KarrLab/bpforms

id: dna
name: DNA nucleotide monophosphates
description: The canonical DNA nucleotide monophosphates, plus the non-canonical DNA
  nucleotide monophosphates based on <a href="https://hoffmanlab.org/proj/dnamod">DNAmod</a>
  and <a href="http://repairtoire.genesilico.pl/damage/">REPAIRtoire</a>
monomers:
  A:
    id: adenine
    name: adenine
    synonyms:
    - 2'-deoxyadenosine-5'-monophosphate
    - DA
    - '[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate'
    - 2'-deoxy-5'-adenylic acid
    - 6-aminopurine
    - A
    identifiers:
    - ns: metacyc.compound
      id: ADENINE
    - ns: chebi
      id: CHEBI:58245
    - ns: pdb-ccd
      id: DA
    - ns: pubchem.compound
      id: '190'
    - ns: chebi
      id: CHEBI:16708
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1ncnc2N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  C:
    id: cytosine
    name: cytosine
    synonyms:
    - 2'-deoxy-5'-cytidylic acid
    - C
    - 4-amino-2-oxo-1,2-dihydropyrimidine
    - DC
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 2'-deoxycytidine-5'-monophosphate
    identifiers:
    - ns: pdb-ccd
      id: DC
    - ns: chebi
      id: CHEBI:57566
    - ns: pubchem.compound
      id: '597'
    - ns: chebi
      id: CHEBI:16040
    - ns: metacyc.compound
      id: CYTOSINE
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1ccc(nc1=O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  G:
    id: guanine
    name: guanine
    synonyms:
    - G
    - 2'-deoxy-5'-guanylic acid
    - 2'-deoxyguanosine-5'-monophosphate
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - DG
    identifiers:
    - ns: pubchem.compound
      id: '764'
    - ns: pdb-ccd
      id: DG
    - ns: chebi
      id: CHEBI:57673
    - ns: metacyc.compound
      id: GUANINE
    - ns: chebi
      id: CHEBI:16235
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  T:
    id: thymine
    name: thymine
    synonyms:
    - 5-methyl-2,4(1H,3H)-pyrimidinedione
    - 5'-thymidylic acid
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - DT
    - thymidine-5'-monophosphate
    - T
    - 5-methyluracil
    identifiers:
    - ns: pubchem.compound
      id: '1135'
    - ns: chebi
      id: CHEBI:26999
    - ns: pdb-ccd
      id: DT
    - ns: metacyc.compound
      id: THYMINE
    - ns: chebi
      id: CHEBI:17821
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  U:
    id: uracil
    name: uracil
    identifiers:
    - ns: metacyc.compound
      id: URACIL
    - ns: pubchem.compound
      id: '1174'
    - ns: chebi
      id: CHEBI:17568
    - ns: chebi
      id: CHEBI:246422
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1ccc(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  dI:
    id: hypoxanthine
    name: hypoxanthine
    synonyms:
    - 2'-deoxyinosine-5'-monophosphate
    - deoxyinosine
    - DI
    - '[(2R,3S,5R)-3-hydroxy-5-(6-oxo-1H-purin-9-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    - I
    - 2'-deoxy-5'-inosinic acid
    identifiers:
    - ns: pubchem.compound
      id: '790'
    - ns: chebi
      id: CHEBI:28806
    - ns: metacyc.compound
      id: HYPOXANTHINE
    - ns: chebi
      id: CHEBI:17368
    - ns: pdb-ccd
      id: DI
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc[nH]c2=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  m2C:
    id: 2-O-methylcytosine
    name: 2-methoxypyrimidin-4-amine
    comments: Pyrimidine substituted with a methoxy group at position C-2 and an amine
      group at C-4.
    synonyms:
    - o-2-methylcytosine
    - 4-amino-2-methoxypyrimidine
    identifiers:
    - ns: dnamod
      id: 2-O-methylcytosine
    - ns: chebi
      id: CHEBI:70854
    structure: COC1=NC(=CCN1C1CC(C(O1)COP(=O)([O-])[O-])O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  f:
    id: 5-formylcytosine
    name: 4-amino-2-oxo-1,2-dihydropyrimidine-5-carbaldehyde
    comments: A nucleobase analogue that is cytosine in which the hydrogen at position
      5 is replaced by a formyl group.
    synonyms:
    - '[(2R,3S,5R)-5-(4-amino-5-methanoyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-formyl-2'-deoxy-cytidine-5'-monophosphate
    - 4-amino-2-oxopyrimidine-5-carbaldehyde
    - 2'-deoxy-5-formylcytidine 5'-(dihydrogen phosphate)
    - cytosine-5-carbaldehyde
    - C
    - 5FC
    identifiers:
    - ns: pdb-ccd
      id: 5FC
    - ns: chebi
      id: CHEBI:76794
    - ns: dnamod
      id: 5-formylcytosine
    structure: O=Cc1cn([C@H]2C[C@@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)nc1N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  h:
    id: 5-(hydroxymethyl)cytosine
    name: 4-amino-5-(hydroxymethyl)pyrimidin-2(1H)-one
    comments: A nucleobase analogue that is cytosine in which the hydrogen at position
      5 is replaced by a hydroxymethyl group.
    synonyms:
    - 4-amino-5-(hydroxymethyl)-2(1h)-pyrimidinone
    - 5HC
    - 5-hydroxymethylcytosine
    - '[(2R,3S,5R)-5-[4-azanyl-5-(hydroxymethyl)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: chebi
      id: CHEBI:76792
    - ns: pdb-ccd
      id: 5HC
    - ns: dnamod
      id: 5-(hydroxymethyl)cytosine
    structure: OCc1cn([C@H]2C[C@H]([C@@H](O2)COP(=O)([O-])[O-])O)c(=O)nc1N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  e3C:
    id: 3-ethylcytosine
    name: 6-amino-1-ethylpyrimidin-2(1H)-one
    comments: A pyrimidone that is cytosine substituted by an ethyl group at position
      3.
    identifiers:
    - ns: chebi
      id: CHEBI:74029
    - ns: dnamod
      id: 3-ethylcytosine
    structure: CCN1C(=CCN(C1=O)C1CC(C(O1)COP(=O)([O-])[O-])O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 17
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 20
      charge: -1
  3mC:
    id: 3-methylcytosine
    name: 6-amino-1-methylpyrimidin-2(1H)-one
    comments: A pyrimidone that is cytosine in which the hydrogen attached to the
      nitrogen at position 3 is substituted by a methyl group. Occurs sparsely. Repaired
      by a direct repair (DR) mechanism. Also repaired in RNA.
    synonyms:
    - 3-methyl-2'-deoxycytidine-5'-monophosphate
    - 3mC
    - n3-methylcytosine
    identifiers:
    - ns: chebi
      id: CHEBI:39992
    - ns: dnamod
      id: 3-methylcytosine
    - ns: repairtoire
      id: 3mC
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1CC=C(N(C1=O)C)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  c:
    id: 5-carboxycytosine
    name: 4-amino-2-oxo-1,2-dihydropyrimidine-5-carboxylic acid
    comments: A nucleobase analogue that is cytosine in which the hydrogen at position
      5 is replaced by a carboxy group.
    synonyms:
    - 4-amino-2-oxopyrimidine-5-carboxylic acid
    - cytosine-5-carboxylic acid
    - 5-carboxylcytosine
    identifiers:
    - ns: dnamod
      id: 5-carboxycytosine
    - ns: chebi
      id: CHEBI:76793
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cc(C(=O)[O-])c(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  ɛC:
    id: 3,N(4)-ethenocytosine
    name: imidazo[1,2-c]pyrimidin-5(6H)-one
    synonyms:
    - 3,n(4)-ethanocytosine
    - ethenocytosine
    identifiers:
    - ns: dnamod
      id: 3,N(4)-ethenocytosine
    - ns: chebi
      id: CHEBI:29147
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1ccc2n(c1=O)ccn2
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  m:
    id: 5-methylcytosine
    name: 4-amino-5-methylpyrimidin-2(1H)-one
    comments: A pyrimidine that is a derivative of cytosine, having a methyl group
      at the 5-position.
    synonyms:
    - C
    - '[(2R,3S,5R)-5-(4-amino-5-methyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-methylcytidine 5'-(dihydrogen phosphate)
    - 4-amino-5-methyl-2(1h)-pyrimidinone
    - 5-methyl-2'-deoxy-cytidine-5'-monophosphate
    - 5CM
    - 4-amino-5-methyl-2-pyrimidinol
    identifiers:
    - ns: dnamod
      id: 5-methylcytosine
    - ns: chebi
      id: CHEBI:27551
    - ns: pdb-ccd
      id: 5CM
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C)c(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  4mC:
    id: N(4)-methylcytosine
    name: 4-(methylamino)pyrimidin-2(1H)-one
    comments: A pyrimidone that is cytosine bearing an N(4)-methyl substituent. Repaired
      by a direct repair (DR) mechanism.
    synonyms:
    - C
    - 4-methyl-2'-deoxycytidine-5'-monophosphate
    - 2'-deoxy-N-methylcytidine 5'-(dihydrogen phosphate)
    - C34
    - 4mC
    - n4-methyl-2'-deoxy-cytidine-5'-monophosphate
    - n(4)-methylcytosine
    - 4-methylamino-1h-pyrimidin-2-one
    - '[(2R,3S,5R)-3-hydroxy-5-(4-methylamino-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: chebi
      id: CHEBI:21839
    - ns: dnamod
      id: N(4)-methylcytosine
    - ns: pdb-ccd
      id: C34
    - ns: repairtoire
      id: 4mC
    structure: CNc1ccn(c(=O)n1)[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 24
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 24
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  1mC:
    id: 1-methylcytosine
    name: 4-amino-1-methylpyrimidin-2(1H)-one
    comments: A pyrimidone that is cytosine in which the hydrogen attached to the
      nitrogen at position 1 is substituted by a methyl group.
    identifiers:
    - ns: dnamod
      id: 1-methylcytosine
    - ns: chebi
      id: CHEBI:39624
    structure: OC1CC(OC1COP(=O)([O-])[O-])[N+]1(C)C=CC(=NC1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  5gmC:
    id: 5-(beta-D-glucosylmethyl)cytosine
    name: (4-amino-2-oxo-1,2-dihydropyrimidin-5-yl)methyl beta-D-glucopyranoside
    comments: A beta-D-glucoside derived from formal condensation of the hydroxy group
      of 5-(hydroxymethyl)cytosine with the anomeric hydroxy group of D-glucopyranose.
    synonyms:
    - beta-glucosyl-5-hydroxymethylcytosine
    - beta-d-glucosyl-5-hydroxymethylcytosine
    - 5-gmc
    - 5-beta-d-glucosylmethylcytosine
    - 5-glucosylmethylcytosine
    identifiers:
    - ns: chebi
      id: CHEBI:131616
    - ns: dnamod
      id: 5-(beta-D-glucosylmethyl)cytosine
    structure: OC[C@H]1O[C@@H](OCc2cn(C3CC(C(O3)COP(=O)([O-])[O-])O)c(=O)[nH]c2=N)[C@@H]([C@H]([C@@H]1O)O)O
    base_monomers:
    - h
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 24
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 24
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  putThy:
    id: alpha-putrescinylthymine
    name: 5-{[(4-aminobutyl)amino]methyl}pyrimidine-2,4(1H,3H)-dione
    comments: An N-substituted putrescine that is thymine in which a hydrogen of the
      methyl group has been replaced by one of the amino groups of putrescine. It
      replaces about half of the thymine residues in the DNA of bacetriophage phiW-14.
    synonyms:
    - n-thyminylputrescine
    - 5-(4-aminobutylaminomethyl)uracil
    - putthy
    identifiers:
    - ns: chebi
      id: CHEBI:132931
    - ns: dnamod
      id: alpha-putrescinylthymine
    structure: '[NH3+]CCCC[NH2+]Cc1cn(C2OC(C(C2)O)COP(=O)([O-])[O-])c(=O)[nH]c1=O'
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  diHT:
    id: 5,6-dihydrothymine
    name: 5,6-dihydrothymine, 5-methyldihydropyrimidine-2,4(1H,3H)-dione
    comments: A pyrimidone obtained by formal addition of hydrogen across the 5,6-position
      of thymine.
    synonyms:
    - 5-methyl-5,6-dihydrouracil
    - 5,6-dihydro-5-methyluracil
    - dihydrothymine
    identifiers:
    - ns: dnamod
      id: 5,6-dihydrothymine
    - ns: chebi
      id: CHEBI:27468
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1CC(C)C(=O)NC1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  e:
    id: 5-formyluracil
    name: 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carbaldehyde
    comments: A pyrimidone resulting from the formal oxidation of the alcoholic hydroxy
      group of 5-hydroxymethyluracil to the corresponding aldehyde. It is a major
      one-electron photooxidation product of thymine in oligodeoxynucleotides.
    synonyms:
    - 5fu
    - fou
    - uracil 5-carbaldehyde
    identifiers:
    - ns: dnamod
      id: 5-formyluracil
    - ns: chebi
      id: CHEBI:80961
    structure: O=Cc1cn(C2CC(C(O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    base_monomers:
    - T
    - g
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 17
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 17
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  1mT:
    id: 1,5-dimethyluracil
    name: 1,5-dimethylpyrimidine-2,4(1H,3H)-dione
    comments: A pyrimidone that is uracil with methyl group substituents at positions
      1 and 5.
    synonyms:
    - 1-methylthymine
    identifiers:
    - ns: dnamod
      id: 1,5-dimethyluracil
    - ns: chebi
      id: CHEBI:74765
    structure: OC1CC(OC1COP(=O)([O-])[O-])[N+]1(C)C=C(C)C(=O)NC1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  O4-meT:
    id: O(4)-methylthymine
    name: 4-methoxy-5-methylpyrimidin-2(1H)-one
    comments: A methylthymine in which the methyl group is located at the O4-position.
    synonyms:
    - 4-methoxy-5-methylpyrimidin-2-one
    - o-4-methylthymine
    identifiers:
    - ns: chebi
      id: CHEBI:134100
    - ns: dnamod
      id: O(4)-methylthymine
    structure: COc1nc(=O)n(cc1C)C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 22
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 18
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 22
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 21
      charge: -1
  3mT:
    id: 3,5-dimethyluracil
    name: 3,5-dimethylpyrimidine-2,4(1H,3H)-dione
    comments: A pyrimidone that is uracil with methyl group substituents at positions
      3 and 5. Repaired by a direct repair (DR) mechanism.
    synonyms:
    - 3-methylthymine
    - 3mT
    - 3-methyl-2'-deoxythymidine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 3mT
    - ns: dnamod
      id: 3,5-dimethyluracil
    - ns: chebi
      id: CHEBI:74766
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cc(C)c(=O)n(c1=O)C
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  xI:
    id: hypoxanthine
    name: 1,7-dihydro-6H-purin-6-one
    comments: A purine nucleobase that consists of purine bearing an oxo substituent
      at position 6.
    synonyms:
    - purine-6-ol
    - purin-6(1h)-one
    - 9h-purin-6(1h)-one
    - 6-oxopurine
    - hyp
    - 6(1h)-purinone
    identifiers:
    - ns: chebi
      id: CHEBI:17368
    - ns: dnamod
      id: hypoxanthine
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1CNC2C1NCNC2=O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  6hmA:
    id: 6-hydroxymethyladenine
    name: (9H-purin-6-ylamino)methanol
    comments: A 6-alkylaminopurine that is adenine where one of the hydrogens of the
      amino group is replaced by a hydroxymethyl group.
    synonyms:
    - n(6)-hydroxymethyl-adenine
    - n(6)-hydroxymethyladenine
    identifiers:
    - ns: chebi
      id: CHEBI:142766
    - ns: dnamod
      id: 6-hydroxymethyladenine
    structure: OCNc1ncnc2c1ncn2C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 24
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 24
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  ncm6A:
    id: N(6)-carbamoylmethyladenine
    name: N(2)-1H-purin-6-ylglycinamide
    comments: A nucleobase analogue that is adenine in which one of the exocyclic
      amino hydrogens is replaced by a carbamoylmethyl group.
    synonyms:
    - 2-(9h-purin-6-ylamino)acetamide
    identifiers:
    - ns: dnamod
      id: N(6)-carbamoylmethyladenine
    - ns: chebi
      id: CHEBI:102525
    structure: NC(=O)CNc1ncnc2c1ncn2C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  6-DMA:
    id: N(6),N(6)-dimethyladenine
    name: N,N-dimethyl-9H-purin-6-amine
    comments: A tertiary amine that is adenine substituted at N-6 by geminal methyl
      groups.
    synonyms:
    - 6-(dimethylamino)purine
    - n,n-dimethyladenine
    - n(6),n(6)-dimethyladenine
    - 6-dimethylaminopurine
    - n,n-dimethyl-1h-purin-6-amine
    - n,n-dimethyl-6-aminopurine
    - 6-dimethyladenine
    - n(6)-dimethyladenine
    identifiers:
    - ns: chebi
      id: CHEBI:60281
    - ns: dnamod
      id: N(6),N(6)-dimethyladenine
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1ncnc2N(C)C
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  m2A:
    id: 9H-purine-2,6-diamine
    name: ''
    comments: A member of the class of 2,6-diaminopurines that is 9H-purine in which
      the hydrogens at positions 2 and 6 are replaced by amino groups.
    synonyms:
    - 2,6-diaminopurine
    - 2-aminoadenine
    - 9h-purine-2,6-diamine
    identifiers:
    - ns: dnamod
      id: 9H-purine-2,6-diamine
    - ns: chebi
      id: CHEBI:40235
    structure: Nc1nc(N)c2c(n1)n(cn2)C1OC(C(C1)O)COP(=O)([O-])[O-]
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 17
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 17
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  HAP:
    id: N(6)-hydroxyadenine
    name: N-hydroxy-1H-purin-6-amine
    comments: A member of the class of 6-aminopurinnes that is adenine in which one
      of the exocyclic amino hydrogens is replaced by a hydroxy group.
    synonyms:
    - 6-n-hydroxylaminopurine
    - 6-hydroxyaminopurine
    - hap
    - n(6)-hydroxyadenine
    - 6-hydroxylaminopurine
    - n-(7h-purin-6-yl)hydroxylamine
    - n-hydroxyadenine
    identifiers:
    - ns: dnamod
      id: N(6)-hydroxyadenine
    - ns: chebi
      id: CHEBI:78235
    structure: ONc1ncnc2c1ncn2C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 23
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 19
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 23
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 22
      charge: -1
  AHAP:
    id: 2-amino-6-hydroxyaminopurine
    name: N(6)-hydroxy-3H-purine-2,6-diamine
    comments: A 2,6-diaminopurine that is the N(6)-hydroxy derivative of 2,6-diamino-3H-purine.
    synonyms:
    - guanine oxime
    - 2-amino-n6-hydroxyadenine
    - 2-amino-n(6)-hydroxyadenine
    identifiers:
    - ns: dnamod
      id: 2-amino-6-hydroxyaminopurine
    - ns: chebi
      id: CHEBI:78685
    structure: ONc1nc(N)nc2c1ncn2C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 24
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 24
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  3mHyp:
    id: 3-methylhypoxanthine
    name: 3-methyl-3,7-dihydro-6H-purin-6-one
    comments: A methylhypoxanthine that is hypoxanthine with the methyl group at position
      3.
    synonyms:
    - 3,7-dihydro-3-methyl-6h-purin-6-one
    - 3-methyl-7h-purin-6(3h)-one
    - 3-methyl-hypoxanthine
    identifiers:
    - ns: dnamod
      id: 3-methylhypoxanthine
    - ns: chebi
      id: CHEBI:145739
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1n(C)cnc2=O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  1mHyp:
    id: 1-methylhypoxanthine
    name: 1-methyl-1,7-dihydro-6H-purin-6-one
    comments: A methylhypoxanthine that is hypoxanthine with the methyl group at position
      1.
    synonyms:
    - 1,7-dihydro-1-methyl-6h-purin-6-one
    - 1-methyl-1,9-dihydro-6h-purin-6-one
    - 1-methyl-hypoxanthine
    identifiers:
    - ns: chebi
      id: CHEBI:73959
    - ns: dnamod
      id: 1-methylhypoxanthine
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1CNC2C1NCN(C2=O)C
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  7mHyp:
    id: 7-methylhypoxanthine
    name: 7-methyl-1,7-dihydro-6H-purin-6-one
    comments: A methylhypoxanthine that is hypoxanthine with the methyl group at position
      7.
    synonyms:
    - 7-methyl-hypoxanthine
    identifiers:
    - ns: chebi
      id: CHEBI:145737
    - ns: dnamod
      id: 7-methylhypoxanthine
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1c[n+](c2c1nc[nH]c2=O)C
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  9mHyp:
    id: 9-methylhypoxanthine
    name: 9-methyl-1,9-dihydro-6H-purin-6-one
    comments: A methylhypoxanthine that is hypoxanthine with the methyl group at position
      9.
    synonyms:
    - 9-methylpoxanthine
    identifiers:
    - ns: chebi
      id: CHEBI:145736
    - ns: dnamod
      id: 9-methylhypoxanthine
    structure: OC1CC(OC1COP(=O)([O-])[O-])[N+]1(C)C=NC2C1NCNC2
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  9mA:
    id: 9-methyladenine
    name: 9-methyl-9H-purin-6-amine
    comments: Adenine substituted with a methyl group at position N-9.
    synonyms:
    - n9-methyladenine
    identifiers:
    - ns: chebi
      id: CHEBI:40526
    - ns: dnamod
      id: 9-methyladenine
    structure: OC1CC(OC1COP(=O)([O-])[O-])[N+]1(C)C=Nc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  1mA:
    id: 1-methyladenine
    name: 1-methyl-1H-purin-6-amine
    comments: Adenine substituted with a methyl group at position N-1. Occurs sparsely.
      Repaired by a direct repair (DR) mechanism. Also repaired in RNA.
    synonyms:
    - n1-methyladenine
    - 1mA
    - 1-methyl-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: dnamod
      id: 1-methyladenine
    - ns: chebi
      id: CHEBI:18083
    - ns: repairtoire
      id: 1mA
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1C=NC2=C(N(C=NC12)C)N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  7mA:
    id: 7-methyladenine
    name: 7-methyl-7H-purin-6-amine
    comments: Adenine substituted with a methyl group at position N-7. Occurs sparsely.
      AlkB activity not confirmed.
    synonyms:
    - 7mA
    - 7-methyl-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: dnamod
      id: 7-methyladenine
    - ns: chebi
      id: CHEBI:28921
    - ns: repairtoire
      id: 7mA
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1CN(c2c1nc[nH+]c2N)C
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  a:
    id: 6-methyladenine
    name: N-methyl-9H-purin-6-amine
    comments: A methyladenine that is 9H-purin-6-amine substituted by a methyl group
      at the amino nitrogen.
    synonyms:
    - 6-map
    - 6-methylaminopurine
    - n6-monomethyladenine
    - n6-methyladenine
    identifiers:
    - ns: dnamod
      id: 6-methyladenine
    - ns: chebi
      id: CHEBI:28871
    structure: CNc1ncnc2c1ncn2C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 23
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 19
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 23
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 22
      charge: -1
  3mA:
    id: 3-methyladenine
    name: 3-methyl-3H-purin-6-amine, 3-methyladenine
    comments: A  methyladenine that is adenine substituted with a methyl group at
      position N-3. Occurs frequently. Repaired by direct repair (DR) mechanisms.
      AlkB activity not confirmed. Also repaired by the BER pathway.
    synonyms:
    - 3mA
    - 6-amino-3-methylpurine
    - 3-methyl-3h-adenine
    - 3-methyl-2'-deoxyadenosine-5'-monophosphate
    - 3-methyl-3h-purin-6-ylamine
    identifiers:
    - ns: chebi
      id: CHEBI:38635
    - ns: dnamod
      id: 3-methyladenine
    - ns: repairtoire
      id: 3mA
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1C=NC2=C([NH+]=CN(C12)C)N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  4mA:
    id: 4-methyladenine
    name: 4-methyl-4,7-dihydro-1H-purin-6-amine
    comments: A methyladenine in which the methyl substituent is located at position
      4.
    identifiers:
    - ns: dnamod
      id: 4-methyladenine
    - ns: chebi
      id: CHEBI:134106
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1C=NC2=C(N=CNC12C)N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  o:
    id: 8-oxoguanine
    name: 2-amino-1H-purine-6,8-dione
    comments: An oxopurine that is guanine which is substituted by an oxo group at
      position 8.
    identifiers:
    - ns: dnamod
      id: 8-oxoguanine
    - ns: chebi
      id: CHEBI:44605
    structure: OC1CC(OC1COP(=O)([O-])[O-])N1C(=O)N=C2C1N=C(N)NC2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  CEG:
    id: N(2)-carboxyethylguanine
    name: N-(6-oxo-6,9-dihydro-1H-purin-2-yl)alanine
    comments: An alanine derivative consisting of alanine having a 6-oxo-6,9-dihydro-1H-purin-2-yl
      group attached to the amino function.
    synonyms:
    - ceguanine
    - n(2)-(1-carboxyethyl)guanine
    identifiers:
    - ns: dnamod
      id: N(2)-carboxyethylguanine
    - ns: chebi
      id: CHEBI:62032
    structure: '[O-]C(=O)C(Nc1[nH]c(=O)c2c(n1)n(cn2)C1CC(C(O1)COP(=O)([O-])[O-])O)C'
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 28
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 28
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  N(2),3-ɛG:
    id: N(2),3-ethenoguanine
    name: 1H-imidazo(2,1-b)purin-4(5H)-one
    comments: A nucleobase analogue obtained by addition of an etheno group across
      positions N2 and 3 of guanine.
    synonyms:
    - n(2),3-epsilong
    identifiers:
    - ns: chebi
      id: CHEBI:134095
    - ns: dnamod
      id: N(2),3-ethenoguanine
    structure: OC1CC(OC1COP(=O)([O-])[O-])[N+]12C=CN=C1NC(=O)c1c2[nH]cn1
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  1,N(2)-ɛG:
    id: 1,N(2)-ethenoguanine
    name: 1,4-dihydro-9H-imidazo[1,2-a]purin-9-one
    comments: A nucleobase analogue obtained by addition of an etheno group across
      positions 1 and N2 of guanine.
    synonyms:
    - 1,n(2)-ethenoguanine
    - 1,n(2)-epsilong
    identifiers:
    - ns: dnamod
      id: 1,N(2)-ethenoguanine
    - ns: chebi
      id: CHEBI:134096
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1[nH]c1nccn1c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  2mG:
    id: N(2)-methylguanine
    name: 2-(methylamino)-1,7-dihydro-6H-purin-6-one
    comments: A methylguanine in which the methyl group is located at the N2-position.
    synonyms:
    - 2-methylamino-6-oxopurine
    - 2-methylguanine
    - 2-methyl-2'-deoxyguanosine-5'-monophosphate
    - n-methyl-guanine
    - 2mG
    - 1,7-dihydro-2-(methylamino)-6h-purin-6-one
    identifiers:
    - ns: chebi
      id: CHEBI:21818
    - ns: repairtoire
      id: 2mG
    - ns: dnamod
      id: N(2)-methylguanine
    structure: CNc1[nH]c(=O)c2c(n1)n(cn2)C1CC(C(O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 21
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 24
      charge: -1
  m6G:
    id: 6-O-methylguanine
    name: 6-methoxy-7H-purin-2-amine
    comments: A methylguanine in which the methyl group is positioned on the oxygen
      at position 6. Formed in DNA by alkylation of the oxygen atom of guanine, most
      often by N-nitroso compounds and sometimes due to methylation by other compounds
      such as endogenous S-adenosylmethionine, it base-pairs to thymine rather than
      cytidine, causing a G:C to A:T transition in DNA.
    synonyms:
    - 6-methoxy-1h-purine-2-amine
    - G
    - '[(2R,3S,5R)-5-(2-azanyl-6-methoxy-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 6OG
    - 6-methoxyguanine
    - 6-o-methyl guanosine-5'-monophosphate
    - o-(6)-methylguanine
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-methoxy-9H-purin-2-amine
    - o(6)-methylguanine
    - 2-amino-6-methoxypurine
    identifiers:
    - ns: dnamod
      id: 6-O-methylguanine
    - ns: pdb-ccd
      id: 6OG
    - ns: chebi
      id: CHEBI:20689
    structure: COc1nc(N)nc2c1ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 27
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 27
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  1mG:
    id: 1-methylguanine
    name: 2-amino-1-methyl-1,9-dihydro-6H-purin-6-one
    comments: Repaired by a direct repair (DR) mechanism.
    synonyms:
    - 2'-deoxy-1-methylguanosine 5'-(dihydrogen phosphate)
    - G
    - 1-methyl-2'-deoxyguanosine-5'-monophosphate
    - '[(2R,3S,5R)-5-(2-amino-1-methyl-6-oxo-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - MG1
    - n1-methylguanine
    - 1mG
    identifiers:
    - ns: chebi
      id: CHEBI:21803
    - ns: dnamod
      id: 1-methylguanine
    - ns: pdb-ccd
      id: MG1
    - ns: repairtoire
      id: 1mG
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)n(c2=O)C
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  dhpUra:
    id: 5-(4,5-dihydroxypentyl)uracil
    name: 5-(4,5-dihydroxypentyl)pyrimidine-2,4(1H,3H)-dione
    comments: A nucleobase analogue that is uracil substituted at position 5 by a
      4,5-dihydroxypentyl group.
    identifiers:
    - ns: dnamod
      id: 5-(4,5-dihydroxypentyl)uracil
    - ns: chebi
      id: CHEBI:132195
    structure: OCC(CCCc1cn(C2CC(C(O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O)O
    base_monomers:
    - U
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 17
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 20
      charge: -1
  b:
    id: uracil-5-carboxylic acid
    name: 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylic acid
    synonyms:
    - 2,4-dihydroxy-5-pyrimidinecarboxylic acid
    - uracil 5-carboxylate
    - isoorotic acid
    - steviolbioside
    - 5-carboxyuracil
    - uracil 5-carboxylic acid
    identifiers:
    - ns: dnamod
      id: uracil-5-carboxylic acid
    - ns: chebi
      id: CHEBI:17477
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cc(C(=O)[O-])c(=O)[nH]c1=O
    base_monomers:
    - U
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
  g:
    id: 5-hydroxymethyluracil
    name: 5-(hydroxymethyl)pyrimidine-2,4(1H,3H)-dione
    comments: A primary alcohol that is uracil bearing a hydroxymethyl substituent
      at the 5-position.
    synonyms:
    - 5-(hydroxymethyl)uracil
    - 5-hydroxymethyl uracil
    - 5-(hydroxymethyl)-2,4(1h,3h)-pyrimidinedione
    identifiers:
    - ns: chebi
      id: CHEBI:16964
    - ns: dnamod
      id: 5-hydroxymethyluracil
    structure: OCc1cn(C2CC(C(O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    base_monomers:
    - U
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 17
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 17
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  1,N2-ethenoG:
    id: 1,N2-ethenoG
    name: 1,N2-etheno-2'-deoxyguanosine-5'-monophosphate
    comments: Arise as side products of lipid peroxidation under oxidative stress.
      exocyclic adducts are repaired with an epoxide intermediate, that is hydrolyzed
      to the repaired base + CHO-CHO.
    identifiers:
    - ns: repairtoire
      id: 1,N2-ethenoG
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc1[nH]ccn1c2=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  1,N6-ethenoA:
    id: 1,N6-ethenoA
    name: 1,N6-etheno-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 1,N6-ethenoA
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc[n+]1c2[nH]cc1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  1eA:
    id: 1eA
    name: 1-ethyl-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 1eA
    structure: CC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 27
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 27
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  1heA:
    id: 1heA
    name: 1-hydroxyethyl-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 1heA
    structure: OCC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 28
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 28
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  1hpA:
    id: 1hpA
    name: 1-hydroxypropyl-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 1hpA
    structure: OCCC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 29
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 29
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  1pA:
    id: 1pA
    name: 1-propyl-2'-deoxyadenosine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 1pA
    structure: CCC[n+]1cnc2c(c1N)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 28
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 28
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  dU:
    id: dU
    name: 2'-deoxyuridine-5'-monophosphate
    comments: A pyrimidine 2'-deoxyribonucleoside having uracil as the nucleobase.
      Cysteine spontaneously loses an amine group, which is replaced by a keto group
      at the C4-atom. This reaction occurs spontaneously and all the time, and is
      the reason why T is used in DNA. This way, dU and T can be distinguished from
      each other.
    synonyms:
    - deoxyuridine
    - U
    - 2'-deoxyuridine-5'-monophosphate
    - dU
    - '[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 1-(2-deoxy-beta-D-erythro-pentofuranosyl)uracil
    - DU
    - 2'-deoxy-5'-uridylic acid
    - 2-deoxyuridine
    - 2'-deoxyuridine
    identifiers:
    - ns: repairtoire
      id: dU
    - ns: pdb-ccd
      id: DU
    - ns: chebi
      id: CHEBI:16450
    - ns: dnamod
      id: 2'-deoxyuridine
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  3,N4-ethenoC:
    id: 3,N4-ethenoC
    name: 3,N4-etheno-2'-deoxycytidine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-oxidanyl-5-(5-oxidanylideneimidazo[1,2-c]pyrimidin-6-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - n3,n4-etheno-2'-deoxycytidine-5'-monophosphate
    - EDC
    - 6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)imidazo[1,2-c]pyrimidin-5(6H)-one
    identifiers:
    - ns: pdb-ccd
      id: EDC
    - ns: repairtoire
      id: 3,N4-ethenoC
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1ccc2n(c1=O)ccn2
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  3eC:
    id: 3eC
    name: 3-ethyl-2'-deoxycytidine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 3eC
    structure: CC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 21
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 24
      charge: -1
  3heC:
    id: 3heC
    name: 3-hydroxyethyl-2'-deoxycytidine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 3heC
    structure: OCC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  3hpC:
    id: 3hpC
    name: 3-hydroxypropyl-2'-deoxycytidine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 3hpC
    structure: OCCC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 27
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 27
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  3mG:
    id: 3mG
    name: 3-methyl-2'-deoxyguanosine-5'-monophosphate
    comments: Occurs sparsely.
    identifiers:
    - ns: repairtoire
      id: 3mG
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1[n+](C)c([nH]c2=O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  3pC:
    id: 3pC
    name: 3-propyl-2'-deoxycytidine-5'-monophosphate
    identifiers:
    - ns: repairtoire
      id: 3pC
    structure: CCC[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  thymidine glycol:
    id: thymidine glycol
    name: 5,6-dihydroxy-5,6-dihydrothymidine-5'-monophosphate
    comments: One of the principal DNA lesions induced by oxidation and ionizing radiation,
      has been investigated in Escherichia coli. Thymine glycol was positioned at
      a unique site in the single-stranded genome of a bacteriophage M13mp19 derivative.
      Replication of the genome in E. coli yielded targeted mutations at a frequency
      of 0.3%; the mutations were exclusively T to C transitions.
    synonyms:
    - '[(2R,3S,5R)-5-[(5R,6S)-5,6-dihydroxy-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (5r,6s)-5,6-dihydro-5,6-dihydroxythymidine-5'-monophosphate
    - CTG
    - T
    - 5,6-dihydroxythymidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: CTG
    - ns: repairtoire
      id: thymidine glycol
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])N1C(=O)NC(=O)[C@]([C@H]1O)(C)O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  6mA:
    id: 6mA
    name: 6-methyl-2'-deoxyadenosine-5'-monophosphate
    comments: AlkB activity not confirmed
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[6-(methylamino)purin-9-yl]oxolan-2-yl]methyl dihydrogen
      phosphate'
    - n6-methyl-deoxy-adenosine-5'-monophosphate
    - 2'-deoxy-N-methyladenosine 5'-(dihydrogen phosphate)
    - 6MA
    - A
    identifiers:
    - ns: pdb-ccd
      id: 6MA
    - ns: repairtoire
      id: 6mA
    structure: CNc1ncnc2c1ncn2[C@@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 24
      charge: -1
  7mG:
    id: 7mG
    name: 7-methyl-2'-deoxyguanosine-5'-monophosphate
    comments: Occurs frequently.
    identifiers:
    - ns: repairtoire
      id: 7mG
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1c[n+](c2c1nc(N)[nH]c2=O)C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  8mG:
    id: 8mG
    name: 8-methyl-2'-deoxyguanosine-5'-monophosphate
    comments: Repaired by a direct repair (DR) mechanism.
    identifiers:
    - ns: repairtoire
      id: 8mG
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1c(C)nc2c1nc(N)[nH]c2=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  O2mT:
    id: O2mT
    name: O2-methyl-2'-deoxythymidine-5'-monophosphate
    comments: AlkB activity not confirmed.
    identifiers:
    - ns: repairtoire
      id: O2mT
    structure: CO[C@@H]1NC(=O)C(=CN1[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O)C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 21
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 24
      charge: -1
  O4mT:
    id: O4mT
    name: O4-methyl-2'-deoxythymidine-5'-monophosphate
    comments: Occurs sparsely. Repaired by the NER pathway.
    identifiers:
    - ns: repairtoire
      id: O4mT
    structure: CO[C@@H]1NC(=O)N(C=C1C)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  O6mG:
    id: O6mG
    name: O6-methyl-2'-deoxyguanosine-5'-monophosphate
    comments: Occurs frequently. Repaired by a direct repair (DR) mechanism.
    identifiers:
    - ns: repairtoire
      id: O6mG
    structure: CO[C@@H]1NC(=[NH+]c2c1ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 28
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 28
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  02I:
    id: 02I
    name: (6s,7s,8s,10r)-4-amino-8-hydroxy-7,8,9,10-tetrahydro-6h-7,10-epoxyazepino[1,2-e]purin-6-yl
      dihydrogen phosphate
    synonyms:
    - (6S,7S,8S,10R)-4-amino-8-hydroxy-7,8,9,10-tetrahydro-6H-7,10-epoxyazepino[1,2-e]purin-6-yl
      dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: 02I
    structure: O[C@H]1C[C@H]2O[C@@H]1[C@@H](OP(=O)([O-])[O-])c1n2c2ncnc(c2n1)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  0AD:
    id: 0AD
    name: 2'-deoxy-n-propylguanosine 5'-(dihydrogen phosphate)
    synonyms:
    - G
    - '[(2R,3S,5R)-3-hydroxy-5-(6-oxo-2-propylamino-1H-purin-9-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-propylguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 0AD
    structure: CCCNc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - G
  0AP:
    id: 0AP
    name: 2'-deoxycytidine 3',5'-bis(dihydrogen phosphate)
    synonyms:
    - 2'-deoxycytidine 3',5'-bis(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-phosphonooxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: 0AP
    structure: Nc1ccn(c(=O)n1)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)OP(=O)(O)O
    base_monomers:
    - C
  0KZ:
    id: 0KZ
    name: '[(1r,2s,4s,5s)-2-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)bicyclo[3.1.0]hex-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,2S,4S,5S)-2-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)bicyclo[3.1.0]hex-1-yl]methyl
      dihydrogen phosphate'
    - '[(1S,2S,4S)-2-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-5-bicyclo[3.1.0]hexanyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 0KZ
    structure: O[C@@H]1C[C@H]([C@@H]2[C@@]1(COP(=O)(O)O)C2)n1cc(C)c(=O)[nH]c1=O
  0R8:
    id: 0R8
    name: '[(2s,5r)-5-{4-amino-5-[(4-ethynylphenyl)ethynyl]-2-oxopyrimidin-1(2h)-yl}tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2S,5R)-5-{4-amino-5-[(4-ethynylphenyl)ethynyl]-2-oxopyrimidin-1(2H)-yl}tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    - '[(2S,5R)-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 0R8
    structure: C#Cc1ccc(cc1)C#Cc1cn([C@H]2CC[C@@H](O2)COP(=O)([O-])[O-])c(=O)nc1N
    base_monomers:
    - C
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  18Q:
    id: 18Q
    name: 2'-deoxy-5-[(thiophen-2-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-(thiophen-2-ylmethylcarbamoyl)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-[(thiophen-2-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 18Q
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(C(=O)NCc2cccs2)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  1AP:
    id: 1AP
    name: 2,6-diaminopurine nucleotide
    synonyms:
    - '[(2R,3S,5R)-5-(2,6-diaminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 2-amino-2'-deoxyadenosine 5'-(dihydrogen phosphate)
    - A
    identifiers:
    - ns: pdb-ccd
      id: 1AP
    structure: Nc1nc(N)c2c(n1)n(cn2)[C@H]1O[C@@H]([C@@H](C1)O)COP(=O)(O)O
    base_monomers:
    - A
  1CC:
    id: 1CC
    name: 5-carboxy-2'-deoxycytidine monophosphate
    synonyms:
    - 4-azanyl-2-oxidanylidene-1-[(2R,4S,5R)-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]pyrimidine-5-carboxylic
      acid
    - 5-carboxy-2'-deoxycytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 1CC
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1cc(C(=O)O)c(nc1=O)N
    base_monomers:
    - C
  1FC:
    id: 1FC
    name: 4-amino-1-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-2-oxo-1,2-dihydropyrimidine-5-carboxylic
      acid
    synonyms:
    - 4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-2-oxo-1,2-dihydropyrimidine-5-carboxylic
      acid
    - 4-azanyl-1-[(2R,3S,4R,5R)-3-fluoranyl-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]-2-oxidanylidene-pyrimidine-5-carboxylic
      acid
    identifiers:
    - ns: pdb-ccd
      id: 1FC
    structure: O[C@H]1[C@@H](COP(=O)(O)O)O[C@H]([C@H]1F)n1cc(C(=O)O)c(nc1=O)N
    base_monomers:
    - C
  1TL:
    id: 1TL
    name: 1-{2,5-anhydro-6-deoxy-4-[(phosphonooxy)methyl]-alpha-l-mannofuranosyl}pyrimidine-2,4(1h,3h)-dione
    synonyms:
    - 1-{2,5-anhydro-6-deoxy-4-[(phosphonooxy)methyl]-alpha-L-mannofuranosyl}pyrimidine-2,4(1H,3H)-dione
    - '[(1R,3S,4R,6R,7S)-6-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methyl-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-4-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 1TL
    structure: C[C@H]1O[C@H]2[C@@H]([C@]1(COP(=O)([O-])[O-])O[C@@H]2n1ccc(=O)[nH]c1=O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 28
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 28
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  1TW:
    id: 1TW
    name: 2-amino-9-(2-se-methyl-5-o-phosphono-2-seleno-beta-d-arabinofuranosyl)-1,9-dihydro-6h-purin-6-one
    synonyms:
    - '[(2R,3R,4S,5R)-5-(2-azanyl-6-oxidanylidene-1H-purin-9-yl)-4-methylselanyl-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2-amino-9-(2-Se-methyl-5-O-phosphono-2-seleno-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one
    identifiers:
    - ns: pdb-ccd
      id: 1TW
    structure: C[Se][C@@H]1[C@H](O)[C@@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)(O)O
  1W5:
    id: 1W5
    name: (1r)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-2-deoxy-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanyl-pyridin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (1R)-1-(6-amino-2-hydroxy-5-nitropyridin-3-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: 1W5
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])c1cc([N+](=O)[O-])c(nc1O)N
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  1WA:
    id: 1WA
    name: 2-amino-8-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-4-hydroxy-1h-imidazo[1,2-a][1,3,5]triazine-5,8-diium
    synonyms:
    - '[(2R,3S,5R)-5-(2-azanyl-4-oxidanyl-1H-imidazo[1,2-a][1,3,5]triazine-5,8-diium-8-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2-amino-8-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-1H-imidazo[1,2-a][1,3,5]triazine-5,8-diium
    identifiers:
    - ns: pdb-ccd
      id: 1WA
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])[n+]1cc[n+]2c1[nH]c(N)nc2O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  2AR:
    id: 2AR
    name: 2'-deoxyaristeromycin-5'-phosphate
    synonyms:
    - '[(1R,2S,4R)-4-(6-amino-9H-purin-9-yl)-2-hydroxycyclopentyl]methyl dihydrogen
      phosphate'
    - '[(1R,2S,4R)-4-(6-aminopurin-9-yl)-2-hydroxy-cyclopentyl]methyl dihydrogen phosphate'
    - A
    identifiers:
    - ns: pdb-ccd
      id: 2AR
    structure: O[C@@H]1C[C@@H](C[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  2BD:
    id: 2BD
    name: n1-(1-hydroxy-3-buten-2(s)-yl)-2'-deoxyinosine mono phosphoric acid
    synonyms:
    - 2'-deoxy-1-[(1S)-1-(hydroxymethyl)prop-2-en-1-yl]inosine 5'-(dihydrogen phosphate)
    - I
    - '[(2R,5R)-3-hydroxy-5-[1-[(2S)-1-hydroxybut-3-en-2-yl]-6-oxo-purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2BD
    structure: OC[C@@H](n1cnc2c(c1=O)ncn2[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O)C=C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 29
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 29
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  2BU:
    id: 2BU
    name: (2s,3s)-n6-(2,3,4-trihydroxybutyl)-2'-deoxyadenosine mono phosphoric acid
    synonyms:
    - 2'-deoxy-N-[(2R,3S)-2,3,4-trihydroxybutyl]adenosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[6-[[(2R,3S)-2,3,4-trihydroxybutyl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - A
    identifiers:
    - ns: pdb-ccd
      id: 2BU
    structure: OC[C@@H]([C@@H](CNc1ncnc2c1ncn2[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O)O)O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 32
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 28
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 32
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 31
      charge: -1
  2DA:
    id: 2DA
    name: 2',3'-dideoxyadenosine-5'-monophosphate
    synonyms:
    - '[(2S,5R)-5-(6-amino-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate'
    - A
    - '[(2S,5R)-5-(6-aminopurin-9-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2DA
    structure: Nc1ncnc2c1ncn2[C@@H]1CC[C@H](O1)COP(=O)([O-])[O-]
    base_monomers:
    - A
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  2DF:
    id: 2DF
    name: n-(2-deoxy-beta-d-erytho-pentofuranosyl-5-phosphate) formamide
    synonyms:
    - N
    - '[(2R,3S,5R)-5-formamido-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate'
    - 2-deoxy-N-formyl-5-O-phosphono-beta-D-erythro-pentofuranosylamine
    identifiers:
    - ns: pdb-ccd
      id: 2DF
    structure: O=CN[C@H]1C[C@H]([C@H](O1)COP(=O)(O)O)O
  2DM:
    id: 2DM
    name: 2-hydroxy-3-(pyren-1-ylmethoxy)propyl dihydrogen phosphate
    synonyms:
    - N
    - '[(2S)-2-hydroxy-3-(pyren-1-ylmethoxy)propyl] dihydrogen phosphate'
    - (2S)-2-hydroxy-3-(pyren-1-ylmethoxy)propyl dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: 2DM
    structure: O[C@@H](COP(=O)([O-])[O-])COCc1ccc2c3c1ccc1c3c(cc2)ccc1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 6
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 9
      charge: -1
  2DT:
    id: 2DT
    name: 3'-deoxythymidine-5'-monophosphate
    synonyms:
    - '[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    - '[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: 2DT
    structure: O=c1[nH]c(=O)n(cc1C)[C@H]1CC[C@H](O1)COP(=O)([O-])[O-]
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  2EG:
    id: 2EG
    name: 2'-deoxy-n-ethylguanosine 5'-phosphate
    synonyms:
    - G
    - '[(2R,3S,5R)-5-(2-ethylamino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-ethylguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 2EG
    structure: CCNc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
  2FE:
    id: 2FE
    name: 2'-fluoro-2'-deoxy-1,n6-ethenoadenine
    synonyms:
    - N
    - '[(2R,3R,4S,5R)-4-fluoro-3-hydroxy-5-imidazo[2,1-f]purin-3-yl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-3H-imidazo[2,1-i]purine
    identifiers:
    - ns: pdb-ccd
      id: 2FE
    structure: F[C@H]1[C@H](O)[C@@H](O[C@H]1n1cnc2c1ncn1c2ncc1)COP(=O)(O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 6
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 6
  2FI:
    id: 2FI
    name: 2'-fluoro-2'-deoxyinosine
    synonyms:
    - N
    - 9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one
    - '[(2R,3R,4S,5R)-4-fluoro-3-hydroxy-5-(6-oxo-1H-purin-9-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2FI
    structure: O[C@@H]1[C@H](COP(=O)(O)O)O[C@H]([C@H]1F)n1cnc2c1nc[nH]c2=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  2GF:
    id: 2GF
    name: '[(2r,5r)-5-(4-amino-5-chloro-2-oxopyrimidin-1(2h)-yl)-3-oxotetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2R,5R)-5-(4-amino-5-chloro-2-oxopyrimidin-1(2H)-yl)-3-oxotetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    - '[(2R,5R)-5-(4-azanyl-5-chloranyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanylidene-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2GF
    structure: O=C1C[C@@H](O[C@H]1COP(=O)(O)O)n1cc(Cl)c(nc1=O)N
  2IA:
    id: 2IA
    name: 2'-deoxy-2'-iodoadenosine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-2'-iodoadenosine 5'-(dihydrogen phosphate)
    - '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-iodanyl-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2IA
    structure: O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@@H]1I)n1cnc2c1ncnc2N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  2JU:
    id: 2JU
    name: 2'-deoxy-5-[(naphthalen-1-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-[(naphthalen-1-ylmethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[5-(naphthalen-1-ylmethylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2JU
    structure: O[C@@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1cc(C(=O)NCc2cccc3c2cccc3)c(=O)[nH]c1=O
  2JV:
    id: 2JV
    name: n-(8-aminopyren-1-yl)-2'-deoxy-5'-o-(trihydroxy-lambda~5~-phosphanyl)guanosine
    synonyms:
    - N-(8-aminopyren-1-yl)-2'-deoxy-5'-O-(trihydroxy-lambda~5~-phosphanyl)guanosine
    - 2-[(8-azanylpyren-1-yl)amino]-9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1H-purin-6-one
    identifiers:
    - ns: pdb-ccd
      id: 2JV
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(O)(O)O)n1cnc2c1nc([nH]c2=O)Nc1ccc2c3c1ccc1c3c(cc2)ccc1N
    base_monomers:
    - G
  2L8:
    id: 2L8
    name: '[(2r,3s,5r)-3-[(1-{[(2r,3s,5r)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)tetrahydrofuran-2-yl]methyl}-1h-1,2,3-triazol-4-yl)methoxy]-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate '
    synonyms:
    - '[(2R,3S,5R)-3-[(1-{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methoxy]-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate (non-preferred name)'
    - '[(2R,3S,5R)-3-[[1-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl]-1,2,3-triazol-4-yl]methoxy]-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2L8
    structure: O[C@@H]1C[C@@H](O[C@H]1Cn1nnc(c1)CO[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O)n1cc(C)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  2LA:
    id: 2LA
    name: 2-amino-5-(aminomethyl)-7-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-3,7-dihydro-4h-pyrrolo[2,3-d]pyrimidin-4-one
    synonyms:
    - 2-amino-5-(aminomethyl)-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
    - '[(2R,3S,5R)-5-[5-(aminomethyl)-2-azanyl-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2LA
    structure: NCc1cn(c2c1c(=O)[nH]c(n2)N)[C@H]1C[C@H]([C@@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 29
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 29
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  2LF:
    id: 2LF
    name: (6s,7s,8s,10r)-2-amino-8-hydroxy-4-oxo-3,6,7,8,9,10-hexahydro-4h-7,10-epoxyazepino[1,2-e]purin-6-yl
      dihydrogen phosphate
    synonyms:
    - (6S,7S,8S,10R)-2-amino-8-hydroxy-4-oxo-3,6,7,8,9,10-hexahydro-4H-7,10-epoxyazepino[1,2-e]purin-6-yl
      dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: 2LF
    structure: O[C@@H]1C[C@H]2O[C@H]1[C@@H](OP(=O)([O-])[O-])c1n2c2nc(N)[nH]c(=O)c2n1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  2PR:
    id: 2PR
    name: 2-amino-9-[2-deoxyribofuranosyl]-9h-purine-5'-monophosphate
    synonyms:
    - G
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-2-amine
    - '[(2R,3S,5R)-5-(2-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 2PR
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)nc2
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  2ST:
    id: 2ST
    name: 5-methyl-2'-se-methyl-2'-selenouridine 5'-(dihydrogen phosphate)
    synonyms:
    - 5-methyl-2'-Se-methyl-2'-selenouridine 5'-(dihydrogen phosphate)
    - '[(2R,3R,4R,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-4-methylselanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: 2ST
    structure: C[Se][C@@H]1[C@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 7
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 7
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  3DR:
    id: 3DR
    name: 1',2'-dideoxyribofuranose-5'-phosphate
    synonyms:
    - N
    - 1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
    - '[(2R,3S)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 3DR
    structure: O[C@H]1CCO[C@@H]1COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  3ZO:
    id: 3ZO
    name: 2'-deoxy-xanthosine-5'-monophosphate
    synonyms:
    - 2'-deoxy-5'-2,3-dihydroxanthylic acid
    - '[(2R,3S,5R)-5-[2,6-bis(oxidanylidene)-3H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 3ZO
    structure: O=c1[nH]c(=O)c2c([nH]1)n(cn2)[C@H]1O[C@H]([C@@H](C1)O)CO[P@@](=O)(O)[O-]
  47C:
    id: 47C
    name: 2'-deoxy-n-(prop-2-en-1-yloxy)cytidine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-N-(prop-2-en-1-yloxy)cytidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[2-oxo-4-(prop-2-enoxyamino)pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: 47C
    structure: C=CCONc1ccn(c(=O)n1)[C@H]1C[C@@H]([C@@H](O1)COP(=O)(O)O)O
    base_monomers:
    - C
  4DG:
    id: 4DG
    name: 2-[(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)methoxy]ethyl dihydrogen phosphate
    synonyms:
    - 2-[(2-azanyl-6-oxo-1H-purin-9-yl)methoxy]ethyl dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: 4DG
    structure: Nc1[nH]c(=O)c2c(n1)n(COCCOP(=O)(O)O)cn2
  4DU:
    id: 4DU
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-1h-imidazo[4,5-c]pyridin-4-amine
    synonyms:
    - '[(2R,3S,5R)-5-(4-azanylimidazo[4,5-c]pyridin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazo[4,5-c]pyridin-4-amine
    identifiers:
    - ns: pdb-ccd
      id: 4DU
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1cnc2c1ccnc2N
  '4E9':
    id: '4E9'
    name: 2'-deoxy-8-[(7-oxo-7h-benzo[de]anthracen-3-yl)amino]guanosine 5'-(dihydrogen
      phosphate)
    synonyms:
    - 2'-deoxy-8-[(7-oxo-7H-benzo[de]anthracen-3-yl)amino]guanosine 5'-(dihydrogen
      phosphate)
    - '[(2R,3S,5R)-5-[2-azanyl-6-oxidanylidene-8-[(7-oxidanylidenebenzo[a]phenalen-3-yl)amino]-1H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: '4E9'
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1c(Nc2ccc3c4c2cccc4C(=O)c2c3cccc2)nc2c1nc(N)[nH]c2=O
  4EN:
    id: 4EN
    name: '[(2r,3s,5r)-5-(4-azanylpyrazolo[3,4-d]pyrimidin-2-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2R,3S,5R)-5-(4-azanylpyrazolo[3,4-d]pyrimidin-2-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 4EN
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@@](=O)(O)[O-])n1nc2c(c1)c(N)ncn2
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  4JA:
    id: 4JA
    name: (2s)-3-[(6-deoxy-beta-d-glucopyranosyl)oxy]-2-hydroxypropyl dihydrogen phosphate
    synonyms:
    - '[(2S)-3-[(2R,3R,4S,5S,6R)-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-propyl]
      dihydrogen phosphate'
    - (2S)-3-[(6-deoxy-beta-D-glucopyranosyl)oxy]-2-hydroxypropyl dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: 4JA
    structure: O[C@@H](COP(=O)([O-])[O-])CO[C@@H]1O[C@H](C)[C@H]([C@@H]([C@H]1O)O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 6
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 9
      charge: -1
  4MF:
    id: 4MF
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-4-methyl-1h-indole
    synonyms:
    - N
    - '[(2R,3S,5R)-3-hydroxy-5-(4-methylindol-1-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methyl-1H-indole
    identifiers:
    - ns: pdb-ccd
      id: 4MF
    structure: O[C@@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1ccc2c1cccc2C
  4PC:
    id: 4PC
    name: 3-(2'-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-methyl-3,7-dihydro-2h-pyrrolo[2,3-d]pyrimidin-2-one
    synonyms:
    - C
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-methyl-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one
    - '[(2R,3S,5R)-3-hydroxy-5-(6-methyl-2-oxo-7H-pyrrolo[2,3-d]pyrimidin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 4PC
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cc2cc([nH]c2nc1=O)C
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  4PD:
    id: 4PD
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-methyl-1,3-dihydro-2h-pyrrolo[2,3-d]pyrimidin-2-one
    synonyms:
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-methyl-1,3-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one
    - C
    - '[(2R,3S,5R)-3-hydroxy-5-(6-methyl-2-oxo-1H-pyrrolo[2,3-d]pyrimidin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 4PD
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cc2cc(nc2[nH]c1=O)C
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  4PE:
    id: 4PE
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-methyl-3h-pyrrolo[2,3-d]pyrimidin-2-ol
    synonyms:
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-methyl-3H-pyrrolo[2,3-d]pyrimidin-2-ol
    - '[(2R,3S,5R)-3-hydroxy-5-(2-hydroxy-6-methyl-pyrrolo[2,3-d]pyrimidin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: 4PE
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cc2cc(nc2nc1O)C
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  4SC:
    id: 4SC
    name: 4'-thio-2'-deoxycytidine-5'-monophosphate group
    synonyms:
    - C
    - 2'-deoxy-5-methyl-5'-O-[oxido(oxo)phosphonio]-4'-thiocytidine
    - '[(2R,3S,5R)-5-[(5R)-4-amino-5-methyl-2-oxo-5,6-dihydropyrimidin-1-yl]-3-hydroxy-thiolan-2-yl]methoxy-oxido-oxo-phosphanium'
    identifiers:
    - ns: pdb-ccd
      id: 4SC
    structure: '[O-][P+](=O)OC[C@H]1S[C@@H](C[C@@H]1O)N1C[C@@H](C)C(=NC1=O)N'
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 14
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 14
  4U3:
    id: 4U3
    name: 5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)
    synonyms:
    - 5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(4-azanyl-5-chloranyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 4U3
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(Cl)c(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  5AT:
    id: 5AT
    name: 5'-amino-5'-deoxythymidine
    synonyms:
    - 1-[(2R,4S,5R)-5-(aminomethyl)-4-hydroxy-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
    - 5'-amino-5'-deoxythymidine
    - T
    identifiers:
    - ns: pdb-ccd
      id: 5AT
    structure: NC[C@H]1O[C@H](C[C@@H]1O)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 11
  5DB:
    id: 5DB
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1h)-one
    synonyms:
    - '[(2R,3S,5R)-5-(4-methoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methoxy-5-methylpyrimidin-2(1H)-one
    identifiers:
    - ns: pdb-ccd
      id: 5DB
    structure: COc1nc(=O)n(cc1C)[C@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
  5EJ:
    id: 5EJ
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-4-ethoxy-5-methylpyrimidin-2(1h)-one
    synonyms:
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-ethoxy-5-methylpyrimidin-2(1H)-one
    - '[(2R,3S,5R)-5-(4-ethoxy-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 5EJ
    structure: CCOc1nc(=O)n(cc1C)[C@H]1C[C@H]([C@H](O1)COP(=O)(O)O)O
  5HT:
    id: 5HT
    name: 5-hydroxy-thymidine
    synonyms:
    - (5R)-5-hydroxy-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-1,3-diazinane-2,4-dione
    - 5-hydroxythymidine
    - T
    identifiers:
    - ns: pdb-ccd
      id: 5HT
    structure: OC[C@H]1O[C@@H](C[C@@H]1O)N1C[C@](C)(O)C(=O)NC1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 11
  5HU:
    id: 5HU
    name: 5-hydroxymethyluridine-2'-deoxy-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[5-(hydroxymethyl)-2,4-dioxo-pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    - 2'-deoxy-5-(hydroxymethyl)uridine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 5HU
    structure: OCc1cn([C@@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
  5IU:
    id: 5IU
    name: 5-iodo-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(5-iodo-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-iodouridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: 5IU
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(I)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  5MD:
    id: 5MD
    name: 2'-deoxy-1-methyl-pseudouridine
    synonyms:
    - N
    - 5-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methyl-pyrimidine-2,4-dione
    - (1R)-1,4-anhydro-2-deoxy-1-(1-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: 5MD
    structure: OC[C@H]1O[C@H](C[C@@H]1O)c1cn(C)c(=O)[nH]c1=O
  5NC:
    id: 5NC
    name: 5-aza-cytidine-5'monophosphate
    synonyms:
    - 4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1,3,5-triazin-2(1H)-one
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-1,3,5-triazin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: 5NC
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc(nc1=O)N
    base_monomers:
    - C
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  5OC:
    id: 5OC
    name: 2'-deoxy-5-hydroxycytidine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-(4-azanyl-5-oxidanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-hydroxycytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 5OC
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)([O-])[O-])n1cc(O)c(nc1=O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  5PC:
    id: 5PC
    name: 5(1-propynyl)-2'-deoxycytidine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-5-prop-1-ynyl-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-prop-1-yn-1-ylcytidine 5'-(dihydrogen phosphate)
    - C
    identifiers:
    - ns: pdb-ccd
      id: 5PC
    structure: CC#Cc1cn([C@@H]2C[C@@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)nc1N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 17
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  5PY:
    id: 5PY
    name: 1-(2'-deoxy-5'-o-phosphono-beta-d-erythro-pentofuranosyl)-5-methylpyrimidin-2(1h)-one
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methylpyrimidin-2(1H)-one
    - T
    identifiers:
    - ns: pdb-ccd
      id: 5PY
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C)cnc1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  5SE:
    id: 5SE
    name: 2'-deoxy-5-(methylselanyl)cytidine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-(methylselanyl)cytidine 5'-(dihydrogen phosphate)
    - U
    - '[(2R,3S,5R)-5-(4-azanyl-5-methylselanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 5SE
    structure: C[Se]c1cn([C@H]2C[C@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)nc1N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 18
      charge: -1
  5UA:
    id: 5UA
    name: 5'-o-carboxy-2'-deoxyadenosine
    synonyms:
    - '[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl hydrogen carbonate'
    - 5'-O-carboxy-2'-deoxyadenosine
    identifiers:
    - ns: pdb-ccd
      id: 5UA
    structure: OC(=O)OC[C@H]1O[C@H](C[C@H]1O)n1cnc2c1ncnc2N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 14
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 14
  63G:
    id: 63G
    name: (6s)-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3h)-one
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(6S)-6-hydroxy-10-oxo-5,6,7,8-tetrahydropyrimido[1,2-a]purin-3-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (6S)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: 63G
    structure: O[C@H]1CCn2c(N1)nc1c(c2=O)ncn1[C@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 31
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 31
  63H:
    id: 63H
    name: (6r)-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3h)-one
    synonyms:
    - (6R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-hydroxy-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one
    - '[(2R,3S,5R)-3-hydroxy-5-[(6R)-6-hydroxy-10-oxo-5,6,7,8-tetrahydropyrimido[1,2-a]purin-3-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 63H
    structure: O[C@H]1CCn2c(N1)nc1c(c2=O)ncn1[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 31
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 31
  64P:
    id: 64P
    name: 5-aminothymidine 5'-(dihydrogen phosphate)
    synonyms:
    - 5-aminothymidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[(5R)-5-amino-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 64P
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1C[C@@](C)(N)C(=O)NC1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  64T:
    id: 64T
    name: 5-hydroxy-thymidine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-hydroxy-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-hydroxythymidine 5'-(dihydrogen phosphate)
    - T
    identifiers:
    - ns: pdb-ccd
      id: 64T
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])N1C[C@](C)(O)C(=O)NC1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  68Z:
    id: 68Z
    name: 1r,2s,4r)-4-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2-oxidanyl-cyclopentyl]methyl
      dihydrogen phosphate
    synonyms:
    - '[(1R,2S,4R)-4-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2-oxidanyl-cyclopentyl]methyl
      dihydrogen phosphate'
    - G
    - '[(1R,2S,4R)-4-(2-amino-6,8-dioxo-1,6,7,8-tetrahydro-9H-purin-9-yl)-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 68Z
    structure: Nc1[nH]c(=O)c2c(n1)n([C@@H]1C[C@H]([C@@H](C1)O)COP(=O)(O)O)c(=O)[nH]2
    base_monomers:
    - G
  6FK:
    id: 6FK
    name: '[(2~{r},3~{s},5~{r})-5-[2-azanyl-8-[ethanoyl(phenyl)amino]-6-oxidanylidene-3~{h}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - G
    - '[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(phenyl)amino]-6-oxidanylidene-3~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 6FK
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1c(nc2c1[nH]c(N)nc2=O)N(c1ccccc1)C(=O)C
    base_monomers:
    - G
  6FM:
    id: 6FM
    name: 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(6-azanyl-2-fluoranyl-purin-9-yl)-2-ethynyl-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-4'-ethynyl-2-fluoroadenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 6FM
    structure: C#C[C@]1(COP(=O)([O-])[O-])O[C@H](C[C@@H]1O)n1cnc2c1nc(F)nc2N
  6HA:
    id: 6HA
    name: 1',5'-anhydro-2',3'-dideoxy-2'-(adenin-9-yl)-6'-o-phosphoryl-d-arabino-hexitol
    synonyms:
    - 2-(6-amino-9H-purin-9-yl)-1,5-anhydro-2,3-dideoxy-6-O-phosphono-D-arabino-hexitol
    - A
    - '[(2R,3S,5S)-5-(6-aminopurin-9-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 6HA
    structure: O[C@H]1C[C@@H](CO[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  6HB:
    id: 6HB
    name: 2'-deoxy-n-[(2s)-2-hydroxybut-3-en-1-yl]adenosine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-N-[(2S)-2-hydroxybut-3-en-1-yl]adenosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-oxidanyl-5-[6-[[(2S)-2-oxidanylbut-3-enyl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 6HB
    structure: C=C[C@H](CNc1ncnc2c1ncn2[C@@H]1C[C@H]([C@@H](O1)COP(=O)(O)O)O)O
    base_monomers:
    - A
  6HC:
    id: 6HC
    name: 1',5'-anhydro-2',3'-dideoxy-2'-(cytosin-1-yl)-6'-o-phosphoryl-d-arabino-hexitol
    synonyms:
    - C
    - 2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,5-anhydro-2,3-dideoxy-6-O-phosphono-D-arabino-hexitol
    - '[(2R,3S,5S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 6HC
    structure: O[C@H]1C[C@@H](CO[C@@H]1COP(=O)([O-])[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  6HG:
    id: 6HG
    name: 1',5'-anhydro-2',3'-dideoxy-2'-(guanin-9-yl)-6'-o-phosphoryl-d-arabino-hexitol
    synonyms:
    - G
    - '[(2R,3S,5S)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen
      phosphate'
    - 2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1,5-anhydro-2,3-dideoxy-6-O-phosphono-D-arabino-hexitol
    identifiers:
    - ns: pdb-ccd
      id: 6HG
    structure: O[C@H]1C[C@@H](CO[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  6HT:
    id: 6HT
    name: 1',5'-anhydro-2',3'-dideoxy-2'-(thymin-1-yl)-6'-o-phosphoryl-d-arabino-hexitol
    synonyms:
    - '[(2R,3S,5S)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxan-2-yl]methyl
      dihydrogen phosphate'
    - 1,5-anhydro-2,3-dideoxy-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-arabino-hexitol
    - T
    identifiers:
    - ns: pdb-ccd
      id: 6HT
    structure: O[C@H]1C[C@@H](CO[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  6MI:
    id: 6MI
    name: 6-methyl-8-(2-deoxy-ribofuranosyl)isoxanthopteridine
    synonyms:
    - N
    - '[(5R)-5-(2-amino-6-methyl-4,7-dioxo-1H-pteridin-8-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2-amino-8-(2-deoxy-5-O-phosphono-beta-D-threo-pentofuranosyl)-6-methylpteridine-4,7(1H,8H)-dione
    identifiers:
    - ns: pdb-ccd
      id: 6MI
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1c(=O)c(C)nc2c1[nH]c(N)nc2=O
  6PO:
    id: 6PO
    name: 9-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-propoxy-9h-purin-2-amine
    synonyms:
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-propoxy-9H-purin-2-amine
    - '[(2R,3S,5R)-5-(2-azanyl-6-propoxy-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 6PO
    structure: CCCOc1nc(N)nc2c1ncn2[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 29
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 29
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  77Y:
    id: 77Y
    name: " 5-(3-(2-(1h-indol-3-yl)acetamide-n-yl)-1-propen-1-yl)-2'-deoxyuridine"
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[5-[(~{E})-3-[2-(1~{H}-indol-3-yl)ethanoylamino]prop-1-enyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: 77Y
    structure: O=C(Cc1c[nH]c2c1cccc2)NC/C=C/c1cn([C@H]2C[C@H]([C@H](O2)COP(=O)(O)O)O)c(=O)[nH]c1=O
  7BG:
    id: 7BG
    name: 2-amino-7-benzyl-9-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-6-oxo-6,9-dihydro-1h-purin-7-ium
    synonyms:
    - '[(2R,3R,4S,5R)-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1H-purin-7-ium-9-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2-amino-7-benzyl-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-6-oxo-6,9-dihydro-1H-purin-7-ium
    identifiers:
    - ns: pdb-ccd
      id: 7BG
    structure: F[C@H]1[C@@H](O)[C@@H](O[C@@H]1n1c[n+](c2c1nc(N)[nH]c2=O)Cc1ccccc1)COP(=O)(O)O
    base_monomers:
    - G
  7DA:
    id: 7DA
    name: 7-deaza-2'-deoxyadenosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(4-aminopyrrolo[3,2-e]pyrimidin-7-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - A
    - 7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine
    identifiers:
    - ns: pdb-ccd
      id: 7DA
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  7GU:
    id: 7GU
    name: 7-deaza-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - G
    - 2-amino-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one
    - '[(2R,3S,5R)-5-(2-amino-4-oxo-3H-pyrrolo[2,3-d]pyrimidin-7-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 7GU
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  8AA:
    id: 8AA
    name: 8-[acetyl(anthracen-2-yl)amino]-2'-deoxy-5'-o-(dihydroxyphosphanyl)guanosine
    synonyms:
    - G
    - 8-[acetyl(anthracen-2-yl)amino]-2'-deoxy-5'-O-(dihydroxyphosphanyl)guanosine
    - '[(2R,3S,5R)-5-[8-[anthracen-2-yl(ethanoyl)amino]-2-azanyl-6-oxidanylidene-3H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphite'
    identifiers:
    - ns: pdb-ccd
      id: 8AA
    structure: '[O-]P(OC[C@H]1O[C@H](C[C@H]1O)n1c(nc2c1[nH]c(N)nc2=O)N(c1ccc2c(c1)cc1c(c2)cccc1)C(=O)C)[O-]'
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 13
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 2
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 1
      charge: -1
  8AG:
    id: 8AG
    name: 8-[acetyl(anthracen-2-yl)amino]-2'-deoxyguanosine 5'-(dihydrogen phosphate)
    synonyms:
    - G
    - '[(2R,3S,5R)-5-[2-amino-8-(anthracen-2-yl-ethanoyl-amino)-6-oxo-7,8-dihydro-1H-purin-9-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 8-[acetyl(anthracen-2-yl)amino]-2'-deoxyguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: 8AG
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1[C@@H](Nc2c1nc(N)[nH]c2=O)N(c1ccc2c(c1)cc1c(c2)cccc1)C(=O)C
    base_monomers:
    - G
  8BA:
    id: 8BA
    name: 8-bromo-deoxyadenosine-5'-monophosphate
    synonyms:
    - (2~{R},3~{S},5~{R})-5-(6-azanyl-8-bromanyl-purin-9-yl)-2-[[oxidanyl-bis(oxidanylidene)-$l^{6}-phosphanyl]oxymethyl]oxolan-3-ol
    identifiers:
    - ns: pdb-ccd
      id: 8BA
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)(=O)O)n1c(Br)nc2c1ncnc2N
    base_monomers:
    - A
  8DT:
    id: 8DT
    name: " 5-(3-(acetamide-n-yl)-1-propen-1-yl)-2'-deoxyuridine"
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[5-[(~{E})-3-acetamidoprop-1-enyl]-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: 8DT
    structure: CC(=O)NC/C=C/c1cn([C@H]2C[C@H]([C@H](O2)COP(=O)(O)O)O)c(=O)[nH]c1=O
  8FG:
    id: 8FG
    name: n-(5'-phospho-2'-deoxyguanosin-8-yl)-2-acetylaminofluorene
    synonyms:
    - G
    - 8-[acetyl(9H-fluoren-2-yl)amino]-2'-deoxyguanosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[2-amino-8-(ethanoyl-(9H-fluoren-2-yl)amino)-6-oxo-1H-purin-9-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 8FG
    structure: Nc1[nH]c(=O)c2c(n1)n([C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O)c(n2)N(c1ccc2c(c1)Cc1c2cccc1)C(=O)C
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 21
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  8MG:
    id: 8MG
    name: 8-methyl-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - 2'-deoxy-8-methylguanosine 5'-(dihydrogen phosphate)
    - G
    - '[(2R,3S,5R)-5-(2-amino-8-methyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 8MG
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1c(C)nc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  8OG:
    id: 8OG
    name: 8-oxo-2'-deoxy-guanosine-5'-monophosphate
    synonyms:
    - G
    - 2'-deoxy-8-oxoguanosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(2-amino-6,8-dioxo-1,7-dihydropurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 8OG
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1c(=O)[nH]c2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  8PY:
    id: 8PY
    name: '[(2~{r},3~{s},5~{r})-5-[2-azanyl-8-[ethanoyl(pyren-2-yl)amino]-6-oxidanylidene-1~{h}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - G
    - '[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(pyren-2-yl)amino]-6-oxidanylidene-1~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 8PY
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1c(nc2c1nc(N)[nH]c2=O)N(c1cc2ccc3c4c2c(c1)ccc4ccc3)C(=O)C
    base_monomers:
    - G
  8RO:
    id: 8RO
    name: '[(2~{r},3~{s},5~{r})-5-(5-methyl-2-oxidanylidene-7-thia-1,3-diazabicyclo[4.1.0]hept-5-en-3-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphite'
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(5-methyl-2-oxidanylidene-7-thia-1,3-diazabicyclo[4.1.0]hept-5-en-3-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphite'
    identifiers:
    - ns: pdb-ccd
      id: 8RO
    structure: OP(OC[C@H]1O[C@@H](C[C@@H]1O)N1CC(=C2N(C1=O)S2)C)O
    base_monomers:
    - C
  8YN:
    id: 8YN
    name: pseudoisocytidine
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-pyrimidin-5-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: 8YN
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1cnc([nH]c1=O)N
    base_monomers:
    - C
  92F:
    id: 92F
    name: 7-amino-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-2-oxo-2,3-dihydropyrido[2,3-d]pyrimidine-6-carbonitrile
    synonyms:
    - 7-amino-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-2-oxo-2,3-dihydropyrido[2,3-d]pyrimidine-6-carbonitrile
    - '[(2~{R},3~{S},5~{R})-5-(7-azanyl-6-cyano-2-oxidanylidene-pyrido[2,3-d]pyrimidin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: 92F
    structure: N#Cc1cc2cn([C@H]3C[C@H]([C@@H](O3)COP(=O)(O)O)O)c(=O)nc2nc1N
  93D:
    id: 93D
    name: (1r)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[2,4-bis(azanyl)pyrimidin-5-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (1R)-1,4-anhydro-2-deoxy-1-(2,4-diaminopyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: 93D
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)([O-])[O-])c1cnc(nc1N)N
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  94O:
    id: 94O
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-2h-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine-2,6(3h)-dione
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[6,17-bis(oxidanylidene)-5,7,9-triazatetracyclo[8.7.0.0^{3,8}.0^{11,16}]heptadeca-1,3,7,9,11(16),12,14-heptaen-5-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-2H-indeno[2',1':5,6]pyrido[2,3-d]pyrimidine-2,6(3H)-dione
    identifiers:
    - ns: pdb-ccd
      id: 94O
    structure: O[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc2cc3C(=O)c4c(c3nc2nc1=O)cccc4
    base_monomers:
    - T
  9O4:
    id: 9O4
    name: (3r,5r)-5-(6-amino-9h-purin-9-yl)oxolan-3-yl dihydrogen phosphate
    synonyms:
    - '[(3~{R},5~{R})-5-(6-aminopurin-9-yl)oxolan-3-yl] dihydrogen phosphate'
    - (3R,5R)-5-(6-amino-9H-purin-9-yl)oxolan-3-yl dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: 9O4
    structure: Nc1ncnc2c1ncn2[C@@H]1OC[C@H](C1)OP(=O)(O)O
  A38:
    id: A38
    name: 8-oxy deoxyadenosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(6-amino-8-oxo-7H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 2'-deoxy-8-oxoadenosine 5'-(dihydrogen phosphate)
    - A
    identifiers:
    - ns: pdb-ccd
      id: A38
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1c(=O)[nH]c2c1ncnc2N
    base_monomers:
    - A
  A3A:
    id: A3A
    name: 2'deoxy-alpha-anomeric-adenosine-5'-phosphate
    synonyms:
    - 2'-deoxy-5'-adenylic acid
    - A
    - '[(2R,3S,5S)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: A3A
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1ncnc2N
    base_monomers:
    - A
  A40:
    id: A40
    name: n2-methyl 2'-deoxyadenosine 5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(6-amino-2-methylamino-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - A
    - 2'-deoxy-2-(methylamino)adenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: A40
    structure: CNc1nc(N)c2c(n1)n(cn2)[C@@H]1C[C@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - A
  A43:
    id: A43
    name: 3'-amino deoxyadenosine 5'-monophosphate
    synonyms:
    - '[(2S,3S,5R)-3-amino-5-(6-aminopurin-9-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    - A
    - 3'-amino-2',3'-dideoxyadenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: A43
    structure: N[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1ncnc2N
    base_monomers:
    - A
  A47:
    id: A47
    name: n6-methoxy adenosine 5'-monophosphate
    synonyms:
    - 2'-deoxy-N-methoxyadenosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[6-(methoxyamino)purin-9-yl]oxolan-2-yl]methyl dihydrogen
      phosphate'
    - A
    identifiers:
    - ns: pdb-ccd
      id: A47
    structure: CONc1ncnc2c1ncn2[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - A
  A5L:
    id: A5L
    name: 9-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-9h-purin-6-amine
    synonyms:
    - '[(2R,3R,4S,5R)-5-(6-aminopurin-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-9H-purin-6-amine
    - A
    identifiers:
    - ns: pdb-ccd
      id: A5L
    structure: O[C@H]1[C@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1F)n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 11
      charge: -1
  AAB:
    id: AAB
    name: 2'-deoxy-ribofuranose-5'-monophosphate
    synonyms:
    - 2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranose
    - '[(2R,3S,5R)-3,5-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: AAB
    structure: O[C@H]1C[C@H]([C@H](O1)COP(=O)(O)O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 16
  ABR:
    id: ABR
    name: (r)-(n-phenyl-2-hydroxy-ethyl)-2'-deoxy-adenosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[6-[[(2R)-2-hydroxy-2-phenyl-ethyl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-[(2R)-2-hydroxy-2-phenylethyl]adenosine 5'-(dihydrogen phosphate)
    - A
    identifiers:
    - ns: pdb-ccd
      id: ABR
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2NC[C@@H](c1ccccc1)O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  ABS:
    id: ABS
    name: (s)-(n-phenyl-2-hydroxy-ethyl)-2'-deoxy-adenosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[6-[[(2S)-2-hydroxy-2-phenyl-ethyl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - A
    - 2'-deoxy-N-[(2S)-2-hydroxy-2-phenylethyl]adenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: ABS
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2NC[C@@H](c1ccccc1)O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  ABT:
    id: ABT
    name: 3'-azido-3'-deoxy-thymidine-5'-alpha borano triphosphate
    synonyms:
    - N
    - '[[(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy-boranylidene-hydroxy-phosphoranyl]
      phosphono hydrogen phosphate'
    - 3'-azido-5'-O-[(1E,3S)-1-boranylidene-1,3,5,5-tetrahydroxy-3,5-dioxido-1lambda~5~-triphosphoxanyl]-3'-deoxythymidine
    identifiers:
    - ns: pdb-ccd
      id: ABT
    structure: '[N-]=[N+]=N[C@@H]1C[C@@H](O[C@@H]1CO[P@@](=[BH2])(O[P@@](=O)(OP(=O)(O)O)O)O)n1cc(C)c(=O)[nH]c1=O'
  AD2:
    id: AD2
    name: 2'-deoxy-adenosine-3'-5'-diphosphate
    synonyms:
    - '[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-phosphonooxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - A
    - 2'-deoxyadenosine 3',5'-bis(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: AD2
    structure: Nc1ncnc2c1ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])OP(=O)(O)O
    base_monomers:
    - A
  AF2:
    id: AF2
    name: 2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-2'-fluoroadenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: AF2
    structure: O[C@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@H]1F)n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 11
      charge: -1
  AFF:
    id: AFF
    name: 2-acetylaminofluorene-3-yl
    synonyms:
    - N
    - N-(9H-fluoren-2-yl)ethanamide
    - N-9H-fluoren-2-ylacetamide
    identifiers:
    - ns: pdb-ccd
      id: AFF
    structure: CC(=O)Nc1ccc2c(c1)Cc1c2cccc1
  AS:
    id: AS
    name: 2-deoxy-adenosine -5'-thio-monophosphate
    synonyms:
    - (2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(dihydroxyphosphinothioyloxymethyl)oxolan-3-ol
    - A
    - 2'-deoxy-5'-O-thiophosphonoadenosine
    identifiers:
    - ns: pdb-ccd
      id: AS
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=S)([O-])[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  ASU:
    id: ASU
    name: 4'-thio-2'4'-dideoxyribofuranose-5'-phosphate
    synonyms:
    - N
    - 2-deoxy-5-O-phosphono-4-thio-alpha-D-erythro-pentofuranose
    - '[(2R,3S,5S)-3,5-dihydroxythiolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: ASU
    structure: O[C@H]1C[C@@H](S[C@H]1COP(=O)([O-])[O-])O
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  ATD:
    id: ATD
    name: thymidine-3'-phosphate
    synonyms:
    - 3'-thymidylic acid
    - '[(2R,3S,5S)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-3-yl]
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: ATD
    structure: OC[C@H]1O[C@@H](C[C@@H]1OP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  ATM:
    id: ATM
    name: 3'-azido-3'-deoxythymidine-5'-monophosphate
    synonyms:
    - '[(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3'-azido-3'-deoxythymidine 5'-(dihydrogen phosphate)
    - T
    identifiers:
    - ns: pdb-ccd
      id: ATM
    structure: '[N-]=[N+]=N[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O'
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 14
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 17
      charge: -1
  B7C:
    id: B7C
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3h)-one
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(2-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: B7C
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc2C=CCNc2nc1=O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  BGM:
    id: BGM
    name: 8-bromo-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(2-amino-8-bromo-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - G
    - 8-bromo-2'-deoxyguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: BGM
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1c(Br)nc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  BMN:
    id: BMN
    name: (1r)-1,4-anhydro-2-deoxy-1-(3-methoxynaphthalen-2-yl)-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - '[(2R,3S,5R)-5-(3-methoxynaphthalen-2-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - (1R)-1,4-anhydro-2-deoxy-1-(3-methoxynaphthalen-2-yl)-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: BMN
    structure: COc1cc2ccccc2cc1[C@H]1C[C@H]([C@@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 27
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 27
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  BRU:
    id: BRU
    name: 5-bromo-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(5-bromo-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-bromo-2'-deoxyuridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: BRU
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(Br)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  BVP:
    id: BVP
    name: (e)-5-(2-bromovinyl)-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-[5-[(E)-2-bromoethenyl]-2,4-dioxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-[(E)-2-bromoethenyl]-2'-deoxyuridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: BVP
    structure: Br/C=C/c1cn([C@H]2C[C@@H]([C@@H](O2)COP(=O)(O)O)O)c(=O)[nH]c1=O
  BZG:
    id: BZG
    name: 6-(benzyloxy)-9-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-9h-purin-2-amine
    synonyms:
    - N
    - '[(2R,3S,5R)-5-(2-azanyl-6-phenylmethoxy-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 6-(benzyloxy)-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-2-amine
    identifiers:
    - ns: pdb-ccd
      id: BZG
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1cnc2c1nc(N)nc2OCc1ccccc1
  C2S:
    id: C2S
    name: cytidine-5'-dithiophosphorate
    synonyms:
    - 2'-deoxy-5'-O-[(dithiophosphono)]cytidine
    - 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]oxolan-2-yl]pyrimidin-2-one
    - C
    identifiers:
    - ns: pdb-ccd
      id: C2S
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@](=S)(S)[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  C36:
    id: C36
    name: 5-methyl-5-fluoro-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - 2'-deoxy-5-fluoro-5-(hydroxymethyl)cytidine 5'-(dihydrogen phosphate)
    - C
    - '[(2R,3S,5R)-5-[(5R)-4-amino-5-fluoro-5-(hydroxymethyl)-2-oxo-6H-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: C36
    structure: OC[C@@]1(F)CN([C@@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)C(=O)N=C1N
    base_monomers:
    - C
  C37:
    id: C37
    name: 5-fluoro-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(4-amino-5-fluoro-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    - 2'-deoxy-5-fluorocytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: C37
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc(F)c(nc1=O)N
    base_monomers:
    - C
  C38:
    id: C38
    name: 5-iodo-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - C
    - 2'-deoxy-5-iodocytidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(4-amino-5-iodo-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: C38
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc(I)c(nc1=O)N
    base_monomers:
    - C
  C42:
    id: C42
    name: 3'-amino-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - 3'-amino-2',3'-dideoxycytidine 5'-(dihydrogen phosphate)
    - C
    - '[(2S,3S,5R)-3-amino-5-(4-amino-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: C42
    structure: N[C@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1ccc(nc1=O)N
    base_monomers:
    - C
  C45:
    id: C45
    name: n4-methoxy-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - 2'-deoxy-N-methoxycytidine 5'-(dihydrogen phosphate)
    - C
    - '[(2R,3S,5R)-3-hydroxy-5-[4-(methoxyamino)-2-oxo-pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: C45
    structure: CONc1ccn(c(=O)n1)[C@H]1C[C@@H]([C@@H](O1)COP(=O)(O)O)O
    base_monomers:
    - C
  C46:
    id: C46
    name: 6h,8h-3,4-dihydropyrimido[4,5-c][1,2]oxazin-7-0ne(cytidine)-5'-monophosphate
    synonyms:
    - C
    - '[(2R,3S,5R)-3-hydroxy-5-(7-oxo-3,4-dihydro-1H-pyrimido[4,5-c][1,2]oxazin-6-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 6-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4,6-dihydro-1H-pyrimido[4,5-c][1,2]oxazin-7(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: C46
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc2CCONc2nc1=O
    base_monomers:
    - C
  C49:
    id: C49
    name: 4-thio,5-fluoro,5-methyl-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - 2'-deoxy-5-fluoro-5-methyl-6-thioxocytidine 5'-(dihydrogen phosphate)
    - C
    - '[(2R,3S)-5-[(5R)-5-fluoro-4-imino-5-methyl-2-oxo-6-sulfanylidene-1,3-diazinan-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: C49
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1C(=O)NC(=N)[C@@](C1=S)(C)F
    base_monomers:
    - C
  C4S:
    id: C4S
    name: 2'-deoxy-4'-thiocytidine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-thiolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    - 2'-deoxy-4'-thiocytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: C4S
    structure: O[C@H]1C[C@@H](S[C@H]1COP(=O)(O)O)n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  C6G:
    id: C6G
    name: 6-(carboxymethoxy)-9-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-9h-purin-2-amine
    synonyms:
    - 6-(carboxymethoxy)-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purin-2-amine
    - 2-[2-azanyl-9-[(2R,4S,5R)-4-oxidanyl-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]oxyethanoic
      acid
    identifiers:
    - ns: pdb-ccd
      id: C6G
    structure: OC(=O)COc1nc(N)nc2c1ncn2[C@@H]1C[C@@H]([C@@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 30
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 26
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 30
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 29
      charge: -1
  C7R:
    id: C7R
    name: 2'-deoxy-5'-o-thiophosphonocytidine
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic
      acid'
    - 2'-deoxy-5'-O-thiophosphonocytidine
    identifiers:
    - ns: pdb-ccd
      id: C7R
    structure: O[C@@H]1C[C@H](O[C@@H]1CO[P@@](=O)(S)[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
  C7S:
    id: C7S
    name: 2'-deoxy-5'-o-thiophosphonocytidine
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic
      acid'
    - 2'-deoxy-5'-O-thiophosphonocytidine
    identifiers:
    - ns: pdb-ccd
      id: C7S
    structure: O[C@@H]1C[C@H](O[C@H]1CO[P@](=O)(S)[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
  CBR:
    id: CBR
    name: 5-bromo-2'-deoxy-cytidine-5'-monophosphate
    synonyms:
    - C
    - '[(2R,3S,5R)-5-(4-amino-5-bromo-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-bromo-2'-deoxycytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: CBR
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(Br)c(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  CDW:
    id: CDW
    name: (4r)-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-1,3-diazabicyclo[2.2.0]hex-5-en-2-one
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(4R)-6-oxo-1,5-diazabicyclo[2.2.0]hex-2-en-5-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    - (4R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1,3-diazabicyclo[2.2.0]hex-5-en-2-one
    identifiers:
    - ns: pdb-ccd
      id: CDW
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1C(=O)N2[C@H]1C=C2
    base_monomers:
    - C
  CFL:
    id: CFL
    name: 4-amino-1-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)pyrimidin-2(1h)-one
    synonyms:
    - 4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidin-2(1H)-one
    - C
    - '[(2R,3R,4S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: CFL
    structure: O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@H]1F)n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  CFZ:
    id: CFZ
    name: 2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3R,4R,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: CFZ
    structure: O[C@H]1[C@H](COP(=O)(O)O)O[C@H]([C@@H]1F)n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  CGY:
    id: CGY
    name: (1r)-1,4-anhydro-2-deoxy-1-[2,6-diamino-5-(dihydroxyamino)pyridin-3-yl]-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[2,6-bis(azanyl)-5-[bis(oxidanyl)amino]pyridin-3-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (1R)-1,4-anhydro-2-deoxy-1-[2,6-diamino-5-(dihydroxyamino)pyridin-3-yl]-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: CGY
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1cc(N(O)O)c(nc1N)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  CJ1:
    id: CJ1
    name: 7-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-7h-pyrrolo[2,3-d]pyrimidine-2,4-diol
    synonyms:
    - 7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-2,4-diol
    - '[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanyl)pyrrolo[2,3-d]pyrimidin-7-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: CJ1
    structure: Oc1nc(O)c2c(n1)n(cc2)[C@H]1O[C@@H]([C@@H](C1)O)COP(=O)(O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
  CMR:
    id: CMR
    name: 2'-deoxy-cytidine-5'-rp-monomethylphosphonate
    synonyms:
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-methyl-phosphinic
      acid'
    - 2'-deoxy-5'-O-[(S)-hydroxy(methyl)phosphoryl]cytidine
    - C
    identifiers:
    - ns: pdb-ccd
      id: CMR
    structure: O[C@@H]1C[C@@H](O[C@@H]1CO[P@](=O)(C)[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  CP1:
    id: CP1
    name: 2-(methylamino)-ethylglycine-carbonylmethylene-cytosine
    synonyms:
    - C
    - 2-[2-(4-amino-2-oxo-pyrimidin-1-yl)ethanoyl-(2-methylaminoethyl)amino]ethanoic
      acid
    - N-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]-N-[2-(methylamino)ethyl]glycine
    identifiers:
    - ns: pdb-ccd
      id: CP1
    structure: CNCCN(C(=O)Cn1ccc(nc1=O)N)CC(=O)O
    base_monomers:
    - C
  CSL:
    id: CSL
    name: (d)-2'-methylselenyl-2'-deoxycytidine-5'-phosphate
    synonyms:
    - C
    - '[(2R,3R,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-4-methylselanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-Se-methyl-2'-selenocytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: CSL
    structure: C[Se][C@H]1[C@@H](O)[C@H](O[C@H]1n1ccc(nc1=O)N)COP(=O)(O)O
    base_monomers:
    - C
  CSM:
    id: CSM
    name: 1-{2,5-anhydro-6-o-methyl-4-[(phosphonooxy)methyl]-alpha-l-mannofuranosyl}pyrimidine-2,4(1h,3h)-dione
    synonyms:
    - 1-{2,5-anhydro-6-O-methyl-4-[(phosphonooxy)methyl]-alpha-L-mannofuranosyl}pyrimidine-2,4(1H,3H)-dione
    - '[(1R,3S,4R,6R,7S)-6-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-(methoxymethyl)-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-4-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: CSM
    structure: COC[C@H]1O[C@@H]2[C@@H]([C@]1(COP(=O)([O-])[O-])O[C@@H]2n1ccc(=O)[nH]c1=O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 30
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 14
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 30
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  CX2:
    id: CX2
    name: 2'-deoxy-5'-o-{(r)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}cytidine
    synonyms:
    - 2'-deoxy-5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}cytidine
    - '[(2R,3S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: CX2
    structure: '[O-][P@@](=O)(OC[C@@H]1O[C@H](C[C@H]1O)n1ccc(nc1=O)N)NCCS'
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 14
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 14
  D00:
    id: D00
    name: 2'-deoxy-n-ethylcytidine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-N-ethylcytidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[4-(ethylamino)-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: D00
    structure: CCNc1ccn(c(=O)n1)[C@@H]1C[C@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
  D3:
    id: D3
    name: 1-(2-deoxy-beta-d-ribofuranosyl)-4-(3-benzamido)phenylimidazole
    synonyms:
    - N
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-{3-[(phenylcarbonyl)amino]phenyl}-1H-imidazole
    - '[(2R,3S,5R)-5-[4-(3-benzamidophenyl)imidazol-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: D3
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc(c1)c1cccc(c1)NC(=O)c1ccccc1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  D33:
    id: D33
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-1h-imidazole
    synonyms:
    - N
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-imidazole
    - '[(2R,3S,5R)-3-hydroxy-5-imidazol-1-yl-oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: D33
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cncc1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  D3N:
    id: D3N
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-1h-perimidin-2(3h)-one
    synonyms:
    - '[(2R,3S,5R)-3-oxidanyl-5-(2-oxidanylidene-3H-perimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-perimidin-2(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: D3N
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1c(=O)[nH]c2c3c1cccc3ccc2
  D3T:
    id: D3T
    name: 2',3'-dideoxy-thymidine-5'-triphosphate
    synonyms:
    - (hydroxy-phosphonooxy-phosphoryl) [(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      hydrogen phosphate
    - T
    identifiers:
    - ns: pdb-ccd
      id: D3T
    structure: O=c1[nH]c(=O)n(cc1C)[C@H]1CC[C@H](O1)CO[P@](=O)(O[P@](=O)(OP(=O)(O)O)O)O
    base_monomers:
    - T
  D4B:
    id: D4B
    name: '[(2~{r},3~{s},5~{r})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[4-azanyl-5-[2-(4-ethynylphenyl)ethynyl]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: D4B
    structure: C#Cc1ccc(cc1)C#Cc1cn([C@@H]2C[C@@H]([C@@H](O2)COP(=O)(O)O)O)c(=O)nc1N
    base_monomers:
    - C
  D4M:
    id: D4M
    name: '[(5r)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-2,5-dihydrofuran-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2,5-dihydrofuran-2-yl]methyl
      dihydrogen phosphate'
    - T
    - '[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,5-dihydrofuran-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: D4M
    structure: O=c1[nH]c(=O)n(cc1C)[C@@H]1C=C[C@H](O1)COP(=O)([O-])[O-]
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  DCT:
    id: DCT
    name: 2',3'-dideoxycytidine 5'-triphosphate
    synonyms:
    - '[(2S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl (hydroxy-phosphonooxy-phosphoryl)
      hydrogen phosphate'
    - C
    identifiers:
    - ns: pdb-ccd
      id: DCT
    structure: Nc1ccn(c(=O)n1)[C@H]1CC[C@@H](O1)CO[P@](=O)(O[P@](=O)(OP(=O)(O)O)O)O
    base_monomers:
    - C
  DCZ:
    id: DCZ
    name: 2'-deoxycytidine
    synonyms:
    - 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidin-2-one
    - 2'-deoxycytidine
    identifiers:
    - ns: pdb-ccd
      id: DCZ
    structure: OC[C@@H]1O[C@H](C[C@@H]1O)n1ccc(nc1=O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 11
  DDG:
    id: DDG
    name: 2',3'-dideoxy-guanosine-5'-monophosphate
    synonyms:
    - G
    - '[(2S,5R)-5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    - '[(2S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DDG
    structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1CC[C@H](O1)COP(=O)([O-])[O-]
    base_monomers:
    - G
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 24
      charge: -1
  DDN:
    id: DDN
    name: 3,4-dihydro-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(4R)-4-hydroxy-2-oxo-3,4-dihydropyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (4R)-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one
    - U
    identifiers:
    - ns: pdb-ccd
      id: DDN
    structure: O[C@H]1C=CN(C(=O)N1)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
  DDX:
    id: DDX
    name: 2',3'-dehydro-2',3'-dideoxyribofuranose-5'-phosphate
    synonyms:
    - N
    - '[(2S,5S)-5-hydroxy-2,5-dihydrofuran-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DDX
    structure: O[C@@H]1C=C[C@H](O1)COP(=O)([O-])[O-]
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 11
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  DFT:
    id: DFT
    name: 1-[2-deoxyribofuranosyl]-2,4-difluoro-5-methyl-benzene-5'monophosphate
    synonyms:
    - N
    - '[(2R,3S,5R)-5-(2,4-difluoro-5-methyl-phenyl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - (1R)-1,4-anhydro-2-deoxy-1-(2,4-difluoro-5-methylphenyl)-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: DFT
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])c1cc(C)c(cc1F)F
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  DG8:
    id: DG8
    name: 2'-deoxy-8-(pyren-1-ylamino)guanosine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-8-(pyren-1-ylamino)guanosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[2-azanyl-6-oxidanylidene-8-(pyren-1-ylamino)-1H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DG8
    structure: Nc1[nH]c(=O)c2c(n1)n([C@@H]1O[C@@H]([C@@H](C1)O)COP(=O)(O)O)c(n2)Nc1ccc2c3c1ccc1c3c(cc2)ccc1
    base_monomers:
    - G
  DGI:
    id: DGI
    name: 2'-deoxyguanosine-5'-diphosphate
    synonyms:
    - G
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl phosphono
      hydrogen phosphate'
    - 2'-deoxyguanosine 5'-(trihydrogen diphosphate)
    identifiers:
    - ns: pdb-ccd
      id: DGI
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@@](=O)(OP(=O)(O)O)O)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  DN:
    id: DN
    name: unknown 2'-deoxynucleotide
    synonyms:
    - N
    - 1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
    - '[(2R,3S)-3-hydroxyoxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DN
    structure: O[C@H]1CCO[C@@H]1COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 13
      charge: -1
  DNR:
    id: DNR
    name: 2'-deoxy-n3-protonated cytidine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - C
    - 2'-deoxy-5'-cytidylic acid
    identifiers:
    - ns: pdb-ccd
      id: DNR
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc([nH+]c1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  DOC:
    id: DOC
    name: 2',3'-dideoxycytidine-5'-monophosphate
    synonyms:
    - '[(2S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    - C
    - '[(2S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DOC
    structure: Nc1ccn(c(=O)n1)[C@H]1CC[C@@H](O1)COP(=O)([O-])[O-]
    base_monomers:
    - C
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 18
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 21
      charge: -1
  DPB:
    id: DPB
    name: (s)-1-[2'-deoxy-3',5'-o-(1-phosphono)benzylidene-b-d-threo-pentofuranosyl]thymine
    synonyms:
    - '[(2S,4aS,6S,7aS)-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2-phenyl-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3]dioxin-2-yl]phosphonic
      acid'
    - 1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-L-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione
    - T
    identifiers:
    - ns: pdb-ccd
      id: DPB
    structure: O=c1[nH]c(=O)n(cc1C)[C@@H]1C[C@@H]2[C@H](O1)CO[C@@](O2)(c1ccccc1)P(=O)([O-])[O-]
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 29
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 32
      charge: -1
  DPY:
    id: DPY
    name: 2-deoxyribofuranosyl-pyridine-2,6-dicarboxylic acid-5'-monophosphate
    synonyms:
    - N
    - (1R)-1,4-anhydro-2-deoxy-1-(2,6-dicarboxypyridin-3-yl)-5-O-phosphono-D-erythro-pentitol
    - 3-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]pyridine-2,6-dicarboxylic
      acid
    identifiers:
    - ns: pdb-ccd
      id: DPY
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1ccc(nc1C(=O)O)C(=O)O
  DRM:
    id: DRM
    name: '{[(1r,2s)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)cyclopentyl]oxy}methylphosphonic
      acid'
    synonyms:
    - '[(1R,2R)-2-(2,4-dioxopyrimidin-1-yl)cyclopentyl]oxymethylphosphonic acid'
    - ({[(1R,2R)-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]oxy}methyl)phosphonic
      acid
    - U
    identifiers:
    - ns: pdb-ccd
      id: DRM
    structure: O=c1ccn(c(=O)[nH]1)[C@@H]1CCC[C@@H]1OCP(=O)([O-])[O-]
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 19
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 22
      charge: -1
  DRP:
    id: DRP
    name: 2-deoxyribofuranosyl-pyridine-5'-monophosphate
    synonyms:
    - N
    - (1R)-1,4-anhydro-2-deoxy-5-O-phosphono-1-pyridin-3-yl-D-erythro-pentitol
    - '[(2R,3S,5R)-3-hydroxy-5-pyridin-3-yl-oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DRP
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1cccnc1
  DRZ:
    id: DRZ
    name: 3',4'-dihydroxy-pentanal-5'-phosphate
    synonyms:
    - N
    - '[(2R,3S)-2,3-dihydroxy-5-oxo-pentyl] dihydrogen phosphate'
    - 2-deoxy-5-O-phosphono-D-erythro-pentose
    identifiers:
    - ns: pdb-ccd
      id: DRZ
    structure: O=CC[C@H]([C@@H](COP(=O)([O-])[O-])O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 15
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 10
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 15
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 13
      charge: -1
  DUZ:
    id: DUZ
    name: 5-(benzylcarbamoyl)-2'-deoxyuridine 5'-(dihydrogen phosphate)
    synonyms:
    - 5-(benzylcarbamoyl)-2'-deoxyuridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-[(phenylmethyl)carbamoyl]pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DUZ
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C(=O)NCc2ccccc2)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  DX:
    id: DX
    name: '[(2~{r},3~{s},5~{r})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DX
    structure: O=c1[nH]c(=O)n2c(n1)n(cc2)[C@@H]1O[C@H]([C@@H](C1)O)COP(=O)(O)O
  DXD:
    id: DXD
    name: (1s,3s,4r)-4-(phosphooxymethyl)-cyclopentane-1,3-diol
    synonyms:
    - N
    - '[(1R,2S,4S)-2,4-dihydroxycyclopentyl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DXD
    structure: O[C@@H]1C[C@@H](C[C@@H]1COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  DZM:
    id: DZM
    name: 3-deaza-3-methyladenine
    synonyms:
    - '[(2R,3S,5R)-5-(4-azanyl-7-methyl-imidazo[4,5-c]pyridin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7-methyl-1H-imidazo[4,5-c]pyridin-4-amine
    - A
    identifiers:
    - ns: pdb-ccd
      id: DZM
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cnc2c1c(C)cnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  E:
    id: E
    name: n-((-)-(7s,8r,9s,10r)[7,8,9-trihydroxy-7,8,9,10-tetra hydrobenzo[a]pyren-10-yl])-2'-deoxy-adenosine-5'-monophosphate
    synonyms:
    - 2'-deoxy-N-[(7S,8R,9S,10R)-7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[pqr]tetraphen-10-yl]adenosine
      5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[6-[[(7S,8R,9S,10R)-7,8,9-trihydroxy-7,8,9,10-tetrahydrobenzo[a]pyren-10-yl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - A
    identifiers:
    - ns: pdb-ccd
      id: E
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2N[C@H]1[C@H](O)[C@H](O)[C@@H](c2c1c1ccc3c4c1c(c2)ccc4ccc3)O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  E1X:
    id: E1X
    name: phosphoric acid mono-[5-(1-ethyl-2,6-dioxo-1,2,3,6-tetrahydro-purin-9-yl)-3-hydroxy-tetrahydro-furan-2-ylmethyl]ester
    synonyms:
    - '[(2R,3S,5R)-5-(1-ethyl-2,6-dioxo-3H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-1-ethylxanthosine 5'-(dihydrogen phosphate)
    - A
    identifiers:
    - ns: pdb-ccd
      id: E1X
    structure: CCn1c(=O)[nH]c2c(c1=O)ncn2[C@@H]1O[C@@H]([C@H](C1)O)COP(=O)([O-])[O-]
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 23
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 26
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 23
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 29
      charge: -1
  EAN:
    id: EAN
    name: '[(1~{s},2~{r},4~{r},6~{s},8~{r})-8-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl]
      dihydrogen phosphate'
    synonyms:
    - '[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl]
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: EAN
    structure: O=c1[nH]c(=O)n(cc1C)[C@@H]1O[C@@H]2[C@@](C1)(O)C[C@H]1[C@]2(C1)OP(=O)(O)O
    base_monomers:
    - T
  EDA:
    id: EDA
    name: 3-[2-deoxy-ribofuranosyl]-3h-1,3,4,5a,8-pentaaza-as-indacene-5'-monophosphate
    synonyms:
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3H-imidazo[2,1-i]purine
    - A
    - '[(2R,3S,5R)-3-hydroxy-5-imidazo[2,1-f]purin-3-yl-oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: EDA
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncn1c2ncc1
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  EDI:
    id: EDI
    name: 2'-deoxy-1-(2-iodoethyl)inosine
    synonyms:
    - '[(2R,3S,5R)-5-[1-(2-iodanylethyl)-6-oxidanylidene-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-1-(2-iodoethyl)inosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: EDI
    structure: ICCn1cnc2c(c1=O)ncn2[C@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
  EHG:
    id: EHG
    name: 9-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-(2-hydroxyethoxy)-9h-purin-2-amine
    synonyms:
    - '[(2R,3S,5R)-5-[2-azanyl-6-(2-hydroxyethyloxy)purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-(2-hydroxyethoxy)-9H-purin-2-amine
    identifiers:
    - ns: pdb-ccd
      id: EHG
    structure: OCCOc1nc(N)nc2c1ncn2[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 29
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 29
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  EXC:
    id: EXC
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5':5,6][1,4]oxazino[2,3-f]isoindol-2(3h)-one
      radical
    synonyms:
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-7,7,9,9-tetramethyl-7,8,9,11-tetrahydropyrimido[4',5':5,6][1,4]oxazino[2,3-f]isoindol-2(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: EXC
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc2oc3cc4c(cc3[nH]c2nc1=O)C(N(C4(C)C)O)(C)C
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  F3H:
    id: F3H
    name: 1,5-anhydro-2,3-dideoxy-3-fluoro-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-6-o-phosphono-d-altritol
    synonyms:
    - 1,5-anhydro-2,3-dideoxy-3-fluoro-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-altritol
    - '[(2R,3R,4S,5R)-4-fluoro-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: F3H
    structure: F[C@H]1[C@H](O)[C@H](OC[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 6
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 6
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  F4H:
    id: F4H
    name: 1,5-anhydro-2,3-dideoxy-3-fluoro-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-6-o-phosphono-d-mannitol
    synonyms:
    - 1,5-anhydro-2,3-dideoxy-3-fluoro-2-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-mannitol
    - '[(2R,3R,4R,5R)-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: F4H
    structure: F[C@H]1[C@@H](O)[C@@H](OC[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O
    base_monomers:
    - T
  F4Q:
    id: F4Q
    name: '[(1~{s},2~{r},4~{r},6~{s},8~{r})-8-(2-azanyl-6-oxidanylidene-1~{h}-purin-9-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl]
      dihydrogen phosphate'
    synonyms:
    - G
    - '[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl]
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: F4Q
    structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1O[C@@H]2[C@@](C1)(O)C[C@H]1[C@@]2(C1)OP(=O)(O)O
    base_monomers:
    - G
  F5H:
    id: F5H
    name: 3,7-anhydro-1,5,6-trideoxy-5-fluoro-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-2-o-phosphono-d-glycero-l-altro-heptitol
    synonyms:
    - 3,7-anhydro-1,5,6-trideoxy-5-fluoro-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-O-phosphono-D-glycero-L-altro-heptitol
    - '[(1S)-1-[(2S,3R,4S,5R)-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxan-2-yl]ethyl]
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: F5H
    structure: F[C@@H]1[C@@H](O)[C@@H](OC[C@@H]1n1cc(C)c(=O)[nH]c1=O)[C@@H](OP(=O)(O)O)C
  F6H:
    id: F6H
    name: 3,7-anhydro-1,5,6-trideoxy-5-fluoro-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-2-o-phosphono-d-glycero-l-allo-heptitol
    synonyms:
    - 3,7-anhydro-1,5,6-trideoxy-5-fluoro-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-O-phosphono-D-glycero-L-allo-heptitol
    - '[(1R)-1-[(2S,3R,4S,5R)-4-fluoranyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxan-2-yl]ethyl]
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: F6H
    structure: F[C@H]1[C@H](O)[C@H](OC[C@@H]1n1cc(C)c(=O)[nH]c1=O)[C@H](OP(=O)([O-])[O-])C
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  F7H:
    id: F7H
    name: 4-azanyl-1-[(1~{s},2~{r},4~{s},6~{s},8~{r})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-5-methyl-pyrimidin-2-one
    synonyms:
    - C
    - 4-azanyl-1-[(1~{S},2~{R},4~{S},6~{S},8~{R})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-5-methyl-pyrimidin-2-one
    identifiers:
    - ns: pdb-ccd
      id: F7H
    structure: Cc1cn([C@H]2C[C@]3([C@@H](O2)[C@]2([C@H](C3)C2)O)O)c(=O)nc1N
    base_monomers:
    - C
  F7K:
    id: F7K
    name: 2-azanyl-9-[(1~{s},2~{r},4~{s},6~{s},8~{r})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-1~{h}-purin-6-one
    synonyms:
    - G
    - 2-azanyl-9-[(1~{S},2~{R},4~{S},6~{S},8~{R})-2,6-bis(oxidanyl)-9-oxatricyclo[4.3.0.0^{2,4}]nonan-8-yl]-1~{H}-purin-6-one
    identifiers:
    - ns: pdb-ccd
      id: F7K
    structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@H]1O[C@@H]2[C@](C1)(O)C[C@H]1[C@]2(O)C1
    base_monomers:
    - G
  FAG:
    id: FAG
    name: "[1',2'-dideoxy[2-amino-5-([9-hydroxy-aflatoxinb2-8-yl]-formyl-amino)-6-oxo-1,6-ihydro-pyrimidin-4-ylamino]-ribofuranose]-5-monophosphate\
      \ group"
    synonyms:
    - N
    - N-(2-amino-5-{formyl[(6aS,8R,9R,9aR)-9-hydroxy-4-methoxy-1,11-dioxo-1,2,3,6a,8,9,9a,11-octahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine
    identifiers:
    - ns: pdb-ccd
      id: FAG
    structure: O=CN(c1c(N[C@H]2C[C@H]([C@H](O2)COP(=O)(O)O)O)nc([nH]c1=O)N)[C@@H]1O[C@@H]2[C@@H]([C@@H]1O)c1c(O2)cc(c2c1oc(=O)c1c2CCC1=O)OC
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
  FAX:
    id: FAX
    name: '[(1r,2s,4r)-4-{[6-amino-5-(formylamino)pyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,2S,4R)-4-{[6-amino-5-(formylamino)pyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,4R)-4-[(6-azanyl-5-formamido-pyrimidin-4-yl)amino]-2-oxidanyl-cyclopentyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: FAX
    structure: O=CNc1c(ncnc1N)N[C@H]1C[C@H]([C@H](C1)O)COP(=O)([O-])[O-]
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  FDG:
    id: FDG
    name: 2-amino-9-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-7,9-dihydro-1h-purine-6,8-dione
    synonyms:
    - '[(2R,3R,4S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7,9-dihydro-1H-purine-6,8-dione
    identifiers:
    - ns: pdb-ccd
      id: FDG
    structure: O[C@H]1[C@H](COP(=O)([O-])[O-])O[C@H]([C@H]1F)n1c(=O)[nH]c2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 11
      charge: -1
  FFD:
    id: FFD
    name: (1r)-1,4-anhydro-2-deoxy-1-(3-fluorophenyl)-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - N
    - '[(2R,3S,5R)-5-(3-fluorophenyl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate'
    - (1R)-1,4-anhydro-2-deoxy-1-(3-fluorophenyl)-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: FFD
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1cccc(c1)F
  FMG:
    id: FMG
    name: 2-amino-9-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-7-methyl-6-oxo-6,9-dihydro-1h-purin-7-ium
    synonyms:
    - G
    - 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7-methyl-6-oxo-6,9-dihydro-1H-purin-7-ium
    - '[(2R,3R,4S,5R)-5-(2-amino-7-methyl-6-oxo-1H-purin-7-ium-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: FMG
    structure: O[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1F)n1c[n+](c2c1nc(N)[nH]c2=O)C
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 11
      charge: -1
  FNU:
    id: FNU
    name: 6-amino-5-fluorouridine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,4R,5R)-5-(6-azanyl-5-fluoro-2,4-dioxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 6-amino-5-fluorouridine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: FNU
    structure: O[C@@H]1[C@@H](O)[C@@H](O[C@@H]1n1c(=O)[nH]c(=O)c(c1N)F)COP(=O)(O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 6
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 6
  FOX:
    id: FOX
    name: ((1r,2s,4r)-4-{[2-amino-5-(formylamino)-6-oxo-3,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl)methyl
      5'-phosphate
    synonyms:
    - G
    - '[(1R,2S,4R)-4-{[2-amino-5-(formylamino)-6-oxo-3,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,4R)-4-[(2-amino-5-formamido-6-oxo-3H-pyrimidin-4-yl)amino]-2-hydroxy-cyclopentyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: FOX
    structure: O=CNc1c(=O)nc([nH]c1N[C@H]1C[C@@H]([C@H](C1)O)COP(=O)(O)O)N
    base_monomers:
    - G
  G2S:
    id: G2S
    name: guanosine-5'-dithiophosphorate
    synonyms:
    - G
    - 2-amino-9-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]oxolan-2-yl]-1H-purin-6-one
    - 2'-deoxy-5'-O-[(dithiophosphono)]guanosine
    identifiers:
    - ns: pdb-ccd
      id: G2S
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@](=S)(S)[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  G31:
    id: G31
    name: 3'-methyl-2',3'-deoxy-guanosine-5'-monophosphate
    synonyms:
    - 2',3'-dideoxy-3'-methylguanosine 5'-(dihydrogen phosphate)
    - G
    - '[(2S,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-methyl-oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: G31
    structure: C[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
  G35:
    id: G35
    name: (5r)-5-carbamimidamido-1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)imidazolidine-2,4-dione
    synonyms:
    - '[(2R,3S,5R)-5-[(5R)-5-carbamimidamido-2,4-dioxo-imidazolidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: G35
    structure: NC(=N)N[C@H]1C(=O)NC(=O)N1[C@@H]1C[C@H]([C@@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 27
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 27
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  G36:
    id: G36
    name: o6-ethyl-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - G
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-ethoxy-9H-purin-2-amine
    - '[(2R,3S,5R)-5-(2-amino-6-ethoxy-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: G36
    structure: CCOc1nc(N)nc2c1ncn2[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - G
  G38:
    id: G38
    name: 3'-amino-2'-deoxy-guanosine-5'-monophosphate
    synonyms:
    - G
    - '[(2S,3S,5R)-3-amino-5-(2-amino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 3'-amino-2',3'-dideoxyguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: G38
    structure: N[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
  G47:
    id: G47
    name: n2-ethanethiol-2'-deoxy-guanosine-5'-monophosphate
    synonyms:
    - G
    - 2'-deoxy-N-(2-sulfanylethyl)guanosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[6-oxo-2-(2-sulfanylethylamino)-1H-purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: G47
    structure: SCCNc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - G
  G49:
    id: G49
    name: n2-methyl-2'-deoxy-guanosine-5'-monophosphate
    synonyms:
    - G
    - '[(2R,3S,5R)-3-hydroxy-5-(2-methylamino-6-oxo-1H-purin-9-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-methylguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: G49
    structure: CNc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
    base_monomers:
    - G
  GCK:
    id: GCK
    name: phosphoric acid 9-(2-guanidinoethoxy-3-(2-deoxy-beta-d-erythropentofuranosyl))-3h-pyrimido-[5,4-b][1,4]-benzooxazin-2-one]-5'-ester
    synonyms:
    - '[amino-[2-[[3-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2-oxo-10H-pyrimido[5,4-b][1,4]benzoxazin-9-yl]oxy]ethylamino]methylidene]azanium'
    - C
    - 9-(2-{[amino(iminio)methyl]amino}ethoxy)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3H-pyrimido[5,4-b][1,4]benzoxazin-2(10H)-one
    identifiers:
    - ns: pdb-ccd
      id: GCK
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1cc2oc3cccc(c3[nH]c2nc1=O)OCCNC(=[NH2+])N
    base_monomers:
    - C
  GF2:
    id: GF2
    name: 2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate)
    - '[(2R,3R,4R,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: GF2
    structure: O[C@@H]1[C@H](COP(=O)([O-])[O-])O[C@@H]([C@@H]1F)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 11
      charge: -1
  GFL:
    id: GFL
    name: 2-amino-9-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-1,9-dihydro-6h-purin-6-one
    synonyms:
    - G
    - '[(2R,3R,4S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-1,9-dihydro-6H-purin-6-one
    identifiers:
    - ns: pdb-ccd
      id: GFL
    structure: O[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@H]1F)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  GMS:
    id: GMS
    name: 2'-deoxyguanosine-5'-monoselenophosphate
    synonyms:
    - G
    - 2'-deoxy-5'-O-selenophosphonoguanosine
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-selanyl-phosphinic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: GMS
    structure: O[C@H]1C[C@@H](O[C@@H]1CO[P@@](=O)([SeH])[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  GN7:
    id: GN7
    name: n7-2'-deoxy-guanosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-7-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - G
    - 2-amino-7-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1,7-dihydro-6H-purin-6-one
    identifiers:
    - ns: pdb-ccd
      id: GN7
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1c(=O)[nH]c(n2)N
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  GNE:
    id: GNE
    name: 1,n2-ethenoguanine
    synonyms:
    - N
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,5-dihydro-9H-imidazo[1,2-a]purin-9-one
    - '[(2R,3S,5R)-3-hydroxy-5-(9-oxo-5H-imidazo[1,2-a]purin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: GNE
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1nc1[nH]ccn1c2=O
  GS:
    id: GS
    name: guanosine-5'-thio-monophosphate
    synonyms:
    - G
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphinic
      acid'
    - 2'-deoxy-5'-O-thiophosphonoguanosine
    identifiers:
    - ns: pdb-ccd
      id: GS
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@](=O)(S)[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  GSR:
    id: GSR
    name: 2'-deoxy-n2-(r)styrene oxide guanosine monophosphate
    synonyms:
    - G
    - 2'-deoxy-N-[(1R)-2-hydroxy-1-phenylethyl]guanosine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[2-[[(1R)-2-hydroxy-1-phenyl-ethyl]amino]-6-oxo-1H-purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: GSR
    structure: OC[C@@H](c1ccccc1)Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 37
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 33
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 37
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 36
      charge: -1
  GSS:
    id: GSS
    name: 2'-deoxy-n2-(s)styrene oxide guanosine monophosphate
    synonyms:
    - G
    - '[(2R,3S,5R)-3-hydroxy-5-[2-[[(1S)-2-hydroxy-1-phenyl-ethyl]amino]-6-oxo-1H-purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-[(1S)-2-hydroxy-1-phenylethyl]guanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: GSS
    structure: OC[C@@H](c1ccccc1)Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 37
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 33
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 37
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 36
      charge: -1
  GX1:
    id: GX1
    name: 2'-deoxy-5'-o-{(s)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}guanosine
    synonyms:
    - '[(2R,3S,5R)-5-(2-azanyl-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic
      acid'
    - 2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}guanosine
    identifiers:
    - ns: pdb-ccd
      id: GX1
    structure: SCCN[P@](=O)(OC[C@@H]1O[C@H](C[C@H]1O)n1cnc2c1nc(N)[nH]c2=O)[O-]
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 17
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 17
  HEU:
    id: HEU
    name: 3-(2-hydroxyethyl)-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - 2'-deoxy-3-(2-hydroxyethyl)uridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-[3-(2-hydroxyethyl)-2,4-dioxo-pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: HEU
    structure: OCCn1c(=O)ccn(c1=O)[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  HN0:
    id: HN0
    name: 2'-deoxy-n-[(2s,3s,5r)-5-hydroxy-2-pentyltetrahydrofuran-3-yl]guanosine
      5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-3-oxidanyl-5-[6-oxidanylidene-2-[[(2S,3S,5R)-5-oxidanyl-2-pentyl-oxolan-3-yl]amino]-1H-purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-[(2S,3S,5R)-5-hydroxy-2-pentyltetrahydrofuran-3-yl]guanosine 5'-(dihydrogen
      phosphate)
    identifiers:
    - ns: pdb-ccd
      id: HN0
    structure: CCCCC[C@@H]1O[C@@H](C[C@H]1Nc1[nH]c(=O)c2c(n1)n(cn2)[C@H]1O[C@H]([C@H](C1)O)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 34
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 37
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 34
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 39
      charge: -1
  HN1:
    id: HN1
    name: (6s,8r)-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-8-hydroxy-6-[(1s)-1-hydroxyhexyl]-4,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3h)-one
    synonyms:
    - '[(2R,3S,5R)-3-oxidanyl-5-[(6S,8R)-8-oxidanyl-6-[(1S)-1-oxidanylhexyl]-10-oxidanylidene-4,6,7,8-tetrahydropyrimido[1,2-a]purin-3-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (6S,8R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-8-hydroxy-6-[(1S)-1-hydroxyhexyl]-4,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: HN1
    structure: CCCCC[C@@H]([C@H]1C[C@H](O)n2c(=N1)[nH]c1c(c2=O)ncn1[C@H]1C[C@H]([C@@H](O1)COP(=O)([O-])[O-])O)O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 40
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 36
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 40
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 38
      charge: -1
  HOL:
    id: HOL
    name: alpha-cholest-5-en-3-yl 3-[(2-deoxy-5-o-phosphono-alpha-d-glycero-pentofuranosyl)oxy]propylcarbamate
    synonyms:
    - N
    - '[(3S,8S,9S,10R,13R,14S,17R)-10,13-dimethyl-17-[(2R)-6-methylheptan-2-yl]-2,3,4,7,8,9,11,12,14,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthren-3-yl]
      N-[3-[(2S,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]oxypropyl]carbamate'
    - (3alpha,8alpha)-cholest-5-en-3-yl {3-[(2-deoxy-5-O-phosphono-alpha-D-erythro-pentofuranosyl)oxy]propyl}carbamate
    identifiers:
    - ns: pdb-ccd
      id: HOL
    structure: CC(CCC[C@@H]([C@@H]1CC[C@@H]2[C@]1(C)CC[C@@H]1[C@@H]2CC=C2[C@]1(C)CC[C@@H](C2)OC(=O)NCCCO[C@H]1C[C@H]([C@@H](O1)COP(=O)([O-])[O-])O)C)C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 54
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 50
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 54
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 53
      charge: -1
  IGU:
    id: IGU
    name: 2'-deoxyisoguanine-5'-monophosphate
    synonyms:
    - G
    - '[(2R,3S,5R)-5-(6-azanyl-2-oxidanylidene-1H-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-2-oxo-2-hydroadenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: IGU
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(=O)[nH]c2N
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  IMC:
    id: IMC
    name: n1-[2-deoxy-ribofuranosyl]-[2-amino-5-methyl-4-oxo-4h-pyrimidine]-5'-monophosphate
    synonyms:
    - 2-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methylpyrimidin-4(1H)-one
    - C
    - '[(2R,3S,5R)-5-(2-amino-5-methyl-4-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: IMC
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)nc1N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  JDT:
    id: JDT
    name: 2'-deoxy-5-ethyluridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-ethyluridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(5-ethyl-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: JDT
    structure: CCc1cn([C@H]2C[C@H]([C@@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  LGP:
    id: LGP
    name: n9-1-hydroxy-prop-2-oxymethyl-guanine-3'-monophosphate
    synonyms:
    - G
    - (2S)-2-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)methoxy]-3-hydroxypropyl dihydrogen
      phosphate
    - '[(2S)-2-[(2-amino-6-oxo-1H-purin-9-yl)methoxy]-3-hydroxy-propyl] dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: LGP
    structure: OC[C@@H](COP(=O)([O-])[O-])OCn1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 7
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 10
      charge: -1
  LHO:
    id: LHO
    name: 2-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-6-methylisoquinoline-1(2h)-thione
    synonyms:
    - 2-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-methylisoquinoline-1(2H)-thione
    - '[(2R,3S,5R)-5-(6-methyl-1-sulfanylidene-isoquinolin-2-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: LHO
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1ccc2c(c1=S)ccc(c2)C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  LSH:
    id: LSH
    name: '[(1r,5r,7r,8s)-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,5R,7R,8S)-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: LSH
    structure: O[C@H]1[C@@H]2NS(=O)(=O)C[C@@]1(COP(=O)(O)O)O[C@@H]2n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
  LST:
    id: LST
    name: '[(1r,5r,7r,8s)-2-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,5R,7R,8S)-2-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-3,3-bis(oxidanylidene)-6-oxa-3$l^{6}-thia-2-azabicyclo[3.2.1]octan-5-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: LST
    structure: O[C@@H]1[C@@H]2[C@H](O[C@@]1(COP(=O)(O)O)CS(=O)(=O)N2C)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
  LTP:
    id: LTP
    name: 4-amino-1-{2-deoxy-5-o-[(r)-hydroxy(phosphonooxy)phosphoryl]-beta-l-erythro-pentofuranosyl}pyrimidin-2(1h)-one
    synonyms:
    - '[(2S,3R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methyl
      phosphono hydrogen phosphate'
    - 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one
    identifiers:
    - ns: pdb-ccd
      id: LTP
    structure: O[C@H]1C[C@H](O[C@H]1CO[P@](=O)(OP(=O)(O)O)O)n1ccc(nc1=O)N
  LWM:
    id: LWM
    name: '[(1r,2s,4r)-4-{[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,2S,4R)-4-{[2-amino-5-(formylamino)-6-oxo-1,6-dihydropyrimidin-4-yl]amino}-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,4R)-4-[(2-azanyl-5-formamido-6-oxidanylidene-1H-pyrimidin-4-yl)amino]-2-oxidanyl-cyclopentyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: LWM
    structure: O=CNc1c(N[C@@H]2C[C@H]([C@H](C2)O)COP(=O)([O-])[O-])nc([nH]c1=O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 15
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 15
  M1G:
    id: M1G
    name: 3-(2-deoxy-beta-d-ribofuranosyl)-pyrido[5,6-a]-purine-10-one-5'-monophosphate
    synonyms:
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)pyrimido[1,2-a]purin-10(3H)-one
    - G
    - '[(2R,3S,5R)-3-hydroxy-5-(10-oxopyrimido[1,2-a]purin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: M1G
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc1ncccn1c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  MA7:
    id: MA7
    name: 1n-methyladenosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(6-amino-1-methyl-purin-1-ium-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - A
    - 2'-deoxy-1-methyladenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: MA7
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc[n+](c2N)C
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  MBZ:
    id: MBZ
    name: 1-[2-deoxyribofuranosyl]-4-methyl-benzoimidazole-5'-monophosphate
    synonyms:
    - N
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-methyl-1H-benzimidazole
    - '[(2R,3S,5R)-3-hydroxy-5-(4-methylbenzimidazol-1-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: MBZ
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1cccc2C
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  MCY:
    id: MCY
    name: 5-methyl-2'-deoxycytidine
    synonyms:
    - C
    - 4-amino-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidin-2-one
    - 2'-deoxy-5-methylcytidine
    identifiers:
    - ns: pdb-ccd
      id: MCY
    structure: OC[C@@H]1O[C@H](C[C@@H]1O)n1cc(C)c(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 11
  MDJ:
    id: MDJ
    name: 4-amino-1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-3-(hydroxymethyl)pyridin-2(1h)-one
    synonyms:
    - 4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-(hydroxymethyl)pyridin-2(1H)-one
    - '[(2R,3S,5R)-5-[4-azanyl-3-(hydroxymethyl)-2-oxo-pyridin-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: MDJ
    structure: OCc1c(N)ccn(c1=O)[C@H]1C[C@H]([C@@H](O1)COP(=O)(O)O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
  MDK:
    id: MDK
    name: 4-amino-1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-3-methylpyridin-2(1h)-one
    synonyms:
    - '[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyridin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 4-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-methylpyridin-2(1H)-one
    identifiers:
    - ns: pdb-ccd
      id: MDK
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1ccc(c(c1=O)C)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  MDQ:
    id: MDQ
    name: 2'-deoxy-3-(oxidomethyl)cytidine 5'-(dihydrogen phosphate)
    synonyms:
    - '[6-azanyl-3-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2-oxo-pyrimidin-1-ium-1-yl]methanolate'
    - 2'-deoxy-3-(oxidomethyl)cytidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: MDQ
    structure: '[O-]C[n+]1c(N)ccn(c1=O)[C@H]1C[C@@H]([C@@H](O1)COP(=O)(O)O)O'
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 25
  MDR:
    id: MDR
    name: 9-(2-deoxy-beta-d-ribofuranosyl)-6-methylpurine
    synonyms:
    - N
    - (2R,3S,5R)-2-(hydroxymethyl)-5-(6-methylpurin-9-yl)oxolan-3-ol
    - 9-(2-deoxy-beta-D-erythro-pentofuranosyl)-6-methyl-9H-purine
    identifiers:
    - ns: pdb-ccd
      id: MDR
    structure: OC[C@H]1O[C@H](C[C@H]1O)n1cnc2c1ncnc2C
  MDU:
    id: MDU
    name: 3-(hydroxymethyl)thymidine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[3-(hydroxymethyl)-5-methyl-2,4-dioxo-pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3-(hydroxymethyl)thymidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: MDU
    structure: OCn1c(=O)n(cc(c1=O)C)[C@H]1C[C@H]([C@@H](O1)COP(=O)(O)O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
  MDV:
    id: MDV
    name: (7s,8s)-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-7,8-dihydro-3h-imidazo[2,1-i]purine-7,8-diol
    synonyms:
    - '[(2R,3S,5R)-5-[(7S,8S)-7,8-dihydroxy-7,8-dihydroimidazo[2,1-f]purin-3-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (7S,8S)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydro-3H-imidazo[2,1-i]purine-7,8-diol
    identifiers:
    - ns: pdb-ccd
      id: MDV
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1cnc2c1ncn1c2=N[C@@H]([C@@H]1O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  ME6:
    id: ME6
    name: '[(2r,3s,5r)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2R,3S,5R)-5-(4-azanyl-3-methyl-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: ME6
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1ccc([n+](c1=O)C)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  MF7:
    id: MF7
    name: n-{2-amino-5-[formyl(methyl)amino]-6-hydroxypyrimidin-4-yl}-2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosylamine
    synonyms:
    - '[(2R,3S,5R)-5-[[2-azanyl-5-[methanoyl(methyl)amino]-6-oxidanyl-pyrimidin-4-yl]amino]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - N-{2-amino-5-[formyl(methyl)amino]-6-hydroxypyrimidin-4-yl}-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine
    identifiers:
    - ns: pdb-ccd
      id: MF7
    structure: O=CN(c1c(N[C@@H]2C[C@@H]([C@@H](O2)COP(=O)(O)O)O)nc(nc1O)N)C
  MFO:
    id: MFO
    name: '[(2~{r},3~{s},5~{r})-5-[2-azanyl-8-[ethanoyl(naphthalen-2-yl)amino]-6-oxidanylidene-3~{h}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - G
    - '[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(naphthalen-2-yl)amino]-6-oxidanylidene-3~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: MFO
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1c(nc2c1[nH]c(N)nc2=O)N(c1ccc2c(c1)cccc2)C(=O)C
    base_monomers:
    - G
  MFT:
    id: MFT
    name: 3-methylthymidine 5'-(dihydrogen phosphate)
    synonyms:
    - 3-methylthymidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(3,5-dimethyl-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: MFT
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1cc(C)c(=O)n(c1=O)C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  MM7:
    id: MM7
    name: (1r)-1,4-anhydro-2-deoxy-1-(2-methoxy-4-methylphenyl)-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - '[(2R,3S,5R)-5-(2-methoxy-4-methyl-phenyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - (1R)-1,4-anhydro-2-deoxy-1-(2-methoxy-4-methylphenyl)-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: MM7
    structure: COc1cc(C)ccc1[C@@H]1C[C@@H]([C@@H](O1)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 24
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 24
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  MMT:
    id: MMT
    name: 5'-o-(dimethylamino)-thymidine
    synonyms:
    - 5'-O-(dimethylamino)thymidine
    - T
    - 1-[(2R,4S,5R)-5-(dimethylaminooxymethyl)-4-hydroxy-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
    identifiers:
    - ns: pdb-ccd
      id: MMT
    structure: CN(OC[C@H]1O[C@@H](C[C@H]1O)n1cc(C)c(=O)[nH]c1=O)C
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 13
  MRG:
    id: MRG
    name: n2-(3-mercaptopropyl)-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - 2'-deoxy-N-(3-sulfanylpropyl)guanosine 5'-(dihydrogen phosphate)
    - G
    - '[(2R,3S,5R)-3-hydroxy-5-[6-oxo-2-(3-sulfanylpropylamino)-1H-purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: MRG
    structure: SCCCNc1[nH]c(=O)c2c(n1)n(cn2)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 31
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 27
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 31
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 30
      charge: -1
  MTR:
    id: MTR
    name: (5-methyl-6-oxo-1,6-dihydro-pyridin-3-yl)-1,2-dideoxy-ribofuranose-5-monophosphate
    synonyms:
    - (1R)-1,4-anhydro-2-deoxy-1-(5-methyl-6-oxo-1,6-dihydropyridin-3-yl)-5-O-phosphono-D-erythro-pentitol
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-6-oxo-1H-pyridin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: MTR
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])c1c[nH]c(=O)c(c1)C
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  N4S:
    id: N4S
    name: n-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2'-deoxycytidine 5'-(dihydrogen
      phosphate)
    synonyms:
    - N-[3-({4-[(3-aminopropyl)amino]butyl}amino)propyl]-2'-deoxycytidine 5'-(dihydrogen
      phosphate)
    - '[(2R,3S,5R)-5-[4-[3-[4-(3-azanylpropylamino)butylamino]propylamino]-2-oxidanylidene-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: N4S
    structure: NCCCNCCCCNCCCNc1ccn(c(=O)n1)[C@@H]1C[C@H]([C@@H](O1)COP(=O)(O)O)O
  N5I:
    id: N5I
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-5-nitro-1h-indole
    synonyms:
    - N
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-nitro-1H-indole
    - '[(2R,3S,5R)-3-hydroxy-5-(5-nitroindol-1-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: N5I
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1ccc2c1ccc(c2)[N+](=O)[O-]
  NCU:
    id: NCU
    name: '[(1r,5r,7r,8s)-7-(4-amino-5-methyl-2-oxopyrimidin-1(2h)-yl)-8-hydroxy-3-methyl-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,5R,7R,8S)-7-(4-amino-5-methyl-2-oxopyrimidin-1(2H)-yl)-8-hydroxy-3-methyl-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl
      dihydrogen phosphate'
    - '[(1R,5R,7R,8S)-7-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-3-methyl-8-oxidanyl-2,6-dioxa-3-azabicyclo[3.2.1]octan-5-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: NCU
    structure: CN1O[C@H]2[C@@H](O[C@](C1)([C@H]2O)COP(=O)([OH-])[O-])n1cc(C)c(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 13
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 20
      charge: -1
  NCX:
    id: NCX
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-5-nitro-1h-indole-3-carboxamide
    synonyms:
    - N
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-nitro-1H-indole-3-carboxamide
    - '[(2R,3S,5R)-5-(3-aminocarbonyl-5-nitro-indol-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: NCX
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(c2c1ccc(c2)[N+](=O)[O-])C(=O)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  NDN:
    id: NDN
    name: 2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: NDN
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1cc([N+](=O)[O-])c(=O)[nH]c1=O
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  NMS:
    id: NMS
    name: 1-(o2-(2-methylamino-2-oxo-ethyl)-o5-hydroxyphosphinyl-beta-d-ribofuranosyl)thymine
    synonyms:
    - '[(2R,3R,4R,5R)-3-hydroxy-4-(2-methylamino-2-oxo-ethoxy)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-methyl-2'-O-[2-(methylamino)-2-oxoethyl]uridine 5'-(dihydrogen phosphate)
    - T
    identifiers:
    - ns: pdb-ccd
      id: NMS
    structure: CNC(=O)CO[C@@H]1[C@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 11
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 29
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 11
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 32
      charge: -1
  NMT:
    id: NMT
    name: 1-(o2-(methylcarbamoyl)-o5-hydroxyphosphinyl-beta-d-ribofuranosyl)thymine
    synonyms:
    - '[(2R,3R,4R,5R)-3-hydroxy-4-(hydroxy-methylamino-methoxy)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-O-[(S)-hydroxy(methylamino)methyl]-5-methyluridine 5'-(dihydrogen phosphate)
    - T
    identifiers:
    - ns: pdb-ccd
      id: NMT
    structure: CN[C@H](O[C@@H]1[C@H](O)[C@H](O[C@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)([O-])[O-])O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 10
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 28
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 10
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 30
      charge: -1
  NP3:
    id: NP3
    name: 1-[2-deoxy-ribofuranosyl]-1h-[3-nitro-pyrrol]-5'-phosphate
    synonyms:
    - N
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3-nitro-1H-pyrrole
    - '[(2R,3S,5R)-3-hydroxy-5-(3-nitropyrrol-1-yl)oxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: NP3
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1ccc(c1)[N+](=O)[O-]
  NR1:
    id: NR1
    name: (3r,4r)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium
    synonyms:
    - (3R,4R)-3-hydroxy-4-[(phosphonooxy)methyl]pyrrolidinium
    - '[(3R,4R)-4-oxidanylpyrrolidin-1-ium-3-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: NR1
    structure: O[C@@H]1C[NH2+]C[C@@H]1COP(=O)(O)O
  NRI:
    id: NRI
    name: phosphoric acid mono-(4-hydroxy-pyrrolidin-3-ylmethyl) ester
    synonyms:
    - '[(3R,4R)-4-hydroxypyrrolidin-3-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: NRI
    structure: O[C@H]1CNC[C@H]1COP(=O)(O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  NTT:
    id: NTT
    name: '[(1r,5r,7r,8s)-8-hydroxy-3-methyl-7-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,5R,7R,8S)-3-methyl-7-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-8-oxidanyl-2,6-dioxa-3-azabicyclo[3.2.1]octan-5-yl]methyl
      dihydrogen phosphate'
    - '[(1R,5R,7R,8S)-8-hydroxy-3-methyl-7-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2,6-dioxa-3-azabicyclo[3.2.1]oct-5-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: NTT
    structure: CN1O[C@H]2[C@H](O[C@@](C1)([C@H]2O)COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 13
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  NYM:
    id: NYM
    name: 3'-deoxy-3'-aminothymidine monophosphate
    synonyms:
    - N
    - '[(2S,3S,5R)-3-amino-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3'-amino-3'-deoxythymidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: NYM
    structure: N[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc(C)c(=O)[nH]c1=O
  OGX:
    id: OGX
    name: 2'-deoxy-5'-o-{(s)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}-8-oxoguanosine
    synonyms:
    - 2'-deoxy-5'-O-{(S)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}-8-oxoguanosine
    - '[(2R,3S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: OGX
    structure: SCCN[P@@](=O)(OC[C@@H]1O[C@H](C[C@H]1O)n1c(=O)[nH]c2c1nc(N)[nH]c2=O)[O-]
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 17
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 17
  OHU:
    id: OHU
    name: 2'-deoxy-5-hydroxyuridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-hydroxyuridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-oxidanyl-5-[5-oxidanyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: OHU
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  P:
    id: P
    name: 2'-deoxy-n1,n2-propano guanosine monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(10-oxo-5,6,7,8-tetrahydropyrimido[1,2-a]purin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - G
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydropyrimido[1,2-a]purin-10(3H)-one
    identifiers:
    - ns: pdb-ccd
      id: P
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc1NCCCn1c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  P2U:
    id: P2U
    name: 2'-deoxy-pseudouridine-5'monophosphate
    synonyms:
    - (1R)-1,4-anhydro-2-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-O-phosphono-D-erythro-pentitol
    - '[(2R,3S,5R)-5-(2,4-dioxo-1H-pyrimidin-5-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: P2U
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])c1c[nH]c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  PBT:
    id: PBT
    name: '[3-hydroxy-5-(5-methyl-2,4-dioxotetrahydro-1(2h)-pyrimidinyl)tetrahydro-2-furanyl]methyl
      dihydrogen phosphate'
    synonyms:
    - N
    - 5'-thymidylic acid
    - '[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: PBT
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1C[C@H](C)C(=O)NC1=O
  PDU:
    id: PDU
    name: 5(1-propynyl)-2'-deoxyuridine-5-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(2,4-dioxo-5-propyl-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    - 2'-deoxy-5-propyluridine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: PDU
    structure: CCCc1cn([C@@H]2C[C@@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 17
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 19
      charge: -1
  PGN:
    id: PGN
    name: 2'-deoxyguanosine-3',5'-diphosphate
    synonyms:
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl]
      dihydrogen phosphate'
    - G
    - 2'-deoxyguanosine 3',5'-bis(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: PGN
    structure: Nc1[nH]c(=O)c2c(n1)n(cn2)[C@@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])OP(=O)(O)O
    base_monomers:
    - G
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 23
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  PPW:
    id: PPW
    name: 7-deaza-8-aza-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - G
    - 6-amino-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-4-one
    - '[(2R,3S,5R)-5-(6-amino-4-oxo-5H-pyrazolo[5,4-d]pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: PPW
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)([O-])[O-])n1ncc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  PRN:
    id: PRN
    name: purine 2'-deoxyribo-5'-monophosphate
    synonyms:
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purine
    - '[(2R,3S,5R)-3-hydroxy-5-purin-9-yl-oxolan-2-yl]methyl dihydrogen phosphate'
    - A
    identifiers:
    - ns: pdb-ccd
      id: PRN
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  PST:
    id: PST
    name: thymidine-5'-thiophosphate
    synonyms:
    - 5'-O-thiophosphonothymidine
    - 1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
    - T
    identifiers:
    - ns: pdb-ccd
      id: PST
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=S)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  PVX:
    id: PVX
    name: n-(2-amino-5-{formyl[(6as,8r,9r,9ar)-9-hydroxy-4-methoxy-1,11-dioxo-1,6a,8,9,9a,11-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosylamine
    synonyms:
    - N-(2-amino-5-{formyl[(6aS,8R,9R,9aR)-9-hydroxy-4-methoxy-1,11-dioxo-1,6a,8,9,9a,11-hexahydrocyclopenta[c]furo[3',2':4,5]furo[2,3-h]chromen-8-yl]amino}-6-oxo-1,6-dihydropyrimidin-4-yl)-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine
    identifiers:
    - ns: pdb-ccd
      id: PVX
    structure: O=CN(c1c(N[C@@H]2C[C@@H]([C@@H](O2)COP(=O)(O)O)O)nc([nH]c1=O)N)[C@H]1O[C@H]2[C@@H]([C@@H]1O)c1c(O2)cc(c2c1oc(=O)c1c2C=CC1=O)OC
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
  PZG:
    id: PZG
    name: '[(2~{r},3~{s},4~{r},5~{r})-5-(2-azanyl-6-oxidanylidene-1~{h}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{h}-pyrazol-4-yl)phosphinic
      acid'
    synonyms:
    - '[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-(3-methyl-1~{H}-pyrazol-4-yl)phosphinic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: PZG
    structure: O[C@H]1[C@@H](CO[P@](=O)(c2c[nH]nc2C)O)O[C@H]([C@@H]1O)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
  QBT:
    id: QBT
    name: '[(2r,3s,5r)-3-hydroxy-5-[(5s)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(5S)-5-methyl-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: QBT
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1C[C@H](C)C(=O)NC1=O
  R:
    id: R
    name: 2'-deoxy-n6-(r)styrene oxide adenosine monophosphate
    synonyms:
    - 2'-deoxy-N-[(1R)-2-hydroxy-1-phenylethyl]adenosine 5'-(dihydrogen phosphate)
    - A
    - '[(2R,3S,5R)-3-hydroxy-5-[6-[[(1R)-2-hydroxy-1-phenyl-ethyl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: R
    structure: OC[C@@H](c1ccccc1)Nc1ncnc2c1ncn2[C@@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 35
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 31
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 35
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 34
      charge: -1
  RBD:
    id: RBD
    name: (r,r)-n6,n6-(2,3-dihydroxy-1,4-butadiyl)-2'-deoxyadenosine-5'-monophosphate
    synonyms:
    - (3R,4R)-1-[9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]purin-6-yl]pyrrolidine-3,4-diol
    - (3R,4R)-1-{9-[(2R,4S,5R)-4-hydroxy-5-{[(trihydroxy-lambda~5~-phosphanyl)oxy]methyl}tetrahydrofuran-2-yl]-9H-purin-6-yl}pyrrolidine-3,4-diol
      (non-preferred name)
    identifiers:
    - ns: pdb-ccd
      id: RBD
    structure: O[C@@H]1C[C@H](O[C@H]1COP(O)(O)O)n1cnc2c1ncnc2N1C[C@@H]([C@H](C1)O)O
    base_monomers:
    - A
  RCE:
    id: RCE
    name: 1-{2,5-anhydro-6-deoxy-4-[(phosphonooxy)methyl]-beta-d-gulofuranosyl}pyrimidine-2,4(1h,3h)-dione
    synonyms:
    - '[(1R,3R,4R,6R,7S)-6-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methyl-7-oxidanyl-2,5-dioxabicyclo[2.2.1]heptan-4-yl]methyl
      dihydrogen phosphate'
    - 1-{2,5-anhydro-6-deoxy-4-[(phosphonooxy)methyl]-beta-D-gulofuranosyl}pyrimidine-2,4(1H,3H)-dione
    identifiers:
    - ns: pdb-ccd
      id: RCE
    structure: C[C@H]1O[C@H]2[C@H]([C@@]1(COP(=O)(O)O)O[C@H]2n1ccc(=O)[nH]c1=O)O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 28
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 28
  RDG:
    id: RDG
    name: 2'-deoxy-n-(furan-2-ylmethyl)guanosine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-[2-(furan-2-ylmethylamino)-6-oxidanylidene-1H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-(furan-2-ylmethyl)guanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: RDG
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1cnc2c1nc(NCc1ccco1)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  RMP:
    id: RMP
    name: 2'-deoxy-adenosine-5'-rp-monomethylphosphonate
    synonyms:
    - '[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-methyl-phosphinic
      acid'
    - 2'-deoxy-5'-O-[(S)-hydroxy(methyl)phosphoryl]adenosine
    - A
    identifiers:
    - ns: pdb-ccd
      id: RMP
    structure: O[C@@H]1C[C@@H](O[C@@H]1CO[P@](=O)(C)[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  S4A:
    id: S4A
    name: 2'-deoxy-4'-thioadenosine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-thiolan-2-yl]methyl dihydrogen
      phosphate'
    - A
    - 2'-deoxy-4'-thioadenosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: S4A
    structure: O[C@@H]1C[C@@H](S[C@@H]1COP(=O)(O)O)n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  S4G:
    id: S4G
    name: 2'-deoxy-4'-thioguanosine 5'-(dihydrogen phosphate)
    synonyms:
    - G
    - '[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-thiolan-2-yl]methyl dihydrogen
      phosphate'
    - 2'-deoxy-4'-thioguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: S4G
    structure: O[C@H]1C[C@@H](S[C@H]1COP(=O)(O)O)n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  S6G:
    id: S6G
    name: 6-thio-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(2-amino-6-sulfanylidene-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - G
    - 2-amino-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1,9-dihydro-6H-purine-6-thione
    identifiers:
    - ns: pdb-ccd
      id: S6G
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=S
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  SAY:
    id: SAY
    name: '[(2r,3s,5r)-3-hydroxy-5-(3-hydroxy-4-methanoyl-phenyl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(3-hydroxy-4-methanoyl-phenyl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: SAY
    structure: O=Cc1ccc(cc1O)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)O
  SC:
    id: SC
    name: 2-deoxy-cytidine-5'-thiophosphorate
    synonyms:
    - C
    - 2'-deoxy-5'-O-thiophosphonocytidine
    - 4-amino-1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-oxolan-2-yl]pyrimidin-2-one
    identifiers:
    - ns: pdb-ccd
      id: SC
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=S)([O-])[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  SDE:
    id: SDE
    name: (s,s)-n6,n6-(2,3-dihydroxy-1,4-butadiyl)-2'-deoxyadenosine-5'-monophosphate
    synonyms:
    - (3S,4S)-1-{9-[(2R,4S,5R)-4-hydroxy-5-{[(trihydroxy-lambda~5~-phosphanyl)oxy]methyl}tetrahydrofuran-2-yl]-9H-purin-6-yl}pyrrolidine-3,4-diol
      (non-preferred name)
    - (3S,4S)-1-[9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]purin-6-yl]pyrrolidine-3,4-diol
    identifiers:
    - ns: pdb-ccd
      id: SDE
    structure: O[C@@H]1C[C@H](O[C@H]1COP(O)(O)O)n1cnc2c1ncnc2N1C[C@@H]([C@H](C1)O)O
    base_monomers:
    - A
  SDG:
    id: SDG
    name: 2-amino-9-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-9h-purine-6-selenol
    synonyms:
    - '[(2R,3S,5R)-5-(2-amino-6-selanyl-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - G
    - 2-amino-9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-9H-purine-6-selenol
    identifiers:
    - ns: pdb-ccd
      id: SDG
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1cnc2c1nc(N)nc2[SeH]
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  SDH:
    id: SDH
    name: (5s)-7-amino-1-[2-deoxy-5-o-(trihydroxy-lambda~5~-phosphanyl)-beta-d-erythro-pentofuranosyl]-1,3,6,8-tetraazaspiro[4.4]non-7-ene-2,4,9-trione
    synonyms:
    - (5S)-7-azanyl-1-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]-1,3,6,8-tetrazaspiro[4.4]non-7-ene-2,4,9-trione
    - (5S)-7-amino-1-[2-deoxy-5-O-(trihydroxy-lambda~5~-phosphanyl)-beta-D-erythro-pentofuranosyl]-1,3,6,8-tetraazaspiro[4.4]non-7-ene-2,4,9-trione
    identifiers:
    - ns: pdb-ccd
      id: SDH
    structure: NC1=NC(=O)[C@@]2(N1)C(=O)NC(=O)N2[C@H]1O[C@H]([C@@H](C1)O)COP(O)(O)O
    base_monomers:
    - G
  SMP:
    id: SMP
    name: 2'-deoxy-adenosine-5'-sp-monomethylphosphonate
    synonyms:
    - 2'-deoxy-5'-O-[(R)-hydroxy(methyl)phosphoryl]adenosine
    - '[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-methyl-phosphinic
      acid'
    - A
    identifiers:
    - ns: pdb-ccd
      id: SMP
    structure: O[C@@H]1C[C@@H](O[C@@H]1CO[P@](=O)(C)[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  SOS:
    id: SOS
    name: '[(1r,2s,4r)-4-({2-amino-5-[benzyl(formyl)amino]-6-oxo-1,6-dihydropyrimidin-4-yl}amino)-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    synonyms:
    - N
    - '[(1R,2S,4R)-4-({2-amino-5-[benzyl(formyl)amino]-6-oxo-1,6-dihydropyrimidin-4-yl}amino)-2-hydroxycyclopentyl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,4R)-4-[[2-amino-5-(methanoyl-(phenylmethyl)amino)-6-oxo-1H-pyrimidin-4-yl]amino]-2-hydroxy-cyclopentyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: SOS
    structure: O=CN(c1c(N[C@@H]2C[C@@H]([C@H](C2)O)COP(=O)([O-])[O-])nc([nH]c1=O)N)Cc1ccccc1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 15
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 18
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 15
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 20
      charge: -1
  SPT:
    id: SPT
    name: 5'-thio-thymidine phosphonic acid
    synonyms:
    - '[(2S,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methylsulfanylphosphonic
      acid'
    - T
    - 5'-S-phosphono-5'-thiothymidine
    identifiers:
    - ns: pdb-ccd
      id: SPT
    structure: O[C@H]1C[C@@H](O[C@@H]1CSP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  T0T:
    id: T0T
    name: (1r)-1-{4-[(e)-2-(2-aminophenyl)ethenyl]phenyl}-1,4-anhydro-2-deoxy-5-o-phosphonato-d-erythro-pentitol
    synonyms:
    - '[(2R,3S,5R)-5-[4-[(E)-2-(2-aminophenyl)ethenyl]phenyl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (1R)-1-{4-[(E)-2-(2-aminophenyl)ethenyl]phenyl}-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: T0T
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)(O)O)c1ccc(cc1)/C=C/c1ccccc1N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  T2S:
    id: T2S
    name: thymidine-5'-dithiophosphorate
    synonyms:
    - 5'-O-[(dithiophosphono)]thymidine
    - 1-[(2R,4S,5R)-4-hydroxy-5-[(hydroxy-sulfanyl-phosphinothioyl)oxymethyl]oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
    - T
    identifiers:
    - ns: pdb-ccd
      id: T2S
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@](=S)(S)[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  T32:
    id: T32
    name: 6'-alpha-methyl carbocyclic thymidine 5'-monophosphate
    synonyms:
    - '[(1R,2S,3S,5S)-5-hydroxy-2-methyl-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,3S,5S)-5-hydroxy-2-methyl-3-(5-methyl-2,4-dioxo-pyrimidin-1-yl)cyclopentyl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: T32
    structure: O[C@H]1C[C@H]([C@H]([C@H]1COP(=O)(O)O)C)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
  T3P:
    id: T3P
    name: thymidine-3'-phosphate
    synonyms:
    - 3'-thymidylic acid
    - '[(2R,3S,5R)-2-(hydroxymethyl)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-3-yl]
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: T3P
    structure: OC[C@H]1O[C@@H](C[C@@H]1OP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  T48:
    id: T48
    name: 6'-alpha-hydroxy carbocyclic thymidine 5'-monophosphate
    synonyms:
    - '[(1R,2S,3S,5S)-2,5-dihydroxy-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclopentyl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,3S,5S)-2,5-dihydroxy-3-(5-methyl-2,4-dioxo-pyrimidin-1-yl)cyclopentyl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: T48
    structure: O[C@H]1C[C@H]([C@H]([C@H]1COP(=O)(O)O)O)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
  T49:
    id: T49
    name: s4'-2'deoxythymidine 5'-monophosphate
    synonyms:
    - 4'-thiothymidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)thiolan-2-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: T49
    structure: O[C@H]1C[C@H](S[C@H]1COP(=O)(O)O)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
  T4S:
    id: T4S
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-4-hydroseleno-5-methylpyrimidin-2(1h)-one
    synonyms:
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-4-selanylpyrimidin-2(1H)-one
    - T
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2-oxo-4-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: T4S
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C)c(nc1=O)[SeH]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  T5O:
    id: T5O
    name: 2'-deoxy-5-methoxyuridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-methoxyuridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methoxy-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: T5O
    structure: COc1cn([C@@H]2C[C@@H]([C@@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 18
      charge: -1
  T5S:
    id: T5S
    name: "\n2'-deoxy-5-(methylselanyl)uridine 5'-phosphate"
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methylselanyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-(methylselanyl)uridine 5'-(dihydrogen phosphate)
    - T
    identifiers:
    - ns: pdb-ccd
      id: T5S
    structure: C[Se]c1cn([C@H]2C[C@@H]([C@@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 16
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 18
      charge: -1
  T64:
    id: T64
    name: (6-4)photoproduct
    synonyms:
    - '[(2R,4S,5R,10S,11R,13R,18R,19S)-4,8,18-trihydroxy-18,24-dimethyl-8-oxido-15,17,22-trioxo-7,9,12,26-tetraoxa-1,14,16,21-tetraaza-8-phosphapentacyclo[18.2.2.1~2,5~.1~10,13~.0~14,19~]hexacosa-20,23-dien-11-yl]methyl
      dihydrogen phosphate (non-preferred name)'
    identifiers:
    - ns: pdb-ccd
      id: T64
    structure: O[C@@H]1C[C@H]2O[C@H]1CO[P@](=O)(O)O[C@@H]1C[C@H](N3[C@H](c4c(cn2c(=O)n4)C)[C@@](C)(O)C(=O)NC3=O)O[C@H]1COP(=O)([O-])[O-]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 45
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 47
      charge: -1
  TA3:
    id: TA3
    name: (4s,5r)-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-5-methyl-1,3-diazabicyclo[2.2.0]hexan-2-one
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(3R,4S)-3-methyl-6-oxo-1,5-diazabicyclo[2.2.0]hexan-5-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (4S,5R)-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-1,3-diazabicyclo[2.2.0]hexan-2-one
    - T
    identifiers:
    - ns: pdb-ccd
      id: TA3
    structure: O[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)N1C(=O)N2[C@H]1[C@@H](C2)C
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  TAF:
    id: TAF
    name: 2'-deoxy-2'-fluoro-arabino-furanosyl thymine-5'-phosphate
    synonyms:
    - '[(2R,3R,4S,5R)-4-fluoro-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
    - T
    identifiers:
    - ns: pdb-ccd
      id: TAF
    structure: O[C@@H]1[C@@H](COP(=O)([O-])[O-])O[C@H]([C@@H]1F)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 11
      charge: -1
  TC1:
    id: TC1
    name: 3-(5-phospho-2-deoxy-beta-d-ribofuranosyl)-2-oxo-1,3-diaza-phenothiazine
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(2-oxo-10H-pyrimido[5,4-b][1,4]benzothiazin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3H-pyrimido[5,4-b][1,4]benzothiazin-2(10H)-one
    - C
    identifiers:
    - ns: pdb-ccd
      id: TC1
    structure: O[C@@H]1C[C@@H](O[C@H]1CO[P@@](=O)(O)[O-])n1cc2sc3ccccc3[nH]c2nc1=O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  TCJ:
    id: TCJ
    name: '[(1~{s},2~{r},4~{r},6~{s},8~{r})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl]
      dihydrogen phosphate'
    synonyms:
    - C
    - '[(1~{S},2~{R},4~{R},6~{S},8~{R})-8-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-1-yl)-6-oxidanyl-9-oxatricyclo[4.3.0.0^{2,4}]nonan-2-yl]
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: TCJ
    structure: O[C@]12C[C@H](O[C@@H]2[C@]2([C@@H](C1)C2)OP(=O)(O)O)n1cc(C)c(nc1=O)N
    base_monomers:
    - C
  TCP:
    id: TCP
    name: 5'-methylthymidine
    synonyms:
    - 5'-O-methylthymidine
    - T
    - 1-[(2R,4S,5R)-4-hydroxy-5-(methoxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
    identifiers:
    - ns: pdb-ccd
      id: TCP
    structure: COC[C@H]1O[C@@H](C[C@@H]1O)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 12
  TCY:
    id: TCY
    name: (2r,3as,4ar,5ar,5bs)-2-(6-amino-9h-purin-9-yl)-3a-hydroxyhexahydrocyclopropa[4,5]cyclopenta[1,2-b]furan-5a(4h)-yl
      dihydrogen phosphate
    synonyms:
    - A
    - (2R,3aS,4aR,5aR,5bS)-2-(6-amino-9H-purin-9-yl)-3a-hydroxyhexahydrocyclopropa[4,5]cyclopenta[1,2-b]furan-5a(4H)-yl
      dihydrogen phosphate
    identifiers:
    - ns: pdb-ccd
      id: TCY
    structure: Nc1ncnc2c1ncn2[C@@H]1O[C@@H]2[C@](C1)(O)C[C@@H]1[C@@]2(C1)OP(=O)(O)O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 18
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 18
  TDY:
    id: TDY
    name: 5-(methylamino)thymidine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[(5R)-5-methyl-5-methylamino-2,4-dioxo-1,3-diazinan-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - T
    - 5-(methylamino)thymidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: TDY
    structure: CN[C@]1(C)CN([C@@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)C(=O)NC1=O
    base_monomers:
    - T
  TED:
    id: TED
    name: 5-[(1e)-14-carboxy-10,13-bis(carboxymethyl)-3,8-dioxo-4,7,10,13-tetraazatetradec-1-en-1-yl]-2'-deoxyuridine
      5'-(dihydrogen phosphate)
    synonyms:
    - 2-[carboxymethyl-[2-[carboxymethyl-[2-[2-[[(E)-3-[1-[(2R,4S,5R)-4-hydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,4-dioxo-pyrimidin-5-yl]prop-2-enoyl]amino]ethylamino]-2-oxo-ethyl]amino]ethyl]amino]ethanoic
      acid
    - 5-[(13E)-1-carboxy-2,5-bis(carboxymethyl)-7,12-dioxo-2,5,8,11-tetraazatetradec-13-en-14-yl]-2'-deoxyuridine
      5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: TED
    structure: O=C(CN(CC(=O)O)CCN(CC(=O)O)CC(=O)O)NCCNC(=O)/C=C/c1cn([C@H]2C[C@@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 45
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 41
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 45
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 43
      charge: -1
  TFF:
    id: TFF
    name: 5'-o-[(r)-{[(r)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(hydroxy)phosphoryl]thymidine
    synonyms:
    - '[[[difluoro-[hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl]methyl]-hydroxy-phosphoryl]-difluoro-methyl]phosphonic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: TFF
    structure: O[C@@H]1C[C@@H](O[C@H]1CO[P@@](=O)(C([P@](=O)(C(P(=O)(O)O)(F)F)O)(F)F)O)n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  TFO:
    id: TFO
    name: '[2-(6-amino-9h-purin-9-yl)-1-methylethoxy]methylphosphonic acid'
    synonyms:
    - '[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethylphosphonic acid'
    - '{[(1R)-2-(6-amino-9H-purin-9-yl)-1-methylethoxy]methyl}phosphonic acid'
    - A
    identifiers:
    - ns: pdb-ccd
      id: TFO
    structure: C[C@@H](Cn1cnc2c1ncnc2N)OCP(=O)([O-])[O-]
    base_monomers:
    - A
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 17
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 20
      charge: -1
  TFT:
    id: TFT
    name: (l)-alpha-threofuranosyl-thymine-3'-monophosphate
    synonyms:
    - (3S,4R,5R)-4-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-3-yl
      dihydrogen phosphate
    - '[(3S,4R,5R)-4-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-3-yl] dihydrogen
      phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: TFT
    structure: O[C@@H]1[C@@H](CO[C@H]1n1cc(C)c(=O)[nH]c1=O)OP(=O)([O-])[O-]
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 24
      charge: -1
  TGP:
    id: TGP
    name: 5'-thio-2'-deoxy-guanosine phosphonic acid
    synonyms:
    - G
    - '[(2S,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methylsulfanylphosphonic
      acid'
    - 2'-deoxy-5'-S-phosphono-5'-thioguanosine
    identifiers:
    - ns: pdb-ccd
      id: TGP
    structure: O[C@H]1C[C@@H](O[C@@H]1CSP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  THM:
    id: THM
    name: thymidine
    synonyms:
    - 1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione
    - thymidine
    identifiers:
    - ns: pdb-ccd
      id: THM
    structure: OC[C@H]1O[C@@H](C[C@@H]1O)n1cc(C)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 11
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 11
  THP:
    id: THP
    name: thymidine-3',5'-diphosphate
    synonyms:
    - '[(2R,3S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-3-phosphonooxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - thymidine 3',5'-bis(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: THP
    structure: O=c1[nH]c(=O)n(cc1C)[C@@H]1C[C@@H]([C@H](O1)COP(=O)(O)O)OP(=O)(O)O
  THX:
    id: THX
    name: phosphonic acid 6-({6-[6-(6-carbamoyl-3,6,7,8-tetrahydro-3,6-diaza-as-indacene-2-carbonyl)-3,6,7,8-tetrahydro-3,6-diaza-as-indocene-2-carbonyl]-3,6,7,8-tetrahydro-3,6-diaza-as-indacene-2-carbonl}-amino)-hexyl
      ester 5-(5-methyl-2,4-dioxo-3,4-dihydro-2h-pyrimidin-1-yl)-tetrahydro-furan-2-ylmethyl
      ester
    synonyms:
    - N
    - 6-[[3-[[3-[(3-aminocarbonyl-2,6-dihydro-1H-pyrrolo[4,5-e]indol-7-yl)carbonyl]-2,6-dihydro-1H-pyrrolo[4,5-e]indol-7-yl]carbonyl]-2,6-dihydro-1H-pyrrolo[4,5-e]indol-7-yl]carbonylamino]hexyl
      [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      hydrogen phosphate
    - 5'-O-[(S)-{[6-({[6-({6-[(6-carbamoyl-3,6,7,8-tetrahydropyrrolo[3,2-e]indol-2-yl)carbonyl]-3,6,7,8-tetrahydropyrrolo[3,2-e]indol-2-yl}carbonyl)-3,6,7,8-tetrahydropyrrolo[3,2-e]indol-2-yl]carbonyl}amino)hexyl]oxy}(hydroxy)phosphoryl]thymidine
    identifiers:
    - ns: pdb-ccd
      id: THX
    structure: O[C@H]1C[C@H](O[C@@H]1CO[P@@](=O)(OCCCCCCNC(=O)c1cc2c([nH]1)ccc1c2CCN1C(=O)c1cc2c([nH]1)ccc1c2CCN1C(=O)c1cc2c([nH]1)ccc1c2CCN1C(=O)N)O)n1cc(C)c(=O)[nH]c1=O
  TLC:
    id: TLC
    name: 2-o,3-ethdiyl-arabinofuranosyl-thymine-5'-monophosphate
    synonyms:
    - '[(3aR,4R,6R,6aS)-3a-hydroxy-6-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)hexahydrofuro[3,4-b]furan-4-yl]methyl
      dihydrogen phosphate'
    - '[(3aR,4R,6R,6aS)-3a-hydroxy-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-3,4,6,6a-tetrahydro-2H-furo[4,3-b]furan-4-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: TLC
    structure: O=c1[nH]c(=O)n(cc1C)[C@@H]1O[C@@H]([C@]2([C@@H]1OCC2)O)COP(=O)([O-])[O-]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 22
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 22
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  TP1:
    id: TP1
    name: 2-(methylamino)-ethylglycine-carbonylmethylene-thymine
    synonyms:
    - N-[2-(methylamino)ethyl]-N-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]glycine
    - T
    - 2-[2-methylaminoethyl-[2-(5-methyl-2,4-dioxo-pyrimidin-1-yl)ethanoyl]amino]ethanoic
      acid
    identifiers:
    - ns: pdb-ccd
      id: TP1
    structure: CNCCN(C(=O)Cn1cc(C)c(=O)[nH]c1=O)CC(=O)O
    base_monomers:
    - T
  TPC:
    id: TPC
    name: 5'-thio-2'-deoxy-cytosine phosphonic acid
    synonyms:
    - '[(2S,3S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methylsulfanylphosphonic
      acid'
    - C
    - 2'-deoxy-5'-S-phosphono-5'-thiocytidine
    identifiers:
    - ns: pdb-ccd
      id: TPC
    structure: O[C@H]1C[C@@H](O[C@@H]1CSP(=O)(O)O)n1ccc(nc1=O)N
    base_monomers:
    - C
  TSP:
    id: TSP
    name: 3'-thio-thymidine-5'-phosphate
    synonyms:
    - '[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-sulfanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - T
    - 3'-thiothymidine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: TSP
    structure: S[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  TT:
    id: TT
    name: '[(1r,3r,4s,9r,10s,12r,15as,15br,18br,18cs)-10-hydroxy-15a,15b-dimethyl-13,15,16,18-tetraoxohexadecahydro-8h-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraazacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - N
    - '[(1R,3R,4S,9R,10S,12R,15aS,15bR,18bR,18cS)-10-hydroxy-15a,15b-dimethyl-13,15,16,18-tetraoxohexadecahydro-8H-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraazacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: TT
    structure: O[C@H]1C[C@@H]2O[C@@H]1COCO[C@H]1C[C@@H](N3[C@@H]4[C@H]5N2C(=O)NC(=O)[C@]5([C@@]4(C)C(=O)NC3=O)C)O[C@@H]1COP(=O)(O)O
  TTD:
    id: TTD
    name: cis-syn cyclobutane thymine dimer
    synonyms:
    - '[(1R,3R,4S,6S,9R,10S,12R,15aS,15bR,18bR,18cS)-6,10-dihydroxy-15a,15b-dimethyl-6-oxido-13,15,16,18-tetraoxohexadecahydro-8H-9,12-epoxy-1,4-methano-2,5,7-trioxa-12a,14,17,18a-tetraaza-6-phosphacyclohexadeca[1,2,3,4-def]biphenylen-3-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: TTD
    structure: O[C@H]1C[C@@H]2O[C@@H]1CO[P@](=O)(O)O[C@H]1C[C@@H](N3[C@@H]4[C@H]5N2C(=O)NC(=O)[C@]5([C@@]4(C)C(=O)NC3=O)C)O[C@@H]1COP(=O)([O-])[O-]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 46
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 49
      charge: -1
  TTI:
    id: TTI
    name: 2'-deoxy-5-telluroxouridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-telluroxouridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-(2,4-dioxo-5-tellanylidene-1,3-diazinan-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: TTI
    structure: O[C@H]1C[C@H](O[C@H]1COP(=O)(O)O)N1CC(=[TeH])C(=O)NC1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  TTM:
    id: TTM
    name: n3-ethyl-thymidine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-(3-ethyl-5-methyl-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 3-ethylthymidine 5'-(dihydrogen phosphate)
    - T
    identifiers:
    - ns: pdb-ccd
      id: TTM
    structure: CCn1c(=O)n(cc(c1=O)C)[C@H]1C[C@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 26
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 22
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 26
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 25
      charge: -1
  TX2:
    id: TX2
    name: 5'-o-{(r)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine
    synonyms:
    - 5'-O-{(R)-hydroxy[(2-sulfanylethyl)amino]phosphoryl}thymidine
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy-N-(2-sulfanylethyl)phosphonamidic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: TX2
    structure: '[O-][P@@](=O)(OC[C@@H]1O[C@H](C[C@H]1O)n1cc(C)c(=O)[nH]c1=O)NCCS'
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 14
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 14
  U33:
    id: U33
    name: 5-bromo-2'-deoxy uridine
    synonyms:
    - 5-bromo-1-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]pyrimidine-2,4-dione
    - U
    - 5-bromo-2'-deoxyuridine
    identifiers:
    - ns: pdb-ccd
      id: U33
    structure: OC[C@@H]1O[C@H](C[C@@H]1O)n1cc(Br)c(=O)[nH]c1=O
  UBI:
    id: UBI
    name: 2'-deoxy-5-[(2-methylpropyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-[(2-methylpropyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[5-(2-methylpropylcarbamoyl)-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: UBI
    structure: CC(CNC(=O)c1cn([C@H]2C[C@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O)C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 24
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 24
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 23
      charge: -1
  UCL:
    id: UCL
    name: 5-chloro-2'-deoxyuridine 5'-(dihydrogen phosphate)
    synonyms:
    - 5-chloro-2'-deoxyuridine 5'-(dihydrogen phosphate)
    - U
    - '[(2R,3S,5R)-5-(5-chloro-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: UCL
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc(Cl)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  UF2:
    id: UF2
    name: 1-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)pyrimidine-2,4(1h,3h)-dione
    synonyms:
    - '[(2R,3R,4S,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione
    identifiers:
    - ns: pdb-ccd
      id: UF2
    structure: O[C@H]1[C@@H](COP(=O)(O)O)O[C@@H]([C@H]1F)n1ccc(=O)[nH]c1=O
  UFP:
    id: UFP
    name: 5-fluoro-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - N
    - '[(2R,3S,5R)-5-(5-fluoro-2,4-dioxo-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-fluorouridine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: UFP
    structure: O[C@H]1C[C@@H](O[C@H]1COP(=O)(O)O)n1cc(F)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  UFR:
    id: UFR
    name: 2'-deoxy-5-formyluridine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methanoyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-formyluridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: UFR
    structure: O=Cc1cn([C@@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
  UFT:
    id: UFT
    name: 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-2'-fluorouridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: UFT
    structure: O[C@@H]1[C@H](COP(=O)([O-])[O-])O[C@H]([C@H]1F)n1ccc(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 8
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 10
      charge: -1
  UMS:
    id: UMS
    name: 2'-methylselenyl-2'-deoxyuridine-5'-phosphate
    synonyms:
    - 2'-Se-methyl-2'-selenouridine 5'-(dihydrogen phosphate)
    - '[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methylselanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: UMS
    structure: C[Se][C@@H]1[C@H](O)[C@H](O[C@@H]1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 7
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 7
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  UMX:
    id: UMX
    name: '[(1r,3r,4r,5s,7s)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,3R,4R,5S,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl
      dihydrogen phosphate'
    - '[(1R,2S,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methyl-5-oxabicyclo[2.2.1]heptan-4-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: UMX
    structure: C[C@H]1C[C@@]2([C@@H]([C@@H]1[C@@H](O2)n1ccc(=O)[nH]c1=O)O)COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 22
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 22
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  UPE:
    id: UPE
    name: 2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-(2-phenylethylcarbamoyl)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: UPE
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C(=O)NCCc2ccccc2)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  UPS:
    id: UPS
    name: 2'-deoxy-5'-o-thiophosphonouridine
    synonyms:
    - 2'-deoxy-5'-O-thiophosphonouridine
    - 1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-oxolan-2-yl]pyrimidine-2,4-dione
    identifiers:
    - ns: pdb-ccd
      id: UPS
    structure: O[C@@H]1C[C@H](O[C@H]1COP(=S)([O-])[O-])n1ccc(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  URT:
    id: URT
    name: ({[(2r,5r)-5-(6-amino-9h-purin-9-yl)-4-fluoro-2,5-dihydrofuran-2-yl]oxy}methyl)phosphonic
      acid
    synonyms:
    - '[(2R,5R)-5-(6-aminopurin-9-yl)-4-fluoro-2,5-dihydrofuran-2-yl]oxymethylphosphonic
      acid'
    identifiers:
    - ns: pdb-ccd
      id: URT
    structure: FC1=C[C@@H](O[C@@H]1n1cnc2c1ncnc2N)OCP(=O)(O)O
  URX:
    id: URX
    name: '[(1r,3r,4r,5r,7s)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,2R,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methyl-5-oxabicyclo[2.2.1]heptan-4-yl]methyl
      dihydrogen phosphate'
    - '[(1R,3R,4R,5R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]hept-1-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: URX
    structure: C[C@@H]1C[C@@]2([C@H]([C@H]1[C@H](O2)n1ccc(=O)[nH]c1=O)O)COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 22
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 22
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  US1:
    id: US1
    name: 2'-deoxy-3'-thiouridine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2R,3S,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-sulfanyl-oxolan-2-yl]methyl dihydrogen
      phosphate'
    - 2'-deoxy-3'-thiouridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: US1
    structure: S[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1ccc(=O)[nH]c1=O
  US2:
    id: US2
    name: 2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methylsulfanyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: US2
    structure: CSc1cn([C@@H]2C[C@H]([C@H](O2)COP(=O)(O)O)O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 20
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 20
  US3:
    id: US3
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1h)-one
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-4-oxo-2-selanyl-pyrimidin-1-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one
    - T
    identifiers:
    - ns: pdb-ccd
      id: US3
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)nc1[SeH]
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  US4:
    id: US4
    name: '[(2r,3s,5r)-3-({[(2r,3s,5r)-5-(6-amino-9h-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl]methoxy}methoxy)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2R,3S,5R)-3-[[(2R,3S,5R)-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxymethoxy]-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - '[(2R,3S,5R)-3-({[(2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-3-hydroxytetrahydrofuran-2-yl]methoxy}methoxy)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl
      dihydrogen phosphate (non-preferred name)'
    identifiers:
    - ns: pdb-ccd
      id: US4
    structure: O[C@@H]1C[C@H](O[C@@H]1COCO[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cc(C)c(=O)[nH]c1=O)n1cnc2c1ncnc2N
  USM:
    id: USM
    name: 2'-s-methyl-2'-thiouridine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-S-methyl-2'-thiouridine 5'-(dihydrogen phosphate)
    - '[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methylsulfanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - U
    identifiers:
    - ns: pdb-ccd
      id: USM
    structure: CS[C@H]1[C@H](O)[C@@H](O[C@H]1n1ccc(=O)[nH]c1=O)COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 7
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 7
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 27
      charge: -1
  UVX:
    id: UVX
    name: '[(1r,3r,4r,7s)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)-7-hydroxy-5-methylidene-2-oxabicyclo[2.2.1]hept-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,3R,4R,7S)-3-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-7-hydroxy-5-methylidene-2-oxabicyclo[2.2.1]hept-1-yl]methyl
      dihydrogen phosphate'
    - '[(1R,4R,6R,7S)-6-(2,4-dioxopyrimidin-1-yl)-7-hydroxy-2-methylidene-5-oxabicyclo[2.2.1]heptan-4-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: UVX
    structure: C=C1C[C@@]2([C@H]([C@H]1[C@H](O2)n1ccc(=O)[nH]c1=O)O)COP(=O)([O-])[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 21
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 24
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 21
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 26
      charge: -1
  VET:
    id: VET
    name: '[(1r,2s,4r)-2-hydroxy-4-[(5r)-5-hydroxy-5-methyl-2,4-dioxo-imidazolidin-1-yl]cyclopentyl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,2S,4R)-2-hydroxy-4-[(5R)-5-hydroxy-5-methyl-2,4-dioxo-imidazolidin-1-yl]cyclopentyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: VET
    structure: O[C@H]1C[C@@H](C[C@H]1COP(=O)(O)O)N1C(=O)NC(=O)[C@]1(C)O
  X4A:
    id: X4A
    name: '[(2r,3s,5s)-2,3,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen phosphate'
    synonyms:
    - N
    - '[(2R,3S,5S)-2,3,5-trihydroxytetrahydrofuran-2-yl]methyl dihydrogen phosphate
      (non-preferred name)'
    - '[(2R,3S,5S)-2,3,5-trihydroxyoxolan-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: X4A
    structure: O[C@@H]1C[C@@H](O[C@]1(O)COP(=O)([O-])[O-])O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 14
      charge: -1
  XAD:
    id: XAD
    name: 9-(2,3-dideoxy-6-o-phosphono-beta-d-erythro-hexopyranosyl)-9h-purin-6-amine
    synonyms:
    - '[(2R,3S,6R)-6-(6-aminopurin-9-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen phosphate'
    - 9-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-9H-purin-6-amine
    - A
    identifiers:
    - ns: pdb-ccd
      id: XAD
    structure: O[C@H]1CC[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XAE:
    id: XAE
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-3h-imidazo[4,5-g]quinazolin-8-amine
    synonyms:
    - N
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3H-imidazo[4,5-g]quinazolin-8-amine
    - '[(2R,3S,5R)-5-(8-aminopyrimido[5,6-f]benzimidazol-3-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XAE
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1cc1ncnc(c1c2)N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  XAL:
    id: XAL
    name: '[(1s,4r,6r)-6-hydroxy-4-(adenin-9-yl)cyclohex-2-en-1-yl]methyl dihydrogen
      phosphate'
    synonyms:
    - '[(1S,4R,6R)-4-(6-amino-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen
      phosphate'
    - '[(1S,4R,6R)-4-(6-aminopurin-9-yl)-6-hydroxy-1-cyclohex-2-enyl]methyl dihydrogen
      phosphate'
    - A
    identifiers:
    - ns: pdb-ccd
      id: XAL
    structure: O[C@H]1C[C@H](C=C[C@@H]1COP(=O)([O-])[O-])n1cnc2c1ncnc2N
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  XAR:
    id: XAR
    name: '[(1r,4s,6s)-4-(6-amino-9h-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - N
    - '[(1R,4S,6S)-4-(6-amino-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen
      phosphate'
    - '[(1R,4S,6S)-4-(6-aminopurin-9-yl)-6-hydroxy-1-cyclohex-2-enyl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XAR
    structure: O[C@H]1C[C@@H](C=C[C@@H]1COP(=O)(O)O)n1cnc2c1ncnc2N
  XCL:
    id: XCL
    name: '[(1s,4r,6r)-6-hydroxy-4-(cytosin-9-yl)cyclohex-2-en-1-yl]methyl dihydrogen
      phosphate'
    synonyms:
    - '[(1S,4R,6R)-4-(4-amino-2-oxopyrimidin-1(2H)-yl)-6-hydroxycyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    - C
    - '[(1S,4R,6R)-4-(4-amino-2-oxo-pyrimidin-1-yl)-6-hydroxy-1-cyclohex-2-enyl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XCL
    structure: O[C@H]1C[C@H](C=C[C@@H]1COP(=O)([O-])[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  XCR:
    id: XCR
    name: '[(1r,4s,6s)-4-(4-amino-2-oxopyrimidin-1(2h)-yl)-6-hydroxycyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - C
    - '[(1R,4S,6S)-4-(4-azanyl-2-oxo-pyrimidin-1-yl)-6-hydroxy-cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XCR
    structure: O[C@H]1C[C@H](C=C[C@H]1COP(=O)([O-])[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XCS:
    id: XCS
    name: (1r)-1-(4-amino-6-methyl-2-oxo-1,2-dihydroquinazolin-8-yl)-1,4-anhydro-2-deoxy-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - N
    - '[(2R,3S,5R)-5-(4-amino-6-methyl-2-oxo-1H-quinazolin-8-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - (1R)-1-(4-amino-6-methyl-2-oxo-1,2-dihydroquinazolin-8-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
    identifiers:
    - ns: pdb-ccd
      id: XCS
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1cc(C)cc2c1[nH]c(=O)nc2N
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  XCT:
    id: XCT
    name: 4-amino-1-(2,3-dideoxy-6-o-phosphono-beta-d-erythro-hexopyranosyl)pyrimidin-2(1h)-one
    synonyms:
    - '[(2R,3S,6R)-6-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen
      phosphate'
    - 4-amino-1-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)pyrimidin-2(1H)-one
    - C
    identifiers:
    - ns: pdb-ccd
      id: XCT
    structure: O[C@H]1CC[C@H](O[C@@H]1COP(=O)([O-])[O-])n1ccc(nc1=O)N
    base_monomers:
    - C
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XCY:
    id: XCY
    name: '{5-[4-{[4-(aminomethyl)benzyl]amino}-2-oxopyrimidin-1(2h)- yl]-3-hydroxytetrahydrofuran-2-yl}methyl
      dihydrogen phosphate'
    synonyms:
    - C
    - N-[4-(aminomethyl)benzyl]-2'-deoxycytidine 5'-(dihydrogen phosphate)
    - '[(2R,3S,5R)-5-[4-[[4-(aminomethyl)phenyl]methylamino]-2-oxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XCY
    structure: NCc1ccc(cc1)CNc1ccn(c(=O)n1)[C@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 32
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 28
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 32
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 30
      charge: -1
  XFC:
    id: XFC
    name: 4-amino-1-(2-deoxy-2-fluoro-5-o-phosphono-beta-d-arabinofuranosyl)-2-oxo-1,2-dihydropyrimidine-5-carbaldehyde
    synonyms:
    - 4-amino-1-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-2-oxo-1,2-dihydropyrimidine-5-carbaldehyde
    - '[(2~{R},3~{R},4~{S},5~{R})-5-(4-azanyl-5-methanoyl-2-oxidanylidene-pyrimidin-1-yl)-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XFC
    structure: O=Cc1cn(c(=O)nc1N)[C@@H]1O[C@H]([C@H]([C@H]1F)O)COP(=O)(O)O
  XGA:
    id: XGA
    name: 6-amino-3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-3,7-dihydro-8h-imidazo[4,5-g]quinazolin-8-one
    synonyms:
    - N
    - 6-amino-3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-3,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
    - '[(2R,3S,5R)-5-(6-amino-8-oxo-7H-pyrimido[5,4-f]benzimidazol-3-yl)-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XGA
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1cc1nc(N)[nH]c(=O)c1c2
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  XGL:
    id: XGL
    name: '[(1s,4r,6r)-6-hydroxy-4-(guanin-9-yl)cyclohex-2-en-1-yl]methyl dihydrogen
      phosphate'
    synonyms:
    - '[(1S,4R,6R)-4-(2-amino-6-oxo-1H-purin-9-yl)-6-hydroxy-1-cyclohex-2-enyl]methyl
      dihydrogen phosphate'
    - G
    - '[(1S,4R,6R)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XGL
    structure: O[C@H]1C[C@H](C=C[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  XGR:
    id: XGR
    name: '[(1r,4s,6s)-4-(2-amino-6-oxo-1,6-dihydro-9h-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - G
    - '[(1R,4S,6S)-4-(2-azanyl-6-oxo-1H-purin-9-yl)-6-hydroxy-cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XGR
    structure: O[C@H]1C[C@H](C=C[C@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XGU:
    id: XGU
    name: 2-amino-9-(2,3-dideoxy-6-o-phosphono-beta-d-erythro-hexopyranosyl)-1,9-dihydro-6h-purin-6-one
    synonyms:
    - G
    - 2-amino-9-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-1,9-dihydro-6H-purin-6-one
    - '[(2R,3S,6R)-6-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XGU
    structure: O[C@H]1CC[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    base_monomers:
    - G
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XPB:
    id: XPB
    name: o6-[4-oxo-4-(3-pyridyl)butyl]-2'-deoxyguanosine-5'-monophosphate
    synonyms:
    - 9-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-6-[4-oxo-4-(pyridin-3-yl)butoxy]-9H-purin-2-amine
    - '[(2R,3S,5R)-5-[2-azanyl-6-(4-oxidanylidene-4-pyridin-3-yl-butoxy)purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XPB
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1cnc2c1nc(N)nc2OCCCC(=O)c1cccnc1
    base_monomers:
    - G
  XTF:
    id: XTF
    name: '[(1r,4r,5s,6r)-5-fluoro-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,4R,5S,6R)-5-fluoranyl-4-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    - '[(1R,4R,5S,6R)-5-fluoro-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XTF
    structure: F[C@H]1[C@H](O)[C@H](C=C[C@@H]1n1cc(C)c(=O)[nH]c1=O)COP(=O)(O)O
    base_monomers:
    - T
  XTH:
    id: XTH
    name: 1-(2,3-dideoxy-6-o-phosphono-beta-d-erythro-hexopyranosyl)-5-methylpyrimidine-2,4(1h,3h)-dione
    synonyms:
    - '[(2R,3S,6R)-3-hydroxy-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxan-2-yl]methyl
      dihydrogen phosphate'
    - 1-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione
    - T
    identifiers:
    - ns: pdb-ccd
      id: XTH
    structure: O[C@H]1CC[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XTL:
    id: XTL
    name: '[(1s,4r,6r)-6-hydroxy-4-(thymin-9-yl)cyclohex-2-en-1-yl]methyl dihydrogen
      phosphate'
    synonyms:
    - '[(1S,4R,6R)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    - '[(1S,4R,6R)-6-hydroxy-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-1-cyclohex-2-enyl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: XTL
    structure: O[C@H]1C[C@H](C=C[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 16
      charge: -1
  XTR:
    id: XTR
    name: '[(1r,4s,6s)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2h)-yl)cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-1-cyclohex-2-enyl]methyl
      dihydrogen phosphate'
    - '[(1R,4S,6S)-6-hydroxy-4-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)cyclohex-2-en-1-yl]methyl
      dihydrogen phosphate'
    - T
    identifiers:
    - ns: pdb-ccd
      id: XTR
    structure: O[C@@H]1C[C@H](C=C[C@@H]1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    base_monomers:
    - T
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  XTY:
    id: XTY
    name: (1r)-1,4-anhydro-2-deoxy-1-(6-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-8-yl)-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - N
    - (1R)-1,4-anhydro-2-deoxy-1-(6-methyl-2,4-dioxo-1,2,3,4-tetrahydroquinazolin-8-yl)-5-O-phosphono-D-erythro-pentitol
    - '[(2R,3S,5R)-3-hydroxy-5-(6-methyl-2,4-dioxo-1H-quinazolin-8-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XTY
    structure: Cc1cc([C@H]2O[C@@H]([C@@H](C2)O)COP(=O)(O)O)c2c(c1)c(=O)[nH]c(=O)[nH]2
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 13
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 13
  XUA:
    id: XUA
    name: 2'-se-methyl-2'-selenoadenosine 5'-(dihydrogen phosphate)
    synonyms:
    - 2'-Se-methyl-2'-selenoadenosine 5'-(dihydrogen phosphate)
    - A
    - '[(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-methylselanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: XUA
    structure: C[Se][C@H]1[C@@H](O)[C@H](O[C@H]1n1cnc2c1ncnc2N)COP(=O)([O-])[O-]
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 7
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 25
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 7
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 28
      charge: -1
  XUG:
    id: XUG
    name: 2'-se-methyl-2'-selenoguanosine 5'-(dihydrogen phosphate)
    synonyms:
    - G
    - '[(2R,3R,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-4-methylselanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-Se-methyl-2'-selenoguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: XUG
    structure: C[Se][C@H]1[C@@H](O)[C@H](O[C@@H]1n1cnc2c1nc(N)[nH]c2=O)COP(=O)([O-])[O-]
    base_monomers:
    - G
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 7
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 27
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 7
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 30
      charge: -1
  Y:
    id: Y
    name: 2'-deoxy-n6-(s)styrene oxide adenosine monophosphate
    synonyms:
    - '[(2R,3S,5R)-3-hydroxy-5-[6-[[(1S)-2-hydroxy-1-phenyl-ethyl]amino]purin-9-yl]oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 2'-deoxy-N-[(1S)-2-hydroxy-1-phenylethyl]adenosine 5'-(dihydrogen phosphate)
    - A
    identifiers:
    - ns: pdb-ccd
      id: Y
    structure: OC[C@@H](c1ccccc1)Nc1ncnc2c1ncn2[C@@H]1C[C@@H]([C@H](O1)COP(=O)([O-])[O-])O
    base_monomers:
    - A
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 35
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 31
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 35
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 34
      charge: -1
  YCO:
    id: YCO
    name: 3-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)-1h-pyrimido[5,4-b][1,4]benzoxazin-2(3h)-one
    synonyms:
    - 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrimido[5,4-b][1,4]benzoxazin-2(3H)-one
    - '[(2R,3S,5R)-3-hydroxy-5-(2-oxo-1H-pyrimido[5,4-b][1,4]benzoxazin-3-yl)oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: YCO
    structure: O[C@@H]1C[C@@H](O[C@H]1COP(=O)([O-])[O-])n1cc2oc3ccccc3nc2[nH]c1=O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  YRR:
    id: YRR
    name: 3-hydroxy-pyrrolidin-2-ylmethyl-monophosphate group
    synonyms:
    - N
    - '[(2R,3S)-3-hydroxypyrrolidin-2-yl]methyl dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: YRR
    structure: O[C@H]1CCN[C@@H]1CO[P@](=O)(O)[O-]
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  Z:
    id: Z
    name: 1-(2-deoxy-5-o-phosphono-beta-d-erythro-pentofuranosyl)pyrimidin-2(1h)-one
    synonyms:
    - 1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)pyrimidin-2(1H)-one
    - C
    - '[(2R,3S,5R)-3-hydroxy-5-(2-oxopyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen
      phosphate'
    identifiers:
    - ns: pdb-ccd
      id: Z
    structure: O[C@H]1C[C@H](O[C@@H]1COP(=O)([O-])[O-])n1cccnc1=O
    base_monomers:
    - C
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 12
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 15
      charge: -1
  ZDU:
    id: ZDU
    name: 5-(3-aminopropyl)-2'-deoxyuridine-5'-monophosphate
    synonyms:
    - '[(2R,3S,5R)-5-[5-(3-aminopropyl)-2,4-dioxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 5-(3-aminopropyl)-2'-deoxyuridine 5'-(dihydrogen phosphate)
    - U
    identifiers:
    - ns: pdb-ccd
      id: ZDU
    structure: NCCCc1cn([C@H]2C[C@@H]([C@H](O2)COP(=O)([O-])[O-])O)c(=O)[nH]c1=O
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 22
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 18
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 22
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 21
      charge: -1
  JSP:
    id: JSP
    name: (1r)-1-(4-amino-1-methyl-2-oxo-1,2-dihydropyrimidin-5-yl)-1,4-anhydro-2-deoxy-5-o-phosphono-d-erythro-pentitol
    synonyms:
    - (1R)-1-(4-amino-1-methyl-2-oxo-1,2-dihydropyrimidin-5-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol
    - '[(2~{R},3~{S},5~{R})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: JSP
    structure: O[C@@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)c1cn(C)c(=O)nc1N
  F74:
    id: F74
    name: 8-chloro-2'-deoxyguanosine 5'-(dihydrogen phosphate)
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(2-azanyl-8-chloranyl-6-oxidanylidene-3~{H}-purin-9-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    - 8-chloro-2'-deoxyguanosine 5'-(dihydrogen phosphate)
    identifiers:
    - ns: pdb-ccd
      id: F74
    structure: O[C@@H]1C[C@H](O[C@H]1COP(=O)(O)O)n1c(Cl)nc2c1[nH]c(N)nc2=O
    base_monomers:
    - G
  AWC:
    id: AWC
    name: 2'-deoxy-5'-o-[(r)-hydroxy(oxo)-lambda~5~-phosphanyl]-5-selenophen-2-yluridine
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-selenophen-2-yl-pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxyphosphinic
      acid'
    - 2'-deoxy-5'-O-[(R)-hydroxy(oxo)-lambda~5~-phosphanyl]-5-selenophen-2-yluridine
    identifiers:
    - ns: pdb-ccd
      id: AWC
    structure: O[P@@H](=O)OC[C@@H]1O[C@H](C[C@H]1O)n1cc(c2ccc[se]2)c(=O)[nH]c1=O
  DZ:
    id: DZ
    name: '[(2~{r},3~{s},5~{r})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{h}-pyridin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(6-azanyl-5-nitro-2-oxidanylidene-1~{H}-pyridin-3-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DZ
    structure: O[C@@H]1C[C@H](O[C@@H]1COP(=O)(O)O)c1cc([N+](=O)[O-])c([nH]c1=O)N
  DP:
    id: DP
    name: '[(2~{r},3~{s},5~{r})-5-(2-azanyl-4-oxidanylidene-imidazo[1,2-a][1,3,5]triazin-8-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    synonyms:
    - '[(2~{R},3~{S},5~{R})-5-(2-azanyl-4-oxidanylidene-imidazo[1,2-a][1,3,5]triazin-8-yl)-3-oxidanyl-oxolan-2-yl]methyl
      dihydrogen phosphate'
    identifiers:
    - ns: pdb-ccd
      id: DP
    structure: O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n1ccn2c1nc(N)nc2=O