KarrLab/bpforms

id: canonical_dna
name: Canonical DNA nucleotide monophosphates
description: The canonical DNA nucleotide monophosphates
monomers:
  A:
    id: adenine
    name: adenine
    synonyms:
    - 6-aminopurine
    identifiers:
    - ns: chebi
      id: CHEBI:16708
    - ns: chebi
      id: CHEBI:58245
    - ns: metacyc.compound
      id: ADENINE
    - ns: pubchem.compound
      id: '190'
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1ncnc2N
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  C:
    id: cytosine
    name: cytosine
    synonyms:
    - 4-amino-2-oxo-1,2-dihydropyrimidine
    identifiers:
    - ns: chebi
      id: CHEBI:16040
    - ns: chebi
      id: CHEBI:57566
    - ns: metacyc.compound
      id: CYTOSINE
    - ns: pubchem.compound
      id: '597'
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1ccc(nc1=O)N
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  G:
    id: guanine
    name: guanine
    synonyms: []
    identifiers:
    - ns: pubchem.compound
      id: '764'
    - ns: chebi
      id: CHEBI:16235
    - ns: chebi
      id: CHEBI:57673
    - ns: metacyc.compound
      id: GUANINE
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1nc(N)[nH]c2=O
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  T:
    id: thymine
    name: thymine
    synonyms:
    - 5-methyluracil
    - 5-methyl-2,4(1H,3H)-pyrimidinedione
    identifiers:
    - ns: chebi
      id: CHEBI:17821
    - ns: chebi
      id: CHEBI:26999
    - ns: metacyc.compound
      id: THYMINE
    - ns: pubchem.compound
      id: '1135'
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cc(C)c(=O)[nH]c1=O
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  U:
    id: uracil
    name: uracil
    identifiers:
    - ns: chebi
      id: CHEBI:17568
    - ns: chebi
      id: CHEBI:246422
    - ns: metacyc.compound
      id: URACIL
    - ns: pubchem.compound
      id: '1174'
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1ccc(=O)[nH]c1=O
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1
  dI:
    id: hypoxanthine
    name: hypoxanthine
    synonyms:
    - deoxyinosine
    identifiers:
    - ns: chebi
      id: CHEBI:17368
    - ns: chebi
      id: CHEBI:28806
    - ns: metacyc.compound
      id: HYPOXANTHINE
    - ns: pubchem.compound
      id: '790'
    structure: OC1CC(OC1COP(=O)([O-])[O-])n1cnc2c1nc[nH]c2=O
    l_bond_atoms:
    - molecule: Monomer
      element: P
      position: 9
    l_displaced_atoms:
    - molecule: Monomer
      element: O
      position: 12
      charge: -1
    r_bond_atoms:
    - molecule: Monomer
      element: O
      position: 1
    r_displaced_atoms:
    - molecule: Monomer
      element: H
      position: 1