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Table 1 KEGG Atom Types.

From: KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics

  Carbon atoms
C1a R-CH3 / methyl
C1b R-CH2-R / methylene
C1c R-CH(-R)-R / tertiary carbon
C1d R-C(-R)2-R / quaternary carbon
C1x ring-CH2-ring / methylene in ring
C1y ring-CH(-R)-ring / tertiary carbon in ring
C1z ring-C(-R)2-ring / quaternary carbon in ring
C2a R=CH2 / alkenyl terminus carbon
C2b R=CH-R / alkenyl secondary carbon
C2c R=C(-R)2 / alkenyl tertiary carbon
C2x ring-CH=ring / alkenyl secondary carbon in ring
C2y ring-C(-R)=ring or ring-C(=R)-ring / alkenyl tertiary carbon in ring
C3a R#CH / alkynyl terminus carbon
C3b R#C-R / alkynyl secondary carbon
C4a R-CH=O / aldehyde carbon
C5a R-C(=O)-R / keto carbon
C5x ring-C(=O)-ring / keto carbon in ring
C6a R-C(=O)-OH / carboxylate carbon
C7a R-C(=O)-O-R / carboxylate ester carbon
C7x ring-C(=O)-O-ring / lactone carbon
C8x ring-CH=ring / aromatic secondary carbon
C8y ring-C(-R)=ring / aromatic tertiary carbon
C0 Undefined carbon
  Nitrogen atoms
N1a R-NH2 / primary amine
N1b R-NH-R / secondary amine
N1c R-N(-R)2 / tertiary amine
N1d R-N(-R)3+ / quaternary ammonium
N1x ring-NH-ring / secondary amine in ring
N1y ring-N(-R)-ring / tertiary amine in ring
N2a R=N-H / primary imine
N2b R=N-R / secondary imine
N2x ring-N=ring / secondary imine in ring
N2y ring-N(-R)+=ring / iminium
N3a R#N / nitrile
N4x ring-NH-ring / aromatic secondary amine
N4y ring-N(-R)-ring / aromatic tertiary amine
N5x ring-N=ring / aromatic secondary imine
N5y ring-N(-R)+=ring / aromatic tertiary imine
N0 Undefined nitrogen
  Oxygen atoms
O1a R-OH / hydroxy
O1b N-OH / N-hydroxy
O1c P-OH / P-hydroxy
O1d S-OH / S-hydroxy
O2a R-O-R / hydroxy ether
O2b P-O-R / hydroxy phosphate bond
O2c P-O-P / pyrophosphate bond
O2x ring-O-ring / cyclic ether
O3a N=O / N-oxo
O3b P=O / P-oxo
O3c S=O / S-oxo
O4a R-CH=O / aldehyde oxygen
O5a R-C(=O)-R / keto oxygen
O5x ring-C(=O)-ring / keto oxygen in ring
O6a R-C(=O)-OH / carboxylate oxygen
O7a R-C(=O)-O-R / carboxylate ester oxygen
O7x ring-C(=O)-O-ring / lactone oxygen
O0 Undefined oxygen
  Sulfur atoms
S1a R-SH / mercapto
S2a R-S-R / sulfide
S2x ring-S-ring / sulfide in ring
S3a R-S-S-R / disulfide
S3x ring-S-S-ring / disulfide in ring
S4a R-SO3 / sulfate
S0 Undefined sulfur
  Phosphorus atoms
P1a P-R / phosphine
P1b P-O / phosphate
  Halogen atoms
X F / fluoride
  Cl / chloride
  Br / bromide
  I / iodide
  Other atoms
Z Other atoms
  1. KEGG Atom Types were defined in 2003 [17], and were used to label the nodes in molecular graphs. KEGG atom label consists of three letters, such as "C1a" meaning a methyl carbon. The first and second letters represent atom species and orbital environments, respectively. The third letter describes the surroundings of a given atom in terms of its bonded neighbors.