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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.