Atom Nomenclature for IGP

The atom nomenclature in PDB data files was revised with the release of data in the PDB Format Version 3.0. These changes make the PDB atom names used by PDB compliant with existing IUPAC nomenclature for standard amino acid and nucleotides (Pure & Appl. Chem., 70, 117-142, 1998) with the exception of the well established convention for C-terminal atoms OXT and HXT. A small number of additional changes were introduced in Version 3 to make atom labeling more conventional. The following chemical diagrams and tables provide the correspondences between atom names used in Version 3 and Version 2 PDB formats.

Labeled Chemical Diagrams

Chemical diagram with format V3 atom labels (heavy atoms)
Chemical diagram with format V3 atom labels (all atoms)
Chemical diagram with format V2 atom labels (heavy atoms)
Chemical diagram with format V2 atom labels (all atoms)

Atom Name Correspondences for IGP

Atom Name (V3) Atom Name (V2)
C1 C1
P P
OP1 OP1
OP2 OP2
OP3 OP3
OP4 OP4
C2 C2
O2 O2
C3 C3
O3 O3
CG CG
CD2 CD2
CE2 CE2
CE3 CE3
CD1 CD1
NE1 NE1
CZ2 CZ2
CZ3 CZ3
CH2 CH2
H11 1H1
H12 2H1
HOP1 1HOP
HOP2 2HOP
H2 H2
HO2 HO2
H3 H3
HO3 HO3
HE3 HE3
HD1 HD1
HN1 HN1
HZ2 HZ2
HZ3 HZ3
HH2 HH2