Atom Nomenclature for DIF

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 DIF

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
CL2 CL2
C3 C3
C4 C4
CL4 CL4
C5 C5
C6 C6
N1 N1
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
O1 O1
O2 O2
H1 H1
H5 H5
H6 H6
HN1 HN1
H9 H9
H10 H10
H11 H11
H12 H12
H131 1H13
H132 2H13
HO1 HO1