Atom Nomenclature for CFF

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 CFF

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
C10 C10
C6 C6
N3 N3
O11 O11
C12 C12
C4 C4
C5 C5
N9 N9
O13 O13
N7 N7
C8 C8
C14 C14
H101 1H10
H102 2H10
H103 3H10
H121 1H12
H122 2H12
H123 3H12
H81 1H8
H141 1H14
H142 2H14
H143 3H14