Atom Nomenclature for CMW

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 CMW

Atom Name (V3) Atom Name (V2)
O4 O4
C6 C6
N2 N2
C5 C5
C4 C4
C3 C3
N1 N1
C2 C2
C1 C1
O1 O1
C7 C7
C8 C8
C9 C9
N3 N3
S S
O3 O3
O2 O2
C10 C10
C16 C16
C15 C15
C13 C13
C14 C14
C12 C12
C11 C11
H2 H2
H4 H4
H1 H1
H3 H3
HA HA
H71C H71C
H72C H72C
H81C H81C
H82C H82C
H91C H91C
H92C H92C
HB HB
H16 H16
H11 H11
H15 H15
H141 H141
H142 H142
H143 H143
H12 H12