Atom Nomenclature for DJL

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 DJL

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
O7 O7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
CL1 CL1
N20 N20
C22 C22
C23 C23
F23 F23
C30 C30
H30 H30
HN20 HN20
HN2A HN2A
HN2B HN2B
H22 H22
H22A H22A
H22B H22B
H23 H23
H23A H23A
H11 H11
H10 H10
H4 H4
H3 H3
H2 H2
H1 H1
H6 H6