Atom Nomenclature for FUN

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 FUN

Atom Name (V3) Atom Name (V2)
N1 N1
S1 S1
O1 O1
O2 O2
C1 C1
C2 C2
CL1 CL1
C3 C3
C4 C4
N2 N2
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
O3 O3
C10 C10
C11 C11
C12 C12
O4 O4
O5 O5
HN11 HN11
HN12 HN12
H3 H3
HN2 HN2
H51 H51
H52 H52
H7 H7
H8 H8
H9 H9
H11 H11
HO4 HO4