Atom Nomenclature for P9B

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 P9B

Atom Name (V3) Atom Name (V2)
C1 C1
N1 N1
O1 O1
S1 S1
C2 C2
O2 O2
C3 C3
C4 C4
C5 C5
C6 C6
N7 N7
C8 C8
O8 O8
N9 N9
C10 C10
C11 C11
F11 F11
C12 C12
F12 F12
C13 C13
F13 F13
C14 C14
F14 F14
C15 C15
F15 F15
HN1 HN1
H2 H2
H3 H3
H5 H5
H6 H6
HN7 HN7
HN9 HN9
HN1A HN1A