Atom Nomenclature for C9N

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 C9N

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
N2 N1
N N2
C1B C5
CN C6
O O1
H1 H1
H2 H2
H3 H3
H31 H4
H32 H5
H5 H8
H6 H9
HB3 H10
HB2 H11
HB1 H12
HN2 H13
HN1 H14
HN3 H15
H H16
H42 H18
H4 H19