Atom Nomenclature for CN2

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 CN2

Atom Name (V3) Atom Name (V2)
O4 O4
C12 C12
C13 C13
S1 S1
N1 N1
C11 C11
C14 C14
C15 C15
C10 C10
C9 C9
C8 C8
C7 C7
C5 C5
C3 C3
C1 C1
O1 O1
C2 C2
O2 O2
C4 C4
O3 O3
C6 C6
C22 C22
C21 C21
C20 C20
C19 C19
C17 C17
C16 C16
O5 O5
O6 O6
C18 C18
H131 1H13
H132 2H13
HS1 HS1
HN1 HN1
H11 H11
H15 H15
H101 1H10
H102 2H10
H91 1H9
H92 2H9
H7 H7
H21 1H2
H22 2H2
H23 3H2
H41 1H4
H42 2H4
H43 3H4
H61 1H6
H62 2H6
H63 3H6
H20 H20
H19 H19
H181 1H18
H182 2H18
H183 3H18