Atom Nomenclature for IN5

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 IN5

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
O4 O4
O5 O5
C7 C7
C8 C8
C9 C9
C10 C10
N1 N1
C4 C4
C5 C5
O1 O1
C6 C6
O2 O2
N2 N2
P1 P1
O3 O3
P2 P2
O6 O6
O7 O7
O8 O8
H1 H1
HO5 HO5
H71 1H7
H72 2H7
H81 1H8
H82 2H8
H9 H9
H101 1H10
H102 2H10
H103 3H10
HO1 HO1
H61 1H6
H62 2H6
H63 3H6
HN2 HN2
HO3 HO3
HO7 HO7
HO8 HO8