Atom Nomenclature for FPT

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 FPT

Atom Name (V3) Atom Name (V2)
C1 C1
N2 N2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
N7 N7
N8 N8
C9 C9
S9 S9
N10 N10
C11 C11
C12 C12
C13 C13
N14 N14
C15 C15
C16 C16
C17 C17
C18 C18
O17 O17
CA CA
CB CB
F18 F18
H3 H3
H5 H5
H6 H6
HN8 HN8
H10 H10
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H15 H15
H16 H16
HA1 1HA
HA2 2HA
HB1 1HB
HB2 2HB
HB3 3HB