Atom Nomenclature for GW6

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 GW6

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
F1 F1
C8 C8
C9 C9
C10 C10
O1 O1
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
F2 F2
C16 C16
O2 O2
C17 C17
C18 C18
C19 C19
C20 C20
O3 O3
C21 C21
O4 O4
C22 C22
C23 C23
C24 C24
C25 C25
O5 O5
C26 C26
O6 O6
S1 S1
C27 C27
F3 F3
H1 H1
H1A H1A
H1B H1B
H2 H2
H3 H3
H3A H3A
H4 H4
H5 H5
H6 H6
H6A H6A
H7 H7
H9 H9
H11 H11
H12 H12
H14 H14
H14A H14A
H14B H14B
H16 H16
HO2 HO2
H17 H17
H17A H17A
H19 H19
H19A H19A
H19B H19B
H23 H23
H24 H24
H25 H25
H27 H27
H27A H27A