Atom Nomenclature for VX7

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 VX7

Atom Name (V3) Atom Name (V2)
O24 O1
C23 C1
C22 C2
C21 C3
C20 C4
C19 C5
C18 C6
C17 C7
N16 N1
C15 C8
C14 C9
C12 C10
O13 O2
N11 N2
C10 C11
C09 C12
C08 C13
O25 O3
C07 C14
C26 C15
C28 C16
C29 C17
C27 C18
C06 C19
C05 C20
C02 C21
C03 C22
C04 C23
C01 C24
H1 H1
H2 H2
H3 H3
H4 H4
H5 H5
H7 H7
H8 H8
H9 H9
H10 H10
H11 H11
H12 H12
H13 H13
H14 H14
H15 H15
H16 H16
H17 H17
H18 H18
H19 H19
H20 H20
H21 H21
H22 H22
H23 H23
H24 H24
H25 H25
H26 H26
H27 H27
H28 H28
H29 H29