Atom Nomenclature for EPE

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 EPE

Atom Name (V3) Atom Name (V2)
N1 N1
C2 C2
C3 C3
N4 N4
C5 C5
C6 C6
C7 C7
C8 C8
O8 O8
C9 C9
C10 C10
S S
O1S O1S
O2S O2S
O3S O3S
H21 1H2
H22 2H2
H31 1H3
H32 2H3
H51 1H5
H52 2H5
H61 1H6
H62 2H6
H71 1H7
H72 2H7
H81 1H8
H82 2H8
HO8 HO8
H91 1H9
H92 2H9
H101 1H10
H102 2H10
HOS3 3HOS