Atom Nomenclature for TMP

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 TMP

Atom Name (V3) Atom Name (V2)
P P
O1P O1P
O2P O2P
O3P O3P
O5' O5*
C5' C5*
C4' C4*
O4' O4*
C3' C3*
O3' O3*
C2' C2*
C1' C1*
N1 N1
C2 C2
O2 O2
N3 N3
C4 C4
O4 O4
C5 C5
C5M C5M
C6 C6
HOP2 2HOP
HOP3 3HOP
H5'1 1H5*
H5'2 2H5*
H4' H4*
H3' H3*
HO3' *HO3
H2'1 1H2*
H2'2 2H2*
H1' H1*
HN3 HN3
H51 1H5
H52 2H5
H53 3H5
H6 H6