Atom Nomenclature for THD

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 THD

Atom Name (V3) Atom Name (V2)
N1' N1'
C2' C2'
CM2 CM2
N3' N3'
C4' C4'
N4' N4'
C5' C5'
C6' C6'
C7' C7'
N3 N3
C2 C2
S1 S1
C5 C5
C4 C4
CM4 CM4
C6 C6
C7 C7
O7 O7
PA PA
O1A O1A
O2A O2A
O3A O3A
PB PB
O1B O1B
O2B O2B
O3B O3B
C8 C8
O9 O9
C9 C9
O10 O10
HM21 1HM2
HM22 2HM2
HM23 3HM2
H4'1 1H4'
H4'2 2H4'
H6' H6'
H7'1 1H7'
H7'2 2H7'
HM41 1HM4
HM42 2HM4
HM43 3HM4
H6C1 1H6C
H6C2 2H6C
H7C1 1H7C
H7C2 2H7C
HO1A HO1A
HO2B HO2B
HO3B HO3B
H9 H9
H9C1 1H9C
H9C2 2H9C
H10 H10