Atom Nomenclature for MD7

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 MD7

Atom Name (V3) Atom Name (V2)
CAN CAN
CAO CAO
CAW CAW
CAS CAS
OAC OAC
CAR CAR
CAD CAD
NAA NAA
CAQ CAQ
OAB OAB
NAP NAP
CAT CAT
CAK CAK
CAM CAM
CAJ CAJ
CAL CAL
CAV CAV
CAU CAU
CAH CAH
CAF CAF
CAE CAE
CAG CAG
CAI CAI
HAN HAN
HANA HANA
HAO HAO
HAOA HAOA
HAW HAW
HOAC HOAC
HNAP HNAP
HAK HAK
HAM HAM
HAJ HAJ
HAL HAL
HAH HAH
HAF HAF
HAE HAE
HAG HAG
HAI HAI