Atom Nomenclature for NHW

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 NHW

Atom Name (V3) Atom Name (V2)
S1 S1
C2 C2
C3 C3
N4 N4
C5 C5
O5 O5
C6 C6
C7 C7
N8 N8
C9 C9
O9 O9
CP CP
C10 C10
O10 O10
C11 C11
C12 C12
C13 C13
C14 C14
N1A N1A
O1A O1A
P1A P1A
C1M C1M
O1M O1M
C1X C1X
C2A C2A
O2A O2A
P2A P2A
C2M C2M
C2X C2X
O2X O2X
N3A N3A
O3A O3A
C3M C3M
C3X C3X
O3X O3X
P3X P3X
C4A C4A
O4A O4A
C4M C4M
C4X C4X
O4X O4X
C5A C5A
O5A O5A
C5M C5M
C5X C5X
O5X O5X
C6A C6A
N6A N6A
O6A O6A
C6M C6M
N7A N7A
O7A O7A
C7M C7M
C8A C8A
O8A O8A
C8M C8M
N9A N9A
O9A O9A
C9M C9M
CAM CAM
CBM CBM
CCM CCM
CDM CDM
CEM CEM
H2 H2
H2A H2A
H3 H3
H3A H3A
HN4 HN4
H6 H6
H6A H6A
H7 H7
H7A H7A
HN8 HN8
HP HP
HPA HPA
H10 H10
HO10 HO10
H12 H12
H12A H12A
H13 H13
H13A H13A
H13B H13B
H14 H14
H14A H14A
H14B H14B
H1X H1X
H2AA H2AA
H2M H2M
H2MA H2MA
H2X H2X
HO2X HO2X
H3M H3M
H3MA H3MA
H3X H3X
H4M H4M
H4MA H4MA
H4X H4X
H5M H5M
H5MA H5MA
H5X H5X
H5XA H5XA
HN6A HN6A
HN6B HN6B
H6M H6M
H6MA H6MA
H7M H7M
H7MA H7MA
H8A H8A
H8M H8M
H8MA H8MA
H9M H9M
H9MA H9MA
HAM HAM
HAMA HAMA
HBM HBM
HBMA HBMA
HCM HCM
HCMA HCMA
HDM HDM
HDMA HDMA
HEM HEM
HEMA HEMA
HEMB HEMB
HO2A HO2A
HO4A HO4A
HO7A HO7A
HO8A HO8A