Atom Nomenclature for PHO

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 PHO

Atom Name (V3) Atom Name (V2)
CHA CHA
CHB CHB
CHC CHC
CHD CHD
NA N A
C1A C1A
C2A C2A
C3A C3A
C4A C4A
CMA CMA
CAA CAA
CBA CBA
CGA CGA
O1A O1A
O2A O2A
NB N B
C1B C1B
C2B C2B
C3B C3B
C4B C4B
CMB CMB
CAB CAB
CBB CBB
NC N C
C1C C1C
C2C C2C
C3C C3C
C4C C4C
CMC CMC
CAC CAC
CBC CBC
ND N D
C1D C1D
C2D C2D
C3D C3D
C4D C4D
CMD CMD
CAD CAD
OBD OBD
CBD CBD
CGD CGD
O1D O1D
O2D O2D
CED CED
C1 C1
C2 C2
C3 C3
C4 C4
C5 C5
C6 C6
C7 C7
C8 C8
C9 C9
C10 C10
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
HHB HHB
HHC HHC
HHD HHD
H2A H2A
H3A H3A
HMA1 HMA1
HMA2 HMA2
HMA3 HMA3
HAA1 HAA1
HAA2 HAA2
HBA1 HBA1
HBA2 HBA2
HMB1 HMB1
HMB2 HMB2
HMB3 HMB3
HAB HAB
HBB1 HBB1
HBB2 HBB2
HMC1 HMC1
HMC2 HMC2
HMC3 HMC3
HAC1 HAC1
HAC2 HAC2
HBC1 HBC1
HBC2 HBC2
HBC3 HBC3
HMD1 HMD1
HMD2 HMD2
HMD3 HMD3
HBD HBD
HED1 HED1
HED2 HED2
HED3 HED3
H11 H11
H12 H12
H2 H2
H41 H41
H42 H42
H43 H43
H51 H51
H52 H52
H61 H61
H62 H62
H71 H71
H72 H72
H8 H8
H91 H91
H92 H92
H93 H93
H101 H101
H102 H102
H111 H111
H112 H112
H121 H121
H122 H122
H13 H13
H141 H141
H142 H142
H143 H143
H151 H151
H152 H152
H161 H161
H162 H162
H171 H171
H172 H172
H18 H18
H191 H191
H192 H192
H193 H193
H201 H201
H202 H202
H203 H203
HNB HNB
HND HND