Atom Nomenclature for LPO

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 LPO

Atom Name (V3) Atom Name (V2)
C1 C1
C2 C2
N3 N3
C4 C4
C5 C5
C6 C6
C7 C7
N8 N8
O9 O9
C10 C10
C11 C11
N12 N12
C13 C13
C14 C14
C15 C15
O16 O16
C17 C17
C18 C18
O19 O19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
CL26 CL26
CL27 CL27
C28 C28
O29 O29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
CL40 CL40
C41 C41
C42 C42
O43 O43
C44 C44
H1 H1
H1A H1A
H2 H2
H2A H2A
HN3 HN3
H4 H4
H4A H4A
H5 H5
HO9 HO9
H11 H11
H14 H14
H15 H15
H17 H17
H17A H17A
H18 H18
H18A H18A
H22 H22
H24 H24
H28 H28
H28A H28A
H28B H28B
H30 H30
H30A H30A
H31 H31
H33 H33
H35 H35
H36 H36
H38 H38
H38A H38A
H39 H39
H39A H39A
H41 H41
H41A H41A
H42 H42
H42A H42A
H44 H44
H44A H44A
H44B H44B