Atom Nomenclature for LMG

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 LMG

Atom Name (V3) Atom Name (V2)
C1 C1
O1 O1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
O5 O5
C6 C6
O6 O6
C7 C7
C8 C8
C9 C9
O7 O7
C10 C10
O9 O9
C11 C11
C12 C12
C13 C13
C14 C14
C15 C15
C16 C16
C17 C17
C18 C18
C19 C19
C20 C20
C21 C21
C22 C22
C23 C23
C24 C24
C25 C25
C26 C26
C27 C27
O8 O8
C28 C28
O10 O10
C29 C29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C39 C39
C40 C40
C41 C41
C42 C42
C43 C43
C44 C44
C45 C45
HC61 1HC6
HC62 2HC6
HC71 1HC7
HC72 2HC7
HC91 1HC9
HC92 2HC9
H111 1H11
H112 2H11
H121 1H12
H122 2H12
H131 1H13
H132 2H13
H141 1H14
H142 2H14
H151 1H15
H152 2H15
H161 1H16
H162 2H16
H171 1H17
H172 2H17
H181 1H18
H182 2H18
H191 1H19
H192 2H19
H201 1H20
H202 2H20
H211 1H21
H212 2H21
H221 1H22
H222 2H22
H231 1H23
H232 2H23
H241 1H24
H242 2H24
H251 1H25
H252 2H25
H261 1H26
H262 2H26
H271 1H27
H272 2H27
H273 3H27
H291 1H29
H292 2H29
H301 1H30
H302 2H30
H311 1H31
H312 2H31
H321 1H32
H322 2H32
H331 1H33
H332 2H33
H341 1H34
H342 2H34
H351 1H35
H352 2H35
H361 1H36
H362 2H36
H371 1H37
H372 2H37
H381 1H38
H382 2H38
H391 1H39
H392 2H39
H401 1H40
H402 2H40
H411 1H41
H412 2H41
H421 1H42
H422 2H42
H431 1H43
H432 2H43
H441 1H44
H442 2H44
H451 1H45
H452 2H45
H453 3H45