Atom Nomenclature for SQD

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 SQD

Atom Name (V3) Atom Name (V2)
O6 O6
C44 C44
C45 C45
C46 C46
O47 O47
C7 C7
O49 O49
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
C21 C21
C22 C22
O48 O48
C23 C23
O10 O10
C24 C24
C25 C25
C26 C26
C27 C27
C28 C28
C29 C29
C30 C30
C31 C31
C32 C32
C33 C33
C34 C34
C35 C35
C36 C36
C37 C37
C38 C38
C1 C1
C2 C2
O2 O2
C3 C3
O3 O3
C4 C4
O4 O4
C5 C5
C6 C6
O5 O5
S S
O7 O7
O8 O8
O9 O9
H441 1H44
H442 2H44
H45 H45
H461 1H46
H462 2H46
H81 1H8
H82 2H8
H91 1H9
H92 2H9
H101 1H10
H102 2H10
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
H223 3H22
H241 1H24
H242 2H24
H251 1H25
H252 2H25
H261 1H26
H262 2H26
H271 1H27
H272 2H27
H281 1H28
H282 2H28
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
H383 3H38
H1 H1
H2 H2
HO2 HO2
H3 H3
HO3 HO3
H4 H4
HO4 HO4
H5 H5
H61 1H6
H62 2H6
HO8 HO8