rdkit reports "Explicit valence for atom # 0 S, 7, is greater than permitted" for six-valent sulfur?
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Evaluación
- Dificultad
- 4/5
- Tiempo estimado
- 3-5 días
- Aptitud para principiantes
- 55/100
Línea de trabajo
Reproduce the error with the supplied ADX PDB block using Chem.MolFromPDBBlock, then trace the PDB parser's bond construction and sulfur valence validation. Compare the parsed CONECT records with the expected six-valent sulfur behavior; done means the case is handled correctly or its unsupported status is clearly established with a regression test.
Escrito por el modelo de indexación a partir del texto del issue.
Descripción
I have a PDB file for the PDBeChem (aka CCD) ligand ADX which has (as far as I can see...) a six-valent sulfur, but I get this:
from rdkit import Chem
mol = Chem.MolFromPDBBlock(ADX)
[13:51:37] Explicit valence for atom # 0 S, 7, is greater than permitted
The "CONECT" record for the S is -
CONECT 1 2 2 3 3 4 8
which looks to me as if it's 6-valent.
Python 3.11.11
rdkit 2024.03.6
MacOS High Sierra 10.13.6 (yes, I know this is old but it's running on a good machine that can't be updated further)
The code I use to convert from the CIF I download from PDBeChem works okay for thousands of other CIF files from PDBeChem, so although it could be the problem I don't think it is.
ADX is read in from a file, and is a string that contains -
HEADER Model coordinates for ADX downloaded from PDBeChem
COMPND ADX
HETATM 1 SB ADX A 1 1.120 -0.280 -5.646 1.00 20.00 S
HETATM 2 O1B ADX A 1 1.559 -1.323 -6.506 1.00 20.00 O
HETATM 3 O2B ADX A 1 -0.013 0.546 -5.868 1.00 20.00 O
HETATM 4 O3B ADX A 1 2.303 0.667 -5.509 1.00 20.00 O
HETATM 5 PA ADX A 1 -0.128 0.012 -3.483 1.00 20.00 P
HETATM 6 O1A ADX A 1 0.457 1.363 -3.330 1.00 20.00 O
HETATM 7 O2A ADX A 1 -1.512 0.117 -4.299 1.00 20.00 O
HETATM 8 O3A ADX A 1 0.899 -0.930 -4.288 1.00 20.00 O
HETATM 9 O5' ADX A 1 -0.409 -0.618 -2.029 1.00 20.00 O
HETATM 10 C5' ADX A 1 -1.323 0.258 -1.367 1.00 20.00 C
HETATM 11 C4' ADX A 1 -1.634 -0.286 0.027 1.00 20.00 C
HETATM 12 O4' ADX A 1 -0.429 -0.350 0.821 1.00 20.00 O
HETATM 13 C3' ADX A 1 -2.560 0.685 0.793 1.00 20.00 C
HETATM 14 O3' ADX A 1 -3.918 0.250 0.712 1.00 20.00 O
HETATM 15 C2' ADX A 1 -2.053 0.615 2.252 1.00 20.00 C
HETATM 16 O2' ADX A 1 -3.085 0.138 3.118 1.00 20.00 O
HETATM 17 C1' ADX A 1 -0.880 -0.386 2.193 1.00 20.00 C
HETATM 18 N9 ADX A 1 0.195 0.033 3.094 1.00 20.00 N
HETATM 19 C8 ADX A 1 1.227 0.869 2.784 1.00 20.00 C
HETATM 20 N7 ADX A 1 1.998 1.026 3.820 1.00 20.00 N
HETATM 21 C5 ADX A 1 1.509 0.308 4.860 1.00 20.00 C
HETATM 22 C6 ADX A 1 1.913 0.092 6.188 1.00 20.00 C
HETATM 23 N6 ADX A 1 3.049 0.702 6.691 1.00 20.00 N
HETATM 24 N1 ADX A 1 1.175 -0.705 6.953 1.00 20.00 N
HETATM 25 C2 ADX A 1 0.089 -1.290 6.482 1.00 20.00 C
HETATM 26 N3 ADX A 1 -0.323 -1.122 5.243 1.00 20.00 N
HETATM 27 C4 ADX A 1 0.350 -0.341 4.405 1.00 20.00 C
HETATM 28 HOB3 ADX A 1 2.436 1.075 -6.376 1.00 20.00 H
HETATM 29 HOA2 ADX A 1 -1.860 -0.781 -4.377 1.00 20.00 H
HETATM 30 H5' ADX A 1 -2.245 0.325 -1.945 1.00 20.00 H
HETATM 31 H5'' ADX A 1 -0.877 1.249 -1.280 1.00 20.00 H
HETATM 32 H4' ADX A 1 -2.094 -1.271 -0.044 1.00 20.00 H
HETATM 33 H3' ADX A 1 -2.460 1.697 0.400 1.00 20.00 H
HETATM 34 HO3' ADX A 1 -4.447 0.891 1.205 1.00 20.00 H
HETATM 35 H2' ADX A 1 -1.702 1.593 2.582 1.00 20.00 H
HETATM 36 HO2' ADX A 1 -3.811 0.774 3.065 1.00 20.00 H
HETATM 37 H1' ADX A 1 -1.222 -1.388 2.454 1.00 20.00 H
HETATM 38 H8 ADX A 1 1.381 1.332 1.821 1.00 20.00 H
HETATM 39 HN61 ADX A 1 3.315 0.548 7.611 1.00 20.00 H
HETATM 40 HN62 ADX A 1 3.582 1.279 6.122 1.00 20.00 H
HETATM 41 H2 ADX A 1 -0.481 -1.931 7.137 1.00 20.00 H
CONECT 1 2 2 3 3 4 8
CONECT 4 28
CONECT 5 6 6 7 8 9
CONECT 7 29
CONECT 9 10
CONECT 10 11 30 31
CONECT 11 12 13 32
CONECT 12 17
CONECT 13 14 15 33
CONECT 14 34
CONECT 15 16 17 35
CONECT 16 36
CONECT 17 18 37
CONECT 18 19 27
CONECT 19 20 20 38
CONECT 20 21
CONECT 21 22 27 27
CONECT 22 23 24 24
CONECT 23 39 40
CONECT 24 25
CONECT 25 26 26 41
CONECT 26 27
END
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