To whom it may concern,
I was trying to save the 3D structure of a chemical which is C1CCC1 in PDB
file. However, I am not sure all of my coordinates are zero as shown:
HETATM 1 C1 UNL 1 0.000 0.000 0.000 1.00
0.00 C
HETATM 2 C2 UNL 1 0.000 0.000 0.000 1.00
0.00 C
HETATM 3 C3 UNL 1 0.000 0.000 0.000 1.00
0.00 C
HETATM 4 C4 UNL 1 0.000 0.000 0.000 1.00
0.00 C
I tried the same chemical with MolToMolBlock and it also gave me zero
coordinates. However, in te example in RDKit website, it showed non-zero
coordinates:
>>> m2 = Chem.MolFromSmiles('C1CCC1')>>> print(Chem.MolToMolBlock(m2))
RDKit 2D
4 4 0 0 0 0 0 0 0 0999 V2000 1.0607 0.0000 0.0000
C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -1.0607 0.0000 C
0 0 0 0 0 0 0 0 0 0 0 0 -1.0607 0.0000 0.0000 C
0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0607 0.0000 C 0
0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0
4 1 1 0M END
Would you please explain me why and how can I have the PDB file with
non-zero coordinates?
Thank you so much for your help
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