Radka,
PDB files simply don't have bonding information. There is just no
way to be absolutely sure whether a bond is single or double,
especially when there are no hydrogens around. While the bond in
question may be long, there are other factors, like the local
geometry, to be considered when bonds are assigned.
Even when hydrogens are around, bond orders can still not be
certain because of different possible ionization states (although
in your case the O should be unlikely to be +ve).
So, the take home message is, always check your molecule and make
necessary edits manually.
Ling
>________________________________
> From: radka <radka2ra...@gmail.com>
>To: openbabel-discuss@lists.sourceforge.net
>Sent: Tuesday, July 16, 2013 2:00 AM
>Subject: [Open Babel] Error in double bond detection
>
>
>Please, can you help me with the following problem?:
>
>I have this PDB file (sugar from Protein Data Bank):
>HETATM 3781 C1 MAN C1129 35.524 5.379 57.298 1.00 26.66
>C
>HETATM 3782 C2 MAN C1129 34.930 6.750 56.924 1.00 26.33
>C
>HETATM 3783 C3 MAN C1129 33.464 6.454 56.622 1.00 26.11
>C
>HETATM 3784 C4 MAN C1129 33.300 5.264 55.639 1.00 27.32
>C
>HETATM 3785 C5 MAN C1129 34.075 4.044 56.187 1.00 26.81
>C
>HETATM 3786 C6 MAN C1129 33.940 2.770 55.387 1.00 29.05
>C
>HETATM 3787 O1 MAN C1129 35.436 5.171 58.706 1.00 28.59
>O
>HETATM 3788 O2 MAN C1129 35.526 7.320 55.789 1.00 25.38
>O
>HETATM 3789 O3 MAN C1129 32.846 7.632 56.180 1.00 27.40
>O
>HETATM 3790 O4 MAN C1129 31.911 5.020 55.451 1.00 27.90
>O
>HETATM 3791 O5 MAN C1129 35.457 4.383 56.289 1.00 22.18
>O
>HETATM 3792 O6 MAN C1129 34.428 2.960 54.081 1.00 30.05
>O
>---
>In this file, the atoms C1 and O1 have a distance 1.426 A. Therefore the
>single bond is between them.
>Note: This C-O bond is the longest C-O bond in this molecule.
>
>But when I convert this file to MOL, OpenBabel reports a double bond between
>C1 and O1.
>All other C-O bonds in the molecule are reported as single.
>
>And OpenBabel insists on the double bond even when I just add hydrogens to
>the PDB file.
>
>I used OpenBabel 2.3.2.
>
>Note: I do the conversion from PDB to MOL, because I need chirality data.
>And when the double bond is found, the chirality is not reported.
>
>Please, do you have some idea, where is a problem?
>
>Thank you very much for help.
>
>
>
>--
>View this message in context:
>http://forums.openbabel.org/Error-in-double-bond-detection-tp4656494.html
>Sent from the General discussion mailing list archive at Nabble.com.
>
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