Thanks Chris for the helpful comments. Sorry to keep on but I'm still left
with the problem on going from cif to smiles where the original number of
elements is not conserved. What I want is to be able to reliably represent
the original cif molecule as a smiles string and from there recreate the
molecule with gen3d. The problem at the moment is that the number of H
atoms is changing. Any work around for this?
On 4 December 2012 15:05, Chris Morley <c.mor...@gaseq.co.uk> wrote:
> Scott
>
> Your "correct smiles" is not right. The sum of the bond orders to the
> charged nitrogen should be 4, and is only 3 (it has no H attached). The
> correct SMILES is in my post below. Even with it, the round trip via xyz:
>
> obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1" -oxyz --gen3D
> | obabel -ixyz -osmi --append formula
> 1 molecule converted
> C(=O)(O)C[C@@H](C(=O)[O])N1CNC=C1 C7H8N2O4
> 1 molecule converted
>
> gives a di-radical rather than a zwitterion because xyz does not
> represent charges (or even bonds) and so OpenBabel didn't get any hints.
> xyz format is poor choice of format for general use. The round trip
> works ok with formats like mol or cml.
>
> Chris
>
> On 04/12/2012 10:51, Scott McKechnie wrote:
> > Hi Chris,
> >
> > Thanks for your reply and apologies for the delayed response. Converting
> > the cif to xyz and viewing the molecule shows the correct structure but
> > converting the xyz file to smi and then generating coordinates and
> > viewing shows the addition of a H atom.
> >
> > The correct smiles is: C(=O)(O)C[C@@H](C(=O)[O-])[N]1C=C[N+]=C1
> > The other smiles is: C(=O)([C@@H](CC(=O)O)N1C=CNC1)O
> >
> > One strange feature is that there doesn't appear to be a double bond
> > between the N atom in the ring and the C atom, leaving the C atom with
> > only three bonds. The smiles conversion seems to want to add a H here to
> > get the correct bonding.
> >
> > Similarly for an ion, using smiles conversion results in the addition of
> > H's.
> >
> > I've attached the cif file.
> >
> > Many thanks,
> >
> > Scott
> >
> >
> > On 30 November 2012 14:53, Chris Morley <c.mor...@gaseq.co.uk
> > <mailto:c.mor...@gaseq.co.uk>> wrote:
> >
> > On 30/11/2012 12:03, scott_m wrote:
> > > Dear all,
> > >
> > > The conversion of (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate
> > from a
> > > .cif file to .smi and subsequent generation of coordinates from
> > the .smi
> > > file results in the addition of an extra H to one of the ring C
> > atoms. The
> > > original cif formula is C7H8N2O4 but this changes to C7H9N2O4,
> > which is no
> > > longer a zwitterion.
> > >
> > > I also noticed that converting an ion to smi and then from smi to
> xyz
> > > resulted in the addition of hydrogen atoms. Can this be avoided?
> > >
> > > Is the smi conversion of ions and zwitterions known to cause
> > problems?
> >
> > Getting added hydrogens right is a recurrent issue. However the
> > conversion from SMILES to xyz (and other formats) seems ok. Your
> problem
> > may be in the conversion of the cif file, but you will need to
> append it
> > for somebody (probably not me) to debug.
> >
> > obabel -:"C(=O)(O)C[C@@H](C(=O)[O-])n1c[nH+]cc1
> > (S)-3-carboxy-2-(imidazol-3-ium-1-yl)propanoate" -oxyz --gen3D
> > --title ""
> > --append formula
> > 21
> > C7H8N2O4
> > C 2.45602 0.70570 1.56344
> > O 3.44592 0.48586 2.25208
> > O 1.43656 1.46670 2.00415
> > C 2.26356 0.11437 0.19030
> > C 3.14546 0.74947 -0.88078
> > H 2.84831 0.31396 -1.84634
> > C 2.83038 2.27406 -0.99631
> > O 1.67090 2.60592 -0.61087
> > O 3.79441 2.97728 -1.40748
> > N 4.60137 0.42805 -0.71225
> > C 5.35900 0.94762 0.25841
> > N 6.58789 0.46124 0.10334
> > H 7.33992 0.61660 0.75954
> > C 6.69161 -0.15933 -1.12882
> > C 5.43119 -0.14873 -1.66026
> > H 0.84536 1.76580 1.27272
> > H 1.20439 0.19509 -0.08254
> > H 2.46795 -0.95767 0.27113
> > H 5.04774 1.61643 1.05753
> > H 7.65241 -0.48371 -1.46628
> > H 5.01646 -0.45579 -2.60586
> > 1 molecule converted
> >
> > Chris
> >
> >
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