[phenixbb] "Aromatic" question

William Scott wgscott at chemistry.ucsc.edu
Wed Oct 10 06:55:25 PDT 2007

It is probably an error in the cif file due to the wrong number of
hydrogens. If you can define a SMILES string, (c1ccccc1 is benzene,
C1CCCCC1 is cyclohexane), you should be able to get the right thing. 
Aromatic rings should be planar to within 1 degree or so. Visually, they
should appear flat.

You can generate a proper SMILES string with a java molecular editor.


Claudia Scotti wrote:
> Dear list,
> I've refined a protein at 2.0 A resolution with its ligand, a small
> molecule which includes a phenyl group. For this, I used elbow to generate
> the cif file, and in this file the atoms of the phenyl ring are correctly
> defined as "aromatic". However, the pdb output of the refinement shows a
> boat configuration for the 6 carbon atoms ring, with a very nice fit to
> the electron density. This would suggest a flexible cyclohexyl-
> substituent instead of the expected, typically planar phenyl ring.
> As my chemistry is poor, I'd really need some suggestions on where I'm
> wrong: did I give the wrong cif file or does phenix recognise a better
> fitting in a boat structure, indicating that my ligand phenyl moiety has
> been reduced somehow to a cyclohexyl one? Or is the aromatic ring of the
> phenyl group not so planar as I've supposed it to be until now?
> Any help would be very appreciated.
> Many many thanks,
> Claudia
> Claudia Scotti
> Dipartimento di Medicina Sperimentale
> Sezione di Patologia Generale
> Universita' di Pavia
> Piazza Botta, 10
> 27100 Pavia
> Italia
> Tel. 0039 0382 986335/8/1
> Facs 0039 0382 303673
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