[phenixbb] "Aromatic" question

William Scott wgscott at chemistry.ucsc.edu
Wed Oct 10 07:03:34 PDT 2007

Oh, the other thing I noticed, when I made 5-bromo-uracil (5BU), was that
elbow.builder failed to put in planar restraints at the bottom of the cif
file. I had to do this manually, or the ring looked puckered.  Fortunately
it was fairly easy to do:

5BU       plan      N1        0.020
5BU       plan      C2        0.020
5BU       plan      O2        0.020
5BU       plan      N3        0.020
5BU       plan      C4        0.020
5BU       plan      O4        0.020
5BU       plan      C5        0.020
5BU       plan      C6        0.020
5BU       plan      C1*       0.020
5BU       plan      H3        0.020
5BU       plan      BR        0.020
5BU       plan      H6        0.020

This keeps the six membered ring and the exocyclic functional groups (two
keto oxygens and one Br atom) constrained to a plane.

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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