Re: CCL:Compendium of bound conformations

 >Dear Colleagues;
 >
 >	I am seekings articles/reviews documenting differences between
 >experimentally-determined (or experimentally-inferred) conformations of
 >"small" (i.e. non-macromolecular) substrates/ligands and their in
 vacuo
 >counterparts calculated using molecular or quantum mechanics.  If anyone
 >has relevant citations, I'd appreciate your sharing those citations with me.
 >
 >Thanks in advance to all responders,
 >
 >S. Shapiro
 >toukie %! at !% zui.unizh.ch
 	Dear Dr. Shapiro,
 	Please see our recent article "Conformational energy penalties of
 protein-bound ligands", by J. Boström, P.-O. Norrby, and T. Liljefors
 in
 J.Comp.-Aid.Mol.Design 12, 383 (1998).  Also relevant are some earlier
 studies referenced therein, in particular Nicklaus et al, Bioorg.Med.Chem.
 3, 411 (1995).  In short, the results are that in vacuo structures can be
 substantially different from bound conformations.  The correct comparison
 is with the solution ensemble, not with gas phase data.  In most cases, if
 you compare inner energies of bound ligands to the inner energy of solvated
 ligands, the differences are below 3 kcal/mol.  Most of the exceptions can
 be traced to imperfections in the force fields or to errors in the
 experimentally determined bound structure.
 	Best regards,
 	Per-Ola Norrby
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  *  Per-Ola Norrby, Associate Professor
  *  The Royal Danish School of Pharmacy, Dept. of Med. Chem.
  *  Universitetsparken 2, DK 2100 Copenhagen, Denmark
  *  tel. +45-35376777-506, +45-35370850    fax +45-35372209
  *  Internet: peo %! at !% compchem.dfh.dk, http://compchem.dfh.dk/PeO/