MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures.
A method has been developed which automatically generates SMARTS patterns for four-atomic torsional fragments, searches experimental structures in the Cambridge Crystallographic Database, and obtains rules for preferred torsion angles in drug-size molecules. These rules can be used for exhaustive conformational analysis using the popular conformer generator OMEGA. This approach results in an overall improvement of quality and coverage of conformational space when comparing conformer ensembles generated by this method with results obtained by using the default OMEGA setup. In particular, the percentage of structures with at least one conformation closer than 0.5 A to the X-ray structure improves from 84% to 92% in a test set of 11 027 experimental structures from the CSD. Moreover, the average RMS distance of the closest conformation to the X-ray structure improves from 0.30 to 0.22 A.
Sadowski
Jens
J
Lead Generation Department, AstraZeneca R&D, S-43183 Mölndal, Sweden. jens.sadowski@astrazeneca.com
Boström
Jonas
J
D002621:Chemistry / Q000295:instrumentation / Q000379:methods*; D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray / Q000379:methods*; D016208:Databases, Factual; D048088:Informatics / Q000379:methods; D008956:Models, Chemical; D008968:Molecular Conformation; D012984:Software