Retrieval of Crystallographically-Derived Molecular Geometry Information

Abstract

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has many uses. However, accessing it by means of conventional substructure searching requires nontrivial user intervention. In consequence, these valuable data have been underutilized and have not been directly accessible to client applications. The situation has been remedied by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Use of a search tree indexed on key values, together with a novel similarity calculation, then enables the distribution matching any given query fragment (or the distributions most closely matching, if an adequate exact match is unavailable) to be found easily and with no user intervention. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.

Structure and Vasorelaxant Activity of Floranol, a Flavonoid Isolated from the Roots ofDioclea grandiflora

“…The C(7)¼O(2) bond length is 1.250(5) . The observed geometry of the ring C agrees well with similar pyranoid geometries checked with the MOGUL [17], an information base of molecular geometry derived from CSD [15], which provides rapid access to information on the preferred values of bond lengths, valence angles, and acyclic torsion angles. The CÀOH bond lengths are very similar (mean value 1.354(7) ), except for C(8)ÀO (6), with a bond lengths of 1.400(5) .…”

Structural basis for the inhibition of the eukaryotic ribosome

“…Crystallographic statistics are reported in Supplementary Information Table 1. Ligands geometry was validated with the software Mogul from the CCDC package 49 . Drawing of chemical structures was performed with MarvinSketch suite (ChemAxon, http://www.chemaxon.com/) and figures of structures were prepared using PyMOL 1.5 (Schrödinger, http://pymol.org/).…”

Fiftieth Anniversary of the Cambridge Structural Database and Thirty Years of Its Use in Croatia

“…By improving this technology, it will be possible to use it quantitatively to assess 'hot spots' of interactions to recognise pharmacophores or chemophores. The CSD System also developed the two extensive knowledge bases Mogul 17,18 and IsoStar. 16 Mogul comprises more than 20 million bond lengths, valence and torsion angles organised into more than 11.5 million chemically searchable distributions, each relating to a specific chemical environment, revealing also data for chemical rings.…”