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Three‐Dimensional Chemical Structure Search Using the Conformational Code for Organic Molecules (CCOM) Program
Author(s) -
Izumi Hiroshi,
Nafie Laurence A.,
Dukor Rina K.
Publication year - 2016
Publication title -
chirality
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.43
H-Index - 77
eISSN - 1520-636X
pISSN - 0899-0042
DOI - 10.1002/chir.22596
Subject(s) - dihedral angle , chemistry , molecule , atom (system on chip) , chirality (physics) , computational chemistry , crystallography , stereochemistry , organic chemistry , computer science , hydrogen bond , physics , chiral symmetry breaking , quantum mechanics , nambu–jona lasinio model , embedded system , quark
Searching the 3D structural fragments of organic molecules is challenging because of structural differences between X‐ray and theoretically calculated geometries and the conformational flexibility of substituents. The codification program called Conformational Code for Organic Molecules (CCOM) can be used to unambiguously convert 3D conformational data for various molecules to 1D data. Two deviations from Rule E‐5.6 of the International Union of Pure and Applied Chemistry (IUPAC) Rules for Nomenclature of Organic Chemistry were introduced to the CCOM program for 3D fragment searching. First, the search for the highest priority atom was limited to a distance of two bonds from the center bond for dihedral angle determination. Second, for indistinguishable atoms in experimentally observed solution structures, the smallest number of atom index in the molecular model was chosen as the priority atom for dihedral angle determination. A search of the 3D conformational fragment mb _3a6c4c of mevastatin ( 1 ) in combination with the SMiles ARbitrary Target Specification (SMARTS) description suggested that a change in the conformation of this fragment may be the driving force for dissociation of mevastatin from its target protein. Chirality 28:370–375, 2016 . © 2016 Wiley Periodicals, Inc.