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Journal of Computer-Aided Molecular Design, Vol. 10, No. 6. (1 December 1996), pp. 607-622, doi:10.1007/bf00134183 Key: citeulike:11603120
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An extensive crystal survey of the Cambridge Structural Database has been carried out to provide hydrogen-bond data for use in drug-design strategies. Previous crystal surveys have generated 1D frequency distributions of hydrogen-bond distances and angles, which are not sufficient to model the hydrogen bond as a ligand-receptor interaction. For each hydrogen-bonding group of interest to the drug designer, geometric hydrogen-bond criteria have been derived. The 3D distribution of complementary atoms about each hydrogen-bonding group has been ascertained by dividing the space about each group into bins of equal volume and counting the number of observed hydrogen-bonding contacts in each bin. Finally, the propensity of each group to form a hydrogen bond has been calculated. Together, these data can be used to predict the potential site points with which a ligand could interact and there-fore could be used in molecular-similarity studies, pharmacophore query searching of databases, or de novo design algorithms.
1. 3D geometry of hydrogen bonds as found in CSD
a) All conformations forming a plausible hydrogen bond were extracted
b) All the above were filtered: hard cutoff values obtained in statistical tests
2. Donor: O-H or N-H (C-H not considered). Acceptor: lone pair at N, O or S. Coordinates: r, alpha, beta, theta (2 planars, 1 torsion)
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