Journal of Computer-Aided Molecular Design

, Volume 10, Issue 6, pp 607–622

Three-dimensional hydrogen-bond geometry and probability information from a crystal survey

  • J. E. J. Mills
  • P. M. Dean
Research Papers

DOI: 10.1007/BF00134183

Cite this article as:
Mills, J.E.J. & Dean, P.M. J Computer-Aided Mol Des (1996) 10: 607. doi:10.1007/BF00134183


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.


Ligand-receptor interactionGeometry of intermolecular interactionsCambridge Structural DatabaseDrug design

Copyright information

© ESCOM Science Publishers B.V 1996

Authors and Affiliations

  • J. E. J. Mills
    • 1
  • P. M. Dean
    • 1
  1. 1.Drug Design Group, Department of PharmacologyUniversity of CambridgeCambridgeU.K.