Determination of molecular topology and atomic hybridization states from heavy atom coordinates

Authors

  • Elaine C. Meng,

    Corresponding author
    1. Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
    • Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
    Search for more papers by this author
  • Richard A. Lewis

    1. Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California 94143-0446
    Current affiliation:
    1. Imperial Cancer Research Fund, Biomolecular Modeling Laboratory, P.O. Box 123, Lincoln's Inn Fields, London WCZA 3PX, England, United Kingdom
    Search for more papers by this author

Abstract

A method is presented for the derivation of hybridization states and connectivity within molecules from the atomic numbers and coordinates of heavy atoms. The algorithm utilizes bond length data from studies of the Cambridge Structural Database (Allen et al., J. Chem. Soc. Perkin Trans. II, S1, (1987)). The program, IDATM, is useful for processing input to hydrogen-adding routines and molecular mechanics programs, as it minimizes the amount of manual preprocessing required. IDATM has been tested on a range of crystallographically determined structures, including poorly determined structures, with a successful assignment of hybridization for over 99% of the atoms in the set.

Ancillary