A semiempirical approach to ligand-binding affinities: Dependence on the Hamiltonian and corrections.

Research output: Contribution to journalArticle


We present a combination of semiempirical quantum-mechanical (SQM) calculations in the conductor-like screening model with the MM/GBSA (molecular-mechanics with generalized Born and surface-area solvation) method for ligand-binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen-bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol-derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen-bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3-1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.


  • Paulius Mikulskis
  • Samuel Genheden
  • Karin Wichmann
  • Ulf Ryde
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Theoretical Chemistry
Original languageEnglish
Pages (from-to)1179-1189
JournalJournal of Computational Chemistry
Issue number12
Publication statusPublished - 2012
Publication categoryResearch

Bibliographic note

The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Theoretical Chemistry (S) (011001039)

Total downloads

No data available

Related research output

Samuel Genheden, 2012, Department of Chemistry, Lund University. 330 p.

Research output: ThesisDoctoral Thesis (compilation)

View all (1)