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Updated: Aug 19, 2025

Quantitative Structure-Activity Relationship, Activity Prediction, and Molecular Dynamics of Non-nucleotide Reverse Transcriptase Inhibitors
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System truncation accelerates binding affinity calculations with the fragment molecular orbital method: A benchmark

Shinya Nakamura1, Tatsuo Akaki1,2, Keiji Nishiwaki1

  • 1Computational Drug Design and Discovery, Department of Pharmaceutical Sciences, Kindai University, Osaka, Japan.

Journal of Computational Chemistry
|November 29, 2022
PubMed
Summary

System truncation in fragment molecular orbital (FMO) calculations significantly speeds up binding affinity computations. Truncating systems to 8 Å for neutral ligands and 12 Å for charged ligands maintains accuracy in FMO/PCM and FMO-MP2 methods.

Keywords:
FMOMP2PCMbinding energy in solutionsystem truncation

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Area of Science:

  • Computational Chemistry
  • Quantum Mechanics
  • Biochemistry

Background:

  • The fragment molecular orbital (FMO) method offers a computationally efficient approach to quantum mechanical calculations.
  • System truncation is a technique used to further enhance the speed of FMO calculations by reducing the number of atoms considered.

Purpose of the Study:

  • To systematically investigate the impact of system truncation on binding affinity calculations using FMO.
  • To evaluate the accuracy of truncated FMO methods (FMO/PCM and FMO-MP2) compared to full system calculations.

Main Methods:

  • Fragment Molecular Orbital (FMO) method combined with polarizable continuum model (PCM) and Møller-Plesset perturbation theory (MP2).
  • Systematic truncation of protein-ligand complexes to varying radii around the ligand.
  • Calculation and comparison of binding energies for truncated versus full systems.

Main Results:

  • Binding energy calculations using FMO/PCM and FMO-MP2 are accurate even with significant system truncation.
  • Neutral ligands can be studied with truncation up to an 8 Å radius with an error of ~0.7 kcal/mol.
  • Charged ligands require a larger truncation radius of 12 Å, with an error of ~1.1 kcal/mol.

Conclusions:

  • System truncation is a viable strategy for accelerating binding affinity calculations in FMO.
  • The optimal truncation radius depends on the charge state of the ligand, balancing computational speed and accuracy.
  • These findings enable more efficient computational screening of drug candidates.