Accurate Prediction of Three-Body Intermolecular Interactions via Electron Deformation Density-Based Machine Learning

Kaycee Low, Michelle L. Coote, Ekaterina I. Izgorodina

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)


This work extends the electron deformation density-based descriptor, originally developed in the electron deformation density-based interaction energy machine learning (EDDIE-ML) algorithm to predict dimer interaction energies, to the prediction of three-body interactions in trimers. Using a sequential learning process to select the training data, the resulting Gaussian process regression (GPR) model predicts the three-body interaction energy within 0.2 kcal mol-1 of the SRS-MP2/cc-pVTZ reference values for the 3B69 and S22-3 trimer data sets. A hybrid kernel function is introduced, which combines contributions from the average and individual atomic environments, allowing the total trimer interaction energy to be predicted in addition to the three-body contribution using the same descriptor. To extend the range and diversity of trimer interaction energies available in the literature, a new data set based on a protein-ligand crystal structure is introduced, consisting of 509 structures of a central ligand with two protein fragments. Benchmark calculations are provided for the new data set, which contains significantly larger molecular interactions than current databases in the literature in addition to charged fragments. Compared to density functional theory (DFT)- and wavefunction-based methods for calculating the three-body interaction energy, our model makes predictions in a significantly shorter time frame by reducing the number of required SCF calculations from 7 to 4 performed at the PBE0 level of theory, showcasing the utility and efficiency of our Δ-ML method particularly when applied to larger systems.

Original languageEnglish
Pages (from-to)1466-1475
Number of pages10
JournalJournal of Chemical Theory and Computation
Issue number5
Early online date14 Feb 2023
Publication statusPublished - 14 Mar 2023


  • Machine learning
  • three-body interactions
  • trimers


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