Quantum-chemical fragmentation methods offer an attractive approach for the accurate calculation of protein--ligand interaction energies. While the Molecular Fractionation with Conjugate Caps (MFCC) scheme offers a rather straightforward approach for this purpose, its accuracy is often not sufficient. Here, we upgrade the MFCC scheme for the calculation of protein--ligand interactions by including many-body contributions. The resulting fragmentation scheme is an extension of our previously developed MFCC-MBE(2) scheme [J. Comput. Chem. 2023, 44, 1634–1644]. For a diverse test set of protein--ligand complexes, we demonstrate that by upgrading the MFCC scheme with many-body contributions, the error in protein--ligand interaction energies can be reduced significantly, and generally yields errors below 20 kJ/mol. Our scheme allows for systematically reducing these errors by including higher-order many-body contributions. As it combines the use of single amino acid fragments with high accuracy, our scheme provides an ideal starting point for the parametrization of accurate machine learning potentials for proteins and protein--ligand interactions.

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