While in previous work the error of the MFCC scheme was reduced by increasing the size of the considered fragments, we explicitly set out to develop a fragmentation scheme that operates in terms of single amino acid fragments. This, in turn, necessitates the inclusion of three-body contributions in order to obtain accurate protein-ligand interaction energies. Here, we considered a test set of eight protein-ligand complexes featuring different types of ligands (ranging form multiply charged ions to zwitterionic molecules). We found that while errors in the protein-ligand interaction energies can amount to several hundreds of kJ/mol for conventional MFCC scheme, with the upgraded MFCC-MBE(2) scheme these errors are generally reduced to below 20-30 kJ/mol.