2023 Volume 23 Pages 14-25
The fragment molecular orbital (FMO) method enables quantum mechanical calculations for macromolecules by dividing the target into fragments. However, most calculations, even for metalloproteins, have been performed by removing metal ions from the structures registered in the Protein Data Bank (PDB). For more realistic and useful calculations, FMO calculations must be performed without removing the metal ions. In this study, we discuss the results obtained from FMO calculations performed using 6-31G* and model core potentials (MCPs) for metal proteins containing Zn and Mg ions. Subsequently, we analyze the differences in atomic charges and interactions.