Abstract: A system computes the interaction energy between a plurality of fragments in a calculation object substance according to the fragment molecular orbital method. The energy of each fragment, the two-body interaction energy of each dimer including two fragments, and the three-body interaction energy of each trimer including three fragments are calculated. The two-body interaction energy of each dimer is corrected by adding, to the two-body interaction energy of the dimer, the contribution of the dimer in the three-body interaction energy of the trimer that includes the dimer.