The fragment molecular orbital (FMO) method enables us to calculate electronic states of large molecules such as proteins. The FMO method has been employed by researchers in the drug discovery and related fields, because inter fragment interaction energy (IFIE), which can be obtained in the FMO calculation, is useful to understand interactions between proteins and their ligands, In the present study, we implemented pair interaction energy decomposition analysis (PIEDA) into the FMO calculation program ABINIT-MP and its GUI program BioStation Viewer. PIEDA is a method which divides the IFIE into four energy components: electrostatic (ES), exchange repulsion (EX), charge-transfer and mixing term (CT+mix), and dispersion (DI) energies. After the implementation, we applied the PIEDA to three protein-ligand systems in order to clarify which energy components play main roles in their binding interactions. The results show that the protein-ligand interactions in complexes of influenza protein neuraminidase-oseltamivir, EGFR tyrosine kinase-erlotinib, and estrogen receptor-ligand consist of clearly different energy components. This indicated that PIEDA is useful to understand details of ligand binding mechanisms.