In structural biology, molecular simulations have played an important role in elucidating functions of the biological system. The understanding of biological phenomena at the molecular level is expected to lead the modeling of disease, drug discovery, and various applications. A variety of life phenomena occur through the combination of site-specific molecular recognition of biomacromolecules. Computer simulations thus provide a promising approach to elucidate these molecular interactions in detail. However, most calculations carried out to date have employed classical mechanical methods based on empirical force fields. Such methods remain limited for performing an accurate analysis of intermolecular interactions such as charge redistribution and charge-transfer (CT) interactions. In contrast to the limitations of classical approaches to molecular simulation, quantum mechanical simulations have been used to successfully characterize weak intermolecular interactions and CT processes. Because several different types of interactions are involved in the interactions of biomolecules, quantum mechanical treatment is necessary to obtain an accurate and systematic understanding of these interactions. The fragment molecular orbital (FMO) method1-4 is one of the most reasonable tools with which to analyze the electronic structure of biomacromolecules.