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Fragment molecular orbital (FMO) method enables ab initio quantum-chemical calculations for biomolecular systems with high accuracy and moderate computational cost. Through this analysis we can evaluate the inter-fragment interaction energies (IFIEs) that provide useful measures for effective interactions between the fragments representing amino-acid residues and ligand molecules. Here I describe how to prepare the input structures and perform the FMO calculations for protein-protein complex system. In addition to the pre-processing, so
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