A calculation method of binding free energy, which includes: calculating solvation energy (”G 1 ) between a solvent and a compound; and calculating an energy change (”G 2 ) between a bound state (»=0) where the compound and a protein are bound, and an unbound state (»=1) where the compound and the protein are not bound, wherein the calculating the energy change (”G 2 ) includes: determining a distance (D th ), within which structure sampling is performed; calculating a change in binding energy (”G 21 ) between the compound and the protein within a distance equal to or shorter than the distance (D th ), calculating a change in solvation energy (”G 23 ) between the solvent and the compound with ignoring an influence of the protein, calculating a change in binding energy (”G 22 ) between the compound and the protein with interpolation, and calculating a correction term (”G 24 ) with respect to a standard state.
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