1. A free energy difference estimation method performed in a computer to estimate a free energy difference between compounds, the method comprising: specifying, by the computer, a change region, in which a partial free energy difference is equal to or greater than a predetermined change value, in a region of a binding constant, by referring to the partial free energy difference for each value of the binding constant indicating a bound state between a target compound and a first candidate compound bindable to the target compound, the partial free energy difference stored in a storage part; and interpolating, by the computer, the partial free energy difference of a second candidate compound in the change region, based on the partial free energy difference acquired in each of a previous region and a following region by using an approximation function.