1. A free energy difference estimation method performed in a computer to estimate a free energy difference between compounds, the method comprising: calculating, by the computer, a partial free enemy difference between a fully bound state and an other state, the fully bound state being when a target compound is bound to a first candidate compound, the other state being when the first candidate compound in water is extracted into vacuum; specifying, by the computer, a first change region, a second change region, and a third change region in a region of a binding constant being from zero to one by referring to the partial free energy difference for each value of the binding constant indicating a bound state between the target compound and the first candidate compound bindable to the target compound, the partial free energy difference stored in a storage part, wherein the first change region is from where the binding constant is equal to zero to where the partial free energy difference is equal to zero, the second change region is where the partial free energy difference is equal to zero and continues until the partial free energy difference becomes less than a predetermined value after a peak, and the third change region is from where the partial free energy difference becomes less than the predetermined value after the peak to where the binding constant is one; and interpolating, by the computer, the partial free energy difference of a second candidate compound in the second change region, based on the partial free energy difference acquired in each of the first change region and the third change region by using an approximation function.