A method for calculating interaction energy between a target molecule and a drug candidate molecule using a calculator, the method comprising: dividing a trajectory over a total time duration of a molecular dynamic simulation of the target molecule and the drug candidate molecule into groups based on molecular mechanic interaction energy between the target molecule and the drug candidate molecule calculated by molecular mechanics, wherein the dividing comprises: obtaining, using the calculator, an average value (E M) of molecular mechanic interaction energy of each of fragments and the drug candidate molecules per a predetermined unit time within the total time duration, for each of the fragments over the total time duration, where the fragments are obtained by dividing the target molecule into partial structures, and the molecular mechanic interaction energy is calculated over the total time duration of the molecular dynamic simulation of the target molecule and the drug candidate molecule; extracting, using the calculator, the fragments having a large interaction with the drug candidate molecule from all of the fragments using the average values (E M) and a predetermined threshold A, wherein the fragments having the large interaction with the drug candidate molecule are identified as fragments having a representative average value (E RM) representing all of the average values (E M) that is equal to or greater than predetermined threshold A; and dividing, using the calculator, the trajectory over the total time duration of the molecular dynamic simulation of the target molecule and the drug candidate molecule into groups using a fluctuation range of the average value (E M) of each of the fragments extracted during the molecular dynamic simulation, and a predetermined threshold B, wherein a time range in which the fluctuation range of the average value (E M) of the fragments is equal to or less than the predetermined threshold B is grouped as a single group among the groups. obtaining, using the calculator, an average value (E M) of molecular mechanic interaction energy of each of fragments and the drug candidate molecules per a predetermined unit time within the total time duration, for each of the fragments over the total time duration, where the fragments are obtained by dividing the target molecule into partial structures, and the molecular mechanic interaction energy is calculated over the total time duration of the molecular dynamic simulation of the target molecule and the drug candidate molecule; extracting, using the calculator, the fragments having a large interaction with the drug candidate molecule from all of the fragments using the average values (E M) and a predetermined threshold A, wherein the fragments having the large interaction with the drug candidate molecule are identified as fragments having a representative average value (E RM) representing all of the average values (E M) that is equal to or greater than predetermined threshold A; and dividing, using the calculator, the trajectory over the total time duration of the molecular dynamic simulation of the target molecule and the drug candidate molecule into groups using a fluctuation range of the average value (E M) of each of the fragments extracted during the molecular dynamic simulation, and a predetermined threshold B, wherein a time range in which the fluctuation range of the average value (E M) of the fragments is equal to or less than the predetermined threshold B is grouped as a single group among the groups.