A method for calculating interaction energy between a target molecule and drug candidate molecules, the method comprising: a) extracting one or more calculation-target water molecules, which are water molecules that influence at least interaction energy between the target molecule and some of the drug candidate molecules, but not the interaction energy between the target molecule and all of the drug candidate molecules; wherein step a) includes a first treatment and a second treatment in one interaction-calculation-target space, which is a space, when the interaction energy is calculated, including the target molecule and one drug candidate molecule among the drug candidate molecules, where the first treatment includes extracting one or more interaction water molecules (W1, W2), which are water molecules that interact with both the target molecule and the one drug candidate molecule, and the second treatment includes extracting one or more calculation-candidate water molecules (W1, W2), which are water molecules extracted from the one or more interaction water molecules (W1, W2), based on a fluctuation width of coordinates of each of the one or more interaction water molecules (W1, W2), or occurrence frequency of each of the one or more interaction water molecules (W1, W2), or both, and wherein step a) further includes a treatment including comparing interaction-calculation-target spaces each including the one or more calculation-candidate water molecules (W1, W2) of the interaction-calculation-target spaces each including the target molecule and the drug candidate molecules, to extract the one or more calculation-target water molecules, which do not have identical coordinates in all of the interaction-calculation-target spaces, from the one or more calculation-candidate water molecules (W1, W2), and b) calculating each interaction energy between the target molecule and each of the drug candidate molecules by only explicitly considering as water molecules the one or more calculation-target water molecules in the calculation of each interaction energy, wherein the method is a method for calculating interaction energy between the target molecule and the drug candidate molecules using a calculator. a) extracting one or more calculation-target water molecules, which are water molecules that influence at least interaction energy between the target molecule and some of the drug candidate molecules, but not the interaction energy between the target molecule and all of the drug candidate molecules; wherein step a) includes a first treatment and a second treatment in one interaction-calculation-target space, which is a space, when the interaction energy is calculated, including the target molecule and one drug candidate molecule among the drug candidate molecules, where the first treatment includes extracting one or more interaction water molecules (W1, W2), which are water molecules that interact with both the target molecule and the one drug candidate molecule, and the second treatment includes extracting one or more calculation-candidate water molecules (W1, W2), which are water molecules extracted from the one or more interaction water molecules (W1, W2), based on a fluctuation width of coordinates of each of the one or more interaction water molecules (W1, W2), or occurrence frequency of each of the one or more interaction water molecules (W1, W2), or both, and wherein step a) further includes a treatment including comparing interaction-calculation-target spaces each including the one or more calculation-candidate water molecules (W1, W2) of the interaction-calculation-target spaces each including the target molecule and the drug candidate molecules, to extract the one or more calculation-target water molecules, which do not have identical coordinates in all of the interaction-calculation-target spaces, from the one or more calculation-candidate water molecules (W1, W2), and wherein step a) includes a first treatment and a second treatment in one interaction-calculation-target space, which is a space, when the interaction energy is calculated, including the target molecule and one drug candidate molecule among the drug candidate molecules, where the first treatment includes extracting one or more interaction water molecules (W1, W2), which are water molecules that interact with both the target molecule and the one drug candidate molecule, and the second treatment includes extracting one or more calculation-candidate water molecules (W1, W2), which are water molecules extracted from the one or more interaction water molecules (W1, W2), based on a fluctuation width of coordinates of each of the one or more interaction water molecules (W1, W2), or occurrence frequency of each of the one or more interaction water molecules (W1, W2), or both, and wherein step a) further includes a treatment including comparing interaction-calculation-target spaces each including the one or more calculation-candidate water molecules (W1, W2) of the interaction-calculation-target spaces each including the target molecule and the drug candidate molecules, to extract the one or more calculation-target water molecules, which do not have identical coordinates in all of the interaction-calculation-target spaces, from the one or more calculation-candidate water molecules (W1, W2), b) calculating each interaction energy between the target molecule and each of the drug candidate molecules by only explicitly considering as water molecules the one or more calculation-target water molecules in the calculation of each interaction energy,