An apparatus for predicting an acid dissociation constant of a molecule, the apparatus comprising: a molecular structure design unit configured to design the molecule; an acid dissociation constant prediction unit configured to: calculate molecular orbital of the designed molecule to obtain electron density of the designed molecule, calculate index value-containing data including index values indicating a bond strength of respective atom pairs of respective interatomic bonds of the designed molecule based on the electron density, determine a hydrogen having the largest electric charge in the designed molecule as a target proton based on the electron density, set a coefficient value (C) included in element pair-containing data to each of the atom pairs according to a pair type of each of the atom pairs, wherein the pair type of the atom pairs includes a first type of an atom pair between the target proton and a first atom directly bonded to the target proton, a second type of an atom pair between the target proton and a second atom not directly bonded to the target proton and a third type of an atom pair between the first atom and the second atom, classify the atom pairs into corresponding pair types, and predict an acid dissociation constant (pKa) of the designed molecule by calculating a sum of products of the index values of the atom pairs and the coefficient values (C) of the element pairs for each of the pair types; a memory configured to store molecular structure data defining the designed molecule, electron density data defining the electron density, the index value-containing data, the element pair-containing data, index value group-containing data including data defining the corresponding pair types, and the predicted acid dissociation constant (pKa); and a prediction result display unit configured to display the predicted acid dissociation constant (pKa) using a display device. a molecular structure design unit configured to design the molecule; an acid dissociation constant prediction unit configured to: calculate molecular orbital of the designed molecule to obtain electron density of the designed molecule, calculate index value-containing data including index values indicating a bond strength of respective atom pairs of respective interatomic bonds of the designed molecule based on the electron density, determine a hydrogen having the largest electric charge in the designed molecule as a target proton based on the electron density, set a coefficient value (C) included in element pair-containing data to each of the atom pairs according to a pair type of each of the atom pairs, wherein the pair type of the atom pairs includes a first type of an atom pair between the target proton and a first atom directly bonded to the target proton, a second type of an atom pair between the target proton and a second atom not directly bonded to the target proton and a third type of an atom pair between the first atom and the second atom, classify the atom pairs into corresponding pair types, and predict an acid dissociation constant (pKa) of the designed molecule by calculating a sum of products of the index values of the atom pairs and the coefficient values (C) of the element pairs for each of the pair types; calculate molecular orbital of the designed molecule to obtain electron density of the designed molecule, calculate index value-containing data including index values indicating a bond strength of respective atom pairs of respective interatomic bonds of the designed molecule based on the electron density, determine a hydrogen having the largest electric charge in the designed molecule as a target proton based on the electron density, set a coefficient value (C) included in element pair-containing data to each of the atom pairs according to a pair type of each of the atom pairs, wherein the pair type of the atom pairs includes a first type of an atom pair between the target proton and a first atom directly bonded to the target proton, a second type of an atom pair between the target proton and a second atom not directly bonded to the target proton and a third type of an atom pair between the first atom and the second atom, classify the atom pairs into corresponding pair types, and predict an acid dissociation constant (pKa) of the designed molecule by calculating a sum of products of the index values of the atom pairs and the coefficient values (C) of the element pairs for each of the pair types; a memory configured to store molecular structure data defining the designed molecule, electron density data defining the electron density, the index value-containing data, the element pair-containing data, index value group-containing data including data defining the corresponding pair types, and the predicted acid dissociation constant (pKa); and a prediction result display unit configured to display the predicted acid dissociation constant (pKa) using a display device.