We have computed free energy for one-electron reduction of the active site of the coenzyme (flavin adenine dinucleotide (FAD)) in aqueous solution by means of the QM/MM method combined with the theory of energy representation (QM/MM-ER). In the present work, we have proposed a novel approach that the excess electron to be attached on the FAD has been regarded as a solute, while the remaining molecules including the active site of FAD have been considered as solvent in the implementation of the method of energy representation. The efficiency and the accuracy of the method have been examined by performing the conventional simulations where the oxidized and the reduced active sites of FAD are regarded as solutes and the surrounding water molecules are treated as solvent. The present approach is computationally more advantageous and is amenable to the extension to the reaction in the protein systems as compared with the conventional one. It has been found that the reduction free energy obtained by the present method is in excellent agreement with that computed by the conventional approach, which guarantees the robustness of the method.