In order to understand the interaction between ethylene-induced esterase(EIE, EC 3.1.1.) from Citrus sinensis and α-naphthyl acetate, a 3D model of EIE was generated based on the crystal structure of the tobacco salicylic acid binding protein 2(SABP2). With the aid of the molecular mechanics and molecular dynamics methods, the final refined model was obtained and its reliability was further assessed. In this study, the docking results show that the main-chain amide of residue His85 and residue Val18 can form hydrogen bonds to the carbonyl oxygen group of α-naphthyl acetate. MM-PBSA method was applied to calculating the binding free energy between EIE mutants and α-naphthyl acetate. Our calculated binding free energy of each of the two mutant complexes is increased compared with that of the one of the wild type, which is unfavorable to the reaction. It is well consistent with the experimental data. The above results clearly indicate that His85 and Val18 in EIE function as the oxyanion role and take part in the catalytic reaction. The new structural insights obtained from this computational study are expected to stimulate further biochemical studies on the structures and mechanisms of EIE and other members of the plant α/β hydrolases. In order to understand the interaction between ethylene-induced esterase (EIE, EC 3.1.1.) From Citrus sinensis and α-naphthyl acetate, a 3D model of EIE was generated based on the crystal structure of the tobacco salicylic acid binding protein 2 ( SABP2). With the aid of the molecular mechanics and molecular dynamics methods, the final refined model was obtained and its reliability was further assessed. In this study, the docking results show that the main-chain amide of residue His85 and residue Val18 can form hydrogen bonds to the carbonyl oxygen group of α-naphthyl acetate. MM-PBSA method was applied to calculating the binding free energy between EIE mutants and α-naphthyl acetate. Our calculated binding free energy of each of the two mutant complexes is increased compared with that of the one of the wild type, which is unfavorable to the reaction. It is well consistent with the experimental data. The above results clearly that that His85 and Val18 in EIE function as the oxyanio The new structural insights obtained from this computational study are expected to stimulate further biochemical studies on the structures and mechanisms of EIE and other members of the plant α / β hydrolases.