The role of amino acid is important to Jasmonate induce plant defense process. Jasmonic acid and amino acid Isoleucine conjugate (JA-Ile) has been found to be necessary to achieve such process effectively. We have examined the origin of such process computationally and showed that Isoleucine is more active compared to other Jasmonic acid conjugates. The epimerization process revealed that Isoleucine conjugated Jasmonic acid is energetically a favoured process compared to JA-Leu and JA-Val. Water has functioned as a catalyst in the whole epimerization process. This study would unravel the importance of Isoleucine in the Jasmonic acid induced plant defense process.