In this current work the conformational properties of the L-Alanyl-L-Glutamine dipeptide which was biological active dipeptide has been investigated by theoretical conformational analysis method using program which is based on Molecular Mechanic calculations in order to determine the structure function relation. The calculations on zwitterionic and neutral form of Ala-Gln which is formed side and main chain torsion angles let us to define their preferable energetically conformers. The side and main chain status of the stable conformations of Ala-Gln were acquired based on the results of the conformational analysis. By using Ramachandran maps, the global conformation, which has the lowest energy of the dipeptide, has been determined. The goal of this work was to explain structure-activity relationship by investigating the bioactive conformation of biological active peptide.