Ab Initio calculations of various configurations of In2Se3 compounds are used to gain insight into the transition from crystalline to amorphous phase. The structures considered are based on wurzite structures with 1/3 of indium sites vacant as observed experimentally. From extensive calculations for possible vacancy configurations in In2Se3 compounds, predictions based on the local coordination of In/Se atoms are made for the energetically favorable vacancy ordering structures. Results indicate that in the most stable In vacancy configurations, Se atoms have coordination of either 2 or 3 (In atoms have coordination of 4). Other coordinations lead to significantly higher formation energies. Results from analyzing the total energy and electronic structure of a range of off-stoichiometry, including vacancies, interstitials and anti-site, configurations, suggest that the energetically most favorable way to form In-rich material is via incorporation of Se vacancies, while Se occupying a vacant site is the most favorable for formation of Se-rich phase. Based on these calculations, predictions are made on how stoichiometry deviations impact structural evolution during phase change.