The application of cluster model calculations to understand the interaction of water molecules with the VPI-5 lattice is presented. The energetically favorable location of water molecules and their influence in altering the local symmetry of the VPI-5 framework are reported. The results indicate the presence of a water molecule in the vicinity of Al1 and P2 sites which are correlating with MAS NMR and X-ray powder diffraction studies. We also carried out thermal analysis and quantified seven different types of water molecules in the hydrated VPI-5. The dehydration to different extents will lead to rupture of the water chain leaving more void space inside VPI-5, and this has been demonstrated by xenon adsorption studies.