With tremendous progress in computer technologies and applications during the last decade, atomistic-level simulation is rapidly becoming an essential tool in materials science for the study of the physical and chemical properties of various materials. Moreover, in parallel with the experimental efforts, computer-aided materials design is also an important factor in the fabrication of novel materials, to be applied in driving engineering innovations and urgent technological needs for achieving a sustainable society. Here, an original approach has been demonstrated that allows us to construct a p - T phase diagrams of various hydrates with complex gas compositions. In order to evaluate the parameters of weak interactions, a time-dependent density-functional formalism and local density (TDLDA) technique entirely in real space have been implemented for the calculations of frequency-dependent polarizabilities and van der Waals dispersion coefficients for atoms within the all-electron mixed-basis approach (TOMBO code) developed at the Institute for Materials Research, Tohoku University. The combination of both methods enables one to calculate thermodynamic properties of clathrate hydrates without resorting to any empirical parameter fittings. Using the proposed method, it is possible to not only confirm the existing experimental data but also predict the unknown region of thermodynamic stability of clathrate hydrates, and also propose the gas storage ability as well as the gas composition for which high-stability region of clathrate hydrates can be achieved. The proposed method is quite general and can be applied to the various nonstoichiometric inclusion compounds with weak guest-host interactions. From this point of view, the present methodology can support experimental explorations of the novel storage materials.