Tris(o-phenylenedioxy)cyclotriphosphazene (TPP) became the compound of choice to investigate the structural features of organic zeolites and their potential applications as soft materials. A van der Waals crystal of the TPP analogue (host) with the thiophene side fragment tris(3,4-thiophenedioxy)cyclotriphosphazene (TTP) was designed to investigate the selective adsorption among some common gases (guest): methane (CH4), carbon dioxide (CO2 nitrogen (N-2), or hydrogen (H-2). The crystal structure of TTP was modeled by applying minimization methods using the COMPASS (condensed-phase optimized molecular potentials for atomic simulation studies) force field. Interaction energies and structural properties of van der Waals complexes of the crystal of TTP and gas molecules were studied using the dispersion corrected density functional theory (DFT-D). The proper functional and basis set were selected after comparing with benchmark data of the coupled-cluster calculations with singles, doubles, and perturbative triple excitations [CCSD(T)] estimated at the complete basis set (CBS) limit. On the basis of our results, the interaction energy between the host and the guest molecules was predicted in the increasing order of host-H-2 << host-N-2 < host-CH4 < host-CO2, suggesting the designed TTP is a good candidate as an organic zeolite for potential fuel storage, hydrogen purification, carbon dioxide removal from the air, as well as safety care in a coal mine.