The first-principles method is challenged by accurate prediction of van der Waals interactions, which are ubiquitous in nature and crucial for determining the structure of molecules and condensed matter. We have contributed to this by constructing a set of pseudopotentials and pseudoatomic orbital basis specialized for molecular systems consisting of C/H/N/O elements. The reliability of the present method is verified from the interaction energies of 45 kinds of complexes (comparing with CCSD(T)) and the crystalline structures of 23 kinds of typical explosive solids (comparing with experiments). Using this method, we have studied the phase transition of octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) under static compression up to 50 GPa. Kinetically, intramolecular deformation has priority in the competition with intermolecular packing deformation by similar to 87%. A possible gamma -> beta phase transition is found at around 2.10 GPa, and the migration of H2O has an effect of kinetically pushing this process. We make it clear that no beta -> delta/epsilon -> delta phase transition occurs at 27 GPa, which has long been a hot debate in experiments. In addition, the P-V relation, bulk modulus, and acoustic velocity are also predicted for alpha-, delta-, and gamma-HMX, which are experimentally unavailable.