Negatively charged molybdenum disulfide layers form stable organic-inorganic layered nanocrystals when reacted with organic cations in solution. The reasons why this self-assembly process leads to a single-phase compound with a well-defined interlayer distance in given conditions are, however, poorly understood to date. Here, for the first time, we quantify the interactions determining the cation packing and stability of the MoS2-organic nanocrystals and find that the main contribution arises from Coulomb forces. The study was performed on the series of new layered compounds of MoS2 with naphthalene derivatives, forming several distinct phases depending on reaction conditions. Starting with structural models derived from powder X-ray diffraction data and TEM, we evaluate their cohesion energy by modeling layer separation with periodic PW-DFT-D calculations. The results provide a reliable approach for estimation of the stability of MoS2-based heterolayered compounds.