We report the synthesis, structure determination, and quantum-chemical analysis of a new family of layered nanocrystals (NCs) obtained by a liquid-phase assembly reaction of exfoliated, negatively charged MoS2 sheets with alkyldiammonium ions. A combined PXRD, TEM, FTIR and DFT study allowed us to determine the atomic structure of these turbostratically disordered NCs and to reveal the topology of cation-MoS2 binding interactions. The diamine molecules sandwiched between the sulfur layers of the adjacent 1T-MoS2 sheets were found to interlink these sheets through the hydrogen bonding interaction network. Quantification of these interactions on the basis of the analysis of calculated electron density distribution showed that the strong NH···S bonds contribute 40-80% of the total cation-MoS2 hydrogen bonding interaction energy (33-38 kcal/mol), being accompanied by the contribution of the weaker, but more numerous CH···S bonds. The short-range ordering in the positions of neighboring MoS2 layers was identified and its relationship with organic-inorganic hydrogen bonding was established. DFT based comparison of energetic characteristics for the assembled NCs and their delaminated and deprotonated models was performed in order to evaluate stability of NCs against delamination and deprotonation. The data obtained in this study show the prospect for crystal engineering of hydrogen-bonding-based new MoS2-organic nanomaterials.