We establish the formula representing cubic nanocrystals (NCs) as hard cubes taking into account the role of the ligands and describe how these results generalize to any other NC shapes. We derive the conditions under which the hard cube representation breaks down and provide explicit expressions for the effective size. We verify the results from the detailed potential of mean force calculations for two nanocubes in different orientations as well as with spherical nanocrystals. Our results explicitly demonstrate the relevance of certain ligand conformations, i.e., “vortices”, and show that edges and corners provide natural sites for their emergence. We also provide both simulations and experimental results with single component cubic perovskite nanocrystals assembled into simple cubic superlattices, which further corroborate theoretical predictions. In this way, we extend the Orbifold Topological Model (OTM) accounting for the role of ligands beyond spherical nanocrystals and discuss its extension to arbitrary nanocrystal shapes. Our results provide detailed predictions for recent superlattices of perovskite nanocubes and spherical nanocrystals. Problems with existing united atom force fields are discussed.