In nanometer clusters (NCs), each atom counts. It is the specific arrangement of these atoms that determines the unique size-dependent functionalities of the NCs and hence their applications. Here, we employ a self-consistent, combined theoretical and experimental approach to determine atom-by-atom the structures of supported Pt NCs on MoS2. The atomic structures are predicted using a genetic algorithm utilizing atomistic force fields and density functional theory, which are then validated using aberration-corrected scanning transmission electron microscopy. We find that relatively small clusters grow with (111) orientation such that Pt[11̅0] is parallel to MoS2[100], which is different from predictions based on lattice-match for thin-film epitaxy. Other 4d and 5d transition metals show similar behavior. The underpinning of this growth mode is the tendency of the NCs to maximize the metal-sulfur interactions rather than to minimize lattice strain.