Subtle differences in the molecular structure of mesogens can lead to very different experimental polymorphisms. The smectic C (SmC) phase can actually be exhibited by one isomer and not the other, or the range of temperature can be completely different. Unveiling the deep connection between atomic structure and the very existence of the SmC phase will lead to the design of new performing liquid crystalline materials for ferroelectric or nonlinear optical applications. Our approach is based on running molecular dynamics simulation from an initial SmC arrangement of molecules. When the temperature is increased, the molecules automatically adjust in a more favorable organization. Such modification in the imposed initial self-assembly is governed by values of the nonbonded energies. Thanks to the combined use of simulation and experimental phase diagrams, we have unveiled part of the deep connection between atomic structure and the very existence of the SmC phase. The actual display of the SmC mesophase stems from a subtle balance between short-range interactions, which reveal arrangement of molecules within a smectic layer, and long-range interactions, which disclose organization of layers.