We present a fully atomistic molecular dynamics simulation of the smectic phase of the ionic liquid crystal (ILC) 1-hexadecyl-3-methylimidazolium nitrate, [C(16)MIm][NO3]. We have characterized the structure of the phase by means of a set of radial distribution functions resolved along the director and in the plane of the smectic layers. The results obtained allow us to discuss the similarities in the microscopic structure of ionic liquids (ILs) and ILCs. In addition to this, we have calculated the orientational order parameters, S, of the methylene groups of the alkyl chain and compared them With the results obtained for phospholipidic membranes from H-2 NMR experiments. We also discuss the orientational order parameters of the imidazolium ring. Finally, we analyze the distribution of voids in the ILC phase. We have found that voids of considerable volume to host a nonpolar gas, e.g. xenon, are localized in the hydrophobic layers and almost absent in the ionic layers.