Periodic, nanostructured porous polymer membranes made from the cross-linked inverted hexagonal phase of self-assembled lyotropic liquid crystals (LLCs) are a promising class of materials for selective separations. In this work, we investigate an experimentally characterized LLC polymer mem-brane using atomistic molecular modeling. In particular, we compare simulated X-ray diffraction (XRD) patterns with experimental XRD data to quantify and understand the differences between simulation and experiment. We find that the nanopores are likely composed of five columns of stacked LLC monomers which surround each hydrophilic core. Evidence suggests that these columns likely move independently of each other over longer time scales than accessible via atomistic simulation. We also find that wide-angle X-ray scattering structural features previously attributed to monomer tail tilt are likely instead due to ordered tail packing. Although this system has been reported as dry, we show that small amounts of water are necessary to reproduce all features from the experimental XRD pattern because of asymmetries introduced by hydrogen bonds between the monomer head groups and water molecules. Finally, we explore the composition and structure of the nanopores and reveal that there exists a composition gradient rather than an abrupt partition between the hydrophilic and hydrophobic regions. A caveat is that the time scales of the dynamics are extremely long for this system, resulting in simulated structures that appear too ordered, thus requiring careful examination of the metastable states observed in order to draw any conclusions. The clear picture of the nanoscopic structure of these membranes provided in this study will enable a better understanding of the mechanisms of small- molecule transport within these nanopores.