In this work, we use molecular simulations to determine the structural and physical properties of the organic matter present in type II shales in the middle of the oil generation window. The construction of molecular models of organic matter constrained by experimental data is discussed. Using a realistic molecular model of organic matter, we generate, by molecular dynamics simulations, structures that mimic bulk organic matter under typical reservoir conditions. Consistent results on density, diffusion, and specific adsorption are found between simulated and experimental data. These structures enable us to provide information on the fluid distribution within the organic matter, the pore size distributions, the isothermal compressibility, and the dynamic of the fluids within the kerogen matrix. This study shows that a consistent description at the molecular level combined with molecular simulations can be useful, in complement of experiments, to investigate the organic matter present in shales.