A hierarchical molecular modeling approach presented predicts adsorption thermodynamics of single components and binary mixtures in zeolites. Atomistic simulations that capture details at the molecular level are performed to calculate the free energies of molecules at discrete adsorption sites. Then a more coarse-grained lattice model is used to calculate the equilibrium loading of adsorbates based on these free energies, and thermodynamic properties can be predicted. Sorbate-sorbate free energies beyond nearest-neighbor interactions are introduced and their impact on the lattice model is investigated. By adding these free energies, the model is better able to accurately describe single-component and binary adsorption of sulfur hexafluoride and neopentane in silicalite. The results from the lattice model agree well with full atomistic grand canonical Monte Carlo simulations performed for the same systems, but the hierarchical approach saves an order of magnitude of computational effort.