The basic idea of Frozen-Density Embedding Theory (FDET) is the constrained minimisation of the Hohenberg-Kohn density functional EHK[ρ] performed using the auxiliary functional EFDETvAB[ΨA,ρB], where ΨA is the embedded NA-electron wave-function and ρB(r⃗ ) a non-negative function in real space integrating to a given number of electrons NB. This choice of independent variables in the total energy functional EFDETvAB[ΨA,ρB] makes it possible to treat the corresponding two components of the total density using different methods in multi-level simulations. We demonstrate, for the first time, the applications of FDET using ρB(r⃗ ) reconstructed from X-ray diffraction data on a molecular crystal. For eight hydrogen-bonded clusters involving a chromophore (represented with ΨA) and the glycylglycine molecule (represented as ρB(r⃗ )), FDET is used to derive excitation energies. It is shown that experimental densities are suitable to be used as ρB(r⃗ ) in FDET based simulations