The basic idea of frozen-density embedding theory (FDET) is the constrained minimization of the Hohenberg–Kohn density functional EHK[ρ] performed using the auxiliary functional [E_{v_{AB}}^{ m FDET}[Psi _A, ho _B]], where ΨA is the embedded NA-electron wavefunction and ρB(r) is 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 [E_{v_{AB}}^{ m FDET}[Psi _A, ho _B]] makes it possible to treat the corresponding two components of the total density using different methods in multi-level simulations. The application of FDET using ρB(r) reconstructed from X-ray diffraction data for a molecular crystal is demonstrated for the first time. For eight hydrogen-bonded clusters involving a chromophore (represented as ΨA) and the glycylglycine molecule [represented as ρB(r)], FDET is used to derive excitation energies. It is shown that experimental densities are suitable for use as ρB(r) in FDET-based simulations.