An infrared free-electron laser can decompose aggregated proteins (including metal complexes) via the excitation of their vibrational bands. In this study, using the results of previous studies on human serum albumin, we prepared hybrid materials of chicken egg white lysozyme protein with the same Schiff-base Zn(II) complexes by incorporating glycylglycine dipeptide derivative moieties. The analysis of secondary structures after irradiation indicated that the inclusion of the Zn(II) complexes into lysozyme induced structural changes in lysozyme, resulting in a more fragile structure than that of the original lysozyme; this is the second reported example of the enhancing effect of a metal complex on protein molecules damaged by IR-FEL irradiation. Their docking features via weak intermolecular interactions were also investigated using fluorescence spectra (quenching, temperature dependence, and decay lifetime) with the aid of computational simulation of docking.