Infrared (IR) spectroscopy of biological macromolecules is an undoubtedly valuable tool for analyzing chemical reactions. Currently, there is a lack of theoretical methods able to model successfully and efficiently simulate and interpret the origin of the spectral signatures. Here, we develop a new method for IR vibrational spectroscopy based on analytic second derivatives of electrostatic embedding QM/MM energy, the computation of electric dipole moments with respect to nuclear perturbations and the localization of normal modes. In addition to the spectrum, the method can provide the origin of each peak from clearly identified molecular motions. As proof of concept, we analyze the IR spectra of flavin adenine dinucleotide in water and in arabidopsis thaliana cryptochrome protein for four redox forms, and the difference IR spectrum before and after illumination with blue light. We show that the main peaks in the difference spectrum are due to N−H hydrogen out-of-plane motions and hydrogen bendings.