Spectral calculations of FAD in cryptochrome with quantum-mechanical environment

Source code and data for the publication:Wieners, L., & Garcia, M. (2026). The Quantum Environment in Cryptochrome Enhances Light Absorption of FAD. bioRxiv.doi: https://doi.org/10.64898/2026.04.24.720615Abstract (preprint version):The light absorption of the protein cryptochrome and its chromophore FAD is important for the regulation of circadian rhythms and in some species for sensing magnetic fields. To compute the absorption spectrum of chromophore, typically only a small region is treated quantum-mechanically due the high computational cost of spectroscopic calculations. We present a formalism that allows a quantum-mechanical treatment of not only the chromophore but also the neighbouring amino acids which differ from species to species. This is achieved by using the real-time time-dependent Hartree-Fock method. This method allows extending the quantum domain from typically only a few dozen atoms up to around 1,200 atoms for the largest calculations. The presented framework allows the treatment of neighbouring tryptophan residues or the cofactor molecule MTHF in the same calculation and allows to extract information of which regions absorb light depending on wavelength. The presented results also show that the environment around the chromophore FAD amplifies the light absorption in cryptochrome. The dataset contains four source code files and two data files containing coordinate input files and result files from spectral calculations, respectively. These can be used to replicate the results of the publication above. In the file Read_me.txt, a description of the files is provided. Further instructions are given in the publication andthe source code files.