Fig. 4: QM/MM Modeling of NeoR.
a Overview of QM/MM excitation energy calculations of eight systems (#1–8) with varying protonation of E136, D140 and E262 as indicated. The total charge of the three carboxylates in each system is given. λMAX refers to the absorption maxima as derived from excited-state energy calculation. b Active site from QM/MM-optimized models, with hydrogen bonds represented as dashed lines. c Water intrusion into NeoR as observed during subsequent 300 ns MD simulations with water densities visualized as red meshes. The retinal and amino acid sidechains are taken from the initial structure of the MD simulations.
