Figure 6.

Probabilities of ligand–protein interactions formed by MSR03 with a neutral quinoline group in the presence of the MIDAS metal ion or a positively charged quinoline group in the absence of the MIDAS metal ion during MD simulations. Interaction types formed by MSR03 with (A, B) neutral quinoline group in the presence of the MIDAS metal ion (induced-fit metadynamics-rescored poses #2 and #5, respectively) or (C) positively charged quinoline group in the absence of the MIDAS metal ion, with protein side chains during simulations and calculated as averages over the four replicas amounting to 1 μs of simulation time are: carbon–carbon atomic interactions (Apolar, pink), aromatic edge-to-face (Aro_E2F, light green) and face-to-face (Aro_F2F, dark green) interactions, electrostatic interactions with the protein negatively charged (Elec_ProN, purple), one-water-mediated and two-water-mediated hydrogen-bond interactions (Hbond_1Wat and Hbond_2Wat, light and dark blue, respectively), and hydrogen bond with the protein as the hydrogen-bond acceptor (Hbond_ProA, light orange). Only interactions with an average probability above 10% are displayed. Error bars refer to the 5th and 95th percentile of the probabilities calculated using a two-state Markov model.