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. 2020 Sep 15;153(11):115101. doi: 10.1063/5.0020458

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© 2020 Author(s).

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FIG. 8. — Conventional MD of SARS-CoV-2 PLpro with Cys270 fixed in the protonated or deprotonated state. (a) Occupancies of the His272⋯Asp286, His272⋯Cys111, and Cys111⋯Trp106 hydrogen bonds from the simulations with Cys270 fixed in the protonated (orange) or deprotonated (red) states. The calculations combined the data from two independent 1-µs trajectories. The first 300 ns data were discarded. (b) Probability distribution of the Cα distance between Tyr268 and Asp164 from the simulations with Cys270 fixed in the protonated (orange) or deprotonated (red) state.