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Caption : figure s1.: root mean square deviation of the non-hydrogen atoms of papain from their starting positions during simulations (a) and the radius of gyration calculated for the papain from the simulation trajectory (b). both the neutral and ion pair (zwitterionic) form of the catalytic dyad were considered and they marked by black and red, respectively.

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Caption : figure s2.: oniom potential energy surfaces (pess) calculated along the (nme)n-c(ace) and the (cys25)sγ…c(amid carbonyl) (a,b), as well as along the (nme)n-c(ace) and the (amid)n…hδ(his159) (c,d) internal distance pairs. the pess were calculated using both b3lyp/6-31g(d,p):amber (a,c) and the m06-2x/6-31g(d,p):amber (b,d) methods.