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. Author manuscript; available in PMC: 2017 Apr 4.
Published in final edited form as: J Phys Chem B. 2016 Feb 29;120(9):2155–2164. doi: 10.1021/acs.jpcb.5b11966

Figure 3.

Figure 3

PD cycles obtained with a PM6/MM as target potential and an inverted EVB reference potential for the SN2 step in the reaction catalyzed by DhlA. (a) Reaction in water and (b) reaction in the protein. (c) Activation free energy computed from PMF PM6/MM and activation free energy obtained from the thermodynamic cycle in the protein.