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. Author manuscript; available in PMC: 2014 Jul 30.
Published in final edited form as: Biochemistry. 2013 Jul 17;52(30):5145–5154. doi: 10.1021/bi400629r

Scheme 3.

Scheme 3

Fundamental reaction pathway in the deacylation stage. Atoms colored in blue are treated by the QM method in the pseudobond first-principles QM/MM calculations. Three boundary carbon atoms (colored in red) are treated with the improved pseudobond parameters. All other atoms belong to the MM subsystem.