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. Author manuscript; available in PMC: 2021 Nov 10.
Published in final edited form as: J Chem Theory Comput. 2020 Oct 13;16(11):7184–7194. doi: 10.1021/acs.jctc.0c00847

Table 4.

Results of Energy Minimizations and FEP Calculations for the Protein-Ligand Complexesa

Complex: 1 with 1/r4 1 with α=0 2 with 1/r4 2 with α=0 3 with 1/r4 3 with α=0
EP-L −112.2 −109.0 −78.6 −73.4 −57.5 −56.5
EP-L 1/r4 −4.2 −1.1 −5.6 −0.8 −1.3 −0.2
ELys-L −33.7 −30.5 −12.5 −7.3 −12.9 −11.9
ELys-L 1/r4 −3.1 −0.3 −4.5 −0.2 −1.2 −0.2
ΔGbinding −2.80±0.01 0 −4.38±0.03 0 −1.47±0.02 0
a

EP-L is the total protein-ligand interaction energy (kcal/mol) with the 1/r4 component on the next row; ELys-L is the interaction energy between the key Lys and the ligand; ΔGbinding is the change in free-energy of binding for turning on the 1/r4 interaction with the phenyl or indolyl ring atoms.