Table 2.

Per-residue free energies of ligand-dimeric SARS-CoV2 M^pro complexes (values kcal/mol)

Residue	Lig1sub2	Lig1Sub2	Lig2Sub1	Lig2Sub2	Lig3Sub1	Lig3Sub2	Lig4Sub1	Lig4Sub2	Lig5Sub1	Lig5Sub2
T24										− 0.809
T25	− 0.604			− 0.740			− 0.567		− 2.816	− 2.750
T26									− 3.063
L27	− 0.550	− 0.569	− 0.669						− 1.807	− 0.874
H41	− 1.806	− 0.925	− 1.217	− 1.955	− 0.595	− 0.785	− 0.865	− 1.337	− 2.202
V42								− 0.549	− 1.561
C44	− 1.030			− 0.646					− 0.756	− 0.558
T45	− 0.818									− 1.562
S46	− 0.603			− 0.658			− 0.659			− 1.445
M49	− 2.051	− 2.381	− 1.779	− 2.172	− 0.888	− 0.589	− 2.127	− 1.954	− 0.630	− 1.429
F140			− 1.353				− 0.577	− 0.671
L141							− 0.578	− 0.525
N142		− 1.571	− 2.836	− 0.786			− 1.080	− 1.421	− 3.386	− 1.418
G143		− 0.986	− 2.027						− 3.138	− 0.713
S144		− 0.651	− 0.624				− 0.794	− 0.767	− 0.684
C145		− 1.297	− 0.717	− 0.506		− 0.633	− 0.601	− 0.731	− 1.229
H163			− 0.686
M165		− 1.214	− 1.549	− 2.264	− 3.263	− 4.215	− 3.455	− 3.395	− 1.935
D166					− 0.683	− 2.464	− 0.810	− 0.955
L167						− 0.545
P168		− 0.719			− 0.547	− 0.652	− 1.085	− 1.072
D187		− 0.650	− 0.556	− 1.468			− 0.971	− 0.803
R188				− 1.194	− 0.513
Q189	− 1.214	− 1.930	− 2.431	− 1.037	− 3.544		− 3.109	− 3.197
A191					− 0.586	− 1.057
Q192					− 0.523	− 1.074

Inhibitor N3, lig1; darunavir, lig2; indinavir, lig3; saquinavir, lig4; tipranavir, 5