Table 5. Computed free energies of binding and average nucleophilic sulphur-Scissile carbon distances^a.

Ligand:	AAALR*NAA	BAAPR*NAA	CAGPR*NAA	DPAGP*AGP	EPLGP*AGP	FPPGP*PGP
FhCL1 ΔGΔd	−10.83 (1.18)3.96 (0.24)	−9.10 (1.30)4.00 (0.25)		−8.30 (0.96)4.41 (0.30)
FhCL2 ΔGΔd	−11.77 (0.75)3.97 (0.24)	−6.30 (1.19)3.95 (0.24)	−10.88 (0.96)3.94 (0.23)	−10.83 (1.30)4.27 (0.34)	−4.11 (1.02)4.82 (0.51)	−b> 10
FhCL3 ΔGΔd	−10.40 (0.84)3.99 (0.26)	−8.28 (0.82)4.06 (0.25)	−12.71 (0.95)4.05 (0.25)	−> 10	−9.56 (1.20)4.40 (0.28)	−b4.08 (0.5)

^aAmino acid sequences of peptide ligands A–F are shown in single letter code with P2 in red and the position of the scissile bond shown by an asterisk; Hyp is indicated by P in ligand F. FhCL1 variants are shown in the leftmost column and are denoted as in Table 4. Mean energies (ΔG) are in kcal/mol, with corresponding standard error of the mean in parentheses. The average distances between the sulphur atom of the catalytic Cys and the backbone carbonyl carbon of scissile ligand residue 4 (Δd) are in Ångstrom, with corresponding standard deviations in parentheses. All measures calculated over the final 4.005 ns of the simulation. Standard errors of the mean for all Δd measures are <0.01 Å;

^bNot calculated, see Methods.