Table 2.

Free Energy Calculations for Native and Designer Complexes^a

receptor	ligand	PDB	type	stability	〈ΔGELE〉	〈ΔGPB〉	〈ΔGPBELE〉	〈ΔGSA〉	〈ΔGvdW〉	〈ΔGNP〉	〈TΔSNM〉	〈ΔGcalc〉	〈ΔGexp〉
barnase	barstar	1BRS	native	stable	−527.0 ± 2.5	588.6 ± 2.3	61.6 ± 0.9	−12.2 ± 0.03	−93.5 ± 0.3	−105.7 ± 0.3	−47.0 ± 1.2	2.9 ± 1.4	−17.3
barnase	barstar NMR	1BTA	grafted	stable	−429.1 ± 2.0	474.2 ± 1.7	45.1 ± 1.1	−12.0 ± 0.05	−87.2 ± 0.5	−99.2 ± 0.5	−45.6 ± 1.2	−8.4 ± 1.6
barnase	NS1 RNA binding domain	1AIL	grafted	unstable	−139.6 ± 4.9	185.4 ± 5.4	51.8 ± 0.8	−11.5 ± 0.06	−71.8 ± 0.5	−83.3 ± 0.5	−49.4 ± 1.0	17.9 ± 1.3
barnase	IF-3 C-terminal domain	1TIG	grafted	unstable	−327.9 ± 1.9	384.7 ± 2.1	55.9 ± 1.1	−10.5 ± 0.04	−69.3 ± 0.4	−79.8 ± 0.4	−43.0 ± 1.1	19.0 ± 1.5
barnase	allergen PHL P2	1WHO	grafted	unstable	−441.1 ± 5.5	487.2 ± 6.5	55.7 ± 0.8	−9.3 ± 0.04	−52.8 ± 0.3	−62.1 ± 0.3	−40.6 ± 1.4	34.2 ± 1.6
lysozyme	antibody D1.3	1VFB	native	stable	121.1 ± 1.1	−68.6 ± 1.0	52.5 ± 0.5	−10.8 ± 0.04	−73.7 ± 0.3	−84.5 ± 0.3	−43.5 ± 1.3	11.5 ± 1.4	−11.5
lysozyme	scorpion toxin BJXTR-IT	1BCG	grafted	stable	−203.7 ± 1.7	245.97 ± 1.7	42.3 ± 0.2	−10.2 ± 0.01	−73.3 ± 0.2	−83.5 ± 0.2	−42.8 ± 1.2	1.6 ± 1.2
lysozyme	MPB1	1BM8	grafted	stable	180.6 ± 1.5	126.8 ± 1.3	53.7 ± 0.5	−10.6 ± 0.03	−70.0 ± 0.3	−80.6 ± 0.3	−41.9 ± 1.9	15.1 ± 2.0
lysozyme	α-amylase inhibitor	1HOE	grafted	unstable	−499.6 ± 2.3	530.4 ± 2.1	30.5 ± 0.6	−8.2 ± 0.03	−48.3 ± 0.3	−56.5 ± 0.3	−38.5 ± 1.2	12.5 ± 1.4
trypsin	BPTI	2PTC	native	stable	234.3 ± 1.5	224.0 ± 1.3	10.3 ± 0.6	−11.1 ± 0.03	−90.4 ± 0.3	−101.5 ± 0.3	−47.5 ± 1.3	−43.7 ± 1.4	−18
trypsin	CheY	1TMY	grafted	stable	−28.8 ± 1.6	70.8 ± 1.4	42.1 ± 0.8	−16.4 ± 0.04	−120.7 ± 0.4	−137.1 ± 0.4	−53.2 ± 1.5	−41.8 ± 1.8
trypsin	tenascin	1TEN	grafted	stable	−405.5 ± 1.1	454.7 ± 1.1	49.1 ± 0.6	−17.6 ± 0.03	−122.5 ± 0.4	−140.1 ± 0.4	−57.3 ± 1.2	−33.6 ± 1.2
trypsin	allergen PHL P2	1WHO	grafted	unstable	−330.3 ± 1.1	358.0 ± 1.0	27.8 ± 0.6	−12.7 ± 0.04	−83.0 ± 0.3	−95.7 ± 0.3	−52.4 ± 1.3	−15.6 ± 1.4

^aUnits in kcal/mol; ΔG_ELE, nonsolvent electrostatic potential energy; ΔG_PB, electrostatic contributions to the solvation free energy calculated with Poisson–Boltzmann equation; ΔG_PBELE, electrostatic potential energy; ΔG_SA, nonpolar contributions to solvation free energy; ΔG_vdW, van der Waals potential energy; ΔG_NP, nonpolar potential energy; TΔS_NM, the entropic contribution calculated with normal−mode analysis to the free energy of binding; ΔG_calc, calculated binding free energy; G_exp, experimental binding free energy.