Table 2.

Structure and energy parameters of natural and designed antibody complexes

PDB entry	Natural antibody						Designed antibody
	Ligand	Kd(nM)b	Predicted binding energy (R.e.u)a	Buried surface area (Å)	Packing score a	Shape complementaritya	Predicted binding energy (R.e.u) a	buried surface area (Å)	Packing score a	Shape complementaritya	buried surface area (Å)	Ligand interface RMSD (Å)	Predicted binding energy rankc
1JPS	Tissue factor	0.1	-25	1950	0.66	0.70	-34.4	2171	0.62	0.59	2171	2.00	17 (5212)
1WEJ	Cytochrome C	15.8	-16	1220	0.70	0.75	-24.5	1535	0.67	0.62	1535	2.00	3 (93)
2CMR	Transmembrane glycoprotein	0.05	-22	2110	0.58	0.72	-26.3	2162	0.57	0.60	2162	1.40	11 (297)
3MXW	Sonic hedgehog protein	0.7	-21	1882	0.70	0.51	-32.2	2011	0.69	0.58	2011	2.72	24 (1274)
1VFB	Lysozyme	3.7	-22	1405	0.67	0.69	-24.3	1493	0.64	0.60	1493	3.20	24 (250)
2JEL	Phosphocarrier protein HPr	3.7	-17	1549	0.66	0.58	-20.4	1353	0.62	0.60	1353	2.70	9 (50)
3K2U	Hepatocyte growth factor activator	0.16	-29.2	1982	0.62	0.68	-26.6	1695	0.58	0.62	1695	3.20	51 (112)
1P2C	Lysozyme	0.098	-17	1467	0.68	0.67	-22.2	1566	0.68	0.60	1566	3.90	138 (659)
1IQD	Coagulation factor VIII	0.014	-32	2134	0.70	0.78	-24.7	1632	0.66	0.67	1632	2.80	762 (2802)

^aSee methods for details.

^bObtained from the “SabDab” database.

^cValues in parentheses signify how many designs with I_RMS<4 Å were computed (Table S6).