Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7 -- Data Supplement - -- Proceedings of the National Academy of Sciences

Supplementary material for Chong et al. (1999) Proc. Natl. Acad. Sci. USA 96 (25), 14330-14335.

Table 6. Bond, angle, and dihedral parameters of the hapten

Bond	K_r	R _eq
O2-N*	750.0	1.210
CA-OS	656.0	1.250
P-CT	227.0	1.810

Angle	K_q	q_eq
CA-CA-O2	70.0	120.0
CA-CB-N*	70.0	120.0
CA-CB-CA	70.0	120.0
CB-N*-O2	70.0	120.0
O2-N*-O2	70.0	120.0
HA-CA-HA	35.0	120.0
CA-OS-P	90.0	120.0
OS-P-CT	90.0	120.0
P-CT-CT	40.0	109.50
P-CT-HC	30.0	109.50

Dihedral	Redundancy	V_n /2	g	n
CA-CA-OS-P	1	1.20	0.0	2
X-P-CT-X	9	1.40	0.0	3

Listed are parameters for the hapten that are not included in the Cornell et al. force field [Cornell, W. D., Cieplak, P., Bayly, C. I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W. & Kollman, P. A. (1995) J. Am. Chem. Soc. 117, 5179-5197]. Definitions of the parameters are as follows: K_r, force constant for bond stretching in kcal/(mol·Å²); R_eq, equilibrium bond length in Å; K_q, force constant for angle bending in kcal/(mol·radians²); q_eq, equilibrium bond angle; V_n/2, barrier height in kcal/mol; g, phase offset in degrees; and n, periodicity of the Fourier transform. The "redundancy" is determined for X-A-B-X as the product of the number of X-A bonds with the number of B-X bonds.