. Author manuscript; available in PMC: 2016 May 30.

Published in final edited form as: J Comput Chem. 2015 Mar 31;36(14):1083–1101. doi: 10.1002/jcc.23897

Table 1.

Parameters for fitted N-ethylsulfamate (NESM; compound 9 in figure 1) compared to the initial guess (see section 4.2.1). RMSE values were calculated as in reference ¹² but without weighting.

Parameter definition		“Blind”^a fit; RMSE = 0.36 kcal/mol		“Targeted”^a fit; RMSE = 0.27 kcal/mol		“Adapted”^a fit; RMSE = 0.27 kcal/mol		Initial guess; RMSE = 0.99 kcal/mol

BOND

Atom types		Force constant^b	Reference length^b	Force constant^b	Reference length^b	Force constant^b	Reference length^b	Force constant^b	Reference length^b

CG321 NG2S3		318.7	1.443	322.4	1.443	329.2	1.444	266.0	1.460

ANGLES

Atom types		Force constant^b	Reference angle^b	Force constant^b	Reference angle^b	Force constant^b	Reference angle^b	Force constant^b	Reference angle^b

CG331 CG321 NG2S3		23.0	108.4	27.3	109.7	37.7	111.6	70.0	109.5
NG2S3 CG321 HGA2		38.0	105.2	38.3	105.2	38.7	105.2	51.5	107.5
CG321 NG2S3 SG3O1		76.5	107.9	58.7	104.9	54.2	104.0	39.5	103.1
CG321 NG2S3 HGP1		51.5	109.5	51.8	109.5	52.2	109.5	35.0	109.0

DIHEDRALS

Atom types	Multiplicity	Amplitude^b	Phase^b	Amplitude^b	Phase^b	Amplitude^b	Phase^b	Amplitude^b	Phase^b

CG331 CG321 NG2S3 SG3O1	1	0.453	180	0.755	180	0.653	180	1.500	180
CG331 CG321 NG2S3 SG3O1	2	1.137	0	0.866	0	0.885	0	0.650	180
CG331 CG321 NG2S3 SG3O1	3	0.391	0	0.628	0	0.667	0	1.000	0
CG331 CG321 NG2S3 SG3O1	4	0.190	180	0.151	180	0.142	180	N/A	N/A
CG331 CG321 NG2S3 SG3O1	6	0.107	0	0.113	0	0.111	0	N/A	N/A

CG331 CG321 NG2S3 HGP1	1	1.110	0	0.741	0	0.790	0	0.000	0
CG331 CG321 NG2S3 HGP1	2	0.477	0	0.321	0	0.325	0	N/A	N/A
CG331 CG321 NG2S3 HGP1	3	0.052	180	0.235	180	0.266	180	N/A	N/A

CG321 NG2S3 SG3O1 OG2P1	3	0.545	0	0.552	0	0.556	0	0.537	0

In the blind fit, bonds and angles are unrestrained, while in the targeted fit, they are restrained towards their initial guess values, as discussed in section 2.10. Dihedrals are restrained towards 0 in all cases. Both the blind and targeted fit were obtained using the uniform bias; conversely, the adapted fit is the same as the targeted fit but using the target-adapted bias.

Conform CHARMM conventions, bond force constants are in kcal mol⁻¹ Å⁻², bond reference lengths in Å, angle force constants in kcal mol⁻¹ radian⁻², reference angles and dihedral phases in degrees, and dihedral amplitudes in kcal mol⁻¹.