Directory UMM :wiley:Public:journals:jcc:suppmat:24:
Table 1. Additional force field parameters used for ligands
N*
O2
O2
HA
O2
HA
CA
CA
O2
OS
CA
HA
HA
H
CA
N
CA
CA
CT
HC
HC
C
CA
O
CT
HC
HC
CX
OS
R
HA
HA
O2
O2
CT
HC
HO
OH
43C9 ester tetrahedral intermediate
C
CT
OX
CA
CA
HA
O2
HC
CA
CA
H
HC
CT
CA
CA
HC
HC
HA
CA
CA
R
N
43C9 amide substrate
HA
HA
N*
C
CA
CA
HA
O2
O2
CA
HA
R
43C9 ester substrate
R=
HA
CA
C
CA
CA
O2
CA
O2
CA
CA
HA
HA
N*
N*
HA
CA
CA
CA
O2
CA
HC
HA
OX
CA
CA
HO
OH
CX
R
N
HA
HA
HA
H
43C9 amide tetrahedral intermediate
CA
HA
R'
HA
HA
CA
R'
N
H
HC
HA
OX
HO
HO
CX
CA
OS
CA
R'
HA
H
17E8 amide substrate
17E8 ester substrate
CA
CA
C
CA
CA
HA
CA
O2
CA
CA
C
OS
CA
HA
HA
CA
CA
O2
CA
CA
HA
HA
HA
CA
CA
HA
HA
HA
HA
17E8 ester tetrahedral intermediate
O2
HC
H1
CT
N
R' =
CT
C
C
CT
HA
O2
HC
CT
HC
CT
HC
HC
O2
HC
CA
HA
HC
HC
CT
HA
HA
CA
CA
CA
CA
CA
OX
HO
HO
CX
N
R'
HC
HC
CT
HA
HC
MASS
H
17E8 amide tetradedral intermediate
HC
m (amu)
CX
12.01
OX
16.00
BOND
K r (kcal mol-1 Å-2)
r eq (Å)
CA-OS
300.0
1.400
*
CA-N
490.0
1.335
=C-N
N*-O2
750.0
1.210
**
N-CX
337.0
1.530
=HF/6-31+G* geometry, K r for N*-CT
CX-OX
320.0
1.260
=HF/6-31+G* geometry, K r for CT-OS
CX-OH
320.0
1.420
=HF/6-31+G* geometry, K r for CT-OS
CX-OS
320.0
1.530
=HF/6-31+G* geometry, K r for CT-OS
CX-CT
310.0
1.526
=CT-CT
1
ANGLE
K θ (kcal mol-1 rad-2)
CA-CA-OS
70.0
CA-N-C
50.0
CA-CA-N
70.0
CA-CB-N*
70.0
CA-CB-CA
70.0
CB-N*-O2
70.0
O2-N*-O2
140.0
CA-N-H
35.0
CA-OS-C
60.0
C-CT-CA
63.0
N-CX-OH
100.0
N-CX-OX
100.0
N-CX-CT
80.0
OH-CX-OX
140.0
CA-N-CX
50.0
CX-N-H
50.0
CX-OH-HO
55.0
CX-CT-HC
50.0
CX-CT-CA
63.0
OH-CX-CT
50.0
OX-CX-CT
50.0
θeq (deg)
120.00
123.20
120.00
120.00
=CT-C-O2
120.00
119.90
=CT-C-O2
120.00
117.00
=CA-N2-H
=CT-C-O2
=O2-P-O2
110.10
=C-OS-CT
108.23
108.23
=O2-P-OS
109.70
119.90
=N-CT-CT
123.20
118.04
=CA-N2-CT
108.50
109.50
=CT-OH-HO
114.00
109.50
=CT-CT-CA
109.50
=OH-CT-CT
117.00
60.0
OS-CX-OH
100.0
OS-CX-OX
100.0
OS-CX-CT
50.0
CT-CT-CX
40.0
N-CT-CX
80.0
CX-CT-H1
50.0
idvf†
V n /2 (kcal/mol-1)
2
2.60
X-CA-OS-X
2
0.325
X-CA-N-X
4
3.45
X-N-CX-X
6
0.00
X-CX-OH-X
3
0.50
X-CA-OS-X
=CA-CA-OS
120.00
CA-OS-CX
DIHEDRAL
*
=CA-N2-CT
108.23
=C-CT-N
=O2-P-OS
=O2-P-O2
=CT-N-H
=CT-CT-HC
=OH-CT-CT
=CM-OS-CT
108.23
=OS-P-OS
109.50
=OS-CT-CT
109.50
109.50
109.50
=OS-P-OS
=CT-CT-CT
=N-CT-CT
=CT-CT-H1
γ (deg)
180.0
-2.
180.0
0.0
2.
0.0
0.0
X-CX-CT-X
9
1.40
X-OS-CX-X
3
σ (Å)
1.15
ε (kcal/mol)
0.0
1.9080
1.7210
0.1094
=CT
0.2104
=OH
NONBONDED
CX
OX
n
180.0
4.
*
*
2.
=X-N-CT-X
3.
=X-CT-OH-X
3.
=X-CT-CT-X
3.
=X-OS-CT-X
* Spellmeyer, D.C.; Grootenhuis, P.D.J.; Miller, M.D.; Kuyper, L.F.; and Kollman, P.A. J. Phys. Chem. 1990, 94 , 4483-4491
** Chong, L.T.; Duan, Y.; Wang, L.; Massova, I.; Kollman P.A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 ,14330-14335
†
Factor by which torsional barrier is divided.
2
N*
O2
O2
HA
O2
HA
CA
CA
O2
OS
CA
HA
HA
H
CA
N
CA
CA
CT
HC
HC
C
CA
O
CT
HC
HC
CX
OS
R
HA
HA
O2
O2
CT
HC
HO
OH
43C9 ester tetrahedral intermediate
C
CT
OX
CA
CA
HA
O2
HC
CA
CA
H
HC
CT
CA
CA
HC
HC
HA
CA
CA
R
N
43C9 amide substrate
HA
HA
N*
C
CA
CA
HA
O2
O2
CA
HA
R
43C9 ester substrate
R=
HA
CA
C
CA
CA
O2
CA
O2
CA
CA
HA
HA
N*
N*
HA
CA
CA
CA
O2
CA
HC
HA
OX
CA
CA
HO
OH
CX
R
N
HA
HA
HA
H
43C9 amide tetrahedral intermediate
CA
HA
R'
HA
HA
CA
R'
N
H
HC
HA
OX
HO
HO
CX
CA
OS
CA
R'
HA
H
17E8 amide substrate
17E8 ester substrate
CA
CA
C
CA
CA
HA
CA
O2
CA
CA
C
OS
CA
HA
HA
CA
CA
O2
CA
CA
HA
HA
HA
CA
CA
HA
HA
HA
HA
17E8 ester tetrahedral intermediate
O2
HC
H1
CT
N
R' =
CT
C
C
CT
HA
O2
HC
CT
HC
CT
HC
HC
O2
HC
CA
HA
HC
HC
CT
HA
HA
CA
CA
CA
CA
CA
OX
HO
HO
CX
N
R'
HC
HC
CT
HA
HC
MASS
H
17E8 amide tetradedral intermediate
HC
m (amu)
CX
12.01
OX
16.00
BOND
K r (kcal mol-1 Å-2)
r eq (Å)
CA-OS
300.0
1.400
*
CA-N
490.0
1.335
=C-N
N*-O2
750.0
1.210
**
N-CX
337.0
1.530
=HF/6-31+G* geometry, K r for N*-CT
CX-OX
320.0
1.260
=HF/6-31+G* geometry, K r for CT-OS
CX-OH
320.0
1.420
=HF/6-31+G* geometry, K r for CT-OS
CX-OS
320.0
1.530
=HF/6-31+G* geometry, K r for CT-OS
CX-CT
310.0
1.526
=CT-CT
1
ANGLE
K θ (kcal mol-1 rad-2)
CA-CA-OS
70.0
CA-N-C
50.0
CA-CA-N
70.0
CA-CB-N*
70.0
CA-CB-CA
70.0
CB-N*-O2
70.0
O2-N*-O2
140.0
CA-N-H
35.0
CA-OS-C
60.0
C-CT-CA
63.0
N-CX-OH
100.0
N-CX-OX
100.0
N-CX-CT
80.0
OH-CX-OX
140.0
CA-N-CX
50.0
CX-N-H
50.0
CX-OH-HO
55.0
CX-CT-HC
50.0
CX-CT-CA
63.0
OH-CX-CT
50.0
OX-CX-CT
50.0
θeq (deg)
120.00
123.20
120.00
120.00
=CT-C-O2
120.00
119.90
=CT-C-O2
120.00
117.00
=CA-N2-H
=CT-C-O2
=O2-P-O2
110.10
=C-OS-CT
108.23
108.23
=O2-P-OS
109.70
119.90
=N-CT-CT
123.20
118.04
=CA-N2-CT
108.50
109.50
=CT-OH-HO
114.00
109.50
=CT-CT-CA
109.50
=OH-CT-CT
117.00
60.0
OS-CX-OH
100.0
OS-CX-OX
100.0
OS-CX-CT
50.0
CT-CT-CX
40.0
N-CT-CX
80.0
CX-CT-H1
50.0
idvf†
V n /2 (kcal/mol-1)
2
2.60
X-CA-OS-X
2
0.325
X-CA-N-X
4
3.45
X-N-CX-X
6
0.00
X-CX-OH-X
3
0.50
X-CA-OS-X
=CA-CA-OS
120.00
CA-OS-CX
DIHEDRAL
*
=CA-N2-CT
108.23
=C-CT-N
=O2-P-OS
=O2-P-O2
=CT-N-H
=CT-CT-HC
=OH-CT-CT
=CM-OS-CT
108.23
=OS-P-OS
109.50
=OS-CT-CT
109.50
109.50
109.50
=OS-P-OS
=CT-CT-CT
=N-CT-CT
=CT-CT-H1
γ (deg)
180.0
-2.
180.0
0.0
2.
0.0
0.0
X-CX-CT-X
9
1.40
X-OS-CX-X
3
σ (Å)
1.15
ε (kcal/mol)
0.0
1.9080
1.7210
0.1094
=CT
0.2104
=OH
NONBONDED
CX
OX
n
180.0
4.
*
*
2.
=X-N-CT-X
3.
=X-CT-OH-X
3.
=X-CT-CT-X
3.
=X-OS-CT-X
* Spellmeyer, D.C.; Grootenhuis, P.D.J.; Miller, M.D.; Kuyper, L.F.; and Kollman, P.A. J. Phys. Chem. 1990, 94 , 4483-4491
** Chong, L.T.; Duan, Y.; Wang, L.; Massova, I.; Kollman P.A. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 ,14330-14335
†
Factor by which torsional barrier is divided.
2