Directory UMM :wiley:Public:journals:jcc:suppmat:21:
Figure 1
Initial geometries of model compounds
Interaction Parameter Optimization
Partial Atomic Charges
I
VDW Parameters
III
Internal Parameter Optimization
Bonds
Angles
II
Torsions
Impropers, Urey-Bradley
IV
Crystal and solution condensed phase MD simulations
Parameter Optimization Complete
Figure 2A
5'
O
α
P
O
3'
O
O
N
H2 N
γ
N
δ
ζ
NH
N
O
χ
P and τ
ε
O
N
N
O
O
NH2
O
O
P
P
O
3'
P
O
O
β
O
5'
O
O
Figure 2B
B
A
C
O
O
CH3
(-)
P
O
O
O
O
(-)
P
O
O
H
O
CH2
α and ζ
γ
CH3
β
O
P
O
H
O
D
E
O
BI/BII
O
Base
χ
O
P
O
(-)
O
CH3
F
G
H
CH3
O
O
CH2
(-2)
P
O
O
Base
(OH)
O
O
O
P and τ
ε
O
O
H
(OH)
O
(-)
O
Figure 3
A
O
B
H
O
CH2
H
1
CH2 CH
2
O
CH2
CH2
CH2
O
H
O
1
O
H
CH2 CH2
H
H
O
C
H
H
3,4
H
O3
H 3C
1
H
O
H
2
O4
P
O1
H
O
CH3
O2
H
Figure 3, continued
H
H
D
5
O
H
4
O
H61
H
H
2
H2
O
H
O
H
H
6
O
H
H
H
H1
O
O
O6
5
1
7
C6
N1
H
2
H21 N
2
C5
H22
C2
C4
4
3
N7
H
C8 H8
H
N3
N9
H
9
8
H9
O
O
H
H
O
H
H
H
O
H
H
H
E
H
8
H
O
O
7
H9
H
H
H
N9
N3
O
O
6
C8 H8
C4
3
H
N7
C5
C2
H
H62
C6
N1
1
H
N6
O
H
H
O
H
Figure 3, continued
F
H
G
O
H
H
H
H
H5
C4
O
6
H
5
O4
H6
C5
N3
C6
C2
H3
1
H
3
H
H
2
H
C5
N3
C6
H6
H
1
O
H
N1
O2
H1
H
O
O
O
H
5
H42
H41
N4
H
H
O
7
H5
8 H
6
H
N3
C6
C2
H
H
H
C5
1
H
O
C4
O
H
O
6
4
N1
O2
H1
H
O
O
H
3
2
H
H
H
3
H
H
H
4
2
H
H
H3
H
C2
O
O
O
C4
CH3
O2
H1
H
O4
H
7
N1
O
H
O
O
H
H
H
H
5
6
O
4
O
H
H
O
H
Figure 4
14
12
10
8
6G
4
2 FH
0
0
0.5
G G
A
G
G
G G
G
H
H
G
H G
G
H G G
H F F F F
F
H
F
H H H
F
G G
F F H
H
G
G
G H H
G F
F H
H
H F F
F
H G
F H
G
H F
H
G
G F
H
F F
F H
F
G F
H
F F
H
G
60
120
180
B
0.4
240
300
360
G
0.3
G
0.2
F
H
0.1
0
F
H
G
0
F
H
G
F
H
G
F
H
G
30
F
H
F
H
G
H
F
G
60
Gamma (degrees)
H
F
G
F
H
G
90
F
G
H
F
H
G
120
Figure 5
14
12
10
8
6
4
2
0
14
12
10
8
6
4
2
0
0.1
A
B
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
240
Gamma (degrees)
300
360
Figure 6
4
A
3
1
2
1
1
1
1
1
11 1
0
0.08
1
1
11
B
0.06
0.04
0.02
0
0.08
C
0.06
0.04
0.02
0
0
60
120
180
240
Alpha (degrees)
300
360
Figure 7
4
A
3
1
2
1
1
1
1
1
11 1
0
0.1
1
1
11
B
0.08
0.06
0.04
0.02
0
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
240
Zeta (degrees)
300
360
Figure 8
8
A
6
4
2
0
8
B
6
4
2
0
0.08
C
0.06
0.04
0.02
0
0.08
D
0.06
0.04
0.02
0
0
60
120
180
240
Beta (degrees)
300
360
Figure 9
8
6
4
2
A
0
8
6
4
2
B
0
0.08
0.06
0.04
0.02
C
0
0.08
0.06
0.04
0.02
D
0
0
60
120
180
240
Epsilon (degrees)
300
360
Figure 10
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0.1
0.08
0.06
0.04
C
0.02
0
0.1
0.08
0.06
0.04
D
0.02
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 11
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 12
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 13
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 14
6
A
J
J
4
J
J JJ
JJ
J
J
J
J
J
2
J
J
1J
J
JJ
J
J
JJ
J
J
0
6
J
J
J
JJ
JJ J JJJ J
1
J
JJ
JJ
J
JJJ
JJ
J
JJ
JJ 1J
JJJ
JJJ
J J
J
J
4
J
J
JJ J
J J
JJ
J
J
2
J
J
J
0
0.1
J
J
J
J
J
J
J
JJ
JJJ
J J J
JJ
JJJ
J
JJJ J J J
JJJJJ
J
J
B
J
J
J
J
JJ
JJ
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
240
300
Pseudorotation angle (degrees)
360
Figure 15
0.12
A
0.08
0.04
0
0.12
B
0.08
0.04
0
0
60
120
180
240
Delta (degrees)
300
360
Figure 16
16
J
J
J
12
J
J
8
J
J
J
J
J
J
J
J
J
J
J
4
J
J
J
J
J
0
0
60
J
JJ J
120
180
240
300
H-O2'-C2'-C3' dihedral (degrees)
360
Figure 17
10
J
JJ
JJ J
JJ
8
6
4
2
0
10
J JJJJJ
JJ J
JJ
JJ
JJ
JJ
JJ
J J JJ JJ JJJ J JJJJJ J
J J
A
J
JJ
J
JJ
JJ J
J
J
J
B
8
J
6
J
J
J
4
J
J
2 J J J J J JJ JJ JJ JJ JJJ J J J JJ J
J J J JJJ
J
J JJJ
0 JJJJJ
JJ
JJ
JJ
JJ
JJJ
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
240
300
Pseudorotation angle (degrees)
360
Figure 18
0.08
A
0.04
0
0.08
B
0.04
0
0.08
C
0.04
0
0.16
D
0.08
0
0.04
E
0.02
0
0.08
F
0.04
0
0.08
G
0.04
0
0
60
120
180
240
300
Dihedral Angle (degrees)
360
Figure 19
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0.04
H
0.02
0
0
60
120
180
240
300
Dihedral Angle (degrees)
360
Initial geometries of model compounds
Interaction Parameter Optimization
Partial Atomic Charges
I
VDW Parameters
III
Internal Parameter Optimization
Bonds
Angles
II
Torsions
Impropers, Urey-Bradley
IV
Crystal and solution condensed phase MD simulations
Parameter Optimization Complete
Figure 2A
5'
O
α
P
O
3'
O
O
N
H2 N
γ
N
δ
ζ
NH
N
O
χ
P and τ
ε
O
N
N
O
O
NH2
O
O
P
P
O
3'
P
O
O
β
O
5'
O
O
Figure 2B
B
A
C
O
O
CH3
(-)
P
O
O
O
O
(-)
P
O
O
H
O
CH2
α and ζ
γ
CH3
β
O
P
O
H
O
D
E
O
BI/BII
O
Base
χ
O
P
O
(-)
O
CH3
F
G
H
CH3
O
O
CH2
(-2)
P
O
O
Base
(OH)
O
O
O
P and τ
ε
O
O
H
(OH)
O
(-)
O
Figure 3
A
O
B
H
O
CH2
H
1
CH2 CH
2
O
CH2
CH2
CH2
O
H
O
1
O
H
CH2 CH2
H
H
O
C
H
H
3,4
H
O3
H 3C
1
H
O
H
2
O4
P
O1
H
O
CH3
O2
H
Figure 3, continued
H
H
D
5
O
H
4
O
H61
H
H
2
H2
O
H
O
H
H
6
O
H
H
H
H1
O
O
O6
5
1
7
C6
N1
H
2
H21 N
2
C5
H22
C2
C4
4
3
N7
H
C8 H8
H
N3
N9
H
9
8
H9
O
O
H
H
O
H
H
H
O
H
H
H
E
H
8
H
O
O
7
H9
H
H
H
N9
N3
O
O
6
C8 H8
C4
3
H
N7
C5
C2
H
H62
C6
N1
1
H
N6
O
H
H
O
H
Figure 3, continued
F
H
G
O
H
H
H
H
H5
C4
O
6
H
5
O4
H6
C5
N3
C6
C2
H3
1
H
3
H
H
2
H
C5
N3
C6
H6
H
1
O
H
N1
O2
H1
H
O
O
O
H
5
H42
H41
N4
H
H
O
7
H5
8 H
6
H
N3
C6
C2
H
H
H
C5
1
H
O
C4
O
H
O
6
4
N1
O2
H1
H
O
O
H
3
2
H
H
H
3
H
H
H
4
2
H
H
H3
H
C2
O
O
O
C4
CH3
O2
H1
H
O4
H
7
N1
O
H
O
O
H
H
H
H
5
6
O
4
O
H
H
O
H
Figure 4
14
12
10
8
6G
4
2 FH
0
0
0.5
G G
A
G
G
G G
G
H
H
G
H G
G
H G G
H F F F F
F
H
F
H H H
F
G G
F F H
H
G
G
G H H
G F
F H
H
H F F
F
H G
F H
G
H F
H
G
G F
H
F F
F H
F
G F
H
F F
H
G
60
120
180
B
0.4
240
300
360
G
0.3
G
0.2
F
H
0.1
0
F
H
G
0
F
H
G
F
H
G
F
H
G
30
F
H
F
H
G
H
F
G
60
Gamma (degrees)
H
F
G
F
H
G
90
F
G
H
F
H
G
120
Figure 5
14
12
10
8
6
4
2
0
14
12
10
8
6
4
2
0
0.1
A
B
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
240
Gamma (degrees)
300
360
Figure 6
4
A
3
1
2
1
1
1
1
1
11 1
0
0.08
1
1
11
B
0.06
0.04
0.02
0
0.08
C
0.06
0.04
0.02
0
0
60
120
180
240
Alpha (degrees)
300
360
Figure 7
4
A
3
1
2
1
1
1
1
1
11 1
0
0.1
1
1
11
B
0.08
0.06
0.04
0.02
0
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
240
Zeta (degrees)
300
360
Figure 8
8
A
6
4
2
0
8
B
6
4
2
0
0.08
C
0.06
0.04
0.02
0
0.08
D
0.06
0.04
0.02
0
0
60
120
180
240
Beta (degrees)
300
360
Figure 9
8
6
4
2
A
0
8
6
4
2
B
0
0.08
0.06
0.04
0.02
C
0
0.08
0.06
0.04
0.02
D
0
0
60
120
180
240
Epsilon (degrees)
300
360
Figure 10
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0.1
0.08
0.06
0.04
C
0.02
0
0.1
0.08
0.06
0.04
D
0.02
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 11
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 12
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 13
10
8
6
4
2
A
0
10
8
6
4
2
B
0
0
60
120
180
240
Chi (degrees)
300
360
Figure 14
6
A
J
J
4
J
J JJ
JJ
J
J
J
J
J
2
J
J
1J
J
JJ
J
J
JJ
J
J
0
6
J
J
J
JJ
JJ J JJJ J
1
J
JJ
JJ
J
JJJ
JJ
J
JJ
JJ 1J
JJJ
JJJ
J J
J
J
4
J
J
JJ J
J J
JJ
J
J
2
J
J
J
0
0.1
J
J
J
J
J
J
J
JJ
JJJ
J J J
JJ
JJJ
J
JJJ J J J
JJJJJ
J
J
B
J
J
J
J
JJ
JJ
C
0.08
0.06
0.04
0.02
0
0.1
D
0.08
0.06
0.04
0.02
0
0
60
120
180
240
300
Pseudorotation angle (degrees)
360
Figure 15
0.12
A
0.08
0.04
0
0.12
B
0.08
0.04
0
0
60
120
180
240
Delta (degrees)
300
360
Figure 16
16
J
J
J
12
J
J
8
J
J
J
J
J
J
J
J
J
J
J
4
J
J
J
J
J
0
0
60
J
JJ J
120
180
240
300
H-O2'-C2'-C3' dihedral (degrees)
360
Figure 17
10
J
JJ
JJ J
JJ
8
6
4
2
0
10
J JJJJJ
JJ J
JJ
JJ
JJ
JJ
JJ
J J JJ JJ JJJ J JJJJJ J
J J
A
J
JJ
J
JJ
JJ J
J
J
J
B
8
J
6
J
J
J
4
J
J
2 J J J J J JJ JJ JJ JJ JJJ J J J JJ J
J J J JJJ
J
J JJJ
0 JJJJJ
JJ
JJ
JJ
JJ
JJJ
0.1
C
0.08
0.06
0.04
0.02
0
0
60
120
180
240
300
Pseudorotation angle (degrees)
360
Figure 18
0.08
A
0.04
0
0.08
B
0.04
0
0.08
C
0.04
0
0.16
D
0.08
0
0.04
E
0.02
0
0.08
F
0.04
0
0.08
G
0.04
0
0
60
120
180
240
300
Dihedral Angle (degrees)
360
Figure 19
0.04
A
0.02
0
0.04
B
0.02
0
0.04
C
0.02
0
0.04
D
0.02
0
0.04
E
0.02
0
0.04
F
0.02
0
0.04
G
0.02
0
0.04
H
0.02
0
0
60
120
180
240
300
Dihedral Angle (degrees)
360