Figure 1
Interaction Parameter Optimization
Partial Atomic Charges
VDW Parameters
Internal Parameter Optimization
Bonds
Angles
Torsions
Impropers, Urey-Bradley
Parameter Optimization Complete
Crystal and solution condensed phase MD simulations
I
II
III
IV
Figure 2A
O
O
O
P
P
O
O
O
O
O
O
O
P
P
O
O
O
O
N
N
N
N
NH
O
NH
2
N
H
2
N
O
P and
τ
5'
3'
3'
Figure 2B
O
CH
2
O
P
O
O
O
H
O
O
O
P
O
H
O
Base
O
O
O
P
O
CH
3
O
O
O
P
O
CH
3
O
Base
CH
2
O
H
(-)
(-2)
O
H
Figure 3
O
CH
2
CH
2
CH
2
CH
2
H
O H
CH
O
2
CH
2
CH
CH
2
O
H
H
O H
H
O H
1
1
2
A
B
H
3
C
O1
P
O2
CH
3
O4
O3
H
O
H
H
O
H
H
O
H
1
2
3,4
Figure 3, continued
H
O
H
C
6
N
1
C
2
N
3
C
5
C
4
N
9
C
8
N
7
H
8
H
9
N
6
H
62
H
61
H
2
H O
H
H
O
H
H
O H
H
O
H
H
O H
H
O
H
H
O
H
H
O
H
C
6
N
1
C
2
N
3
C
5
C
4
N
9
C
8
N
7
H
8
H
9
O
6
N
2
H
O
H
H
O
H
H
O H
H
O
H
H
O H
Figure 3, continued
C
4
C
5
C
6
N
1
C
2
N
3
O
4
H
3
O
2
H
1
H
5
H
6
H
O
H
H
O
H
H
O
H
H
O
H
H O
H
H
O
H
C
4
C
5
C
6
N
1
C
2
N
3
O
4
H
3
O
2
H
1
CH
3
H
6
H
O
H
H
O
H
H
O
H
H
O
H
H O
H
H O
H
H
O
H
C
4
C
5
C
6
N
1
C
2
N
3
N
4
O
2
H
1
H
5
H
6
H
O H
H
O
H
Figure 4
G G G G G G G G G G G G G G G G G G G G G G G G G H H H H H H H H H H H H H H H H H H H H H H H H H F F F F F F F F F F F F F F F F F F F F F F F F F 0 2 4 6 8 10 12 140 60 120 180 240 300 360
A
G G G G G G G G G G GG H H H
H H H H H H H H
H F F F F
F F F F F F F F 0 0.1 0.2 0.3 0.4 0.5
0 30 60 90 120
Gamma (degrees)
Figure 5
0 2 4 6 8 10 12 14
A
0 2 4 6 8 10 12 14
B
0 0.02 0.04 0.06 0.08 0.1
C
0 0.02 0.04 0.06 0.08 0.1
0 60 120 180 240 300 360
Gamma (degrees)
Figure 6
1
1 1 1 1 1
1 1 1
1 1 1 0
1 2 3 4
A
0 0.02 0.04 0.06 0.08
B
0 0.02 0.04 0.06 0.08
0 60 120 180 240 300 360
Alpha (degrees)
Figure 7
1
1 1 1 1 1
1 1 1
1 1 1 0
1 2 3 4
A
0 0.02 0.04 0.06 0.08 0.1
B
0 0.02 0.04 0.06 0.08 0.1
0 60 120 180 240 300 360
Zeta (degrees)
Figure 8
0 2 4 6 8
A
0 2 4 6 8
B
0 0.02 0.04 0.06 0.08
0 60 120 180 240 300 360
Beta (degrees) 0
0.02 0.04 0.06 0.08
C
Figure 9
0 2 4 6 8
A
0 2 4 6 8
B
0 0.02 0.04 0.06 0.08
C
0 0.02 0.04 0.06 0.08
0 60 120 180 240 300 360
Epsilon (degrees)
Figure 10
0 2 4 6 8 10
A
0 2 4 6 8 10
B
0 0.02 0.04 0.06 0.08 0.1
C
0 0.02 0.04 0.06 0.08 0.1
0 60 120 180 240 300 360
Chi (degrees)
Figure 11
0 2 4 6 8 10
A
0 2 4 6 8 10
0 60 120 180 240 300 360
Chi (degrees)
Figure 12
0 2 4 6 8 10
A
0 2 4 6 8 10
0 60 120 180 240 300 360
Chi (degrees)
Figure 13
0 2 4 6 8 10
A
0 2 4 6 8 10
0 60 120 180 240 300 360
Chi (degrees)
Figure 14
JJJ J J JJ JJ JJ JJ JJJ JJ J JJ JJ JJ JJJ J J J J J J J J J J J J J JJJ J JJ J JJJ JJJ JJJ J J J J J J JJ JJ J J J J J J J J J J1
1
1
0 2 4 6A
JJ JJ JJ J JJ J J J J J J J J J J J J J J J J J J J J J J JJJJ JJ J J J J JJ J J JJ J JJ J JJJJ JJ J JJ J JJ JJJ J J J J J J J J J J J J J J J 0 2 4 6B
0 0.02 0.04 0.06 0.08 0.1C
0 0.02 0.04 0.06 0.08 0.10 60 120 180 240 300 360
Pseudorotation angle (degrees)
Figure 15
0 0.04 0.08
0.12
A
0 0.04 0.08 0.12
0 60 120 180 240 300 360
Delta (degrees)
Figure 16
J
J J J J J J J J J J J J J J J J
J
J
J
J
J
J
J
J
0 4 8 12 16
0 60 120 180 240 300 360
Figure 17
JJ JJ JJ J JJ J J J J JJ J J J J J J J J J J J JJ J J JJJ J JJ J JJ J JJ J JJ J JJ JJJ JJ J JJ J JJ J JJJ J JJ J JJJ JJJ J JJJ JJ 0 2 4 6 8 10A
J J J J J J J J J J J J J J J J J J J J JJ J J J J JJ JJ J JJ JJ J JJJ JJ J JJ JJ JJ JJ JJJJ J JJ JJJ JJ J J J J J J JJ J J JJ J JJ JJJ J 0 2 4 6 8 10B
0 0.02 0.04 0.06 0.08 0.10 60 120 180 240 300 360
Pseudorotation angle (degrees)
Figure 18
0 0.04 0.08
A
0 0.04 0.08
B
0 0.04 0.08
C
0 0.08 0.16
D
0 0.02
0.04
E
0 0.04 0.08
F
0 0.04 0.08
0 60 120 180 240 300 360
Dihedral Angle (degrees)
Figure 19
0 0.02 0.04
0 60 120 180 240 300 360
Dihedral Angle (degrees)
H
0 0.02 0.04
A
0 0.02 0.04
B
0 0.02 0.04
C
0 0.02 0.04
D
0 0.02 0.04
E
0 0.02 0.04
F
0 0.02 0.04