Directory UMM :wiley:Public:journals:jcc:suppmat:21:

(1)

[image:1.612.93.508.57.708.2]

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

(2)

[image:2.612.98.546.76.346.2]

Figure 2A

O

P

O

P

O

N

NH

O

NH

2

N

H

2

N

O















P and

τ

5'

3'

(3)

[image:3.612.104.508.76.661.2]

Figure 2B

O

CH

2

O

P

O

H

O

P

O

H

O

Base

O

P

O

CH

3

O

P

O

CH

3

O

Base

CH

2

O

H

(-)

(-2)

O

H

















































(4)

[image:4.612.145.492.65.495.2]

Figure 3

O

CH

2

CH

2

CH

2

CH

2

H

O H

CH

O

2

CH

2

CH

2

O

H

O H

H

O H

1

2

A

B

H

3

C

O1

P

O2

CH

3

O4

O3

H

O

H

O

H

O

H

1

2

3,4

(5)

[image:5.612.178.487.87.575.2]

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

O

H

O H

H

O

H

O H

H

O

H

O

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

O

H

O H

H

O

H

O H

(6)

[image:6.612.94.564.83.655.2]

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

O

H

O

H

O

H

H O

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

O

H

O

H

O

H

H O

H

H O

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

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[image:7.612.89.524.97.410.2]

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 14

0 60 120 180 240 300 360

A

G G G G G G G G G G G

G 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)

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[image:8.612.97.537.95.682.2]

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)

(9)

[image:9.612.92.534.113.570.2]

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)

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[image:10.612.90.537.92.546.2]

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)

(11)

[image:11.612.96.537.97.688.2]

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

(12)

[image:12.612.95.534.95.692.2]

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)

(13)

[image:13.612.95.533.98.691.2]

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)

(14)

[image:14.612.90.518.98.407.2]

Figure 11

0 2 4 6 8 10

A

0 2 4 6 8 10

0 60 120 180 240 300 360

Chi (degrees)

(15)

[image:15.612.90.519.113.422.2]

Figure 12

0 2 4 6 8 10

A

0 2 4 6 8 10

0 60 120 180 240 300 360

Chi (degrees)

(16)

[image:16.612.89.519.100.408.2]

Figure 13

0 2 4 6 8 10

A

0 2 4 6 8 10

0 60 120 180 240 300 360

Chi (degrees)

(17)

[image:17.612.96.533.98.704.2]

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 J

1

0 2 4 6

A

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 6

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

Pseudorotation angle (degrees)

(18)

[image:18.612.90.534.91.406.2]

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)

(19)

[image:19.612.93.523.90.298.2]

Figure 16

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

(20)

[image:20.612.99.535.90.535.2]

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 10

A

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 10

B

0 0.02 0.04 0.06 0.08 0.1

0 60 120 180 240 300 360

Pseudorotation angle (degrees)

(21)

[image:21.612.151.510.82.677.2]

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)

(22)

[image:22.612.149.497.80.712.2]

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