suppmat.doc 75KB Jun 05 2011 09:30:45 PM

Supplemental Material
Pavelites, Bash, Gao and MacKerell, Jr. ÒA Molecular Mechanics Force Field for NAD+,
NADH and the Pyrophosphate Groups of NucleotidesÓ Journal of Computational Chemistry.
Submitted

Table S1. Average crystal, ab initio and empirical geometries for NIC+. Bond lengths are given
in and angles in given in degrees.
Bond
Survey
CHARMM
HF/6-31G(d)
N2-H1
1.017
1.003
N2-C3
1.347±0.010
1.341
1.343
C3-H4
1.098
1.072

C3-C5
1.367±0.018
1.373
1.366
H6-C5
1.093
1.072
C5-C7
1.384±0.005
1.385
1.395
H8-C7
1.094
1.074
C7-C9
1.388±0.004
1.393
1.387
C9-C10
1.383±0.011

1.375
1.381
C10-H11
1.097
1.072
C10-N2
1.342±0.011
1.342
1.329
C9-C12
1.499±0.012
1.510
1.517
C12-013
1.232±0.011
1.224
1.196
N14-C12
1.322±0.015
1.352

1.338
H15-N14
0.995
0.992
H16-N14
1.000
0.998
Angle
Survey
CHARMM
HF/6-31G(d)
C3-N2-H1
120.3
118.5
H4-C3-N2
118.5
116.8
C5-C3-N2
121.8 ± 1.5
121.3

119.3
H6-C5-C3
121.4
120.0
C7-C5-C3
119.6 ± 1.1
119.7
118.8
H8-C7-C5
120.4
118.1
C9-C7-C5
118.9 ± 0.7
118.7
120.8
C10-C9-C7
118.5 ± 0.8
118.7
117.6
H11-C1O-C9

119.9
121.6
C12-C9-C7
123.8 ± 1.0
119.4
127.6
013-C12-C'9
119.8 ± 0.0
118.3
117.7
N14-C12-('19
117.6 ± 0.5
117.7
118.0
H15-N14-C12
122.9
125.2
H16-N14-C12
114.8
117.3

C9-C10-N2
122.1 ± 1.3
121.8
120.2
C10-N2-C3
119.0 ± 1.6
119.8
123.3
C12-C9-C10
117.6 ± 0.9
121.8
114.8
013-C12-N14
122.5 ± 0.5
123.8
124.2
Dihedral Angle
Survey
CHARMM
HF/6-31G(d)

H4-C3-N2-H1
0.6
0.0
H4-C3-C5-H6
0.1
0.0
H6-C5-C7-H8
2.4
0.0
H8-C7-C9-C12
0.4
0.0
C12-C9-C10-H11
1.9
0.0
N14-C12-C9-C10
164.2±10.3
158.3
179.5

013-C12-C9-C10
H15-N14-C12-C9
H16-N14-C12-C9
N2-C3-C5-C7
C3-C5-C7-C9
C5-C7-C9-C10
C7-C9-C10-N2
C9-C10-N2-C3
C10-N2-C3-C5

8.4±12.2
1.4±1.2
1.6±0.9
1.2±1.4
0.9±2.1
1.1±1.3
0.9±0.6

16.8
9.6

172.7
0.0
0.7
1.2
1.1
0.5
0.1

0.5
0.1
180.0
0.0
0.0
0.0
0.0
0.0
0.0

Table S2. NICH crystal, ab initio and empirical geometries. Bond lengths in are given in and
angles are given in degrees.

Bond
N2-H1
N2-C3
C3-H4
C3-C5
H6-C5
C5-C7
H8-C7
H17-C7
C7-C9
C9-C10
C10-H11
C10-N2
C9-C12
C12-013
N14-C12
H15-N14
H16-N14
Angle
N2-C3-C5

C3-C5-C7
C5-C7-C9
C7-C9-C10
C9-C10-N2
C10-N2-C3
H1-N2-C3
H4-C3-C5
H6-C5-C7
H8-C7-C9
H17-C7-C9
H8-C7-H17
H11-C10-C9
C7-C9-C12
C9-C12-013
C9-C12-N14
013-C12-N14
C12-N14-H15
C12-N14-H16
Dihedral Angle
H1-N2-C3-H4
N2-C3-C5-H6
C3-C5-C7-H8

FIXDARa
1.470**
1.369

FIXDARb
1.467**
1.408

1.328

1.328

1.510

1.514

1.524
1.352

1.524
1.357

1.392
1.495
1.246
1.332

1.354
1.496
1.238
1.342

FIXDARa
123.5
123.3
108.1
123.2
121.7
118.2

FIXDARb
121.3
124.0
108.6
123.2
121.7
118.2

122.6
119.7
118.3
122.0

122.7
120.4
118.2
121.4

FIXDARa

FIXDARb

FIXCUK
1.468**
1.383
0.950
1.324
1.094
1.479
0.950
1.572**
1.527
1.361
1.090
1.359
1.456
1.253
1.334
0.949
0.950
FIXCUK
122.4
123.2
109.5
119.9
123.4
118.1
120.3**
118.8
118.4
115.6**
105.6
104.2**
118.3
120.1
120.3
121.0
118.6
120.0
120.0
FIXCUK
-0.5**
173.6
110.0**

CHARMM
1.015
1.371
1.095
1.326
1.090
1.512
1.111
1.111
1.539
1.353
1.094
1.381
1.531
1.228
1.356
0.997
0.998
CHARMM
120.7
123.7
109.6
119.9
123.1
118.0
119.8
118.8
117.4
111.7
107.8
108.8
119.1
122.2
122.1
115.7
122.1
121.8
115.9
CHARMM
5.6
-170.4
-128.3

HF/6-31G(d)
0.992
1.392
1.073
1.320
1.075
1.511
1.092
1.090
1.519
1.334
1.072
1.365
1.482
1.206
1.361
0.992
0.995
HF/6-31G(d)
122.2
122.9
110.5
121.6
123.4
119.0
119.4
122.6
118.2
110.6
111.1
105.7
120.1
122.3
123.2
116.1
120.7
121.9
116.1
HF/6-31G(d)
-12.5
179.1
126.8

C3-C5-C7-H17
134.9**
-112.6
117.9
H4-C3-C5-H6
-6.4
12.8
-0.1
H4-C3-C5-C7
173.6
169.1
-177.5
C5-C7-C9-C12
166.7
166.4
161.4
-148.9
-175.3
C5-C7-C9-C10
-12.9
-10.4
-18.9
7.8
4.4
C7-C9-C12-013
-163.9
-163.1
13.7
161.2
177.2
C7-C9-C12-N14
15.7
17.6
-162.5
-20.6
-1.6
C7-C9-C10-H11
-172.6
-175.4
-179.7
C7-C9-C10-N2
2.6
1.9
7.3
7.1
0.9
HS-C7-C9-C12
-72.7**
-25.7
-53.9
H8-C7-C9-C10
107.0**
131.0
125.8
H17-C7-C9-C10
-139.4
109.5
-117.2
H17-C7-C9-C12
41.9
93.8
63.1
C9-C12-N14-H15
-0.1
1.6
-17.1
C9-C12-N14-H16
-180.0
178.7
-171.8
C9-C10-N2-H1
179.6**
174.5
-168.7
C9-C10-N2-C3
7.3
13.2
7.2
-26.1
-6.4
C10-N2-C3-C5
-4.8
-10.5
-8.0
29.3
6.0
C3-C5-C7-C9
15.5
13.1
18.7
4.6
-4.7
**Covalently bound to a carbon, not hydrogen as in NICH. Cambridge crystal database
identifiers: FIXCUK: (R,R:S,S)-N-Benzyl-4-(1-(4-cyanophenyl)-1-hydroxymethyl)-1,4dihydronicotinamide, FIXDAR: (R,R:S,S)-N-Benzyl-4-(1-hydroxy-1-phenylmethyl)1,4-dihydronicotinamide. a and b indicate individual, unique molecules in the crystal.

Table S3. Inorganic phosphate crystal, empirical and ab initio geometry data;bond lengths,
angles and dihedral angles. Distances in and angles in degrees.
Bond
Internal Coord
r1
C1-O11
r2
P1-O11
r3
O12-P1
r4
O13-P1
r5
O14-P1
r6
P2-O12
r7
O22-P2
r8
O23-P2
r9
O24-P2
r10
C1-H11
r11
C1-H12
r12
C1-H13
r2r6
r2+r6/2
r4r5
r4+r5/2
r789
r7+r8+r9/3
r479 r4+r5+r7+r8+r9/5
Ang1e Internal Coord
a1
P1-O11-C1
a2
O12-P1-O11
a3
O13-P1-O11
a4
O14-P1-O11
a5
P2-O12-P1
a6
O22-P2-O12
a7
O23-P2-O12
a8
O24-P2-O12
a9
H11-C1-O11
a10
H12-C1-O11
a11
H13-C1-O11
a3a4
a3+a4/2.0
a678
a6+a7+a8/3.0
a368 a3+a4+a6+a7+a8/5.0
Dihedra1 Internal Coord
d1
O12-P1-O11-C1
d2
O13-P1-O11-C1
d3
O14-P1-O11-C1
d4
P2-O12-P1-011
d5
O22-P2-O12-P1
d6
O23-P2-O12-P1
d7
O24-P2-O12-P1
d8
H11-C1-O11-P1
d9
H12-C1-O11-P1

Diphosphate
1.438±0.030
1.597±0.021
1.606±0.040
1.499±0.025
1.475±0.035
1.620±0.020
1.514±0.057
1.499±0.058
1.514±0.080

Triphosphate
1.463± 0.085
1.605± 0.120
1.564± 0.043
1.478± 0.048
1.525± 0.039
1.673±0.055
1.559±0.060
1.464± 0.037
1.599±0.075

1.609±0.021
1.487±0.030
1.509±0.066
1.500±0.052
Diphosphate
119.8±4.5
99.4±3.6
111.2±1.7
107.9±1.0
131.5±1.6
103.8±4.8
107.1±5.5
107.7±4.5

1.639±0.093
1.502±0.044
1.541±0.059
1.525±0.054
Triphosphate
122.0±3.6
102.1±4.1
108.6±2.2
108.9±7.9
134.0±1.7
104.9±3.1
107.0±3.0
100.2±3.1

109.6±1.4
106.2±4.9
107.5±3.9
Diphosphate
See
Table S4
entries
1-6

108.8±5.8
104.0±3.1
105.9±4.4
Triphosphate
See
Table S4
entries
7-10

CHARMM
1.428
1.602
1.568
1.488
1.486
1.647
1.529
1.527
1.528
1.108
1.117
1.115
1.623
1.487
1.528
1.512
CHARMM
120.2
107.7
105.9
108.2
144.4
104.9
107.0
105.5
110.3
112.3
109.2
107.1
105.8
106.3
CHARMM
63.9
-179.7
-57.5
-47.2
-152.6
-32.4
88.2
-149.5
27.7

Ab Initio
1.394
1.670
1.561
1.499
1.498
1.740
1.512
1.518
1.515
1.096
1.093
1.084
1.705
1.498
1.515
1.508
Ab Initio
118.3
103.3
103.5
105.7
152.5
104.4
104.4
102.1
107.4
110.7
112.1
104.6
103.7
104.1
Ab Initio
70.3
-174.4
-49.9
-72.6
-92.5
28.7
147.9
-167.8
74.4

d10
H13-C1-O11-P1
-90.5
-41-.8
Empirical and ab initio values are from the fully optimized structures of methyl diphosphate. Six
diphosphate and four triphosphate crystal structures were used for determination of the averages.

Table S4 . Dihedral angles for the Diphosphate and Triphosphate crystal structures.
IC
CDPCHMa CDPCHMb HMADPH KADPHDO1 KADPHDO2
O12-P1-O11-C1
46.5
-175.3
-57.3
-66.3
-63.6
O13-P1-O11-C1
-63.3
-64.5
56.4
47.4
51.3
O14-P1-O11-C1
168.7
72.7
-173.7
-179.2
-177.5
P2-O12-P1-O11
87.4
-124.3
-63.6
157.7
157.3
O22-P2-O12-P1
-124.3
-159.4
68.2
165.9
164.9
O23-P2-O12-P1
122.5
87.4
-176.1
36.6
38.0
O24-P2-O12-P1
-12.5
-31.2
-60.3
-79.6
-80.1
IC
RBADPMIO ADENTPa
ADENTPb ADENTP02a ADENTP02b
O12-P1-O11-C1
-67.0
64.2
-51.5
-66.2
54.9
O13-P1-O11-C1
50.0
176.9
-165.8
175.6
172.1
O14-P1-O11-C1
179.3
-52.8
58.8
51.0'
-60.8
P2-O12-P1-O11
155.0
164.3
-69.4
-153.4
69.2
O22-P2-O12-P1
168.5
125.4
166.4
-132.8
-169.8
O23-P2-O12-P1
38.2
-10.2
-67.2
-2.4
70.7
O24-P2-O12-P1
-76.5
-127.4
50.5
115.8
-51.3
Cambridge crystal database identifiers: CDPCHM: Cytidine 5'-diphosphate choline
monohydrate, HMADPH: tris(Hydroxymethyl)-methylammonium adenosine-5'diphosphate dihydrate, KADPHD01, KADPHD02: Potassium adenosine-5'-diphosphate
dihydrate, RBADPM10: Rubidium adenosine-5'-diphosphate monohydrate, ADENDP20:
Adenosine-5'-diphosphoric acid trihydrate, ADENTP: Disodium adenosine-triphosphate
trihydrate. a and b indicate individual, unique molecules in the crystal.

Table S5. Vibrational frequency assignments and relative contributions of the
assignments to the frequency for NIC+. Frequencies in cm-1
Mode

CHARMM
Freq
Assignment
55.8
tAMIDE (111)
144.1
wAMIDE (78)
tRING (18)
215.6
dAMIDE (87)

6

Ab initio
Assignment
tAMIDE (100)
wAMIDE (56)
tRING (35)
318.9
dAMIDE (60)
dC=O(15)
337.1
tNH2 (48)
wNH2 (33)
356.2
rC=O(32)
sC9C12 (25)
dRING (24)
386.0
tRING (66)

7
8

400.3
474.9

tRING (84)
rC=O (19)
tRING (17)

444.5
516.8

9

514.5

532.4

10

566.3

11

613.9

dC=O (42)
sC12N14 (22)
wNH2 (55)
tNH2 (28)
dRING (87)

12

648.1

678.5

13

677.8

14

746.5

tRING (61)
dRING (19)
tRING (43)
dRING (26)
wC=O (68)

15

801.3

rNH2 (23)

779.7

16

836.3

837.3

17

988.4

wC5H (44)
wC3H (23)
wC10H (80)

18

999.5

wC3H (61)
wC7H (15)

964.1

1
2
3
4
5

Freq
59.0
153.7

353.1

tNH2 (83)

398.4

tRING (62)

413.2

tRING (45)
sC9C12 (17)
dRING (16)
tRING (69)
wN2H (35)
wC3H (27)
WC10H (22)
dC=O (28)
rC=O (20)
wNH2 (72)

570.3
658.8

713.3
732.2

878.0

rC=O (25)
dC=O (23)
dRING (18)
tRING (65)
wN2H (19)
dRING (49)
wC=O (16)
wC=O (68)
dRING (19)
wC10H (42)
wC3H (26)
dRING (38)
sN2C3 (16)
wC5H (38)
wC7H (22)
wC3H (21)
wN2H (39)
WC10H (25)
wC5H (18)

19

1008.4

dRING (32)
sC5C7 (23)

970.1

20

1016.1

1007.9

21

1040.5

22

1085.9

23

1124.6

dRING (30)
sN2C3 (27)
wC7H (60)
wC5H (37)
sC5C7(29)
sC10N2 (28)
sC3C5 (18)
sC9C10 (15)

24

1142.9

1120.9

25

1200.2

26

1270.0

27

1317.8

28

1323.4

sC3C5 (23)
sC7C9 (21)
sN2C3 (16)
dC5H (28)
sC10N2 (22)
dN2H (32)
dC3H (24)
dC10H (18)
dC10H (21)
dC7H (21)
rNH2 (23)
dC7H (20)

29

1429.7

sC12N14 (39)

1569.1

30

1468.8

1604.8

31

1554.0

dC3H (20)
dC5H (20)
dN2H (27)

32

1613.1

1948.6

33

1647.2

sC7C9 (20)
scNH2 (18)
sC3C5 (20)
sC9C10 (17)

34

1674.0

2046.9

35

1966.7

36

3067.2

scNH2 (53)
dN2H (19)
sC=O (71)
wN2H (29)
sC7H (91)

37
38
39

3084.6
3100.2
3102.7

sC5H (77)
sC3H (84)
sC10H (99)

2995.2
2997.8
2999.2

1024.1
1066.2
1073.3

1208.2
1273.7
1479.3
1554.5

1665.0

1997.4

2080.7
2993.2

dC5H (23)
sN2C3 (22)
sC3C5 (17)
rNH2 (74)
dRING (47)
sC5C7 (15)
wC7H (42)
wC5H (35)
sC10N2 (28)
sC5C7 (23)
sC3C5 (20)
dC5H (42)
dRING (24)
dN2H (25)
sN2C3 (17)
dN2H (25)
scNH2 (28)
sC9C12 (25)
dN2H (19)
sN2C3 (18)
sC10N2 (16)
sC9C10 (33)
sC7C9 (25)
sC5C7 (20)
sC3C5 (18)
scNH2 (55)
sC12N14 (19)
sC=O (64)
sC12N14 (21)
dC3H (36)
dC10H (29)
dC7H (21)
dC3H (49)
dC10H (28)
dC7H (51)
dC10H (26)
sC5H (64)
sC7H (21)
sC7H (77)
sC3H (90)
sC10H (70)
sC5H (21)

40
3420.0
sN2H (100)
3446.5
sNH2 (99)
41
3446.9
sNH2 (86)
3457.3
sN2H (99)
42
3583.2
sNH2a (85)
3562.3 1
sNH2a (99)
Stretching modes are represented by an "s" followed by the atoms in the bond stretch.
For example, sC7H is the stretching niode of the hydrogens attached the C7 carbon.
Angle deformations are represented by a "d" and a descriptor as in dRING, which are the
ring angle deformations, and dN2H which are the amide hydrogen angle deformations.
Wagging is represented by a "w" and a descriptor such as wAMIDE which is the amide
carbon improper dihedral wag and wC7H which is the wagging of the hydrogens attached
to atom C7. Other abbreviations: "t" for dihedral torsion, "r" for rocking, "sc" for
scissoring, "sym" for symmetric and "asy" for asymmetric. Ab initio frequencies, at the
HF/6-31G(d) level have been scaled by 0.9 (see text).

Table S6. Vibrational frequency assignments and relative contributions of the
assignments to the frequency for NICH. Frequencies in cm-1
Mode
1
2

Ab initio
Assignment
tAMIDE (69)
tRING (31)
98.4
tRING (63)
tAMIDE (27)

Freq
64.7

3

209.3

4

221.9

5

274.0

6

283.1

7

355.3

8

421.7

9

465.3

10

CHARMM
Freq
Assignment
99.8
wNH2 (84)
127.3

dAMIDE (65)
dC=O (16)
wAMIDE (52)
wN2H (19)
wN2H (60)
tNH2 (20)

203.0

tNH2 (65)
wN2H (16)
dRING (39)
sC9CI2 (27)
rC=O (18)
tRING (101)

368.9

515.5

523.2

rC=O (31)
dC=O (23)
dAMIDE (16)
tRING (100)

11

537.6

wNH2 (84)

609.7

12

565.0

639.2

13

605.1

14

722.4

15

736.9

16

765.3

dRING (69)
dC=O (19)
dRING (42)
rC=O (21)
dC=O (15)
dRING (24)
sC7C9 (21)
sC9CI2 (16)
wC5H (44)
wC3H (23)
tRING (16)
wC=O (83)

266.3
289.4

406.4
490.3

579.0

684.6

rC=O (39)
tAMIDE (29)
wNH2 (20)
tRING (16)
tRING (87)
tNH2 (66)
scC7H (19)
rC=O (56)
tAMIDE (17)
dC=O (-17)
tRING (56)
wAMIDE (46)
scNH2 (19)
tRING (18)
scNH2 (34)
dRING (27)
sC9CI2 (20)
tRING (30)
wC=O (27)
tAMIDE (23)
scC7H (16)
dRING (34)
wC7H (23)
dRING (27)
scNH2 (23)
wN2H (28)
dRING (28)

715.6

sC9C10 (35)
wC=O (18)

774.6

wC5H (74)

786.3

wNH2 (39)

17
18

902.1
958.9

982.4

sC5C7 (64)
dRING (33)
sN2C3 (22)
sC7C9 (19)
wC3H (58)
wC5H (28)
wC10H (31)
wC3H (18)
wC10H (55)

19

972.3

20

977.9

21

835.7
889.3

1004.7

22

1011.4

tC7H (64)

1034.4

23

1077.4

rNH2 (35)
sC12N14 (35)

1092.5

24

1100.5

1142.8

25

1150.0

dRING (32)
rNH2 (25)
sC9C12 (16)
sC10N2 (32)

26

1206.4

dC3H (26)
dC5H (24)

1218.0

27

1215.1

wC7H (77)

1327.9

28

1303.4

dC10H (40)
rC7H (32)

1388.7

29

1349.3

sC12N14 (23)

1415.5

30

1382.6

rC7H (28)
sC7C9 (18)

1476.6

979.3
995.9

1176.1

sC9C10 (34)
wC=O (16)
sC5C7 (47)
dRING (34)
sC9C10 (31)
wC3H (24)
sN2C3 (17)
wC10H (26)
wC3H (26)
rNH2 (49)
sNH2 (45)
scNH2 (-16)
DRING (46)
sC9C12 (24)
sC9C10 (-20)
wC3H (23)
wN2H (17)
WC10H (16)
wAMIDE (41)
sC12N14 (29)
wN2H (34)
wC3H (27)
wC10H (22)
dN2H (23)
dC3H (21)
sC10N2 (16)
tC7H (50)
sC9C12 (34)
dAMIDE (24)
tRING (23)
wC7H (-18)
sC9C12 (38)
scNH2 (24)
tC7H (21)
dC10H (16)
dC5H (37)
rC7H (22)
tC7H (-18)
dC3H (18)
tC7H (63)
rC7H (-40)
sC=O (29)
dC10H (22)
rC=O (22)

dRING (19)
rC7H (41)
wC7H (34)
32
1494.5
1551.2
rC7H (22)
dRING (17)
33
1498.2
1558.3
dN2H (43)
34
1619.3
1653.4
dC3H (31)
sN2C3 (26)
sC3C5 (23)
35
1636.3
sC9C10 (46)
1667.7
rNH2 (52)
scNH2 (-18)
sNH2a (17)
36
1717.5
sC3C5 (54)
1744.8
dC10H (28)
sC=O (24)
37
1749.8
sC=O (53)
1962.5
dC=O (109)
rC=O (-39)
38
2815.6
sC7Hsym (60)
2802.8
sC7C9 (53)
sC7Hasy (40)
sC7Hsym (25)
sC7Hasy (24)
39
2850.2
sC7Hasy (60)
2843.9
sC7C9 (50)
sC7Hsym (40)
sC7Hsym (27)
sC7Hasy (24)
40
3033.4
sC5H (86)
2989.6
sC5H (99)
41
3063.6
sC3H (86)
3092.2
sC10H (96)
42
3085.7
sC10H (99)
3092.7
sC3H (96)
43
3457.6
sNH2 (98)
3444.4
sNH2a (48)
sC7Hsym (22)
sC7Hasy (22)
scNH2 (18)
44
3520.6
sN2H (100)
3454.6
sN2H (99)
45
3572.5
sNH2a (98)
3566.2
sNH2a (38)
rNH2 (35)
sC7Hasy (24)
sC7Hsym (24)
scNH2 (-21)
For key to normal mode abbreviations, see Table S5. Ab initio frequencies, at the HF/631G(d) level have been scaled by 0.9 (see text).
31

1402.3

dC3H (43)
dC5H (28)
dN2H (57)
sC10N2 (16)
scC7H (97)
scNH2 (78)

1531.2

Table S7. Vibrational frequency assignments and relative contributions for methyl
diphosphate. Frequencies in cm-1
Mode

5

Ab initio
Freq
Assignment
28.8
tP2-O12 (150)
tP1-O12 (-49)
49.3
tP1- O12 (151)
tP2-O12 (-47)
86.8
dP-O-P (80)
tP1-O11 (27)
129.9
tP1-O11 (62)
dP-O-P (25)
162.6
tCH3 (98)

6

210.5

dP-O-C (51)
scO-P-O (26)

234.3

7

248.3

sP-O (104)

250.5

8

281.2

312.1

9

292.4

dPO3as' (50)
rO=P=O (23)
dPO3as (43)

10

372.1

430.0

11

389.9

scO=P=O (31)
scO-P-O (20)
dPO3as (19)
rO=P=O (45)
dPO3as' (18)

12

455.7

473.3

13

493.0

14

508.7

15

516.7

16

546.4

tO=P=O (29)
wO=P=O (22)
rPO3' (16)
rPO3' (38)
rPO3 (25)
rPO3 (37)
dPO3as (17)
dPO3sym (57)
scO=P=O (21)
wO=P=O (19)
tO=P=O (33)

1
2
3
4

CHARMM
Freq
Assignment
37.6
tP2-O12 (83)
52.0
95.5
110.,5
163.0

319.6

461.4

tP1-O12 (94)
tP2-O12 (18)
dP-O-P (97)
sP-O (16)
tP1-O11(54)
tCH3 (43)
tCH3 (56)
tP1-O11 (41)
sP-O (36)
dP-O-C (29)
scO-P-O (24)
sP-O (33)
dPO3as (23)
scO-P-O (16)
dP-O-C (16)
dPO3as' (55)
rO=P=O (22)
dPO3as (28)
dP-O-C (21)
scO-P-O (19)
wO=P=O (29)
scO=P=O (19)
rPO3 (30)
scO-P-O (26)
dPO3as (17)
rPO3' (59)
rO=P=O (19)

487.6

rPO3' (47)

500.5

dPO3sym (26)

509.8

dPO3sym (32)

533.8

scO=P=O (37)
tO=P=O (21)

17

586.6

dPO3sym (32)
sP-0 (20)
scO=P=O (19)
sP-O (58)
wO=P=O (29)

635.6

scO=P=O (22)
sP-O (22)

18

684.4

730.4
887.2

1067.0

sP=O (65)
sP-O (35)
sP=O (67)
sP-O (30)
sP=O (65)
sP-O (31)
sP=O (92)

sP-O (37)
wO=P=O (28)
sP=O (20)
sP=O (65)
sP-O (26)
sP=O (45)
sP-O (32)
sC-O (67)

19

877.9

20

957.9

21

1043.0

22
23

1080.9

sP=O (94)

1124.5

24
25
26

1101.1
1145.7
1170.0

sC-O (84)
sP=O (93)
dCH3as'(67)
dCH3as (29)

1143.8
1146.6
1192.7

27

1204.7

1020.3
1054.1
1057.9

dCH3as' (43)
dCH3as (31)
rCH3' (17)
sP=O (70)
sP-O (30)
SP=O (91)
sP=O (90)
dCH3as (46)
dCH3a.s' (22)
rCH3' (15)
sP=O (91)

dCH3as (61)
1256.9
dCH3as' (25)
28
1454.7
dCH3s (50)
1436.3
rCH3 (78)
rCH3' (42)
dCH3as (17)
29
1488.6
dCH3s (49)
1470.9
rCH3' (61)
rCH3' (35)
dCH3as' (28)
30
1506.6
rCH3 (82)
1638.4
dCH3s (84)
rCH3' (16)
31
2767.0
sC-H (100)
2853.7
sC-H (100)
32
2813.4
sC-H (100)
2913.9
sC-H (100)
33
2942.7
sC-H (100)
2916.1
sC-H (100)
For key to normal mode abbreviations, see table S5. Ab initio frequencies, at the HF/631G+(d) level have been scaled by 0.9 (see text).

Table S8. NIC+/NICH dipole moments in Debye.
ab initio

Model 1

Model 2

8.26
-6.66
-4.62
1.64

7.77
-6.09
-4.76
0.77

7.17
-5.78
-4.13
0.98

6.98
6.57
1.77
1.56
ab initio

6.17
6.11
0.84
-0.01
emp

4.82
-2.50
-4.02
0.94

3.65
-1.23
-3.40
-0.51

3.72
3.21
1.83
0.43

2.18
1.10
1.88
0.05

NIC+ trans
Total
x
y
z
+
NIC cis
Total
x
y
z
NICH trans
total
x
y
z
NICH cis
Total
x
y
z

Table S9. Unitcell parameters and energies of the NAD+-Li+ crystal minimizations for
both Models 1 and 2. Energies in kcal/mol, distances in , angles in degrees and forces in
mdyn.
Cutoff
Model 1
exper
10-9-7
13-12-10
16-15-13
19-18-16
22-21-19
25-24-22
Model 2
exper
10-9-7
13-12-10
16-15-13
19-18-16
22-21-19
25-24-22

a

b

c

Total Energy

Lattice Energy
VDWElec

GRMS

10-073
10.349
9.984
10.130
10.318
10.122
10.112

15-839
15.477
15.418
15.452
15.428
15.462
15.346

17.821
17.311
17-887
17.679
17.654
17.994
17.918

-554.94
-595.25
-614.18
-624.51
-629.21
-633.75

-36.96
-45.10
-46.36
-47.63
-47.21
-48.68

-215.61
-202.82
-201.01
-198.40
-196-06
-192.96

0.00053
0.04190
0.00071
0.00057
0.00068
0.00027

10.073
9.684
9.862
9.906
10.088
9.926
9.924.

15.839
15.274
15.581
15.446
15.352
15.473
15.352

17.821
18.658
17.964
18.264
17.862
18.170
18.188

-542.84
-587.27
-604.96
-614.57
-620.91
-624.53

-37.25
-44.14
-47.22
-47.08
-47.94
-47.83

-226.71
-214.97
-209.56
-204.73
-202.44
-200.82

0.00084
0.00063
0.00048
0.00042
0.00054
0.00056

Table S10. Interaction distances involving the nicotinamide ring in the NAD-LI+ crystal
from x-ray crystallography and the calculations using Models 1 and 2.
Interaction pair
NNI - AO2
NC6 - AO2
NC5 - AC5
NC4 - OH2
NC3 - AO2
NC2 - AO2
NC2 - AO5'
NC2 - OH2
NO7 - AC8
NO7 - OH2
NN7 - OH2
Aver Diff
RMS Diff

exper
3.03
3.33
3.43
3.43
3.44
3.10
3.46
3.16
3.14
2.74
2.86

min
3.36
3.64
3.98
3.30
3.24
3.12
3.33
2.94
3.22
3.15
2.75
0.08
0.27

model 1
dyn ave
3.58
3.27
3.64
3.83
3.54
3.66
3.24
3.50
3.21
4.11
3.20
0.33
0.52

rms
0.21
0.17
0.21
0.21
0.22
0.20
0.19
0.18
0.18
0.42
0.18

min
3.33
3.57
4.06
3.17
3.11
3.07
3.21
2.88
3.11
3.13
2.78
0.03
0.31

model 2
dyn ave
3.45
3.25
3.44
4.04
3.24
3.29
3.14
3.29
3.09
3.36
3.13
0.15
0.33

rms
0.21
0.16
0.21
0.24
0.14
0.20
0.18
0.19
0.34
0.39
0.19

Distances in . Interactions between non-hydrogen atoms less than 3.5 in the crystal
structure are included. Average and RMS difference are the average and root-meansquare differences between the calculated and experimental results.

Table S11. NAD crystal experimental and calculated dihedrals for Model 2 with the final
diphosphate parameters. Angles indegrees.
Dihedral

Exper

Minimized

Diff

AP -O3 -NP -NO5'
AC5'-AO5'-AP -O3
AC5'-AO5'-AP -AO2
AP-O3-NP-NO1
AP-O3-NP-NO2
AP -AO5'-AC5'-AC4'
A05'-AC5'-AC4'-AC3'
AC5'-AC4'-AC3'-AO3'
AO4'-AC3'-*AC4-AC5'
AC2'-AC4'-*AC3-AO3'
AC4'-AC3'-AC2'-AC1'
AC3'-AC2'-AC1'-AN9
AO4'-AC1'-AN9 -AC4
AC1'-AC4 -*AN9-AC8
AC4-AN9-AC8-AN7
AC8-AN9-AC4-AC5
AC8-AN7-AC5-AC6
AN7 -AC5 -AC6 -AN1
AC5 -AC6 -AN1 -AC2
AN9 -AC5 -*AC4-AN3
AC5 -AN1 -*AC6-AN6
AC5 -AN1 -*AC6-AN6
AC1'-AC3'-*AC2-AO2'
NC5'-NO5'-NP -NO2
NP -NO5'-NC5'-NC4'
N05'-NC5'-NC4'-NC3'
NC5'-NC4'-NC3'-NC2'
NC4'-NC3'-NC2'-NC1'
NC3'-NC2'-NC11'-NO4'
NC2'-NC1'-NO4'-NC4'
NC3'-NC2'-NC1'-NN1
NC2'-NC1'-NN1 -NC2
NC1'-NN1 -NC2 -NC3
NN1 -NC2 -NC3 -NC4
NC2 -NC3 -NC4 -NC5
NC3 -NC4 -NC5 -NC6
NC4 -NC5 -NC6 -NN1
NC5 -NC6 -NN1 -NC2
NN1 -NC2 -NC3 -NC7
NC2 -NC3 -NC7 -NO7
NC2 -NC3 -NC7 -NN7

72.5
-124.6
122.5
-171.7
-37.8
162.8
48.0
141.6
-121.5
-120.5
-35.4
153.0
-121.4
-175.1
2.0
-0.6
175.5
-175.9
1.1
179.7
178.1
178.1
-123.4
-167.5
179.0
46.5
-151.9
43.1
-31.1
7.0
93.1
70.7
-177.5
-3.7
1.9
1.3
-2.5
0.5
179.4
-9.2
160.9

52.5
-125.2
120.5
167.7
-71.7
164.7
46.4
151.8
-121.4
-120.4
-38.5
146.9
-144.8
-176.7
-3.2
1.4
177.1
-178.2
-0.1
178.4
179.8
179.8
-124.8
-157.5
146.0
54.7
-157.0
37.7
-25.7
3.6
97.1
73.2
176.3
-1.7
1.9
-0.7
-0.9
1.1
177.3
14.0
-162.2

-20.0
-0.6
-2.0
-20.6
-34.0
1.9
-1.6
10.2
0.0
0.1
-3.1
-6.1
-23.4
-1.7
-5.2
2.0
1.6
-2.2
-1.2
-1.3
1.7
1.7
-1.4
10.0
-33.0
8.2
-5.1
-5.4
5.4
-3.5
4.1
2.5
-6.2
2.0
-0.1
-2.0
1.6
0.7
-2.1
23.2
36.9

Dynamics
aver RMS fluc
54.8
19.5
-131.1
17.6
115.2
17.7
170.2
19.5
-69.1
32.3
161.0
9.1
49.9
12.3
150.0
9.7
-121.0
3.6
-121.3
3.3
-38.9
4.8
149.2
5.5
-145.3
25.3
-178.3
7.6
-1.8
5.5
0.4
3.7
178.7
6.1
-178.5
5.8
-1.1
5.8
178.7
4.6
179.0
5.1
179.0
5.1
-123.4
4.4
-155.3
15.6
149.8
29.9
56.3
11.6
-155.7
5.9
36.0
8.7
-24.9
9.0
4.1
7.8
98.2
8.8
72.1
7.9
177.9
9.1
-1.7
5.4
1.5
4.9
-0.3
5.7
-0.7
5.8
0.5
5.6
178.3
7.6
16.9
28.1
-158.4
42.7

-17.7
-6.5
-7.3
-18.1
-31.4
-1.8
1.9
8.4
0.5
-0.8
-3.5
-3.8
-23.9
-3.2
-3.8
1.1
3.1
-2.6
-2.2
-1.0
0.9
0.9
0.0
12.2
-29.2
9.8
-3.8
-7.1
6.2
-3.0
5.2
1.4
-4.6
2.0
-0.5
-1.7
1.8
0.1
-1.1
26.1
40.7

NP -O3 -AP -AO5'
132.5
164.6
32.1
O3 -NP -NO5'-NC5'
79.1
78.7
-0.4
RMS difference
12.8
* prior to the third atom indicates an improper torsion angle.

161.1
81.3

29.6
9.9

28.6
2.2
12.7

Table S12. NAD crystal experimental and calculated interaction distances for Model 2.
Distances given in .
Interaction pair

exper

Minimized

NAD1 NC6 -NAD1 N05'
3.23
NAD1 AN7 -NAD1 NO1
3.22
NAD1 AC8 -NAD1 O3
3.45
NAD1 AC8 -NAD1 NO1
3.41
NAD1 AO1 -NAD1 NO2
2.95
NAD1 AO5'-NAD1 AC2'
3.22
NAD1 AO2'-WATX OH2 2.66
NAD1 NN1 -C009 AO2
3.03
NAD1 NC6 -C009 AO2
3.33
NAD1 NC5 -C020 AC5
3.43
NAD1 NC4 -C020 OH2
3.43
NAD1 NC3 -C009 AO2
3.44
NAD1 NC2 -C009 AO2
3.10
NAD1 NC2 -C009 AO5'
3.46
NAD1 NC2 -C020 OH2
3.16
NAD1 AN7 -C008 OH2
3.38
NAD1 AN9 -C020 NO4'
3.19
NAD1 AN1 -C003 NC2'
3.44
NAD1 AN1 -C003 NO2'
2.77
NAD1 AC2 -C003 NO3'
3.38
NAD1 AN3 -C020 NO4'
3.16
NAD1 AC4 -C020 NO4'
3.15
NAD1 AN6 -C003 NO2Õ 3.41
NAD1 AN6 -C008 AO2'
3.09
NAD1 AN6 -C008 AO3'
2.91
NAD1 AO1 -C020 AN7
3.14
NAD1 AO1 -C020 AN6
2.89
NAD1 AO1 -C020 NO1
3.25
NAD1 NO2 -C020AN7
3.38
NAD1 NO2 -C020 NO1
3.13
NAD1 AO4'-C020 NO4'
2.94
NAD1 AO4'-C020 NC6
3.43
NAD1 AC1'-C015 AO2
3.31
NAD1 AC1'-C020 NO4'
3.16
NAD1 AO3'-C015 AO2
2.59
NAD1 AO3'-C015 NC3'
3.24
NAD1 AO3'-C015 NO3'
2.70
NAD1 AC5'-C020 NO1
3.48
Interactions involving the amide group
NAD1 NO7 -C009 AC8
3.14

Diff

3.52
3.73
3.23
4.07
2.76
3.06
2.71
3.35
3.59
4.07
3.15
3.10
3.07
3.23
2.89
3.30
3.00
3.73
2.93
3.12
3.87
3.31
3.19
3.02
2.95
3.16
2.73
3.41
3.71
3.62
3.08
2.99
3.35
3.31
2.65
3.20
2.68
3.52

0.30
0.52
-0.21
0.65
-0.19
-0.16
0.05
0.32
0.26
0.65
-0.28
-0.35
-0-03
-0.24
-0.27
-0.08
-0.20
0.29
0.15
-0.25
0.71
0.16
-0.22
-0.07
0.04
0.01
-0.15
0.15
0.33
0.49
0.14
-0.43
0.04
0.15
0.06
-0.04
-0.01
0.04

Dynamics
Aver rms flu
3.54
0.23
3.76
0.14
3.35
0.13
4.02
0.17
2.76
0.11
3.13
0.10
2.78
0.12
3.28
0.15
3.49
0.23
4.08
0.22
3.21
0.13
3.27
0.25
3.14
0.19
3.25
0.16
2.98
0.19
3.27
0.28
3.09
0.15
3.87
0.22
3.04
0.16
3.28
0.15
3.71
0.18
3.32
0.16
3.40
0.17
3.12
0.15
3.09
0.22
3.06
0.10
2.79
0.12
3.46
0.19
3.85
0.21
3.67
0.13
3.17
0.16
3.21
0.18
3.44
0.13
3.27
0.12
2.71
0.10
3.22
0.10
2.70
0.08
3.64
0.25

3.14

-0.01

3.23

0.26

Diff
0.31
01.54
-0.10
0.60
-0.19
-0.08
0.12
0.25
0.16
0.65
-0.22
-0.17
0.03
-0.21
-0.18
-0.11
-0.10
0.42
0.26
-0.10
0.54
0.17
-0.01
0.03
0.18
-0.08
-0.10
0.20
0.46
0.53
0.23
-0.22
0.13
0.12
0.12
-0.02
0.00
0.16
0.09

NAD1 NO7 -C020 OH2
2.74
3.12
0.38
3.20
0.26
0.46
NAD1 NN7 -C020 OH2
2.86
2.79
-0.07
2.95
0.35
0.09
NAD1 NO2 -C013 NN7
2.88
2.85
-0.04
2.93
0.17
0.05
Interactions involving the Lithium ion
ION1 LIT -NAD1 AC5
3.19
3.12
-0.08
3.25
0.13
0.06
ION1 LIT -NAD1 AN7
2.13
2.28
0.15
2.37
0.15
0.24
ION1 LIT -NAD1 ACS
3.01
3.08
0.07
3.12
0.15
0.11
ION1 LIT -NAD1 NP
3.31
3.21
-0-10
3.27
0.08
-0.04
ION1 LIT -NAD1 NO1
1.92
2.05
0.12
2.07
0.06
0.15
ION1 LIT -NAD1 AH8
3.17
3.47
0.30
3.44
0.18
0.27
ION1 L1T -NAD1 AH61
2.75
2.84
0.08
2.98
0.17
0.23
NAD1 AO1 -C020 LIT
1.88
2.13
0.24
2.14
0.08
0.26
NAD1 NO2 -C020 LIT
1.86
2.08
0.23
2.12
0.07
0.26
Average difference
0.07
0.16
RMS difference
0.27
0.26
The selected interactions are those less than 3.5 A between non-hydrogen atoms of
NAD and the environment in the crystal following the overlay with water. Values in
parenthesis for the average and rms differences represent those values with all
differences greater than 1.0 A.

Table S13) Alcohol Dehydrogenase bound NAD experimental and calculated dihedrals.
Dihedral angles in degrees.
Dihedral
AP -O3 -NP -NO5'
AC5'-AO5'-AP -O3
AC5'-AO5'-AP -AO2
AP -O3 -NP -NO1
AP -O3 -NP -NO2
AP -AO5'-AC5'-AC4'
AO1 -AP -AO5'-AC5'
AO5'-AC5'-AC4'-AC3'
AC5'-AC4'-AC3'-AO3'
AO4'-AC3'-*AC4-AC5'
AC4'-AC3'-AC2'-AC1'
AC3'-AC2'-AC1'-AN9
AO4'-AC1'-AN9 -AC4
AC1'-AC4 -*AN9-AC8
AC4 -AN9 -AC8 -AN7
AC8 -AN9 -AC4 -AC5
AC8 -AN7 -AC5 -AC6
AN7 -AC5 -AC6 -AN1
AC5 -AC6 -AN1 -AC2
AN9 -AC5 -*AC4-AN3
AC5 -AN1 -*AC6-AN6
AC5 -AN1 -*AC6-AN6
AC1'-AC3'-*AC2-AO2'
NC5'-NO5'-NP -NO2
NP -NO5'-NC5'-NC4'
NO5'-NC5'-NC4'-NC3'
NC5'-NC4'-NC3'-NC2'
NC4'-NC3'-NC2'-NC1'
NC3'-NC2'-NC1'-NO4'
NC2'-NC1'-NO4'-NC4'
NO2'-NC2'-NC1'-NO4'
NC3'-NC2'-NC1'-NN1
NO3'-NC3'-NC2'-NC1'
NC2'-NC1'-NN1 -NC2
NC1'-NN1 -NC2 -NC3
NN1 -NC2 -NC3 -NC4
NC2 -NC3 -NC4 -NC5
NC3 -NC4 -NC5 -NC6
NC4 -NC5 -NC6 -NN1
NC5 -NC6 -NN1 -NC2
NN1 -NC2 -NC3 -NC7

Experimental
-155.7
-85.4
36.5
96.4
-36.5
-137.7
163.4
47.5
103.6
-11.5
-17.5
167.5
-107.7
-174.4
0.6
-0.9
178.1
-178.4
-0.5
178.3
179.2
179.2
96.0
-55.7
-170.9
52.6
-95.0
-38.7
45.4
-34.8
167.3
163.2
83.6
140.0
173.3
1.0
-0.4
-0.1
0.0
0.6
-175.4

Dynamics
Aver
RMS flu
-173.8
11.9
53.8
10.8
-178.7
10.8
75.6
12.4
-61.9
12.6
166.5
14.2
-55.9
11.3
-64.6
7.8
124.8
8.1
18.4
14.8
-27.1
5.4
157.9
10.9
-124.8
17.1
175.1
8.9
0.0
4.7
0.2
3.9
-180.0
5.4
-178.5
6.4
-1.4
5.6
-179.9
5.0
179.3
5.2
179.3
5.2
126.9
39.6
-54.8
9.1
-166.1
9.1
44.7
9.3
-93.0
5.0
-38.1
3.8
37.5
5.1
-22.0
7.0
160.3
5.1
156.4
5.1
82.0
5.0
142.1
7.5
166.9
7.6
0.2
5.7
-2.0
5.3
2.2
5.2
-0.4
5.4
-1.4
5.8
-174.8
7.9

Difference
-18.1
139.2
144.8
-20.8
-25.4
-55.8
140.8
-112.1
21.2
29.9
-9.6
-9.6
-17.1
-10.5
-0.6
1.1
1.9
-0.1
-0.9
1.8
0.1
0.1
30.9
0.9
4.8
-7.9
2.0
0.6
-7.9
12.8
-7.0
-6.8
-1.6
2.1
-6.4
-0.8
-1.6
2.3
-0.4
-2.0
0.6

NC2 -NC3 -NC7 -NO7
-160.6
-161.3
10.0
-0.7
NC2 -NC3 -NC7 -NN7
19.9
23.6
10.8
3.7
RMS Difference
43.3(14.2)
* prior to the third atom indicates an improper torsion angle. The rms difference in paranthesis
represents the value with all dihedral differences > 100û removed.

Table S14) Alcohol Dehydrogenase bound NAD experimental and calculated interaction
distances. Distances in .
Interaction

Experiment

AO4'- CG1
3.29
AC1'- OD1
3.41
AN3 - OD1
3.45
AN6 - NH1
3.03
AO2'- OD1
2.81
AO3'- CG
3.45
AO3'- OD1
3.46
AO3'- OD2
2.68
AO3'- NZ
2.77
AC5'- N
3.40
AO1 - NE
2.64
AO1 - CZ
3.23
AO1 - NH2
3.00
AO2 - CA
3.17
O3 - CB
3.28
NO1 - N
3.30
NO1 - CB
3.36
NO1 - NH1
2.83
NO2 - N
3.22
NO2 - N
2.95
NC5' - O
3.22
NO2' - OG
2.80
NO2' - NE2
3.30
NO2' - CD2
3.26
NC3' - O
3.15
NO3' - NE2
3.15
NO3' - C
3.38
NO3' - O
2.57
NO3' - N
3.09
NC4' - O
3.39
NC5 - SG
3.35
NC4 - OG1
3.44
NC4 - CG2
3.44
NC2 - O
2.93
NC5 - O1
3.09
NC4 - C1
3.36
NC4 - O1
3.31
Interactions involving the amide group
NC7 - CG2
3.48
NO7 - N
2.86

Dynamics
Average RMS flu
3.99
0.25
3.86
0.29
4.02
0.43
3.63
0.49
2.74
0.16
3.56
0.17
3.84
0.26
2.63
0.10
2.85
0.14
4.64
0.19
2.73
0.10
3.16
0.08
2.71
0.11
3.45
0.18
3.38
0.22
3.15
0.25
3.61
0.25
2.72
0.11
3.23
0.18
2.95
0.15
3.31
0.19
2.78
0.10
3.13
0.19
3.09
0.17
3.46
0.17
3.19
0.24
3.51
0.14
2.74
0.13
3.29
0.24
3.68
0.23
3.37
0.12
3.44
0.21
3.40
0.15
3.01
0.14
3.15
0.18
3.60
0.24
3.33
0.18
3.89
2.98

0.22
0.16

Difference
0.70
0.45
0.57
0.60
-0.07
0.11
0.38
-0.05
0.08
1.24
0.09
-0.07
-0.29
0.28
0.10
-0.15
0.25
-0.11
0.01
0.00
0.09
-0.02
-0.17
-0.17
0.31
0.04
0.13
0.17
0.20
0.29
0.02
0.00
-0.04
0.08
0.06
0.24
0.02
0.41
0.12

NN7 - O
2.98
2.96
0.15
-0.02
NN7 - O
2.93
3.03
0.20
0.10
Interactions involving the zinc ion
NC5 - ZN
3.34
3.50
0.14
0.16
Interactions involving water
AN1 - OH2
3.26
5.16
2.03
1.90
AN6 - OH2
3.12
7.05
3.02
3.93
AO2'- OH2
2.94
3.53
0.68
0.59
AO3'- OH2
3.20
3.96
0.85
0.76
AC5'- OH2
3.26
3.75
0.25
0.49
AO2 - OH2
2.72
2.67
0.11
-0.05
AO2 - OH2
2.65
2.80
0.17
0.15
NO2 - OH2
2.71
2.73
0.20
0.02
AO4'- OH2
3.09
7.20
4.86
4.11
AN7 - OH2
2.92
8.95
4.27
6.03
AC8 - OH2
3.40
6.26
1.47
2.86
AC2'- OH2
3.47
18.93
8.31
15.46
AO2'- OH2
2.65
19.56
8.57
16.91
AC5'- OH2
3.39
7.46
4.89
4.07
AO5'- OH2
2.73
8.42
4.59
5.69
Average Difference
1.21 (0.20)
RMS Difference
3.40 (0.28)
See Table S12 legend. The average and rms differences in paranthesis represents the values with
all distance differences > 1.0 removed.

Table S15. Bond Parameters. Equilibrium bond lengths in and force constants are given
in kcal/mol/.
bond type
NIC+/NICH
CN1A CN3
CN1A NN1
CN1A ON1
CN3A CN3
CN3B CN3
CN3B NN2
CN3A HN3
CN3B HN3
CN3A HN3B
CN3B HN3B
NICH
CN3 CN8
CN3C NN2
CN3C HN3
CN3C CN3
Phosphate
ON2 P2
ON3 P2

Kb

bo

302.0
560.0
860.0
450.0
420.0
420.0
350.0
350.0
350.0
350.0

1.480
1.360
1.230
1.360
1.350
1.315
1.09
1.09
1.09
1.09

222.5
420.0
374.0
420.0

1.490
1.355
1.09
1.320

300.0
480.0

1.68
1.53

Table S16. Angle Parameters. Equilibrium bond angles are given in degrees and force
constants are given in kcal/mol/.
angle type
K

KUB
So
NIC+/NICH
CN3A CN3 CN3B
40.0
118.0
CN3A CN3 CN1A
40.0
110.2
CN3B CN3 CN1A
10.0
131.8
CN3 CN1A NN1
85.0
113.0
80.0
2.46
ON1 CN1A CN3
85.0
118.5
20.0
2.43
ON1 CNLA NN1
85.0
128.5
20.0
2.17
CN3B CN3 HN3
30.0
122.0
CN3A CN3 HN3
30.0
119.0
CN3 CN3A CN3
50.0
118.0
CN3 CN3A HN3
30.0
121.0
CN3 CN3B NN2
120.0
122.0
HN3 CN3B NN2
30.0
117.5
CN3 CN3B HN3
30.0
120.5
CN6 CN9 ON2
75.7
110.1
CN1A NN1 HN1
35.0
120.0
CN3B NN2 CN3B
30.0
120.0
CN3B NN2 CN6B
70.0
121.7
HN3B CN3B NN2
80.0
117.5
CN3 CN3A HN3B
80.0
121.0
CN3 CN3B HN3B
80.0
120.5
CN3B CN3 HN3B
30.0
122.0
CN3A CN3 HN3B
30.0
119.0
NICH
CN3 CN8 CN3
125.0
108.0
CN3 CN3 CNS
53.5
108.5
CN8 CN3 CN1A
125.0
124.2
CN3 CNS HN7
55.0
110.1
CN8 CN3 HN3
30.0
116.0
CN8 CN3 HN3B
30.0
122.0
CN3 CN3C NN2
60.0
122.0
CN3C NN2 CN3C
20.0
114.0
CN3C CN3 CN8
43.5
128.0
CN3 CN3C HN3
42.0
119.0
HN3 CN3C NN2
42.0
119.0
CN3C CN3 HN3
42.0
116.0
CN3C NN2 HN2
39.0
123.0
CN3C CN3 CN1A
5.0
107.8
CN3B CN3 CN8
53.5
108.5
CN3B NN2 HN2
32.0
117.4
Phosphate
P ON2 P
15.0
140.0
-40.0
2.800

P2
P2
CN9
ON2
ON2
ON3

ON2
ON2
ON2
P2
P2
P2

P
P2
P2
ON2
ON3
ON3

15.0
15.0
20.0
80.0
98.9
104.0

140.0
140.0
120.0
104.3
111.6
120.0

-40.0
-40.0
35.0

2.800
2.800
2.33

Table S17. Dihedral Angle Parameters. Equilibrium dihedral angles in degrees force
constants are given in kcal/mol/radian.
Dihedral
NIC+/NICH
CN3 NN2 CN3B
HN2 NN2 CN3B
HN3B CN3 CN3A
HN3B CN3 CN3B
NN2 CN3B CN3
CN3 CN1A CN3
CN1A CN3 CN3B
CN1A CN3 CN3A
CN3 CN1A CN3
CN1A CN3 CN3
CN3A CN3 CN1A
CN3B CN3 CN1A
CN3A CN3 CN1A
CN3A CN3 CN1A
CN3B CN3 CN1A
CN3B CN3 CN1A
CN3 CN3A CN3
CN3 CN3A CN3
NN2 CN3B CN3
CN3B NN2 CN3B
X CN3 CN3A
X CN3 CN3B
X CN3 CN8
X NN1 CN1A
X NN2 CN3B
NICH
CN8 CN3 CN1A
CN8 CN3 CN1A
C,N8 CN3 CN1A
CN8 CN3 CN1A
CN8 CN3 CN1A
CN8 CN3 CN1A
CN3C CN3 CN1A
CN3C CN3 CN1A
CN3C CN3 CN1A
CN3C CN3 CN1A
HN2 NN2 CN3C
CN3 NN2 CN3C
NN2 CN3C CN3

K

n



HN3B
HN3B
HN3B
HN3B
HN3B
HN3B
HN3B
HN3B
HN3
HN3
ON1
ON1
NN1
NN1
NN1
NN1
CN1A
CN3B
CN3A
CN3
X
X
X
X
X

7.0
3.0
2.0
1.0
7.0
7.0
1.0
5.0
7.0
1.0
2.38
2.38
0.35
0.62
0.35
0.62
3.0
6.0
7.0
4.0
1.0
1.0
1.0
2.5
1.0

2
2
2
2
2
2
2
2
2
2
2
2
1
2
1
2
2
2
2
2
2
2
3
2
2

180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
0.0
0.0
0.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0
180.0

ON1
ON1
ON1
NN1
NN1
NN1
ON1
ON1
NN1
NN1
HN3
HN3
HN3

1.00
1.00
0.40
0.50
0.35
0.40
0.30
1.95
1.10
1.95
4.0
7.0
7.0

2
3
6
2
3
6
1
2
1
2
2
2
2

180.0
0.0
0.0
180.0
180.0
0.0
0.0
180.0
180.0
180.0
180.0
180.0
180.0

CN8 CN3
CN3C CN3
CN1A CN3
X CN3
X NN2
CN3C NN2
Phosphate
P2 ON2
P2 ON2
P ON2
P ON2
P2 ON2
P2 ON2
P ON2
P ON2
P ON2
P ON2
P ON2
P ON2
P2 ON2
P2 ON2
P2 ON2
P2 ON2

CN3C
CN8
CN3C
CN3C
CN3C
CN3C

NN2
CN3
NN2
X
X
CN3

0.1
4.0
2.5
0.1
0.1
0.1

2
3
2
2
2
2

180.0
180.0
180.0
180.0
180.0
180.0

P
P
P2
P2
P2
P2
P
P
P
P
P2
P2
P
P
P2
P2

ON2
ON2
ON2
ON2
ON2
ON2
ON2
ON2
ON3
ON3
ON3
ON3
ON3
ON3
ON3
ON3

0.03
0.03
0.03
0.03
0.03
0.03
0.03
0.03
0.10
0.03
0.10
0.03
0.10
0.03
0.10
0.03

2
3
2
3
2
3
2
3
2
3
2
3
2
3
2
3

0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0

Table S18. Improper Dihedral Angle Parameters Equilibrium. Improper dihedral angles
in degrees and force constant in are given in kcal/mol - A.
Improper Dihedral
NIC+/NICH
HN3B
X
HN3B
X
HN3B
X
HN2 CN3
HN1 HN1
ON1
X
HN7 CN3
NICH
HN3
X

K

o

X
X
X
CN3B
CNIA
X
CN3

CN3
CN3A
CN3B
NN2
NN1
CNIA
CN8

15.0
13.0
13.0
50.0
-5.0
40.0
18.0

0.0
0.0
0.0
0.0
0.0
0.0
0.0

X

CN3C

53.0

0.0

Table S19. Nonbonded Parameters. Epsilon is in kcal/mol and Rmin are in
Atom

Rmin/2
NIC+/NICH
CN3A
-0.180
1.80
CN3B
-0.180
1.80
CN1A
-0.070
2.00
HN3B
-0.046
0.90
HN3N
-0.046
0.90
NICH
CN3C
-0.180
1.80
phosphate
P2
-0.585
2.15
Previously developed parameters used in this study are
published elsewhere.2d

Supplemental Figures
Figure S1. Adiabatic energy surface for the amide rotation in NIC+ for the empirical (F),
HF/6-31G(d) (B) and MP2/6-31G(d)//6-31G(d) (E) levels of theory. Energies in
kcal/mol.
Figure S2. Adiabatic energy surface for the amide rotation in NICH for the empirical (F),
HF/6-31G(d) (B) and MP2/6-31G(d)//6-31G(d) (E) levels of theory. Energies in
kcal/mol.
Figure S3. Angle variations versus amide dihedral rotation angle for NIC+ at the
empirical and HF/6-31G(d) levels of theory. Data is included for the C10-C9-C12 (emp.
(J), HF/6-31G(d), (E)), C7-C9-C12 (emp. (B), HF/6-31G(d), (G)), and C9-C12-N14
(emp. (F), HF/6-31G(d), (A)) angles.
Figure S4. Angle variations versus amide dihedral rotation angle for NICH at the
empirical and HF/6-31G(d) levels of theory. Data is included for the O13-C9-C12 (emp.
(J), HF/6-31G(d), (E)), C7-C9-C12 (emp. (B), HF/6-31G(d), (G)), and C9-C12-N14
(emp. (F), HF/6-31G(d), (A)) angles.

Figure S1

6

J
5

B

4

B
H
J

Potential Energy, kcal/mol

3

H

B

2
B

B

J
B

B

J

B

H

H
B

B
B

B

J B
H

1

B

B
B

0
0

30

60

90

C10-C9-C12-N14 Dihedral Angle, degrees

120

150

B H
J

B

H
JB

180

Figure S2

9
B

8

B

F
F

7

E

E

B

6

F

F

5

B
F

4

E

Potential Energy, kcal/mol
F

E

F

F

B
E

F

3
B
2

E
F

B

F

F

F
F

FE

F

1

F
B
E
F

0
0

30

60

90

C10-C9-C12-N14 Dihedral Angle, degrees

120

150

F
E
EB
B
180

Figure S3

130
J

J

J

J

J

J

Ñ
J

J

J

J

Ñ

J

E

J

125

J
Ñ
E

J
J
J

E

Angle, degrees

J

Ñ
E

120

F

F

A

F

F

F

115
B

B

B

F

F
A

B

Ñ

B

E
Ñ
F

B
J

B

Ñ
A

J
B

B

B

B

A
F

F

F

F
A

F

F
B

F
B
A

B
F

F

F

B

B

A
E
E

B
B

F

B

110
0

30

60

90

C10-C9-C12-N14 Dihedral Angle, degrees

120

150

180

Figure S4

124
E

B
B

E

B

B

B

B
F

A
J

J

J

F
J

F

118

J

B

Ñ
J

Ñ

J

J

EE

E

J

J
Ñ

F

F

J

J

B
J

ÑÑ
B
J

F

AA
F

J

J

Ñ

F
F

A

F
Ñ

Ñ
116

J

J

B
E

B

J

F

B

B

B
120

B

B

B

E

Angle, degrees

B

E

B
E

122

E

Ñ

F
F

Ñ
F

F

F

F
A

F

A

F
A

A

A
A
114
0

30

60

90

C10-C9-C12-N14 Dihedral Angle, degrees

120

150

180