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

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Supplemental Material

Pavelites, Bash, Gao and MacKerell, Jr. ÒA Molecular Mechanics Force Field for NAD+_,

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[image:2.612.88.559.84.718.2]

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

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013-C12-C9-C10 8.4±12.2 16.8 0.5

H15-N14-C12-C9 9.6 0.1

H16-N14-C12-C9 172.7 180.0

N2-C3-C5-C7 1.4±1.2 0.0 0.0

C3-C5-C7-C9 1.6±0.9 0.7 0.0

C5-C7-C9-C10 1.2±1.4 1.2 0.0

C7-C9-C10-N2 0.9±2.1 1.1 0.0

C9-C10-N2-C3 1.1±1.3 0.5 0.0

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[image:4.612.87.558.95.713.2]

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

Bond FIXDARa FIXDARb FIXCUK CHARMM HF/6-31G(d)

N2-H1 1.470** 1.467** 1.468** 1.015 0.992

N2-C3 1.369 1.408 1.383 1.371 1.392

C3-H4 0.950 1.095 1.073

C3-C5 1.328 1.328 1.324 1.326 1.320

H6-C5 1.094 1.090 1.075

C5-C7 1.510 1.514 1.479 1.512 1.511

H8-C7 0.950 1.111 1.092

H17-C7 1.572** 1.111 1.090

C7-C9 1.524 1.524 1.527 1.539 1.519

C9-C10 1.352 1.357 1.361 1.353 1.334

C10-H11 1.090 1.094 1.072

C10-N2 1.392 1.354 1.359 1.381 1.365

C9-C12 1.495 1.496 1.456 1.531 1.482

C12-013 1.246 1.238 1.253 1.228 1.206

N14-C12 1.332 1.342 1.334 1.356 1.361

H15-N14 0.949 0.997 0.992

H16-N14 0.950 0.998 0.995

Angle FIXDARa FIXDARb FIXCUK CHARMM HF/6-31G(d)

N2-C3-C5 123.5 121.3 122.4 120.7 122.2

C3-C5-C7 123.3 124.0 123.2 123.7 122.9

C5-C7-C9 108.1 108.6 109.5 109.6 110.5

C7-C9-C10 123.2 123.2 119.9 119.9 121.6

C9-C10-N2 121.7 121.7 123.4 123.1 123.4

C10-N2-C3 118.2 118.2 118.1 118.0 119.0

H1-N2-C3 120.3** 119.8 119.4

H4-C3-C5 118.8 118.8 122.6

H6-C5-C7 118.4 117.4 118.2

H8-C7-C9 115.6** 111.7 110.6

H17-C7-C9 105.6 107.8 111.1

H8-C7-H17 104.2** 108.8 105.7

H11-C10-C9 118.3 119.1 120.1

C7-C9-C12 122.6 122.7 120.1 122.2 122.3

C9-C12-013 119.7 120.4 120.3 122.1 123.2

C9-C12-N14 118.3 118.2 121.0 115.7 116.1

013-C12-N14 122.0 121.4 118.6 122.1 120.7

C12-N14-H15 120.0 121.8 121.9

C12-N14-H16 120.0 115.9 116.1

Dihedral Angle FIXDARa FIXDARb FIXCUK CHARMM HF/6-31G(d)

H1-N2-C3-H4 -0.5** 5.6 -12.5

N2-C3-C5-H6 173.6 -170.4 179.1

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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

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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 Diphosphate Triphosphate CHARMM Ab Initio

r1 C1-O11 1.438±0.030 1.463± 0.085 1.428 1.394

r2 P1-O11 1.597±0.021 1.605± 0.120 1.602 1.670

r3 O12-P1 1.606±0.040 1.564± 0.043 1.568 1.561

r4 O13-P1 1.499±0.025 1.478± 0.048 1.488 1.499

r5 O14-P1 1.475±0.035 1.525± 0.039 1.486 1.498

r6 P2-O12 1.620±0.020 1.673±0.055 1.647 1.740

r7 O22-P2 1.514±0.057 1.559±0.060 1.529 1.512

r8 O23-P2 1.499±0.058 1.464± 0.037 1.527 1.518

r9 O24-P2 1.514±0.080 1.599±0.075 1.528 1.515

r10 C1-H11 1.108 1.096

r11 C1-H12 1.117 1.093

r12 C1-H13 1.115 1.084

r2r6 r2+r6/2 1.609±0.021 1.639±0.093 1.623 1.705

r4r5 r4+r5/2 1.487±0.030 1.502±0.044 1.487 1.498

r789 r7+r8+r9/3 1.509±0.066 1.541±0.059 1.528 1.515 r479 r4+r5+r7+r8+r9/5 1.500±0.052 1.525±0.054 1.512 1.508 Ang1e Internal Coord Diphosphate Triphosphate CHARMM Ab Initio

a1 P1-O11-C1 119.8±4.5 122.0±3.6 120.2 118.3

a2 O12-P1-O11 99.4±3.6 102.1±4.1 107.7 103.3

a3 O13-P1-O11 111.2±1.7 108.6±2.2 105.9 103.5

a4 O14-P1-O11 107.9±1.0 108.9±7.9 108.2 105.7

a5 P2-O12-P1 131.5±1.6 134.0±1.7 144.4 152.5

a6 O22-P2-O12 103.8±4.8 104.9±3.1 104.9 104.4

a7 O23-P2-O12 107.1±5.5 107.0±3.0 107.0 104.4

a8 O24-P2-O12 107.7±4.5 100.2±3.1 105.5 102.1

a9 H11-C1-O11 110.3 107.4

a10 H12-C1-O11 112.3 110.7

a11 H13-C1-O11 109.2 112.1

a3a4 a3+a4/2.0 109.6±1.4 108.8±5.8 107.1 104.6

a678 a6+a7+a8/3.0 106.2±4.9 104.0±3.1 105.8 103.7

a368 a3+a4+a6+a7+a8/5.0 107.5±3.9 105.9±4.4 106.3 104.1 Dihedra1 Internal Coord Diphosphate Triphosphate CHARMM Ab Initio

d1 O12-P1-O11-C1 See See 63.9 70.3

d2 O13-P1-O11-C1 Table S4 Table S4 -179.7 -174.4

d3 O14-P1-O11-C1 entries entries -57.5 -49.9

d4 P2-O12-P1-011 1-6 7-10 -47.2 -72.6

d5 O22-P2-O12-P1 -152.6 -92.5

d6 O23-P2-O12-P1 -32.4 28.7

d7 O24-P2-O12-P1 88.2 147.9

d8 H11-C1-O11-P1 -149.5 -167.8

[image:6.612.88.561.104.711.2]

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[image:8.612.90.560.85.321.2]

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

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[image:9.612.96.518.114.703.2]

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

Mode Ab initio CHARMM

Freq Assignment Freq Assignment

1 59.0 tAMIDE (100) 55.8 tAMIDE (111)

2 153.7 wAMIDE (56) 144.1 wAMIDE (78)

tRING (35) tRING (18)

3 318.9 dAMIDE (60) 215.6 dAMIDE (87)

dC=O(15)

4 337.1 tNH2 (48) 353.1 tNH2 (83)

wNH2 (33)

5 356.2 rC=O(32) 398.4 tRING (62)

sC9C12 (25) dRING (24)

6 386.0 tRING (66) 413.2 tRING (45)

sC9C12 (17) dRING (16)

7 400.3 tRING (84) 444.5 tRING (69)

8 474.9 rC=O (19) 516.8 wN2H (35)

tRING (17) wC3H (27)

WC10H (22)

9 514.5 dC=O (42) 532.4 dC=O (28)

sC12N14 (22) rC=O (20)

10 566.3 wNH2 (55) 570.3 wNH2 (72)

tNH2 (28)

11 613.9 dRING (87) 658.8 rC=O (25)

dC=O (23) dRING (18)

12 648.1 tRING (61) 678.5 tRING (65)

dRING (19) wN2H (19)

13 677.8 tRING (43) 713.3 dRING (49)

dRING (26) wC=O (16)

14 746.5 wC=O (68) 732.2 wC=O (68)

dRING (19)

15 801.3 rNH2 (23) 779.7 wC10H (42)

wC3H (26)

16 836.3 wC5H (44) 837.3 dRING (38)

wC3H (23) sN2C3 (16)

17 988.4 wC10H (80) 878.0 wC5H (38)

wC7H (22) wC3H (21)

18 999.5 wC3H (61) 964.1 wN2H (39)

wC7H (15) WC10H (25)

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19 1008.4 dRING (32) 970.1 dC5H (23)

sC5C7 (23) sN2C3 (22)

sC3C5 (17)

20 1016.1 dRING (30) 1007.9 rNH2 (74)

sN2C3 (27)

21 1040.5 wC7H (60) 1024.1 dRING (47)

wC5H (37) sC5C7 (15)

22 1085.9 sC5C7(29) 1066.2 wC7H (42)

sC10N2 (28) wC5H (35)

23 1124.6 sC3C5 (18) 1073.3 sC10N2 (28)

sC9C10 (15) sC5C7 (23)

sC3C5 (20)

24 1142.9 sC3C5 (23) 1120.9 dC5H (42)

sC7C9 (21) dRING (24)

sN2C3 (16)

25 1200.2 dC5H (28) 1208.2 dN2H (25)

sC10N2 (22) sN2C3 (17)

26 1270.0 dN2H (32) 1273.7 dN2H (25)

dC3H (24) dC10H (18)

27 1317.8 dC10H (21) 1479.3 scNH2 (28)

dC7H (21) sC9C12 (25)

28 1323.4 rNH2 (23) 1554.5 dN2H (19)

dC7H (20) sN2C3 (18)

sC10N2 (16)

29 1429.7 sC12N14 (39) 1569.1 sC9C10 (33)

sC7C9 (25)

30 1468.8 dC3H (20) 1604.8 sC5C7 (20)

dC5H (20) sC3C5 (18)

31 1554.0 dN2H (27) 1665.0 scNH2 (55)

sC12N14 (19)

32 1613.1 sC7C9 (20) 1948.6 sC=O (64)

scNH2 (18) sC12N14 (21)

33 1647.2 sC3C5 (20) 1997.4 dC3H (36)

sC9C10 (17) dC10H (29)

dC7H (21)

34 1674.0 scNH2 (53) 2046.9 dC3H (49)

dN2H (19) dC10H (28)

35 1966.7 sC=O (71) 2080.7 dC7H (51)

wN2H (29) dC10H (26)

36 3067.2 sC7H (91) 2993.2 sC5H (64)

sC7H (21)

37 3084.6 sC5H (77) 2995.2 sC7H (77)

38 3100.2 sC3H (84) 2997.8 sC3H (90)

39 3102.7 sC10H (99) 2999.2 sC10H (70)

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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

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[image:12.612.94.517.116.715.2]

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

1 64.7 tAMIDE (69) 99.8 wNH2 (84)

tRING (31)

2 98.4 tRING (63) 127.3 rC=O (39)

tAMIDE (27) tAMIDE (29)

wNH2 (20) tRING (16)

3 209.3 dAMIDE (65) 203.0 tRING (87)

dC=O (16)

4 221.9 wAMIDE (52) 266.3 tNH2 (66)

wN2H (19) scC7H (19)

5 274.0 wN2H (60) 289.4 rC=O (56)

tNH2 (20) tAMIDE (17)

dC=O (-17)

6 283.1 tNH2 (65) 368.9 tRING (56)

wN2H (16)

7 355.3 dRING (39) 406.4 wAMIDE (46)

sC9CI2 (27) scNH2 (19)

rC=O (18) tRING (18)

8 421.7 tRING (101) 490.3 scNH2 (34)

dRING (27) sC9CI2 (20)

9 465.3 rC=O (31) 515.5 tRING (30)

dC=O (23) wC=O (27)

dAMIDE (16)

10 523.2 tRING (100) 579.0 tAMIDE (23)

scC7H (16)

11 537.6 wNH2 (84) 609.7 dRING (34)

wC7H (23)

12 565.0 dRING (69) 639.2 dRING (27)

dC=O (19) scNH2 (23)

13 605.1 dRING (42) 684.6 wN2H (28)

rC=O (21) dRING (28)

dC=O (15)

14 722.4 dRING (24) 715.6 sC9C10 (35)

sC7C9 (21) wC=O (18)

sC9CI2 (16)

15 736.9 wC5H (44) 774.6 wC5H (74)

wC3H (23) tRING (16)

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sC9C10 (34) wC=O (16)

17 902.1 sC5C7 (64) 835.7 sC5C7 (47)

18 958.9 dRING (33) 889.3 dRING (34)

sN2C3 (22) sC9C10 (31)

sC7C9 (19)

19 972.3 wC3H (58) 979.3 wC3H (24)

wC5H (28) sN2C3 (17)

20 977.9 wC10H (31) 995.9 wC10H (26)

wC3H (18) wC3H (26)

21 982.4 wC10H (55) 1004.7 rNH2 (49)

sNH2 (45) scNH2 (-16)

22 1011.4 tC7H (64) 1034.4 DRING (46)

sC9C12 (24) sC9C10 (-20)

23 1077.4 rNH2 (35) 1092.5 wC3H (23)

sC12N14 (35) wN2H (17)

WC10H (16)

24 1100.5 dRING (32) 1142.8 wAMIDE (41)

rNH2 (25) sC12N14 (29)

sC9C12 (16)

25 1150.0 sC10N2 (32) 1176.1 wN2H (34)

wC3H (27) wC10H (22)

26 1206.4 dC3H (26) 1218.0 dN2H (23)

dC5H (24) dC3H (21)

sC10N2 (16)

27 1215.1 wC7H (77) 1327.9 tC7H (50)

sC9C12 (34) dAMIDE (24) tRING (23) wC7H (-18)

28 1303.4 dC10H (40) 1388.7 sC9C12 (38)

rC7H (32) scNH2 (24)

tC7H (21) dC10H (16)

29 1349.3 sC12N14 (23) 1415.5 dC5H (37)

rC7H (22) tC7H (-18) dC3H (18)

30 1382.6 rC7H (28) 1476.6 tC7H (63)

sC7C9 (18) rC7H (-40)

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dRING (19)

31 1402.3 dC3H (43) 1531.2 rC7H (41)

dC5H (28) wC7H (34)

32 1494.5 dN2H (57) 1551.2 rC7H (22)

sC10N2 (16) dRING (17)

33 1498.2 scC7H (97) 1558.3 dN2H (43)

34 1619.3 scNH2 (78) 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)

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[image:15.612.93.525.110.710.2]

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

1 28.8 tP2-O12 (150) 37.6 tP2-O12 (83)

tP1-O12 (-49)

2 49.3 tP1- O12 (151) 52.0 tP1-O12 (94)

tP2-O12 (-47) tP2-O12 (18)

3 86.8 dP-O-P (80) 95.5 dP-O-P (97)

tP1-O11 (27) sP-O (16)

4 129.9 tP1-O11 (62) 110.,5 tP1-O11(54)

dP-O-P (25) tCH3 (43)

5 162.6 tCH3 (98) 163.0 tCH3 (56)

tP1-O11 (41)

6 210.5 dP-O-C (51) 234.3 sP-O (36)

scO-P-O (26) dP-O-C (29)

scO-P-O (24)

7 248.3 sP-O (104) 250.5 sP-O (33)

dPO3as (23) scO-P-O (16) dP-O-C (16)

8 281.2 dPO3as' (50) 312.1 dPO3as' (55)

rO=P=O (23) rO=P=O (22)

9 292.4 dPO3as (43) 319.6 dPO3as (28)

dP-O-C (21) scO-P-O (19)

10 372.1 scO=P=O (31) 430.0 wO=P=O (29)

scO-P-O (20) scO=P=O (19)

dPO3as (19)

11 389.9 rO=P=O (45) 461.4 rPO3 (30)

dPO3as' (18) scO-P-O (26)

dPO3as (17)

12 455.7 tO=P=O (29) 473.3 rPO3' (59)

wO=P=O (22) rO=P=O (19)

rPO3' (16)

13 493.0 rPO3' (38) 487.6 rPO3' (47)

rPO3 (25)

14 508.7 rPO3 (37) 500.5 dPO3sym (26)

dPO3as (17)

15 516.7 dPO3sym (57) 509.8 dPO3sym (32)

scO=P=O (21) wO=P=O (19)

16 546.4 tO=P=O (33) 533.8 scO=P=O (37)

(16)

17 586.6 dPO3sym (32) 635.6 scO=P=O (22)

sP-0 (20) sP-O (22)

scO=P=O (19)

18 684.4 sP-O (58) 730.4 sP-O (37)

wO=P=O (29) wO=P=O (28)

sP=O (20)

19 877.9 sP=O (65) 887.2 sP=O (65)

sP-O (35) sP-O (26)

20 957.9 sP=O (67) 1020.3 sP=O (45)

sP-O (30) sP-O (32)

21 1043.0 sP=O (65) 1054.1 sC-O (67)

sP-O (31)

22 1067.0 sP=O (92) 1057.9 dCH3as' (43)

dCH3as (31) rCH3' (17)

23 1080.9 sP=O (94) 1124.5 sP=O (70)

sP-O (30)

24 1101.1 sC-O (84) 1143.8 SP=O (91)

25 1145.7 sP=O (93) 1146.6 sP=O (90)

26 1170.0 dCH3as'(67) 1192.7 dCH3as (46)

dCH3as (29) dCH3a.s' (22)

rCH3' (15)

27 1204.7 dCH3as (61) 1256.9 sP=O (91)

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)

(17)

[image:17.612.91.523.85.416.2]

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

ab initio Model 1 Model 2

NIC+ trans

Total 8.26 7.77 7.17

x -6.66 -6.09 -5.78

y -4.62 -4.76 -4.13

z 1.64 0.77 0.98

NIC+_cis

Total 6.98 6.17

x 6.57 6.11

y 1.77 0.84

z 1.56 -0.01

ab initio emp

NICH trans

total 4.82 3.65

x -2.50 -1.23

y -4.02 -3.40

z 0.94 -0.51

NICH cis

Total 3.72 2.18

x 3.21 1.10

y 1.83 1.88

(18)

[image:18.612.90.524.114.382.2]

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 a b c Total Energy Lattice Energy GRMS

VDWElec Model 1

exper 10-073 15-839 17.821

10-9-7 10.349 15.477 17.311 -554.94 -36.96 -215.61 0.00053 13-12-10 9.984 15.418 17-887 -595.25 -45.10 -202.82 0.04190 16-15-13 10.130 15.452 17.679 -614.18 -46.36 -201.01 0.00071 19-18-16 10.318 15.428 17.654 -624.51 -47.63 -198.40 0.00057 22-21-19 10.122 15.462 17.994 -629.21 -47.21 -196-06 0.00068 25-24-22 10.112 15.346 17.918 -633.75 -48.68 -192.96 0.00027 Model 2

exper 10.073 15.839 17.821

10-9-7 9.684 15.274 18.658 -542.84 -37.25 -226.71 0.00084 13-12-10 9.862 15.581 17.964 -587.27 -44.14 -214.97 0.00063 16-15-13 9.906 15.446 18.264 -604.96 -47.22 -209.56 0.00048 19-18-16 10.088 15.352 17.862 -614.57 -47.08 -204.73 0.00042 22-21-19 9.926 15.473 18.170 -620.91 -47.94 -202.44 0.00054 25-24-22 9.924. 15.352 18.188 -624.53 -47.83 -200.82 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 exper model 1 model 2

min dyn ave rms min dyn ave rms

NNI - AO2 3.03 3.36 3.58 0.21 3.33 3.45 0.21

NC6 - AO2 3.33 3.64 3.27 0.17 3.57 3.25 0.16

NC5 - AC5 3.43 3.98 3.64 0.21 4.06 3.44 0.21

NC4 - OH2 3.43 3.30 3.83 0.21 3.17 4.04 0.24

NC3 - AO2 3.44 3.24 3.54 0.22 3.11 3.24 0.14

NC2 - AO2 3.10 3.12 3.66 0.20 3.07 3.29 0.20

NC2 - AO5' 3.46 3.33 3.24 0.19 3.21 3.14 0.18

NC2 - OH2 3.16 2.94 3.50 0.18 2.88 3.29 0.19

NO7 - AC8 3.14 3.22 3.21 0.18 3.11 3.09 0.34

NO7 - OH2 2.74 3.15 4.11 0.42 3.13 3.36 0.39

NN7 - OH2 2.86 2.75 3.20 0.18 2.78 3.13 0.19

Aver Diff 0.08 0.33 0.03 0.15

[image:18.612.90.524.480.704.2]

(19)

(20)

[image:20.612.86.555.94.726.2]

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

Dihedral Exper Minimized Diff Dynamics

aver RMS fluc

AP -O3 -NP -NO5' 72.5 52.5 -20.0 54.8 19.5 -17.7

AC5'-AO5'-AP -O3 -124.6 -125.2 -0.6 -131.1 17.6 -6.5

AC5'-AO5'-AP -AO2 122.5 120.5 -2.0 115.2 17.7 -7.3

AP-O3-NP-NO1 -171.7 167.7 -20.6 170.2 19.5 -18.1

AP-O3-NP-NO2 -37.8 -71.7 -34.0 -69.1 32.3 -31.4

AP -AO5'-AC5'-AC4' 162.8 164.7 1.9 161.0 9.1 -1.8

A05'-AC5'-AC4'-AC3' 48.0 46.4 -1.6 49.9 12.3 1.9

AC5'-AC4'-AC3'-AO3' 141.6 151.8 10.2 150.0 9.7 8.4

AO4'-AC3'-*AC4-AC5' -121.5 -121.4 0.0 -121.0 3.6 0.5 AC2'-AC4'-*AC3-AO3' -120.5 -120.4 0.1 -121.3 3.3 -0.8 AC4'-AC3'-AC2'-AC1' -35.4 -38.5 -3.1 -38.9 4.8 -3.5

AC3'-AC2'-AC1'-AN9 153.0 146.9 -6.1 149.2 5.5 -3.8

AO4'-AC1'-AN9 -AC4 -121.4 -144.8 -23.4 -145.3 25.3 -23.9 AC1'-AC4 -*AN9-AC8 -175.1 -176.7 -1.7 -178.3 7.6 -3.2

AC4-AN9-AC8-AN7 2.0 -3.2 -5.2 -1.8 5.5 -3.8

AC8-AN9-AC4-AC5 -0.6 1.4 2.0 0.4 3.7 1.1

AC8-AN7-AC5-AC6 175.5 177.1 1.6 178.7 6.1 3.1

AN7 -AC5 -AC6 -AN1 -175.9 -178.2 -2.2 -178.5 5.8 -2.6

AC5 -AC6 -AN1 -AC2 1.1 -0.1 -1.2 -1.1 5.8 -2.2

AN9 -AC5 -*AC4-AN3 179.7 178.4 -1.3 178.7 4.6 -1.0

AC5 -AN1 -*AC6-AN6 178.1 179.8 1.7 179.0 5.1 0.9

AC1'-AC3'-*AC2-AO2' -123.4 -124.8 -1.4 -123.4 4.4 0.0 NC5'-NO5'-NP -NO2 -167.5 -157.5 10.0 -155.3 15.6 12.2 NP -NO5'-NC5'-NC4' 179.0 146.0 -33.0 149.8 29.9 -29.2

N05'-NC5'-NC4'-NC3' 46.5 54.7 8.2 56.3 11.6 9.8

NC5'-NC4'-NC3'-NC2' -151.9 -157.0 -5.1 -155.7 5.9 -3.8

NC4'-NC3'-NC2'-NC1' 43.1 37.7 -5.4 36.0 8.7 -7.1

NC3'-NC2'-NC11'-NO4' -31.1 -25.7 5.4 -24.9 9.0 6.2

NC2'-NC1'-NO4'-NC4' 7.0 3.6 -3.5 4.1 7.8 -3.0

NC3'-NC2'-NC1'-NN1 93.1 97.1 4.1 98.2 8.8 5.2

NC2'-NC1'-NN1 -NC2 70.7 73.2 2.5 72.1 7.9 1.4

NC1'-NN1 -NC2 -NC3 -177.5 176.3 -6.2 177.9 9.1 -4.6

NN1 -NC2 -NC3 -NC4 -3.7 -1.7 2.0 -1.7 5.4 2.0

NC2 -NC3 -NC4 -NC5 1.9 1.9 -0.1 1.5 4.9 -0.5

NC3 -NC4 -NC5 -NC6 1.3 -0.7 -2.0 -0.3 5.7 -1.7

NC4 -NC5 -NC6 -NN1 -2.5 -0.9 1.6 -0.7 5.8 1.8

NC5 -NC6 -NN1 -NC2 0.5 1.1 0.7 0.5 5.6 0.1

NN1 -NC2 -NC3 -NC7 179.4 177.3 -2.1 178.3 7.6 -1.1

NC2 -NC3 -NC7 -NO7 -9.2 14.0 23.2 16.9 28.1 26.1

(21)

NP -O3 -AP -AO5' 132.5 164.6 32.1 161.1 29.6 28.6

O3 -NP -NO5'-NC5' 79.1 78.7 -0.4 81.3 9.9 2.2

RMS difference 12.8 12.7

(22)

[image:22.612.90.558.94.711.2]

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

Interaction pair exper Minimized Diff Dynamics Diff Aver rms flu

NAD1 NC6 -NAD1 N05' 3.23 3.52 0.30 3.54 0.23 0.31

NAD1 AN7 -NAD1 NO1 3.22 3.73 0.52 3.76 0.14 01.54

NAD1 AC8 -NAD1 O3 3.45 3.23 -0.21 3.35 0.13 -0.10

NAD1 AC8 -NAD1 NO1 3.41 4.07 0.65 4.02 0.17 0.60

NAD1 AO1 -NAD1 NO2 2.95 2.76 -0.19 2.76 0.11 -0.19

NAD1 AO5'-NAD1 AC2' 3.22 3.06 -0.16 3.13 0.10 -0.08

NAD1 AO2'-WATX OH2 2.66 2.71 0.05 2.78 0.12 0.12

NAD1 NN1 -C009 AO2 3.03 3.35 0.32 3.28 0.15 0.25

NAD1 NC6 -C009 AO2 3.33 3.59 0.26 3.49 0.23 0.16

NAD1 NC5 -C020 AC5 3.43 4.07 0.65 4.08 0.22 0.65

NAD1 NC4 -C020 OH2 3.43 3.15 -0.28 3.21 0.13 -0.22

NAD1 NC3 -C009 AO2 3.44 3.10 -0.35 3.27 0.25 -0.17

NAD1 NC2 -C009 AO2 3.10 3.07 -0-03 3.14 0.19 0.03

NAD1 NC2 -C009 AO5' 3.46 3.23 -0.24 3.25 0.16 -0.21

NAD1 NC2 -C020 OH2 3.16 2.89 -0.27 2.98 0.19 -0.18

NAD1 AN7 -C008 OH2 3.38 3.30 -0.08 3.27 0.28 -0.11

NAD1 AN9 -C020 NO4' 3.19 3.00 -0.20 3.09 0.15 -0.10

NAD1 AN1 -C003 NC2' 3.44 3.73 0.29 3.87 0.22 0.42

NAD1 AN1 -C003 NO2' 2.77 2.93 0.15 3.04 0.16 0.26

NAD1 AC2 -C003 NO3' 3.38 3.12 -0.25 3.28 0.15 -0.10

NAD1 AN3 -C020 NO4' 3.16 3.87 0.71 3.71 0.18 0.54

NAD1 AC4 -C020 NO4' 3.15 3.31 0.16 3.32 0.16 0.17

NAD1 AN6 -C003 NO2Õ 3.41 3.19 -0.22 3.40 0.17 -0.01

NAD1 AN6 -C008 AO2' 3.09 3.02 -0.07 3.12 0.15 0.03

NAD1 AN6 -C008 AO3' 2.91 2.95 0.04 3.09 0.22 0.18

NAD1 AO1 -C020 AN7 3.14 3.16 0.01 3.06 0.10 -0.08

NAD1 AO1 -C020 AN6 2.89 2.73 -0.15 2.79 0.12 -0.10

NAD1 AO1 -C020 NO1 3.25 3.41 0.15 3.46 0.19 0.20

NAD1 NO2 -C020AN7 3.38 3.71 0.33 3.85 0.21 0.46

NAD1 NO2 -C020 NO1 3.13 3.62 0.49 3.67 0.13 0.53

NAD1 AO4'-C020 NO4' 2.94 3.08 0.14 3.17 0.16 0.23

NAD1 AO4'-C020 NC6 3.43 2.99 -0.43 3.21 0.18 -0.22

NAD1 AC1'-C015 AO2 3.31 3.35 0.04 3.44 0.13 0.13

NAD1 AC1'-C020 NO4' 3.16 3.31 0.15 3.27 0.12 0.12

NAD1 AO3'-C015 AO2 2.59 2.65 0.06 2.71 0.10 0.12

NAD1 AO3'-C015 NC3' 3.24 3.20 -0.04 3.22 0.10 -0.02

NAD1 AO3'-C015 NO3' 2.70 2.68 -0.01 2.70 0.08 0.00

NAD1 AC5'-C020 NO1 3.48 3.52 0.04 3.64 0.25 0.16

Interactions involving the amide group

(23)

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

(24)

Table S13) Alcohol Dehydrogenase bound NAD experimental and calculated dihedrals. Dihedral angles in degrees.

Dihedral Experimental Dynamics Difference

Aver RMS flu

AP -O3 -NP -NO5' -155.7 -173.8 11.9 -18.1

AC5'-AO5'-AP -O3 -85.4 53.8 10.8 139.2

AC5'-AO5'-AP -AO2 36.5 -178.7 10.8 144.8

AP -O3 -NP -NO1 96.4 75.6 12.4 -20.8

AP -O3 -NP -NO2 -36.5 -61.9 12.6 -25.4

AP -AO5'-AC5'-AC4' -137.7 166.5 14.2 -55.8

AO1 -AP -AO5'-AC5' 163.4 -55.9 11.3 140.8

AO5'-AC5'-AC4'-AC3' 47.5 -64.6 7.8 -112.1

AC5'-AC4'-AC3'-AO3' 103.6 124.8 8.1 21.2

AO4'-AC3'-*AC4-AC5' -11.5 18.4 14.8 29.9

AC4'-AC3'-AC2'-AC1' -17.5 -27.1 5.4 -9.6

AC3'-AC2'-AC1'-AN9 167.5 157.9 10.9 -9.6

AO4'-AC1'-AN9 -AC4 -107.7 -124.8 17.1 -17.1

AC1'-AC4 -*AN9-AC8 -174.4 175.1 8.9 -10.5

AC4 -AN9 -AC8 -AN7 0.6 0.0 4.7 -0.6

AC8 -AN9 -AC4 -AC5 -0.9 0.2 3.9 1.1

AC8 -AN7 -AC5 -AC6 178.1 -180.0 5.4 1.9

AN7 -AC5 -AC6 -AN1 -178.4 -178.5 6.4 -0.1

AC5 -AC6 -AN1 -AC2 -0.5 -1.4 5.6 -0.9

AN9 -AC5 -*AC4-AN3 178.3 -179.9 5.0 1.8

AC5 -AN1 -*AC6-AN6 179.2 179.3 5.2 0.1

AC1'-AC3'-*AC2-AO2' 96.0 126.9 39.6 30.9

NC5'-NO5'-NP -NO2 -55.7 -54.8 9.1 0.9

NP -NO5'-NC5'-NC4' -170.9 -166.1 9.1 4.8

NO5'-NC5'-NC4'-NC3' 52.6 44.7 9.3 -7.9

NC5'-NC4'-NC3'-NC2' -95.0 -93.0 5.0 2.0

NC4'-NC3'-NC2'-NC1' -38.7 -38.1 3.8 0.6

NC3'-NC2'-NC1'-NO4' 45.4 37.5 5.1 -7.9

NC2'-NC1'-NO4'-NC4' -34.8 -22.0 7.0 12.8

NO2'-NC2'-NC1'-NO4' 167.3 160.3 5.1 -7.0

NC3'-NC2'-NC1'-NN1 163.2 156.4 5.1 -6.8

NO3'-NC3'-NC2'-NC1' 83.6 82.0 5.0 -1.6

NC2'-NC1'-NN1 -NC2 140.0 142.1 7.5 2.1

NC1'-NN1 -NC2 -NC3 173.3 166.9 7.6 -6.4

NN1 -NC2 -NC3 -NC4 1.0 0.2 5.7 -0.8

NC2 -NC3 -NC4 -NC5 -0.4 -2.0 5.3 -1.6

NC3 -NC4 -NC5 -NC6 -0.1 2.2 5.2 2.3

NC4 -NC5 -NC6 -NN1 0.0 -0.4 5.4 -0.4

NC5 -NC6 -NN1 -NC2 0.6 -1.4 5.8 -2.0

[image:24.612.83.562.103.721.2]

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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)

(26)

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

Interaction Experiment Dynamics Difference

Average RMS flu

AO4'- CG1 3.29 3.99 0.25 0.70

AC1'- OD1 3.41 3.86 0.29 0.45

AN3 - OD1 3.45 4.02 0.43 0.57

AN6 - NH1 3.03 3.63 0.49 0.60

AO2'- OD1 2.81 2.74 0.16 -0.07

AO3'- CG 3.45 3.56 0.17 0.11

AO3'- OD1 3.46 3.84 0.26 0.38

AO3'- OD2 2.68 2.63 0.10 -0.05

AO3'- NZ 2.77 2.85 0.14 0.08

AC5'- N 3.40 4.64 0.19 1.24

AO1 - NE 2.64 2.73 0.10 0.09

AO1 - CZ 3.23 3.16 0.08 -0.07

AO1 - NH2 3.00 2.71 0.11 -0.29

AO2 - CA 3.17 3.45 0.18 0.28

O3 - CB 3.28 3.38 0.22 0.10

NO1 - N 3.30 3.15 0.25 -0.15

NO1 - CB 3.36 3.61 0.25 0.25

NO1 - NH1 2.83 2.72 0.11 -0.11

NO2 - N 3.22 3.23 0.18 0.01

NO2 - N 2.95 2.95 0.15 0.00

NC5' - O 3.22 3.31 0.19 0.09

NO2' - OG 2.80 2.78 0.10 -0.02

NO2' - NE2 3.30 3.13 0.19 -0.17

NO2' - CD2 3.26 3.09 0.17 -0.17

NC3' - O 3.15 3.46 0.17 0.31

NO3' - NE2 3.15 3.19 0.24 0.04

NO3' - C 3.38 3.51 0.14 0.13

NO3' - O 2.57 2.74 0.13 0.17

NO3' - N 3.09 3.29 0.24 0.20

NC4' - O 3.39 3.68 0.23 0.29

NC5 - SG 3.35 3.37 0.12 0.02

NC4 - OG1 3.44 3.44 0.21 0.00

NC4 - CG2 3.44 3.40 0.15 -0.04

NC2 - O 2.93 3.01 0.14 0.08

NC5 - O1 3.09 3.15 0.18 0.06

NC4 - C1 3.36 3.60 0.24 0.24

NC4 - O1 3.31 3.33 0.18 0.02

Interactions involving the amide group

NC7 - CG2 3.48 3.89 0.22 0.41

[image:26.612.94.560.102.711.2]

(27)

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)

(28)

[image:28.612.90.325.97.398.2]

Table S15. Bond Parameters. Equilibrium bond lengths in and force constants are given in kcal/mol/.

bond type Kb bo

NIC+/NICH

CN1A CN3 302.0 1.480

CN1A NN1 560.0 1.360

CN1A ON1 860.0 1.230

CN3A CN3 450.0 1.360

CN3B CN3 420.0 1.350

CN3B NN2 420.0 1.315

CN3A HN3 350.0 1.09

CN3B HN3 350.0 1.09

CN3A HN3B 350.0 1.09

CN3B HN3B 350.0 1.09

NICH

CN3 CN8 222.5 1.490

CN3C NN2 420.0 1.355

CN3C HN3 374.0 1.09

CN3C CN3 420.0 1.320

Phosphate

ON2 P2 300.0 1.68

(29)

[image:29.612.90.523.82.722.2]

Table S16. Angle Parameters. Equilibrium bond angles are given in degrees and force constants are given in kcal/mol/.

angle type K_ _ K_UB S_o

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

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P2 ON2 P 15.0 140.0 -40.0 2.800

P2 ON2 P2 15.0 140.0 -40.0 2.800

CN9 ON2 P2 20.0 120.0 35.0 2.33

ON2 P2 ON2 80.0 104.3

ON2 P2 ON3 98.9 111.6

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[image:31.612.92.522.107.717.2]

Table S17. Dihedral Angle Parameters. Equilibrium dihedral angles in degrees force constants are given in kcal/mol/radian.

Dihedral K_ n 

NIC+/NICH

CN3 NN2 CN3B HN3B 7.0 2 180.0

HN2 NN2 CN3B HN3B 3.0 2 180.0

HN3B CN3 CN3A HN3B 2.0 2 180.0

HN3B CN3 CN3B HN3B 1.0 2 180.0

NN2 CN3B CN3 HN3B 7.0 2 180.0

CN3 CN1A CN3 HN3B 7.0 2 180.0

CN1A CN3 CN3B HN3B 1.0 2 180.0

CN1A CN3 CN3A HN3B 5.0 2 180.0

CN3 CN1A CN3 HN3 7.0 2 180.0

CN1A CN3 CN3 HN3 1.0 2 180.0

CN3A CN3 CN1A ON1 2.38 2 180.0

CN3B CN3 CN1A ON1 2.38 2 180.0

CN3A CN3 CN1A NN1 0.35 1 180.0

CN3A CN3 CN1A NN1 0.62 2 0.0

CN3B CN3 CN1A NN1 0.35 1 0.0

CN3B CN3 CN1A NN1 0.62 2 0.0

CN3 CN3A CN3 CN1A 3.0 2 180.0

CN3 CN3A CN3 CN3B 6.0 2 180.0

NN2 CN3B CN3 CN3A 7.0 2 180.0

CN3B NN2 CN3B CN3 4.0 2 180.0

X CN3 CN3A X 1.0 2 180.0

X CN3 CN3B X 1.0 2 180.0

X CN3 CN8 X 1.0 3 180.0

X NN1 CN1A X 2.5 2 180.0

X NN2 CN3B X 1.0 2 180.0

NICH

CN8 CN3 CN1A ON1 1.00 2 180.0

CN8 CN3 CN1A ON1 1.00 3 0.0

C,N8 CN3 CN1A ON1 0.40 6 0.0

CN8 CN3 CN1A NN1 0.50 2 180.0

CN8 CN3 CN1A NN1 0.35 3 180.0

CN8 CN3 CN1A NN1 0.40 6 0.0

CN3C CN3 CN1A ON1 0.30 1 0.0

CN3C CN3 CN1A ON1 1.95 2 180.0

CN3C CN3 CN1A NN1 1.10 1 180.0

CN3C CN3 CN1A NN1 1.95 2 180.0

HN2 NN2 CN3C HN3 4.0 2 180.0

CN3 NN2 CN3C HN3 7.0 2 180.0

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CN8 CN3 CN3C NN2 0.1 2 180.0

CN3C CN3 CN8 CN3 4.0 3 180.0

CN1A CN3 CN3C NN2 2.5 2 180.0

X CN3 CN3C X 0.1 2 180.0

X NN2 CN3C X 0.1 2 180.0

CN3C NN2 CN3C CN3 0.1 2 180.0

Phosphate

P2 ON2 P ON2 0.03 2 0.0

P2 ON2 P ON2 0.03 3 0.0

P ON2 P2 ON2 0.03 2 0.0

P ON2 P2 ON2 0.03 3 0.0

P2 ON2 P2 ON2 0.03 2 0.0

P2 ON2 P2 ON2 0.03 3 0.0

P ON2 P ON2 0.03 2 0.0

P ON2 P ON2 0.03 3 0.0

P ON2 P ON3 0.10 2 0.0

P ON2 P ON3 0.03 3 0.0

P ON2 P2 ON3 0.10 2 0.0

P ON2 P2 ON3 0.03 3 0.0

P2 ON2 P ON3 0.10 2 0.0

P2 ON2 P ON3 0.03 3 0.0

P2 ON2 P2 ON3 0.10 2 0.0

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[image:33.612.90.523.96.268.2]

Table S18. Improper Dihedral Angle Parameters Equilibrium. Improper dihedral angles in degrees and force constant in are given in kcal/mol - A.

Improper Dihedral K_ _o

NIC+/NICH

HN3B X X CN3 15.0 0.0

HN3B X X CN3A 13.0 0.0

HN3B X X CN3B 13.0 0.0

HN2 CN3 CN3B NN2 50.0 0.0

HN1 HN1 CNIA NN1 -5.0 0.0

ON1 X X CNIA 40.0 0.0

HN7 CN3 CN3 CN8 18.0 0.0

NICH

HN3 X 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

[image:33.612.91.327.325.492.2]

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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

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[image:35.612.103.507.116.383.2]

Figure S1

B _B

B B B

B B

B

B _B B B J

J

J J H

H