vlfv 7klvmrxuqdolv wkh2zqhu 6rflhwlhv

Electronic Supplementary Information

to

How do hydrophobic nucleobases differ from natural DNA

nucleobases? Comparison of structural features and duplex

properties from QM calculations and MD simulations

Indu Negi,a Preetleen Kathuria,a Purshotam Sharma*a and Stacey D.

Wetmore*b

aComputational Biochemistry Laboratory, Department of Chemistry and

Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh,

160014, India.

bDepartment of Chemistry and Biochemistry, University of Lethbridge,

Lethbridge, Alberta, T1K 3M4, Canada.

*Email: [email protected], [email protected]

Table of Contents

Details of MD simulations…….………………………………..….…......S3-S5

Figure S1: Relative energy as a function of rotation about the glycosidic bond for the natural DNA nucleosides.…………………….…………...…..S6

Figure S2: Structures of syn and anti minima for rotation about the

glycosidic bond in natural nucleosides, obtained from glycosidic torsional

profiles…………………………………………………………………….……S7

Figure S3: Optimized geometries of the hydrophobic base pairs……....S8

Figure S4: Orientation and magnitude of the dipole moments in the hydrophobic and natural nucleobases……………………………………...S9

Figures S5–S8: Relative stacking interaction energies between natural and hydrophobic bases as a function of the angle of rotation.……...………………………………………………………….S10–S13

Figure S9: Frequency of the glycosidic dihedral angle in nucleosides within

the hydrophobic and T:A control base pairs in DNA duplexes…………...S14

Figure S10: Backbone rmsd for DNA oligonucleotides containing a

hydrophobic or T:A control base pair…………………….…….………….S15

Figure S11: The oligonucleotide sequence used to simulate DNA

containing a hydrophobic or T:A control base pair. ………………...…...S16

Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics.This journal is © the Owner Societies 2017

[S2]

Tables S1–S4: Stacking energies as a function of α for stacked

natural:hydrophobic base dimers..………...………..……………….S17–S20

Table S5: Stacking energies as a function of α for stacked natural:natural base dimers..…….…………..…………………………..........................…S21

Table S6: Average base pseudostep parameters, minor groove dimensions DNA bend and base pair width for oligonucleotide containing a hydrophobic or T:A control base pair………………………………………...……………S22

Table S7: Hydrogen-bonding occupancies for the base pairs flanking the

hydrophobic or T:A control pair………………………………….…………S23

Table S8: Average interaction energies and standard deviation for the

hydrophobic or T:A control base pairs in DNA duplexes ..……………...S24

Tables S9–S26: Cartesian coordinates of the anti and syn structures of the hydrophobic and natural bases………………………………...…….S25–S42

Tables S27–S46: Cartesian coordinates of stacked base pairs…S42–S62

Tables S47–S51: Cartesian coordinates of mol2 files for the hydrophobic

bases…………………………………………………………………...S63–S70

[S3]

Details of MD simulations: MD simulations were carried out on a

complementary 11-mer DNA oligonucleotide (5-TCACAXTTCCA-3, 5-

AGTGTYAAGGT-3), where each hydrophobic base pair (5SICS:FEMO,

5SICS:MMO2, 5SICS:NaM and TPT3:NaM) was placed reiteratively at the

X:Y position. Since our quantum mechanical calculations suggest that all

hydrophobic bases prefer an anti orientation about the glycosidic bond,

initial structures for MD simulations were built with the hydrophobic bases

in the anti orientation. Simulations were started with planar mutual

orientations of the opposing hydrophobic bases, which is in synchrony with

a previous MD study that showed the 5SICS:NaM pair adopts a planar

geometry in DNA.1 Partial charges for each modified base were calculated

based on the B3LYP/6-31+G(d,p) optimized geometry using the RESP ESP

charge Derive (RED) server.2 The Antechamber program of AmberTools3

was used to assign AMBER atom types.4 The ff14SB force field,5 which

uses ff99bsc06 parameters for DNA, was used for all simulations, and was

supplemented with additional force field parameters from the General

AMBER Force Field (GAFF)7 as required. Sodium counterions used for

DNA charge neutralization were assigned the Joung and Cheatham force

field parameters.8

Initial DNA structures were prepared using the make-na server

(structure.usc.edu/make-na), which automatically builds nucleic acid

helices for a given sequence using the nucleic acid builder (NAB) script.9

The particle mesh Ewald method was used to approximate the Coulombic

interactions, with a 10 Å cutoff to approximate the nonbonded interactions.

The periodic boundary condition was implemented, bonds involving

hydrogen atoms were constrained using the SHAKE algorithm, and a 2 fs

time step was used throughout the simulation. Energy minimization was

first performed with the DNA held fixed using a force constant of 500 kcal

mol−1 Å−2, during 500 steps of steepest descent and 500 subsequent steps

of conjugate gradient minimization. In the second minimization step, the

entire box containing the DNA, ions and water was energy minimized using

1000 steps of steepest descent and 1500 steps of conjugate gradient

minimization. The system was then heated to 300 K using the Langevin

[S4]

temperature equilibration scheme, with the DNA restrained via a 10 kcal

mol−1 Å−2 force constant, and a 20 ps MD simulation was then performed at

constant volume. This was followed by a 100 ns unrestrained MD simulation

on each system.

The stability of the simulations was analysed using the root-mean-

square deviation (rmsd) with respect to the initial production simulation

frame (Figure S10). Representative structures were obtained by clustering

each MD simulation with respect to the atoms forming the dihedral angles

of the hydrophobic or control base pair (i.e., the 6th and 17th bases; Figure

S11), using the K-means clustering algorithm of ptraj.10 To compare the

modified DNA structural features, the base step parameters at the

modification site were calculated using a pseudostep consisting of the base

pairs 5 and 3 with respect to the hydrophobic base pair. The use of

pseudostep parameters rather than the traditional step parameters defined

for adjacent base pairs in natural DNA11 is justified since no protocol is

currently available in the literature to calculate parameters of DNA steps

involving hydrophobic bases. van der Waals stacking interaction energies

between the hydrophobic and flanking base pairs were calculated using the

“lie” command of cpptraj, whereas the percentage occupancies of

hydrogen-bonding interactions within base pairs were calculated using the

‘hbond’ command of cpptraj. The extent of DNA bending was analysed by

measuring the angle between the center of mass within three blocks of the

DNA, with the central block comprised of the hydrophobic base pair and the

corresponding flanking 5 and 3 base pairs, and the other two blocks

consisting of the three base pairs neighbouring each side of the central

block.

References 1. S. Jahiruddin and A. Datta, J. Phys. Chem. B, 2015, 119, 5839-5845. 2. F. Y. Dupradeau, A. Pigache, T. Zaffran, C. Savineau, R. Lelong, N. Grivel, D. Lelong, W. Rosanski and P. Cieplak, Phys. Chem. Chem. Phys., 2010, 12, 7821-7839. 3. J. Wang, W. Wang, P. A. Kollman and D. A. Case, J. Mol. Graph. Model., 2006, 25, 247-260. 4. W. D.Cornell, P. Cieplak, C. I. Bayly, I. R. Gould, K. M. Merz, D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell and P. A. Kollman, J. Am. Chem. Soc., 1995, 117, 5179-5197.

[S5]

5. J. A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K. E. Hauser and C. Simmerling, J. Chem. Theory Comput., 2015, 11, 3696-3713. 6. A. Pérez, I. Marchán, D. Svozil, J. Sponer, T. E. Cheatham III, C. A. Laughton and M. Orozco, Biophys. J., 2007, 92, 3817-3829. 7. J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman and D. A. Case, J. Comput. Chem., 2004, 25, 1157-1174. 8. I. S. Joung and T. E. Cheatham III, J. Phys. Chem. B, 2008, 112, 9020-9041. 9. N. B. Leontis and J. SantaLucia, Molecular Modeling of Nucleic Acids; American Chemical Society, 1998. 10. J. Shao, S. W. Tanner, N. Thompson and T. E. Cheatham III, J. Chem. Theory Comput., 2007, 3, 2312-2334. 11. P. Kathuria, P. Sharma and S. D. Wetmore, Nucleic Acids Res., 2015, 43, 7388-7397.

[S6]

Figure S1. B3LYP-D3/6-31+G(d,p) relative energy (kJ mol–1) as a function of rotation

about the glycosidic bond (, deg) for the natural DNA nucleosides. The glycosidic

dihedral angle is shown for the general representation of the nucleoside dX (X =

Adenine, Thymine, Cytosine and Guanine).

[S7]

Figure S2. B3LYP-D3/6-31+G(d,p) optimized structures of the syn and anti minima

for rotation about the glycosidic bond in the natural nucleosides. B3LYP-D3/6-

311+G(2df,p) relative anti/syn energy difference (kJ mol–1) is provided in parentheses.

The -dihedral angle ((C4C5O5H)) is constrained in all structures to prevent

interactions between the nucleobase and the 5–OH group that are non-native to DNA.

The dihedral angle that determines the orientation of the base with respect to sugar

is indicated in blue in the syn conformations.

[S8]

Figure S3. B3LYP-D3/6-31+G(d,p) optimized geometries of the hydrophobic base

pairs.

[S9]

Figure S4: Orientation of the B3LYP-D3/6-31+G(d,p) dipole moments in the

hydrophobic (top) and natural (bottom) nucleobases, with the magnitude provided in

parentheses.

[S10]

Figure S5. Relative stacking interaction energies (kJ mol–1) between adenine and a

hydrophobic base plotted as a function of the angle of rotation (α, deg).

[S11]

Figure S6. Relative stacking interaction energies (kJ mol–1) between cytosine and a


[S12]

Figure S7. Relative stacking interaction energies (kJ mol–1) between guanine and a


[S13]

Figure S8. Relative stacking interaction energies (kJ mol–1) between thymine and a


[S14]

Figure S9. Frequency (% occupancy) of the glycosidic dihedral angle (deg) in

nucleosides within the hydrophobic and T:A control pairs obtained from MD

simulations on DNA duplexes.

[S15]

Figure S10. Backbone rmsd for DNA oligonucleotides (5-TCACAXTTCCA-3, 5-

AGTGTYAAGGT-3) containing a hydrophobic or T:A control base pair where black

represents 5SICS:FEMO, red 5SICS:MMO2, blue 5SICS:NaM, orange NaM:TPT3

and green T:A.

.

[S16]

Figure S11. Oligonucleotide sequence used to simulate DNA containing a

hydrophobic or T:A control base pair. The position of the hydrophobic or T:A base pair

is highlighted in red.

[S17]

Table S1. B3LYP-D3/6-311+G(2df,p) stacking energies (kJ mol) as a function of α

(deg) for stacked dimers between A and a hydrophobic base.

α FEMO AMMO2 A–NaM A–5SICS A–TPT3

0 –20.2 –20.2 –20.7 –37.9 –33.7

30 –26.2 –19.5 –22.9 –32.3 –27.7

60 –26.0 –21.1 –20.9 –23.7 –16.3

90 –24.1 –23.8 –10.5 –19.9 –17.8

120 –20.1 –27.0 –11.6 –21.8 –14.6

150 –19.7 –28.2 –17.6 –22.5 –17.0

180 –26.4 –22.5 –21.3 –21.7 –18.0

210 –27.2 –18.9 –24.4 –19.7 –16.1

240 –28.5 –19.7 –24.6 –24.9 –21.9

270 –29.1 –24.5 –21.1 –25.5 –22.5

300 –26.7 –24.4 –10.8 –18.2 –14.5

330 –30.1 –25.2 –16.9 –31.1 –26.7

[S18]


(deg) for stacked dimers between C and a hydrophobic base.

α C–FEMO

C–MMO2 C–NaM C–5SICS C–TPT3

0 –23.4 –9.4 –24.8 –38.6 –38.7

30 –31.2 –7.6 –30.2 –36.8 –36.9

60 –22.2 –15.7 –25.9 –35.1 –32.6

90 –13.7 –18.8 –21.9 –39.3 –36.9

120 –9.5 –20.1 –22.5 –36.0 –28.9

150 –10.2 –19.9 –20.8 –27.4 –22.3

180 –14.0 –17.7 –19.4 –20.9 –14.5

210 –18.6 –18.0 –23.9 –16.5 –8.9

240 –24.1 –20.0 –27.1 –14.0 –9.4

270 –25.7 –22.9 –24.7 –8.6 –7.4

300 –23.8 –25.8 –22.0 –19.9 –22.3

330 –24.5 –23.2 –23.8 –40.3 –41.9

[S19]


(deg) for stacked dimers between G and a hydrophobic base.

α G–FEMO G–MMO2 G–NaM G–5SICS G–TPT3

0 –28.2 –25.6 –30.6 –34.1 –27.7

30 –21.9 –30.9 –26.4 –34.1 –30.1

60 –15.1 –31.8 –21.9 –35.4 –31.0

90 –23.8 –24.6 –23.2 –30.9 –24.1

120 –30.3 –22.0 –20.3 –5.8 –1.7

150 –32.6 –23.9 –28.4 –8.3 –4.6

180 –34.0 –29.7 –29.7 –18.6 –17.0

210 –29.4 –35.8 –25.1 –25.4 –24.4

240 –27.2 –31.8 –24.6 –34.0 –33.4

270 –29.4 –21.7 –25.9 –42.4 –43.7

300 –35.1 –24.0 –21.8 –42.6 –40.9

330 –33.5 –21.4 –25.4 –34.5 –29.3

[S20]


(deg) for stacked dimers between T and a hydrophobic base.

α T–FEMO T–MMO2 T–NaM T–5SICS T–TPT3

0 –21.0 –25.4 –32.1 –26.7 –18.0

30 –19.6 –26.0 –27.5 –21.8 –17.3

60 –14.8 –24.3 –19.1 –22.5 –22.8

90 –21.8 –29.4 –29.1 –30.4 –26.9

120 –31.8 –20.2 –37.0 –20.9 –15.5

150 –38.4 –20.8 –36.0 –26.6 –27.8

180 –33.2 –26.2 –33.3 –31.6 –32.6

210 –24.3 –29.7 –31.2 –31.1 –34.2

240 –18.7 –25.7 –29.5 –40.1 –41.9

270 –26.4 –8.7 –32.0 –42.6 –41.3

300 –20.2 –22.8 –33.4 –43.7 –39.7

330 –14.4 –25.0 –32.4 –36.6 –29.2

[S21]

Table S5. B3LYP-D3/6-311+G(2df,p) stacking energies (kJ mol–1) as a function of α

(deg) for stacked dimers of natural bases.

Angles A–A A–C A–G A–T C–C C–G C–T G–G G–T T–T

0 2.4 –9.8 –23.1 –37.5 19.4 –28.9 –34.9 14.2 –18.4 22.9

30 –16.7 –17.0 –19.3 –23.3 2.3 –14.7 –31.7 –13.7 –18.3 –14.6

60 –24.0 –24.0 –13.3 –15.5 –15.8 –5.6 –24.5 –29.1 –23.6 –31.6

90 –25.2 –32.8 –16.6 –26.0 –28.1 –7.6 –13.8 –38.4 –22.2 –24.4

120 –21.6 –33.2 –24.0 –25.5 –32.4 –16.5 –7.5 –39.9 –22.6 –24.3

150 –20.7 –27.7 –24.9 –22.8 –37.0 –27.8 –15.9 –29.9 –28.0 –33.9

180 –22.0 –26.3 –32.9 –25.7 –38.7 –34.9 –19.1 –28.5 –30.5 –36.8

210 –20.3 –23.2 –33.5 –29.2 –36.9 –32.6 –16.2 –30.0 –25.5 –24.6

240 –22.1 –20.9 –30.4 –31.9 –32.4 –29.6 –14.6 –39.9 –36.6 –24.5

270 –25.2 –21.1 –26.0 –29.3 –28.0 –31.1 –21.2 –38.3 –39.8 –24.7

300 –23.6 –15.2 –20.6 –25.0 –15.8 –35.1 –29.5 –28.4 –39.7 –31.7

330 –16.7 –18.1 –24.5 –36.4 2.3 –40.3 –35.7 –13.0 –31.7 –14.5

[S22]

Table S6. Average base pseudostep parameters, minor groove dimensions, DNA bend and base pair width for oligonucleotides

containing a hydrophobic or T:A control base pair.a

Base pair Shift (Å)

Slide (Å)

Rise (Å)

Tilt (deg)

Roll (deg)

Twist (deg)

Minor groove

(Å)

Bend (deg)

C1'–C1' distance

(Å)

T:A –0.110 (0.717)

–1.415 (0.825)

6.702 (0.360)

0.6 (4.6)

1.7 (6.6)

66.9 (5.3)

8.768 (1.646)

150.4 (7.4)

10.639 (0.245)

SICS:FEMO –0.044 (0.805)

–1.011 (0.870)

11.306 (0.565)

1.1 (4.8)

–13.9 (8.5)

68.8 (5.0)

11.301 (1.520)

171.0 (4.8)

8.812 (0.517)

SICS:MMO2 0.030

(0.720) –2.823 (0.895)

7.4 (0.617)

–0.3 (4.8)

8.5 (6.8)

58.5 (4.7)

10.754 (1.315)

152.2 (7.4)

10.551 (0.429)

SICS:NAM 0.150

(0.869) –2.807 (1.220)

9.140 (1.613)

0.2 (5.8)

6.5 (11.1)

59.4 (8.0)

11.806 (1.335)

163.0 (9.0)

10.034 (0.807)

TPT3:NAM 0.019

(0.680) –2.693 (0.829)

7.332 (0.578)

–0.8 (4.6)

6.0 (6.6)

59.3 (4.5)

10.388 (1.366)

153.0 (7.9)

10.693 (0.382)

aBase step parameters at the modification site were calculated using a pseudostep consisting of the base pairs 5 and 3 with respect to

the hydrophobic base pair.

[S23]

Table S7. Hydrogen-bonding occupancies (%) for the 5– and 3–base pairs flanking the

hydrophobic or control pair.a

Base pair Flanking base pairs Hydrogen bond Occupancy

T:A

5–A:T N1···H3–N3 O4···H6–N6

99.69 94.71

3–T:A O4···H6–N6 N1···H3–N3

96.66 99.76

5SICS:FEMO

5–A:T N1···H3–N3 O4···H6–N6

99.14 91.48

3–T:A O4···H6–N6 N1···H3–N3

98.49 99.37

5SICS:MMO2

5–A:T N1···H3–N3 O4···H6–N6

99.31 95.91

3–T:A O4···H6–N6 N1···H3–N3

95.71 99.56

5SICS:NaM

5–A:T N1···H3–N3 O4···H6–N6

92.18 98.11

3–T:A O4···H6–N6 N1···H3–N3

99.52 95.46

TPT3:NaM

5–A:T N1···H3–N3 O4···H6–N6

99.07 97.40

3–T:A O4···H6–N6 N1···H3–N3

95.62 99.61

aHydrogen-bonding interactions were determined using a cut-off of 3.4 Å for the donor–acceptor distance and 120o for the donor–hydrogen–acceptor angle.

[S24]

Table S8. Average interaction energies and standard deviation (in parentheses, kJ

mol–1) for the hydrophobic or T:A control base pairs in DNA duplexes.

Base pair Intrabase pair Flanking base pair

T:A –42.84 (5.0) –84.4 (8.8)

5SICS:FEMO –33.2 (3.4) –65.5 (7.6)

5SICS:MMO2 –10.5 (3.4) –90.7 (9.7)

5SICS:NaM –18.5 (5.9) –32.3 (13.9)

TPT3:NaM –14.7 (3.4) –126 (11.3)

[S25]

TABLE S9. Cartesian coordinates of anti 5SICS ( = 210.5o)

Energy (in hartrees) = -1260.79578

ATOM X Y Z

C -0.73063400 1.04208600 -0.10837300 C -2.08550400 0.48842500 -0.05851900 C -2.30033400 -0.91677500 -0.02123400 C -1.16148009 -1.78394900 -0.04128000 C 0.08114800 -1.25551000 -0.14975700 H -3.05765700 2.40796700 -0.05917200 C -3.21707500 1.33628600 -0.03369100 C -3.61899100 -1.42316700 0.04428000 H -1.28552800 -2.85936000 0.02062200 H 0.98196100 -1.85211100 -0.17764300 C -4.72034900 -0.58183900 0.06566000 C -4.49534700 0.81559200 0.02129800 H -3.75897800 -2.50127900 0.07563600 H -5.34737100 1.49070500 0.03324000 N 0.28852900 0.10848800 -0.23022600 S -0.39798300 2.69640000 0.00795200 C -6.12870700 -1.11859600 0.13547100 H -6.63896800 -0.76034200 1.03735800 H -6.71923400 -0.78076800 -0.72419400 H -6.14485900 -2.21197800 0.14901200 O 3.15924300 -2.36001000 0.80144200 C 4.00158400 -1.98300100 -0.29361000 H 3.77995900 -2.58734200 -1.18366100 H 5.06354700 -2.10862500 -0.03569200 C 3.75148800 -0.52099800 -0.62697800 H 4.46113900 -0.21681000 -1.40554100 O 2.41689600 -0.36460000 -1.14350100 C 1.68709100 0.57580800 -0.36499700 H 1.64110100 1.53851500 -0.87541800 C 3.87813700 0.44608800 0.56656900 H 4.47616200 0.01024300 1.37680400 C 2.42294400 0.67096800 0.97499100 H 2.09723100 -0.14296900 1.62885400 H 2.24237400 1.62824100 1.46927100 O 4.50236200 1.63092200 0.06135400 H 3.31214100 -3.28736100 1.01928400 H 4.43316800 2.33246000 0.72225000

[S26]

Table S10. Cartesian coordinates of syn 5SICS structure ( = 60.8o)


ATOM X Y Z

C -0.49139800 0.32084300 -0.09413000 C -1.96388900 0.26461700 -0.06104600 C -2.66064800 -0.96377300 0.08781300 C -1.89551200 -2.16669100 0.21243900 C -0.54599500 -2.09795200 0.18655800 H -2.21169000 2.38796300 -0.29349900 C -2.73318800 1.44539000 -0.17743200 C -4.07312800 -0.97977200 0.11902600 H -2.38412700 -3.12604700 0.33994100 H 0.06721100 -2.98309800 0.29391300 C -4.81461700 0.18629300 0.00686200 C -4.11431000 1.40648600 -0.14387300 H -4.57838700 -1.93560900 0.23719400 H -4.67604300 2.33291200 -0.23436500 N 0.15670000 -0.91148400 0.02734900 S 0.34299900 1.76810000 -0.26879400 C -6.32276900 0.17593200 0.04226500 H -6.69856200 0.79850200 0.86265000 H -6.73877900 0.58210400 -0.88724500 H -6.71732700 -0.83514900 0.17632500 O 3.71973200 2.14338700 -0.31796600 C 3.73448100 1.51778500 0.96765500 H 2.91951100 1.89016600 1.60018400 H 4.69668900 1.71177300 1.46489100 C 3.55290300 -0.00055200 0.82676700 H 4.19989400 -0.50755500 1.55038000 O 2.19352200 -0.38369700 1.14050200 C 1.62972500 -1.07749900 0.04638400 H 1.77834400 -2.15182700 0.19983200 C 3.83915700 -0.56374300 -0.57900300 H 4.50264500 0.08943600 -1.15063400 C 2.43535600 -0.66019000 -1.18908600 H 2.11930900 0.31731700 -1.55265000 H 2.37472800 -1.40351700 -1.98958300 O 4.43339600 -1.86065100 -0.39177200 H 3.83498200 3.09442800 -0.20697900 H 4.69649500 -2.20636900 -1.25439300

[S27]

Table S11. Cartesian coordinates of anti FEMO structure ( = 196.4o)


ATOM X Y Z

O 2.71325400 -2.20011800 1.13802200 C 3.47600700 -1.99818800 -0.05459400 H 3.19432700 -2.72267900 -0.83086000 H 4.55410800 -2.09561100 0.14598000 C 3.20495000 -0.59747800 -0.58221100 H 3.90414400 -0.39295300 -1.40348700 O 1.86105700 -0.53340700 -1.08300200 C 1.15678600 0.56185700 -0.48539800 H 1.25512700 1.44892100 -1.12493500 C 3.34250400 0.51459400 0.47596400 H 3.93428600 0.18012800 1.33666600 C 1.88742100 0.80633200 0.84761300 H 1.55010500 0.07726100 1.58980500 H 1.73063300 1.81848200 1.22995900 O 3.98132200 1.62423800 -0.17122800 H 2.88033400 -3.08696200 1.47839300 H 4.00967800 2.36860900 0.44398400 C -2.59334500 0.95198800 0.07643600 C -1.24249900 1.24836000 -0.09298100 C -0.74896200 -1.09910400 -0.37138900 C -2.09611300 -1.38349100 -0.19666300 C -3.04834600 -0.38492200 0.02743000 H -3.32438300 1.73007200 0.25229700 H -0.04174000 -1.89988600 -0.54761000 F -2.49759300 -2.67907100 -0.24808700 C -4.42901800 -0.69534000 0.20090000 C -5.60529800 -0.94490900 0.35102300 H -6.63784000 -1.17638500 0.48111100 O -0.72321900 2.51737300 -0.03937700 C -1.61687100 3.61270600 0.12169800 H -2.14677400 3.55906500 1.08160700 H -0.99536800 4.50895600 0.10088300 H -2.34684400 3.65601400 -0.69683500 C -0.30401100 0.21991500 -0.32774600

[S28]

Table S12. Cartesian coordinates of syn FEMO structure ( = 58.7o)


ATOM X Y Z

O 3.28157700 1.90258400 -0.00341200 C 3.65326500 1.00974800 1.05263400 H 3.27328700 1.36549400 2.01990600 H 4.74876900 0.92025500 1.11248700 C 3.07921500 -0.37596100 0.79690600 H 3.59640800 -1.08369300 1.45994500 O 1.67723400 -0.38907500 1.10150000 C 0.96839600 -1.06547700 0.05178700 H 0.99124100 -2.14797600 0.24904400 C 3.23385800 -0.87624200 -0.65666500 H 3.93999500 -0.25782500 -1.22174700 C 1.80673400 -0.77925600 -1.20553000 H 1.61733500 0.23592000 -1.55823800 H 1.61660500 -1.49421200 -2.01219500 O 3.70461800 -2.23141000 -0.58015300 H 3.70883500 2.75368900 0.14955100 H 3.81098600 -2.57389400 -1.47717400 C -2.20808000 1.08244200 -0.15823700 C -0.85927300 0.72522000 -0.15108700 C -1.48093900 -1.58149300 0.18904800 C -2.82034100 -1.21611500 0.16998400 C -3.22078800 0.11118000 0.00226200 H -2.51183100 2.11242200 -0.29163300 H -1.22917100 -2.62591100 0.34199000 F -3.76018700 -2.18176700 0.33016400 C -4.59853400 0.47821600 -0.00729900 C -5.76611200 0.80171400 -0.01780000 H -6.79634500 1.07627700 -0.02424200 O 0.15604900 1.61354000 -0.31939800 C -0.13266000 2.99902700 -0.42115500 H -0.65400500 3.36503200 0.47312800 H 0.83879300 3.48742700 -0.50359200 H -0.73473900 3.22312400 -1.31214900 C -0.47645900 -0.62722300 0.02767800

[S29]

Table S13. Cartesian coordinates of anti MMO2 structure ( = 196o)


ATOM X Y Z

O 2.85666000 -1.97941800 1.11510600 C 3.50153300 -1.63722600 -0.11496600 H 3.32489000 -2.40555500 -0.88017100 H 4.58721300 -1.52398800 0.02946400 C 2.93932000 -0.31746000 -0.62046700 H 3.55705000 0.02199000 -1.46303800 O 1.59306200 -0.51925200 -1.07100000 C 0.72186500 0.45660000 -0.47952500 H 0.67995100 1.34181900 -1.12857600 C 2.89772400 0.79950200 0.44246800 H 3.55636100 0.57412500 1.28994600 C 1.42119100 0.82797000 0.83949900 H 1.23026000 0.05068100 1.58517800 H 1.09419800 1.79620200 1.22857700 O 3.32016900 2.00761300 -0.20901100 H 3.21089500 -2.81606400 1.43857800 H 3.20688300 2.74515800 0.40459900 C -2.21469100 -1.98480000 -0.18833800 C -0.92034100 -1.47905600 -0.36112200 C -0.66623200 -0.11112100 -0.31328500 C -1.74981700 0.75884500 -0.07315600 C -3.04315300 0.25988000 0.09591600 C -3.28900500 -1.12306500 0.03883100 H -2.38341400 -3.05726400 -0.23563900 H -0.08608000 -2.14674700 -0.54442100 H -3.87470200 0.93238500 0.27615700 C -4.69670200 -1.64232700 0.22339200 H -5.09896700 -1.36086900 1.20404400 H -5.37417900 -1.23205300 -0.53511800 H -4.73204900 -2.73298900 0.14802200 O -1.42963700 2.09410100 -0.01353700 C -2.47389300 3.04007200 0.17053600 H -1.99426200 4.02012800 0.15697900 H -3.21247500 2.98537000 -0.63982900 H -2.98040000 2.89643800 1.13408000

[S30]

Table S14. Cartesian coordinates of syn MMO2 structure ( = 60o)


ATOM X Y Z

O -2.72544600 2.00446700 0.03362800 C -3.17474400 1.15162900 -1.02520000 H -2.78776800 1.49207300 -1.99519600 H -4.27496400 1.13735300 -1.06630400 C -2.68844700 -0.27140600 -0.79393700 H -3.26132600 -0.93572400 -1.45699200 O -1.29626100 -0.36780800 -1.11640300 C -0.61953800 -1.11780200 -0.09080300 H -0.73063100 -2.19080500 -0.31020500 C -2.85853300 -0.77855800 0.65633300 H -3.50916700 -0.11764100 1.23989300 C -1.42040600 -0.79637000 1.18219500 H -1.15209500 0.19517400 1.55018300 H -1.27067900 -1.53808500 1.97341100 O -3.43294500 -2.09396100 0.57075000 H -3.04533800 2.89854900 -0.13488600 H -3.53564000 -2.44404200 1.46521900 C 3.16463500 -1.57256000 -0.29676100 C 1.78528300 -1.81213100 -0.30080700 C 0.85469900 -0.79756500 -0.08258100 C 1.35079200 0.50952100 0.14005800 C 2.72698000 0.75600700 0.13658500 C 3.64881700 -0.28198900 -0.08071400 H 3.85688700 -2.39144100 -0.47111200 H 1.42103200 -2.81981300 -0.48550100 H 3.10174500 1.75952400 0.30632800 C 5.12978900 0.01947100 -0.08589300 H 5.39221700 0.69465300 -0.90934200 H 5.43882000 0.50833500 0.84548800 H 5.72257400 -0.89266800 -0.19949500 O 0.41329000 1.47247900 0.35849800 C 0.81414800 2.82332800 0.51161900 H -0.11245400 3.38657500 0.62998100 H 1.44426200 2.96243600 1.40081400 H 1.35257400 3.18468600 -0.37463900

[S31]

Table S15. Cartesian coordinates of anti NaM structure ( = 194.5o)


ATOM X Y Z

O 2.65030200 -2.42461300 1.17574800 C 3.38277200 -2.33414800 -0.04932100 H 2.98586600 -3.03212100 -0.79923500 H 4.44866700 -2.55723000 0.11283800 C 3.26157700 -0.92026600 -0.59676200 H 3.95853500 -0.81367600 -1.43884700 O 1.92163100 -0.70679300 -1.06235700 C 1.38651900 0.49825900 -0.49797300 H 1.61147300 1.33998500 -1.16670300 C 3.56133400 0.18472800 0.43622600 H 4.11790700 -0.20764600 1.29588200 C 2.16347300 0.67311900 0.81889700 H 1.74389100 0.00983600 1.58084600 H 2.14752400 1.70442200 1.18127100 O 4.33227300 1.18788700 -0.24221000 H 2.72452500 -3.31994500 1.52646500 H 4.45764100 1.93757300 0.35409900 C -4.95106300 -1.07994600 0.19923600 C -4.32128700 0.14728400 0.24865000 C -2.91651700 0.25275000 0.06156100 C -2.16222900 -0.93857600 -0.18121300 C -2.83855600 -2.18644900 -0.22753700 C -4.20407000 -2.25974800 -0.04119000 H -2.82073900 2.39806000 0.29557100 H -6.02582200 -1.14412100 0.34406000 H -4.89661900 1.05146500 0.43256200 C -2.23837100 1.50321500 0.10917200 C -0.75613000 -0.83170100 -0.36889900 H -2.25876800 -3.08705500 -0.41353700 H -4.71000700 -3.22007900 -0.07893600 C -0.87224400 1.56367300 -0.07508600 H -0.17046800 -1.72481100 -0.55818100 O -0.13422200 2.71860600 -0.03438700 C -0.81419300 3.95247500 0.15811000 H -1.32368400 3.98017800 1.13010700 H -0.04457200 4.72521600 0.12908700 H -1.54439100 4.13369900 -0.64108800 C -0.10782300 0.37959000 -0.32397100

[S32]

Table S16. Cartesian coordinates of syn dNaM structure ( = 59.2o) Energy (in hartrees) = –921.75311

ATOM X Y Z

O 3.72231100 1.65745700 0.06022800 C 3.97502800 0.70925600 1.10315900 H 3.61715100 1.08489000 2.07125900 H 5.05342900 0.50091800 1.17884100 C 3.25701400 -0.59964900 0.80927600 H 3.68772500 -1.37407200 1.46001700 O 1.85977100 -0.46608300 1.09978200 C 1.09379000 -1.05088200 0.03308100 H 1.00754900 -2.13329100 0.21330900 C 3.37562900 -1.08213400 -0.65413000 H 4.14541000 -0.52553900 -1.19998500 C 1.97067100 -0.83348100 -1.21172900 H 1.88804900 0.19979900 -1.55262800 H 1.71725600 -1.51511000 -2.02979500 O 3.71102100 -2.47902900 -0.60396400 H 4.18729000 2.47601400 0.26993900 H 3.79232200 -2.81002300 -1.50786400 C -5.35558000 0.15801100 0.06164900 C -4.29328400 1.02877900 -0.07419700 C -2.95439400 0.55254700 -0.05144000 C -2.72769200 -0.84954400 0.11512700 C -3.83953500 -1.72096600 0.25458200 C -5.12948300 -1.23079500 0.22811700 H -2.02342100 2.48208500 -0.31614600 H -6.37321400 0.53780900 0.04234600 H -4.47028000 2.09404000 -0.20050500 C -1.83699400 1.42183900 -0.18945800 C -1.38441900 -1.31620100 0.14378200 H -3.65781100 -2.78523500 0.38326800 H -5.97321700 -1.90604700 0.33539100 C -0.54702100 0.92778300 -0.16665200 H -1.21030900 -2.38022100 0.28805900 O 0.56770600 1.69262200 -0.30738800 C 0.43868100 3.10014300 -0.41953900 H -0.05677200 3.52642700 0.46281700 H 1.45969600 3.47769500 -0.48536600 H -0.11942800 3.38401400 -1.32218800 C -0.30206200 -0.47702200 0.00503300

[S33]

Table S17. Cartesian coordinates of anti dTPT3 structure ( = 209.6o)

Energy (in hartrees) = –1542.23267

ATOM X Y Z

O 3.07066400 -2.14014900 0.82884300 C 3.88457200 -1.68144200 -0.25617800 H 3.75106500 -2.31759200 -1.14165700 H 4.94897100 -1.68007500 0.02149000 C 3.47392400 -0.26210500 -0.61351900 H 4.15345400 0.10988400 -1.38933400 O 2.13625000 -0.26458300 -1.14700500 C 1.29155700 0.58525400 -0.38454800 H 1.12496300 1.52759600 -0.90876700 C 3.47529700 0.72960700 0.56581500 H 4.10965200 0.37582400 1.38832600 C 1.99937400 0.79207200 0.95852700 H 1.76302000 -0.03956800 1.62829900 H 1.70457100 1.73240400 1.43007000 O 3.96582800 1.97015400 0.04833500 H 3.32488400 -3.04110900 1.06228100 H 3.81444300 2.66824600 0.69912500 C -2.47899300 -1.35259100 -0.00611900 C -2.38916400 0.04692800 -0.03417400 C -1.16023100 0.77131600 -0.12197600 C -0.09433800 -1.42634300 -0.18125400 C -1.27198500 -2.10323300 -0.06564200 C -3.83377000 -1.80677300 0.09561200 C -4.71940900 -0.76666900 0.14366700 H 0.86728300 -1.91724300 -0.22970900 H -1.27288600 -3.18593700 -0.02224500 H -4.12095400 -2.85152000 0.12923400 H -5.79776600 -0.83100600 0.21588000 S -3.95951900 0.79852700 0.07691700 S -1.07395600 2.45949000 -0.05235800 N -0.03972000 -0.05109900 -0.24551300

[S34]

Table S18. Cartesian coordinates of syn dTPT3 structure ( = 61.1o)


ATOM X Y Z

O -3.28577600 -2.16014600 -0.31901000 C -3.30544900 -1.53225100 0.96533700 H -2.46896000 -1.87359300 1.58696900 H -4.25324900 -1.75860300 1.47615300 C -3.17885800 -0.00847500 0.81597600 H -3.85043700 0.48184800 1.52817900 O -1.83579700 0.42524000 1.14243500 C -1.28167700 1.12417800 0.04788800 H -1.45727400 2.19684500 0.18557100 C -3.46453800 0.53449000 -0.59743600 H -4.10330800 -0.14112400 -1.17081200 C -2.05621400 0.66259000 -1.19054400 H -1.70502000 -0.31306100 -1.52806600 H -2.00495600 1.39066400 -2.00537600 O -4.09378300 1.81713300 -0.42896300 H -3.36614900 -3.11439000 -0.20474700 H -4.36449700 2.14407000 -1.29651700 C 2.99243600 1.07012500 0.11223100 C 2.28513000 -0.12969400 -0.03054500 C 0.85497000 -0.24542600 -0.06845400 C 0.88258000 2.17922100 0.20486000 C 2.23918300 2.27098400 0.23567200 C 4.41033900 0.87374800 0.11604500 C 4.74040300 -0.44592200 -0.02182300 H 0.25778300 3.05660800 0.30905200 H 2.71510400 3.23594300 0.36310600 H 5.13310200 1.67536900 0.21703100 H 5.73653800 -0.86933800 -0.05026100 S 3.35931800 -1.49751600 -0.16034400 S 0.10230000 -1.74025700 -0.24086400 N 0.19406400 0.98770200 0.04544600

[S35]

Table S19. Cartesian coordinates of anti Adenine structure ( = 235.8o)


ATOM X Y Z

O -2.90109800 2.09593800 0.39453500 C -3.56255400 1.45236500 -0.70210600 H -3.28667600 1.92339800 -1.65449800 H -4.65501200 1.50258300 -0.58174500 C -3.14315600 -0.01003300 -0.75161700 H -3.75129200 -0.51811500 -1.50946500 O -1.76323300 -0.10930100 -1.13789500 C -0.98184000 -0.71333800 -0.10715300 H -0.70384000 -1.73159700 -0.39475500 C -3.27787400 -0.75989000 0.58608600 H -4.01499800 -0.28203800 1.24328300 C -1.85992500 -0.68625100 1.15408200 H -1.72591200 0.26289800 1.67842300 H -1.62493300 -1.50794700 1.83634700 O -3.67641300 -2.09694700 0.26626000 H -3.16638700 3.02305000 0.42668100 H -3.70011700 -2.62292500 1.07641600 C 1.53885700 -0.49474900 -0.06174800 C 0.40649400 1.38739700 0.21017100 C 2.38600800 0.60937800 0.08889000 H -0.46530600 2.02239100 0.28637700 C 3.76867000 0.34065200 0.03792000 C 3.24504900 -1.88948500 -0.27743200 H 3.62986100 -2.89486500 -0.42761400 N 0.26105000 0.02179100 0.02564900 N 1.66007100 1.77841000 0.25432600 N 1.91292800 -1.76901300 -0.24169100 N 4.17697100 -0.92830100 -0.15192900 N 4.70221000 1.31464400 0.19454900 H 5.66748700 1.08657700 0.01324700 H 4.41209700 2.28008600 0.19521100

[S36]

Table S20. Cartesian coordinates of syn Adenine structure (=82.4o)


ATOM X Y Z

O -2.24998800 2.25869000 -0.58649500 C -3.03085200 1.37559700 -1.38821000 H -2.65152300 1.32623800 -2.41801400 H -4.08549800 1.69236200 -1.41445700 C -2.96679100 -0.01918600 -0.78588200 H -3.73586400 -0.64385000 -1.25736800 O -1.67320300 -0.59755400 -1.04926600 C -1.11494700 -1.09097900 0.16858800 H -1.40205600 -2.14343700 0.29924000 C -3.16147500 -0.05860700 0.74525900 H -3.63482300 0.85754400 1.11409800 C -1.73151800 -0.22092700 1.26458900 H -1.22940100 0.74761800 1.28811500 H -1.68463300 -0.68987000 2.25172900 O -3.98301500 -1.20255500 1.02672000 H -2.28128100 3.14841500 -0.95693400 H -4.13347100 -1.25076200 1.97984900 C 1.23830800 -0.04570200 0.26439200 C 1.06448100 -2.12819700 -0.45964300 C 2.46983700 -0.57187900 -0.14548400 H 0.57960100 -3.05912200 -0.72335600 C 3.58854600 0.27926300 -0.03326000 C 2.17126800 1.89367400 0.80887000 H 2.08188700 2.90564400 1.19570100 N 0.32915500 -1.07835600 0.06933000 N 2.34204000 -1.87543700 -0.59608600 N 1.03912400 1.18521100 0.75817800 N 3.41187300 1.52387100 0.44533700 N 4.83796700 -0.12473100 -0.37572100 H 5.58062700 0.55684500 -0.38515600 H 4.96382500 -1.00852800 -0.84369500

[S37]

Table S21. Cartesian coordinates of anti Cytosine structure (=216.7o)


ATOM X Y Z

O -2.00926200 2.20525700 0.74941700 C -2.86157500 1.82754100 -0.33890300 H -2.62903700 2.41457700 -1.23762100 H -3.91996900 1.97924700 -0.08059300 C -2.64055900 0.35588300 -0.65267200 H -3.35264100 0.05808000 -1.43177200 O -1.30729000 0.16580300 -1.15572500 C -0.58922800 -0.76369800 -0.34718100 H -0.53630800 -1.73818500 -0.83467200 C -2.79745600 -0.59239400 0.55242800 H -3.40104900 -0.13674500 1.34769400 C -1.35064100 -0.83024500 0.98266900 H -1.02459000 -0.01174100 1.63066000 H -1.19380100 -1.78208300 1.49646500 O -3.43135000 -1.77551800 0.05510800 H -2.14560900 3.13851500 0.95262000 H -3.40626200 -2.45928300 0.73741700 C 2.35756100 1.46025500 0.04425800 C 1.07355600 1.02817600 -0.09936900 C 1.82249500 -1.29158800 -0.07820800 C 3.37431900 0.44766700 0.05998600 H 0.21781700 1.69226100 -0.13465100 O 1.49340400 -2.47436700 -0.04049900 N 3.11363900 -0.84583800 -0.00464200 N 0.79550200 -0.29742500 -0.20884500 H 2.58778200 2.51469600 0.13279600 N 4.68586800 0.81005400 0.17741600 H 5.37461500 0.08160700 0.05627500 H 4.96913900 1.76253700 0.01342100

[S38]

Table S22. Cartesian coordinates of syn Cytosine structure (=72.0o)


ATOM X Y Z

O 2.62686600 2.11568900 -0.09534000 C 2.95770600 1.35291800 1.06063700 H 2.44626300 1.73204700 1.95586500 H 4.04464400 1.36586900 1.24182700 C 2.53066900 -0.09319900 0.84589400 H 3.06774100 -0.73000700 1.55985100 O 1.11582700 -0.23134300 1.09156500 C 0.50728900 -0.88441700 -0.01632700 H 0.53647000 -1.97145300 0.14430400 C 2.77906700 -0.62270600 -0.58224900 H 3.51763000 -0.01461600 -1.11370100 C 1.38881100 -0.53850100 -1.21918200 H 1.18969100 0.48224200 -1.54330100 H 1.25915100 -1.24030500 -2.04884800 O 3.24103500 -1.97839700 -0.44700600 H 2.89357700 3.03345800 0.03112200 H 3.42564300 -2.32976300 -1.32774200 C -3.13034700 -1.20242700 0.51487300 C -1.79734100 -1.45262500 0.43512400 C -1.37409600 0.77784500 -0.45278000 C -3.55757000 0.09258000 0.06367100 H -1.37263600 -2.39672700 0.76023300 O -0.56636800 1.61177600 -0.82992700 N -2.72520700 1.00864300 -0.38683800 N -0.91306000 -0.53959700 -0.06026400 H -3.81939600 -1.94545300 0.89634300 N -4.88600500 0.40291900 0.06911100 H -5.54579700 -0.16686200 0.57319700 H -5.13707800 1.35921300 -0.13552600

[S39]

Table S23. Cartesian coordinates of anti Guanine structure ( = 239.6o) Energy (in hartrees) = –963.91993

ATOM X Y Z

O 3.38455600 -1.93252100 0.21821100 C 3.90519800 -1.14124600 -0.85653100 H 3.63884600 -1.57708400 -1.82811200 H 5.00059700 -1.06334100 -0.78759100 C 3.31104900 0.25847000 -0.78083600 H 3.82406700 0.89200700 -1.51406500 O 1.91544800 0.21731900 -1.11825200 C 1.10641700 0.63307900 -0.01814000 H 0.69559700 1.62754300 -0.21451200 C 3.40461400 0.91701800 0.60737600 H 4.22086400 0.48894100 1.20187200 C 2.03052400 0.62286300 1.21031300 H 2.03545300 -0.37022300 1.66503600 H 1.72480500 1.35778500 1.96021900 O 3.62009300 2.31529900 0.38370600 H 3.75961900 -2.82032900 0.17253800 H 3.64685700 2.77059600 1.23541300 C -1.35724900 0.08059100 0.01749000 C 0.00685600 -1.64487000 0.23470800 C -2.05827300 -1.12160000 0.13353200 H 0.95259500 -2.16543000 0.28505000 C -3.49508900 -1.09235800 0.08707600 C -3.15610700 1.37949900 -0.17339000 N -0.02871500 -0.26174800 0.09370900 N -1.18554500 -2.18595100 0.26401600 N -1.84606800 1.34243700 -0.11595800 N -3.94822300 0.26332100 -0.08026500 O -4.32318200 -1.98891700 0.15638400 H -4.95233600 0.34072300 -0.19316200 N -3.79369900 2.58261300 -0.38783500 H -4.71161100 2.71249900 0.01431000 H -3.18256100 3.38349500 -0.30264800

[S40]

Table S24. Cartesian coordinates of syn Guanine structure ( = 74.2o)


ATOM X Y Z

O -2.33770800 2.25975200 -0.66671000 C -3.12729500 1.33439100 -1.41719800 H -2.76067300 1.24345000 -2.44844100 H -4.18120300 1.65173100 -1.44202200 C -3.06036400 -0.03559900 -0.76320900 H -3.85262300 -0.66390800 -1.19090300 O -1.78384800 -0.64075600 -1.03954800 C -1.26620900 -1.19985300 0.16695200 H -1.65100100 -2.22080400 0.29681300 C -3.22429800 -0.02233000 0.77493300 H -3.61866300 0.93611700 1.12854600 C -1.80019300 -0.28391000 1.27061800 H -1.22908600 0.64574100 1.27579000 H -1.76981000 -0.74978400 2.25973300 O -4.12503100 -1.09150400 1.10115500 H -2.38601900 3.12564100 -1.08863800 H -4.26857400 -1.09898600 2.05656000 C 1.15160000 -0.35975100 0.11994500 C 0.82536800 -2.50731200 -0.27591300 C 2.34428700 -1.02703100 -0.16898000 H 0.27246800 -3.42886400 -0.40095600 C 3.57864500 -0.28615000 -0.16858200 C 2.09058200 1.64316000 0.40205100 N 0.16928800 -1.32775000 0.06246900 N 2.11686100 -2.36805100 -0.41135800 N 0.97414500 0.95760800 0.40093200 N 3.31914800 1.09228400 0.13893400 O 4.72915400 -0.64398200 -0.37378800 H 4.15878800 1.65523000 0.21158700 N 2.06010100 2.98167700 0.73347700 H 2.75235500 3.58770800 0.31506100 H 1.12396400 3.36459500 0.74311100

[S41]

Table S25. Cartesian coordinates of anti Thymine structure ( = 229.4o)


ATOM X Y Z

O -1.95459900 2.32005800 0.41824400 C -2.79183600 1.86980200 -0.65524800 H -2.44257400 2.26999700 -1.61602100 H -3.83350800 2.18407500 -0.49522200 C -2.74380200 0.35093900 -0.71820900 H -3.47815500 0.01130200 -1.45830900 O -1.43765600 -0.07448100 -1.14144200 C -0.84534700 -0.93608400 -0.17032200 H -0.91326500 -1.97665900 -0.49034000 C -3.02538500 -0.35527200 0.62317700 H -3.57595800 0.29597100 1.31305400 C -1.62042500 -0.68429300 1.13038800 H -1.20864900 0.18404800 1.65155200 H -1.59377800 -1.54931600 1.79873600 O -3.78865000 -1.52493500 0.31278100 H -1.98214400 3.28356900 0.46181000 H -3.92622600 -2.03883000 1.11941600 C 2.28278700 1.08147900 0.10799200 C 0.98653800 0.69608000 0.04210400 C 1.50059000 -1.67118200 -0.15725700 C 3.31733100 0.05103700 0.03343900 H 0.16871600 1.40763500 0.07472400 O 1.18557300 -2.85141000 -0.24730200 N 2.81988300 -1.25580100 -0.09946300 N 0.58281500 -0.62364700 -0.08843100 H 3.50862700 -1.99800300 -0.14635700 C 2.71916900 2.51182300 0.24515200 H 3.31805500 2.65037500 1.15169200 H 3.35473000 2.80599700 -0.59692800 H 1.85670900 3.18316000 0.28661000 O 4.52668400 0.25037200 0.07941100

[S42]

Table S26. Cartesian coordinates of syn Thymine structure ( = 75.5o)


ATOM X Y Z

O 3.04392300 1.94202200 0.40459100 C 3.28073400 0.92953000 1.37838300 H 2.79988000 1.17003000 2.33642000 H 4.35993700 0.79044500 1.55017100 C 2.70885900 -0.38539400 0.87189200 H 3.10951700 -1.20451400 1.48202300 O 1.27206300 -0.37389500 1.00316300 C 0.68885300 -0.76764000 -0.23516000 H 0.60288400 -1.86182000 -0.26532300 C 3.00914400 -0.67832100 -0.61485000 H 3.84437200 -0.07370200 -0.98262000 C 1.68864400 -0.32252700 -1.30502100 H 1.62777000 0.75393700 -1.45501600 H 1.55002000 -0.85000000 -2.25340700 O 3.31693400 -2.07895300 -0.70479800 H 3.40205000 2.78232000 0.71350600 H 3.55398600 -2.28748500 -1.61784600 C -2.99195900 -0.82601200 0.26727900 C -1.68694300 -1.15059500 0.12663200 C -0.98169600 1.07235100 -0.53437700 C -3.38989600 0.55168400 -0.01646500 H -1.33731500 -2.15534100 0.33802900 O -0.16148300 1.91768500 -0.85192100 N -2.32897600 1.38003200 -0.40548800 N -0.68738000 -0.27793300 -0.29115500 H -2.56038100 2.34874100 -0.59470500 C -4.05232000 -1.79490700 0.70458700 H -4.54431700 -1.44215500 1.61709100 H -4.83354300 -1.88399700 -0.05776700 H -3.63042900 -2.78613200 0.89359400 O -4.53024700 0.99513700 0.06333400

[S43]

Table S27. Cartesian coordinates of stacking interactions.

Cartesian coordinates of Adenine–FEMO structure (α=0o)

Counterpoise corrected Energy (in hartrees) = –989.83045

ATOM X Y Z

N -0.95941300 -2.55979200 -1.04962100 C -2.18233100 -1.94607500 -1.27860700 H -2.78767400 -2.19544800 -2.14972300 N -2.50504400 -1.06043400 -0.35163500 C -1.43463100 -1.09843800 0.53357400 C -1.15438700 -0.39858800 1.73532800 N -2.01064000 0.52544900 2.24831400 H -1.77060200 1.00083400 3.10796600 H -2.87718000 0.73096300 1.77009900 N 0.00046300 -0.65755800 2.39264700 C 0.83991600 -1.57900800 1.86867100 H 1.75939100 -1.75028100 2.43990700 N 0.70251500 -2.31192800 0.74631400 C -0.45540600 -2.02541300 0.12371000 H -0.51260100 -3.26953300 -1.61868400 C 1.37296900 -0.13096900 -1.97722000 C 2.00865200 0.31523400 -0.79618800 C 1.38701400 1.28018800 0.01399300 C 0.11860000 1.81549700 -0.34317300 C -0.48546900 1.34709400 -1.52786900 C 0.12516800 0.38678800 -2.34114200 H 1.86956100 -0.88243500 -2.59724400 H 1.85313300 1.64342700 0.93055900 H -0.38236800 0.05432400 -3.25072000 F -1.70173900 1.83977300 -1.89941200 O 3.22921900 -0.25501600 -0.52966000 C -0.51198200 2.79652900 0.48157400 C -1.03937700 3.63613400 1.19822800 H -1.50932700 4.37342600 1.82139900 C 3.90690500 0.17136200 0.66034100 H 4.12028600 1.25713500 0.62389300 H 3.30260800 -0.05547500 1.55985700 H 4.84766800 -0.39692700 0.68523200

[S44]

Table S28. Cartesian coordinates of Adenine–MMO2 structure (α=0o)


ATOM X Y Z

N 0.71286900 -2.33240300 1.13170500 C 1.74479500 -1.74148300 1.84623500 H 1.99247600 -2.06482500 2.85696400 N 2.35987600 -0.78018700 1.17887600 C 1.69443700 -0.74158800 -0.04035500 C 1.85698200 0.05855200 -1.20048200 N 2.81321800 1.02231600 -1.28377700 H 2.89352800 1.56956700 -2.13034600 H 3.43467300 1.18553500 -0.50341100 N 1.03569300 -0.14239800 -2.25779700 C 0.09091200 -1.10453700 -2.15789400 H -0.54635700 -1.22565300 -3.04123900 N -0.17389100 -1.93073000 -1.12686500 C 0.66223500 -1.69937300 -0.09833500 H 0.10946900 -3.08777700 1.43588300 C -0.14902600 2.10249700 0.51435700 C -1.14589700 1.62766200 -0.34982200 C -2.01037400 0.58228500 0.04447000 C -1.87859300 0.00111400 1.32107500 C -0.87520700 0.48179300 2.18598500 C -0.01796900 1.51794100 1.79585500 H -1.27022700 2.06140000 -1.34740400 H -2.53428300 -0.80789300 1.64924400 H -0.77039000 0.03175100 3.17937700 H 0.75637400 1.87878700 2.48159800 O -2.94543300 0.20676400 -0.89223000 C -3.84300800 -0.85059200 -0.53347100 H -4.44690600 -0.57252800 0.35214100 H -4.49794300 -0.99414100 -1.40523200 H -3.28764900 -1.78439900 -0.31923000 C 0.77623200 3.22419800 0.08699400 H 1.83106000 2.89351500 0.10912300 H 0.54258900 3.56784600 -0.93438100 H 0.68958400 4.08769600 0.77208200

[S45]

Table S29. Cartesian coordinates of Adenine–NaM structure (=0o)


ATOM X Y Z

N 0.93605000 -1.00279800 2.39295800 C 2.17843800 -0.38707900 2.34852100 H 2.62538700 0.05309700 3.23955900 N 2.72557300 -0.39895500 1.14507400 C 1.78988300 -1.06074600 0.35936400 C 1.76020000 -1.40610400 -1.01627700 N 2.77971500 -1.09329000 -1.86061400 H 2.71664100 -1.35891500 -2.83430600 H 3.59013700 -0.59962500 -1.51229400 N 0.68461000 -2.06735800 -1.50480500 C -0.31959000 -2.37039600 -0.65154400 H -1.16534600 -2.90546400 -1.09817500 N -0.42332900 -2.10623500 0.66572300 C 0.66323500 -1.44956700 1.11145100 H 0.33634400 -1.11757800 3.20189800 C -2.21716500 0.96563700 1.48707800 C -0.99707300 1.60707500 1.59032500 C -0.13961300 1.75510000 0.45548100 C -0.57754100 1.21674400 -0.81034400 C -1.84200400 0.55650600 -0.89929000 C -2.64677300 0.43385500 0.23073800 H 1.44467000 2.81673300 1.50169700 H -2.87567700 0.85061200 2.35325500 H -0.67191900 2.01291700 2.55459200 C 1.12289100 2.41206700 0.53532100 C 0.27648000 1.36299200 -1.94535900 H -2.15220500 0.15719200 -1.86761400 C 1.50236000 2.00864200 -1.83696400 C 1.93203800 2.53872500 -0.58753200 H -0.05132600 0.95601800 -2.90880500 H 2.14464300 2.11164900 -2.71841500 H 2.90021300 3.04528200 -0.51533200 O -3.87577300 -0.17795200 0.26358100 C -4.36243400 -0.73178600 -0.96578000 H -3.67790000 -1.51726900 -1.34050200 H -5.34372100 -1.16736800 -0.72844600 H -4.47208800 0.05681200 -1.73524500

[S46]

Table S30. Cartesian coordinates of Adenine–5SICS structure (=0o)


ATOM X Y Z

N 1.09641100 -1.89957600 -1.44520400 C 0.47916900 -1.25872400 -2.50959600 H 1.01213900 -1.06239100 -3.43957700 N -0.77757800 -0.92954800 -2.26462000 C -0.99474200 -1.38185500 -0.96882600 C -2.12569000 -1.34402600 -0.11321800 N -3.30414600 -0.78543400 -0.49971900 H -4.08498900 -0.78026900 0.14283000 H -3.39245300 -0.38061000 -1.42174700 N -2.03026900 -1.88006600 1.12628500 C -0.85156000 -2.43120900 1.49396700 H -0.82855900 -2.85039400 2.50630800 N 0.29314700 -2.53533400 0.79073100 C 0.15702000 -1.99184200 -0.43262300 H 2.04813200 -2.24576800 -1.40538100 C 2.28309600 0.75352500 0.22152600 C 0.89944300 1.23983500 0.15997500 C 0.01706200 1.07566900 1.28164200 C 0.50031700 0.42705800 2.47474400 C 1.79198200 -0.01934400 2.51324300 H 1.08029300 2.00282000 -1.85508200 H 3.58017900 -0.19142300 1.47523400 C 0.40405700 1.88078800 -1.00471000 C -1.31615400 1.55655400 1.19239100 H -0.15550800 0.29299800 3.33784000 H 2.23773100 -0.52022000 3.37520300 C -1.79261500 2.18581400 0.04096600 C -0.90751300 2.34122200 -1.06156000 H -1.98003400 1.42557400 2.05458600 H -1.26880000 2.83342200 -1.97147400 N 2.62270400 0.14811000 1.42573300 S 3.45055000 0.86043800 -0.99364100 C -3.21308400 2.69688800 -0.05103300 H -3.22396300 3.78517700 -0.24558400 H -3.74833200 2.21207300 -0.88817600 H -3.77125700 2.50282700 0.87951200

[S47]

Table S31. Cartesian coordinates of Adenine–TPT3 structure (=0o)


ATOM X Y Z

N 0.07053900 -1.58176400 -1.89528900 C -0.04133600 -0.43588700 -2.66927900 H 0.61063500 -0.26389800 -3.52532900 N -0.99246600 0.38400300 -2.25586100 C -1.53378200 -0.26243700 -1.15136400 C -2.58090600 0.07571800 -0.25597500 N -3.28766200 1.23165300 -0.37629800 H -4.02616600 1.43262800 0.28463500 H -3.07195600 1.87993600 -1.12129200 N -2.88703500 -0.77754700 0.74952800 C -2.17449700 -1.92193500 0.85426500 H -2.46293500 -2.57635200 1.68469900 N -1.16344600 -2.36631600 0.08223100 C -0.89053300 -1.49155700 -0.90307200 H 0.72041600 -2.34872000 -2.02430200 C 0.23124100 0.77633800 1.60665900 C 1.18776300 0.77596300 0.56306800 C 2.14074200 -0.27720700 0.34833700 C 1.10099100 -1.34926200 2.32321900 C 0.19584400 -0.33350800 2.51501600 C -0.59150300 1.95251500 1.58281600 C -0.25541100 2.80111900 0.55106600 H 2.67047700 -2.06875100 1.17423900 H 1.15591600 -2.23593000 2.95813400 H -0.52252700 -0.38018400 3.33557300 H -1.39242600 2.15378200 2.29914400 H -0.71585600 3.75974100 0.30235300 N 2.01246900 -1.30191000 1.29138000 S 3.30970200 -0.35653700 -0.86510900 S 1.06754600 2.21102200 -0.43028100

[S48]

Table S32. Cartesian coordinates of Cytosine–FEMO structure (=0o)


ATOM X Y Z

N 1.41972700 1.90363900 0.99557500 C 0.16790100 2.23478400 1.41523500 H 0.04844700 2.48123800 2.47418200 C -0.86903200 2.24670200 0.51856100 H -1.88369500 2.50778800 0.82399500 C -0.53545900 1.89477700 -0.84375400 N -1.52837300 1.88922900 -1.78280200 H -1.29354000 1.64265400 -2.73627900 H -2.48164600 2.12376200 -1.54685900 N 0.68725500 1.57011000 -1.25945800 C 1.73586400 1.55521800 -0.36611500 O 2.90093800 1.27240500 -0.63639700 H 2.20184400 1.88836500 1.64208000 C 0.84891700 -1.26868700 1.70569000 C 1.07139400 -1.59875900 0.34937700 C 0.00171200 -1.58342100 -0.56139700 C -1.30912700 -1.23754300 -0.13120000 C -1.49355400 -0.91419600 1.22866700 C -0.43524300 -0.92653500 2.14316500 H 1.69164000 -1.28519000 2.40230900 H 0.14291900 -1.83335900 -1.61348700 H -0.62733800 -0.66821900 3.18807100 F -2.73796900 -0.57805800 1.67423300 O 2.36631900 -1.91944300 0.02328400 C -2.39554200 -1.22252100 -1.05842300 C -3.31579400 -1.21412600 -1.86448700 H -4.12921500 -1.20432600 -2.56523400 C 2.63348500 -2.26048000 -1.34400400 H 2.05163800 -3.15201400 -1.64795200 H 2.38934800 -1.41461100 -2.01531800 H 3.70986200 -2.47938900 -1.38980900

[S49]

Table S33. Cartesian coordinates of Cytosine–MMO2 structure (=0o)


ATOM X Y Z

N -0.13128200 -2.00805000 1.05788400 C 0.95751000 -1.53150300 1.72141600 H 0.92770600 -1.56740500 2.81421100 C 2.02267300 -1.03738300 1.01383600 H 2.90974400 -0.64834600 1.51658000 C 1.89663500 -1.06449900 -0.42644300 N 2.92713700 -0.58493300 -1.18525900 H 2.83767500 -0.60446800 -2.19356500 H 3.76723200 -0.21535900 -0.76447400 N 0.83392600 -1.52950000 -1.08040900 C -0.24147300 -2.02810400 -0.37842900 O -1.27058700 -2.48124800 -0.87443100 H -0.93077600 -2.37836400 1.56145400 C 0.71937100 2.02035300 -0.20287900 C -0.38606300 1.53983900 -0.91922200 C -1.51443600 1.01810500 -0.24827600 C -1.54082400 0.97488000 1.15965900 C -0.42743100 1.45899900 1.87512200 C 0.69136700 1.97628600 1.21076600 H -0.39186200 1.56164000 -2.01386800 H -2.40098900 0.57649600 1.70143600 H -0.44514600 1.42666000 2.97010700 H 1.54789700 2.34822800 1.78354300 O -2.53260700 0.57897700 -1.06267900 C -3.69666800 0.04191500 -0.42324500 H -4.17830100 0.80154600 0.22275000 H -4.37780800 -0.24586200 -1.23733800 H -3.43834700 -0.84598700 0.18603400 C 1.92783300 2.57913800 -0.92698900 H 2.83837400 2.00597900 -0.67222500 H 1.79066400 2.54286600 -2.02049700 H 2.11006300 3.62977100 -0.63467900

[S50]

Table S34. Cartesian coordinates of Cytosine–NaM structure (=0o)


ATOM X Y Z

N -0.18477700 1.83083300 1.45872000 C -1.42949700 1.38174300 1.77782400 H -1.62987200 1.18385700 2.83473900 C -2.36089700 1.19907100 0.78862100 H -3.36702000 0.84034500 1.01229300 C -1.92907400 1.50901200 -0.55618000 N -2.81449400 1.34633600 -1.58442500 H -2.51094100 1.56368300 -2.52553200 H -3.75565800 1.01707500 -1.42567700 N -0.71283600 1.94854100 -0.87371000 C 0.23013000 2.13530500 0.11310200 O 1.37895000 2.53498300 -0.06269600 H 0.52012600 1.97315300 2.17479500 C 2.01706400 -0.94599900 1.48104200 C 0.74938400 -1.39733100 1.79729100 C -0.23890100 -1.60036300 0.78383600 C 0.11700500 -1.32219100 -0.58724800 C 1.43224300 -0.85615200 -0.89651900 C 2.36503400 -0.67173300 0.12110100 H -1.81141000 -2.27265400 2.12801800 H 2.77561500 -0.78956600 2.25386900 H 0.48709900 -1.60617700 2.84028400 C -1.55282500 -2.06483200 1.08345000 C -0.86769700 -1.52396300 -1.60147200 H 1.67856300 -0.65233600 -1.94108300 C -2.14101600 -1.97787700 -1.27895500 C -2.48961600 -2.25151300 0.07392800 H -0.60257300 -1.31423500 -2.64408200 H -2.88382500 -2.12699200 -2.07021500 H -3.49633800 -2.60873600 0.31492300 O 3.65300700 -0.23004300 -0.05740600 C 4.06282400 0.06235300 -1.39958700 H 3.43737100 0.86578200 -1.83467100 H 5.10822700 0.39508300 -1.32606000 H 3.99476900 -0.84095200 -2.03629400

[S51]

Table S35. Cartesian coordinates of Cytosine–5SICS structure (=0o)


ATOM X Y Z

N -0.97303600 1.96518900 -1.03330700 C -0.28675400 1.28576200 -1.99259600 H -0.86242600 0.91311600 -2.84472000 C 1.06470900 1.09887300 -1.85837800 H 1.64282100 0.55865500 -2.61000900 C 1.66872700 1.65769800 -0.66930200 N 3.01343700 1.50304500 -0.48073800 H 3.43514800 1.89476700 0.35219600 H 3.58867100 1.01092100 -1.14881300 N 1.00205700 2.32307800 0.27201100 C -0.35617600 2.51612200 0.14630900 O -1.07059300 3.11213400 0.94931100 H -1.97362500 2.11516200 -1.11228500 C -2.02096200 -1.07905800 0.01511400 C -0.57453700 -1.29466800 0.14219500 C 0.14067300 -0.79586800 1.28384100 C -0.57363100 -0.07831000 2.30980500 C -1.92054000 0.11273800 2.17382200 H -0.40250700 -2.37535400 -1.72269900 H -3.59042900 -0.22098600 0.98857000 C 0.14726500 -1.99815700 -0.85621600 C 1.53972900 -1.02009800 1.37894500 H -0.04731000 0.30857000 3.18520400 H -2.53684300 0.64392000 2.90221900 C 2.23953700 -1.71386300 0.39014600 C 1.51808100 -2.20178300 -0.73437800 H 2.07457200 -0.63479600 2.25459300 H 2.05529800 -2.74803400 -1.51779400 N -2.58825100 -0.37415600 1.07023000 S -3.01530500 -1.59120800 -1.24979600 C 3.72959900 -1.95105300 0.49429800 H 3.95335200 -3.03375200 0.48793700 H 4.25654200 -1.50556600 -0.36954000 H 4.14259300 -1.51446800 1.41839700

[S52]

Table S36. Cartesian coordinates of Cytosine–TPT3 structure (=0o)


ATOM X Y Z

N -0.76827800 -1.73456700 -1.30950900 C -0.74920700 -0.60284700 -2.06560700 H -0.06581100 -0.58792400 -2.91949500 C -1.56575900 0.44825700 -1.73724500 H -1.57352500 1.36874000 -2.32345900 C -2.40733500 0.26091100 -0.57635100 N -3.24303300 1.27474100 -0.20021500 H -3.83176300 1.14234100 0.61276300 H -3.28445200 2.14419300 -0.71182300 N -2.42984600 -0.84396000 0.16661600 C -1.61307700 -1.90567000 -0.15513500 O -1.55036700 -2.96995400 0.45625800 H -0.17233600 -2.52464800 -1.53430200 C 0.25322200 0.68778800 1.51025600 C 1.13942000 0.71990400 0.40679000 C 2.00800300 -0.36492800 0.04326700 C 1.03009900 -1.53753600 1.99243000 C 0.20531900 -0.49076600 2.32685800 C -0.49302900 1.90753900 1.63747200 C -0.17009000 2.81917900 0.65654500 H 2.47441300 -2.24744000 0.68433900 H 1.06891800 -2.47627000 2.54883600 H -0.46087700 -0.56469900 3.18840800 H -1.23233400 2.09382500 2.42094900 H -0.58363600 3.82045600 0.51780300 N 1.87521500 -1.45632100 0.90757500 S 3.08995500 -0.40935800 -1.25003000 S 1.04757800 2.23815900 -0.45753400

[S53]

Table S37. Cartesian coordinates of Guanine–FEMO structure (=0o)


ATOM X Y Z

N 0.78975500 -2.58921200 0.25494900 C 1.47784100 -2.14113700 1.37887600 H 2.46107300 -2.53249600 1.63770000 N 0.81195600 -1.22541800 2.05392800 C -0.36860400 -1.06030600 1.34517200 C -1.49428900 -0.18680500 1.59069300 O -1.70896400 0.63311100 2.47695500 N -2.48903500 -0.38246900 0.55193600 H -3.28899300 0.24079000 0.63149900 C -2.40766900 -1.25467400 -0.51079500 N -3.45013900 -1.23011000 -1.42216800 H -4.37353400 -1.01243500 -1.06134500 H -3.43336300 -2.00893100 -2.07354100 N -1.37647100 -2.05429300 -0.72289500 C -0.40282900 -1.90227100 0.21721800 H 1.09045100 -3.28352400 -0.41977900 C 1.22245800 -0.03378300 -2.07237600 C 2.07208200 0.29298100 -0.99099100 C 1.67536900 1.26246500 -0.05467800 C 0.42177300 1.92187000 -0.18382900 C -0.39937200 1.57053100 -1.27473900 C -0.01353100 0.60677000 -2.21216700 H 1.54537500 -0.79042100 -2.79276300 H 2.30953300 1.53523400 0.78955900 H -0.68450800 0.36776200 -3.04169900 F -1.60784400 2.18386400 -1.42806200 O 3.26133200 -0.39227500 -0.94500700 C 0.02000700 2.90733000 0.76891300 C -0.31008500 3.74910400 1.59300600 H -0.60761700 4.48921000 2.31169600 C 4.15183100 -0.08928300 0.13775100 H 4.45623500 0.97484500 0.11067900 H 3.67606800 -0.31182700 1.11237100 H 5.02856900 -0.73589900 -0.00998000

[S54]

Table S38. Cartesian coordinates of Guanine–MMO2 structure (=0o)


ATOM X Y Z

N -0.66413800 -2.25884200 -0.55249600 C -1.06105300 -1.78195500 -1.79848200 H -1.96137400 -2.15088100 -2.28859500 N -0.24104100 -0.86960100 -2.28100600 C 0.74154800 -0.73695800 -1.31134500 C 1.90646500 0.11839400 -1.26900100 O 2.33637000 0.94652100 -2.06473700 N 2.62525600 -0.11077200 -0.02898400 H 3.43075900 0.49824800 0.09338300 C 2.28250200 -0.99619800 0.96866300 N 3.08102300 -1.00430400 2.10014200 H 4.06663300 -0.79912500 1.97088400 H 2.89940500 -1.79178800 2.71497100 N 1.21839400 -1.77901100 0.91743300 C 0.49619700 -1.59526800 -0.22255500 H -1.12586800 -2.95677900 0.01972100 C -0.26781300 2.21671900 0.09054700 C -1.45116100 1.61970000 -0.36692400 C -2.11981500 0.64657800 0.40866300 C -1.60001500 0.26268000 1.66057100 C -0.41047000 0.86557400 2.11599000 C 0.25285400 1.83020700 1.34778000 H -1.87691200 1.89955100 -1.33603600 H -2.09807900 -0.48698800 2.27867000 H -0.00390700 0.56901200 3.08918400 H 1.17657000 2.28821600 1.71796200 O -3.26921200 0.13680000 -0.14970300 C -3.97929400 -0.85342400 0.60368200 H -4.31230100 -0.44495900 1.57763400 H -4.85177800 -1.12461600 -0.00847800 H -3.34692400 -1.74564700 0.77794400 C 0.44618900 3.26025300 -0.74503300 H 1.47525000 2.93475800 -0.98500600 H -0.08719200 3.44765900 -1.69175000 H 0.52518900 4.21666500 -0.19592700

[S55]

Table S39. Cartesian coordinates of Guanine–NaM structure (=0o)


ATOM X Y Z

N -0.67892600 -2.27642200 0.24492700 C -1.11959400 -2.21933600 -1.07416300 H -2.09441300 -2.60863200 -1.36583400 N -0.24162700 -1.65892600 -1.88209500 C 0.82686900 -1.33062800 -1.06120800 C 2.08313600 -0.68576800 -1.37169400 O 2.53916700 -0.25960800 -2.42726600 N 2.87078200 -0.56037200 -0.15896500 H 3.74923500 -0.06538900 -0.29322500 C 2.51108800 -0.98045900 1.10234600 N 3.39443000 -0.69981900 2.13137300 H 4.38308300 -0.69227600 1.90171800 H 3.17383800 -1.18660300 2.99480300 N 1.36232000 -1.57531000 1.37479900 C 0.57431200 -1.70700100 0.27180100 H -1.16982700 -2.65649200 1.04636700 C -2.10842300 0.41967300 1.90794800 C -0.85350200 0.98485500 2.03628200 C -0.16878900 1.53276000 0.90668600 C -0.81993400 1.48327200 -0.38074700 C -2.11754300 0.89528200 -0.49550800 C -2.74957600 0.37294100 0.63026000 H 1.60971600 2.15279200 1.99483300 H -2.63514400 -0.00043900 2.77004000 H -0.36605100 1.01855200 3.01684300 C 1.12534500 2.12095900 1.01220900 C -0.13873900 2.02957100 -1.51058400 H -2.59048400 0.86917800 -1.47987200 C 1.12289700 2.59685200 -1.37693400 C 1.76299100 2.64447800 -0.10622500 H -0.62874700 1.99451500 -2.49036800 H 1.63065400 3.01118200 -2.25477600 H 2.75721500 3.09417800 -0.01421700 O -3.99130600 -0.21344800 0.63923600 C -4.68594600 -0.29061100 -0.61233100 H -4.10904500 -0.88731100 -1.34521700 H -5.64291600 -0.78518400 -0.39189800 H -4.86640200 0.72127500 -1.02404800

[S56]

Table S40. Cartesian coordinates of Guanine–5SICS structure (=0o)


ATOM X Y Z

N -1.10683500 1.48624600 2.08411200 C -0.37945700 0.85255400 3.08750600 H -0.83399400 0.59433500 4.04333900 N 0.87108900 0.61924700 2.74204800 C 0.97550400 1.12053000 1.45320000 C 2.10176200 1.14756000 0.54696300 O 3.25242200 0.74112400 0.66779700 N 1.70169100 1.77947700 -0.69700000 H 2.43264400 1.78523100 -1.40438100 C 0.45727300 2.28656500 -0.99873400 N 0.27928500 2.78989600 -2.27659300 H 1.08398300 3.22314500 -2.71817000 H -0.58435000 3.31260500 -2.38631800 N -0.56465000 2.26291200 -0.16036600 C -0.24887800 1.66615100 1.02245500 H -2.08055500 1.76739800 2.10791300 C -2.17787700 -0.74495500 -0.70976600 C -0.77196700 -1.16599300 -0.74023300 C -0.17857100 -1.81300400 0.39684100 C -0.97557700 -2.04786700 1.57469700 C -2.28308500 -1.64850900 1.58435800 H -0.42738600 -0.45135000 -2.75166500 H -3.80820900 -0.73987600 0.51053100 C 0.02979400 -0.94419200 -1.88945100 C 1.18391700 -2.20898400 0.33761100 H -0.54222500 -2.53833000 2.44914800 H -2.95594500 -1.78732200 2.43320100 C 1.96321000 -1.98549900 -0.79884000 C 1.36207800 -1.34383600 -1.91688700 H 1.62559800 -2.70174200 1.21132700 H 1.96261000 -1.16237400 -2.81531100 N -2.83351000 -1.02912200 0.48244600 S -3.03324700 0.02376000 -1.94606300 C 3.41405600 -2.40838700 -0.85885300 H 3.57895300 -3.11884100 -1.68976000 H 4.06715200 -1.53562700 -1.04351200 H 3.73171600 -2.88978900 0.08054800

[S57]

Table S41. Cartesian coordinates of Guanine–TPT3 structure (=0o)


ATOM X Y Z

N 0.66640700 1.84496400 -1.91641900 C 1.32127800 2.76463500 -1.10229800 H 1.19813300 3.83794700 -1.24277000 N 2.07312200 2.18988300 -0.18467600 C 1.90816100 0.83002200 -0.40120500 C 2.47352500 -0.30462200 0.29406300 O 3.23963400 -0.37363200 1.24911400 N 1.98697800 -1.53024000 -0.31252800 H 2.30328900 -2.37279000 0.16157400 C 1.12602100 -1.63277100 -1.38257400 N 0.74187100 -2.90955700 -1.75699800 H 1.42059000 -3.65278100 -1.62587900 H 0.26328700 -2.93934300 -2.65209600 N 0.61951900 -0.58870700 -2.01592400 C 1.03276200 0.59230500 -1.47801600 H 0.03580000 2.03775200 -2.68642700 C -0.69389700 0.86808900 1.65311900 C -1.29252200 -0.17494400 0.90629600 C -2.18143100 0.03931300 -0.20157600 C -1.82870500 2.45000400 0.23966600 C -0.98010600 2.22807300 1.29723800 C 0.14771100 0.36526900 2.70180200 C 0.17317100 -1.01168100 2.73270300 H -3.01068600 1.59447200 -1.23413600 H -2.10943100 3.44575900 -0.10959100 H -0.54356900 3.06732100 1.84189200 H 0.70479800 0.99935900 3.39656500 H 0.72762400 -1.65069400 3.42340500 N -2.38588500 1.39928300 -0.45550500 S -2.93495600 -1.14138200 -1.14145400 S -0.81859400 -1.75233600 1.49605400

[S58]

Table S42. Cartesian coordinates of Thymine–FEMO structure (=0o)


ATOM X Y Z

N -0.73374900 -2.41413600 -0.11717500 C 0.03575300 -2.06017700 0.97830400 H 0.91206000 -2.69009700 1.15415900 C -0.27342300 -1.00233500 1.78280300 C 0.54962400 -0.60100100 2.97794500 H 1.41570500 -1.27228900 3.10177700 H 0.90947700 0.43746700 2.86892700 H -0.06313600 -0.62803900 3.89644600 C -1.47424300 -0.21230600 1.46521200 O -1.87431000 0.76418700 2.09794600 N -2.18895900 -0.66182200 0.32403200 H -3.02386200 -0.13450600 0.07978600 C -1.89213600 -1.73660100 -0.51053000 O -2.56248200 -2.06352200 -1.48428000 H -0.47881400 -3.20562100 -0.69625100 C 1.08987700 -0.46461000 -2.05716700 C 1.90077800 -0.13516600 -0.94724200 C 1.56419300 0.95844600 -0.13195700 C 0.41049900 1.74146400 -0.41279300 C -0.37454500 1.38355200 -1.52787500 C -0.04796500 0.29673600 -2.34559000 H 1.36506800 -1.31865300 -2.68215800 H 2.17053600 1.23644200 0.73081000 H -0.68764800 0.05774100 -3.19948800 F -1.48753900 2.11354100 -1.82527700 O 2.99300900 -0.94434800 -0.75163100 C 0.06977200 2.85302300 0.41703100 C -0.20897000 3.80199500 1.13705100 H -0.46090400 4.63662600 1.76372300 C 3.84143800 -0.64295100 0.36483100 H 4.27329800 0.37188200 0.26801800 H 3.28003400 -0.71533700 1.31632800 H 4.64134900 -1.39672800 0.34098300

[S59]

Table S43. Cartesian coordinates of Thymine–MMO2 structure (=0o)


ATOM X Y Z

N -0.43648700 -2.14775500 0.35970000 C -0.32730400 -1.33225300 1.47349000 H 0.42034100 -1.64514100 2.20749700 C -1.09512000 -0.21763800 1.64649800 C -0.99198700 0.68190400 2.84942200 H -0.22394300 0.31426200 3.55014100 H -0.73785900 1.71177100 2.54187000 H -1.96226700 0.73936100 3.37392800 C -2.07514600 0.12299700 0.60223000 O -2.83135400 1.09340800 0.62209500 N -2.10444700 -0.77916900 -0.49340400 H -2.77227400 -0.56891000 -1.23136000 C -1.33121000 -1.92061300 -0.69078500 O -1.41503900 -2.65339600 -1.67080100 H 0.14765500 -2.96961500 0.25923700 C 0.21864200 1.90827200 -0.96045100 C 1.14842500 1.59503100 0.04125100 C 1.97760700 0.45662600 -0.06870200 C 1.87795300 -0.38287300 -1.19571500 C 0.94199500 -0.06384300 -2.19975900 C 0.11977200 1.06437900 -2.09146400 H 1.24658600 2.23032300 0.92755000 H 2.50745500 -1.26837400 -1.30402000 H 0.86229100 -0.71487000 -3.07734800 H -0.60216800 1.29675200 -2.88194700 O 2.84721700 0.25838800 0.97879000 C 3.70713300 -0.88523600 0.90795000 H 4.36555400 -0.82980900 0.01928200 H 4.31190900 -0.86064300 1.82618400 H 3.11683100 -1.82134000 0.86828400 C -0.66895500 3.13063600 -0.83816000 H -1.73667700 2.84366100 -0.84891400 H -0.46735300 3.67905700 0.09697700 H -0.50697400 3.82044900 -1.68692600

[S60]

Table S44. Cartesian coordinates of Thymine–NaM structure (=0o)


ATOM X Y Z

N -0.40433100 0.97243700 2.02427600 C 0.00698700 1.80150100 0.99424500 H 0.98069900 2.27700900 1.14058300 C -0.74523200 2.01251300 -0.12445000 C -0.31638900 2.90944300 -1.25513600 H 0.66968500 3.35780700 -1.04852700 H -0.26465400 2.34179100 -2.20112200 H -1.05488000 3.71582800 -1.41077900 C -2.04360600 1.32709400 -0.23123500 O -2.82481400 1.42104800 -1.17719000 N -2.36686600 0.50367400 0.87901700 H -3.25872900 0.01658700 0.83310700 C -1.61559500 0.27353800 2.02896300 O -1.96479500 -0.45726500 2.95005700 H 0.17632000 0.83551900 2.84334100 C 2.13216500 -1.34989700 1.20378200 C 0.91356200 -1.98893900 1.07201900 C 0.09130200 -1.78571700 -0.08020000 C 0.56345300 -0.89247400 -1.11127300 C 1.82586100 -0.23994700 -0.95887300 C 2.59575700 -0.46575500 0.17951700 H -1.51684800 -3.10831900 0.54921200 H 2.76379600 -1.50307000 2.08395900 H 0.56230800 -2.66534600 1.85899900 C -1.16889700 -2.43238800 -0.24023400 C -0.25537500 -0.68751700 -2.26301600 H 2.16233300 0.43150200 -1.75213900 C -1.47989100 -1.33210700 -2.39131600 C -1.94335800 -2.21254900 -1.37312500 H 0.09849800 -0.01028600 -3.04879200 H -2.09491900 -1.16292400 -3.28193900 H -2.91007500 -2.71438800 -1.48622000 O 3.81938600 0.10402000 0.43233500 C 4.33906200 1.00089300 -0.55784400 H 3.66112900 1.86483600 -0.69925100 H 5.31008900 1.34179300 -0.17070400 H 4.47655800 0.48030800 -1.52535300

[S61]

Table S45. Cartesian coordinates of Thymine–5SICS structure (=0o)


ATOM X Y Z

N 0.71893300 -2.26418600 -0.33593400 C -0.22283400 -2.36690400 0.67402500 H 0.12731800 -2.85303900 1.58874100 C -1.49686100 -1.89661700 0.54164600 C -2.53534900 -1.99827600 1.62702500 H -2.12266800 -2.49642500 2.52011000 H -2.90022700 -0.99463400 1.90873700 H -3.41369900 -2.56491900 1.27028000 C -1.87532600 -1.25625800 -0.72866200 O -2.98253000 -0.78731400 -0.98968900 N -0.83562800 -1.20477400 -1.69383200 H -1.06797300 -0.76709200 -2.58221800 C 0.46968700 -1.67704700 -1.58043600 O 1.31581500 -1.59412200 -2.46452900 H 1.65780200 -2.62333900 -0.20824700 C 2.25226600 0.68235800 0.35126400 C 0.88837700 1.19516700 0.17344800 C -0.08067000 1.07366000 1.22695000 C 0.29549500 0.44179300 2.46669500 C 1.57032600 -0.02976700 2.61363400 H 1.23964100 1.90979400 -1.83683200 H 3.42853900 -0.26089100 1.72013100 C 0.49777600 1.82025100 -1.03874800 C -1.39227900 1.57941400 1.02551700 H -0.42726100 0.34009300 3.27928000 H 1.93769400 -0.52049200 3.51739100 C -1.76528700 2.19271900 -0.17176600 C -0.79518400 2.30583600 -1.20579900 H -2.12292800 1.48093600 1.83652100 H -1.07487600 2.78512100 -2.15067500 N 2.48533600 0.09682600 1.59013600 S 3.51138400 0.73879500 -0.77232300 C -3.16300000 2.73035700 -0.38327100 H -3.13509800 3.81409800 -0.60022600 H -3.64308600 2.23819600 -1.24908800 H -3.79489200 2.56818700 0.50529000

[S62]

Table S46. Cartesian coordinates of Thymine–TPT3 structure (=0o)


ATOM X Y Z

N -0.47930700 -2.23203200 0.10419000 C -1.48024000 -1.72943100 0.91844800 H -1.51238200 -2.14790500 1.92814400 C -2.36460400 -0.78029800 0.49549700 C -3.45941700 -0.22090500 1.36457900 H -3.43950800 -0.68123400 2.36645600 H -3.35113200 0.87343100 1.46703600 H -4.44761400 -0.39869900 0.90446300 C -2.24139900 -0.27702000 -0.88236700 O -2.96379800 0.57484000 -1.39852500 N -1.18380400 -0.85968900 -1.62880300 H -1.07395000 -0.53083800 -2.58513400 C -0.27051000 -1.82767400 -1.21813400 O 0.62152400 -2.28332300 -1.92601000 H 0.16280800 -2.93718300 0.44656200 C 0.09074300 1.47911500 0.96209100 C 1.12464900 0.96105100 0.14559700 C 2.06572900 -0.03453100 0.57760600 C 0.85119500 0.04026200 2.73395800 C -0.04134100 0.99287900 2.30531500 C -0.69916000 2.46017200 0.27328800 C -0.26413300 2.66466000 -1.01765400 H 2.48688300 -1.13713800 2.24471300 H 0.83560900 -0.39323600 3.73603100 H -0.82179900 1.36057200 2.97407300 H -1.54788900 2.98545900 0.71920500 H -0.68080700 3.35050200 -1.75848300 N 1.84044800 -0.43168200 1.89946700 S 3.32258400 -0.70351300 -0.32682200 S 1.11601300 1.67965400 -1.44943400

[S63]

Table S47. Mol2 file of the FEMO base.

1 O3' 0.0000 0.0000 0.0000 OS 1 LI -0.558500

2 P 5.0720 2.3560 0.4640 P 1 LI 1.220100

3 O1P 6.0930 1.5280 1.1240 O2 1 LI -0.792800

4 O2P 5.3510 3.3990 -0.5330 O2 1 LI -0.792800

5 O5' 3.9690 1.3130 -0.1630 OS 1 LI -0.497900

6 C5' 2.9420 1.8350 -1.0110 CI 1 LI 0.059500

7 H5'1 3.3530 2.1430 -1.9800 H1 1 LI 0.046600

8 H5'2 2.4590 2.7030 -0.5380 H1 1 LI 0.046600

9 C4' 1.8780 0.7780 -1.2580 CT 1 LI 0.196300

10 H4' 0.9930 1.2810 -1.6730 H1 1 LI 0.072400

11 O4' 2.3580 -0.1840 -2.2050 OS 1 LI -0.395200

12 C1' 2.0030 -1.5010 -1.7610 CT 1 LI 0.193900

13 H1' 0.9740 -1.7190 -2.0830 H1 1 LI 0.045000

14 C2' 2.0270 -1.3940 -0.2280 CT 1 LI -0.108100

15 H2'1 3.0570 -1.4210 0.1310 HC 1 LI 0.049300

16 H2'2 1.4450 -2.1820 0.2590 HC 1 LI 0.049300

17 C3' 1.4360 -0.0000 0.0000 CT 1 LI 0.154600

18 H3' 1.8150 0.4660 0.9150 H1 1 LI 0.058500

19 C1 2.9100 -2.5280 -2.3900 CA 1 LI -0.024400

20 C12 4.3140 -2.5150 -2.2130 CA 1 LI 0.120600

21 C10 5.1110 -3.4830 -2.8230 CA 1 LI -0.192100

22 H11 6.1850 -3.4830 -2.6980 HA 1 LI 0.159600

23 C6 4.5410 -4.4990 -3.6200 CA 1 LI 0.001100

24 C4 3.1530 -4.4960 -3.7750 CA 1 LI 0.253700

[S64]

25 F5 2.5660 -5.4540 -4.5360 F 1 LI -0.192300

26 C2 2.3520 -3.5320 -3.1810 CA 1 LI -0.251600

27 H3 1.2810 -3.5640 -3.3490 HA 1 LI 0.186800

28 C7 5.3570 -5.4880 -4.2410 c1 1 LI 0.020300

29 C8 6.0630 -6.3230 -4.7630 c1 1 LI -0.411800

30 H9 6.6740 -7.0620 -5.2280 HA 1 LI 0.308800

31 O13 4.8090 -1.5270 -1.4220 OS 1 LI -0.210100

32 C14 6.2130 -1.4000 -1.2690 CT 1 LI -0.011300

33 H15 6.7040 -1.2400 -2.2370 H1 1 LI 0.065300

34 H16 6.3550 -0.5230 -0.6370 H1 1 LI 0.065300

35 H17 6.6460 -2.2820 -0.7810 H1 1 LI 0.065300

Table S48. Mol2 file of the MMO2 base.

1 O3' 0.0000 0.0000 0.0000 OS 1 LI -0.560100

2 P 5.4400 1.8540 0.3940 P 1 LI 1.220300

3 O1P 6.3840 0.7870 0.7580 O2 1 LI -0.792700

4 O2P 5.7360 2.9590 -0.5300 O2 1 LI -0.792700

5 O5' 4.0690 1.1040 -0.1090 OS 1 LI -0.500900

6 C 3.0290 1.8970 -0.6850 CI 1 LI 0.070700

7 H32 3.3860 2.4250 -1.5790 H1 1 LI 0.041100

8 H31 2.6580 2.6380 0.0390 H1 1 LI 0.041100

9 C30 1.8780 0.9930 -1.0920 CT 1 LI 0.198900

10 H29 1.0190 1.6240 -1.3560 H1 1 LI 0.070100

11 O28 2.2660 0.2180 -2.2330 OS 1 LI -0.393700

12 C27 1.9680 -1.1680 -2.0140 CT 1 LI 0.143300

13 H26 0.9480 -1.3760 -2.3620 H1 1 LI 0.048900

14 C25 2.0260 -1.3230 -0.4860 CT 1 LI -0.115900

[S65]

15 H24 3.0700 -1.3960 -0.1660 HC 1 LI 0.052100

16 H23 1.4770 -2.1990 -0.1320 HC 1 LI 0.052100

17 C22 1.4350 -0.0000 0.0000 CT 1 LI 0.153600

18 H21 1.8120 0.2900 0.9870 H1 1 LI 0.055800

19 C18 2.9430 -2.0340 -2.7680 CA 1 LI 0.002600

20 C17 4.1540 -1.5420 -3.2460 CA 1 LI -0.165500

21 H16 4.3780 -0.4940 -3.0820 HA 1 LI 0.159300

22 C15 5.0540 -2.3670 -3.9290 CA 1 LI -0.261000

23 H14 5.9900 -1.9560 -4.2960 HA 1 LI 0.162000

24 C13 4.7570 -3.7130 -4.1470 CA 1 LI 0.049000

25 C12 3.5400 -4.2220 -3.6650 CA 1 LI -0.173600

26 H11 3.3060 -5.2670 -3.8290 HA 1 LI 0.122900

27 C10 2.6470 -3.3940 -2.9810 CA 1 LI 0.118500

28 O9 1.4480 -3.8250 -2.4690 OS 1 LI -0.215300

29 C8 1.0640 -5.1730 -2.6900 CT 1 LI -0.015200

30 H7 0.0830 -5.2840 -2.2260 H1 1 LI 0.063400

31 H6 0.9880 -5.3960 -3.7620 H1 1 LI 0.063400

32 H5 1.7700 -5.8710 -2.2230 H1 1 LI 0.063400

33 C4 5.7110 -4.6210 -4.8860 CT 1 LI -0.089500

34 H3 6.0300 -5.4610 -4.2560 HC 1 LI 0.041200

35 H2 5.2440 -5.0460 -5.7820 HC 1 LI 0.041200

36 H1 6.6080 -4.0800 -5.2010 HC 1 LI 0.041200

Table S49. Mol2 file of the NaM base.

1 O3' 0.0000 0.0000 0.0000 OS 1 LI -0.560000

2 P 5.4520 1.8130 0.3990 P 1 LI 1.220300

3 O1P 6.3960 0.7340 0.7280 O2 1 LI -0.792700

[S66]

4 O2P 5.7480 2.9450 -0.4910 O2 1 LI -0.792700

5 O5' 4.0800 1.0800 -0.1240 OS 1 LI -0.501800

6 C 3.0400 1.8910 -0.6740 CI 1 LI 0.071600

7 H35 3.3910 2.4330 -1.5620 H1 1 LI 0.040700

8 H34 2.6830 2.6220 0.0670 H1 1 LI 0.040700

9 C33 1.8770 1.0020 -1.0830 CT 1 LI 0.208300

10 H32 1.0230 1.6440 -1.3340 H1 1 LI 0.067400

11 O31 2.2490 0.2370 -2.2370 OS 1 LI -0.395000

12 C30 1.9610 -1.1500 -2.0250 CT 1 LI 0.142500

13 H29 0.9420 -1.3640 -2.3720 H1 1 LI 0.050900

14 C28 2.0250 -1.3190 -0.4980 CT 1 LI -0.093600

15 H27 3.0700 -1.3910 -0.1830 HC 1 LI 0.046100

16 H26 1.4780 -2.1980 -0.1480 HC 1 LI 0.046100

17 C25 1.4350 -0.0000 0.0000 CT 1 LI 0.151000

18 H24 1.8130 0.2810 0.9890 H1 1 LI 0.054700

19 C21 2.9410 -2.0070 -2.7840 CA 1 LI -0.007900

20 C20 4.1190 -1.5020 -3.2790 CA 1 LI -0.215800

21 H19 4.3300 -0.4490 -3.1350 HA 1 LI 0.161200

22 C18 5.0530 -2.3200 -3.9720 CA 1 LI 0.089700

23 C17 4.7490 -3.7050 -4.1560 CA 1 LI 0.060900

24 C16 5.6810 -4.5230 -4.8490 CA 1 LI -0.191500

25 H15 5.4510 -5.5760 -4.9900 HA 1 LI 0.137700

26 C14 6.8590 -3.9960 -5.3360 CA 1 LI -0.128800

27 H13 7.5610 -4.6350 -5.8640 HA 1 LI 0.137400

28 C12 7.1590 -2.6240 -5.1540 CA 1 LI -0.167800

29 H11 8.0880 -2.2200 -5.5430 HA 1 LI 0.140500

30 C10 6.2710 -1.8070 -4.4860 CA 1 LI -0.172500

[S67]

31 H9 6.4930 -0.7520 -4.3440 HA 1 LI 0.138000

32 C8 3.5280 -4.2200 -3.6410 CA 1 LI -0.246600

33 H7 3.3100 -5.2720 -3.7870 HA 1 LI 0.142700

34 C6 2.6500 -3.3940 -2.9720 CA 1 LI 0.152600

35 O5 1.4580 -3.8050 -2.4360 OS 1 LI -0.213800

36 C4 1.0710 -5.1590 -2.6210 CT 1 LI -0.007400

37 H3 1.7840 -5.8440 -2.1450 H1 1 LI 0.062300

38 H2 0.0950 -5.2590 -2.1450 H1 1 LI 0.062300

39 H1 0.9870 -5.4040 -3.6860 H1 1 LI 0.062300

Table S50. Mol2 file of the 5SICS base.

1 O3' 0.0000 0.0000 0.0000 OS 1 LI -0.552300

2 P 4.4870 1.1190 0.6750 P 1 LI 1.219600

3 O1P 5.4930 1.1430 -0.3960 O2 1 LI -0.793300

4 O2P 3.2270 1.8770 0.6620 O2 1 LI -0.793300

5 O5' 4.1440 -0.4630 0.9490 OS 1 LI -0.489100

6 C 2.7550 4.4930 -0.0580 C 1 LI 0.029000

7 C16 3.8340 5.4770 0.0000 CA 1 LI 0.184000

8 C15 5.0990 5.1430 0.5520 CA 1 LI 0.113400

9 C14 5.2960 3.8200 1.0590 CA 1 LI -0.273400

10 H 6.2580 3.5210 1.4590 HA 1 LI 0.163300

11 C13 4.2680 2.9380 1.0470 CA 1 LI -0.092100

12 H12 4.3430 1.9270 1.4200 H4 1 LI 0.166000

13 N 3.0270 3.2770 0.5460 NC 1 LI 0.075400

14 C1* 1.9700 2.2460 0.5920 CT 1 LI 0.203200

15 H1* 1.0230 2.7840 0.6390 H2 1 LI 0.061600

16 O4* 2.1530 1.4510 1.7550 OS 1 LI -0.395100

[S68]

17 C4* 1.8630 0.0700 1.4760 CT 1 LI 0.150600

18 H4* 1.0190 -0.2400 2.1040 H1 1 LI 0.089800

19 C5* 3.0660 -0.7850 1.8320 CI 1 LI 0.030900

20 H5*1 3.3440 -0.5850 2.8750 H1 1 LI 0.067100

21 H5*2 2.7840 -1.8440 1.7390 H1 1 LI 0.067100

22 C3* 1.4310 0.0000 -0.0000 CT 1 LI 0.164300

23 H3*2 1.8140 -0.9030 -0.4910 H1 1 LI 0.059500

24 C2* 2.0230 1.2770 -0.5910 CT 1 LI -0.033400

25 H2*1 3.0650 1.1010 -0.8730 HC 1 LI 0.028700

26 H2*2 1.4760 1.6620 -1.4540 HC 1 LI 0.028700

27 C11 6.1280 6.1120 0.5790 CA 1 LI -0.289900

28 H10 7.0900 5.8350 1.0020 HA 1 LI 0.168600

29 C9 5.9320 7.3920 0.0840 CA 1 LI 0.098800

30 C8 4.6650 7.7150 -0.4580 CA 1 LI -0.135800

31 H7 4.4940 8.7150 -0.8470 HA 1 LI 0.143500

32 C6 3.6470 6.7840 -0.5040 CA 1 LI -0.238100

33 H5 2.6810 7.0340 -0.9270 HA 1 LI 0.153800

34 C4 7.0290 8.4250 0.1130 CT 1 LI -0.153300

35 H3 7.2780 8.7600 -0.9010 HC 1 LI 0.062300

36 H2 6.7190 9.3110 0.6780 HC 1 LI 0.062300

37 H1 7.9390 8.0310 0.5730 HC 1 LI 0.062300

38 S 1.2800 4.7800 -0.8300 s2 1 LI -0.414700

Table S51. Mol2 file of the TPT3 base.

1 O3' 0.0000 0.0000 0.0000 OS 1 LI -0.553000

2 P 5.4610 1.6570 0.4570 P 1 LI 1.219500

3 O1P 6.4670 0.5850 0.5010 O2 1 LI -0.793300

[S69]

4 O2P 5.6950 3.0090 -0.0710 O2 1 LI -0.793300

5 O5' 4.1460 1.0220 -0.2950 OS 1 LI -0.487300

6 C5* 3.0630 1.8940 -0.6300 CT 1 LI 0.015500

7 H5*1 3.3350 2.5470 -1.4700 H1 1 LI 0.073100

8 H5*2 2.7820 2.5210 0.2280 H1 1 LI 0.073100

9 C4* 1.8610 1.0580 -1.0320 CT 1 LI 0.125300

10 H4* 1.0170 1.7320 -1.2170 H1 1 LI 0.098800

11 O4* 2.1510 0.3490 -2.2510 OS 1 LI -0.395100

12 C1* 1.9810 -1.0480 -2.0720 CT 1 LI 0.258000

13 H1* 1.0420 -1.3820 -2.5140 H2 1 LI 0.036700

14 C2* 2.0240 -1.2900 -0.5610 CT 1 LI -0.031900

15 H2*1 3.0630 -1.3900 -0.2350 HC 1 LI 0.023900

16 H2*2 1.4720 -2.1910 -0.2810 HC 1 LI 0.023900

17 C3* 1.4300 -0.0000 0.0000 CT 1 LI 0.167200

18 H3*2 1.8140 0.2330 1.0000 H1 1 LI 0.064100

19 N 3.0520 -1.7600 -2.8020 NC 1 LI 0.116700

20 C 2.7780 -3.0330 -3.2970 CA 1 LI 0.029700

21 C10 3.8690 -3.6110 -4.0100 CB 1 LI -0.027100

22 C9 5.1240 -3.0030 -4.1620 CB 1 LI 0.366400

23 C8 5.3250 -1.7280 -3.5640 CA 1 LI -0.321300

24 H 6.2780 -1.2150 -3.6240 HA 1 LI 0.185600

25 C7 4.2820 -1.1510 -2.9030 CA 1 LI -0.145000

26 H6 4.3470 -0.1880 -2.4180 H4 1 LI 0.192500

27 C5 6.0290 -3.8170 -4.9190 C* 1 LI -0.443200

28 H4 7.0480 -3.5340 -5.1530 HA 1 LI 0.214500

29 C3 5.4520 -4.9940 -5.3090 CA 1 LI -0.068600

30 H2 5.9090 -5.7830 -5.8910 H4 1 LI 0.211800

[S70]

31 S 3.8030 -5.1730 -4.7780 S 1 LI -0.047900

32 S1 1.3090 -3.8300 -3.0530 S 1 LI -0.389300

vlfv 7klvmrxuqdolv wkh2zqhu 6rflhwlhv

Documents