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

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* CHARMM27 All-Hydrogen Nucleic Acid Topology File * Foloppe, N. and MacKerell, A.D., Jr.

* All-atom emiprical force field for nucleic acids: * 1) Parameter optimization based on small molecule and * condensed phase macromolecular target data.

* J. Computational Chemistry, Submitted * and

* MacKerell, A.D., Jr. and Banavali, N.

* All-atom emiprical force field for nucleic acids:

* 2) Application to molecular dynamics simulations of DNA * and RNA in solution

* J. Computational Chemistry, Submitted *

MASS 1 HT 1.008000 H ! TIPS3P WATER HYDROGEN MASS 2 HN1 1.008000 H ! Nucleic acid amine proton

MASS 3 HN2 1.008000 H ! Nucleic acid ring nitrogen proton MASS 4 HN3 1.008000 H ! Nucleic acid aromatic carbon proton MASS 5 HN3B 1.008000 H ! NAD+ aromatic hydrogen

MASS 6 HN3C 1.008000 H ! Standard aromatic hydrogen (as in benzene) MASS 7 HNP 1.008000 H ! pure aromatic H

MASS 8 HN4 1.008000 H ! Nucleic acid phosphate hydroxyl proton MASS 9 HN5 1.008000 H ! Nucleic acid ribose hydroxyl proton MASS 10 HN6 1.008000 H ! Nucleic acid ribose aliphatic proton

MASS 11 HN7 1.008000 H ! Nucleic acid proton (equivalent to protein HA) MASS 12 HN8 1.008000 H ! Bound to CN8 in nucleic acids/model compounds MASS 13 HN9 1.008000 H ! Bound to CN9 in nucleic acids/model compounds MASS 20 CN1 12.011000 C ! Nucleic acid carbonyl carbon

MASS 21 CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon

MASS 22 CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2) MASS 23 CN2 12.011000 C ! Nucleic acid aromatic carbon to amide MASS 24 CN3 12.011000 C ! Nucleic acid aromatic carbon

MASS 25 CN3A 12.011000 C ! NAD+ aromatic carbon MASS 26 CN3B 12.011000 C ! NAD+ aromatic carbon MASS 27 CN3C 12.011000 C ! NADH aromatic carbon

MASS 28 CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC MASS 29 CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5 MASS 30 CN4 12.011000 C ! Nucleic acid purine C8 and ADE C2 MASS 31 CN5 12.011000 C ! Nucleic acid purine C4 and C5 MASS 32 CN5G 12.011000 C ! Nucleic acid guanine C5

MASS 33 CN7 12.011000 C ! Nucleic acid carbon (equivalent to protein CT1) MASS 34 CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1'

MASS 35 CN7C 12.011000 C ! C2' in arabinose

MASS 36 CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives

MASS 37 CN8 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 38 CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2) MASS 39 CN9 12.011000 C ! Nucleic acid carbon (equivalent to protein CT3) MASS 50 NN1 14.007000 N ! Nucleic acid amide nitrogen

MASS 51 NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha) MASS 52 NN2 14.007000 N ! Nucleic acid protonated ring nitrogen

MASS 53 NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE MASS 54 NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha)

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MASS 58 NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3

MASS 59 NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3 MASS 60 NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3 MASS 61 NN4 14.007000 N ! Nucleic acid purine N7

MASS 62 NN5 14.007000 N ! Nucleic acid sp2 amine nitrogen MASS 70 OT 15.999400 O ! TIPS3P WATER OXYGEN

MASS 71 ON1 15.999400 O ! Nucleic acid carbonyl oxygen

MASS 72 ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2 MASS 73 ON2 15.999400 O ! Nucleic acid phosphate ester oxygen MASS 74 ON3 15.999400 O ! Nucleic acid =O in phosphate

MASS 75 ON4 15.999400 O ! Nucleic acid phosphate hydroxyl oxygen MASS 76 ON5 15.999400 O ! Nucleic acid ribose hydroxyl oxygen MASS 77 ON6 15.999400 O ! Nucleic acid deoxyribose ring oxygen MASS 78 ON6B 15.999400 O ! Nucleic acid ribose ring oxygen MASS 82 P 30.974000 P ! phosphorus

MASS 83 P2 30.974000 P ! pyrophosphate phosphorus MASS 90 SOD 22.989770 NA ! Sodium Ion

MASS 102 CPH1 12.011000 C ! For imidazole model compound (NF) MASS 103 CPH2 12.011000 C ! For imidazole model compound (NF) MASS 104 HR3 1.008000 H ! For imidazole model compound (NF) MASS 105 HR1 1.008000 H ! For imidazole model compound (NF) MASS 106 NR1 14.007000 H ! For nitrogen in imidazol (NF) MASS 107 NR2 14.007000 H ! For nitrogen in imidazol (NF) ! oligonucleotide connectivity information

DECL +P DECL +O1P DECL +O2P DECL +O5' DECL -O3'

DEFA FIRS none LAST none AUTOGENERATE ANGLES DIHEDRALS

!Note that the default nucleotides are RNA. The !patches DEO1 and DEO2 must be applied to create !the corresponding DNA nucleotides.

RESI GUA -1.00 ! O6 ATOM P P 1.50 ! || ATOM O1P ON3 -0.78 ! C6 ATOM O2P ON3 -0.78 ! / \

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ATOM C2 CN2 0.75 ! O3' H3' O2' H2'' ATOM N1 NN2G -0.34 ! | |

ATOM H1 HN2 0.26 ! H2' ATOM N2 NN1 -0.68 !

ATOM H21 HN1 0.32 ATOM H22 HN1 0.35 ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 GROUP

ATOM C2' CN7B 0.14 ATOM H2'' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H2' HN5 0.43 GROUP

ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57

BOND P O1P P O2P P O5'

BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N2 C2 N1 N2 H21

BOND N2 H22 N1 H1 N1 C6 C6 C5 BOND C5 N7 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2'

BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8

BOND C2 N3 C4 C5 N7 C8 C6 O6

IMPH N2 N3 N1 C2 O6 N1 C5 C6 H22 H21 C2 N2 DONO H21 N2

DONO H22 N2 DONO H1 N1 DONO H2' O2' ACCE O6 C6 ACCE N3 ACCE N7 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5'

! Chi and sugar-phosphate backbone in B-DNA like conformation

BILD -O3' P O5' C5' 1.6001 101.45 -46.90 119.00 1.4401 !alpha BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802

BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801

BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284 !gamma BILD C5' C4' C3' O3' 1.5160 116.10 140.00 115.12 1.4212 !delta BILD C4' C3' O3' +P 1.5284 111.92 155.00 119.05 1.6001 !epsilon BILD C3' O3' +P +O5' 1.4212 119.05 -95.20 101.45 1.5996 !zeta BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160

BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212

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BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374

BILD C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 BILD C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 BILD N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 BILD C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 BILD C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 BILD N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 BILD N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 BILD H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 BILD N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 BILD C6 C2 *N1 H1 1.393 124.9 180.0 117.4 1.03 BILD C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 BILD N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI ADE -1.00 ! H61 H62!

ATOM P P 1.50 ! \ / ATOM O1P ON3 -0.78 ! N6 ATOM O2P ON3 -0.78 ! | ATOM O5' ON2 -0.57 ! C6 ATOM C5' CN8B -0.08 ! // \

ATOM H5' HN8 0.09 ! N1 C5--N7\\ ATOM H5'' HN8 0.09 ! | || C8-H8 GROUP ! C2 C4--N9/ ATOM C4' CN7 0.16 ! / \\ / \ ATOM H4' HN7 0.09 ! H2 N3 \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! \ ATOM H1' HN7 0.09 ! \ GROUP ! O1P H5' H4' O4' \ ATOM C5 CN5 0.28 ! | | \ / \ \ ATOM N7 NN4 -0.71 ! -P-O5'-C5'---C4' C1' ATOM C8 CN4 0.34 ! | | \ / \ ATOM H8 HN3 0.12 ! O2P H5'' C3'--C2' H1' ATOM N9 NN2 -0.05 ! / \ / \ ATOM N1 NN3A -0.74 ! O3' H3' O2' H2'' ATOM C2 CN4 0.50 ! | |

ATOM H2 HN3 0.13 ! H2' ATOM N3 NN3A -0.75

ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 GROUP

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ATOM H2' HN5 0.43 GROUP

ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57

BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N9 C1' C2' N9 C4 N9 C8 C4 N3 BOND C2 N1 C6 N6

BOND N6 H61 N6 H62 C6 C5 C5 N7

BOND C2' C3' C2' O2' O2' H2' C3' O3' O3' +P BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C8 H8 C2 H2

BOND N1 C6 C2 N3 C4 C5 N7 C8 IMPH H62 C6 H61 N6 N6 N1 C5 C6

DONO H61 N6 DONO H62 N6 DONO H2' O2' ACCE N3

ACCE N7 ACCE N1 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5'

BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801

BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212

BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 !puck BILD C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896

BILD O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C4 *N9 C8 1.4896 125.97 -179.94 106.0 1.367

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BILD O4' C2' C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI CYT -1.00

ATOM P P 1.50 !

ATOM O1P ON3 -0.78 ! H42 H41 ATOM O2P ON3 -0.78 ! \ / ATOM O5' ON2 -0.57 ! N4 ATOM C5' CN8B -0.08 ! | ATOM H5' HN8 0.09 ! C4 ATOM H5'' HN8 0.09 ! / \\ GROUP ! H5-C5 N3 ATOM C4' CN7 0.16 ! || | ATOM H4' HN7 0.09 ! H6-C6 C2 ATOM O4' ON6B -0.50 ! \ / \\ ATOM C1' CN7B 0.16 ! N1 O2 ATOM H1' HN7 0.09 ! \ GROUP ! \ ATOM N1 NN2 -0.13 ! \ ATOM C6 CN3 0.05 ! O1P H5' H4' O4' \ ATOM H6 HN3 0.17 ! | | \ / \ \ ATOM C2 CN1 0.52 ! -P-O5'-C5'---C4' C1' ATOM O2 ON1C -0.49 ! | | \ / \ ATOM N3 NN3 -0.66 ! O2P H5'' C3'--C2' H1' ATOM C4 CN2 0.65 ! / \ / \ ATOM N4 NN1 -0.75 ! O3' H3' O2' H2'' ATOM H41 HN1 0.37 ! | |

ATOM H42 HN1 0.33 ! H2' ATOM C5 CN3 -0.13 !

ATOM H5 HN3 0.07 ! GROUP

BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6

BOND C2 N3 C4 N4 N4 H41 N4 H42 BOND C4 C5 C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2'

BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6

BOND C2 O2 C5 C6 N3 C4 IMPH O2 N1 N3 C2 N4 N3 C5 C4 IMPH H42 C4 H41 N4

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ACCE O2 C2 ACCE N3 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5'

BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801

BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 -30.00 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364

BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI THY -1.00 ! H51 O4

ATOM P P 1.50 ! | ||

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ATOM H6 HN3 0.17 ! / \ / \ ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.41 ! | |

ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 !

ATOM C4 CN1 0.50 ! ATOM O4 ON1 -0.45 ! ATOM C5 CN3T -0.15 ATOM C5M CN9 -0.11 ATOM H51 HN9 0.07 ATOM H52 HN9 0.07 ATOM H53 HN9 0.07 GROUP

BOND O5' C5' C5' C4' C4' O4' C4' C3' O4' C1' BOND C1' N1 C1' C2' N1 C2 N1 C6

BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C2' C3' C3' O3' O3' +P BOND C2' O2' O2' H2'

BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C6 H6 C5M H51 C5M H52 C5M H53 BOND C2 O2 C4 O4 C5 C6

IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 DONO H3 N3

DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5'

BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801

BILD P O5' C5' C4' 1.5996 119.00 -146.00 110.04 1.5160 !beta BILD O5' C5' C4' C3' 1.4401 108.83 60.00 116.10 1.5284

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BILD C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 BILD N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 BILD N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 BILD C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 BILD C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 BILD C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 BILD C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 BILD H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0. 115.0 0.0 0.0 RESI URA -1.00 ! O4

ATOM P P 1.50 ! ||

ATOM O1P ON3 -0.78 ! C4 H3 ATOM O2P ON3 -0.78 ! / \ / ATOM O5' ON2 -0.57 ! H5-C5 N3 ATOM C5' CN8B -0.08 ! || | ATOM H5' HN8 0.09 ! H6-C6 C2 ATOM H5'' HN8 0.09 ! \ / \\ GROUP ! N1 O2 ATOM C4' CN7 0.16 ! \ ATOM H4' HN7 0.09 ! \ ATOM O4' ON6B -0.50 ! \ ATOM C1' CN7B 0.16 ! O1P H5' H4' O4' \ ATOM H1' HN7 0.09 ! | | \ / \ \ GROUP ! -P-O5'-C5'---C4' C1' ATOM N1 NN2B -0.34 ! | | \ / \ ATOM C6 CN3 0.20 ! O2P H5'' C3'--C2' H1' ATOM H6 HN3 0.14 ! / \ / \ ATOM C2 CN1T 0.55 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.45 ! | |

ATOM N3 NN2U -0.46 ! H2' ATOM H3 HN2 0.36 !

ATOM C4 CN1 0.53 ! ATOM O4 ON1 -0.48 ! ATOM C5 CN3 -0.15 ! ATOM H5 HN3 0.10 ! GROUP

BOND P O1P P O2P P O5'

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BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C2' C3' C3' O3' O3' +P

BOND C2' O2' O2' H2'

BOND C1' H1' C2' H2'' C3' H3' C4' H4' C5' H5' BOND C5' H5'' C5 H5 C6 H6

BOND C2 O2 C4 O4 C5 C6 IMPH O2 N1 N3 C2 O4 N3 C5 C4 DONO H3 N3

DONO H2' O2' ACCE O2 C2 ACCE O4 C4 ACCE O1P P ACCE O2P P ACCE O2' ACCE O3' ACCE O4' ACCE O5'

BILD -O3' P O5' C5' 1.6001 101.45 -39.25 119.00 1.4401 BILD -O3' O5' *P O1P 1.6001 101.45 -115.82 109.74 1.4802 BILD -O3' O5' *P O2P 1.6001 101.45 115.90 109.80 1.4801 BILD P O5' C5' C4' 1.5996 119.00 -151.39 110.04 1.5160 BILD O5' C5' C4' C3' 1.4401 108.83 -179.85 116.10 1.5284 BILD C5' C4' C3' O3' 1.5160 116.10 76.70 115.12 1.4212 BILD C4' C3' O3' +P 1.5284 111.92 159.13 119.05 1.6001 BILD C3' O3' +P +O5' 1.4212 119.05 -98.86 101.45 1.5996 BILD O4' C3' *C4' C5' 1.4572 104.06 -120.04 116.10 1.5160 BILD C2' C4' *C3' O3' 1.5284 100.16 -124.08 115.12 1.4212 BILD C4' C3' C2' C1' 1.5284 100.16 39.58 102.04 1.5251 BILD C3' C2' C1' N1 1.5284 101.97 144.39 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -96.0 117.06 1.3746 BILD C1' C2 *N1 C6 1.4896 117.06 -180.0 121.3 1.379 BILD C2 N1 C6 C5 1.379 121.3 0.0 122.8 1.338 BILD C6 N1 C2 N3 1.380 121.3 0.0 114.8 1.373 BILD N1 N3 *C2 O2 1.379 114.8 -180.0 122.0 1.218 BILD N1 C2 N3 C4 1.379 114.8 0.0 127.0 1.383 BILD C5 N3 *C4 O4 1.440 114.7 180.0 119.8 1.227 BILD C2 C4 *N3 H3 1.373 127.0 180.0 116.5 1.03 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 BILD C1' C3' *C2' O2' 1.5284 102.04 -114.67 110.81 1.4212 BILD H2' O2' C2' C3' 0.9600 114.97 148.63 111.92 1.5284 BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 ! Selected patches to create DNA, and individual bases included ! methylated analogs

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! see AUTOgen ANGLes DIHEdrals in STRUCTURE section of the ! documentation

PRES DEO1 0.000 ! Patch to make DEOXYribose in PYRIMIDINES DELETE ATOM O2' ! necessary due to auto-generate dihedrals GROUP !

ATOM C4' CN7 0.16 ! ATOM H4' HN7 0.09 ! ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.16 ! ATOM H1' HN7 0.09 ! GROUP

ATOM C2' CN8 -0.18 ATOM H2' HN8 0.09 ATOM H2'' HN8 0.09 BOND C2' H2'

THET C1' C2' H2' C3' C2' H2' H2' C2' H2''

DIHE H2' C2' C1' O4' H2' C2' C1' N1 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0

PRES DEO2 0.000 ! Patch to make DEOXYribose in PURINES DELETE ATOM O2' ! necessary due to auto-generate dihedrals GROUP !

ATOM C4' CN7 0.16 ! ATOM H4' HN7 0.09 ! ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.16 ! ATOM H1' HN7 0.09 ! GROUP

ATOM C2' CN8 -0.18 ATOM H2' HN8 0.09 ATOM H2'' HN8 0.09 BOND C2' H2'

THET C1' C2' H2' C3' C2' H2' H2' C2' H2''

DIHE H2' C2' C1' O4' H2' C2' C1' N9 H2' C2' C1' H1' DIHE H2' C2' C3' C4' H2' C2' C3' O3' H2' C2' C3' H3' BILD C1' C3' *C2' H2' 0.0 0.0 -115.0 0.0 0.0

PRES PYRC 0.00 ! Patch to generate CYTOSINE base ! use in generate statement

! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P

(12)

DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM N1 NN2 -0.50 ATOM H1 HN2 0.37 ATOM C6 CN3 0.05 ATOM H6 HN3 0.17 ATOM C2 CN1 0.52 ATOM O2 ON1C -0.49 ATOM N3 NN3 -0.66 ATOM C4 CN2 0.65 ATOM N4 NN1 -0.75 ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 ATOM C5 CN3 -0.13 ATOM H5 HN3 0.07 BOND N1 H1

IMPH H1 C6 C2 N1

BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0

PRES PYRU 0.00 ! Patch to generate URACIL base ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS

DELE ATOM P DELE ATOM O1P DELE ATOM O2P DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM N1 NN2B -0.82 ! ATOM H1 HN2 0.48 ! ATOM C6 CN3 0.20 ! ATOM H6 HN3 0.14 ! BOND N1 H1

BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0

(13)

ATOM N1 NN2B -0.80 ! ATOM H1 HN2 0.46 ! ATOM C6 CN3 0.17 ! ATOM H6 HN3 0.17 ! BOND N1 H1

BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0

PRES PURG 0.00 ! Patch to generate GUANINE base ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS

(14)

ATOM N2 NN1 -0.68 ! ATOM H21 HN1 0.32 ! ATOM H22 HN1 0.35 ! ATOM C6 CN1 0.54 ! ATOM O6 ON1 -0.51 ! ATOM C5 CN5G 0.00 ! ATOM N7 NN4 -0.60 ! ATOM C8 CN4 0.25 ! ATOM H8 HN3 0.16 ! BOND N9 H9

IMPH H9 C8 C4 N9

BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0

PRES PURA 0.00 ! Patch to generate ADENINE base ! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS

DELE ATOM P DELE ATOM O1P DELE ATOM O2P DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM C5 CN5 0.28 ATOM N7 NN4 -0.71 ATOM C8 CN4 0.34 ATOM H8 HN3 0.12 ATOM N9 NN2 -0.37 ATOM H9 HN2 0.32 ATOM N1 NN3A -0.74 ATOM C2 CN4 0.50 ATOM H2 HN3 0.13 ATOM N3 NN3A -0.75 ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 BOND N9 H9

BILD C5 C4 N9 H9 0.0 0.0 180.0 0.0 0.0

(15)

ATOM H5T HN5 0.43 ATOM O5' ON5 -0.66 ATOM C5' CN8B 0.05 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 !

DELETE ATOM P DELETE ATOM O1P DELETE ATOM O2P !

BOND H5T O5' DONO H5T O5'

BILD H5T O5' C5' C4' 0.0000 0.00 180.00 0.00 0.0000 PRES 5PHO -1.00 ! 5'terminal PHOSPHATE patch

! use in generate statement GROUP

ATOM C5' CN8B -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM P P 1.50 ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O5' ON2 -0.62 ATOM O5T ON4 -0.68 ATOM H5T HN4 0.34 BOND O5T P H5T O5T DONO H5T O5T

BILD C4' C5' O5' P 0.0000 000.00 -146.00 000.00 0.0000 BILD C5' O5' P O5T 0.0000 000.00 -46.90 000.00 0.0000 BILD O5T O5' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 BILD O5T O5' *P O2P 0.0000 000.00 115.90 000.00 0.0000 BILD H5T O5T P O5' 0.0000 000.00 -95.20 000.00 0.0000 PRES 5POM -1.00 ! 5'terminal Methyl-Phosphate patch

ATOM C5' CN8B -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM P P 1.50 ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O5' ON2 -0.57 ATOM O5T ON2 -0.57 ATOM C5T CN9 -0.17 ATOM H5T1 HN9 0.09 ATOM H5T2 HN9 0.09 ATOM H5T3 HN9 0.09

BOND O5T P O5T C5T C5T H5T1 C5T H5T2 BOND C5T H5T3

(16)

BILD H5T1 C5T O5T P 0.0000 000.00 180.20 000.00 0.0000 BILD H5T2 C5T O5T P 0.0000 000.00 60.00 000.00 0.0000 BILD H5T3 C5T O5T P 0.0000 000.00 -60.00 000.00 0.0000 PRES 3TER 0.00 ! 3'terminal HYDROXYL patch

ATOM C3' CN7 0.14 ATOM H3' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H3T HN5 0.43 BOND O3' H3T

DONO H3T O3'

BILD H3T O3' C3' C4' 0.9600 114.97 148.63 111.92 1.5284 PRES 3PHO -1.00 ! 3'terminal PHOSPHATE patch

ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM P3 P 1.50 ATOM O1P3 ON3 -0.82 ATOM O2P3 ON3 -0.82 ATOM O3' ON2 -0.62 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34

BOND O3' P3 P3 O1P3 P3 O2P3 P3 O3T O3T H3T DONO H3T O3T

ACCE O3T ACCE O1P2 ACCE O1P3

! Build in B-DNA-like conformation (NF)

BILD C4' C3' O3' P3 0.0000 000.00 155.00 000.00 0.0000 BILD C3' O3' P3 O3T 0.0000 000.00 -95.20 000.00 0.0000 BILD O3T O3' *P3 O1P3 0.0000 000.00 -115.82 000.00 0.0000 BILD O3T O3' *P3 O2P3 0.0000 000.00 115.90 000.00 0.0000 BILD H3T O3T P3 O3' 0.0000 000.00 -46.90 000.00 0.0000 PRES 9MG 0.000 ! 9-Methyl guanine patch

! use in generate statement ! DELETE PHOSPHATE AND RIBOSE ATOMS

(17)

DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM N9 NN2B -0.02 ATOM C4 CN5 0.26 ATOM C9 CN9 -0.27 ATOM N3 NN3G -0.74 ATOM C2 CN2 0.75 ATOM N1 NN2G -0.34 ATOM H1 HN2 0.26 ATOM N2 NN1 -0.68 ATOM H21 HN1 0.32 ATOM H22 HN1 0.35 ATOM C6 CN1 0.54 ATOM O6 ON1 -0.51 ATOM C5 CN5G 0.00 ATOM N7 NN4 -0.60 ATOM C8 CN4 0.25 ATOM H8 HN3 0.16 ATOM H91 HN9 0.09 ATOM H92 HN9 0.09 ATOM H93 HN9 0.09

BOND N9 C9 C9 H91 C9 H92 C9 H93

BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 BILD C8 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 BILD N9 H91 *C9 H92 0.0 0.0 -115.0 0.0 0.0 BILD H91 H92 *C9 H93 0.0 0.0 115.0 0.0 0.0 PRES 9EG 0.000 ! 9-Ethyl guanine patch

ATOM C9 CN8 -0.18 ATOM H91 HN8 0.09 ATOM H92 HN8 0.09 GROUP

(18)

ATOM H9B1 HN9 0.09 ATOM H9B2 HN9 0.09 ATOM H9B3 HN9 0.09

BOND N9 C9 C9 H91 C9 H92 C9 H93 BOND C9 C9B C9B H9B1 C9B H9B2 C9B H9B3

BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 BILD C8 N9 C9 C9B 0.0 0.0 0.0 0.0 0.0 BILD N9 C9B *C9 H91 0.0 0.0 -115.0 0.0 0.0 BILD C9B H91 *C9 H92 0.0 0.0 115.0 0.0 0.0 BILD N9 C9 C9B H9B1 0.0 0.0 180.0 0.0 0.0 BILD C9 H9B1 *C9B H9B2 0.0 0.0 -115.0 0.0 0.0 BILD H9B1 H9B2 *C9B H9B3 0.0 0.0 115.0 0.0 0.0 PRES 9MA 0.00 ! 9-Methyl adenine patch

DELE ATOM P DELE ATOM O1P DELE ATOM O2P DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3'

! all atoms included in patch to get correct atom ! order to simplify analysis

GROUP

ATOM C5 CN5 0.28 ATOM N7 NN4 -0.71 ATOM C8 CN4 0.34 ATOM H8 HN3 0.12 ATOM N9 NN2 -0.05 ATOM C9 CN9 -0.27 ATOM N1 NN3A -0.74 ATOM C2 CN4 0.50 ATOM H2 HN3 0.13 ATOM N3 NN3A -0.75 ATOM C4 CN5 0.43 ATOM C6 CN2 0.46 ATOM N6 NN1 -0.77 ATOM H61 HN1 0.38 ATOM H62 HN1 0.38 ATOM H91 HN9 0.09 ATOM H92 HN9 0.09 ATOM H93 HN9 0.09

(19)

BILD C8 C4 *N9 C9 0.0 0.0 180.0 0.0 0.0 BILD C4 N9 C9 H91 0.0 0.0 180.0 0.0 0.0 BILD N9 H91 *C9 H92 0.0 0.0 -115.0 0.0 0.0 BILD H91 H92 *C9 H93 0.0 0.0 115.0 0.0 0.0 PRES 1MC 0.000 ! 1-Methyl Cytosine patch

ATOM N1 NN2 -0.13 ATOM C1 CN9 -0.27 ATOM C6 CN3 0.05 ATOM H6 HN3 0.17 ATOM C2 CN1 0.52 ATOM O2 ON1C -0.49 ATOM N3 NN3 -0.66 ATOM C4 CN2 0.65 ATOM N4 NN1 -0.75 ATOM H41 HN1 0.37 ATOM H42 HN1 0.33 ATOM C5 CN3 -0.13 ATOM H5 HN3 0.07 ATOM H11 HN9 0.09 ATOM H12 HN9 0.09 ATOM H13 HN9 0.09

BOND N1 C1 C1 H11 C1 H12 C1 H13

BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 PRES 1MT 0.00 ! 1-Methyl Thymine patch

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DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM N1 NN2B -0.34 ATOM C1 CN9 -0.27 ATOM C6 CN3 0.17 ATOM H6 HN3 0.17 ATOM C2 CN1T 0.51 ATOM O2 ON1 -0.41 ATOM N3 NN2U -0.46 ATOM H3 HN2 0.36 ATOM C4 CN1 0.50 ATOM O4 ON1 -0.45 ATOM C5 CN3T -0.15 ATOM C5M CN9 -0.11 ATOM H51 HN9 0.07 ATOM H52 HN9 0.07 ATOM H53 HN9 0.07 ATOM H11 HN9 0.09 ATOM H12 HN9 0.09 ATOM H13 HN9 0.09

BOND N1 C1 C1 H11 C1 H12 C1 H13

BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 PRES 1MU 0.00 ! 1-Methyl Uracil patch

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DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM N1 NN2B -0.34 ATOM C1 CN9 -0.27 ATOM C6 CN3 0.20 ATOM H6 HN3 0.14 ATOM C2 CN1T 0.55 ATOM O2 ON1 -0.45 ATOM N3 NN2U -0.46 ATOM H3 HN2 0.36 ATOM C4 CN1 0.53 ATOM O4 ON1 -0.48 ATOM C5 CN3 -0.15 ATOM H5 HN3 0.10 ATOM H11 HN9 0.09 ATOM H12 HN9 0.09 ATOM H13 HN9 0.09

BOND N1 C1 C1 H11 C1 H12 C1 H13

BILD C6 C2 *N1 C1 0.0 0.0 180.0 0.0 0.0 BILD C2 N1 C1 H11 0.0 0.0 180.0 0.0 0.0 BILD N1 H11 *C1 H12 0.0 0.0 -115.0 0.0 0.0 BILD H11 H12 *C1 H13 0.0 0.0 115.0 0.0 0.0 ! Model compounds used for parameter optimization

RESI THF 0.00 ! tetrahydrofuran !

! Figure 3A, interaction with water !

GROUP

ATOM O4' ON6 -0.50 ! H41' O4' H11' ATOM C4' CN8 0.07 ! \ / \ / ATOM C3' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM C2' CN8 -0.18 ! | |

ATOM C1' CN8 0.07 ! H31'--C3'--C2'--H21' ATOM H11' HN8 0.09 ! / \

ATOM H12' HN8 0.09 ! H32' H22' ATOM H21' HN8 0.09 !

ATOM H22' HN8 0.09 ! ATOM H31' HN8 0.09 ! ATOM H32' HN8 0.09 ! ATOM H41' HN8 0.09 ! ATOM H42' HN8 0.09 !

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4'

BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42'

PATC FIRS NONE LAST NONE

RESI THFO 0.00 ! 3'-hydroxyl-tetrahydrofuran !

(22)

GROUP

ATOM O4' ON6 -0.50 ! H41' O4' H11' ATOM C1' CN7B 0.07 ! \ / \ / ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM C4' CN7 0.07 ! | |

ATOM H11' HN7 0.09 ! H31'--C3'--C2'--H21' ATOM H12' HN7 0.09 ! / \

ATOM H21' HN8 0.09 ! O3' H22' ATOM H22' HN8 0.09 ! |

ATOM H41' HN7 0.09 ! H32' ATOM H42' HN7 0.09

GROUP

ATOM C3' CN7 0.14 ATOM H31' HN7 0.09 ATOM O3' ON5 -0.66 ATOM H32' HN5 0.43

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' H32'

IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC H32' O3' C3' C4' 0.9492 108.72 44.80 110.98 1.5211 PATC FIRS NONE LAST NONE

RESI DMPA -1.00 ! Dimethylphosphate !

! Model compound A !

GROUP !

ATOM P1 P 1.500 ! H11! ATOM O3 ON3 -0.780 ! | ATOM O4 ON3 -0.780 ! H13- C1-H12 ATOM O1 ON2 -0.570 ! \ ATOM O2 ON2 -0.570 ! O3 O1 ATOM C1 CN9 -0.170 ! \\ / ATOM H11 HN9 0.090 ! (-) P1 ATOM H12 HN9 0.090 ! // \ ATOM H13 HN9 0.090 ! O4 O2 ATOM C2 CN9 -0.170 ! / ATOM H21 HN9 0.090 ! H23-C2-H22 ATOM H22 HN9 0.090 ! | ATOM H23 HN9 0.090 ! H21 !

(23)

! IC FOR THE g,g conformation (3-21G* opt. structure)

IC O3 P1 O1 C1 1.4723 107.31 000.0 117.79 1.4356 IC O4 P1 O2 C2 1.4722 000.0 000.0 117.79 1.4357 IC O1 P1 O2 C2 1.6343 000.0 73.8 117.79 1.4357 IC O2 P1 O1 C1 1.6344 000.0 73.7 117.79 1.4356 IC H11 C1 O1 P1 1.0827 107.8 174.8 117.79 1.6343 IC H12 C1 O1 P1 1.0800 110.4 54.1 117.79 1.6343 IC H13 C1 O1 P1 1.0848 110.7 294.3 117.79 1.6343 IC H21 C2 O2 P1 1.0827 107.9 174.7 117.79 1.6344 IC H22 C2 O2 P1 1.0800 110.4 54.1 117.79 1.6344 IC H23 C2 O2 P1 1.0848 110.7 294.2 117.79 1.6344

RESI T5PH -1.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -1) !

! Model compound B !

GROUP

ATOM C5' CN8B -0.08 !

ATOM H5' HN8 0.09 ! O1P H5T ATOM H5'' HN8 0.09 ! || / ATOM O5' ON2 -0.62 ! O2P==P==O3P ATOM P P 1.50 ! | ATOM O1P ON3 -0.82 ! O5' ATOM O2P ON3 -0.82 ! | ATOM O3P ON4 -0.68 ! H5'' | ATOM H5T HN4 0.34 ! \ |

GROUP ! H5'--C5' O4' H1' ATOM O4' ON6 -0.50 ! \ / \ / ATOM C1' CN7B 0.07 ! H4'--C4' C1'--H1'' ATOM H1' HN7 0.09 ! | |

ATOM H1'' HN7 0.09 ! H3'--C3'--C2'--H2' ATOM C4' CN7 0.16 ! / \ ATOM H4'' HN7 0.09 ! H3'' H2'' GROUP !

ATOM C2' CN8 -0.18 ATOM H2' HN8 0.09 ATOM H2'' HN8 0.09 GROUP

ATOM C3' CN7 -0.18 ATOM H3' HN7 0.09 ATOM H3'' HN7 0.09

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P O3P H5T

(24)

IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.0 0.0 0.0 IC O4' C4' C5' H5' 0.0 0.0 180.0 0.0 0.0 IC O4' C4' C5' H5'' 0.0 0.0 -60.0 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 IC O5' P O3P H5T 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI TH5P -2.00 ! 5'-phosphate-methyl-tetrahydrofuran (phosphate -2) !

! Model compound B with dianionic phosphate, vibrational analysis !

GROUP ! O1P (-2) ATOM O4' ON6 -0.50 ! ||

ATOM C1' CN7B 0.07 ! O2P==P==O2P ATOM H1' HN7 0.09 ! | ATOM H1'' HN7 0.09 ! H5'' | ATOM C4' CN7 0.16 ! \ |

ATOM H4'' HN7 0.09 ! H5'--C5' O4' H1' GROUP ! \ / \ / ATOM C2' CN8 -0.18 ! H4'--C4' C1'--H1'' ATOM H2' HN8 0.09 ! | |

ATOM H2'' HN8 0.09 ! H3'--C3'--C2'--H2' GROUP ! / \ ATOM C3' CN7 -0.18 ! H3'' H2'' ATOM H3' HN7 0.09 !

ATOM H3'' HN7 0.09 GROUP

ATOM C5' CN8B -0.18 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 GROUP

ATOM O5' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C4' C5' BOND C1' H1' C1' H1'' C2' H2' C2' H2'' C3' H3' C3' H3'' BOND C4' H4'' C5' H5' C5' H5'' C5' O5' O5' P P O1P BOND P O2P P O3P

(25)

IC H3' C3' C4' O4' 1.1127 108.68 81.68 105.43 1.4416 IC H3'' C3' C4' O4' 1.1069 112.41 -156.66 105.43 1.4416 IC H4'' C4' O4' C1' 1.1127 106.71 -95.75 109.61 1.4471 IC C5' C4' O4' C1' 1.5325 108.43 144.82 109.61 1.4471 IC H51' C5' C4' O4' 1.1092 110.48 180.00 108.43 1.4416 IC H52' C5' C4' O4' 1.1104 110.01 -60.00 108.43 1.4416 IC O4' C4' C5' O5' 0.0 0.0 60.00 0.0 0.0 IC C4' C5' O5' P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O1P 0.0 0.0 -60.0 0.0 0.0 IC C5' O5' P O2P 0.0 0.0 180.0 0.0 0.0 IC C5' O5' P O3P 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI T3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran !

! Model compound C !

GROUP

ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.07 !

ATOM H11' HN7 0.09 ! H41' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | |

ATOM H42' HN7 0.09 ! H31'--C3'--C2'--H21' GROUP ! / \

ATOM C2' CN8 -0.18 ! O3' H22' ATOM H21' HN8 0.09 ! |

ATOM H22' HN8 0.09 ! O1P==P==O2P GROUP ! |

ATOM C3' CN7 0.01 ! O3T (-1) ATOM H31' HN7 0.09 ! \

ATOM O3' ON2 -0.62 ! H3T ATOM P P 1.50 !

ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T

(26)

IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI R3PH -1.00 ! monoanionic 3'phosphate-tetrahydrofuran !

! Model compound C, monoanionic with 2'hydroxyl !

GROUP

ATOM O4' ON6B -0.50 ! ATOM C1' CN7B 0.07 !

ATOM H11' HN7 0.09 ! H41' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.07 ! H42'--C4' C1'--H12' ATOM H41' HN7 0.09 ! | |

ATOM C2' CN7B 0.14 ! O3' O2' ATOM H21' HN7 0.09 ! | | ATOM O2' ON5 -0.66 ! O1P==P==O2P H22' ATOM H22' HN5 0.43 ! |

GROUP ! O3T (-1) ATOM C3' CN7 0.01 ! \

ATOM H31' HN7 0.09 ! H3T ATOM O3' ON2 -0.62 !

ATOM P P 1.50 ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3'

BOND C1' H11' C1' H12' C2' H21' C2' O2' O2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T H3T

IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC O2' C2' C3' C4' 1.0822 110.88 283.41 100.86 1.5211 IC H22' O2' C2' C3' 1.0822 110.88 0.00 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 60.0 0.0 0.0 IC O3T P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC H3T O3T P O3' 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE

(27)

!

! Model compound D !

GROUP

ATOM O4' ON6 -0.50 !

ATOM C1' CN7B 0.07 ! H41' O4' H11' ATOM H11' HN7 0.09 ! \ / \ / ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C4' CN7 0.07 ! | |

GROUP ! O3' H22' ATOM C2' CN8 -0.18 ! |

ATOM H21' HN8 0.09 ! O1P==P==O2P ATOM H22' HN8 0.09 ! |

GROUP ! O3T (-1) ATOM C3' CN7 0.01 ! \

ATOM H31' HN7 0.09 ! C3T--H3T3 GROUP ! / \

ATOM O3' ON2 -0.57 ! H3T1 H3T2 ATOM P P 1.50 !

ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O3T ON2 -0.57 ATOM C3T CN8B -0.17 ATOM H3T1 HN8 0.09 ATOM H3T2 HN8 0.09 ATOM H3T3 HN8 0.09

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H41' BOND C4' H42' O3' P P O1P P O2P P O3T O3T C3T BOND C3T H3T1 C3T H3T2 C3T H3T3

IC C4' O4' C1' C2' 1.4055 108.09 23.45 106.18 1.5457 IC O4' C1' C2' C3' 1.4127 106.18 3.96 103.11 1.5346 IC C1' C2' C3' C4' 1.5457 103.11 -26.93 100.86 1.5211 IC C2' C3' C4' O4' 1.5346 100.86 41.73 103.15 1.4055 IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC H41' C4' O4' C1' 1.0891 110.89 77.76 108.09 1.4127 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0000 000.00 180.00 000.00 0.0000 IC C3' O3' P O3T 0.0000 000.00 -95.22 000.00 0.0000 IC O3T O3' *P O1P 0.0000 000.00 -115.82 000.00 0.0000 IC O3T O3' *P O2P 0.0000 000.00 115.90 000.00 0.0000 IC C3T O3T P O3' 0.0000 000.00 -46.90 000.00 0.0000 IC H3T1 C3T O3T P 0.0000 000.00 180.00 000.00 0.0000 IC H3T2 C3T O3T P 0.0000 000.00 60.00 000.00 0.0000 IC H3T3 C3T O3T P 0.0000 000.00 -60.00 000.00 0.0000 PATC FIRS NONE LAST NONE

(28)

!

! Model compound E, with imidazole !

GROUP

ATOM O4' ON6 -0.50 ! H41' O4' Imidazole ATOM C1' CN7B 0.16 ! \ / \ /

ATOM H12' HN7 0.09 ! H42'--C4' C1'--H12' ATOM C4' CN7 0.07 ! | |

GROUP ! H32' H22' ATOM C2' CN8 -0.18 !

ATOM H21' HN8 0.09 ! ATOM H22' HN8 0.09 ! GROUP ! ATOM C3' CN7 -0.18 ! ATOM H31' HN7 0.09 ! ATOM H32' HN7 0.09 !

GROUP ! Imidazole: transferred from isolated imidazole (IMIA) ATOM CG CPH1 -0.05 ! C1' HE1

ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / | ATOM ND1 NR1 -0.04 ! HG-CG | ATOM CE1 CPH2 0.25 ! \ | ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! |

! HD2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'

BOND C4' H41' C4' H42'

BOND ND1 CE1 CE1 NE2 NE2 CD2 CD2 CG CG ND1 BOND CE1 HE1 CD2 HD2 CG HG

IMPH ND1 CG CE1 C1' ND1 CE1 CG C1' IMPH CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPH CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPH CG CD2 ND1 HG CG ND1 CD2 HG IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0 IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0

IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0

(29)

RESI THMI 0.00 ! thf-ch3-imidazole !

! Model compound E with imidazole base and 5'methyl, vibrational analysis !

GROUP ! Sugar: transferred from thf ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.16 ! \ /

ATOM H12' HN7 0.09 ! H51'-C5' O4' Imidazole ATOM C4' CN7 0.16 ! \ / \ /

ATOM H42' HN7 0.09 ! H42'--C4' C1'--H12' GROUP ! | |

ATOM C2' CN8 -0.18 ! H31'--C3'--C2'--H21' ATOM H21' HN8 0.09 ! / \

ATOM H22' HN8 0.09 ! H32' H22' GROUP

ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09 GROUP

ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09

ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! |

! HD2

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C1' ND1 BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32'

BOND C4' H42' C4' C5' C5' H51' C5' H52' C5' H53' BOND ND1 CE1 NE2 CD2 CG ND1

BOND CE1 HE1 CD2 HD2 CG HG BOND CG CD2 CE1 NE2

IMPH ND1 CG CE1 C1' ND1 CE1 CG C1' IMPH CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPH CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPH CG CD2 ND1 HG CG ND1 CD2 HG ! ic table for thfim, from Nicolas:

IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0 IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC C5' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0

(30)

IC C4' O4' C1' ND1 0.0 0.0 256.98 0.0 0.0 IC O4' C1' ND1 CE1 0.0 0.0 180.00 0.0 0.0

IC C1' ND1 CE1 NE2 0.0 0.0 181.56 0.0 0.0 IC ND1 CE1 NE2 CD2 0.0 0.0 0.34 0.0 0.0

IC CE1 NE2 CD2 CG 0.0 0.0 0.00 0.0 0.0 IC HE1 CE1 NE2 CD2 0.0 0.0 180.40 0.0 0.0 IC CE1 NE2 CD2 HD2 0.0 0.0 179.83 0.0 0.0 IC NE2 CD2 CG HG 0.0 0.0 178.45 0.0 0.0 PATC FIRS NONE LAST NONE

RESI TADE 0.00 ! thf with adenine !

! Model compound E with adenine !

GROUP

ATOM C5 CN5 0.28 ! H61 H62! ATOM N7 NN4 -0.71 ! \ / ATOM C8 CN4 0.34 ! N6 ATOM H8 HN3 0.12 ! | ATOM N9 NN2 -0.05 ! C6 ATOM C1' CN7B 0.16 ! // \

ATOM N1 NN3A -0.74 ! N1 C5--N7\\ ATOM C2 CN4 0.50 ! | || C8-H8 ATOM H2 HN3 0.13 ! C2 C4--N9/ ATOM N3 NN3A -0.75 ! / \\ / \ ATOM C4 CN5 0.43 ! H2 N3 \ ATOM C6 CN2 0.46 ! \ ATOM N6 NN1 -0.77 ! \ ATOM H61 HN1 0.38 ! \ ATOM H62 HN1 0.38 ! H42' O4' \ ATOM O4' ON6 -0.50 ! \ / \ \ ATOM H12' HN7 0.09 ! H41'-C4' C1' ATOM C4' CN7 0.07 ! \ / \ ATOM H41' HN7 0.09 ! H31'--C3'--C2' H12' ATOM H42' HN7 0.09 ! / / \ GROUP ! H32' H21' H22' ATOM C2' CN8 -0.18 !

ATOM H21' HN8 0.09 ATOM H22' HN8 0.09 GROUP

ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42'

BOND C1' N9

BOND N9 C4 N9 C8 C4 N3 C2 N1 C6 N6

BOND N6 H61 N6 H62 C6 C5 C5 N7 C8 H8 C2 H2 BOND N1 C6 C2 N3 C4 C5 N7 C8

IMPH H62 C6 H61 N6 N6 N1 C5 C6 ! ic table for thfim, from Nicolas:

(31)

IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0

IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 180.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.97 -180.00 106.0 1.367

IC C4 N9 C8 N7 1.376 106.0 0.0 113.6 1.312 IC C8 N9 C4 C5 1.367 106.0 0.0 105.6 1.382 IC C8 N7 C5 C6 0.0 0.0 180.0 0.0 0.0 IC N7 C5 C6 N1 0.0 0.0 180.0 0.0 0.0 IC C5 C6 N1 C2 0.0 0.0 0.0 0.0 0.0 IC N9 C5 *C4 N3 1.376 105.6 -180.0 126.9 1.342 IC C5 N1 *C6 N6 1.409 117.6 -180.0 121.2 1.337 IC N1 C6 N6 H61 1.337 121.2 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 119.00 1.01 IC C5 N1 *C6 N6 1.409 117.6 -180.0 119.0 1.337 IC N1 C6 N6 H61 1.337 119.0 0.0 119.0 1.01 IC H61 C6 *N6 H62 1.01 119.0 180.0 121.00 1.01 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 IC N1 N3 *C2 H2 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI TCYT 0.00 ! THF with cytosine !

! Model compound E with cytosine !

GROUP

ATOM N1 NN2 -0.13 !

ATOM C1' CN7B 0.16 ! H42 H41 ATOM C6 CN3 0.05 ! \ / ATOM H6 HN3 0.17 ! N4 ATOM C2 CN1 0.52 ! | ATOM O2 ON1C -0.49 ! C4 ATOM N3 NN3 -0.66 ! / \\ ATOM C4 CN2 0.65 ! H5-C5 N3 ATOM N4 NN1 -0.75 ! || | ATOM H41 HN1 0.37 ! H6-C6 C2 ATOM H42 HN1 0.33 ! \ / \\ ATOM C5 CN3 -0.13 ! N1 O2 ATOM H5 HN3 0.07 ! \ ATOM O4' ON6 -0.50 ! \ ATOM H12' HN7 0.09 ! \ ATOM C4' CN7 0.07 ! H42' O4' \ ATOM H41' HN7 0.09 ! \ / \ \ ATOM H42' HN7 0.09 ! H41'-C4' C1' GROUP ! \ / \ ATOM C2' CN8 -0.18 ! H31'--C3'--C2' H12' ATOM H21' HN8 0.09 ! / / \ ATOM H22' HN8 0.09 ! H32' H21' H22' GROUP

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BOND C1' H12' C2' H21' C2' H22' C3' H31' C3' H32' BOND C4' H41' C4' H42'

BOND C1' N1

BOND N1 C2 N1 C6 C4 N4 N4 H41 N4 H42 BOND C2 N3 C4 C5 C5 H5 C6 H6

BOND C2 O2 C5 C6 N3 C4

IMPH O2 N1 N3 C2 N4 N3 C5 C4 IMPH H42 C4 H41 N4

BILD C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 BILD O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi BILD C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364

BILD C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 BILD C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 BILD N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 BILD N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 BILD C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 BILD N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 BILD H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 BILD C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 BILD N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0

IC C2' C3' C4' O4' 0.0 0.0 33.390 0.0 0.0 IC H12' C1' C2' C3' 0.0 0.0 268.35 0.0 0.0 IC H21' C2' C3' C4' 0.0 0.0 82.530 0.0 0.0 IC H22' C2' C3' C4' 0.0 0.0 204.06 0.0 0.0 IC H31' C3' C4' O4' 0.0 0.0 155.99 0.0 0.0 IC H32' C3' C4' O4' 0.0 0.0 276.70 0.0 0.0 IC H41' C4' O4' C1' 0.0 0.0 132.30 0.0 0.0 IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0

IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.79 -180.00 120.6 1.364

IC C2 N1 C6 C5 1.399 120.6 0.0 121.0 1.337 IC C6 N1 C2 N3 1.364 120.6 0.0 118.9 1.356 IC N1 N3 *C2 O2 1.399 118.9 180.0 121.9 1.237 IC N1 C2 N3 C4 1.399 118.9 0.0 120.0 1.334 IC C5 N3 *C4 N4 1.426 121.8 180.00 118.9 1.337 IC N3 C4 N4 H41 1.337 117.9 0.00 118.9 1.01 IC H41 C4 *N4 H42 1.01 118.9 180.00 120.7 1.01 IC C6 C4 *C5 H5 0.0 0.0 180.0 0.0 0.0 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI TGUA 0.00 ! thf with guanine !

! Model compound E with guanine !

GROUP

ATOM N9 NN2B -0.02 ! O6 ATOM C4 CN5 0.26 ! || ATOM C1' CN7B 0.16 ! C6 ATOM N3 NN3G -0.74 ! / \

(33)

ATOM H22 HN1 0.35 ! | \ ATOM C6 CN1 0.54 ! H22 \ ATOM O6 ON1 -0.51 ! \ ATOM C5 CN5G 0.00 ! H42' O4' \ ATOM N7 NN4 -0.60 ! \ / \ \ ATOM C8 CN4 0.25 ! H41'-C4' C1' ATOM H8 HN3 0.16 ! \ / \ ATOM O4' ON6 -0.50 ! H31'--C3'--C2' H12' ATOM H12' HN7 0.09 ! / / \ ATOM C4' CN7 0.07 ! H32' H21' H22' ATOM H41' HN7 0.09

ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09

BOND C1' N9

BOND N9 C4 N9 C8 C4 N3 C2 N2 C2 N1 N2 H21 BOND N2 H22 N1 H1 N1 C6 C6 C5 C5 N7 C8 H8 BOND C2 N3 C4 C5 N7 C8 C6 O6

IMPH N2 N3 N1 C2 O6 N1 C5 C6 H22 H21 C2 N2 IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0

IC C3' C2' C1' N9 1.5284 101.97 147.80 113.71 1.4896 IC O4' C1' N9 C4 1.5251 113.71 -97.2 125.59 1.3783 !chi IC C1' C4 *N9 C8 1.4896 125.59 -179.99 106.0 1.374

IC C4 N9 C8 N7 1.377 106.0 0.0 113.5 1.304 IC C8 N9 C4 C5 1.374 106.0 0.0 105.6 1.377 IC N9 C5 *C4 N3 1.377 105.6 180.0 128.4 1.355 IC C5 C4 N3 C2 1.377 128.4 0.0 111.8 1.327 IC C4 N3 C2 N1 1.355 111.8 0.0 124.0 1.375 IC N1 N3 *C2 N2 1.375 124.0 180.0 119.7 1.341 IC N3 C2 N2 H21 1.327 119.7 180.0 127.0 1.01 IC H21 C2 *N2 H22 1.01 127.0 -180.0 116.5 1.01 IC N3 C2 N1 C6 1.327 124.0 0.0 124.9 1.393 IC C6 C2 *N1 H1 1.393 124.9 180.00 117.4 1.03 IC C5 N1 *C6 O6 1.415 111.7 180.0 120.0 1.239 IC N9 N7 *C8 H8 0.0 0.0 180.0 0.0 0.0 PATC FIRS NONE LAST NONE

(34)

! Model compound E with thymine !

GROUP

ATOM N1 NN2B -0.34 ! H51 O4 ATOM C1' CN7B 0.16 ! | ||

ATOM C6 CN3 0.17 ! H52-C5M C4 H3 ATOM H6 HN3 0.17 ! | \ / \ / ATOM C2 CN1T 0.51 ! H53 C5 N3 ATOM O2 ON1 -0.41 ! || | ATOM N3 NN2U -0.46 ! H6-C6 C2 ATOM H3 HN2 0.36 ! \ / \\ ATOM C4 CN1 0.50 ! N1 O2 ATOM O4 ON1 -0.45 ! \ ATOM C5 CN3T -0.15 ! \ ATOM C5M CN9 -0.11 ! \ ATOM H51 HN9 0.07 ! H42' O4' \ ATOM H52 HN9 0.07 ! \ / \ \ ATOM H53 HN9 0.07 ! H41'-C4' C1' ATOM O4' ON6 -0.50 ! \ / \ ATOM H12' HN7 0.09 ! H31'--C3'--C2' H12' ATOM C4' CN7 0.07 ! / / \ ATOM H41' HN7 0.09 ! H32' H21' H22' ATOM H42' HN7 0.09

GROUP

BOND C1' N1

BOND N1 C2 N1 C6 C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 C5M C6 H6 C5M H51 C5M H52 C5M H53

BOND C2 O2 C4 O4 C5 C6

IMPH O2 N1 N3 C2 O4 N3 C5 C4 C5M C4 C6 C5 IC C1' C2' C3' C4' 0.0 0.0 324.92 0.0 0.0

(35)

IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI TURA 0.00 ! THF with uracil on C1' !

! Model compound E with uracil !

GROUP

ATOM N1 NN2B -0.34 ! O4 ATOM C1' CN7B 0.16 ! ||

ATOM C6 CN3 0.20 ! C4 H3 ATOM H6 HN3 0.14 ! / \ / ATOM C2 CN1T 0.55 ! H5-C5 N3 ATOM O2 ON1 -0.45 ! || | ATOM N3 NN2U -0.46 ! H6-C6 C2 ATOM H3 HN2 0.36 ! \ / \\ ATOM C4 CN1 0.53 ! N1 O2 ATOM O4 ON1 -0.48 ! \ ATOM C5 CN3 -0.15 ! \ ATOM H5 HN3 0.10 ! \ ATOM O4' ON6 -0.50 ! H42' O4' \ ATOM H12' HN7 0.09 ! \ / \ \ ATOM C4' CN7 0.07 ! H41'-C4' C1' ATOM H41' HN7 0.09 ! \ / \ ATOM H42' HN7 0.09 ! H31'--C3'--C2' H12' GROUP ! / / \ ATOM C2' CN8 -0.18 ! H32' H21' H22' ATOM H21' HN8 0.09

BOND C1' N1

BOND N1 C2 N1 C6

BOND C2 N3 N3 H3 N3 C4 C4 C5 BOND C5 H5 C6 H6

BOND C2 O2 C4 O4 C5 C6

(36)

IC H42' C4' O4' C1' 0.0 0.0 220.70 0.0 0.0

IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC C3' C2' C1' N1 1.5284 101.97 147.89 113.71 1.4896 IC O4' C1' N1 C2 1.5251 113.71 180.0 125.59 1.3783 !chi IC C1' C2 *N1 C6 1.4896 117.06 -179.96 122.08 1.3704 IC C2 N1 C6 C5 1.3746 122.08 -0.02 121.23 1.3432 IC C6 N1 C2 N3 1.3704 122.08 0.06 115.38 1.3813 IC N1 N3 *C2 O2 1.3746 115.38 -179.95 121.70 1.2191 IC N1 C2 N3 C4 1.3746 115.38 -0.07 126.46 1.3795 IC C5 N3 *C4 O4 1.4439 114.07 179.98 120.59 1.2327 IC C2 C4 *N3 H3 1.3813 126.46 180.00 116.77 1.0900 IC C4 C6 *C5 C5M 1.4439 120.78 -179.94 121.63 1.5000 IC N1 C5 *C6 H6 0.0 0.0 180.0 0.0 0.0 IC C6 C5 C5M H51 0.0 0.0 0.0 0.0 0.0 IC C5 H51 *C5M H52 0.0 0.0 115.0 0.0 0.0 IC H51 H52 *C5M H53 0.0 0.0 -115.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI TM3P -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) !

! Model compound F !

GROUP

ATOM O4' ON6 -0.50 ! H52' H53' ATOM C1' CN7B 0.07 ! \ /

ATOM H11' HN7 0.09 ! H51'-C5' O4' H11' ATOM H12' HN7 0.09 ! \ / \ / ATOM C4' CN7 0.16 ! H42'--C4' C1'--H12' ATOM H42' HN7 0.09 ! | |

GROUP ! H31'--C3'--C2'--H21' ATOM C2' CN8 -0.18 ! / \

ATOM H21' HN8 0.09 ! O3' H22' ATOM H22' HN8 0.09 ! |

GROUP ! O1P==P==O2P ATOM C3' CN7 -0.09 ! || ATOM H31' HN7 0.09 ! O3P (-2) GROUP !

ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 GROUP

ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C2' H22' C3' H31' C4' H42' BOND O3' P P O1P P O2P P O3P

BOND C4' C5' C5' H51' C5' H52' C5' H53'

(37)

IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI RM3P -2.00 ! 4'-methyl,3'-phosphate tetrahydrofuran (phosphate -2) !

! Model compound F, monoanionic with 2'hydroxyl !

GROUP

ATOM O4' ON6B -0.50 ATOM C1' CN7B 0.07 ATOM H11' HN7 0.09 ATOM H12' HN7 0.09 ATOM C4' CN7 0.16 ATOM H42' HN7 0.09 GROUP

ATOM C2' CN7B 0.14 ATOM H21' HN7 0.09 ATOM O2' ON5 -0.66 ATOM H22' HN5 0.43 GROUP

ATOM C3' CN7 -0.09 ATOM H31' HN7 0.09 GROUP

ATOM O3' ON2 -0.40 ATOM P P 1.10 ATOM O1P ON3 -0.90 ATOM O2P ON3 -0.90 ATOM O3P ON3 -0.90 GROUP

ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09

BOND C1' O4' C1' C2' C2' C3' C3' C4' C4' O4' C3' O3' BOND C1' H11' C1' H12' C2' H21' C3' H31' C4' H42'

BOND C2' O2' O2' H22'

BOND O3' P P O1P P O2P P O3P BOND C4' C5' C5' H51' C5' H52' C5' H53'

(38)

IC C3' C4' O4' C1' 1.5211 103.15 -41.62 108.09 1.4127 IC H11' C1' C2' C3' 1.0856 111.62 123.53 103.11 1.5346 IC H12' C1' C2' C3' 1.0818 113.32 -114.11 103.11 1.5346 IC H21' C2' C3' C4' 1.0846 110.65 91.68 100.86 1.5211 IC H22' C2' C3' C4' 1.0822 110.88 -148.45 100.86 1.5211 IC H31' C3' C4' O4' 1.0806 113.53 162.89 103.15 1.4055 IC C5' C4' O4' C1' 0.0000 000.00 77.76 108.09 1.4127 IC H51' C5' C4' O4' 0.0 0.0 180.0 0.0 0.0 IC H52' C5' C4' O4' 0.0 0.0 -60.0 0.0 0.0 IC H53' C5' C4' O4' 0.0 0.0 60.0 0.0 0.0 IC H42' C4' O4' C1' 1.0808 108.72 -162.12 108.09 1.4127 IC O3' C3' C4' O4' 1.4028 110.98 -77.39 103.15 1.4055 IC P O3' C3' C4' 0.0 0.0 180.00 0.0 0.0 IC O1P P O3' C3' 0.0 0.0 -60.0 0.0 0.0 IC O2P P O3' C3' 0.0 0.0 180.0 0.0 0.0 IC O3P P O3' C3' 0.0 0.0 60.0 0.0 0.0 PATC FIRS NONE LAST NONE

RESI THAO 0.00 ! Nucleoside analogue with imidazole !

! Model compound G with imidazole !

GROUP

ATOM O4' ON6 -0.50 ! H5T ATOM C4' CN7 0.16 ! / ATOM H42' HN7 0.09 ! H51' O5' ATOM C1' CN7B 0.16 ! \ |

ATOM H12' HN7 0.09 !H52'--C5' O4' Imidazole GROUP ! \ / \ /

ATOM C2' CN8 -0.18 ! H42'--C4' C1'--H12' ATOM H21' HN8 0.09 ! | |

ATOM H31' HN7 0.09 ! O3' H22' ATOM C3' CN7 0.14 ! |

ATOM O3' ON5 -0.66 ! H32' ATOM H32' HN5 0.43 !

GROUP

ATOM C5' CN8B 0.05 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM O5' ON5 -0.66 ATOM H5T HN5 0.43

ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / || ATOM ND1 NR1 -0.04 ! HG-CG || ATOM CE1 CPH2 0.25 ! \\ || ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! |

! HD2

(39)

BOND O3' H32' BOND C1' ND1

BOND ND1 CE1 NE2 CD2 CG ND1 BOND CE1 HE1 CD2 HD2 CG HG BOND CG CD2 CE1 NE2

! KEEPS HYDROGENS IN RING PLANE

IMPH ND1 CG CE1 C1' ND1 CE1 CG C1' IMPH CD2 CG NE2 HD2 CD2 NE2 CG HD2 IMPH CE1 ND1 NE2 HE1 CE1 NE2 ND1 HE1 IMPH CG CD2 ND1 HG

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

DECL +P DECL +O1P DECL +O2P DECL +O5' DECL -O3'

ATOM C3' CN7 0.01 ATOM H3' HN7 0.09 ATOM O3' ON2 -0.57

ATOM P P 1.50 ! \ / ATOM O1P ON3 -0.78 ! N6 ATOM O2P ON3 -0.78 ! | ATOM O5' ON2 -0.57 ! C6 ATOM C5' CN8B -0.08 ! // \

BILD O4' C2' *C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' *C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' *C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' *C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' *C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI CYT -1.00

ATOM H6 HN3 0.17 ! / \ / \ ATOM C2 CN1T 0.51 ! O3' H3' O2' H2'' ATOM O2 ON1 -0.41 ! | |

BOND P O1P P O2P P O5'

ATOM C4' CN7 0.16 ! ATOM H4' HN7 0.09 ! ATOM O4' ON6 -0.50 ! ATOM C1' CN7B 0.16 ! ATOM H1' HN7 0.09 ! GROUP

! DELETE PHOSPHATE AND RIBOSE ATOMS DELE ATOM P

BILD C5 C6 N1 H1 0.0 0.0 180.0 0.0 0.0

DELE ATOM P DELE ATOM O1P DELE ATOM O2P DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

ATOM C5' CN8B -0.08 ATOM H5' HN8 0.09 ATOM H5'' HN8 0.09 ATOM P P 1.50 ATOM O1P ON3 -0.78 ATOM O2P ON3 -0.78 ATOM O5' ON2 -0.57 ATOM O5T ON2 -0.57 ATOM C5T CN9 -0.17 ATOM H5T1 HN9 0.09 ATOM H5T2 HN9 0.09 ATOM H5T3 HN9 0.09

DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

DELE ATOM P DELE ATOM O1P DELE ATOM O2P DELE ATOM O5' DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3'

DELE ATOM C5' DELE ATOM H5' DELE ATOM H5'' DELE ATOM C4' DELE ATOM H4' DELE ATOM O4' DELE ATOM C1' DELE ATOM H1' DELE ATOM C2' DELE ATOM H2'' DELE ATOM O2' DELE ATOM H2' DELE ATOM C3' DELE ATOM O3' DELE ATOM H3' GROUP

GROUP

GROUP !

GROUP ! O1P (-2) ATOM O4' ON6 -0.50 ! ||

ATOM O1P ON3 -0.82 ATOM O2P ON3 -0.82 ATOM O3T ON4 -0.68 ATOM H3T HN4 0.34

GROUP

ATOM HG HR3 0.09 ! \ / ATOM CD2 CPH1 0.22 ! ND1---CE1 ATOM HD2 HR3 0.10 ! / | ATOM ND1 NR1 -0.04 ! HG-CG | ATOM CE1 CPH2 0.25 ! \ | ATOM HE1 HR1 0.13 ! CD2---NE2 ATOM NE2 NR2 -0.70 ! |

ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09

GROUP

ATOM N1 NN2 -0.13 !

ATOM C3' CN7 -0.18 ATOM H31' HN7 0.09 ATOM H32' HN7 0.09

GROUP

ATOM C5' CN8B -0.27 ATOM H51' HN8 0.09 ATOM H52' HN8 0.09 ATOM H53' HN8 0.09

GROUP

BILD O4' C2' C1' H1' 0.0 0.0 -115.0 0.0 0.0 BILD C1' C3' C2' H2'' 0.0 0.0 115.0 0.0 0.0 BILD C2' C4' C3' H3' 0.0 0.0 115.0 0.0 0.0 BILD C3' O4' C4' H4' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' C5' H5' 0.0 0.0 -115.0 0.0 0.0 BILD C4' O5' C5' H5'' 0.0 0.0 115.0 0.0 0.0 RESI CYT -1.00