1 0 2 db2000.dat D-ADENOSINE - with 5' - OH end group and 3' - O(minus) DA5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.52 109.59 -127.70 15 C8 CK B 14 12 11 1.37 131.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.30 113.93 177.00 18 C5 CB S 17 15 14 1.39 104.00 0.00 19 C6 CA B 18 17 15 1.40 132.42 180.00 20 N6 N2 B 19 18 17 1.34 123.50 0.00 21 H61 H E 20 19 18 1.01 120.00 180.00 22 H62 H E 20 19 18 1.01 120.00 0.00 23 N1 NC S 19 18 17 1.34 117.43 180.00 24 C2 CQ B 23 19 18 1.33 118.80 0.00 25 H2 H5 E 24 23 19 1.08 120.00 180.00 26 N3 NC S 24 23 19 1.32 129.17 0.00 27 C4 CB E 26 24 23 1.35 110.80 0.00 28 C3' CT M 9 6 5 1.53 115.78 -329.11 29 H3' H1 E 28 9 6 1.09 109.50 30.00 30 C2' CT B 28 9 6 1.53 102.80 -86.30 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 33 O3' OS M 28 9 6 1.42 116.52 -203.47 CHARGE A5E, dft/cc-pVTZ, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1680 .1024 -.1692 .2153 .1451 -.5436 -.0475 .6038 -.7136 .3558 .3558 -.7313 .5726 .0119 -.7649 .5499 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-ADENOSINE - with 5' - phosphate group and 3' - O(minus) group DA INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.52 109.59 -127.70 17 C8 CK B 16 14 13 1.37 131.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.30 113.93 177.00 20 C5 CB S 19 17 16 1.39 104.00 0.00 21 C6 CA B 20 19 17 1.40 132.42 180.00 22 N6 N2 B 21 20 19 1.34 123.50 0.00 23 H61 H E 22 21 20 1.01 120.00 180.00 24 H62 H E 22 21 20 1.01 120.00 0.00 25 N1 NC S 21 20 19 1.34 117.43 180.00 26 C2 CQ B 25 21 20 1.33 118.80 0.00 27 H2 H5 E 26 25 21 1.08 120.00 180.00 28 N3 NC S 26 25 21 1.32 129.17 0.00 29 C4 CB E 28 26 25 1.35 110.80 0.00 30 C3' CT M 11 8 7 1.53 115.78 -329.11 31 H3' H1 E 30 11 8 1.09 109.50 30.00 32 C2' CT B 30 11 8 1.53 102.80 -86.30 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 35 O3' OS M 30 11 8 1.42 116.52 -203.47 CHARGE A deoxy -resp charges, dft/cc-pVTZ, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1680 .1024 -.1692 .2153 .1451 -.5436 -.0475 .6038 -.7136 .3558 .3558 -.7313 .5726 .0119 -.7649 .5499 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-ADENOSINE - with 5' - phosphate group and 3' - OH group DA3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.52 109.59 -127.70 17 C8 CK B 16 14 13 1.37 131.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.30 113.93 177.00 20 C5 CB S 19 17 16 1.39 104.00 0.00 21 C6 CA B 20 19 17 1.40 132.42 180.00 22 N6 N2 B 21 20 19 1.34 123.50 0.00 23 H61 H E 22 21 20 1.01 120.00 180.00 24 H62 H E 22 21 20 1.01 120.00 0.00 25 N1 NC S 21 20 19 1.34 117.43 180.00 26 C2 CQ B 25 21 20 1.33 118.80 0.00 27 H2 H5 E 26 25 21 1.08 120.00 180.00 28 N3 NC S 26 25 21 1.32 129.17 0.00 29 C4 CB E 28 26 25 1.35 110.80 0.00 30 C3' CT M 11 8 7 1.53 115.78 -329.11 31 H3' H1 E 30 11 8 1.09 109.50 30.00 32 C2' CT B 30 11 8 1.53 102.80 -86.30 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 35 O3' OH M 30 11 8 1.42 116.52 -203.47 36 H3T HO M 35 30 11 0.96 114.97 180.00 CHARGE A3E, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1680 .1024 -.1692 .2153 .1451 -.5436 -.0475 .6038 -.7136 .3558 .3558 -.7313 .5726 .0119 -.7649 .5499 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-ADENOSINE - with 5' - OH group and 3' - OH group DAN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.52 109.59 -127.70 15 C8 CK B 14 12 11 1.37 131.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.30 113.93 177.00 18 C5 CB S 17 15 14 1.39 104.00 0.00 19 C6 CA B 18 17 15 1.40 132.42 180.00 20 N6 N2 B 19 18 17 1.34 123.50 0.00 21 H61 H E 20 19 18 1.01 120.00 180.00 22 H62 H E 20 19 18 1.01 120.00 0.00 23 N1 NC S 19 18 17 1.34 117.43 180.00 24 C2 CQ B 23 19 18 1.33 118.80 0.00 25 H2 H5 E 24 23 19 1.08 120.00 180.00 26 N3 NC S 24 23 19 1.32 129.17 0.00 27 C4 CB E 26 24 23 1.35 110.80 0.00 28 C3' CT M 9 6 5 1.53 115.78 -329.11 29 H3' H1 E 28 9 6 1.09 109.50 30.00 30 C2' CT B 28 9 6 1.53 102.80 -86.30 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 33 O3' OH M 28 9 6 1.42 116.52 -203.47 34 H3T HO M 33 28 9 0.96 114.97 180.00 CHARGE ADE resp, dft/cc-pvtz, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1680 .1024 -.1692 .2153 .1451 -.5436 -.0475 .6038 -.7136 .3558 .3558 -.7313 .5726 .0119 -.7649 .5499 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - OH end group and 3' - O(minus) RA5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.52 109.59 -127.70 15 C8 CK B 14 12 11 1.37 131.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.30 113.93 177.00 18 C5 CB S 17 15 14 1.39 104.00 0.00 19 C6 CA B 18 17 15 1.40 132.42 180.00 20 N6 N2 B 19 18 17 1.34 123.50 0.00 21 H61 H E 20 19 18 1.01 120.00 180.00 22 H62 H E 20 19 18 1.01 120.00 0.00 23 N1 NC S 19 18 17 1.34 117.43 180.00 24 C2 CQ B 23 19 18 1.33 118.80 0.00 25 H2 H5 E 24 23 19 1.08 120.00 180.00 26 N3 NC S 24 23 19 1.32 129.17 0.00 27 C4 CB E 26 24 23 1.35 110.80 0.00 28 C3' CT M 9 6 5 1.53 115.78 -329.11 29 H3' H1 E 28 9 6 1.09 109.50 30.00 30 C2' CT B 28 9 6 1.53 102.80 -86.30 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 32 O2' OH S 30 28 9 1.43 109.50 240.00 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 34 O3' OS M 28 9 6 1.42 116.52 -203.47 CHARGE RA5E, dft/cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .0264 .1660 -.0994 .2280 .1154 -.5462 -.0196 .5848 -.6928 .3475 .3475 -.7181 .5805 .0031 -.7390 .4398 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - phosphate group and 3' - O(minus) grou RA INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.52 109.59 -127.70 17 C8 CK B 16 14 13 1.37 131.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.30 113.93 177.00 20 C5 CB S 19 17 16 1.39 104.00 0.00 21 C6 CA B 20 19 17 1.40 132.42 180.00 22 N6 N2 B 21 20 19 1.34 123.50 0.00 23 H61 H E 22 21 20 1.01 120.00 180.00 24 H62 H E 22 21 20 1.01 120.00 0.00 25 N1 NC S 21 20 19 1.34 117.43 180.00 26 C2 CQ B 25 21 20 1.33 118.80 0.00 27 H2 H5 E 26 25 21 1.08 120.00 180.00 28 N3 NC S 26 25 21 1.32 129.17 0.00 29 C4 CB E 28 26 25 1.35 110.80 0.00 30 C3' CT M 11 8 7 1.53 115.78 -329.11 31 H3' H1 E 30 11 8 1.09 109.50 30.00 32 C2' CT B 30 11 8 1.53 102.80 -86.30 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 34 O2' OH S 32 30 11 1.43 109.50 240.00 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 36 O3' OS M 30 11 8 1.42 116.52 -203.47 CHARGE RA, dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .0264 .1660 -.0994 .2280 .1154 -.5462 -.0196 .5848 -.6928 .3475 .3475 -.7181 .5805 .0031 -.7390 .4398 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - phosphate group and 3' - OH group RA3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.52 109.59 -127.70 17 C8 CK B 16 14 13 1.37 131.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.30 113.93 177.00 20 C5 CB S 19 17 16 1.39 104.00 0.00 21 C6 CA B 20 19 17 1.40 132.42 180.00 22 N6 N2 B 21 20 19 1.34 123.50 0.00 23 H61 H E 22 21 20 1.01 120.00 180.00 24 H62 H E 22 21 20 1.01 120.00 0.00 25 N1 NC S 21 20 19 1.34 117.43 180.00 26 C2 CQ B 25 21 20 1.33 118.80 0.00 27 H2 H5 E 26 25 21 1.08 120.00 180.00 28 N3 NC S 26 25 21 1.32 129.17 0.00 29 C4 CB E 28 26 25 1.35 110.80 0.00 30 C3' CT M 11 8 7 1.53 115.78 -329.11 31 H3' H1 E 30 11 8 1.09 109.50 30.00 32 C2' CT B 30 11 8 1.53 102.80 -86.30 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 34 O2' OH S 32 30 11 1.43 109.50 240.00 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 36 O3' OH M 30 11 8 1.42 116.52 -203.47 37 H3T HO M 36 30 11 0.96 114.97 180.00 CHARGE RA3E, cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .0264 .1660 -.0994 .2280 .1154 -.5462 -.0196 .5848 -.6928 .3475 .3475 -.7181 .5805 .0031 -.7390 .4398 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-ADENOSINE - with 5' - OH group and 3' - OH group RAN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.52 109.59 -127.70 15 C8 CK B 14 12 11 1.37 131.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.30 113.93 177.00 18 C5 CB S 17 15 14 1.39 104.00 0.00 19 C6 CA B 18 17 15 1.40 132.42 180.00 20 N6 N2 B 19 18 17 1.34 123.50 0.00 21 H61 H E 20 19 18 1.01 120.00 180.00 22 H62 H E 20 19 18 1.01 120.00 0.00 23 N1 NC S 19 18 17 1.34 117.43 180.00 24 C2 CQ B 23 19 18 1.33 118.80 0.00 25 H2 H5 E 24 23 19 1.08 120.00 180.00 26 N3 NC S 24 23 19 1.32 129.17 0.00 27 C4 CB E 26 24 23 1.35 110.80 0.00 28 C3' CT M 9 6 5 1.53 115.78 -329.11 29 H3' H1 E 28 9 6 1.09 109.50 30.00 30 C2' CT B 28 9 6 1.53 102.80 -86.30 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 32 O2' OH S 30 28 9 1.43 109.50 240.00 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 34 O3' OH M 28 9 6 1.42 116.52 -203.47 35 H3T HO M 34 28 9 0.96 114.97 180.00 CHARGE resp RADE, dft/cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .0264 .1660 -.0994 .2280 .1154 -.5462 -.0196 .5848 -.6928 .3475 .3475 -.7181 .5805 .0031 -.7390 .4398 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-THYMINE - with 5' - OH end group and 3' - O(minus) DT5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.53 109.59 -127.70 15 C6 CM B 14 12 11 1.37 123.04 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.34 121.22 177.30 18 C7 CT 3 17 15 14 1.50 121.63 180.00 19 H71 HC E 18 17 15 1.09 109.50 60.00 20 H72 HC E 18 17 15 1.09 109.50 180.00 21 H73 HC E 18 17 15 1.09 109.50 300.00 22 C4 C B 17 15 14 1.44 120.78 0.00 23 O4 O E 22 17 15 1.23 125.35 180.00 24 N3 NA B 22 17 15 1.38 114.07 0.00 25 H3 H E 24 22 17 1.09 116.77 180.00 26 C2 C S 24 22 17 1.38 126.46 0.00 27 O2 O E 26 24 22 1.22 121.70 180.00 28 C3' CT M 9 6 5 1.53 115.78 -329.11 29 H3' H1 E 28 9 6 1.09 109.50 30.00 30 C2' CT B 28 9 6 1.53 102.80 -86.30 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 33 O3' OS M 28 9 6 1.42 116.52 -203.47 CHARGE T5 dft/cc-pvtz, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1082 .1074 -.0282 -.2552 .2796 -.0388 -.1326 .0606 .0606 .0606 .5608 -.5455 -.4824 .3542 .5892 -.5880 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-THYMINE - with 5' - phosphate group and 3' - O(minus) group DT INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.53 109.59 -127.70 17 C6 CM B 16 14 13 1.37 123.04 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.34 121.22 177.30 20 C7 CT 3 19 17 16 1.50 121.63 180.00 21 H71 HC E 20 19 17 1.09 109.50 60.00 22 H72 HC E 20 19 17 1.09 109.50 180.00 23 H73 HC E 20 19 17 1.09 109.50 300.00 24 C4 C B 19 17 16 1.44 120.78 0.00 25 O4 O E 24 19 17 1.23 125.35 180.00 26 N3 NA B 24 19 17 1.38 114.07 0.00 27 H3 H E 26 24 19 1.09 116.77 180.00 28 C2 C S 26 24 19 1.38 126.46 0.00 29 O2 O E 28 26 24 1.22 121.70 180.00 30 C3' CT M 11 8 7 1.53 115.78 -329.11 31 H3' H1 E 30 11 8 1.09 109.50 30.00 32 C2' CT B 30 11 8 1.53 102.80 -86.30 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 35 O3' OS M 30 11 8 1.42 116.52 -203.47 CHARGE deoxy -resp T, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1082 .1074 -.0282 -.2552 .2796 -.0388 -.1326 .0606 .0606 .0606 .5608 -.5455 -.4824 .3542 .5892 -.5880 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-THYMINE - with 5' - phosphate group and 3' - OH group DT3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.53 109.59 -127.70 17 C6 CM B 16 14 13 1.37 123.04 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.34 121.22 177.30 20 C7 CT 3 19 17 16 1.50 121.63 180.00 21 H71 HC E 20 19 17 1.09 109.50 60.00 22 H72 HC E 20 19 17 1.09 109.50 180.00 23 H73 HC E 20 19 17 1.09 109.50 300.00 24 C4 C B 19 17 16 1.44 120.78 0.00 25 O4 O E 24 19 17 1.23 125.35 180.00 26 N3 NA B 24 19 17 1.38 114.07 0.00 27 H3 H E 26 24 19 1.09 116.77 180.00 28 C2 C S 26 24 19 1.38 126.46 0.00 29 O2 O E 28 26 24 1.22 121.70 180.00 30 C3' CT M 11 8 7 1.53 115.78 -329.11 31 H3' H1 E 30 11 8 1.09 109.50 30.00 32 C2' CT B 30 11 8 1.53 102.80 -86.30 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 35 O3' OH M 30 11 8 1.42 116.52 -203.47 36 H3T HO M 35 30 11 0.96 114.97 180.00 CHARGE T3, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1082 .1074 -.0282 -.2552 .2796 -.0388 -.1326 .0606 .0606 .0606 .5608 -.5455 -.4824 .3542 .5892 -.5880 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-THYMINE - with 5' - OH group and 3' - OH group DTN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.53 109.59 -127.70 15 C6 CM B 14 12 11 1.37 123.04 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.34 121.22 177.30 18 C7 CT 3 17 15 14 1.50 121.63 180.00 19 H71 HC E 18 17 15 1.09 109.50 60.00 20 H72 HC E 18 17 15 1.09 109.50 180.00 21 H73 HC E 18 17 15 1.09 109.50 300.00 22 C4 C B 17 15 14 1.44 120.78 0.00 23 O4 O E 22 17 15 1.23 125.35 180.00 24 N3 NA B 22 17 15 1.38 114.07 0.00 25 H3 H E 24 22 17 1.09 116.77 180.00 26 C2 C S 24 22 17 1.38 126.46 0.00 27 O2 O E 26 24 22 1.22 121.70 180.00 28 C3' CT M 9 6 5 1.53 115.78 -329.11 29 H3' H1 E 28 9 6 1.09 109.50 30.00 30 C2' CT B 28 9 6 1.53 102.80 -86.30 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 33 O3' OH M 28 9 6 1.42 116.52 -203.47 34 H3T HO M 33 28 9 0.96 114.97 180.00 CHARGE deoxy-THY-B, dft/cc-pvtz, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1082 .1074 -.0282 -.2552 .2796 -.0388 -.1326 .0606 .0606 .0606 .5608 -.5455 -.4824 .3542 .5892 -.5880 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - OH end group and 3' - O(minus) RU5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.53 109.59 -127.70 15 C6 CM B 14 12 11 1.37 123.04 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.34 121.22 177.30 18 H5 HA E 17 15 14 1.09 120.00 180.00 19 C4 C B 17 15 14 1.44 120.78 0.00 20 O4 O E 19 17 15 1.23 125.35 180.00 21 N3 NA B 19 17 15 1.38 114.07 0.00 22 H3 H E 21 19 17 1.09 116.77 180.00 23 C2 C S 21 19 17 1.38 126.46 0.00 24 O2 O E 23 21 19 1.22 121.70 180.00 25 C3' CT M 9 6 5 1.53 115.78 -329.11 26 H3' H1 E 25 9 6 1.09 109.50 30.00 27 C2' CT B 25 9 6 1.53 102.80 -86.30 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 29 O2' OH S 27 25 9 1.43 109.50 240.00 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 31 O3' OS M 25 9 6 1.42 116.52 -203.47 CHARGE RU5E, cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .0834 .1150 -.0115 -.1206 .2211 -.3171 .1640 .5728 -.5528 -.3409 .3077 .4625 -.5597 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - phosphate group and 3' - O(minus) group RU INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.53 109.59 -127.70 17 C6 CM B 16 14 13 1.37 123.04 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.34 121.22 177.30 20 H5 HA E 19 17 16 1.09 120.00 180.00 21 C4 C B 19 17 16 1.44 120.78 0.00 22 O4 O E 21 19 17 1.23 125.35 180.00 23 N3 NA B 21 19 17 1.38 114.07 0.00 24 H3 H E 23 21 19 1.09 116.77 180.00 25 C2 C S 23 21 19 1.38 126.46 0.00 26 O2 O E 25 23 21 1.22 121.70 180.00 27 C3' CT M 11 8 7 1.53 115.78 -329.11 28 H3' H1 E 27 11 8 1.09 109.50 30.00 29 C2' CT B 27 11 8 1.53 102.80 -86.30 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 31 O2' OH S 29 27 11 1.43 109.50 240.00 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 33 O3' OS M 27 11 8 1.42 116.52 -203.47 CHARGE RU dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .0834 .1150 -.0115 -.1206 .2211 -.3171 .1640 .5728 -.5528 -.3409 .3077 .4625 -.5597 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - phosphate group and 3' - OH group RU3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.53 109.59 -127.70 17 C6 CM B 16 14 13 1.37 123.04 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.34 121.22 177.30 20 H5 HA E 19 17 16 1.09 120.00 180.00 21 C4 C B 19 17 16 1.44 120.78 0.00 22 O4 O E 21 19 17 1.23 125.35 180.00 23 N3 NA B 21 19 17 1.38 114.07 0.00 24 H3 H E 23 21 19 1.09 116.77 180.00 25 C2 C S 23 21 19 1.38 126.46 0.00 26 O2 O E 25 23 21 1.22 121.70 180.00 27 C3' CT M 11 8 7 1.53 115.78 -329.11 28 H3' H1 E 27 11 8 1.09 109.50 30.00 29 C2' CT B 27 11 8 1.53 102.80 -86.30 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 31 O2' OH S 29 27 11 1.43 109.50 240.00 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 33 O3' OH M 27 11 8 1.42 116.52 -203.47 34 H3T HO M 33 27 11 0.96 114.97 180.00 CHARGE RU3E, dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .0834 .1150 -.0115 -.1206 .2211 -.3171 .1640 .5728 -.5528 -.3409 .3077 .4625 -.5597 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-URACIL - with 5' - OH group and 3' - OH group RUN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 6 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.53 109.59 -127.70 15 C6 CM B 14 12 11 1.37 123.04 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.34 121.22 177.30 18 H5 HA E 17 15 14 1.09 120.00 180.00 19 C4 C B 17 15 14 1.44 120.78 0.00 20 O4 O E 19 17 15 1.23 125.35 180.00 21 N3 NA B 19 17 15 1.38 114.07 0.00 22 H3 H E 21 19 17 1.09 116.77 180.00 23 C2 C S 21 19 17 1.38 126.46 0.00 24 O2 O E 23 21 19 1.22 121.70 180.00 25 C3' CT M 9 6 5 1.53 115.78 -329.11 26 H3' H1 E 25 9 6 1.09 109.50 30.00 27 C2' CT B 25 9 6 1.53 102.80 -86.30 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 29 O2' OH S 27 25 9 1.43 109.50 240.00 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 31 O3' OH M 25 9 6 1.42 116.52 -203.47 32 H3T HO M 31 25 9 0.96 114.97 180.00 CHARGE resp RURA dft/cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .0834 .1150 -.0115 -.1206 .2211 -.3171 .1640 .5728 -.5528 -.3409 .3077 .4625 -.5597 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-GUANOSINE - with 5' - OH end group and 3' - O(minus) group DG5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.49 108.06 -127.70 15 C8 CK B 14 12 11 1.38 129.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.31 114.00 -179.90 18 C5 CB S 17 15 14 1.39 103.90 0.00 19 C6 C B 18 17 15 1.42 130.40 180.00 20 O6 O E 19 18 17 1.23 128.80 0.00 21 N1 NA B 19 18 17 1.40 111.38 180.00 22 H1 H E 21 19 18 1.00 117.36 179.90 23 C2 CA B 21 19 18 1.38 125.24 -0.10 24 N2 N2 B 23 21 19 1.34 116.02 180.00 25 H21 H E 24 23 21 1.01 127.00 -0.82 26 H22 H E 24 23 21 1.01 116.53 -179.44 27 N3 NC S 23 21 19 1.33 123.30 0.00 28 C4 CB E 27 23 21 1.36 112.20 0.00 29 C3' CT M 9 6 5 1.53 115.78 -329.11 30 H3' H1 E 29 9 6 1.09 109.50 30.00 31 C2' CT B 29 9 6 1.53 102.80 -86.30 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 34 O3' OS M 29 9 6 1.42 116.52 -203.47 CHARGE deoxy gua, dft/cc-pvtz, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1557 .0886 -.0379 .1353 .1508 -.5139 .0585 .5071 -.5301 -.5405 .3750 .6834 -.7508 .3443 .3443 -.6502 .2909 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-GUANOSINE - with 5' - phosphate group and 3' - O(minus) grou DG INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.49 108.06 -127.70 17 C8 CK B 16 14 13 1.38 129.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.31 114.00 -179.90 20 C5 CB S 19 17 16 1.39 103.90 0.00 21 C6 C B 20 19 17 1.42 130.40 180.00 22 O6 O E 21 20 19 1.23 128.80 0.00 23 N1 NA B 21 20 19 1.40 111.38 180.00 24 H1 H E 23 21 20 1.00 117.36 179.90 25 C2 CA B 23 21 20 1.38 125.24 -0.10 26 N2 N2 B 25 23 21 1.34 116.02 180.00 27 H21 H E 26 25 23 1.01 127.00 -0.82 28 H22 H E 26 25 23 1.01 116.53 -179.44 29 N3 NC S 25 23 21 1.33 123.30 0.00 30 C4 CB E 29 25 23 1.36 112.20 0.00 31 C3' CT M 11 8 7 1.53 115.78 -329.11 32 H3' H1 E 31 11 8 1.09 109.50 30.00 33 C2' CT B 31 11 8 1.53 102.80 -86.30 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 36 O3' OS M 31 11 8 1.42 116.52 -203.47 CHARGE gua, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1557 .0886 -.0379 .1353 .1508 -.5139 .0585 .5071 -.5301 -.5405 .3750 .6834 -.7508 .3443 .3443 -.6502 .2909 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-GUANOSINE - with 5' - phosphate group and 3' - OH group DG3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.49 108.06 -127.70 17 C8 CK B 16 14 13 1.38 129.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.31 114.00 -179.90 20 C5 CB S 19 17 16 1.39 103.90 0.00 21 C6 C B 20 19 17 1.42 130.40 180.00 22 O6 O E 21 20 19 1.23 128.80 0.00 23 N1 NA B 21 20 19 1.40 111.38 180.00 24 H1 H E 23 21 20 1.00 117.36 179.90 25 C2 CA B 23 21 20 1.38 125.24 -0.10 26 N2 N2 B 25 23 21 1.34 116.02 180.00 27 H21 H E 26 25 23 1.01 127.00 -0.82 28 H22 H E 26 25 23 1.01 116.53 -179.44 29 N3 NC S 25 23 21 1.33 123.30 0.00 30 C4 CB E 29 25 23 1.36 112.20 0.00 31 C3' CT M 11 8 7 1.53 115.78 -329.11 32 H3' H1 E 31 11 8 1.09 109.50 30.00 33 C2' CT B 31 11 8 1.53 102.80 -86.30 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 36 O3' OH M 31 11 8 1.42 116.52 -203.47 37 H3T HO M 36 31 11 0.96 114.97 180.00 CHARGE gua, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1557 .0886 -.0379 .1353 .1508 -.5139 .0585 .5071 -.5301 -.5405 .3750 .6834 -.7508 .3443 .3443 -.6502 .2909 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-GUANOSINE - with 5' - OH group and 3' - OH group DGN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.49 108.06 -127.70 15 C8 CK B 14 12 11 1.38 129.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.31 114.00 -179.90 18 C5 CB S 17 15 14 1.39 103.90 0.00 19 C6 C B 18 17 15 1.42 130.40 180.00 20 O6 O E 19 18 17 1.23 128.80 0.00 21 N1 NA B 19 18 17 1.40 111.38 180.00 22 H1 H E 21 19 18 1.00 117.36 179.90 23 C2 CA B 21 19 18 1.38 125.24 -0.10 24 N2 N2 B 23 21 19 1.34 116.02 180.00 25 H21 H E 24 23 21 1.01 127.00 -0.82 26 H22 H E 24 23 21 1.01 116.53 -179.44 27 N3 NC S 23 21 19 1.33 123.30 0.00 28 C4 CB E 27 23 21 1.36 112.20 0.00 29 C3' CT M 9 6 5 1.53 115.78 -329.11 30 H3' H1 E 29 9 6 1.09 109.50 30.00 31 C2' CT B 29 9 6 1.53 102.80 -86.30 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 34 O3' OH M 29 9 6 1.42 116.52 -203.47 35 H3T HO M 34 29 9 0.96 114.97 180.00 CHARGE deoxy-GUA-B, dft/cc-pvtz, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1557 .0886 -.0379 .1353 .1508 -.5139 .0585 .5071 -.5301 -.5405 .3750 .6834 -.7508 .3443 .3443 -.6502 .2909 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - OH end group and 3' - O(minus) group RG5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.49 108.06 -127.70 15 C8 CK B 14 12 11 1.38 129.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.31 114.00 -179.90 18 C5 CB S 17 15 14 1.39 103.90 0.00 19 C6 C B 18 17 15 1.42 130.40 180.00 20 O6 O E 19 18 17 1.23 128.80 0.00 21 N1 NA B 19 18 17 1.40 111.38 180.00 22 H1 H E 21 19 18 1.00 117.36 179.90 23 C2 CA B 21 19 18 1.38 125.24 -0.10 24 N2 N2 B 23 21 19 1.34 116.02 180.00 25 H21 H E 24 23 21 1.01 127.00 -0.82 26 H22 H E 24 23 21 1.01 116.53 -179.44 27 N3 NC S 23 21 19 1.33 123.30 0.00 28 C4 CB E 27 23 21 1.36 112.20 0.00 29 C3' CT M 9 6 5 1.53 115.78 -329.11 30 H3' H1 E 29 9 6 1.09 109.50 30.00 31 C2' CT B 29 9 6 1.53 102.80 -86.30 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 33 O2' OH S 31 29 9 1.43 109.50 240.00 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 35 O3' OS M 29 9 6 1.42 116.52 -203.47 CHARGE RG5E, cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .1132 .1019 -.0871 .1966 .1168 -.5279 .0827 .4649 -.5150 -.4848 .3601 .6423 -.7501 .3488 .3488 -.6313 .2440 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - phosphate group and 3' - O(minus) grou RG INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.49 108.06 -127.70 17 C8 CK B 16 14 13 1.38 129.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.31 114.00 -179.90 20 C5 CB S 19 17 16 1.39 103.90 0.00 21 C6 C B 20 19 17 1.42 130.40 180.00 22 O6 O E 21 20 19 1.23 128.80 0.00 23 N1 NA B 21 20 19 1.40 111.38 180.00 24 H1 H E 23 21 20 1.00 117.36 179.90 25 C2 CA B 23 21 20 1.38 125.24 -0.10 26 N2 N2 B 25 23 21 1.34 116.02 180.00 27 H21 H E 26 25 23 1.01 127.00 -0.82 28 H22 H E 26 25 23 1.01 116.53 -179.44 29 N3 NC S 25 23 21 1.33 123.30 0.00 30 C4 CB E 29 25 23 1.36 112.20 0.00 31 C3' CT M 11 8 7 1.53 115.78 -329.11 32 H3' H1 E 31 11 8 1.09 109.50 30.00 33 C2' CT B 31 11 8 1.53 102.80 -86.30 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 35 O2' OH S 33 31 11 1.43 109.50 240.00 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 37 O3' OS M 31 11 8 1.42 116.52 -203.47 CHARGE RG, dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .1132 .1019 -.0871 .1966 .1168 -.5279 .0827 .4649 -.5150 -.4848 .3601 .6423 -.7501 .3488 .3488 -.6313 .2440 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - phosphate group and 3' - OH group RG3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N9 N* S 14 13 11 1.49 108.06 -127.70 17 C8 CK B 16 14 13 1.38 129.20 81.59 18 H8 H5 E 17 16 14 1.08 120.00 0.00 19 N7 NB S 17 16 14 1.31 114.00 -179.90 20 C5 CB S 19 17 16 1.39 103.90 0.00 21 C6 C B 20 19 17 1.42 130.40 180.00 22 O6 O E 21 20 19 1.23 128.80 0.00 23 N1 NA B 21 20 19 1.40 111.38 180.00 24 H1 H E 23 21 20 1.00 117.36 179.90 25 C2 CA B 23 21 20 1.38 125.24 -0.10 26 N2 N2 B 25 23 21 1.34 116.02 180.00 27 H21 H E 26 25 23 1.01 127.00 -0.82 28 H22 H E 26 25 23 1.01 116.53 -179.44 29 N3 NC S 25 23 21 1.33 123.30 0.00 30 C4 CB E 29 25 23 1.36 112.20 0.00 31 C3' CT M 11 8 7 1.53 115.78 -329.11 32 H3' H1 E 31 11 8 1.09 109.50 30.00 33 C2' CT B 31 11 8 1.53 102.80 -86.30 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 35 O2' OH S 33 31 11 1.43 109.50 240.00 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 37 O3' OH M 31 11 8 1.42 116.52 -203.47 38 H3T HO M 37 31 11 0.96 114.97 180.00 CHARGE RG3E, dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .1132 .1019 -.0871 .1966 .1168 -.5279 .0827 .4649 -.5150 -.4848 .3601 .6423 -.7501 .3488 .3488 -.6313 .2440 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE R-GUANOSINE - with 5' - OH group and 3' - OH group RGN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N9 N* S 12 11 9 1.49 108.06 -127.70 15 C8 CK B 14 12 11 1.38 129.20 81.59 16 H8 H5 E 15 14 12 1.08 120.00 0.00 17 N7 NB S 15 14 12 1.31 114.00 -179.90 18 C5 CB S 17 15 14 1.39 103.90 0.00 19 C6 C B 18 17 15 1.42 130.40 180.00 20 O6 O E 19 18 17 1.23 128.80 0.00 21 N1 NA B 19 18 17 1.40 111.38 180.00 22 H1 H E 21 19 18 1.00 117.36 179.90 23 C2 CA B 21 19 18 1.38 125.24 -0.10 24 N2 N2 B 23 21 19 1.34 116.02 180.00 25 H21 H E 24 23 21 1.01 127.00 -0.82 26 H22 H E 24 23 21 1.01 116.53 -179.44 27 N3 NC S 23 21 19 1.33 123.30 0.00 28 C4 CB E 27 23 21 1.36 112.20 0.00 29 C3' CT M 9 6 5 1.53 115.78 -329.11 30 H3' H1 E 29 9 6 1.09 109.50 30.00 31 C2' CT B 29 9 6 1.53 102.80 -86.30 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 33 O2' OH S 31 29 9 1.43 109.50 240.00 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 35 O3' OH M 29 9 6 1.42 116.52 -203.47 36 H3T HO M 35 29 9 0.96 114.97 180.00 CHARGE resp RGUA, dft/cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .1132 .1019 -.0871 .1966 .1168 -.5279 .0827 .4649 -.5150 -.4848 .3601 .6423 -.7501 .3488 .3488 -.6313 .2440 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C1' C2' C4 C5 C4 N9 DONE D-CYTOSINE - with 5' - OH end group and 3' - O(minus) group DC5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.49 108.10 -127.70 15 C6 CM B 14 12 11 1.36 121.10 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.36 121.00 180.00 18 H5 HA E 17 15 14 1.09 120.00 180.00 19 C4 CA B 17 15 14 1.43 116.90 0.00 20 N4 N2 B 19 17 15 1.32 120.10 180.00 21 H41 H E 20 19 17 1.01 117.70 180.00 22 H42 H E 20 19 17 1.01 120.27 0.00 23 N3 NC S 19 17 15 1.33 121.70 0.00 24 C2 C S 23 19 17 1.36 120.50 0.00 25 O2 O E 24 23 19 1.24 122.40 180.00 26 C3' CT M 9 6 5 1.53 115.78 -329.11 27 H3' H1 E 26 9 6 1.09 109.50 30.00 28 C2' CT B 26 9 6 1.53 102.80 -86.30 29 H2'1 HC E 28 26 9 1.09 109.50 120.00 30 H2'2 HC E 28 26 9 1.09 109.50 240.00 31 O3' OS M 26 9 6 1.42 116.52 -203.47 CHARGE C5E, cc-pvtz, polarization corected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1421 .0851 -.1318 -.0115 .2099 -.4696 .1833 .7010 -.7417 .3526 .3526 -.7555 .8464 -.6524 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group DC INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.49 108.10 -127.70 17 C6 CM B 16 14 13 1.36 121.10 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.36 121.00 180.00 20 H5 HA E 19 17 16 1.09 120.00 180.00 21 C4 CA B 19 17 16 1.43 116.90 0.00 22 N4 N2 B 21 19 17 1.32 120.10 180.00 23 H41 H E 22 21 19 1.01 117.70 180.00 24 H42 H E 22 21 19 1.01 120.27 0.00 25 N3 NC S 21 19 17 1.33 121.70 0.00 26 C2 C S 25 21 19 1.36 120.50 0.00 27 O2 O E 26 25 21 1.24 122.40 180.00 28 C3' CT M 11 8 7 1.53 115.78 -329.11 29 H3' H1 E 28 11 8 1.09 109.50 30.00 30 C2' CT B 28 11 8 1.53 102.80 -86.30 31 H2'1 HC E 30 28 11 1.09 109.50 120.00 32 H2'2 HC E 30 28 11 1.09 109.50 240.00 33 O3' OS M 28 11 8 1.42 116.52 -203.47 CHARGE deoxy -resp C, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1421 .0851 -.1318 -.0115 .2099 -.4696 .1833 .7010 -.7417 .3526 .3526 -.7555 .8464 -.6524 .1645 .0623 -.0561 .0486 .0486 -.4998 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-CYTOSINE - with 5' - phosphate group and 3' - OH group DC3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.49 108.10 -127.70 17 C6 CM B 16 14 13 1.36 121.10 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.36 121.00 180.00 20 H5 HA E 19 17 16 1.09 120.00 180.00 21 C4 CA B 19 17 16 1.43 116.90 0.00 22 N4 N2 B 21 19 17 1.32 120.10 180.00 23 H41 H E 22 21 19 1.01 117.70 180.00 24 H42 H E 22 21 19 1.01 120.27 0.00 25 N3 NC S 21 19 17 1.33 121.70 0.00 26 C2 C S 25 21 19 1.36 120.50 0.00 27 O2 O E 26 25 21 1.24 122.40 180.00 28 C3' CT M 11 8 7 1.53 115.78 -329.11 29 H3' H1 E 28 11 8 1.09 109.50 30.00 30 C2' CT B 28 11 8 1.53 102.80 -86.30 31 H2'1 HC E 30 28 11 1.09 109.50 120.00 32 H2'2 HC E 30 28 11 1.09 109.50 240.00 33 O3' OH M 28 11 8 1.42 116.52 -203.47 34 H3T HO M 30 25 8 0.96 114.97 180.00 CHARGE deoxy -resp C, dft/cc-pvtz, polarization corrected 1.0735 -.7545 -.7545 -.4128 -.0111 .0662 .0662 .0721 .0887 -.3124 .1421 .0851 -.1318 -.0115 .2099 -.4696 .1833 .7010 -.7417 .3526 .3526 -.7555 .8464 -.6524 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE D-CYTOSINE - with 5' - OH group and 3' - OH group DCN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.49 108.10 -127.70 15 C6 CM B 14 12 11 1.36 121.10 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.36 121.00 180.00 18 H5 HA E 17 15 14 1.09 120.00 180.00 19 C4 CA B 17 15 14 1.43 116.90 0.00 20 N4 N2 B 19 17 15 1.32 120.10 180.00 21 H41 H E 20 19 17 1.01 117.70 180.00 22 H42 H E 20 19 17 1.01 120.27 0.00 23 N3 NC S 19 17 15 1.33 121.70 0.00 24 C2 C S 23 19 17 1.36 120.50 0.00 25 O2 O E 24 23 19 1.24 122.40 180.00 26 C3' CT M 9 6 5 1.53 115.78 -329.11 27 H3' H1 E 26 9 6 1.09 109.50 30.00 28 C2' CT B 26 9 6 1.53 102.80 -86.30 29 H2'1 HC E 28 26 9 1.09 109.50 120.00 30 H2'2 HC E 28 26 9 1.09 109.50 240.00 31 O3' OH M 26 9 6 1.42 116.52 -203.47 32 H3T HO M 31 26 9 0.96 114.97 180.00 CHARGE deoxy-CYT-B: CYT, df/cc-pvtz, polarization corrected .4109 -.5671 -.0111 .0662 .0662 .0721 .0887 -.3124 .1421 .0851 -.1318 -.0115 .2099 -.4696 .1833 .7010 -.7417 .3526 .3526 -.7555 .8464 -.6524 .1645 .0623 -.0561 .0486 .0486 -.5918 .3999 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - OH end group and 3' - O(minus) group RC5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.49 108.10 -127.70 15 C6 CM B 14 12 11 1.36 121.10 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.36 121.00 180.00 18 H5 HA E 17 15 14 1.09 120.00 180.00 19 C4 CA B 17 15 14 1.43 116.90 0.00 20 N4 N2 B 19 17 15 1.32 120.10 180.00 21 H41 H E 20 19 17 1.01 117.70 180.00 22 H42 H E 20 19 17 1.01 120.27 0.00 23 N3 NC S 19 17 15 1.33 121.70 0.00 24 C2 C S 23 19 17 1.36 120.50 0.00 25 O2 O E 24 23 19 1.24 122.40 180.00 26 C3' CT M 9 6 5 1.53 115.78 -329.11 27 H3' H1 E 26 9 6 1.09 109.50 30.00 28 C2' CT B 26 9 6 1.53 102.80 -86.30 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 30 O2' OH S 28 26 9 1.43 109.50 240.00 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 32 O3' OS M 26 9 6 1.42 116.52 -203.47 CHARGE RC5E , dft/cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .0175 .1427 -.0827 -.0403 .2017 -.4449 .1759 .6770 -.7460 .3542 .3542 -.7264 .8021 -.6611 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - phosphate group and 3' - O(minus) group RC INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.49 108.10 -127.70 17 C6 CM B 16 14 13 1.36 121.10 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.36 121.00 180.00 20 H5 HA E 19 17 16 1.09 120.00 180.00 21 C4 CA B 19 17 16 1.43 116.90 0.00 22 N4 N2 B 21 19 17 1.32 120.10 180.00 23 H41 H E 22 21 19 1.01 117.70 180.00 24 H42 H E 22 21 19 1.01 120.27 0.00 25 N3 NC S 21 19 17 1.33 121.70 0.00 26 C2 C S 25 21 19 1.36 120.50 0.00 27 O2 O E 26 25 21 1.24 122.40 180.00 28 C3' CT M 11 8 7 1.53 115.78 -329.11 29 H3' H1 E 28 11 8 1.09 109.50 30.00 30 C2' CT B 28 11 8 1.53 102.80 -86.30 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 32 O2' OH S 30 28 11 1.43 109.50 240.00 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 34 O3' OS M 28 11 8 1.42 116.52 -203.47 CHARGE RC, dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .0175 .1427 -.0827 -.0403 .2017 -.4449 .1759 .6770 -.7460 .3542 .3542 -.7264 .8021 -.6611 .2522 .0191 .0041 .1033 -.4963 .3720 -.4749 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - phosphate group and 3' - OH group RC3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 P P M 3 2 1 1.60 119.04 200.00 5 O1P O2 E 4 3 2 1.48 109.61 150.00 6 O2P O2 E 4 3 2 1.48 109.58 20.00 7 O5' OS M 4 3 2 1.60 101.43 -98.89 8 C5' CT M 7 4 3 1.44 119.00 -39.22 9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 11 C4' CT M 8 7 4 1.52 110.00 180.00 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 13 O4' OS S 11 8 7 1.46 108.86 -86.31 14 C1' CT B 13 11 8 1.42 110.04 105.60 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 16 N1 N* S 14 13 11 1.49 108.10 -127.70 17 C6 CM B 16 14 13 1.36 121.10 81.59 18 H6 H4 E 17 16 14 1.08 120.00 0.00 19 C5 CM B 17 16 14 1.36 121.00 180.00 20 H5 HA E 19 17 16 1.09 120.00 180.00 21 C4 CA B 19 17 16 1.43 116.90 0.00 22 N4 N2 B 21 19 17 1.32 120.10 180.00 23 H41 H E 22 21 19 1.01 117.70 180.00 24 H42 H E 22 21 19 1.01 120.27 0.00 25 N3 NC S 21 19 17 1.33 121.70 0.00 26 C2 C S 25 21 19 1.36 120.50 0.00 27 O2 O E 26 25 21 1.24 122.40 180.00 28 C3' CT M 11 8 7 1.53 115.78 -329.11 29 H3' H1 E 28 11 8 1.09 109.50 30.00 30 C2' CT B 28 11 8 1.53 102.80 -86.30 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 32 O2' OH S 30 28 11 1.43 109.50 240.00 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 34 O3' OH M 28 11 8 1.42 116.52 -203.47 35 H3T HO M 34 28 11 0.96 114.97 180.00 CHARGE RC3E, dft/cc-pvtz, polarization corrected 1.0720 -.7552 -.7552 -.4085 .0556 .0602 .0602 .0219 .1055 -.2599 .0175 .1427 -.0827 -.0403 .2017 -.4449 .1759 .6770 -.7460 .3542 .3542 -.7264 .8021 -.6611 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE R-CYTOSINE - with 5' - OH group and 3' - OH group RCN INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 3 DUMM DU M 2 1 0 1.00 90.00 0.00 4 H5T HO M 3 2 1 1.00 120.00 180.00 5 O5' OH M 4 3 2 0.96 101.43 -98.89 6 C5' CT M 5 4 3 1.44 119.00 -39.22 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 9 C4' CT M 6 5 4 1.52 110.00 -180.00 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 11 O4' OS S 9 6 5 1.46 108.86 -86.31 12 C1' CT B 11 9 5 1.42 110.04 105.60 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 14 N1 N* S 12 11 9 1.49 108.10 -127.70 15 C6 CM B 14 12 11 1.36 121.10 81.59 16 H6 H4 E 15 14 12 1.08 120.00 0.00 17 C5 CM B 15 14 12 1.36 121.00 180.00 18 H5 HA E 17 15 14 1.09 120.00 180.00 19 C4 CA B 17 15 14 1.43 116.90 0.00 20 N4 N2 B 19 17 15 1.32 120.10 180.00 21 H41 H E 20 19 17 1.01 117.70 180.00 22 H42 H E 20 19 17 1.01 120.27 0.00 23 N3 NC S 19 17 15 1.33 121.70 0.00 24 C2 C S 23 19 17 1.36 120.50 0.00 25 O2 O E 24 23 19 1.24 122.40 180.00 26 C3' CT M 9 6 5 1.53 115.78 -329.11 27 H3' H1 E 26 9 6 1.09 109.50 30.00 28 C2' CT B 26 9 6 1.53 102.80 -86.30 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 30 O2' OH S 28 26 9 1.43 109.50 240.00 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 32 O3' OH M 26 9 6 1.42 116.52 -203.47 33 H3T HO M 32 26 9 0.96 114.97 180.00 CHARGE resp RCYT, dft/cc-pvtz, polarization corrected .4086 -.5634 .0556 .0602 .0602 .0219 .1055 -.2599 .0175 .1427 -.0827 -.0403 .2017 -.4449 .1759 .6770 -.7460 .3542 .3542 -.7264 .8021 -.6611 .2522 .0191 .0041 .1033 -.4963 .3720 -.5798 .4128 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C1' C2' C2 N1 DONE N-methyl-ADENINE AME INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 8 N9 N* M 5 4 3 1.52100 109.6030 295.5360 9 C8 CK M 8 5 4 1.37000 131.1870 81.6070 10 H8 H5 E 9 8 5 1.08000 120.0060 .0050 11 N7 NB M 9 8 5 1.30000 113.8870 177.0200 12 C5 CB M 11 9 8 1.38900 104.0390 .0040 13 C6 CA M 12 11 9 1.40000 132.4290 180.0430 14 N6 N2 B 13 12 11 1.34000 123.4980 359.9610 15 H61 H E 14 13 12 1.01000 119.9420 180.0440 16 H62 H E 14 13 12 1.01000 120.0050 .0060 17 N1 NC M 13 12 11 1.34000 117.4080 179.9600 18 C2 CQ M 17 13 12 1.33000 118.8320 .0080 19 H2 H5 E 18 17 13 1.08000 120.0130 179.9930 20 N3 NC M 18 17 13 1.31900 129.1490 359.9310 21 C4 CB M 20 18 17 1.35000 110.8300 .0830 CHARGE + ADE new-resp polarization corrected, dft/cc-pvtz .110341 -.178023 .110341 .110341 -.078080 .105117 .145537 -.513780 -.017376 .581790 -.751139 .379088 .379088 -.725359 .566714 .019429 -.748533 .504503 IMPROPER C8 C4 N9 C1' C6 H61 N6 H62 N7 N9 C8 H8 N1 N3 C2 H2 C5 N1 C6 N6 LOOP CLOSING EXPLICIT C4 C5 C4 N9 DONE N-methyl-CYTOSINE CME INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 .0000 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 .0000 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 .0000 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 .0000 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 .0000 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 .0000 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 .0000 8 N1 N* M 5 4 3 1.49000 108.1190 295.5500 .0000 9 C6 CM M 8 5 4 1.36000 121.1340 81.5730 .0000 10 H6 H4 E 9 8 5 1.08000 119.9490 .0420 .0000 11 C5 CM M 9 8 5 1.36000 121.0290 180.0410 .0000 12 H5 HA E 11 9 8 1.09000 119.9940 180.0670 .0000 13 C4 CA M 11 9 8 1.43000 116.8750 359.9720 .0000 14 N4 N2 B 13 11 9 1.31900 120.0770 179.9930 .0000 15 H41 H E 14 13 11 1.01000 117.7460 180.0300 .0000 16 H42 H E 14 13 11 1.01000 120.2950 .0610 .0000 17 N3 NC M 13 11 9 1.33000 121.7030 .0750 .0000 18 C2 C M 17 13 11 1.36000 120.5330 359.9230 .0000 19 O2 O E 18 17 13 1.23900 122.4570 180.0510 .0000 CHARGE + deoxy-CYT-B: polarization corrected charges, CYT, df/cc-pvtz .072305 -.066987 .072305 .072305 -.120009 -.022683 .170764 -.534862 .199549 .852027 -.917553 .409639 .409639 -.787560 .816641 -.625521 IMPROPER C6 C2 N1 C1' N1 N3 C2 O2 C4 H41 N4 H42 N1 C5 C6 H6 C6 C4 C5 H5 N3 C5 C4 N4 LOOP CLOSING EXPLICIT C2 N1 DONE N-methyl-GUANINE GME INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 8 N9 N* M 5 4 3 1.49000 108.0830 295.5380 9 C8 CK M 8 5 4 1.38000 129.2070 81.5690 10 H8 H5 E 9 8 5 1.08000 119.9900 .0590 11 N7 NB M 9 8 5 1.31000 114.0170 180.1070 12 C5 CB M 11 9 8 1.39000 103.8950 .0350 13 C6 C M 12 11 9 1.42000 130.4290 179.9530 14 O6 O E 13 12 11 1.23100 128.7830 .0290 15 N1 NA M 13 12 11 1.40000 111.4060 180.0170 16 H1 H E 15 13 12 1.00100 117.3610 179.9310 17 C2 CA M 15 13 12 1.38000 125.2260 359.8940 18 N2 N2 B 17 15 13 1.34100 116.0360 180.0230 19 H21 H E 18 17 15 1.01000 126.9570 359.1960 20 H22 H E 18 17 15 1.01000 116.5580 180.5620 21 N3 NC M 17 15 13 1.33000 123.3460 .0130 22 C4 CB M 21 17 15 1.36000 112.1600 359.9980 CHARGE + deoxy-GUA-B, polarization corrected, dft/cc-pvtz .101967 -.155686 .101967 .101967 -.055116 .086175 .140052 -.473394 -.023631 .540370 -.534593 -.550934 .374369 .645312 -.692954 .331359 .331359 -.683661 .415072 IMPROPER C8 C4 N9 C1' C5 N1 C6 O6 C6 C2 N1 H1 C2 H21 N2 H22 N7 N9 C8 H8 N1 N3 C2 N2 LOOP CLOSING EXPLICIT C4 C5 C4 N9 DONE N-methyl- THYMINE TME INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 4 H11' H1 M 3 2 1 1.10000 92.5070 92.0960 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 8 N1 N* M 5 4 3 1.53000 109.5990 295.5450 9 C6 CM M 8 5 4 1.36900 123.0650 81.6170 10 H6 H4 E 9 8 5 1.08100 120.0030 359.9610 11 C5 CM M 9 8 5 1.34000 121.2490 177.3250 12 C7 CT 3 11 9 8 1.50000 121.6610 179.9620 13 H71 HC E 12 11 9 1.09000 109.5000 59.9870 14 H72 HC E 12 11 9 1.08900 109.5040 179.9530 15 H73 HC E 12 11 9 1.09000 109.5220 300.0240 16 C4 C M 11 9 8 1.44000 120.7500 359.9570 17 O4 O E 16 11 9 1.23000 125.3460 180.0040 18 N3 NA M 16 11 9 1.38000 114.1000 .0440 19 H3 H E 18 16 11 1.08900 116.7820 180.0400 20 C2 C M 18 16 11 1.38000 126.4030 359.9360 21 O2 O E 20 18 16 1.22100 121.6390 179.9800 CHARGE + THY dft/cc-pvtz, polarization corrected .074001 -.067546 .074001 .074001 -.031294 -.189777 .194132 -.030526 -.231950 .089475 .089475 .089475 .547155 -.539763 -.438227 .339487 .485470 -.527589 IMPROPER C6 C2 N1 C1' C4 C6 C5 C7 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C2 N1 DONE N-methyl-URACIL UME INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 .00000 .0000 .0000 2 DUMM DU M 1 0 -1 1.00000 .0000 .0000 3 DUMM DU M 2 1 0 1.00000 90.0000 .0000 4 H11' H1 M 3 2 1 3.88600 92.5070 92.0960 5 C1' CT M 4 3 2 1.09000 102.0370 71.2940 6 H12' H1 E 5 4 3 1.09000 109.4780 183.2340 7 H13' H1 E 5 4 3 1.09000 107.8200 59.2900 8 N1 N* M 5 4 3 1.53000 109.5990 295.5450 9 C6 CM M 8 5 4 1.36900 123.0650 81.6170 10 H6 H4 E 9 8 5 1.08100 120.0030 359.9610 11 C5 CM M 9 8 5 1.34000 121.2490 177.3250 12 H5 HA E 11 9 8 1.09100 120.0290 179.9930 13 C4 C M 11 9 8 1.44000 120.7500 359.9570 14 O4 O E 13 11 9 1.23000 125.3460 180.0040 15 N3 NA M 13 11 9 1.38000 114.1000 .0440 16 H3 H E 15 13 11 1.08900 116.7820 180.0400 17 C2 C M 15 13 11 1.38000 126.4030 359.9360 18 O2 O E 17 15 13 1.22100 121.6390 179.9800 CHARGE + URA dft/cc-pvtz, polarization corrected .078008 -.082649 .078008 .078008 -.006301 -.113902 .190428 -.361481 .177457 .646954 -.569023 -.440391 .326261 .549017 -.550394 IMPROPER C6 C2 N1 C1' C4 C6 C5 H5 N1 N3 C2 O2 C5 N3 C4 O4 C2 C4 N3 H3 N1 C5 C6 H6 LOOP CLOSING EXPLICIT C2 N1 DONE STOP