1 0 2 dbnp94.dat P-amidate, D-ADENOSINE - with 5' - OH end group and 3' - NH (minus) AN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0431 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1838 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0268 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.1607 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1877 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6175 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0725 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.6897 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9123 21 H61 H E 20 19 18 1.01 120.00 0.00 0.4167 22 H62 H E 20 19 18 1.01 120.00 180.00 0.4167 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7624 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5716 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0598 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.7417 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3800 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 33 N3' NS M 28 9 6 1.44 111.00 -203.47 34 HN3' H E 33 28 9 1.01 118.00 21.00 CHARGE A5E 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.0625 0.1178 -0.4196 0.0431 0.1838 -0.0268 0.1607 0.1877 -0.6175 0.0725 0.6897 -0.9123 0.4167 0.4167 -0.7624 0.5716 0.0598 -0.7417 0.3800 0.3335 0.0493 -0.1261 0.0352 0.0352 -0.8488 0.3772 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' - NH (minus) group DANP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0431 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1838 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0268 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.1607 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1877 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6175 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0725 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.6897 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9123 23 H61 H E 22 21 20 1.01 120.00 0.00 0.4167 24 H62 H E 22 21 20 1.01 120.00 180.00 0.4167 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7624 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5716 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0598 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.7417 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3800 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 N3' NS M 30 1l 8 1.44 111.00 -203.47 36 HN3' H E 35 30 11 1.01 118.00 21.00 CHARGE deoxy -resp charges A 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 0.0754 0.0754 0.0625 0.1178 -0.4196 0.0431 0.1838 -0.0268 0.1607 0.1877 -0.6175 0.0725 0.6897 -0.9123 0.4167 0.4167 -0.7624 0.5716 0.0598 -0.7417 0.3800 0.3335 0.0493 -0.1261 0.0352 0.0352 -0.8488 0.3772 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 DAN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0431 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1838 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0268 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.1607 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1877 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6175 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0725 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.6897 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9123 23 H61 H E 22 21 20 1.01 120.00 0.00 0.4167 24 H62 H E 22 21 20 1.01 120.00 180.00 0.4167 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7624 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5716 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0598 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.7417 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3800 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6549 36 H3T HO M 35 30 11 0.96 114.97 180.00 0.4396 CHARGE A3E 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 0.0431 0.1838 -0.0268 0.1607 0.1877 -0.6175 0.0725 0.6897 -0.9123 0.4167 0.4167 -0.7624 0.5716 0.0598 -0.7417 0.3800 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0431 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1838 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0268 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.1607 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1877 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6175 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0725 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.6897 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9123 21 H61 H E 20 19 18 1.01 120.00 0.00 0.4167 22 H62 H E 20 19 18 1.01 120.00 180.00 0.4167 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7624 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5716 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0598 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.7417 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3800 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 33 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6549 34 H3T HO M 33 28 9 0.96 114.97 180.00 0.4396 CHARGE ADE resp 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 0.0431 0.1838 -0.0268 0.1607 0.1877 -0.6175 0.0725 0.6897 -0.9123 0.4167 0.4167 -0.7624 0.5716 0.0598 -0.7417 0.3800 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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' - NH (minus) RAN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 60.00 0.0679 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0394 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2007 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0251 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.2006 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1553 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6073 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0515 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.7009 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9019 21 H61 H E 20 19 18 1.01 120.00 0.00 0.4115 22 H62 H E 20 19 18 1.01 120.00 180.00 0.4115 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7615 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5875 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0473 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.6997 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3053 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 30 C2' CT B 28 9 6 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 9 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 34 N3' NS M 28 9 6 1.44 111.00 -203.47 35 HN3' H E 34 28 9 1.01 118.00 21.00 CHARGE RA5E 0.4295 -0.6223 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0394 0.2007 -0.0251 0.2006 0.1553 -0.6073 0.0515 0.7009 -0.9019 0.4115 0.4115 -0.7615 0.5875 0.0473 -0.6997 0.3053 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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' - NH (minus) group RANP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0394 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2007 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0251 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.2006 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1553 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6073 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0515 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.7009 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9019 23 H61 H E 22 21 20 1.01 120.00 0.00 0.4115 24 H62 H E 22 21 20 1.01 120.00 180.00 0.4115 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7615 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5875 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0473 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.6997 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3053 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 32 C2' CT B 30 11 8 1.53 102.80 -86.30 0.0670 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 0.0972 34 O2' OH S 32 30 11 1.43 109.50 240.00 -0.6139 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 0.4186 36 N3' NS M 30 11 8 1.44 111.00 -203.47 37 HN3' H E 36 30 11 1.01 118.00 21.00 CHARGE RA 1.1662 -0.7760 -0.7760 -0.4989 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0394 0.2007 -0.0251 0.2006 0.1553 -0.6073 0.0515 0.7009 -0.9019 0.4115 0.4115 -0.7615 0.5875 0.0473 -0.6997 0.3053 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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 RAN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0394 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2007 16 N9 N* S 14 13 11 1.52 109.59 -127.70 -0.0251 17 C8 CK B 16 14 13 1.37 131.20 81.59 0.2006 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1553 19 N7 NB S 17 16 14 1.30 113.93 177.00 -0.6073 20 C5 CB S 19 17 16 1.39 104.00 0.00 0.0515 21 C6 CA B 20 19 17 1.40 132.42 180.00 0.7009 22 N6 N2 B 21 20 19 1.34 123.50 0.00 -0.9019 23 H61 H E 22 21 20 1.01 120.00 0.00 0.4115 24 H62 H E 22 21 20 1.01 120.00 180.00 0.4115 25 N1 NC S 21 20 19 1.34 117.43 180.00 -0.7615 26 C2 CQ B 25 21 20 1.33 118.80 0.00 0.5875 27 H2 H5 E 26 25 21 1.08 120.00 180.00 0.0473 28 N3 NC S 26 25 21 1.32 129.17 0.00 -0.6997 29 C4 CB E 28 26 25 1.35 110.80 0.00 0.3053 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0615 32 C2' CT B 30 11 8 1.53 102.80 -86.30 0.0670 33 H2'1 H1 E 32 30 11 1.09 109.50 120.00 0.0972 34 O2' OH S 32 30 11 1.43 109.50 240.00 -0.6139 35 HO'2 HO E 34 32 30 0.96 107.00 180.00 0.4186 36 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6541 34 H3T HO M 36 30 11 0.96 114.97 180.00 0.4376 CHARGE RA3E 1.1662 -0.7760 -0.7760 -0.4989 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0394 0.2007 -0.0251 0.2006 0.1553 -0.6073 0.0515 0.7009 -0.9019 0.4115 0.4115 -0.7615 0.5875 0.0473 -0.6997 0.3053 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 60.00 0.0679 9 C4' CT M 6 5 4 1.52 110.00 180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0394 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2007 14 N9 N* S 12 11 9 1.52 109.59 -127.70 -0.0251 15 C8 CK B 14 12 11 1.37 131.20 81.59 0.2006 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1553 17 N7 NB S 15 14 12 1.30 113.93 177.00 -0.6073 18 C5 CB S 17 15 14 1.39 104.00 0.00 0.0515 19 C6 CA B 18 17 15 1.40 132.42 180.00 0.7009 20 N6 N2 B 19 18 17 1.34 123.50 0.00 -0.9019 21 H61 H E 20 19 18 1.01 120.00 0.00 0.4115 22 H62 H E 20 19 18 1.01 120.00 180.00 0.4115 23 N1 NC S 19 18 17 1.34 117.43 180.00 -0.7615 24 C2 CQ B 23 19 18 1.33 118.80 0.00 0.5875 25 H2 H5 E 24 23 19 1.08 120.00 180.00 0.0473 26 N3 NC S 24 23 19 1.32 129.17 0.00 -0.6997 27 C4 CB E 26 24 23 1.35 110.80 0.00 0.3053 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0615 30 C2' CT B 28 9 6 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 9 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 9 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 32 30 28 0.96 107.00 180.00 0.4186 34 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6541 35 H3T HO M 34 28 9 0.96 114.97 180.00 0.4376 CHARGE resp RADE 0.4295 -0.6223 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0394 0.2007 -0.0251 0.2006 0.1553 -0.6073 0.0515 0.7009 -0.9019 0.4115 0.4115 -0.7615 0.5875 0.0473 -0.6997 0.3053 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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' -NH (minus) DTN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0680 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1804 14 N1 N* S 12 11 9 1.53 109.59 -127.70 -0.0239 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.2209 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2607 17 C5 CM B 15 14 12 1.34 121.22 177.30 0.0025 18 C7 CT 3 17 15 14 1.50 121.63 180.00 -0.2269 19 H71 HC E 18 17 15 1.09 109.50 60.00 0.0770 20 H72 HC E 18 17 15 1.09 109.50 180.00 0.0770 21 H73 HC E 18 17 15 1.09 109.50 300.00 0.0770 22 C4 C B 17 15 14 1.44 120.78 0.00 0.5194 23 O4 O E 22 17 15 1.23 125.35 180.00 -0.5563 24 N3 NA B 22 17 15 1.38 114.07 0.00 -0.4340 25 H3 H E 24 22 17 1.09 116.77 180.00 0.3420 26 C2 C S 24 22 17 1.38 126.46 0.00 0.5677 27 O2 O E 26 24 22 1.22 121.70 180.00 -0.5881 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 33 N3' NS M 29 9 6 1.44 111.00 -203.47 34 HN3' H E 33 29 9 1.01 118.00 21.00 CHARGE T5E 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.0625 0.1178 -0.4196 0.0680 0.1804 -0.0239 -0.2209 0.2607 0.0025 -0.2269 0.0770 0.0770 0.0770 0.5194 -0.5563 -0.4340 0.3420 0.5677 -0.5881 0.3335 0.0493 -0.1261 0.0352 0.0352 -0.8488 0.3772 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' - NH (minus) group DTNP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804 16 N1 N* S 14 13 11 1.53 109.59 -127.70 -0.0239 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.2209 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607 19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025 20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269 21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770 22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770 23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770 24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194 25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563 26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340 27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420 28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677 29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 N3' NS M 30 11 8 1.44 111.00 -203.47 36 HN3' H E 35 30 11 1.01 118.00 21.00 CHARGE deoxy -resp T 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 0.0754 0.0754 0.0625 0.1178 -0.4196 0.0680 0.1804 -0.0239 -0.2209 0.2607 0.0025 -0.2269 0.0770 0.0770 0.0770 0.5194 -0.5563 -0.4340 0.3420 0.5677 -0.5881 0.3335 0.0493 -0.1261 0.0352 0.0352 -0.8488 0.3772 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 DTN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804 16 N1 N* S 14 13 11 1.53 109.59 -127.70 -0.0239 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.2209 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607 19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025 20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269 21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770 22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770 23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770 24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194 25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563 26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340 27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420 28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677 29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881 30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985 32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854 33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718 34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718 35 O3' OH M 30 11 8 1.42 116.52 -203.47 -0.6549 36 H3T HO M 35 30 11 0.96 114.97 180.00 0.4396 CHARGE T3E 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 0.0680 0.1804 -0.0239 -0.2209 0.2607 0.0025 -0.2269 0.0770 0.0770 0.0770 0.5194 -0.5563 -0.4340 0.3420 0.5677 -0.5881 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 4 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0680 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1804 14 N1 N* S 12 11 9 1.53 109.59 -127.70 -0.0239 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.2209 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2607 17 C5 CM B 15 14 12 1.34 121.22 177.30 0.0025 18 C7 CT 3 17 15 14 1.50 121.63 180.00 -0.2269 19 H71 HC E 18 17 15 1.09 109.50 60.00 0.0770 20 H72 HC E 18 17 15 1.09 109.50 180.00 0.0770 21 H73 HC E 18 17 15 1.09 109.50 300.00 0.0770 22 C4 C B 17 15 14 1.44 120.78 0.00 0.5194 23 O4 O E 22 17 15 1.23 125.35 180.00 -0.5563 24 N3 NA B 22 17 15 1.38 114.07 0.00 -0.4340 25 H3 H E 24 22 17 1.09 116.77 180.00 0.3420 26 C2 C S 24 22 17 1.38 126.46 0.00 0.5677 27 O2 O E 26 24 22 1.22 121.70 180.00 -0.5881 28 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 9 6 1.09 109.50 30.00 0.0985 30 C2' CT B 28 9 6 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 9 1.09 109.50 120.00 0.0718 32 H2'2 HC E 30 28 9 1.09 109.50 240.00 0.0718 33 O3' OH M 28 9 6 1.42 116.52 -203.47 -0.6549 34 H3T HO M 33 28 9 0.96 114.97 180.00 0.4396 CHARGE deoxy-THY-B: 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 0.0680 0.1804 -0.0239 -0.2209 0.2607 0.0025 -0.2269 0.0770 0.0770 0.0770 0.5194 -0.5563 -0.4340 0.3420 0.5677 -0.5881 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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' - NH (minus) RUN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0674 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1824 14 N1 N* S 12 11 9 1.53 109.59 -127.70 0.0418 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.1126 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2188 17 C5 CM B 15 14 12 1.34 121.22 177.30 -0.3635 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1811 19 C4 C B 17 15 14 1.44 120.78 0.00 0.5952 20 O4 O E 19 17 15 1.23 125.35 180.00 -0.5761 21 N3 NA B 19 17 15 1.38 114.07 0.00 -0.3549 22 H3 H E 21 19 17 1.09 116.77 180.00 0.3154 23 C2 C S 21 19 17 1.38 126.46 0.00 0.4687 24 O2 O E 23 21 19 1.22 121.70 180.00 -0.5477 25 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 27 C2' CT B 25 9 6 1.53 102.80 -86.30 0.0670 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 0.0972 29 O2' OH S 27 25 9 1.43 109.50 240.00 -0.6139 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 0.4186 31 N3' NS M 25 9 6 1.44 111.00 -203.47 32 HN3' H E 31 25 9 1.01 118.00 21.00 CHARGE RU5E 0.4295 -0.6223 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0674 0.1824 0.0418 -0.1126 0.2188 -0.3635 0.1811 0.5952 -0.5761 -0.3549 0.3154 0.4687 -0.5477 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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' - NH (minus) group RUNP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0674 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1824 16 N1 N* S 14 13 11 1.53 109.59 -127.70 0.0418 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.1126 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2188 19 C5 CM B 17 16 14 1.34 121.22 177.30 -0.3635 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1811 21 C4 C B 19 17 16 1.44 120.78 0.00 0.5952 22 O4 O E 21 19 17 1.23 125.35 180.00 -0.5761 23 N3 NA B 21 19 17 1.38 114.07 0.00 -0.3549 24 H3 H E 23 21 19 1.09 116.77 180.00 0.3154 25 C2 C S 23 21 19 1.38 126.46 0.00 0.4687 26 O2 O E 25 23 21 1.22 121.70 180.00 -0.5477 27 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 29 C2' CT B 27 11 8 1.53 102.80 -86.30 0.0670 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 0.0972 31 O2' OH S 29 27 11 1.43 109.50 240.00 -0.6139 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 0.4186 33 N3' NS M 27 11 8 1.44 111.00 -203.47 34 HN3' H E 33 27 11 1.01 118.00 21.00 CHARGE RU 1.1662 -0.7760 -0.7760 -0.4989 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0674 0.1824 0.0418 -0.1126 0.2188 -0.3635 0.1811 0.5952 -0.5761 -0.3549 0.3154 0.4687 -0.5477 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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 RUN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0674 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1824 16 N1 N* S 14 13 11 1.53 109.59 -127.70 0.0418 17 C6 CM B 16 14 13 1.37 123.04 81.59 -0.1126 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2188 19 C5 CM B 17 16 14 1.34 121.22 177.30 -0.3635 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1811 21 C4 C B 19 17 16 1.44 120.78 0.00 0.5952 22 O4 O E 21 19 17 1.23 125.35 180.00 -0.5761 23 N3 NA B 21 19 17 1.38 114.07 0.00 -0.3549 24 H3 H E 23 21 19 1.09 116.77 180.00 0.3154 25 C2 C S 23 21 19 1.38 126.46 0.00 0.4687 26 O2 O E 25 23 21 1.22 121.70 180.00 -0.5477 27 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 28 H3' H1 E 27 11 8 1.09 109.50 30.00 0.0615 29 C2' CT B 27 11 8 1.53 102.80 -86.30 0.0670 30 H2'1 H1 E 29 27 11 1.09 109.50 120.00 0.0972 31 O2' OH S 29 27 11 1.43 109.50 240.00 -0.6139 32 HO'2 HO E 31 29 27 0.96 107.00 180.00 0.4186 33 O3' OH M 27 11 8 1.42 116.52 -203.47 -0.6541 34 H3T HO M 34 27 11 0.96 114.97 180.00 0.4376 CHARGE RU3E 1.1662 -0.7760 -0.7760 -0.4989 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0674 0.1824 0.0418 -0.1126 0.2188 -0.3635 0.1811 0.5952 -0.5761 -0.3549 0.3154 0.4687 -0.5477 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 6 1.42 110.04 105.60 0.0674 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1824 14 N1 N* S 12 11 9 1.53 109.59 -127.70 0.0418 15 C6 CM B 14 12 11 1.37 123.04 81.59 -0.1126 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2188 17 C5 CM B 15 14 12 1.34 121.22 177.30 -0.3635 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1811 19 C4 C B 17 15 14 1.44 120.78 0.00 0.5952 20 O4 O E 19 17 15 1.23 125.35 180.00 -0.5761 21 N3 NA B 19 17 15 1.38 114.07 0.00 -0.3549 22 H3 H E 21 19 17 1.09 116.77 180.00 0.3154 23 C2 C S 21 19 17 1.38 126.46 0.00 0.4687 24 O2 O E 23 21 19 1.22 121.70 180.00 -0.5477 25 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 26 H3' H1 E 25 9 6 1.09 109.50 30.00 0.0615 27 C2' CT B 25 9 6 1.53 102.80 -86.30 0.0670 28 H2'1 H1 E 27 25 9 1.09 109.50 120.00 0.0972 29 O2' OH S 27 25 9 1.43 109.50 240.00 -0.6139 30 HO'2 HO E 29 27 25 0.96 107.00 180.00 0.4186 31 O3' OH M 25 9 6 1.42 116.52 -203.47 -0.6541 32 H3T HO M 31 25 9 0.96 114.97 180.00 0.4376 CHARGE resp RURA 0.4295 -0.6223 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0674 0.1824 0.0418 -0.1126 0.2188 -0.3635 0.1811 0.5952 -0.5761 -0.3549 0.3154 0.4687 -0.5477 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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' - NH (minus) group DGN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.0625 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1178 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.4196 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0358 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1746 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0577 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.0736 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1997 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5725 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1991 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4918 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5699 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.5053 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3520 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7432 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9230 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4235 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4235 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6636 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1814 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.3335 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0493 31 C2' CT B 29 9 6 1.53 102.80 -86.30 -0.1261 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 0.0352 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 0.0352 34 N3' NS M 29 9 6 1.44 111.00 -203.47 -0.8488 35 HN3' H E 34 29 9 1.01 118.00 21.00 0.3772 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' - NH (minus) group DGNP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.0625 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1178 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.4196 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0358 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1746 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0577 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.0736 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1997 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5725 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1991 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4918 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5699 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.5053 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3520 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7432 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9230 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4235 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4235 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6636 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1814 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.3335 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0493 33 C2' CT B 31 11 8 1.53 102.80 -86.30 -0.1261 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 0.0352 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 0.0352 36 N3' NS M 31 11 8 1.44 111.00 -203.47 -0.8488 37 HN3' H E 36 31 11 1.01 118.00 21.00 0.3772 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 DGN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0358 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1746 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0577 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.0736 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1997 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5725 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1991 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4918 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5699 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.5053 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3520 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7432 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9230 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4235 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4235 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6636 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1814 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0985 33 C2' CT B 31 11 8 1.53 102.80 -86.30 -0.0854 34 H2'1 HC E 33 31 11 1.09 109.50 120.00 0.0718 35 H2'2 HC E 33 31 11 1.09 109.50 240.00 0.0718 36 O3' OH M 31 11 8 1.42 116.52 -203.47 -0.6549 37 H3T HO M 36 31 11 0.96 114.97 180.00 0.4396 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0358 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1746 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0577 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.0736 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1997 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5725 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1991 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4918 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5699 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.5053 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3520 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7432 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9230 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4235 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4235 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6636 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1814 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0985 31 C2' CT B 29 9 6 1.53 102.80 -86.30 -0.0854 32 H2'1 HC E 31 29 9 1.09 109.50 120.00 0.0718 33 H2'2 HC E 31 29 9 1.09 109.50 240.00 0.0718 34 O3' OH M 29 9 6 1.42 116.52 -203.47 -0.6549 35 H3T HO M 34 29 9 0.96 114.97 180.00 0.4396 CHARGE deoxy-GUA-B: 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 0.0358 0.1746 0.0577 0.0736 0.1997 -0.5725 0.1991 0.4918 -0.5699 -0.5053 0.3520 0.7432 -0.9230 0.4235 0.4235 -0.6636 0.1814 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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' - NH (minus) group RGN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0191 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2006 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0492 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.1374 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1640 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5709 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1744 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4770 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5597 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.4787 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3424 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7657 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9672 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4364 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4364 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6323 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1222 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 31 C2' CT B 29 9 6 1.53 102.80 -86.30 0.0670 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 0.0972 33 O2' OH S 31 29 9 1.43 109.50 240.00 -0.6139 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 0.4186 35 N3' NS M 29 9 6 1.44 111.00 -203.47 36 HN3' H E 35 29 9 1.01 118.00 21.00 CHARGE RG5E 0.4295 -0.6223 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0191 0.2006 0.0492 0.1374 0.1640 -0.5709 0.1744 0.4770 -0.5597 -0.4787 0.3424 0.7657 -0.9672 0.4364 0.4364 -0.6323 0.1222 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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' - NH (minus) group RGNP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0191 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2006 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0492 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.1374 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1640 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5709 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1744 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4770 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5597 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.4787 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3424 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7657 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9672 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4364 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4364 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6323 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1222 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 33 C2' CT B 31 11 8 1.53 102.80 -86.30 0.0670 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 0.0972 35 O2' OH S 33 31 11 1.43 109.50 240.00 -0.6139 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 0.4186 37 N3' NS M 31 11 8 1.44 111.00 -203.47 38 HN3' H E 37 31 11 1.01 118.00 21.00 CHARGE RG 1.1662 -0.7760 -0.7760 -0.4989 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0191 0.2006 0.0492 0.1374 0.1640 -0.5709 0.1744 0.4770 -0.5597 -0.4787 0.3424 0.7657 -0.9672 0.4364 0.4364 -0.6323 0.1222 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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 RGN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0191 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2006 16 N9 N* S 14 13 11 1.49 108.06 -127.70 0.0492 17 C8 CK B 16 14 13 1.38 129.20 81.59 0.1374 18 H8 H5 E 17 16 14 1.08 120.00 0.00 0.1640 19 N7 NB S 17 16 14 1.31 114.00 -179.90 -0.5709 20 C5 CB S 19 17 16 1.39 103.90 0.00 0.1744 21 C6 C B 20 19 17 1.42 130.40 180.00 0.4770 22 O6 O E 21 20 19 1.23 128.80 0.00 -0.5597 23 N1 NA B 21 20 19 1.40 111.38 180.00 -0.4787 24 H1 H E 23 21 20 1.00 117.36 179.90 0.3424 25 C2 CA B 23 21 20 1.38 125.24 -0.10 0.7657 26 N2 N2 B 25 23 21 1.34 116.02 180.00 -0.9672 27 H21 H E 26 25 23 1.01 127.00 -0.82 0.4364 28 H22 H E 26 25 23 1.01 116.53 -179.44 0.4364 29 N3 NC S 25 23 21 1.33 123.30 0.00 -0.6323 30 C4 CB E 29 25 23 1.36 112.20 0.00 0.1222 31 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 32 H3' H1 E 31 11 8 1.09 109.50 30.00 0.0615 33 C2' CT B 31 11 8 1.53 102.80 -86.30 0.0670 34 H2'1 H1 E 33 31 11 1.09 109.50 120.00 0.0972 35 O2' OH S 33 31 11 1.43 109.50 240.00 -0.6139 36 HO'2 HO E 35 33 31 0.96 107.00 180.00 0.4186 37 O3' OH M 31 11 8 1.42 116.52 -203.47 -0.6541 38 H3T HO M 37 31 11 0.96 114.97 180.00 0.4376 CHARGE RG3E 1.1662 -0.7760 -0.7760 -0.4989 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0191 0.2006 0.0492 0.1374 0.1640 -0.5709 0.1744 0.4770 -0.5597 -0.4787 0.3424 0.7657 -0.9672 0.4364 0.4364 -0.6323 0.1222 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0191 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2006 14 N9 N* S 12 11 9 1.49 108.06 -127.70 0.0492 15 C8 CK B 14 12 11 1.38 129.20 81.59 0.1374 16 H8 H5 E 15 14 12 1.08 120.00 0.00 0.1640 17 N7 NB S 15 14 12 1.31 114.00 -179.90 -0.5709 18 C5 CB S 17 15 14 1.39 103.90 0.00 0.1744 19 C6 C B 18 17 15 1.42 130.40 180.00 0.4770 20 O6 O E 19 18 17 1.23 128.80 0.00 -0.5597 21 N1 NA B 19 18 17 1.40 111.38 180.00 -0.4787 22 H1 H E 21 19 18 1.00 117.36 179.90 0.3424 23 C2 CA B 21 19 18 1.38 125.24 -0.10 0.7657 24 N2 N2 B 23 21 19 1.34 116.02 180.00 -0.9672 25 H21 H E 24 23 21 1.01 127.00 -0.82 0.4364 26 H22 H E 24 23 21 1.01 116.53 -179.44 0.4364 27 N3 NC S 23 21 19 1.33 123.30 0.00 -0.6323 28 C4 CB E 27 23 21 1.36 112.20 0.00 0.1222 29 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 30 H3' H1 E 29 9 6 1.09 109.50 30.00 0.0615 31 C2' CT B 29 9 6 1.53 102.80 -86.30 0.0670 32 H2'1 H1 E 31 29 9 1.09 109.50 120.00 0.0972 33 O2' OH S 31 29 9 1.43 109.50 240.00 -0.6139 34 HO'2 HO E 33 31 29 0.96 107.00 180.00 0.4186 35 O3' OH M 29 9 6 1.42 116.52 -203.47 -0.6541 36 H3T HO M 35 29 9 0.96 114.97 180.00 0.4376 CHARGE resp RGUA 0.4295 -0.6223 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0191 0.2006 0.0492 0.1374 0.1640 -0.5709 0.1744 0.4770 -0.5597 -0.4787 0.3424 0.7657 -0.9672 0.4364 0.4364 -0.6323 0.1222 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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' - NH (minus) group DCN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 5 1.42 110.04 105.60 -0.0116 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1963 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0339 15 C6 CM B 14 12 11 1.36 121.10 81.59 -0.0183 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2293 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5222 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1863 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8439 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9773 21 H41 H E 20 19 17 1.01 117.70 0.00 0.4314 22 H42 H E 20 19 17 1.01 120.27 180.00 0.4314 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7748 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7959 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6548 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 28 C2' CT B 26 9 6 1.53 102.80 -86.30 -0.0854 29 H2'1 HC E 28 26 9 1.09 109.50 -200.00 0.0718 30 H2'2 HC E 28 26 9 1.09 109.50 -320.00 0.0718 31 N3' NS M 26 9 6 1.44 111.00 -203.47 32 HN3' H E 31 26 9 1.01 118.00 21.00 CHARGE C5E 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.0625 0.1178 -0.4196 -0.0116 0.1963 -0.0339 -0.0183 0.2293 -0.5222 0.1863 0.8439 -0.9773 0.4314 0.4314 -0.7748 0.7959 -0.6548 0.3335 0.0493 -0.1261 0.0352 0.0352 -0.8488 0.3772 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' - NH (minus) group DCNP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 -0.0116 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1963 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0339 17 C6 CM B 16 14 13 1.36 121.10 81.59 -0.0183 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2293 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5222 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1863 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8439 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9773 23 H41 H E 22 21 19 1.01 117.70 0.00 0.4314 24 H42 H E 22 21 19 1.01 120.27 180.00 0.4314 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7748 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7959 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6548 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0985 30 C2' CT B 28 11 8 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 11 1.09 109.50 -200.00 0.0718 32 H2'2 HC E 30 28 11 1.09 109.50 -320.00 0.0718 33 N3' NS M 28 11 8 1.44 111.00 -203.47 34 HN3' H E 33 28 11 1.01 118.00 21.00 CHARGE deoxy -resp C 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 0.0754 0.0754 0.0625 0.1178 -0.4196 -0.0116 0.1963 -0.0339 -0.0183 0.2293 -0.5222 0.1863 0.8439 -0.9773 0.4314 0.4314 -0.7748 0.7959 -0.6548 0.3335 0.0493 -0.1261 0.0352 0.0352 -0.8488 0.3772 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 DCN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1659 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954 8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0754 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0754 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691 14 C1' CT B 13 11 8 1.42 110.04 105.60 -0.0116 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1963 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0339 17 C6 CM B 16 14 13 1.36 121.10 81.59 -0.0183 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2293 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5222 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1863 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8439 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9773 23 H41 H E 22 21 19 1.01 117.70 0.00 0.4314 24 H42 H E 22 21 19 1.01 120.27 180.00 0.4314 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7748 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7959 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6548 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0985 30 C2' CT B 28 11 8 1.53 102.80 -86.30 -0.0854 31 H2'1 HC E 30 28 11 1.09 109.50 -200.00 0.0718 32 H2'2 HC E 30 28 11 1.09 109.50 -320.00 0.0718 33 O3' OH M 28 11 8 1.42 116.52 -203.47 -0.6549 31 H3T HO M 30 25 8 0.96 114.97 180.00 0.4396 CHARGE C3E 1.1659 -0.7761 -0.7761 -0.4954 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 -0.0116 0.1963 -0.0339 -0.0183 0.2293 -0.5222 0.1863 0.8439 -0.9773 0.4314 0.4314 -0.7748 0.7959 -0.6548 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4422 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6318 6 C5' CT M 5 4 3 1.44 119.00 -39.22 -0.0069 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0754 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0754 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1629 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1176 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3691 12 C1' CT B 11 9 5 1.42 110.04 105.60 -0.0116 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.1963 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0339 15 C6 CM B 14 12 11 1.36 121.10 81.59 -0.0183 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.2293 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5222 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1863 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8439 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9773 21 H41 H E 20 19 17 1.01 117.70 0.00 0.4314 22 H42 H E 20 19 17 1.01 120.27 180.00 0.4314 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7748 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7959 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6548 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.0713 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0985 28 C2' CT B 26 9 6 1.53 102.80 -86.30 -0.0854 29 H2'1 HC E 28 26 9 1.09 109.50 -200.00 0.0718 30 H2'2 HC E 28 26 9 1.09 109.50 -320.00 0.0718 31 O3' OH M 26 9 6 1.42 116.52 -203.47 -0.6549 32 H3T HO M 31 26 9 0.96 114.97 180.00 0.4396 CHARGE deoxy-CYT-B: CYT 0.4422 -0.6318 -0.0069 0.0754 0.0754 0.1629 0.1176 -0.3691 -0.0116 0.1963 -0.0339 -0.0183 0.2293 -0.5222 0.1863 0.8439 -0.9773 0.4314 0.4314 -0.7748 0.7959 -0.6548 0.0713 0.0985 -0.0854 0.0718 0.0718 -0.6549 0.4396 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' - NH (minus) group RCN5 INT 1 CORRECT NOMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0066 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2029 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0484 15 C6 CM B 14 12 11 1.36 121.10 81.59 0.0053 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.1958 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5215 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1928 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8185 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9530 21 H41 H E 20 19 17 1.01 117.70 0.00 0.4234 22 H42 H E 20 19 17 1.01 120.27 180.00 0.4234 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7584 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7538 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6252 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 28 C2' CT B 26 9 6 1.53 102.80 -86.30 0.0670 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 0.0972 30 O2' OH S 28 26 9 1.43 109.50 240.00 -0.6139 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 0.4186 32 N3' NS M 26 9 6 1.44 111.00 -203.47 33 HN3' H E 32 26 9 1.01 118.00 21.00 CHARGE RC5E 0.4295 -0.6223 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0066 0.2029 -0.0484 0.0053 0.1958 -0.5215 0.1928 0.8185 -0.9530 0.4234 0.4234 -0.7584 0.7538 -0.6252 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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' - NH (minus) group RCNP INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0066 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2029 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0484 17 C6 CM B 16 14 13 1.36 121.10 81.59 0.0053 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.1958 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5215 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1928 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8185 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9530 23 H41 H E 22 21 19 1.01 117.70 0.00 0.4234 24 H42 H E 22 21 19 1.01 120.27 180.00 0.4234 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7584 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7538 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6252 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0615 30 C2' CT B 28 11 8 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 11 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 31 30 28 0.96 107.00 180.00 0.4186 34 N3' NS M 28 11 8 1.44 111.00 -203.47 35 HN3' H E 34 28 11 1.01 118.00 21.00 CHARGE RC 1.1662 -0.7760 -0.7760 -0.4989 0.1060 0.0596 0.0596 0.0440 0.1353 -0.4861 0.0066 0.2029 -0.0484 0.0053 0.1958 -0.5215 0.1928 0.8185 -0.9530 0.4234 0.4234 -0.7584 0.7538 -0.6252 0.3368 0.0105 0.0482 0.0929 -0.6532 0.3880 -0.7175 0.3446 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 RCN3 INT 1 CORRECT OMIT DU BEG 0.0 1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 P P M 3 2 1 1.60 119.04 200.00 1.1662 5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760 6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760 7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4989 8 C5' CT M 7 4 3 1.44 119.00 -39.22 0.0558 9 H5'1 H1 E 8 7 4 1.09 109.50 -60.00 0.0679 10 H5'2 H1 E 8 7 4 1.09 109.50 60.00 0.0679 11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1065 12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1174 13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3548 14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0066 15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.2029 16 N1 N* S 14 13 11 1.49 108.10 -127.70 -0.0484 17 C6 CM B 16 14 13 1.36 121.10 81.59 0.0053 18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.1958 19 C5 CM B 17 16 14 1.36 121.00 180.00 -0.5215 20 H5 HA E 19 17 16 1.09 120.00 180.00 0.1928 21 C4 CA B 19 17 16 1.43 116.90 0.00 0.8185 22 N4 N2 B 21 19 17 1.32 120.10 180.00 -0.9530 23 H41 H E 22 21 19 1.01 117.70 0.00 0.4234 24 H42 H E 22 21 19 1.01 120.27 180.00 0.4234 25 N3 NC S 21 19 17 1.33 121.70 0.00 -0.7584 26 C2 C S 25 21 19 1.36 120.50 0.00 0.7538 27 O2 O E 26 25 21 1.24 122.40 180.00 -0.6252 28 C3' CT M 11 8 7 1.53 115.78 -329.11 0.2022 29 H3' H1 E 28 11 8 1.09 109.50 30.00 0.0615 30 C2' CT B 28 11 8 1.53 102.80 -86.30 0.0670 31 H2'1 H1 E 30 28 11 1.09 109.50 120.00 0.0972 32 O2' OH S 30 28 11 1.43 109.50 240.00 -0.6139 33 HO'2 HO E 31 30 28 0.96 107.00 180.00 0.4186 34 O3' OH M 28 11 8 1.42 116.52 -203.47 -0.6541 35 H3T HO M 34 28 11 0.96 114.97 180.00 0.4376 CHARGE RC3E 1.1662 -0.7760 -0.7760 -0.4989 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0066 0.2029 -0.0484 0.0053 0.1958 -0.5215 0.1928 0.8185 -0.9530 0.4234 0.4234 -0.7584 0.7538 -0.6252 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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 0.0000 2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000 3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000 4 H5T HO M 3 2 1 1.00 120.00 180.00 0.4295 5 O5' OH M 4 3 2 0.96 101.43 -98.89 -0.6223 6 C5' CT M 5 4 3 1.44 119.00 -39.22 0.0558 7 H5'1 H1 E 6 5 4 1.09 109.50 60.00 0.0679 8 H5'2 H1 E 6 5 4 1.09 109.50 -60.00 0.0679 9 C4' CT M 6 5 5 1.52 110.00 -180.00 0.1065 10 H4' H1 E 9 6 5 1.09 109.50 -200.00 0.1174 11 O4' OS S 9 6 5 1.46 108.86 -86.31 -0.3548 12 C1' CT B 11 9 5 1.42 110.04 105.60 0.0066 13 H1' H2 E 12 11 9 1.09 109.50 -240.00 0.2029 14 N1 N* S 12 11 9 1.49 108.10 -127.70 -0.0484 15 C6 CM B 14 12 11 1.36 121.10 81.59 0.0053 16 H6 H4 E 15 14 12 1.08 120.00 0.00 0.1958 17 C5 CM B 15 14 12 1.36 121.00 180.00 -0.5215 18 H5 HA E 17 15 14 1.09 120.00 180.00 0.1928 19 C4 CA B 17 15 14 1.43 116.90 0.00 0.8185 20 N4 N2 B 19 17 15 1.32 120.10 180.00 -0.9530 21 H41 H E 20 19 17 1.01 117.70 0.00 0.4234 22 H42 H E 20 19 17 1.01 120.27 180.00 0.4234 23 N3 NC S 19 17 15 1.33 121.70 0.00 -0.7584 24 C2 C S 23 19 17 1.36 120.50 0.00 0.7538 25 O2 O E 24 23 19 1.24 122.40 180.00 -0.6252 26 C3' CT M 9 6 5 1.53 115.78 -329.11 0.2022 27 H3' H1 E 26 9 6 1.09 109.50 30.00 0.0615 28 C2' CT B 26 9 6 1.53 102.80 -86.30 0.0670 29 H2'1 H1 E 28 26 9 1.09 109.50 120.00 0.0972 30 O2' OH S 28 26 9 1.43 109.50 240.00 -0.6139 31 HO'2 HO E 30 28 26 0.96 107.00 180.00 0.4186 32 O3' OH M 26 9 6 1.42 116.52 -203.47 -0.6541 33 H3T HO M 32 26 9 0.96 114.97 180.00 0.4376 CHARGE resp RCYT 0.4295 -0.6223 0.0558 0.0679 0.0679 0.1065 0.1174 -0.3548 0.0066 0.2029 -0.0484 0.0053 0.1958 -0.5215 0.1928 0.8185 -0.9530 0.4234 0.4234 -0.7584 0.7538 -0.6252 0.2022 0.0615 0.0670 0.0972 -0.6139 0.4186 -0.6541 0.4376 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 STOP