dna.rtp 29.9 KB
Newer Older
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235
[ bondedtypes ]
; Column 1 : default bondtype
; Column 2 : default angletype
; Column 3 : default proper dihedraltype
; Column 4 : default improper dihedraltype
; Column 5 : This controls the generation of dihedrals from the bonding.
;            All possible dihedrals are generated automatically. A value of
;            1 here means that all these are retained. A value of
;            0 here requires generated dihedrals be removed if
;              * there are any dihedrals on the same central atoms
;                specified in the residue topology, or
;              * there are other identical generated dihedrals
;                sharing the same central atoms, or
;              * there are other generated dihedrals sharing the
;                same central bond that have fewer hydrogen atoms
; Column 6 : number of neighbors to exclude from non-bonded interactions
; Column 7 : 1 = generate 1,4 interactions between pairs of hydrogen atoms
;            0 = do not generate such
; Column 8 : 1 = remove proper dihedrals if found centered on the same
;                bond as an improper dihedral
;            0 = do not generate such
; bonds  angles  dihedrals  impropers all_dihedrals nrexcl HH14 RemoveDih
     1       1          9          4        1         3      1     0

                 
; 5' (XXF), 3' (XXT), non-terminal (XX), and monomer (XXN) nuc's 

[ DA5 ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT            0.04310     9
   H1'    H2            0.18380    10
    N9    N*           -0.02680    11
    C8    CK            0.16070    12
    H8    H5            0.18770    13
    N7    NB           -0.61750    14
    C5    CB            0.07250    15
    C6    CA            0.68970    16
    N6    N2           -0.91230    17
   H61    H             0.41670    18
   H62    H             0.41670    19
    N1    NC           -0.76240    20
    C2    CQ            0.57160    21
    H2    H5            0.05980    22
    N3    NC           -0.74170    23
    C4    CB            0.38000    24
   C3'    CT            0.07130    25
   H3'    H1            0.09850    26
   C2'    CT           -0.08540    27
  H2'1    HC            0.07180    28
  H2'2    HC            0.07180    29
   O3'    OS           -0.52320    30
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    N6
    C6    N1
    N6   H61
    N6   H62
    N1    C2
    C2    H2
    C2    N3
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
 [ impropers ]
    C4    C8    N9   C1'
    C6   H61    N6   H62
    N9    N7    C8    H8
    N1    N3    C2    H2
    C5    N6    C6    N1
                        
[ DA ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT            0.04310    11
   H1'    H2            0.18380    12
    N9    N*           -0.02680    13
    C8    CK            0.16070    14
    H8    H5            0.18770    15
    N7    NB           -0.61750    16
    C5    CB            0.07250    17
    C6    CA            0.68970    18
    N6    N2           -0.91230    19
   H61    H             0.41670    20
   H62    H             0.41670    21
    N1    NC           -0.76240    22
    C2    CQ            0.57160    23
    H2    H5            0.05980    24
    N3    NC           -0.74170    25
    C4    CB            0.38000    26
   C3'    CT            0.07130    27
   H3'    H1            0.09850    28
   C2'    CT           -0.08540    29
  H2'1    HC            0.07180    30
  H2'2    HC            0.07180    31
   O3'    OS           -0.52320    32
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    N6
    C6    N1
    N6   H61
    N6   H62
    N1    C2
    C2    H2
    C2    N3
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
  -O3'     P
 [ impropers ]
    C4    C8    N9   C1'  
    C6   H61    N6   H62
    N9    N7    C8    H8
    N1    N3    C2    H2
    C5    N6    C6    N1  
                        
[ DA3 ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT            0.04310    11
   H1'    H2            0.18380    12
    N9    N*           -0.02680    13
    C8    CK            0.16070    14
    H8    H5            0.18770    15
    N7    NB           -0.61750    16
    C5    CB            0.07250    17
    C6    CA            0.68970    18
    N6    N2           -0.91230    19
   H61    H             0.41670    20
   H62    H             0.41670    21
    N1    NC           -0.76240    22
    C2    CQ            0.57160    23
    H2    H5            0.05980    24
    N3    NC           -0.74170    25
    C4    CB            0.38000    26
   C3'    CT            0.07130    27
   H3'    H1            0.09850    28
   C2'    CT           -0.08540    29
  H2'1    HC            0.07180    30
  H2'2    HC            0.07180    31
   O3'    OH           -0.65490    32
   H3T    HO            0.43960    33
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    N6
    C6    N1
    N6   H61
    N6   H62
    N1    C2
    C2    H2
    C2    N3
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
  -O3'     P
 [ impropers ]
    C4    C8    N9   C1'  
    C6   H61    N6   H62
    N9    N7    C8    H8
    N1    N3    C2    H2
    C5    N6    C6    N1  

[ DAN ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT            0.04310     9
   H1'    H2            0.18380    10
    N9    N*           -0.02680    11
    C8    CK            0.16070    12
    H8    H5            0.18770    13
    N7    NB           -0.61750    14
    C5    CB            0.07250    15
    C6    CA            0.68970    16
    N6    N2           -0.91230    17
   H61    H             0.41670    18
   H62    H             0.41670    19
    N1    NC           -0.76240    20
    C2    CQ            0.57160    21
    H2    H5            0.05980    22
    N3    NC           -0.74170    23
    C4    CB            0.38000    24
   C3'    CT            0.07130    25
   H3'    H1            0.09850    26
   C2'    CT           -0.08540    27
  H2'1    HC            0.07180    28
  H2'2    HC            0.07180    29
   O3'    OH           -0.65490    30
   H3T    HO            0.43960    31
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    N6
    C6    N1
    N6   H61
    N6   H62
    N1    C2
    C2    H2
    C2    N3
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
 [ impropers ]
    C4    C8    N9   C1'
    C6   H61    N6   H62
    N9    N7    C8    H8
    N1    N3    C2    H2
    C5    N6    C6    N1


                 
[ DT5 ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT            0.06800     9
   H1'    H2            0.18040    10
    N1    N*           -0.02390    11
    C6    CM           -0.22090    12
    H6    H4            0.26070    13
    C5    CM            0.00250    14
    C7    CT           -0.22690    15
   H71    HC            0.07700    16
   H72    HC            0.07700    17
   H73    HC            0.07700    18
    C4    C             0.51940    19
    O4    O            -0.55630    20
    N3    NA           -0.43400    21
    H3    H             0.34200    22
    C2    C             0.56770    23
    O2    O            -0.58810    24
   C3'    CT            0.07130    25
   H3'    H1            0.09850    26
   C2'    CT           -0.08540    27
  H2'1    HC            0.07180    28
  H2'2    HC            0.07180    29
   O3'    OS           -0.52320    30
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    C7
    C5    C4
    C7   H71
    C7   H72
    C7   H73
    C4    O4
    C4    N3
    N3    H3
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
 [ impropers ]
    C2    C6    N1   C1'
    C4    C6    C5    C7
    N1    N3    C2    O2
    C5    N3    C4    O4
    C4    C2    N3    H3  
    N1    C5    C6    H6
                        
[ DT ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT            0.06800    11
   H1'    H2            0.18040    12
    N1    N*           -0.02390    13
    C6    CM           -0.22090    14
    H6    H4            0.26070    15
    C5    CM            0.00250    16
    C7    CT           -0.22690    17
   H71    HC            0.07700    18
   H72    HC            0.07700    19
   H73    HC            0.07700    20
    C4    C             0.51940    21
    O4    O            -0.55630    22
    N3    NA           -0.43400    23
    H3    H             0.34200    24
    C2    C             0.56770    25
    O2    O            -0.58810    26
   C3'    CT            0.07130    27
   H3'    H1            0.09850    28
   C2'    CT           -0.08540    29
  H2'1    HC            0.07180    30
  H2'2    HC            0.07180    31
   O3'    OS           -0.52320    32
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    C7
    C5    C4
    C7   H71
    C7   H72
    C7   H73
    C4    O4
    C4    N3
    N3    H3
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
  -O3'     P
 [ impropers ]
    C2    C6    N1   C1'
    C4    C6    C5    C7
    N1    N3    C2    O2
    C5    N3    C4    O4
    C4    C2    N3    H3  
    N1    C5    C6    H6
                        
[ DT3 ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT            0.06800    11
   H1'    H2            0.18040    12
    N1    N*           -0.02390    13
    C6    CM           -0.22090    14
    H6    H4            0.26070    15
    C5    CM            0.00250    16
    C7    CT           -0.22690    17
   H71    HC            0.07700    18
   H72    HC            0.07700    19
   H73    HC            0.07700    20
    C4    C             0.51940    21
    O4    O            -0.55630    22
    N3    NA           -0.43400    23
    H3    H             0.34200    24
    C2    C             0.56770    25
    O2    O            -0.58810    26
   C3'    CT            0.07130    27
   H3'    H1            0.09850    28
   C2'    CT           -0.08540    29
  H2'1    HC            0.07180    30
  H2'2    HC            0.07180    31
   O3'    OH           -0.65490    32
   H3T    HO            0.43960    33
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    C7
    C5    C4
    C7   H71
    C7   H72
    C7   H73
    C4    O4
    C4    N3
    N3    H3
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
  -O3'     P
 [ impropers ]
    C2    C6    N1   C1'
    C4    C6    C5    C7
    N1    N3    C2    O2
    C5    N3    C4    O4
    C4    C2    N3    H3  
    N1    C5    C6    H6
                        
[ DTN ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT            0.06800     9
   H1'    H2            0.18040    10
    N1    N*           -0.02390    11
    C6    CM           -0.22090    12
    H6    H4            0.26070    13
    C5    CM            0.00250    14
    C7    CT           -0.22690    15
   H71    HC            0.07700    16
   H72    HC            0.07700    17
   H73    HC            0.07700    18
    C4    C             0.51940    19
    O4    O            -0.55630    20
    N3    NA           -0.43400    21
    H3    H             0.34200    22
    C2    C             0.56770    23
    O2    O            -0.58810    24
   C3'    CT            0.07130    25
   H3'    H1            0.09850    26
   C2'    CT           -0.08540    27
  H2'1    HC            0.07180    28
  H2'2    HC            0.07180    29
   O3'    OH           -0.65490    30
   H3T    HO            0.43960    31
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    C7
    C5    C4
    C7   H71
    C7   H72
    C7   H73
    C4    O4
    C4    N3
    N3    H3
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
 [ impropers ]
    C2    C6    N1   C1'
    C4    C6    C5    C7
    N1    N3    C2    O2
    C5    N3    C4    O4
    C4    C2    N3    H3  
    N1    C5    C6    H6

                     

[ DG5 ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT            0.03580     9
   H1'    H2            0.17460    10
    N9    N*            0.05770    11
    C8    CK            0.07360    12
    H8    H5            0.19970    13
    N7    NB           -0.57250    14
    C5    CB            0.19910    15
    C6    C             0.49180    16
    O6    O            -0.56990    17
    N1    NA           -0.50530    18
    H1    H             0.35200    19
    C2    CA            0.74320    20
    N2    N2           -0.92300    21
   H21    H             0.42350    22
   H22    H             0.42350    23
    N3    NC           -0.66360    24
    C4    CB            0.18140    25
   C3'    CT            0.07130    26
   H3'    H1            0.09850    27
   C2'    CT           -0.08540    28
  H2'1    HC            0.07180    29
  H2'2    HC            0.07180    30
   O3'    OS           -0.52320    31
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    O6
    C6    N1
    N1    H1
    N1    C2
    C2    N2
    C2    N3
    N2   H21
    N2   H22
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
 [ impropers ]
    C4    C8    N9   C1'
    C5    N1    C6    O6
    C6    C2    N1    H1
    C2   H21    N2   H22
    N9    N7    C8    H8
    N2    N1    C2    N3
                        
[ DG ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT            0.03580    11
   H1'    H2            0.17460    12
    N9    N*            0.05770    13
    C8    CK            0.07360    14
    H8    H5            0.19970    15
    N7    NB           -0.57250    16
    C5    CB            0.19910    17
    C6    C             0.49180    18
    O6    O            -0.56990    19
    N1    NA           -0.50530    20
    H1    H             0.35200    21
    C2    CA            0.74320    22
    N2    N2           -0.92300    23
   H21    H             0.42350    24
   H22    H             0.42350    25
    N3    NC           -0.66360    26
    C4    CB            0.18140    27
   C3'    CT            0.07130    28
   H3'    H1            0.09850    29
   C2'    CT           -0.08540    30
  H2'1    HC            0.07180    31
  H2'2    HC            0.07180    32
   O3'    OS           -0.52320    33
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    O6
    C6    N1
    N1    H1
    N1    C2
    C2    N2
    C2    N3
    N2   H21
    N2   H22
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
  -O3'     P
 [ impropers ]
    C4    C8    N9   C1'
    C5    N1    C6    O6
    C6    C2    N1    H1
    C2   H21    N2   H22
    N9    N7    C8    H8
    N2    N1    C2    N3
                        
[ DG3 ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT            0.03580    11
   H1'    H2            0.17460    12
    N9    N*            0.05770    13
    C8    CK            0.07360    14
    H8    H5            0.19970    15
    N7    NB           -0.57250    16
    C5    CB            0.19910    17
    C6    C             0.49180    18
    O6    O            -0.56990    19
    N1    NA           -0.50530    20
    H1    H             0.35200    21
    C2    CA            0.74320    22
    N2    N2           -0.92300    23
   H21    H             0.42350    24
   H22    H             0.42350    25
    N3    NC           -0.66360    26
    C4    CB            0.18140    27
   C3'    CT            0.07130    28
   H3'    H1            0.09850    29
   C2'    CT           -0.08540    30
  H2'1    HC            0.07180    31
  H2'2    HC            0.07180    32
   O3'    OH           -0.65490    33
   H3T    HO            0.43960    34
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    O6
    C6    N1
    N1    H1
    N1    C2
    C2    N2
    C2    N3
    N2   H21
    N2   H22
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
  -O3'     P
 [ impropers ]
    C4    C8    N9   C1'
    C5    N1    C6    O6
    C6    C2    N1    H1
    C2   H21    N2   H22
    N9    N7    C8    H8
    N2    N1    C2    N3
                        
[ DGN ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT            0.03580     9
   H1'    H2            0.17460    10
    N9    N*            0.05770    11
    C8    CK            0.07360    12
    H8    H5            0.19970    13
    N7    NB           -0.57250    14
    C5    CB            0.19910    15
    C6    C             0.49180    16
    O6    O            -0.56990    17
    N1    NA           -0.50530    18
    H1    H             0.35200    19
    C2    CA            0.74320    20
    N2    N2           -0.92300    21
   H21    H             0.42350    22
   H22    H             0.42350    23
    N3    NC           -0.66360    24
    C4    CB            0.18140    25
   C3'    CT            0.07130    26
   H3'    H1            0.09850    27
   C2'    CT           -0.08540    28
  H2'1    HC            0.07180    29
  H2'2    HC            0.07180    30
   O3'    OH           -0.65490    31
   H3T    HO            0.43960    32
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N9
   C1'   C2'
    N9    C8
    N9    C4
    C8    H8
    C8    N7
    N7    C5
    C5    C6
    C5    C4
    C6    O6
    C6    N1
    N1    H1
    N1    C2
    C2    N2
    C2    N3
    N2   H21
    N2   H22
    N3    C4
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
 [ impropers ]
    C4    C8    N9   C1'
    C5    N1    C6    O6
    C6    C2    N1    H1
    C2   H21    N2   H22
    N9    N7    C8    H8
    N2    N1    C2    N3
                      
[ DC5 ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT           -0.01160     9
   H1'    H2            0.19630    10
    N1    N*           -0.03390    11
    C6    CM           -0.01830    12
    H6    H4            0.22930    13
    C5    CM           -0.52220    14
    H5    HA            0.18630    15
    C4    CA            0.84390    16
    N4    N2           -0.97730    17
   H41    H             0.43140    18
   H42    H             0.43140    19
    N3    NC           -0.77480    20
    C2    C             0.79590    21
    O2    O            -0.65480    22
   C3'    CT            0.07130    23
   H3'    H1            0.09850    24
   C2'    CT           -0.08540    25
  H2'1    HC            0.07180    26
  H2'2    HC            0.07180    27
   O3'    OS           -0.52320    28
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    H5
    C5    C4
    C4    N4
    C4    N3
    N4   H41
    N4   H42
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
 [ impropers ]
   C1'    N1    C6    C2
    N1    N3    C2    O2 
    C4   H41    N4   H42
    N1    C5    C6    H6
    C6    C4    C5    H5
    C5    N4    C4    N3
                        
[ DC ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT           -0.01160    11
   H1'    H2            0.19630    12
    N1    N*           -0.03390    13
    C6    CM           -0.01830    14
    H6    H4            0.22930    15
    C5    CM           -0.52220    16
    H5    HA            0.18630    17
    C4    CA            0.84390    18
    N4    N2           -0.97730    19
   H41    H             0.43140    20
   H42    H             0.43140    21
    N3    NC           -0.77480    22
    C2    C             0.79590    23
    O2    O            -0.65480    24
   C3'    CT            0.07130    25
   H3'    H1            0.09850    26
   C2'    CT           -0.08540    27
  H2'1    HC            0.07180    28
  H2'2    HC            0.07180    29
   O3'    OS           -0.52320    30
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    H5
    C5    C4
    C4    N4
    C4    N3
    N4   H41
    N4   H42
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
  -O3'     P
 [ impropers ]
    C2    C6    N1   C1'
    N1    N3    C2    O2 
    C4   H41    N4   H42
    N1    C5    C6    H6
    C6    C4    C5    H5
    C5    N4    C4    N3
                        
[ DC3 ]
 [ atoms ]
     P    P             1.16590     1
   O1P    O2           -0.77610     2
   O2P    O2           -0.77610     3
   O5'    OS           -0.49540     4
   C5'    CT           -0.00690     5
  H5'1    H1            0.07540     6
  H5'2    H1            0.07540     7
   C4'    CT            0.16290     8
   H4'    H1            0.11760     9
   O4'    OS           -0.36910    10
   C1'    CT           -0.01160    11
   H1'    H2            0.19630    12
    N1    N*           -0.03390    13
    C6    CM           -0.01830    14
    H6    H4            0.22930    15
    C5    CM           -0.52220    16
    H5    HA            0.18630    17
    C4    CA            0.84390    18
    N4    N2           -0.97730    19
   H41    H             0.43140    20
   H42    H             0.43140    21
    N3    NC           -0.77480    22
    C2    C             0.79590    23
    O2    O            -0.65480    24
   C3'    CT            0.07130    25
   H3'    H1            0.09850    26
   C2'    CT           -0.08540    27
  H2'1    HC            0.07180    28
  H2'2    HC            0.07180    29
   O3'    OH           -0.65490    30
   H3T    HO            0.43960    31
 [ bonds ]
     P   O1P
     P   O2P
     P   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    H5
    C5    C4
    C4    N4
    C4    N3
    N4   H41
    N4   H42
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
  -O3'     P
 [ impropers ]
    C2    C6    N1   C1'
    N1    N3    C2    O2
    C4   H41    N4   H42
    N1    C5    C6    H6
    C6    C4    C5    H5
    C5    N4    C4    N3

[ DCN ]
 [ atoms ]
   H5T    HO            0.44220     1
   O5'    OH           -0.63180     2
   C5'    CT           -0.00690     3
  H5'1    H1            0.07540     4
  H5'2    H1            0.07540     5
   C4'    CT            0.16290     6
   H4'    H1            0.11760     7
   O4'    OS           -0.36910     8
   C1'    CT           -0.01160     9
   H1'    H2            0.19630    10
    N1    N*           -0.03390    11
    C6    CM           -0.01830    12
    H6    H4            0.22930    13
    C5    CM           -0.52220    14
    H5    HA            0.18630    15
    C4    CA            0.84390    16
    N4    N2           -0.97730    17
   H41    H             0.43140    18
   H42    H             0.43140    19
    N3    NC           -0.77480    20
    C2    C             0.79590    21
    O2    O            -0.65480    22
   C3'    CT            0.07130    23
   H3'    H1            0.09850    24
   C2'    CT           -0.08540    25
  H2'1    HC            0.07180    26
  H2'2    HC            0.07180    27
   O3'    OH           -0.65490    28
   H3T    HO            0.43960    29
 [ bonds ]
   H5T   O5'
   O5'   C5'
   C5'  H5'1
   C5'  H5'2
   C5'   C4'
   C4'   H4'
   C4'   O4'
   C4'   C3'
   O4'   C1'
   C1'   H1'
   C1'    N1
   C1'   C2'
    N1    C6
    N1    C2
    C6    H6
    C6    C5
    C5    H5
    C5    C4
    C4    N4
    C4    N3
    N4   H41
    N4   H42
    N3    C2
    C2    O2
   C3'   H3'
   C3'   C2'
   C3'   O3'
   C2'  H2'1
   C2'  H2'2
   O3'   H3T
 [ impropers ]
    C2    C6    N1   C1'
    N1    N3    C2    O2
    C4   H41    N4   H42
    N1    C5    C6    H6
    C6    C4    C5    H5
    N3    C4    N4    C5