/usr/share/gromacs/top/amber03.ff/dna.rtp is in gromacs-data 2018.1-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | [ 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
|