data_128
#
_chem_comp.id 128
_chem_comp.name "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE"
_chem_comp.type "RNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C16 H17 N8 O19 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2001-02-28
_chem_comp.pdbx_modified_date 2017-04-18
_chem_comp.pdbx_ambiguous_flag Y
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 718.270
_chem_comp.one_letter_code N
_chem_comp.three_letter_code 128
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1I5D
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
128 PG PG P 0 1 N N N 12.178 64.572 12.762 -8.719 0.060 1.297 PG 128 1
128 O1G O1G O 0 1 N N N 13.105 64.540 11.548 -9.440 -0.818 0.349 O1G 128 2
128 O2G O2G O 0 1 N N N 12.740 63.706 13.882 -9.312 1.554 1.202 O2G 128 3
128 O3G O3G O 0 1 N N N 11.613 65.972 13.203 -8.908 -0.498 2.795 O3G 128 4
128 PB PB P 0 1 N N N 9.506 64.044 11.199 -6.332 0.221 -0.453 PB 128 5
128 O1B O1B O 0 1 N N N 10.301 64.699 10.050 -6.916 1.311 -1.266 O1B 128 6
128 O2B O2B O 0 1 N N N 8.309 64.832 11.713 -6.416 -1.163 -1.272 O2B 128 7
128 O3B O3B O 0 1 N N N 10.649 63.852 12.341 -7.153 0.080 0.925 O3B 128 8
128 PA PA P 0 1 N N N 7.864 61.441 11.015 -3.585 1.201 -0.979 PA 128 9
128 O1A O1A O 0 1 N N N 7.076 61.920 12.290 -3.624 0.679 -2.363 O1A 128 10
128 O2A O2A O 0 1 N N N 6.954 60.885 9.950 -3.740 2.804 -1.005 O2A 128 11
128 O3A O3A O 0 1 N N N 8.720 62.684 10.506 -4.792 0.559 -0.129 O3A 128 12
128 "O5'" "O5'" O 0 1 N N N 9.071 60.587 11.746 -2.180 0.809 -0.297 "O5'" 128 13
128 "C5'" "C5'" C 0 1 N N N 9.957 61.195 12.796 -0.915 1.141 -0.873 "C5'" 128 14
128 "C4'" "C4'" C 0 1 N N R 11.301 60.300 12.755 0.208 0.623 0.028 "C4'" 128 15
128 "O4'" "O4'" O 0 1 N N N 11.638 59.758 14.039 0.199 -0.814 0.040 "O4'" 128 16
128 "C3'" "C3'" C 0 1 N N R 11.372 59.140 11.902 1.572 1.071 -0.527 "C3'" 128 17
128 "O3'" "O3'" O 0 1 N N N 12.594 59.262 11.203 2.309 1.723 0.533 "O3'" 128 18
128 "C2'" "C2'" C 0 1 N N R 11.585 57.905 12.803 2.356 -0.260 -0.727 "C2'" 128 19
128 "O2'" "O2'" O 0 1 N N N 12.482 56.946 12.199 3.647 -0.022 -0.146 "O2'" 128 20
128 "C1'" "C1'" C 0 1 N N R 12.122 58.446 14.165 1.571 -1.241 0.176 "C1'" 128 21
128 N9 N9 N 0 1 Y N N 11.312 57.778 15.377 1.730 -2.617 -0.299 N9 128 22
128 C8 C8 C 0 1 Y N N 11.757 57.676 16.665 0.924 -3.262 -1.188 C8 128 23
128 N7 N7 N 0 1 Y N N 10.842 57.070 17.433 1.357 -4.473 -1.385 N7 128 24
128 C5 C5 C 0 1 Y N N 9.815 56.783 16.629 2.466 -4.682 -0.636 C5 128 25
128 C6 C6 C 0 1 Y N N 8.565 56.139 16.942 3.340 -5.766 -0.444 C6 128 26
128 N6 N6 N 0 1 N N N 8.329 55.717 18.198 3.142 -6.962 -1.112 N6 128 27
128 N1 N1 N 0 1 Y N N 7.623 55.943 15.935 4.361 -5.616 0.393 N1 128 28
128 C2 C2 C 0 1 Y N N 7.939 56.393 14.693 4.559 -4.479 1.034 C2 128 29
128 N3 N3 N 0 1 Y N N 9.109 57.001 14.406 3.767 -3.438 0.886 N3 128 30
128 C4 C4 C 0 1 Y N N 10.084 57.222 15.339 2.723 -3.492 0.065 C4 128 31
128 C1F C1F C 0 1 N N N 13.043 57.851 11.131 3.681 1.354 0.273 C1F 128 32
128 C2F C2F C 0 1 N N N 12.697 57.105 9.928 4.218 2.203 -0.838 C2F 128 33
128 C3F C3F C 0 1 N N N 13.628 56.738 9.019 5.436 2.717 -0.829 C3F 128 34
128 C4F C4F C 0 1 N N N 14.957 56.991 9.104 6.321 2.465 0.330 C4F 128 35
128 C5F C5F C 0 1 N N N 15.365 57.680 10.226 5.695 1.978 1.579 C5F 128 36
128 C6F C6F C 0 1 N N N 14.459 58.131 11.267 4.473 1.473 1.538 C6F 128 37
128 N2F N2F N 1 1 N N N 11.346 56.728 9.649 3.344 2.478 -2.001 N2F 128 38
128 N4F N4F N 1 1 N N N 15.889 56.644 8.231 7.610 2.666 0.253 N4F 128 39
128 N6F N6F N 1 1 N N N 15.050 58.812 12.333 3.860 1.004 2.801 N6F 128 40
128 O2F O2F O 0 1 N N N 10.415 56.991 10.363 3.302 1.693 -2.931 O2F 128 41
128 O3F O3F O -1 1 N N N 11.078 56.117 8.639 2.667 3.491 -2.028 O3F 128 42
128 O4F O4F O 0 1 N N N 17.060 56.908 8.367 8.434 2.417 1.378 O4F 128 43
128 O5F O5F O -1 1 N N N 15.613 56.057 7.236 8.183 3.133 -0.955 O5F 128 44
128 O6F O6F O 0 1 N N N 16.250 58.976 12.322 4.480 1.088 3.847 O6F 128 45
128 O7F O7F O -1 1 N N N 14.464 59.262 13.267 2.737 0.535 2.796 O7F 128 46
128 HOG2 HOG2 H 0 0 N N N 13.560 63.316 13.601 -8.885 2.185 1.797 HOG2 128 47
128 HOG3 HOG3 H 0 0 N N N 11.944 66.645 12.621 -9.829 -0.537 3.087 HOG3 128 48
128 HOB2 HOB2 H 0 0 N N N 8.231 65.644 11.226 -6.051 -1.923 -0.799 HOB2 128 49
128 HOA2 HOA2 H 0 0 N N N 6.053 60.926 10.249 -3.723 3.215 -0.129 HOA2 128 50
128 "H5'" "H5'1" H 0 1 N N N 10.181 62.245 12.556 -0.833 0.681 -1.858 "H5'" 128 51
128 "H5''" "H5'2" H 0 0 N N N 9.482 61.139 13.786 -0.833 2.224 -0.970 "H5''" 128 52
128 "H4'" "H4'" H 0 1 N N N 12.108 60.985 12.456 0.075 1.003 1.041 "H4'" 128 53
128 "H3'" "H3'" H 0 1 N N N 10.494 59.023 11.249 1.490 1.678 -1.429 "H3'" 128 54
128 "H2'" "H2'" H 0 1 N N N 10.607 57.435 12.983 2.410 -0.574 -1.770 "H2'" 128 55
128 "H1'" "H1'" H 0 1 N N N 13.211 58.341 14.275 1.898 -1.152 1.212 "H1'" 128 56
128 H8 H8 H 0 1 N N N 12.714 58.034 17.015 0.053 -2.832 -1.660 H8 128 57
128 HN61 HN61 H 0 0 N N N 7.430 55.282 18.240 2.393 -7.059 -1.721 HN61 128 58
128 HN62 HN62 H 0 0 N N N 9.031 55.057 18.465 3.752 -7.703 -0.972 HN62 128 59
128 H2 H2 H 0 1 N N N 7.220 56.258 13.898 5.401 -4.400 1.705 H2 128 60
128 H3F H3F H 0 1 N N N 13.283 56.197 8.150 5.781 3.315 -1.660 H3F 128 61
128 H4F H4F H 0 1 N N N 17.548 56.580 7.621 9.372 2.595 1.225 H4F 128 62
128 H5F H5F H 0 1 N N N 16.417 57.896 10.337 6.231 2.033 2.515 H5F 128 63
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
128 PG O1G DOUB N N 1
128 PG O2G SING N N 2
128 PG O3G SING N N 3
128 PG O3B SING N N 4
128 O2G HOG2 SING N N 5
128 O3G HOG3 SING N N 6
128 PB O1B DOUB N N 7
128 PB O2B SING N N 8
128 PB O3B SING N N 9
128 PB O3A SING N N 10
128 O2B HOB2 SING N N 11
128 PA O1A DOUB N N 12
128 PA O2A SING N N 13
128 PA O3A SING N N 14
128 PA "O5'" SING N N 15
128 O2A HOA2 SING N N 16
128 "O5'" "C5'" SING N N 17
128 "C5'" "C4'" SING N N 18
128 "C5'" "H5'" SING N N 19
128 "C5'" "H5''" SING N N 20
128 "C4'" "O4'" SING N N 21
128 "C4'" "C3'" SING N N 22
128 "C4'" "H4'" SING N N 23
128 "O4'" "C1'" SING N N 24
128 "C3'" "O3'" SING N N 25
128 "C3'" "C2'" SING N N 26
128 "C3'" "H3'" SING N N 27
128 "O3'" C1F SING N N 28
128 "C2'" "O2'" SING N N 29
128 "C2'" "C1'" SING N N 30
128 "C2'" "H2'" SING N N 31
128 "O2'" C1F SING N N 32
128 "C1'" N9 SING N N 33
128 "C1'" "H1'" SING N N 34
128 N9 C8 SING Y N 35
128 N9 C4 SING Y N 36
128 C8 N7 DOUB Y N 37
128 C8 H8 SING N N 38
128 N7 C5 SING Y N 39
128 C5 C6 SING Y N 40
128 C5 C4 DOUB Y N 41
128 C6 N6 SING N N 42
128 C6 N1 DOUB Y N 43
128 N6 HN61 SING N N 44
128 N6 HN62 SING N N 45
128 N1 C2 SING Y N 46
128 C2 N3 DOUB Y N 47
128 C2 H2 SING N N 48
128 N3 C4 SING Y N 49
128 C1F C2F SING N N 50
128 C1F C6F SING N N 51
128 C2F C3F DOUB N N 52
128 C2F N2F SING N N 53
128 C3F C4F SING N N 54
128 C3F H3F SING N N 55
128 C4F C5F SING N N 56
128 C4F N4F DOUB N N 57
128 O4F H4F SING N N 58
128 C5F C6F DOUB N N 59
128 C5F H5F SING N N 60
128 C6F N6F SING N N 61
128 N2F O2F DOUB N N 62
128 N2F O3F SING N N 63
128 N4F O4F SING N N 64
128 N4F O5F SING N N 65
128 N6F O6F DOUB N N 66
128 N6F O7F SING N N 67
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
128 SMILES ACDLabs 12.01 "P(=O)(O)(O)OP(=O)(O)OP(=O)(O)OCC1OC(C2C1OC3(O2)C(=C/C(C=C3[N+](=O)[O-])=[N+](/O)[O-])[N+](=O)[O-])n4cnc5c(N)ncnc45"
128 InChI InChI 1.03
;InChI=1S/C16H17N8O19P3/c17-13-10-14(19-4-18-13)21(5-20-10)15-12-11(7(39-15)3-38-45(34,35)43-46(36,37)42-44(31,32)33)40-16(41-12)8(23(27)28)1-6(22(25)26)2-9(16)24(29)30/h1-2,4-5,7,11-12,15H,3H2,(H,25,26)(H,34,35)(H,36,37)(H2,17,18,19)(H2,31,32,33)/t7-,11-,12-,15-/m1/s1
;
128 InChIKey InChI 1.03 XFMMHXLUHKBKQE-UHEGPQQHSA-N
128 SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@H]4O[C]5(O[C@@H]34)C(=C[C@@](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O"
128 SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH]4O[C]5(O[CH]34)C(=C[C](C=C5[N+]([O-])=O)=[N+](O)[O-])[N+]([O-])=O"
128 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N"
128 SMILES "OpenEye OEToolkits" 1.7.6 "c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)OC5(O4)C(=CC(=[N+](O)[O-])C=C5[N+](=O)[O-])[N+](=O)[O-])N"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
128 "SYSTEMATIC NAME" ACDLabs 12.01
;2',3'-O-{(1R)-4-[hydroxy(oxo)-lambda~5~-azanylidene]-2,6-dinitrocyclohexa-2,5-diene-1,1-diyl}adenosine 5'-(tetrahydrogen triphosphate)
;
128 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6
;(3aR,4R,6R,6aR)-4-(6-aminopurin-9-yl)-3',5'-dinitro-N-oxidanyl-6-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]spiro[3a,4,6,6a-tetrahydrofuro[3,4-d][1,3]dioxole-2,4'-cyclohexa-2,5-diene]-1'-imine oxide
;
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
128 "Create component" 2001-02-28 RCSB
128 "Other modification" 2015-09-12 RCSB
128 "Other modification" 2017-04-18 RCSB
#