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 
# 
