data_IOO # _chem_comp.id IOO _chem_comp.name ; N7-(3,4-difluorobenzyl) guanosine 5'-monophosphate ; _chem_comp.type "L-RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C17 H19 F2 N5 O8 P" _chem_comp.mon_nstd_parent_comp_id G _chem_comp.pdbx_synonyms "[(2R,3S,4R,5R)-5-[2-azanyl-7-[[3,4-bis(fluoranyl)phenyl]methyl]-6-oxidanylidene-1H-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2022-04-04 _chem_comp.pdbx_modified_date 2022-08-22 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 490.332 _chem_comp.one_letter_code ? _chem_comp.three_letter_code IOO _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 7ZEG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 IOO "C2'" C2 C 0 1 N N N 3.021 -22.020 9.641 3.147 -3.622 -0.758 "C2'" IOO 1 IOO C1 C5 C 0 1 Y N N 0.548 -21.627 8.560 2.466 -1.352 0.560 C1 IOO 2 IOO "C1'" C4 C 0 1 Y N N 1.632 -21.782 7.795 1.512 -2.122 -0.115 "C1'" IOO 3 IOO N1 N2 N 0 1 N N N 4.233 -22.222 10.153 3.487 -4.771 -1.426 N1 IOO 4 IOO N4 N1 N 0 1 N N N 1.921 -21.879 10.470 4.121 -2.912 -0.123 N4 IOO 5 IOO C2 "C1'" C 0 1 N N R 2.214 -21.813 5.395 -0.984 -1.918 -0.460 C2 IOO 6 IOO C3 "C2'" C 0 1 N N R 1.855 -23.080 4.591 -1.660 -2.914 0.516 C3 IOO 7 IOO "C3'" "C3'" C 0 1 N N S 2.326 -22.757 3.173 -3.158 -2.747 0.164 "C3'" IOO 8 IOO "C4'" "C4'" C 0 1 N N R 2.695 -21.268 3.276 -3.233 -1.370 -0.525 "C4'" IOO 9 IOO "C5'" "C5'" C 0 1 N N N 2.095 -20.585 2.059 -4.195 -0.458 0.240 "C5'" IOO 10 IOO C6 C6 C 0 1 N N N 0.669 -21.685 9.892 3.815 -1.776 0.542 C6 IOO 11 IOO C8 C8 C 0 1 Y N N -0.045 -21.496 6.490 0.549 -0.376 0.823 C8 IOO 12 IOO C11 CAY C 0 1 N N N -1.949 -21.220 8.062 2.439 0.759 1.911 C11 IOO 13 IOO C12 CAZ C 0 1 Y N N -2.219 -19.847 8.255 2.983 1.827 0.997 C12 IOO 14 IOO C13 CBA C 0 1 Y N N -3.077 -17.737 7.419 4.778 2.713 -0.318 C13 IOO 15 IOO C14 CBB C 0 1 Y N N -2.793 -19.091 7.237 4.277 1.735 0.521 C14 IOO 16 IOO C15 CBC C 0 1 Y N N -2.787 -17.135 8.641 3.983 3.786 -0.682 C15 IOO 17 IOO C16 CBD C 0 1 Y N N -1.942 -19.239 9.476 2.184 2.894 0.631 C16 IOO 18 IOO C17 CBE C 0 1 Y N N -2.219 -17.887 9.666 2.683 3.875 -0.208 C17 IOO 19 IOO F1 FBF F 0 1 N N N -3.062 -15.790 8.835 4.473 4.745 -1.497 F1 IOO 20 IOO F2 FBG F 0 1 N N N -1.927 -17.284 10.893 1.905 4.922 -0.562 F2 IOO 21 IOO N3 N3 N 0 1 N N N 2.849 -21.954 8.321 1.890 -3.236 -0.753 N3 IOO 22 IOO N7 N7 N 1 1 Y N N -0.497 -21.454 7.744 1.815 -0.298 1.110 N7 IOO 23 IOO N9 N9 N 0 1 Y N N 1.274 -21.663 6.529 0.314 -1.484 0.062 N9 IOO 24 IOO "O2'" "O2'" O 0 1 N N N 2.511 -24.262 5.107 -1.223 -4.251 0.264 "O2'" IOO 25 IOO "O3'" "O3'" O 0 1 N N N 3.503 -23.509 2.809 -3.583 -3.777 -0.730 "O3'" IOO 26 IOO "O4'" "O4'" O 0 1 N N N 1.993 -20.824 4.414 -1.908 -0.809 -0.510 "O4'" IOO 27 IOO "O5'" "O5'" O 0 1 N N N 2.357 -19.151 2.053 -4.347 0.774 -0.469 "O5'" IOO 28 IOO OP1 O6 O 0 1 N N N -0.299 -21.559 10.638 4.680 -1.134 1.113 OP1 IOO 29 IOO O1 OAT O 0 1 N N N 3.694 -18.717 0.083 -4.901 2.346 1.426 O1 IOO 30 IOO OP3 OAU O 0 1 N Y N 3.604 -17.018 1.758 -5.121 3.245 -0.923 OP3 IOO 31 IOO OP2 OAV O 0 1 N N N 5.022 -19.012 2.212 -6.826 1.489 0.036 OP2 IOO 32 IOO P PAS P 0 1 N N N 3.750 -18.523 1.576 -5.290 1.972 0.048 P IOO 33 IOO H21 H1 H 0 1 N N N 5.021 -22.325 9.546 4.411 -5.068 -1.442 H21 IOO 34 IOO H22 H2 H 0 1 N N N 4.355 -22.271 11.144 2.805 -5.288 -1.883 H22 IOO 35 IOO H1 H3 H 0 1 N N N 2.024 -21.916 11.464 5.040 -3.223 -0.149 H1 IOO 36 IOO "H1'" H4 H 0 1 N N N 3.259 -21.850 5.736 -0.869 -2.366 -1.447 "H1'" IOO 37 IOO "H2'" H5 H 0 1 N N N 0.763 -23.213 4.592 -1.469 -2.633 1.552 "H2'" IOO 38 IOO "H3'" H6 H 0 1 N N N 1.508 -22.901 2.452 -3.764 -2.753 1.071 "H3'" IOO 39 IOO "H4'" H7 H 0 1 N N N 3.783 -21.120 3.338 -3.571 -1.489 -1.554 "H4'" IOO 40 IOO "H5'" H8 H 0 1 N N N 1.007 -20.747 2.061 -5.164 -0.947 0.331 "H5'" IOO 41 IOO "H5''" H9 H 0 0 N N N 2.530 -21.029 1.152 -3.793 -0.258 1.233 "H5''" IOO 42 IOO H8 H10 H 0 1 N N N -0.646 -21.409 5.597 -0.205 0.330 1.140 H8 IOO 43 IOO H11 H11 H 0 1 N N N -2.563 -21.592 7.228 3.253 0.336 2.500 H11 IOO 44 IOO H12 H12 H 0 1 N N N -2.207 -21.768 8.980 1.696 1.196 2.578 H12 IOO 45 IOO H13 H13 H 0 1 N N N -3.518 -17.161 6.619 5.791 2.642 -0.686 H13 IOO 46 IOO H14 H14 H 0 1 N N N -3.022 -19.560 6.291 4.898 0.898 0.804 H14 IOO 47 IOO H15 H15 H 0 1 N N N -1.511 -19.818 10.279 1.172 2.963 1.000 H15 IOO 48 IOO "HO2'" H16 H 0 0 N N N 2.200 -24.439 5.987 -1.618 -4.911 0.850 "HO2'" IOO 49 IOO "HO3'" H17 H 0 0 N Y N 3.283 -24.431 2.743 -3.556 -4.665 -0.348 "HO3'" IOO 50 IOO HOP3 H18 H 0 0 N Y N 3.518 -16.603 0.908 -5.661 4.007 -0.671 HOP3 IOO 51 IOO HOP2 H19 H 0 0 N N N 5.593 -19.372 1.543 -7.150 1.228 -0.837 HOP2 IOO 52 # 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 IOO O1 P DOUB N N 1 IOO P OP3 SING N N 2 IOO P "O5'" SING N N 3 IOO P OP2 SING N N 4 IOO "O5'" "C5'" SING N N 5 IOO "C5'" "C4'" SING N N 6 IOO "O3'" "C3'" SING N N 7 IOO "C3'" "C4'" SING N N 8 IOO "C3'" C3 SING N N 9 IOO "C4'" "O4'" SING N N 10 IOO "O4'" C2 SING N N 11 IOO C3 "O2'" SING N N 12 IOO C3 C2 SING N N 13 IOO C2 N9 SING N N 14 IOO C8 N9 SING Y N 15 IOO C8 N7 DOUB Y N 16 IOO N9 "C1'" SING Y N 17 IOO C14 C13 DOUB Y N 18 IOO C14 C12 SING Y N 19 IOO C13 C15 SING Y N 20 IOO N7 C11 SING N N 21 IOO N7 C1 SING Y N 22 IOO "C1'" N3 SING N N 23 IOO "C1'" C1 DOUB Y N 24 IOO C11 C12 SING N N 25 IOO C12 C16 DOUB Y N 26 IOO N3 "C2'" DOUB N N 27 IOO C1 C6 SING N N 28 IOO C15 F1 SING N N 29 IOO C15 C17 DOUB Y N 30 IOO C16 C17 SING Y N 31 IOO "C2'" N1 SING N N 32 IOO "C2'" N4 SING N N 33 IOO C17 F2 SING N N 34 IOO C6 N4 SING N N 35 IOO C6 OP1 DOUB N N 36 IOO N1 H21 SING N N 37 IOO N1 H22 SING N N 38 IOO N4 H1 SING N N 39 IOO C2 "H1'" SING N N 40 IOO C3 "H2'" SING N N 41 IOO "C3'" "H3'" SING N N 42 IOO "C4'" "H4'" SING N N 43 IOO "C5'" "H5'" SING N N 44 IOO "C5'" "H5''" SING N N 45 IOO C8 H8 SING N N 46 IOO C11 H11 SING N N 47 IOO C11 H12 SING N N 48 IOO C13 H13 SING N N 49 IOO C14 H14 SING N N 50 IOO C16 H15 SING N N 51 IOO "O2'" "HO2'" SING N N 52 IOO "O3'" "HO3'" SING N N 53 IOO OP3 HOP3 SING N N 54 IOO OP2 HOP2 SING N N 55 # 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 IOO InChI InChI 1.06 "InChI=1S/C17H18F2N5O8P/c18-8-2-1-7(3-9(8)19)4-23-6-24(14-11(23)15(27)22-17(20)21-14)16-13(26)12(25)10(32-16)5-31-33(28,29)30/h1-3,6,10,12-13,16,25-26H,4-5H2,(H4-,20,21,22,27,28,29,30)/p+1/t10-,12-,13-,16-/m1/s1" IOO InChIKey InChI 1.06 BIHPVAUGYOUOAQ-XNIJJKJLSA-O IOO SMILES_CANONICAL CACTVS 3.385 "NC1=Nc2n(c[n+](Cc3ccc(F)c(F)c3)c2C(=O)N1)[C@@H]4O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]4O" IOO SMILES CACTVS 3.385 "NC1=Nc2n(c[n+](Cc3ccc(F)c(F)c3)c2C(=O)N1)[CH]4O[CH](CO[P](O)(O)=O)[CH](O)[CH]4O" IOO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C[n+]2cn(c3c2C(=O)NC(=N3)N)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)F)F" IOO SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C[n+]2cn(c3c2C(=O)NC(=N3)N)C4C(C(C(O4)COP(=O)(O)O)O)O)F)F" # _pdbx_chem_comp_identifier.comp_id IOO _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[[3,4-bis(fluoranyl)phenyl]methyl]-6-oxidanylidene-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id IOO _pdbx_chem_comp_synonyms.name "[(2R,3S,4R,5R)-5-[2-azanyl-7-[[3,4-bis(fluoranyl)phenyl]methyl]-6-oxidanylidene-1H-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site IOO "Create component" 2022-04-04 PDBE IOO "Modify linking type" 2022-04-05 PDBE IOO "Initial release" 2022-04-13 RCSB IOO "Modify descriptor" 2022-08-22 RCSB #