data_PMO # _chem_comp.id PMO _chem_comp.name "N1-(5'-PHOSPHO-ALPHA-RIBOSYL)-5-METHOXYBENZIMIDAZOLE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H17 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "PHOSPORIC ACID MONO-[3,4-DIHYDROXY-5-(5-METHOXY-BENZOIMIDAZOL-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-07-09 _chem_comp.pdbx_modified_date 2020-06-17 _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 360.256 _chem_comp.one_letter_code ? _chem_comp.three_letter_code PMO _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1JHQ _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 PMO N3 N3 N 0 1 Y N N 56.299 41.401 14.042 -0.968 2.003 2.446 N3 PMO 1 PMO N1 N1 N 0 1 Y N N 56.638 40.834 11.882 -0.090 0.273 1.448 N1 PMO 2 PMO C2 C2 C 0 1 Y N N 55.853 40.717 12.982 -0.567 1.538 1.299 C2 PMO 3 PMO C7A C7A C 0 1 Y N N 57.700 41.668 12.327 -0.210 -0.056 2.785 C7A PMO 4 PMO C3A C3A C 0 1 Y N N 57.465 42.033 13.640 -0.776 1.067 3.411 C3A PMO 5 PMO C4 C4 C 0 1 Y N N 58.319 42.908 14.314 -1.027 1.037 4.785 C4 PMO 6 PMO C5 C5 C 0 1 Y N N 59.462 43.381 13.692 -0.708 -0.090 5.514 C5 PMO 7 PMO C6 C6 C 0 1 Y N N 59.705 43.018 12.345 -0.148 -1.200 4.887 C6 PMO 8 PMO C7 C7 C 0 1 Y N N 58.838 42.162 11.677 0.099 -1.184 3.532 C7 PMO 9 PMO O10 O10 O 0 1 N N N 60.409 44.257 14.157 -0.947 -0.120 6.853 O10 PMO 10 PMO C11 C11 C 0 1 N N N 60.104 44.698 15.466 -0.524 -1.402 7.320 C11 PMO 11 PMO P P P 0 1 N N N 59.397 39.331 6.103 -0.986 -0.232 -5.110 P PMO 12 PMO O1P O1P O 0 1 N N N 58.998 38.126 5.320 -1.028 -1.712 -5.107 O1P PMO 13 PMO O2P O2P O 0 1 N N N 59.628 40.489 5.208 -2.393 0.342 -5.641 O2P PMO 14 PMO O3P O3P O 0 1 N N N 60.508 39.189 7.099 0.198 0.268 -6.078 O3P PMO 15 PMO "O5'" O5* O 0 1 N N N 58.028 39.619 6.929 -0.719 0.300 -3.614 "O5'" PMO 16 PMO "C5'" C5* C 0 1 N N N 57.542 38.674 7.890 0.536 -0.241 -3.201 "C5'" PMO 17 PMO "C4'" C4* C 0 1 N N R 58.055 39.057 9.267 0.852 0.228 -1.780 "C4'" PMO 18 PMO "O4'" O4* O 0 1 N N N 57.509 40.370 9.642 -0.152 -0.239 -0.865 "O4'" PMO 19 PMO "C3'" C3* C 0 1 N N S 57.622 38.125 10.389 2.177 -0.403 -1.283 "C3'" PMO 20 PMO "O3'" O3* O 0 1 N N N 58.400 38.269 11.586 3.302 0.383 -1.679 "O3'" PMO 21 PMO "C2'" C2* C 0 1 N N R 56.207 38.690 10.608 1.970 -0.353 0.256 "C2'" PMO 22 PMO "O2'" O2* O 0 1 N N N 55.752 38.244 11.909 2.343 0.923 0.778 "O2'" PMO 23 PMO "C1'" C1* C 0 1 N N S 56.420 40.211 10.551 0.449 -0.581 0.388 "C1'" PMO 24 PMO H21 1H2 H 0 1 N N N 54.928 40.115 13.012 -0.606 2.078 0.365 H21 PMO 25 PMO H41 1H4 H 0 1 N N N 58.089 43.227 15.344 -1.466 1.893 5.275 H41 PMO 26 PMO H61 1H6 H 0 1 N N N 60.584 43.408 11.806 0.093 -2.079 5.467 H61 PMO 27 PMO H71 1H7 H 0 1 N N N 59.052 41.875 10.633 0.534 -2.047 3.051 H71 PMO 28 PMO H111 1H11 H 0 0 N N N 60.874 45.410 15.844 -0.697 -1.473 8.394 H111 PMO 29 PMO H112 2H11 H 0 0 N N N 59.079 45.135 15.521 -1.090 -2.181 6.808 H112 PMO 30 PMO H113 3H11 H 0 0 N N N 59.962 43.840 16.164 0.538 -1.532 7.114 H113 PMO 31 PMO HOP2 2HOP H 0 0 N N N 59.882 41.256 5.706 -2.514 0.000 -6.538 HOP2 PMO 32 PMO HOP3 3HOP H 0 0 N N N 60.762 39.956 7.597 0.190 1.235 -6.051 HOP3 PMO 33 PMO "H5'1" 1H5* H 0 0 N N N 56.431 38.575 7.863 1.319 0.098 -3.879 "H5'1" PMO 34 PMO "H5'2" 2H5* H 0 0 N N N 57.799 37.623 7.618 0.486 -1.330 -3.221 "H5'2" PMO 35 PMO "H4'" H4* H 0 1 N N N 59.165 39.025 9.171 0.916 1.316 -1.747 "H4'" PMO 36 PMO "H3'" H3* H 0 1 N N N 57.714 37.040 10.148 2.277 -1.431 -1.632 "H3'" PMO 37 PMO "HO3'" *HO3 H 0 0 N N N 58.129 37.687 12.286 4.089 -0.064 -1.340 "HO3'" PMO 38 PMO "H2'" H2* H 0 1 N N N 55.439 38.365 9.866 2.528 -1.150 0.748 "H2'" PMO 39 PMO "HO2'" *HO2 H 0 0 N N N 54.878 38.592 12.044 3.283 1.041 0.583 "HO2'" PMO 40 PMO "H1'" H1* H 0 1 N N N 55.510 40.752 10.201 0.251 -1.627 0.620 "H1'" PMO 41 # # 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 PMO N3 C2 DOUB Y N 1 PMO N3 C3A SING Y N 2 PMO N1 C2 SING Y N 3 PMO N1 C7A SING Y N 4 PMO N1 "C1'" SING N N 5 PMO C2 H21 SING N N 6 PMO C7A C3A DOUB Y N 7 PMO C7A C7 SING Y N 8 PMO C3A C4 SING Y N 9 PMO C4 C5 DOUB Y N 10 PMO C4 H41 SING N N 11 PMO C5 C6 SING Y N 12 PMO C5 O10 SING N N 13 PMO C6 C7 DOUB Y N 14 PMO C6 H61 SING N N 15 PMO C7 H71 SING N N 16 PMO O10 C11 SING N N 17 PMO C11 H111 SING N N 18 PMO C11 H112 SING N N 19 PMO C11 H113 SING N N 20 PMO P O1P DOUB N N 21 PMO P O2P SING N N 22 PMO P O3P SING N N 23 PMO P "O5'" SING N N 24 PMO O2P HOP2 SING N N 25 PMO O3P HOP3 SING N N 26 PMO "O5'" "C5'" SING N N 27 PMO "C5'" "C4'" SING N N 28 PMO "C5'" "H5'1" SING N N 29 PMO "C5'" "H5'2" SING N N 30 PMO "C4'" "O4'" SING N N 31 PMO "C4'" "C3'" SING N N 32 PMO "C4'" "H4'" SING N N 33 PMO "O4'" "C1'" SING N N 34 PMO "C3'" "O3'" SING N N 35 PMO "C3'" "C2'" SING N N 36 PMO "C3'" "H3'" SING N N 37 PMO "O3'" "HO3'" SING N N 38 PMO "C2'" "O2'" SING N N 39 PMO "C2'" "C1'" SING N N 40 PMO "C2'" "H2'" SING N N 41 PMO "O2'" "HO2'" SING N N 42 PMO "C1'" "H1'" SING N N 43 # # 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 PMO SMILES ACDLabs 10.04 "O=P(O)(O)OCC3OC(n2cnc1cc(OC)ccc12)C(O)C3O" PMO SMILES_CANONICAL CACTVS 3.341 "COc1ccc2n(cnc2c1)[C@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O" PMO SMILES CACTVS 3.341 "COc1ccc2n(cnc2c1)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O" PMO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "COc1ccc2c(c1)ncn2[C@@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O" PMO SMILES "OpenEye OEToolkits" 1.5.0 "COc1ccc2c(c1)ncn2C3C(C(C(O3)COP(=O)(O)O)O)O" PMO InChI InChI 1.03 "InChI=1S/C13H17N2O8P/c1-21-7-2-3-9-8(4-7)14-6-15(9)13-12(17)11(16)10(23-13)5-22-24(18,19)20/h2-4,6,10-13,16-17H,5H2,1H3,(H2,18,19,20)/t10-,11-,12-,13+/m1/s1" PMO InChIKey InChI 1.03 VYUPJUKSTVHSQI-LPWJVIDDSA-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 PMO "SYSTEMATIC NAME" ACDLabs 10.04 "5-methoxy-1-(5-O-phosphono-alpha-D-ribofuranosyl)-1H-benzimidazole" PMO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5S)-3,4-dihydroxy-5-(5-methoxybenzimidazol-1-yl)oxolan-2-yl]methyl dihydrogen phosphate" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site PMO "Create component" 2001-07-09 RCSB PMO "Modify descriptor" 2011-06-04 RCSB PMO "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PMO _pdbx_chem_comp_synonyms.name "PHOSPORIC ACID MONO-[3,4-DIHYDROXY-5-(5-METHOXY-BENZOIMIDAZOL-1-YL)-TETRAHYDRO-FURAN-2-YLMETHYL] ESTER" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##