data_N5I # _chem_comp.id N5I _chem_comp.name "1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-5-NITRO-1H-INDOLE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C13 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-03-21 _chem_comp.pdbx_modified_date 2021-03-01 _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 358.241 _chem_comp.one_letter_code N _chem_comp.three_letter_code N5I _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits" _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 N5I O3P O3P O 0 1 N Y N -20.164 64.193 45.222 0.339 -0.227 -4.868 O3P N5I 1 N5I OR2 OR2 O 0 1 N N N -11.094 68.879 41.671 2.199 6.489 4.264 OR2 N5I 2 N5I NRO NRO N 1 1 N N N -11.577 67.770 41.849 1.888 6.522 3.049 NRO N5I 3 N5I OR1 OR1 O -1 1 N N N -10.832 66.803 41.911 1.577 7.590 2.470 OR1 N5I 4 N5I CZ3 CZ3 C 0 1 Y N N -13.021 67.604 41.987 1.888 5.311 2.306 CZ3 N5I 5 N5I CE3 CE3 C 0 1 Y N N -13.527 66.329 42.191 1.543 5.334 0.950 CE3 N5I 6 N5I CD2 CD2 C 0 1 Y N N -14.915 66.184 42.318 1.545 4.128 0.220 CD2 N5I 7 N5I CH2 CH2 C 0 1 Y N N -13.844 68.740 41.911 2.232 4.116 2.935 CH2 N5I 8 N5I CZ2 CZ2 C 0 1 Y N N -15.206 68.628 42.032 2.241 2.908 2.231 CZ2 N5I 9 N5I CE2 CE2 C 0 1 Y N N -15.733 67.338 42.237 1.893 2.946 0.876 CE2 N5I 10 N5I NE1 NE1 N 0 1 Y N N -17.026 66.918 42.395 1.818 1.923 -0.049 NE1 N5I 11 N5I CD1 CD1 C 0 1 Y N N -17.046 65.558 42.568 1.433 2.429 -1.266 CD1 N5I 12 N5I CG CG C 0 1 Y N N -15.780 65.064 42.539 1.257 3.787 -1.131 CG N5I 13 N5I "C1'" C1* C 0 1 N N R -18.261 67.759 42.392 2.101 0.516 0.211 "C1'" N5I 14 N5I "O4'" O4* O 0 1 N N N -19.381 66.974 42.806 2.678 -0.093 -0.958 "O4'" N5I 15 N5I "C4'" C4* C 0 1 N N R -20.259 66.740 41.703 2.156 -1.432 -1.088 "C4'" N5I 16 N5I "C3'" C3* C 0 1 N N S -19.515 67.224 40.464 1.309 -1.697 0.152 "C3'" N5I 17 N5I "O3'" O3* O 0 1 N N N -20.441 67.731 39.498 2.127 -2.250 1.180 "O3'" N5I 18 N5I "C2'" C2* C 0 1 N N N -18.637 68.330 41.029 0.878 -0.312 0.578 "C2'" N5I 19 N5I "C5'" C5* C 0 1 N N N -20.649 65.266 41.665 1.348 -1.500 -2.377 "C5'" N5I 20 N5I "O5'" O5* O 0 1 N N N -21.014 64.815 42.966 2.211 -1.232 -3.468 "O5'" N5I 21 N5I P P P 0 1 N N N -20.212 63.635 43.716 1.592 -1.245 -4.964 P N5I 22 N5I O2P O2P O 0 1 N N N -21.078 62.391 43.723 0.886 -2.697 -5.051 O2P N5I 23 N5I O1P O1P O 0 1 N N N -18.806 63.542 43.147 2.575 -0.951 -6.059 O1P N5I 24 N5I HOP3 3HOP H 0 0 N N N -20.155 63.463 45.830 -0.163 -0.014 -5.684 HOP3 N5I 25 N5I HE3 HE3 H 0 1 N N N -12.871 65.473 42.250 1.274 6.266 0.460 HE3 N5I 26 N5I HH2 HH2 H 0 1 N N N -13.400 69.712 41.756 2.499 4.107 3.990 HH2 N5I 27 N5I HZ2 HZ2 H 0 1 N N N -15.848 69.494 41.972 2.510 1.980 2.725 HZ2 N5I 28 N5I HD1 HD1 H 0 1 N N N -17.938 64.965 42.707 1.317 1.781 -2.124 HD1 N5I 29 N5I HG HG H 0 1 N N N -15.485 64.032 42.659 0.954 4.461 -1.920 HG N5I 30 N5I "H1'" H1* H 0 1 N N N -18.031 68.592 43.072 2.853 0.503 1.007 "H1'" N5I 31 N5I "H4'" H4* H 0 1 N N N -21.211 67.286 41.777 3.008 -2.117 -1.157 "H4'" N5I 32 N5I "H3'" H3* H 0 1 N N N -18.944 66.442 39.943 0.475 -2.383 -0.018 "H3'" N5I 33 N5I H3T H3T H 0 1 N Y N -21.293 67.843 39.904 2.928 -1.706 1.218 H3T N5I 34 N5I "H2'1" 1H2* H 0 0 N N N -19.176 69.285 41.114 0.008 0.008 -0.009 "H2'1" N5I 35 N5I "H2'2" 2H2* H 0 0 N N N -17.771 68.576 40.397 0.635 -0.225 1.641 "H2'2" N5I 36 N5I "H5'1" 1H5* H 0 0 N N N -21.504 65.136 40.985 0.551 -0.756 -2.359 "H5'1" N5I 37 N5I "H5'2" 2H5* H 0 0 N N N -19.789 64.678 41.311 0.917 -2.495 -2.497 "H5'2" N5I 38 N5I HOP2 2HOP H 0 0 N N N -21.259 62.126 42.829 0.508 -2.990 -5.907 HOP2 N5I 39 # # 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 N5I O3P P SING N N 1 N5I O3P HOP3 SING N N 2 N5I OR2 NRO DOUB N N 3 N5I NRO OR1 SING N N 4 N5I NRO CZ3 SING N N 5 N5I CZ3 CH2 DOUB Y N 6 N5I CZ3 CE3 SING Y N 7 N5I CE3 CD2 DOUB Y N 8 N5I CE3 HE3 SING N N 9 N5I CD2 CE2 SING Y N 10 N5I CD2 CG SING Y N 11 N5I CH2 CZ2 SING Y N 12 N5I CH2 HH2 SING N N 13 N5I CZ2 CE2 DOUB Y N 14 N5I CZ2 HZ2 SING N N 15 N5I CE2 NE1 SING Y N 16 N5I NE1 "C1'" SING N N 17 N5I NE1 CD1 SING Y N 18 N5I CD1 CG DOUB Y N 19 N5I CD1 HD1 SING N N 20 N5I CG HG SING N N 21 N5I "C1'" "C2'" SING N N 22 N5I "C1'" "O4'" SING N N 23 N5I "C1'" "H1'" SING N N 24 N5I "O4'" "C4'" SING N N 25 N5I "C4'" "C3'" SING N N 26 N5I "C4'" "C5'" SING N N 27 N5I "C4'" "H4'" SING N N 28 N5I "C3'" "O3'" SING N N 29 N5I "C3'" "C2'" SING N N 30 N5I "C3'" "H3'" SING N N 31 N5I "O3'" H3T SING N N 32 N5I "C2'" "H2'1" SING N N 33 N5I "C2'" "H2'2" SING N N 34 N5I "C5'" "O5'" SING N N 35 N5I "C5'" "H5'1" SING N N 36 N5I "C5'" "H5'2" SING N N 37 N5I "O5'" P SING N N 38 N5I P O1P DOUB N N 39 N5I P O2P SING N N 40 N5I O2P HOP2 SING N N 41 # # 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 N5I SMILES ACDLabs 10.04 "[O-][N+](=O)c2cc1ccn(c1cc2)C3OC(C(O)C3)COP(=O)(O)O" N5I SMILES_CANONICAL CACTVS 3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O" N5I SMILES CACTVS 3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2ccc3cc(ccc23)[N+]([O-])=O" N5I SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1cc2c(ccn2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)cc1[N+](=O)[O-]" N5I SMILES "OpenEye OEToolkits" 1.5.0 "c1cc2c(ccn2C3CC(C(O3)COP(=O)(O)O)O)cc1[N+](=O)[O-]" N5I InChI InChI 1.03 "InChI=1S/C13H15N2O8P/c16-11-6-13(23-12(11)7-22-24(19,20)21)14-4-3-8-5-9(15(17)18)1-2-10(8)14/h1-5,11-13,16H,6-7H2,(H2,19,20,21)/t11-,12+,13+/m0/s1" N5I InChIKey InChI 1.03 FQCJFJRLZCIFHB-YNEHKIRRSA-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 N5I "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-nitro-1H-indole" N5I "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-nitroindol-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 N5I "Create component" 2007-03-21 PDBJ N5I "Modify descriptor" 2011-06-04 RCSB N5I "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id N5I _pdbx_chem_comp_synonyms.name "5-NITRO-1-INDOLYL-2'-DEOXYRIBOSIDE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##