data_XB9 # _chem_comp.id XB9 _chem_comp.name N-carbamoyl-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C6 H13 N2 O7 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-10-27 _chem_comp.pdbx_modified_date 2024-03-15 _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 256.150 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XB9 _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 8UJT _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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 XB9 N2 N1 N 0 1 N N N N N N -41.598 -5.212 4.680 -4.827 2.202 -0.602 N2 XB9 1 XB9 N1 N2 N 0 1 N N N N N N -39.418 -4.780 5.049 -3.316 0.424 -0.568 N1 XB9 2 XB9 C2 C1 C 0 1 N N N N N N -40.659 -4.320 4.969 -3.966 1.415 0.072 C2 XB9 3 XB9 O1 O1 O 0 1 N N N N N N -40.920 -3.140 5.160 -3.776 1.599 1.259 O1 XB9 4 XB9 "C1'" C2 C 0 1 N N R N N N -39.142 -6.192 4.830 -2.380 -0.432 0.165 "C1'" XB9 5 XB9 "C2'" C3 C 0 1 N N N N N N -37.750 -6.216 4.238 -2.374 -1.857 -0.431 "C2'" XB9 6 XB9 "C3'" C4 C 0 1 N N S N N N -36.997 -7.234 5.065 -0.897 -2.299 -0.336 "C3'" XB9 7 XB9 "C4'" C5 C 0 1 N N R N N N -37.759 -7.369 6.360 -0.184 -1.088 0.307 "C4'" XB9 8 XB9 "C5'" C6 C 0 1 N N N N N N -37.098 -6.554 7.468 1.206 -0.901 -0.305 "C5'" XB9 9 XB9 "O3'" O2 O 0 1 N N N N N N -37.047 -8.475 4.375 -0.772 -3.453 0.498 "O3'" XB9 10 XB9 "O4'" O3 O 0 1 N N N N N N -39.067 -6.863 6.094 -1.026 0.043 -0.004 "O4'" XB9 11 XB9 "O5'" O4 O 0 1 N N N N N N -37.191 -5.156 7.168 1.891 0.148 0.382 "O5'" XB9 12 XB9 OP1 O5 O 0 1 N N N N N N -36.551 -2.682 7.389 4.292 -0.552 0.040 OP1 XB9 13 XB9 OP2 O6 O 0 1 N N N N N N -34.771 -4.401 7.586 3.387 1.248 -1.479 OP2 XB9 14 XB9 P P1 P 0 1 N N N N N N -36.220 -4.082 7.867 3.384 0.616 0.001 P XB9 15 XB9 O2 O7 O 0 1 N Y N N N N -36.441 -4.315 9.444 3.886 1.722 1.058 O2 XB9 16 XB9 H1 H1 H 0 1 N N N N N N -42.554 -4.927 4.612 -4.979 2.056 -1.549 H1 XB9 17 XB9 H2 H2 H 0 1 N N N N N N -41.349 -6.169 4.530 -5.299 2.913 -0.140 H2 XB9 18 XB9 H3 H3 H 0 1 N N N N N N -38.668 -4.154 5.261 -3.468 0.277 -1.515 H3 XB9 19 XB9 H4 H4 H 0 1 N N N N N N -39.872 -6.656 4.150 -2.643 -0.462 1.222 H4 XB9 20 XB9 H5 H5 H 0 1 N N N N N N -37.783 -6.522 3.182 -3.010 -2.520 0.156 H5 XB9 21 XB9 H6 H6 H 0 1 N N N N N N -37.278 -5.226 4.318 -2.700 -1.837 -1.471 H6 XB9 22 XB9 H7 H7 H 0 1 N N N N N N -35.965 -6.902 5.250 -0.492 -2.497 -1.328 H7 XB9 23 XB9 H8 H8 H 0 1 N N N N N N -37.801 -8.427 6.658 -0.108 -1.221 1.386 H8 XB9 24 XB9 H9 H9 H 0 1 N N N N N N -37.606 -6.757 8.422 1.772 -1.828 -0.210 H9 XB9 25 XB9 H10 H10 H 0 1 N N N N N N -36.039 -6.840 7.549 1.107 -0.641 -1.359 H10 XB9 26 XB9 H11 H11 H 0 1 N N N N N N -36.580 -9.135 4.874 -1.251 -4.227 0.171 H11 XB9 27 XB9 H12 H12 H 0 1 N N N N N N -34.358 -3.656 7.165 2.812 2.020 -1.579 H12 XB9 28 XB9 H13 H13 H 0 1 N N N N N N -36.755 -3.512 9.842 4.780 2.050 0.890 H13 XB9 29 # 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 XB9 "C2'" "C1'" SING N N 1 XB9 "C2'" "C3'" SING N N 2 XB9 "O3'" "C3'" SING N N 3 XB9 N2 C2 SING N N 4 XB9 "C1'" N1 SING N N 5 XB9 "C1'" "O4'" SING N N 6 XB9 C2 N1 SING N N 7 XB9 C2 O1 DOUB N N 8 XB9 "C3'" "C4'" SING N N 9 XB9 "O4'" "C4'" SING N N 10 XB9 "C4'" "C5'" SING N N 11 XB9 "O5'" "C5'" SING N N 12 XB9 "O5'" P SING N N 13 XB9 OP1 P DOUB N N 14 XB9 OP2 P SING N N 15 XB9 P O2 SING N N 16 XB9 N2 H1 SING N N 17 XB9 N2 H2 SING N N 18 XB9 N1 H3 SING N N 19 XB9 "C1'" H4 SING N N 20 XB9 "C2'" H5 SING N N 21 XB9 "C2'" H6 SING N N 22 XB9 "C3'" H7 SING N N 23 XB9 "C4'" H8 SING N N 24 XB9 "C5'" H9 SING N N 25 XB9 "C5'" H10 SING N N 26 XB9 "O3'" H11 SING N N 27 XB9 OP2 H12 SING N N 28 XB9 O2 H13 SING N N 29 # 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 XB9 SMILES ACDLabs 12.01 "OC1CC(NC(=O)N)OC1COP(=O)(O)O" XB9 InChI InChI 1.06 "InChI=1S/C6H13N2O7P/c7-6(10)8-5-1-3(9)4(15-5)2-14-16(11,12)13/h3-5,9H,1-2H2,(H3,7,8,10)(H2,11,12,13)/t3-,4+,5+/m0/s1" XB9 InChIKey InChI 1.06 HSXUVWHNWPQKRN-VPENINKCSA-N XB9 SMILES_CANONICAL CACTVS 3.385 "NC(=O)N[C@H]1C[C@H](O)[C@@H](CO[P](O)(O)=O)O1" XB9 SMILES CACTVS 3.385 "NC(=O)N[CH]1C[CH](O)[CH](CO[P](O)(O)=O)O1" XB9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1[C@@H]([C@H](O[C@H]1NC(=O)N)COP(=O)(O)O)O" XB9 SMILES "OpenEye OEToolkits" 2.0.7 "C1C(C(OC1NC(=O)N)COP(=O)(O)O)O" # 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 XB9 "SYSTEMATIC NAME" ACDLabs 12.01 N-carbamoyl-2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosylamine XB9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-(aminocarbonylamino)-3-oxidanyl-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 XB9 "Create component" 2023-10-27 RCSB XB9 "Initial release" 2024-03-20 RCSB #