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 
# 
