data_OWR
# 
_chem_comp.id                                    OWR 
_chem_comp.name                                  "1-[2-deoxy-5-O-(dihydroxyphosphanyl)-beta-D-erythro-pentofuranosyl]-1H-naphtho[2,3-d]imidazole" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C16 H17 N2 O6 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-05-18 
_chem_comp.pdbx_modified_date                    2022-08-26 
_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                        364.290 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     OWR 
_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        8CTZ 
_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 
OWR C1    C1  C 0 1 Y N N 3.367 35.620 14.066 5.211  0.824  0.145  C1    OWR 1  
OWR "C1'" C2  C 0 1 N N R 6.084 39.537 15.891 0.141  -0.710 -0.260 "C1'" OWR 2  
OWR C10   C3  C 0 1 Y N N 2.777 35.338 16.371 5.590  -1.102 -1.359 C10   OWR 3  
OWR C11   C4  C 0 1 Y N N 1.982 34.236 16.048 6.918  -0.806 -1.333 C11   OWR 4  
OWR C12   C5  C 0 1 Y N N 1.880 33.819 14.726 7.414  0.269  -0.598 C12   OWR 5  
OWR C13   C6  C 0 1 Y N N 2.572 34.516 13.734 6.596  1.075  0.129  C13   OWR 6  
OWR C2    C7  C 0 1 Y N N 3.469 36.032 15.382 4.690  -0.306 -0.628 C2    OWR 7  
OWR "C2'" C8  C 0 1 N N N 7.538 39.276 16.284 0.062  -1.972 0.622  "C2'" OWR 8  
OWR C3    C9  C 0 1 Y N N 4.265 37.138 15.680 3.314  -0.568 -0.621 C3    OWR 9  
OWR "C3'" C10 C 0 1 N N S 8.013 40.647 16.771 -1.429 -2.053 1.033  "C3'" OWR 10 
OWR C4    C11 C 0 1 Y N N 4.912 37.776 14.693 2.472  0.240  0.111  C4    OWR 11 
OWR "C4'" C12 C 0 1 N N R 6.840 41.601 16.572 -2.115 -1.193 -0.058 "C4'" OWR 12 
OWR C5    C13 C 0 1 Y N N 4.811 37.373 13.419 2.969  1.332  0.859  C5    OWR 13 
OWR "C5'" C14 C 0 1 N N N 7.319 42.932 15.998 -3.448 -0.640 0.450  "C5'" OWR 14 
OWR C6    C15 C 0 1 Y N N 4.062 36.316 13.089 4.326  1.619  0.880  C6    OWR 15 
OWR C8    C16 C 0 1 Y N N 6.120 39.108 13.466 0.811  1.279  1.138  C8    OWR 16 
OWR N7    N1  N 0 1 Y N N 5.550 38.209 12.669 1.896  1.918  1.458  N7    OWR 17 
OWR N9    N2  N 0 1 Y N N 5.724 38.831 14.701 1.101  0.238  0.312  N9    OWR 18 
OWR "O3'" O1  O 0 1 N N N 8.384 40.615 18.158 -1.897 -3.403 0.988  "O3'" OWR 19 
OWR "O4'" O2  O 0 1 N N N 5.978 40.944 15.638 -1.171 -0.125 -0.287 "O4'" OWR 20 
OWR "O5'" O3  O 0 1 N N N 8.171 42.667 14.877 -4.112 0.049  -0.611 "O5'" OWR 21 
OWR OP3   O4  O 0 1 N Y N 9.203 45.021 14.785 -5.928 1.546  -1.784 OP3   OWR 22 
OWR OP2   O5  O 0 1 N N N 9.472 43.468 12.797 -6.664 -0.357 -0.126 OP2   OWR 23 
OWR P     P1  P 0 1 N N N 8.591 43.922 13.945 -5.546 0.760  -0.431 P     OWR 24 
OWR H1    H1  H 0 1 N N N 5.428 39.246 16.725 0.447  -0.983 -1.270 H1    OWR 25 
OWR H2    H2  H 0 1 N N N 2.856 35.656 17.400 5.231  -1.940 -1.937 H2    OWR 26 
OWR H3    H3  H 0 1 N N N 1.447 33.709 16.824 7.605  -1.420 -1.896 H3    OWR 27 
OWR H4    H4  H 0 1 N N N 1.272 32.965 14.469 8.476  0.466  -0.607 H4    OWR 28 
OWR H5    H5  H 0 1 N N N 2.494 34.202 12.704 7.005  1.903  0.690  H5    OWR 29 
OWR H6    H6  H 0 1 N N N 7.602 38.527 17.087 0.349  -2.855 0.052  H6    OWR 30 
OWR H7    H7  H 0 1 N N N 8.127 38.938 15.419 0.695  -1.862 1.503  H7    OWR 31 
OWR H8    H8  H 0 1 N N N 4.360 37.479 16.700 2.915  -1.397 -1.186 H8    OWR 32 
OWR H9    H9  H 0 1 N N N 8.860 40.978 16.152 -1.584 -1.623 2.023  H9    OWR 33 
OWR H10   H10 H 0 1 N N N 6.330 41.771 17.532 -2.264 -1.775 -0.968 H10   OWR 34 
OWR H11   H11 H 0 1 N N N 7.879 43.487 16.766 -4.074 -1.462 0.797  H11   OWR 35 
OWR H12   H12 H 0 1 N N N 6.454 43.528 15.673 -3.264 0.050  1.273  H12   OWR 36 
OWR H13   H13 H 0 1 N N N 3.998 36.003 12.057 4.696  2.455  1.454  H13   OWR 37 
OWR H14   H14 H 0 1 N N N 6.779 39.909 13.165 -0.181 1.538  1.480  H14   OWR 38 
OWR H15   H15 H 0 1 N N N 8.673 41.478 18.429 -1.434 -4.000 1.592  H15   OWR 39 
OWR H16   H16 H 0 1 N Y N 8.631 45.779 14.781 -6.781 1.999  -1.747 H16   OWR 40 
OWR H17   H17 H 0 1 N N N 9.013 43.595 11.975 -6.759 -1.020 -0.824 H17   OWR 41 
OWR OP1   O6  O 0 1 N N N 7.202 44.453 13.363 -5.484 1.717  0.695  OP1   OWR 42 
# 
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 
OWR N7    C5    SING Y N 1  
OWR N7    C8    DOUB Y N 2  
OWR OP2   P     SING N N 3  
OWR C6    C5    DOUB Y N 4  
OWR C6    C1    SING Y N 5  
OWR C5    C4    SING Y N 6  
OWR C8    N9    SING Y N 7  
OWR C13   C1    DOUB Y N 8  
OWR C13   C12   SING Y N 9  
OWR P     OP3   SING N N 10 
OWR P     "O5'" SING N N 11 
OWR C1    C2    SING Y N 12 
OWR C4    N9    SING Y N 13 
OWR C4    C3    DOUB Y N 14 
OWR N9    "C1'" SING N N 15 
OWR C12   C11   DOUB Y N 16 
OWR "O5'" "C5'" SING N N 17 
OWR C2    C3    SING Y N 18 
OWR C2    C10   DOUB Y N 19 
OWR "O4'" "C1'" SING N N 20 
OWR "O4'" "C4'" SING N N 21 
OWR "C1'" "C2'" SING N N 22 
OWR "C5'" "C4'" SING N N 23 
OWR C11   C10   SING Y N 24 
OWR "C2'" "C3'" SING N N 25 
OWR "C4'" "C3'" SING N N 26 
OWR "C3'" "O3'" SING N N 27 
OWR "C1'" H1    SING N N 28 
OWR C10   H2    SING N N 29 
OWR C11   H3    SING N N 30 
OWR C12   H4    SING N N 31 
OWR C13   H5    SING N N 32 
OWR "C2'" H6    SING N N 33 
OWR "C2'" H7    SING N N 34 
OWR C3    H8    SING N N 35 
OWR "C3'" H9    SING N N 36 
OWR "C4'" H10   SING N N 37 
OWR "C5'" H11   SING N N 38 
OWR "C5'" H12   SING N N 39 
OWR C6    H13   SING N N 40 
OWR C8    H14   SING N N 41 
OWR "O3'" H15   SING N N 42 
OWR OP3   H16   SING N N 43 
OWR OP2   H17   SING N N 44 
OWR P     OP1   DOUB N N 45 
# 
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 
OWR SMILES           ACDLabs              12.01 "O=P(O)(O)OCC1OC(CC1O)n1cnc2cc3ccccc3cc21"                                                                                                                    
OWR InChI            InChI                1.03  "InChI=1S/C16H17N2O6P/c19-14-7-16(24-15(14)8-23-25(20,21)22)18-9-17-12-5-10-3-1-2-4-11(10)6-13(12)18/h1-6,9,14-16,19H,7-8H2,(H2,20,21,22)/t14-,15+,16+/m0/s1" 
OWR InChIKey         InChI                1.03  HNXFPKXDQSBACZ-ARFHVFGLSA-N                                                                                                                                   
OWR SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3cc4ccccc4cc23"                                                                                                    
OWR SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3cc4ccccc4cc23"                                                                                                         
OWR SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2cc3c(cc2c1)ncn3[C@H]4C[C@@H]([C@H](O4)COP(=O)(O)O)O"                                                                                                   
OWR SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2cc3c(cc2c1)ncn3C4CC(C(O4)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 
OWR "SYSTEMATIC NAME" ACDLabs              12.01 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-naphtho[2,3-d]imidazole"                  
OWR "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{S},5~{R})-5-benzo[f]benzimidazol-3-yl-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 
OWR "Create component" 2022-05-18 RCSB 
OWR "Initial release"  2022-08-31 RCSB 
# 
