data_CI0
# 
_chem_comp.id                                    CI0 
_chem_comp.name                                  "1-(1-{(2S)-1-[(3R,5R)-3,5-dimethylpiperazin-1-yl]-1-oxopropan-2-yl}piperidin-4-yl)-1,3-dihydro-2H-benzimidazol-2-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H31 N5 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-11-22 
_chem_comp.pdbx_modified_date                    2023-01-20 
_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                        385.503 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CI0 
_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        7SVP 
_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 
CI0 N1  N1  N 0 1 N N N 41.148 -20.979 50.110 -4.172 -0.570 0.001  N1  CI0 1  
CI0 N3  N2  N 0 1 N N N 42.523 -15.268 54.630 3.487  -0.217 0.044  N3  CI0 2  
CI0 C4  C1  C 0 1 N N N 39.323 -20.443 53.116 -2.291 -1.510 -2.412 C4  CI0 3  
CI0 C5  C2  C 0 1 N N N 41.781 -18.973 54.131 -0.274 0.185  0.279  C5  CI0 4  
CI0 C6  C3  C 0 1 N N N 42.606 -17.741 54.477 1.152  -0.085 0.766  C6  CI0 5  
CI0 C7  C4  C 0 1 N N N 40.349 -17.729 52.686 0.287  -0.558 -1.958 C7  CI0 6  
CI0 C8  C5  C 0 1 N N N 41.087 -16.428 52.976 1.730  -0.850 -1.538 C8  CI0 7  
CI0 C10 C6  C 0 1 Y N N 43.648 -14.772 53.957 4.571  0.657  0.029  C10 CI0 8  
CI0 C13 C7  C 0 1 Y N N 45.802 -13.302 53.105 7.040  1.892  0.248  C13 CI0 9  
CI0 C15 C8  C 0 1 Y N N 44.009 -13.591 54.610 5.663  -0.045 0.542  C15 CI0 10 
CI0 C17 C9  C 0 1 N N R 41.812 -21.062 47.745 -5.319 1.570  -0.218 C17 CI0 11 
CI0 C20 C10 C 0 1 N N N 44.942 -21.389 49.857 -4.639 0.970  2.473  C20 CI0 12 
CI0 C21 C11 C 0 1 N N N 42.500 -21.368 50.524 -5.088 -1.038 1.052  C21 CI0 13 
CI0 C1  C12 C 0 1 N N N 40.797 -21.487 48.781 -4.676 0.405  -0.978 C1  CI0 14 
CI0 C11 C13 C 0 1 Y N N 44.363 -15.230 52.866 4.724  1.976  -0.372 C11 CI0 15 
CI0 C12 C14 C 0 1 Y N N 45.448 -14.470 52.453 5.957  2.589  -0.262 C12 CI0 16 
CI0 C14 C15 C 0 1 Y N N 45.089 -12.836 54.198 6.897  0.578  0.649  C14 CI0 17 
CI0 C16 C16 C 0 1 N N N 42.203 -14.413 55.674 3.900  -1.397 0.544  C16 CI0 18 
CI0 C18 C17 C 0 1 N N N 41.789 -19.561 47.489 -5.984 2.517  -1.219 C18 CI0 19 
CI0 C19 C18 C 0 1 N N R 43.528 -20.955 49.494 -5.719 0.184  1.728  C19 CI0 20 
CI0 C2  C19 C 0 1 N N N 40.329 -20.207 50.848 -2.902 -1.017 -0.059 C2  CI0 21 
CI0 C3  C20 C 0 1 N N S 40.602 -20.133 52.347 -2.013 -0.610 -1.206 C3  CI0 22 
CI0 C9  C21 C 0 1 N N N 41.752 -16.483 54.349 2.126  0.096  -0.401 C9  CI0 23 
CI0 N2  N3  N 0 1 N N N 41.243 -18.885 52.773 -0.606 -0.746 -0.808 N2  CI0 24 
CI0 N4  N4  N 0 1 N N N 43.115 -13.395 55.651 5.208  -1.325 0.853  N4  CI0 25 
CI0 N5  N5  N 0 1 N N N 43.158 -21.481 48.169 -6.333 1.041  0.705  N5  CI0 26 
CI0 O1  O1  O 0 1 N N N 39.382 -19.611 50.347 -2.474 -1.748 0.809  O1  CI0 27 
CI0 O2  O2  O 0 1 N N N 41.271 -14.559 56.459 3.198  -2.379 0.693  O2  CI0 28 
CI0 H1  H1  H 0 1 N N N 39.522 -20.389 54.197 -1.970 -2.527 -2.187 H1  CI0 29 
CI0 H2  H2  H 0 1 N N N 38.548 -19.710 52.849 -3.359 -1.506 -2.629 H2  CI0 30 
CI0 H3  H3  H 0 1 N N N 38.976 -21.454 52.857 -1.742 -1.138 -3.277 H3  CI0 31 
CI0 H4  H4  H 0 1 N N N 40.947 -19.058 54.843 -0.972 0.043  1.104  H4  CI0 32 
CI0 H5  H5  H 0 1 N N N 42.420 -19.865 54.207 -0.346 1.209  -0.086 H5  CI0 33 
CI0 H6  H6  H 0 1 N N N 42.973 -17.828 55.510 1.403  0.616  1.562  H6  CI0 34 
CI0 H7  H7  H 0 1 N N N 43.461 -17.671 53.789 1.221  -1.105 1.144  H7  CI0 35 
CI0 H8  H8  H 0 1 N N N 39.925 -17.681 51.672 0.213  0.470  -2.312 H8  CI0 36 
CI0 H9  H9  H 0 1 N N N 39.537 -17.850 53.418 -0.003 -1.240 -2.758 H9  CI0 37 
CI0 H10 H10 H 0 1 N N N 41.858 -16.270 52.207 1.808  -1.882 -1.197 H10 CI0 38 
CI0 H11 H11 H 0 1 N N N 40.371 -15.593 52.954 2.395  -0.695 -2.388 H11 CI0 39 
CI0 H12 H12 H 0 1 N N N 46.655 -12.740 52.754 8.001  2.378  0.331  H12 CI0 40 
CI0 H13 H13 H 0 1 N N N 41.568 -21.570 46.800 -4.560 2.112  0.346  H13 CI0 41 
CI0 H14 H14 H 0 1 N N N 45.206 -20.990 50.848 -3.877 1.299  1.766  H14 CI0 42 
CI0 H15 H15 H 0 1 N N N 44.994 -22.488 49.879 -5.089 1.839  2.953  H15 CI0 43 
CI0 H16 H16 H 0 1 N N N 45.648 -21.003 49.107 -4.182 0.333  3.229  H16 CI0 44 
CI0 H17 H17 H 0 1 N N N 42.536 -22.460 50.649 -5.869 -1.656 0.608  H17 CI0 45 
CI0 H18 H18 H 0 1 N N N 42.736 -20.881 51.482 -4.534 -1.621 1.788  H18 CI0 46 
CI0 H19 H19 H 0 1 N N N 39.809 -21.095 48.497 -3.850 0.775  -1.585 H19 CI0 47 
CI0 H20 H20 H 0 1 N N N 40.759 -22.586 48.816 -5.420 -0.070 -1.617 H20 CI0 48 
CI0 H21 H21 H 0 1 N N N 44.088 -16.142 52.356 3.882  2.522  -0.770 H21 CI0 49 
CI0 H22 H22 H 0 1 N N N 46.029 -14.797 51.604 6.077  3.616  -0.574 H22 CI0 50 
CI0 H23 H23 H 0 1 N N N 45.366 -11.923 54.705 7.744  0.038  1.045  H23 CI0 51 
CI0 H24 H24 H 0 1 N N N 40.780 -19.258 47.173 -6.452 3.342  -0.683 H24 CI0 52 
CI0 H25 H25 H 0 1 N N N 42.060 -19.028 48.412 -5.232 2.908  -1.904 H25 CI0 53 
CI0 H26 H26 H 0 1 N N N 42.511 -19.313 46.697 -6.742 1.974  -1.784 H26 CI0 54 
CI0 H27 H27 H 0 1 N N N 43.523 -19.856 49.440 -6.482 -0.145 2.434  H27 CI0 55 
CI0 H28 H28 H 0 1 N N N 41.304 -20.949 52.574 -2.217 0.428  -1.473 H28 CI0 56 
CI0 H29 H29 H 0 1 N N N 40.949 -16.556 55.097 2.086  1.127  -0.754 H29 CI0 57 
CI0 H31 H31 H 0 1 N N N 43.134 -12.625 56.289 5.743  -2.041 1.229  H31 CI0 58 
CI0 H32 H32 H 0 1 N N N 43.186 -22.480 48.203 -6.857 1.790  1.134  H32 CI0 59 
# 
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 
CI0 C18 C17 SING N N 1  
CI0 C17 N5  SING N N 2  
CI0 C17 C1  SING N N 3  
CI0 N5  C19 SING N N 4  
CI0 C1  N1  SING N N 5  
CI0 C19 C20 SING N N 6  
CI0 C19 C21 SING N N 7  
CI0 N1  C21 SING N N 8  
CI0 N1  C2  SING N N 9  
CI0 O1  C2  DOUB N N 10 
CI0 C2  C3  SING N N 11 
CI0 C3  N2  SING N N 12 
CI0 C3  C4  SING N N 13 
CI0 C12 C11 DOUB Y N 14 
CI0 C12 C13 SING Y N 15 
CI0 C7  N2  SING N N 16 
CI0 C7  C8  SING N N 17 
CI0 N2  C5  SING N N 18 
CI0 C11 C10 SING Y N 19 
CI0 C8  C9  SING N N 20 
CI0 C13 C14 DOUB Y N 21 
CI0 C10 C15 DOUB Y N 22 
CI0 C10 N3  SING N N 23 
CI0 C5  C6  SING N N 24 
CI0 C14 C15 SING Y N 25 
CI0 C9  C6  SING N N 26 
CI0 C9  N3  SING N N 27 
CI0 C15 N4  SING N N 28 
CI0 N3  C16 SING N N 29 
CI0 N4  C16 SING N N 30 
CI0 C16 O2  DOUB N N 31 
CI0 C4  H1  SING N N 32 
CI0 C4  H2  SING N N 33 
CI0 C4  H3  SING N N 34 
CI0 C5  H4  SING N N 35 
CI0 C5  H5  SING N N 36 
CI0 C6  H6  SING N N 37 
CI0 C6  H7  SING N N 38 
CI0 C7  H8  SING N N 39 
CI0 C7  H9  SING N N 40 
CI0 C8  H10 SING N N 41 
CI0 C8  H11 SING N N 42 
CI0 C13 H12 SING N N 43 
CI0 C17 H13 SING N N 44 
CI0 C20 H14 SING N N 45 
CI0 C20 H15 SING N N 46 
CI0 C20 H16 SING N N 47 
CI0 C21 H17 SING N N 48 
CI0 C21 H18 SING N N 49 
CI0 C1  H19 SING N N 50 
CI0 C1  H20 SING N N 51 
CI0 C11 H21 SING N N 52 
CI0 C12 H22 SING N N 53 
CI0 C14 H23 SING N N 54 
CI0 C18 H24 SING N N 55 
CI0 C18 H25 SING N N 56 
CI0 C18 H26 SING N N 57 
CI0 C19 H27 SING N N 58 
CI0 C3  H28 SING N N 59 
CI0 C9  H29 SING N N 60 
CI0 N4  H31 SING N N 61 
CI0 N5  H32 SING N N 62 
# 
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 
CI0 SMILES           ACDLabs              12.01 "CC(C(=O)N1CC(C)NC(C)C1)N1CCC(CC1)N1c2ccccc2NC1=O"                                                                                                                     
CI0 InChI            InChI                1.03  "InChI=1S/C21H31N5O2/c1-14-12-25(13-15(2)22-14)20(27)16(3)24-10-8-17(9-11-24)26-19-7-5-4-6-18(19)23-21(26)28/h4-7,14-17,22H,8-13H2,1-3H3,(H,23,28)/t14-,15-,16+/m1/s1" 
CI0 InChIKey         InChI                1.03  LWPPVRZWNRKLJH-OAGGEKHMSA-N                                                                                                                                            
CI0 SMILES_CANONICAL CACTVS               3.385 "C[C@@H]1CN(C[C@@H](C)N1)C(=O)[C@H](C)N2CCC(CC2)N3C(=O)Nc4ccccc34"                                                                                                     
CI0 SMILES           CACTVS               3.385 "C[CH]1CN(C[CH](C)N1)C(=O)[CH](C)N2CCC(CC2)N3C(=O)Nc4ccccc34"                                                                                                          
CI0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1CN(C[C@H](N1)C)C(=O)[C@H](C)N2CCC(CC2)N3c4ccccc4NC3=O"                                                                                                        
CI0 SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CN(CC(N1)C)C(=O)C(C)N2CCC(CC2)N3c4ccccc4NC3=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 
CI0 "SYSTEMATIC NAME" ACDLabs              12.01 "1-(1-{(2S)-1-[(3R,5R)-3,5-dimethylpiperazin-1-yl]-1-oxopropan-2-yl}piperidin-4-yl)-1,3-dihydro-2H-benzimidazol-2-one"            
CI0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[1-[(2~{S})-1-[(3~{R},5~{R})-3,5-dimethylpiperazin-1-yl]-1-oxidanylidene-propan-2-yl]piperidin-4-yl]-1~{H}-benzimidazol-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
CI0 "Create component" 2021-11-22 RCSB 
CI0 "Initial release"  2023-01-25 RCSB 
# 
