data_Y3S
# 
_chem_comp.id                                    Y3S 
_chem_comp.name                                  "(2R)-4-(3-fluoranylthiophen-2-yl)carbonyl-N-(4-methoxyphenyl)-2-methyl-piperazine-1-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H20 F N3 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-02-03 
_chem_comp.pdbx_modified_date                    2022-12-14 
_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                        377.433 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y3S 
_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        8BW4 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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 
Y3S N1  N1  N 0 1 N N N -20.237 17.005 27.963 2.266  0.465  -0.427 N1  Y3S 1  
Y3S N3  N2  N 0 1 N N N -18.570 13.375 25.086 -2.269 -0.846 0.484  N3  Y3S 2  
Y3S C4  C1  C 0 1 Y N N -21.928 17.526 29.616 4.488  -0.484 -0.425 C4  Y3S 3  
Y3S C5  C2  C 0 1 Y N N -20.839 17.919 28.852 3.639  0.584  -0.170 C5  Y3S 4  
Y3S C6  C3  C 0 1 N N N -20.286 15.632 28.048 1.649  -0.721 -0.256 C6  Y3S 5  
Y3S C7  C4  C 0 1 N N N -18.769 15.589 26.062 -0.497 0.388  -0.651 C7  Y3S 6  
Y3S C8  C5  C 0 1 N N N -18.896 14.774 24.811 -1.597 0.459  0.415  C8  Y3S 7  
Y3S C10 C6  C 0 1 Y N N -16.485 13.334 23.710 -4.397 0.264  0.075  C10 Y3S 8  
Y3S C13 C7  C 0 1 Y N N -15.753 14.603 23.959 -5.536 0.625  0.744  C13 Y3S 9  
Y3S C15 C8  C 0 1 N N R -19.246 13.518 27.395 -0.358 -2.119 -0.340 C15 Y3S 10 
Y3S C17 C9  C 0 1 Y N N -20.368 19.227 28.950 4.150  1.770  0.339  C17 Y3S 11 
Y3S C1  C10 C 0 1 N N N -24.116 20.408 31.572 8.497  -0.203 0.298  C1  Y3S 12 
Y3S C11 C11 C 0 1 Y N N -14.566 13.850 22.029 -5.411 2.391  -0.709 C11 Y3S 13 
Y3S C12 C12 C 0 1 Y N N -14.772 14.826 22.936 -6.078 1.807  0.292  C12 Y3S 14 
Y3S C14 C13 C 0 1 N N N -19.441 12.781 26.090 -1.459 -2.048 0.726  C14 Y3S 15 
Y3S C16 C14 C 0 1 N N N -17.865 13.271 27.982 -0.980 -2.450 -1.699 C16 Y3S 16 
Y3S C18 C15 C 0 1 Y N N -20.972 20.123 29.817 5.503  1.887  0.591  C18 Y3S 17 
Y3S C2  C16 C 0 1 Y N N -22.057 19.716 30.582 6.351  0.820  0.336  C2  Y3S 18 
Y3S C3  C17 C 0 1 Y N N -22.532 18.416 30.480 5.841  -0.366 -0.173 C3  Y3S 19 
Y3S C9  C18 C 0 1 N N N -17.595 12.679 24.482 -3.605 -0.939 0.335  C9  Y3S 20 
Y3S F1  F1  F 0 1 N N N -15.970 15.408 25.016 -6.072 -0.104 1.747  F1  Y3S 21 
Y3S N2  N3  N 0 1 N N N -19.492 14.956 27.174 0.313  -0.814 -0.410 N2  Y3S 22 
Y3S O1  O1  O 0 1 N N N -22.691 20.571 31.443 7.683  0.936  0.584  O1  Y3S 23 
Y3S O2  O2  O 0 1 N N N -20.996 15.041 28.871 2.297  -1.707 0.038  O2  Y3S 24 
Y3S O3  O3  O 0 1 N N N -17.563 11.451 24.566 -4.153 -2.023 0.417  O3  Y3S 25 
Y3S S1  S1  S 0 1 Y N N -15.812 12.496 22.211 -4.044 1.472  -1.153 S1  Y3S 26 
Y3S H1  H1  H 0 1 N N N -19.725 17.392 27.196 1.760  1.237  -0.724 H1  Y3S 27 
Y3S H2  H2  H 0 1 N N N -22.305 16.517 29.534 4.091  -1.409 -0.817 H2  Y3S 28 
Y3S H3  H3  H 0 1 N N N -17.705 15.678 26.328 -0.950 0.331  -1.641 H3  Y3S 29 
Y3S H4  H4  H 0 1 N N N -19.187 16.591 25.884 0.135  1.274  -0.589 H4  Y3S 30 
Y3S H5  H5  H 0 1 N N N -18.205 15.166 24.050 -2.320 1.229  0.144  H5  Y3S 31 
Y3S H6  H6  H 0 1 N N N -19.928 14.840 24.437 -1.154 0.695  1.383  H6  Y3S 32 
Y3S H7  H7  H 0 1 N N N -19.991 13.143 28.112 0.363  -2.891 -0.071 H7  Y3S 33 
Y3S H8  H8  H 0 1 N N N -19.529 19.543 28.348 3.490  2.602  0.537  H8  Y3S 34 
Y3S H9  H9  H 0 1 N N N -24.507 21.147 32.287 8.161  -1.050 0.896  H9  Y3S 35 
Y3S H10 H10 H 0 1 N N N -24.592 20.558 30.592 8.417  -0.450 -0.761 H10 Y3S 36 
Y3S H11 H11 H 0 1 N N N -24.337 19.394 31.936 9.536  0.023  0.541  H11 Y3S 37 
Y3S H12 H12 H 0 1 N N N -13.776 13.858 21.292 -5.702 3.319  -1.179 H12 Y3S 38 
Y3S H13 H13 H 0 1 N N N -14.214 15.750 22.894 -6.975 2.234  0.717  H13 Y3S 39 
Y3S H14 H14 H 0 1 N N N -20.489 12.867 25.769 -1.006 -1.991 1.715  H14 Y3S 40 
Y3S H15 H15 H 0 1 N N N -19.184 11.720 26.222 -2.090 -2.934 0.660  H15 Y3S 41 
Y3S H16 H16 H 0 1 N N N -17.764 13.823 28.928 -1.701 -1.677 -1.966 H16 Y3S 42 
Y3S H17 H17 H 0 1 N N N -17.734 12.195 28.170 -0.197 -2.494 -2.456 H17 Y3S 43 
Y3S H18 H18 H 0 1 N N N -17.098 13.616 27.273 -1.485 -3.414 -1.642 H18 Y3S 44 
Y3S H19 H19 H 0 1 N N N -20.600 21.134 29.898 5.900  2.810  0.987  H19 Y3S 45 
Y3S H20 H20 H 0 1 N N N -23.375 18.101 31.077 6.501  -1.198 -0.367 H20 Y3S 46 
# 
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 
Y3S C11 S1  SING Y N 1  
Y3S C11 C12 DOUB Y N 2  
Y3S S1  C10 SING Y N 3  
Y3S C12 C13 SING Y N 4  
Y3S C10 C13 DOUB Y N 5  
Y3S C10 C9  SING N N 6  
Y3S C13 F1  SING N N 7  
Y3S C9  O3  DOUB N N 8  
Y3S C9  N3  SING N N 9  
Y3S C8  N3  SING N N 10 
Y3S C8  C7  SING N N 11 
Y3S N3  C14 SING N N 12 
Y3S C7  N2  SING N N 13 
Y3S C14 C15 SING N N 14 
Y3S N2  C15 SING N N 15 
Y3S N2  C6  SING N N 16 
Y3S C15 C16 SING N N 17 
Y3S N1  C6  SING N N 18 
Y3S N1  C5  SING N N 19 
Y3S C6  O2  DOUB N N 20 
Y3S C5  C17 DOUB Y N 21 
Y3S C5  C4  SING Y N 22 
Y3S C17 C18 SING Y N 23 
Y3S C4  C3  DOUB Y N 24 
Y3S C18 C2  DOUB Y N 25 
Y3S C3  C2  SING Y N 26 
Y3S C2  O1  SING N N 27 
Y3S O1  C1  SING N N 28 
Y3S N1  H1  SING N N 29 
Y3S C4  H2  SING N N 30 
Y3S C7  H3  SING N N 31 
Y3S C7  H4  SING N N 32 
Y3S C8  H5  SING N N 33 
Y3S C8  H6  SING N N 34 
Y3S C15 H7  SING N N 35 
Y3S C17 H8  SING N N 36 
Y3S C1  H9  SING N N 37 
Y3S C1  H10 SING N N 38 
Y3S C1  H11 SING N N 39 
Y3S C11 H12 SING N N 40 
Y3S C12 H13 SING N N 41 
Y3S C14 H14 SING N N 42 
Y3S C14 H15 SING N N 43 
Y3S C16 H16 SING N N 44 
Y3S C16 H17 SING N N 45 
Y3S C16 H18 SING N N 46 
Y3S C18 H19 SING N N 47 
Y3S C3  H20 SING N N 48 
# 
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 
Y3S InChI            InChI                1.06  "InChI=1S/C18H20FN3O3S/c1-12-11-21(17(23)16-15(19)7-10-26-16)8-9-22(12)18(24)20-13-3-5-14(25-2)6-4-13/h3-7,10,12H,8-9,11H2,1-2H3,(H,20,24)/t12-/m1/s1" 
Y3S InChIKey         InChI                1.06  IFZPOZKASMLFRK-GFCCVEGCSA-N                                                                                                                            
Y3S SMILES_CANONICAL CACTVS               3.385 "COc1ccc(NC(=O)N2CCN(C[C@H]2C)C(=O)c3sccc3F)cc1"                                                                                                       
Y3S SMILES           CACTVS               3.385 "COc1ccc(NC(=O)N2CCN(C[CH]2C)C(=O)c3sccc3F)cc1"                                                                                                        
Y3S SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1CN(CCN1C(=O)Nc2ccc(cc2)OC)C(=O)c3c(ccs3)F"                                                                                                    
Y3S SMILES           "OpenEye OEToolkits" 2.0.7 "CC1CN(CCN1C(=O)Nc2ccc(cc2)OC)C(=O)c3c(ccs3)F"                                                                                                         
# 
_pdbx_chem_comp_identifier.comp_id           Y3S 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(2~{R})-4-(3-fluoranylthiophen-2-yl)carbonyl-~{N}-(4-methoxyphenyl)-2-methyl-piperazine-1-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y3S "Create component"   2021-02-03 RCSB 
Y3S "Initial release"    2021-02-17 RCSB 
Y3S "Modify coordinates" 2022-12-14 PDBE 
# 
