data_Y9H
# 
_chem_comp.id                                    Y9H 
_chem_comp.name                                  "(5S)-2-[4-(2-fluoroethyl)piperidin-1-yl]pyrimido[1,2-a]benzimidazole" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H19 F N4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-18 
_chem_comp.pdbx_modified_date                    2023-06-02 
_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                        298.358 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y9H 
_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        8FUG 
_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 
Y9H C8  C1  C 0 1 Y N N 133.445 106.507 123.466 2.010  0.654  -0.204 C8  Y9H 1  
Y9H C5  C2  C 0 1 N N N 137.736 107.721 121.753 -3.145 1.524  -0.135 C5  Y9H 2  
Y9H C6  C3  C 0 1 N N N 136.502 107.479 120.875 -1.975 1.279  -1.093 C6  Y9H 3  
Y9H N1  N1  N 0 1 N N N 136.026 106.095 121.040 -1.434 -0.064 -0.846 N1  Y9H 4  
Y9H C2  C4  C 0 1 N N N 138.869 106.714 121.450 -4.169 0.396  -0.286 C2  Y9H 5  
Y9H N2  N2  N 0 1 Y N N 134.454 106.798 122.628 0.700  0.804  -0.455 N2  Y9H 6  
Y9H N3  N3  N 0 1 Y N N 132.756 107.343 124.291 2.968  1.554  -0.031 N3  Y9H 7  
Y9H C4  C5  C 0 1 N N N 137.047 105.155 120.559 -2.350 -1.212 -0.877 C4  Y9H 8  
Y9H C1  C6  C 0 1 N N N 139.633 107.036 120.153 -5.354 0.656  0.646  C1  Y9H 9  
Y9H C10 C7  C 0 1 Y N N 130.869 106.951 125.894 5.444  1.389  0.451  C10 Y9H 10 
Y9H C11 C8  C 0 1 Y N N 130.035 105.958 126.406 6.455  0.495  0.659  C11 Y9H 11 
Y9H C12 C9  C 0 1 Y N N 130.148 104.629 125.989 6.211  -0.870 0.630  C12 Y9H 12 
Y9H C13 C10 C 0 1 Y N N 131.087 104.208 125.043 4.939  -1.348 0.390  C13 Y9H 13 
Y9H C14 C11 C 0 1 Y N N 131.907 105.218 124.545 3.898  -0.456 0.177  C14 Y9H 14 
Y9H C15 C12 C 0 1 Y N N 133.461 104.184 122.899 1.754  -1.709 -0.222 C15 Y9H 15 
Y9H C16 C13 C 0 1 Y N N 134.512 104.464 122.019 0.435  -1.549 -0.469 C16 Y9H 16 
Y9H C17 C14 C 0 1 N N N 140.400 108.348 120.163 -6.433 -0.402 0.406  C17 Y9H 17 
Y9H C3  C15 C 0 1 N N N 138.305 105.278 121.433 -3.517 -0.939 0.080  C3  Y9H 18 
Y9H C7  C16 C 0 1 Y N N 134.990 105.772 121.901 -0.090 -0.244 -0.589 C7  Y9H 19 
Y9H C9  C17 C 0 1 Y N N 131.824 106.575 124.943 4.145  0.928  0.206  C9  Y9H 20 
Y9H F1  F1  F 0 1 N N N 141.233 108.411 121.297 -7.517 -0.164 1.257  F1  Y9H 21 
Y9H N4  N4  N 0 1 Y N N 132.928 105.217 123.623 2.547  -0.604 -0.083 N4  Y9H 22 
Y9H H15 H1  H 0 1 N N N 138.108 108.740 121.570 -2.776 1.545  0.891  H15 Y9H 23 
Y9H H16 H2  H 0 1 N N N 137.445 107.621 122.809 -3.616 2.477  -0.372 H16 Y9H 24 
Y9H H6  H3  H 0 1 N N N 136.767 107.649 119.821 -2.327 1.347  -2.123 H6  Y9H 25 
Y9H H5  H4  H 0 1 N N N 135.704 108.176 121.170 -1.199 2.023  -0.920 H5  Y9H 26 
Y9H H17 H5  H 0 1 N N N 139.590 106.773 122.279 -4.519 0.359  -1.317 H17 Y9H 27 
Y9H H4  H6  H 0 1 N N N 136.658 104.128 120.618 -2.732 -1.347 -1.889 H4  Y9H 28 
Y9H H3  H7  H 0 1 N N N 137.301 105.391 119.515 -1.821 -2.111 -0.561 H3  Y9H 29 
Y9H H2  H8  H 0 1 N N N 138.905 107.074 119.329 -5.020 0.605  1.682  H2  Y9H 30 
Y9H H1  H9  H 0 1 N N N 140.351 106.223 119.970 -5.764 1.646  0.444  H1  Y9H 31 
Y9H H7  H10 H 0 1 N N N 130.781 107.977 126.221 5.645  2.450  0.477  H7  Y9H 32 
Y9H H8  H11 H 0 1 N N N 129.287 106.221 127.139 7.456  0.855  0.848  H8  Y9H 33 
Y9H H9  H12 H 0 1 N N N 129.481 103.895 126.416 7.021  -1.564 0.797  H9  Y9H 34 
Y9H H10 H13 H 0 1 N N N 131.170 103.180 124.723 4.754  -2.412 0.368  H10 Y9H 35 
Y9H H11 H14 H 0 1 N N N 133.080 103.179 123.005 2.175  -2.698 -0.127 H11 Y9H 36 
Y9H H12 H15 H 0 1 N N N 134.953 103.671 121.432 -0.208 -2.409 -0.582 H12 Y9H 37 
Y9H H19 H16 H 0 1 N N N 141.016 108.417 119.254 -6.767 -0.351 -0.631 H19 Y9H 38 
Y9H H18 H17 H 0 1 N N N 139.688 109.186 120.187 -6.023 -1.391 0.607  H18 Y9H 39 
Y9H H14 H18 H 0 1 N N N 138.050 104.986 122.462 -3.145 -0.895 1.103  H14 Y9H 40 
Y9H H13 H19 H 0 1 N N N 139.077 104.600 121.040 -4.253 -1.739 -0.006 H13 Y9H 41 
# 
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 
Y9H C1  C17 SING N N 1  
Y9H C1  C2  SING N N 2  
Y9H C17 F1  SING N N 3  
Y9H C4  N1  SING N N 4  
Y9H C4  C3  SING N N 5  
Y9H C6  N1  SING N N 6  
Y9H C6  C5  SING N N 7  
Y9H N1  C7  SING N N 8  
Y9H C3  C2  SING N N 9  
Y9H C2  C5  SING N N 10 
Y9H C7  C16 SING Y N 11 
Y9H C7  N2  DOUB Y N 12 
Y9H C16 C15 DOUB Y N 13 
Y9H N2  C8  SING Y N 14 
Y9H C15 N4  SING Y N 15 
Y9H C8  N4  SING Y N 16 
Y9H C8  N3  DOUB Y N 17 
Y9H N4  C14 SING Y N 18 
Y9H N3  C9  SING Y N 19 
Y9H C14 C9  DOUB Y N 20 
Y9H C14 C13 SING Y N 21 
Y9H C9  C10 SING Y N 22 
Y9H C13 C12 DOUB Y N 23 
Y9H C10 C11 DOUB Y N 24 
Y9H C12 C11 SING Y N 25 
Y9H C5  H15 SING N N 26 
Y9H C5  H16 SING N N 27 
Y9H C6  H6  SING N N 28 
Y9H C6  H5  SING N N 29 
Y9H C2  H17 SING N N 30 
Y9H C4  H4  SING N N 31 
Y9H C4  H3  SING N N 32 
Y9H C1  H2  SING N N 33 
Y9H C1  H1  SING N N 34 
Y9H C10 H7  SING N N 35 
Y9H C11 H8  SING N N 36 
Y9H C12 H9  SING N N 37 
Y9H C13 H10 SING N N 38 
Y9H C15 H11 SING N N 39 
Y9H C16 H12 SING N N 40 
Y9H C17 H19 SING N N 41 
Y9H C17 H18 SING N N 42 
Y9H C3  H14 SING N N 43 
Y9H C3  H13 SING N N 44 
# 
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 
Y9H SMILES           ACDLabs              12.01 "FCCC1CCN(CC1)c1nc2nc3ccccc3n2cc1"                                                                                  
Y9H InChI            InChI                1.06  "InChI=1S/C17H19FN4/c18-9-5-13-6-10-21(11-7-13)16-8-12-22-15-4-2-1-3-14(15)19-17(22)20-16/h1-4,8,12-13H,5-7,9-11H2" 
Y9H InChIKey         InChI                1.06  DWSFKWXDRBTTCG-UHFFFAOYSA-N                                                                                         
Y9H SMILES_CANONICAL CACTVS               3.385 "FCCC1CCN(CC1)c2ccn3c(n2)nc4ccccc34"                                                                                
Y9H SMILES           CACTVS               3.385 "FCCC1CCN(CC1)c2ccn3c(n2)nc4ccccc34"                                                                                
Y9H SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)nc3n2ccc(n3)N4CCC(CC4)CCF"                                                                              
Y9H SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)nc3n2ccc(n3)N4CCC(CC4)CCF"                                                                              
# 
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 
Y9H "SYSTEMATIC NAME" ACDLabs              12.01 "(5S)-2-[4-(2-fluoroethyl)piperidin-1-yl]pyrimido[1,2-a]benzimidazole" 
Y9H "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[4-(2-fluoranylethyl)piperidin-1-yl]pyrimido[1,2-a]benzimidazole"   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y9H "Create component" 2023-01-18 RCSB 
Y9H "Initial release"  2023-06-07 RCSB 
# 
