data_O1M
#
_chem_comp.id O1M
_chem_comp.name 4-(4-fluorophenyl)piperazine-1-carboxamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H14 F N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-06-04
_chem_comp.pdbx_modified_date 2019-08-16
_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 223.247
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code O1M
_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 5QSJ
_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
O1M N1 N1 N 0 1 N N N N N N -18.054 -29.787 4.483 -2.766 -0.043 -0.272 N1 O1M 1
O1M C4 C1 C 0 1 N N N N N N -18.385 -30.800 3.457 -2.098 1.097 -0.919 C4 O1M 2
O1M C5 C2 C 0 1 Y N N N N N -16.904 -29.314 0.422 1.362 -0.072 -0.325 C5 O1M 3
O1M C6 C3 C 0 1 Y N N N N N -16.382 -28.246 -0.096 2.159 -1.202 -0.457 C6 O1M 4
O1M C7 C4 C 0 1 Y N N N N N -16.189 -28.179 -1.449 3.507 -1.133 -0.165 C7 O1M 5
O1M C8 C5 C 0 1 Y N N N N N -16.556 -29.234 -2.190 4.064 0.062 0.260 C8 O1M 6
O1M C10 C6 C 0 1 Y N N N N N -17.256 -30.330 -0.376 1.924 1.126 0.095 C10 O1M 7
O1M N N2 N 0 1 N N N N N N -20.286 -30.066 5.229 -4.598 -0.963 0.844 N O1M 8
O1M C C7 C 0 1 N N N N N N -19.136 -29.297 5.226 -3.952 0.111 0.349 C O1M 9
O1M O O1 O 0 1 N N N N N N -19.094 -28.250 5.839 -4.439 1.219 0.462 O O1M 10
O1M C1 C8 C 0 1 N N N N N N -16.995 -28.829 4.087 -2.107 -1.357 -0.326 C1 O1M 11
O1M C2 C9 C 0 1 N N N N N N -16.981 -28.423 2.602 -0.662 -1.197 0.157 C2 O1M 12
O1M C3 C10 C 0 1 N N N N N N -18.289 -30.235 2.039 -0.653 1.165 -0.414 C3 O1M 13
O1M C9 C11 C 0 1 Y N N N N N -17.074 -30.270 -1.679 3.272 1.189 0.392 C9 O1M 14
O1M F F1 F 0 1 N N N N N N -16.399 -29.265 -3.410 5.382 0.126 0.551 F O1M 15
O1M N2 N3 N 0 1 N N N N N N -17.106 -29.513 1.771 -0.003 -0.140 -0.622 N2 O1M 16
O1M H1 H1 H 0 1 N N N N N N -19.412 -31.156 3.628 -2.102 0.958 -2.000 H1 O1M 17
O1M H2 H2 H 0 1 N N N N N N -17.684 -31.643 3.551 -2.622 2.019 -0.666 H2 O1M 18
O1M H3 H3 H 0 1 N N N N N N -16.102 -27.416 0.535 1.725 -2.134 -0.788 H3 O1M 19
O1M H4 H4 H 0 1 N N N N N N -15.754 -27.302 -1.906 4.127 -2.011 -0.267 H4 O1M 20
O1M H5 H5 H 0 1 N N N N N N -17.698 -31.215 0.057 1.307 2.007 0.194 H5 O1M 21
O1M H6 H6 H 0 1 N N N N N N -21.090 -29.761 5.739 -4.177 -1.837 0.817 H6 O1M 22
O1M H7 H7 H 0 1 N N N N N N -20.313 -30.927 4.722 -5.484 -0.863 1.226 H7 O1M 23
O1M H8 H8 H 0 1 N N N N N N -16.022 -29.285 4.321 -2.634 -2.058 0.321 H8 O1M 24
O1M H9 H9 H 0 1 N N N N N N -17.125 -27.915 4.686 -2.115 -1.729 -1.351 H9 O1M 25
O1M H10 H10 H 0 1 N N N N N N -16.031 -27.915 2.381 -0.659 -0.928 1.213 H10 O1M 26
O1M H11 H11 H 0 1 N N N N N N -17.818 -27.734 2.414 -0.126 -2.137 0.020 H11 O1M 27
O1M H12 H12 H 0 1 N N N N N N -19.145 -29.562 1.879 -0.112 1.935 -0.964 H12 O1M 28
O1M H13 H13 H 0 1 N N N N N N -18.346 -31.075 1.331 -0.650 1.408 0.649 H13 O1M 29
O1M H14 H14 H 0 1 N N N N N N -17.365 -31.099 -2.307 3.708 2.120 0.723 H14 O1M 30
#
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
O1M F C8 SING N N 1
O1M C8 C9 DOUB Y N 2
O1M C8 C7 SING Y N 3
O1M C9 C10 SING Y N 4
O1M C7 C6 DOUB Y N 5
O1M C10 C5 DOUB Y N 6
O1M C6 C5 SING Y N 7
O1M C5 N2 SING N N 8
O1M N2 C3 SING N N 9
O1M N2 C2 SING N N 10
O1M C3 C4 SING N N 11
O1M C2 C1 SING N N 12
O1M C4 N1 SING N N 13
O1M C1 N1 SING N N 14
O1M N1 C SING N N 15
O1M C N SING N N 16
O1M C O DOUB N N 17
O1M C4 H1 SING N N 18
O1M C4 H2 SING N N 19
O1M C6 H3 SING N N 20
O1M C7 H4 SING N N 21
O1M C10 H5 SING N N 22
O1M N H6 SING N N 23
O1M N H7 SING N N 24
O1M C1 H8 SING N N 25
O1M C1 H9 SING N N 26
O1M C2 H10 SING N N 27
O1M C2 H11 SING N N 28
O1M C3 H12 SING N N 29
O1M C3 H13 SING N N 30
O1M C9 H14 SING N N 31
#
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
O1M SMILES ACDLabs 12.01 N2(C(N)=O)CCN(c1ccc(cc1)F)CC2
O1M InChI InChI 1.03 InChI=1S/C11H14FN3O/c12-9-1-3-10(4-2-9)14-5-7-15(8-6-14)11(13)16/h1-4H,5-8H2,(H2,13,16)
O1M InChIKey InChI 1.03 XARVCWHXIZRCGB-UHFFFAOYSA-N
O1M SMILES_CANONICAL CACTVS 3.385 NC(=O)N1CCN(CC1)c2ccc(F)cc2
O1M SMILES CACTVS 3.385 NC(=O)N1CCN(CC1)c2ccc(F)cc2
O1M SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1cc(ccc1N2CCN(CC2)C(=O)N)F
O1M SMILES "OpenEye OEToolkits" 2.0.6 c1cc(ccc1N2CCN(CC2)C(=O)N)F
#
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
O1M "SYSTEMATIC NAME" ACDLabs 12.01 4-(4-fluorophenyl)piperazine-1-carboxamide
O1M "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 4-(4-fluorophenyl)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
O1M 'Create component' 2019-06-04 RCSB
O1M 'Initial release' 2019-08-21 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
O1M N1 N 4.299 2.910 1
O1M C4 C 5.598 2.160 2
O1M C5 C 4.299 -1.590 3
O1M C6 C 5.598 -2.340 4
O1M C7 C 5.598 -3.840 5
O1M C8 C 4.299 -4.590 6
O1M C10 C 3.000 -2.340 7
O1M N N 3.000 5.160 8
O1M C C 4.299 4.410 9
O1M O O 5.598 5.160 10
O1M C1 C 3.000 2.160 11
O1M C2 C 3.000 0.660 12
O1M C3 C 5.598 0.660 13
O1M C9 C 3.000 -3.840 14
O1M F F 4.299 -6.090 15
O1M N2 N 4.299 -0.090 16
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
O1M F C8 SINGLE NONE 1
O1M C8 C9 DOUBLE NONE 2
O1M C8 C7 SINGLE NONE 3
O1M C9 C10 SINGLE NONE 4
O1M C7 C6 DOUBLE NONE 5
O1M C10 C5 DOUBLE NONE 6
O1M C6 C5 SINGLE NONE 7
O1M C5 N2 SINGLE NONE 8
O1M N2 C3 SINGLE NONE 9
O1M N2 C2 SINGLE NONE 10
O1M C3 C4 SINGLE NONE 11
O1M C2 C1 SINGLE NONE 12
O1M C4 N1 SINGLE NONE 13
O1M C1 N1 SINGLE NONE 14
O1M N1 C SINGLE NONE 15
O1M C N SINGLE NONE 16
O1M C O DOUBLE NONE 17
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
O1M MurckoScaffold S1 scaffold c1ccc(N2CCNCC2)cc1 InChI=1S/C10H14N2/c1-2-4-10(5-3-1)12-8-6-11-7-9-12/h1-5,11H,6-9H2 YZTJYBJCZXZGCT-UHFFFAOYSA-N
O1M phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
O1M piperazine F2 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-UHFFFAOYSA-N
O1M Z198194394 F3 fragment NC(=O)N1CCN(c2ccc(F)cc2)CC1 InChI=1S/C11H14FN3O/c12-9-1-3-10(4-2-9)14-5-7-15(8-6-14)11(13)16/h1-4H,5-8H2,(H2,13,16) XARVCWHXIZRCGB-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
O1M N1 S1 1
O1M C4 S1 1
O1M C5 S1 1
O1M C6 S1 1
O1M C7 S1 1
O1M C8 S1 1
O1M C10 S1 1
O1M C1 S1 1
O1M C2 S1 1
O1M C3 S1 1
O1M C9 S1 1
O1M N2 S1 1
O1M C5 F1 1
O1M C10 F1 1
O1M C9 F1 1
O1M C8 F1 1
O1M C7 F1 1
O1M C6 F1 1
O1M N1 F2 1
O1M C4 F2 1
O1M C3 F2 1
O1M N2 F2 1
O1M C2 F2 1
O1M C1 F2 1
O1M N F3 1
O1M C F3 1
O1M O F3 1
O1M N1 F3 1
O1M C4 F3 1
O1M C3 F3 1
O1M N2 F3 1
O1M C2 F3 1
O1M C1 F3 1
O1M C5 F3 1
O1M C10 F3 1
O1M C9 F3 1
O1M C8 F3 1
O1M F F3 1
O1M C7 F3 1
O1M C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id O1M
_pdbe_chem_comp_rdkit_properties.exactmw 223.112
_pdbe_chem_comp_rdkit_properties.amw 223.251
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.364
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 113.223
_pdbe_chem_comp_rdkit_properties.tpsa 49.570
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.646
_pdbe_chem_comp_rdkit_properties.CrippenMR 58.945
_pdbe_chem_comp_rdkit_properties.chi0v 7.628
_pdbe_chem_comp_rdkit_properties.chi1v 3.958
_pdbe_chem_comp_rdkit_properties.chi2v 1.543
_pdbe_chem_comp_rdkit_properties.chi3v 1.543
_pdbe_chem_comp_rdkit_properties.chi4v 0.866
_pdbe_chem_comp_rdkit_properties.chi0n 21.628
_pdbe_chem_comp_rdkit_properties.chi1n 10.853
_pdbe_chem_comp_rdkit_properties.chi2n 1.543
_pdbe_chem_comp_rdkit_properties.chi3n 1.543
_pdbe_chem_comp_rdkit_properties.chi4n 0.866
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.780
_pdbe_chem_comp_rdkit_properties.kappa1 2.911
_pdbe_chem_comp_rdkit_properties.kappa2 4.384
_pdbe_chem_comp_rdkit_properties.kappa3 2.238
_pdbe_chem_comp_rdkit_properties.Phi 0.798
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
O1M UniChem PDBe O1M
O1M UniChem ZINC ZINC000000386756
O1M UniChem Mcule MCULE-1873141231
O1M UniChem eMolecules 20125400
O1M UniChem SureChEMBL SCHEMBL16221494
O1M UniChem PubChem 851859
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
O1M N1 2.481 0.168 0.065 ETKDGv3 1
O1M C4 1.759 1.019 -0.891 ETKDGv3 2
O1M C5 -1.778 -0.187 -0.120 ETKDGv3 3
O1M C6 -2.343 -0.883 -1.308 ETKDGv3 4
O1M C7 -3.662 -1.090 -1.411 ETKDGv3 5
O1M C8 -4.570 -0.625 -0.344 ETKDGv3 6
O1M C10 -2.620 0.236 0.845 ETKDGv3 7
O1M N 4.630 -0.927 0.738 ETKDGv3 8
O1M C 3.920 0.068 -0.005 ETKDGv3 9
O1M O 4.573 0.865 -0.731 ETKDGv3 10
O1M C1 1.750 -0.479 1.165 ETKDGv3 11
O1M C2 0.315 0.047 1.287 ETKDGv3 12
O1M C3 0.400 0.402 -1.233 ETKDGv3 13
O1M C9 -4.075 0.004 0.727 ETKDGv3 14
O1M F -5.905 -0.837 -0.453 ETKDGv3 15
O1M N2 -0.356 0.048 -0.022 ETKDGv3 16
O1M H1 1.614 2.027 -0.447 ETKDGv3 17
O1M H2 2.335 1.133 -1.835 ETKDGv3 18
O1M H3 -1.692 -1.241 -2.094 ETKDGv3 19
O1M H4 -4.065 -1.602 -2.275 ETKDGv3 20
O1M H5 -2.253 0.771 1.710 ETKDGv3 21
O1M H6 5.673 -0.964 0.694 ETKDGv3 22
O1M H7 4.136 -1.654 1.299 ETKDGv3 23
O1M H8 2.271 -0.288 2.129 ETKDGv3 24
O1M H9 1.721 -1.576 0.986 ETKDGv3 25
O1M H10 -0.233 -0.603 2.005 ETKDGv3 26
O1M H11 0.330 1.082 1.691 ETKDGv3 27
O1M H12 -0.178 1.135 -1.837 ETKDGv3 28
O1M H13 0.562 -0.512 -1.844 ETKDGv3 29
O1M H14 -4.738 0.349 1.510 ETKDGv3 30
#