data_F5F
#
_chem_comp.id F5F
_chem_comp.name 3-[(1R,2S,4R,6S)-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1H-pyridin-2-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H21 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-31
_chem_comp.pdbx_modified_date 2020-10-09
_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 247.333
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code F5F
_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 7BQL
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
F5F C1 C1 C 0 1 N N N N N N -24.215 30.198 -23.023 3.360 -0.324 0.747 C1 F5F 1
F5F C2 C2 C 0 1 N N N N N N -23.672 31.215 -23.781 3.723 -0.135 -0.540 C2 F5F 2
F5F C4 C3 C 0 1 N N N N N N -25.793 32.200 -23.994 1.473 -0.007 -1.223 C4 F5F 3
F5F C5 C4 C 0 1 N N N N N N -26.344 31.168 -23.224 1.048 -0.193 0.097 C5 F5F 4
F5F C6 C5 C 0 1 N N N N N N -25.536 30.187 -22.755 1.994 -0.359 1.092 C6 F5F 5
F5F C7 C6 C 0 1 N N R N N N -27.843 31.051 -22.876 -0.422 -0.225 0.429 C7 F5F 6
F5F C10 C7 C 0 1 N N S N N N -28.663 30.886 -24.159 -1.092 -1.370 -0.333 C10 F5F 7
F5F C11 C8 C 0 1 N N N N N N -30.077 30.491 -23.761 -2.584 -1.402 0.004 C11 F5F 8
F5F C12 C9 C 0 1 N N R N N N -30.722 31.648 -22.996 -3.227 -0.074 -0.401 C12 F5F 9
F5F C13 C10 C 0 1 N N N N N N -29.884 32.095 -21.794 -2.557 1.071 0.362 C13 F5F 10
F5F C14 C11 C 0 1 N N S N N N -28.387 32.233 -22.065 -1.065 1.103 0.025 C14 F5F 11
F5F C15 C12 C 0 1 N N N N N N -28.052 29.812 -25.052 -0.449 -2.698 0.071 C15 F5F 12
F5F C16 C13 C 0 1 N N N N N N -32.077 31.180 -22.470 -4.720 -0.106 -0.064 C16 F5F 13
F5F C17 C14 C 0 1 N N N N N N -27.722 32.211 -20.701 -0.405 2.230 0.776 C17 F5F 14
F5F C18 C15 C 0 1 N N N N N N -26.622 32.896 -20.502 0.199 3.190 0.120 C18 F5F 15
F5F N3 N1 N 0 1 N N N N N N -24.468 32.200 -24.256 2.787 0.022 -1.513 N3 F5F 16
F5F O8 O1 O 0 1 N N N N N N -26.080 29.156 -21.982 1.614 -0.553 2.377 O8 F5F 17
F5F O9 O2 O 0 1 N N N N N N -26.442 33.090 -24.436 0.649 0.141 -2.113 O9 F5F 18
F5F H1 H1 H 0 1 N N N N N N -23.581 29.410 -22.644 4.114 -0.451 1.509 H1 F5F 19
F5F H2 H2 H 0 1 N N N N N N -22.613 31.225 -23.995 4.771 -0.108 -0.800 H2 F5F 20
F5F H4 H4 H 0 1 N N N N N N -27.975 30.141 -22.273 -0.549 -0.379 1.501 H4 F5F 21
F5F H5 H5 H 0 1 N N N N N N -28.688 31.843 -24.701 -0.965 -1.216 -1.405 H5 F5F 22
F5F H6 H6 H 0 1 N N N N N N -30.666 30.272 -24.664 -3.062 -2.217 -0.540 H6 F5F 23
F5F H7 H7 H 0 1 N N N N N N -30.043 29.598 -23.119 -2.711 -1.556 1.075 H7 F5F 24
F5F H8 H8 H 0 1 N N N N N N -30.868 32.500 -23.676 -3.100 0.080 -1.472 H8 F5F 25
F5F H9 H9 H 0 1 N N N N N N -30.262 33.073 -21.460 -3.015 2.017 0.074 H9 F5F 26
F5F H10 H10 H 0 1 N N N N N N -30.018 31.356 -20.991 -2.684 0.917 1.433 H10 F5F 27
F5F H11 H11 H 0 1 N N N N N N -28.176 33.181 -22.582 -0.938 1.257 -1.047 H11 F5F 28
F5F H12 H12 H 0 1 N N N N N N -27.030 30.107 -25.334 -0.927 -3.513 -0.472 H12 F5F 29
F5F H13 H13 H 0 1 N N N N N N -28.021 28.857 -24.508 0.614 -2.674 -0.169 H13 F5F 30
F5F H14 H14 H 0 1 N N N N N N -28.664 29.697 -25.959 -0.576 -2.852 1.143 H14 F5F 31
F5F H15 H15 H 0 1 N N N N N N -32.558 31.999 -21.916 -4.847 -0.260 1.008 H15 F5F 32
F5F H16 H16 H 0 1 N N N N N N -32.716 30.884 -23.315 -5.178 0.840 -0.352 H16 F5F 33
F5F H17 H17 H 0 1 N N N N N N -31.933 30.319 -21.800 -5.197 -0.922 -0.607 H17 F5F 34
F5F H18 H18 H 0 1 N N N N N N -28.153 31.633 -19.897 -0.429 2.247 1.856 H18 F5F 35
F5F H19 H19 H 0 1 N N N N N N -26.146 32.883 -19.533 0.672 3.998 0.658 H19 F5F 36
F5F H20 H20 H 0 1 N N N N N N -26.192 33.473 -21.307 0.223 3.174 -0.960 H20 F5F 37
F5F H21 H21 H 0 1 N N N N N N -25.392 28.551 -21.731 2.352 -0.658 2.994 H21 F5F 38
F5F H3 H3 H 0 1 N N N N N N -24.072 32.935 -24.806 3.070 0.152 -2.431 H3 F5F 39
#
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
F5F C15 C10 SING N N 1
F5F O9 C4 DOUB N N 2
F5F N3 C4 SING N N 3
F5F N3 C2 SING N N 4
F5F C10 C11 SING N N 5
F5F C10 C7 SING N N 6
F5F C4 C5 SING N N 7
F5F C2 C1 DOUB N N 8
F5F C11 C12 SING N N 9
F5F C5 C7 SING N N 10
F5F C5 C6 DOUB N N 11
F5F C1 C6 SING N N 12
F5F C12 C16 SING N N 13
F5F C12 C13 SING N N 14
F5F C7 C14 SING N N 15
F5F C6 O8 SING N N 16
F5F C14 C13 SING N N 17
F5F C14 C17 SING N N 18
F5F C17 C18 DOUB N N 19
F5F C1 H1 SING N N 20
F5F C2 H2 SING N N 21
F5F C7 H4 SING N N 22
F5F C10 H5 SING N N 23
F5F C11 H6 SING N N 24
F5F C11 H7 SING N N 25
F5F C12 H8 SING N N 26
F5F C13 H9 SING N N 27
F5F C13 H10 SING N N 28
F5F C14 H11 SING N N 29
F5F C15 H12 SING N N 30
F5F C15 H13 SING N N 31
F5F C15 H14 SING N N 32
F5F C16 H15 SING N N 33
F5F C16 H16 SING N N 34
F5F C16 H17 SING N N 35
F5F C17 H18 SING N N 36
F5F C18 H19 SING N N 37
F5F C18 H20 SING N N 38
F5F O8 H21 SING N N 39
F5F N3 H3 SING N N 40
#
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
F5F InChI InChI 1.03 InChI=1S/C15H21NO2/c1-4-11-8-9(2)7-10(3)13(11)14-12(17)5-6-16-15(14)18/h4-6,9-11,13H,1,7-8H2,2-3H3,(H2,16,17,18)/t9-,10+,11-,13-/m1/s1
F5F InChIKey InChI 1.03 SWIJWROLKBJDFO-LSCVPOLPSA-N
F5F SMILES_CANONICAL CACTVS 3.385 C[C@@H]1C[C@H](C)[C@H]([C@@H](C1)C=C)C2=C(O)C=CNC2=O
F5F SMILES CACTVS 3.385 C[CH]1C[CH](C)[CH]([CH](C1)C=C)C2=C(O)C=CNC2=O
F5F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H]1C[C@@H]([C@H]([C@@H](C1)C=C)C2=C(C=CNC2=O)O)C
F5F SMILES "OpenEye OEToolkits" 2.0.7 CC1CC(C(C(C1)C=C)C2=C(C=CNC2=O)O)C
#
_pdbx_chem_comp_identifier.comp_id F5F
_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
3-[(1~{R},2~{S},4~{R},6~{S})-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1~{H}-pyridin-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
F5F 'Create component' 2020-03-31 PDBJ
F5F 'Initial release' 2020-10-14 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
F5F C1 C 5.104 -3.750 1
F5F C2 C 6.404 -4.500 2
F5F C4 C 7.702 -2.250 3
F5F C5 C 6.404 -1.500 4
F5F C6 C 5.104 -2.250 5
F5F C7 C 6.404 0.000 6
F5F C10 C 5.104 0.750 7
F5F C11 C 5.104 2.250 8
F5F C12 C 6.404 3.000 9
F5F C13 C 7.702 2.250 10
F5F C14 C 7.702 0.750 11
F5F C15 C 3.805 0.000 12
F5F C16 C 6.404 4.500 13
F5F C17 C 9.002 0.000 14
F5F C18 C 10.301 0.750 15
F5F N3 N 7.702 -3.750 16
F5F O8 O 3.805 -1.500 17
F5F O9 O 9.002 -1.500 18
#
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
F5F C10 C15 SINGLE BEGINWEDGE 1
F5F O9 C4 DOUBLE NONE 2
F5F N3 C4 SINGLE NONE 3
F5F N3 C2 SINGLE NONE 4
F5F C10 C11 SINGLE NONE 5
F5F C10 C7 SINGLE NONE 6
F5F C4 C5 SINGLE NONE 7
F5F C2 C1 DOUBLE NONE 8
F5F C11 C12 SINGLE NONE 9
F5F C7 C5 SINGLE BEGINDASH 10
F5F C5 C6 DOUBLE NONE 11
F5F C1 C6 SINGLE NONE 12
F5F C12 C16 SINGLE BEGINWEDGE 13
F5F C12 C13 SINGLE NONE 14
F5F C7 C14 SINGLE NONE 15
F5F C6 O8 SINGLE NONE 16
F5F C14 C13 SINGLE NONE 17
F5F C14 C17 SINGLE BEGINWEDGE 18
F5F C17 C18 DOUBLE NONE 19
#
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
F5F MurckoScaffold S1 scaffold 'O=c1[nH]cccc1C1CCCCC1' InChI=1S/C11H15NO/c13-11-10(7-4-8-12-11)9-5-2-1-3-6-9/h4,7-9H,1-3,5-6H2,(H,12,13) NSDAFIXBLIOQQP-UHFFFAOYSA-N
F5F cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
F5F pyridine F2 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
F5F C1 S1 1
F5F C2 S1 1
F5F C4 S1 1
F5F C5 S1 1
F5F C6 S1 1
F5F C7 S1 1
F5F C10 S1 1
F5F C11 S1 1
F5F C12 S1 1
F5F C13 S1 1
F5F C14 S1 1
F5F N3 S1 1
F5F O9 S1 1
F5F C7 F1 1
F5F C10 F1 1
F5F C11 F1 1
F5F C12 F1 1
F5F C13 F1 1
F5F C14 F1 1
F5F C2 F2 1
F5F C1 F2 1
F5F C6 F2 1
F5F C5 F2 1
F5F C4 F2 1
F5F N3 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id F5F
_pdbe_chem_comp_rdkit_properties.exactmw 247.157
_pdbe_chem_comp_rdkit_properties.amw 247.338
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.533
_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 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 137.210
_pdbe_chem_comp_rdkit_properties.tpsa 53.090
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.415
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.950
_pdbe_chem_comp_rdkit_properties.chi0v 8.764
_pdbe_chem_comp_rdkit_properties.chi1v 4.605
_pdbe_chem_comp_rdkit_properties.chi2v 2.143
_pdbe_chem_comp_rdkit_properties.chi3v 2.143
_pdbe_chem_comp_rdkit_properties.chi4v 1.440
_pdbe_chem_comp_rdkit_properties.chi0n 29.764
_pdbe_chem_comp_rdkit_properties.chi1n 14.961
_pdbe_chem_comp_rdkit_properties.chi2n 2.143
_pdbe_chem_comp_rdkit_properties.chi3n 2.143
_pdbe_chem_comp_rdkit_properties.chi4n 1.440
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.510
_pdbe_chem_comp_rdkit_properties.kappa1 2.671
_pdbe_chem_comp_rdkit_properties.kappa2 5.006
_pdbe_chem_comp_rdkit_properties.kappa3 2.217
_pdbe_chem_comp_rdkit_properties.Phi 0.743
#
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
F5F UniChem PDBe F5F
F5F UniChem ZINC ZINC000473132466
F5F UniChem PubChem 122397578
F5F UniChem Nikkaji J3.488.877I
#
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
F5F C1 4.098 -0.240 0.648 ETKDGv3 1
F5F C2 4.466 -0.868 -0.469 ETKDGv3 2
F5F C4 2.092 -1.110 -1.125 ETKDGv3 3
F5F C5 1.690 -0.334 0.084 ETKDGv3 4
F5F C6 2.673 0.014 0.963 ETKDGv3 5
F5F C7 0.218 0.052 0.289 ETKDGv3 6
F5F C10 -0.672 -1.202 0.602 ETKDGv3 7
F5F C11 -1.776 -1.463 -0.456 ETKDGv3 8
F5F C12 -2.606 -0.218 -0.874 ETKDGv3 9
F5F C13 -1.841 1.116 -0.718 ETKDGv3 10
F5F C14 -0.327 0.911 -0.889 ETKDGv3 11
F5F C15 -1.270 -1.126 2.017 ETKDGv3 12
F5F C16 -3.961 -0.163 -0.155 ETKDGv3 13
F5F C17 0.401 2.236 -1.016 ETKDGv3 14
F5F C18 0.365 3.186 -0.074 ETKDGv3 15
F5F N3 3.479 -1.329 -1.392 ETKDGv3 16
F5F O8 2.420 0.611 2.202 ETKDGv3 17
F5F O9 1.232 -1.602 -1.902 ETKDGv3 18
F5F H1 4.858 0.087 1.346 ETKDGv3 19
F5F H2 5.515 -1.041 -0.671 ETKDGv3 20
F5F H4 0.137 0.733 1.154 ETKDGv3 21
F5F H5 -0.030 -2.113 0.605 ETKDGv3 22
F5F H6 -2.442 -2.288 -0.119 ETKDGv3 23
F5F H7 -1.277 -1.856 -1.368 ETKDGv3 24
F5F H8 -2.836 -0.337 -1.957 ETKDGv3 25
F5F H9 -2.214 1.837 -1.479 ETKDGv3 26
F5F H10 -2.043 1.559 0.283 ETKDGv3 27
F5F H11 -0.178 0.380 -1.852 ETKDGv3 28
F5F H12 -0.453 -1.124 2.770 ETKDGv3 29
F5F H13 -1.866 -0.201 2.149 ETKDGv3 30
F5F H14 -1.916 -2.007 2.218 ETKDGv3 31
F5F H15 -4.548 0.708 -0.518 ETKDGv3 32
F5F H16 -4.546 -1.083 -0.369 ETKDGv3 33
F5F H17 -3.832 -0.070 0.942 ETKDGv3 34
F5F H18 0.976 2.423 -1.918 ETKDGv3 35
F5F H19 -0.199 3.055 0.843 ETKDGv3 36
F5F H20 0.907 4.114 -0.222 ETKDGv3 37
F5F H21 1.529 0.597 2.678 ETKDGv3 38
F5F H3 3.776 -1.846 -2.249 ETKDGv3 39
#