data_0FV
#
_chem_comp.id 0FV
_chem_comp.name "(2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H19 F O7 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "2-fluorogeranyl diphosphate"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-01-04
_chem_comp.pdbx_modified_date 2020-06-17
_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 332.200
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 0FV
_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 3V1X
_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
0FV C1 C1 C 0 1 N N N N N N -27.315 34.780 3.440 0.290 -1.708 -0.620 C1 0FV 1
0FV O1 O1 O 0 1 N N N N N N -28.758 34.837 3.394 -0.580 -0.633 -0.257 O1 0FV 2
0FV C2 C2 C 0 1 N N N N N N -26.829 34.802 2.036 1.704 -1.196 -0.724 C2 0FV 3
0FV F2 F2 F 0 1 N N N N N N -26.340 35.990 1.591 2.024 -0.285 -1.668 F2 0FV 4
0FV C3 C3 C 0 1 N N N N N N -26.917 33.740 1.262 2.624 -1.636 0.103 C3 0FV 5
0FV C4 C4 C 0 1 N N N N N N -27.480 32.446 1.762 2.240 -2.547 1.241 C4 0FV 6
0FV C5 C5 C 0 1 N N N N N N -26.425 33.832 -0.151 4.062 -1.230 -0.085 C5 0FV 7
0FV C6 C6 C 0 1 N N N N N N -25.170 32.998 -0.298 4.369 -0.017 0.796 C6 0FV 8
0FV C7 C7 C 0 1 N N N N N N -23.935 33.757 0.092 5.808 0.389 0.608 C7 0FV 9
0FV C8 C8 C 0 1 N N N N N N -22.738 33.458 -0.398 6.098 1.589 0.168 C8 0FV 10
0FV C9 C9 C 0 1 N N N N N N -21.542 34.245 0.048 4.996 2.514 -0.279 C9 0FV 11
0FV C10 C10 C 0 1 N N N N N N -22.497 32.385 -1.423 7.534 2.043 0.110 C10 0FV 12
0FV PA PA P 0 1 N N N N N N -29.219 36.402 3.369 -2.167 -0.819 -0.057 PA 0FV 13
0FV O1A O1A O 0 1 N N N N N N -29.346 36.863 1.987 -2.751 -1.416 -1.279 O1A 0FV 14
0FV O2A O2A O 0 1 N N N N N N -30.641 36.477 4.064 -2.439 -1.790 1.198 O2A 0FV 15
0FV O3A O3A O 0 1 N N N N N N -28.112 37.352 4.092 -2.845 0.615 0.217 O3A 0FV 16
0FV PB PB P 0 1 N N N N N N -28.395 38.246 5.417 -4.360 1.158 0.193 PB 0FV 17
0FV O1B O1B O 0 1 N N N N N N -29.319 37.802 6.485 -4.430 2.586 0.933 O1B 0FV 18
0FV O2B O2B O 0 1 N N N N N N -27.035 38.274 6.248 -4.848 1.321 -1.333 O2B 0FV 19
0FV O3B O3B O 0 1 N N N N N N -28.764 39.722 4.933 -5.240 0.197 0.893 O3B 0FV 20
0FV H1 H1 H 0 1 N N N N N N -26.990 33.854 3.937 0.241 -2.487 0.140 H1 0FV 21
0FV H2 H2 H 0 1 N N N N N N -26.921 35.648 3.989 -0.020 -2.117 -1.581 H2 0FV 22
0FV H3 H3 H 0 1 N N N N N N -27.789 32.561 2.811 2.214 -3.578 0.888 H3 0FV 23
0FV H4 H4 H 0 1 N N N N N N -28.351 32.165 1.152 2.974 -2.456 2.042 H4 0FV 24
0FV H5 H5 H 0 1 N N N N N N -26.713 31.660 1.690 1.256 -2.266 1.616 H5 0FV 25
0FV H6 H6 H 0 1 N N N N N N -26.200 34.881 -0.394 4.713 -2.057 0.197 H6 0FV 26
0FV H7 H7 H 0 1 N N N N N N -27.199 33.455 -0.835 4.234 -0.972 -1.130 H7 0FV 27
0FV H8 H8 H 0 1 N N N N N N -25.258 32.110 0.345 3.718 0.811 0.515 H8 0FV 28
0FV H9 H9 H 0 1 N N N N N N -25.075 32.683 -1.348 4.198 -0.275 1.841 H9 0FV 29
0FV H10 H10 H 0 1 N N N N N N -24.023 34.573 0.794 6.601 -0.308 0.836 H10 0FV 30
0FV H11 H11 H 0 1 N N N N N N -21.851 34.992 0.793 4.596 3.047 0.584 H11 0FV 31
0FV H12 H12 H 0 1 N N N N N N -20.802 33.565 0.496 5.393 3.232 -0.997 H12 0FV 32
0FV H13 H13 H 0 1 N N N N N N -21.095 34.755 -0.818 4.202 1.933 -0.747 H13 0FV 33
0FV H14 H14 H 0 1 N N N N N N -23.448 31.886 -1.663 7.802 2.522 1.051 H14 0FV 34
0FV H15 H15 H 0 1 N N N N N N -22.080 32.837 -2.335 8.181 1.182 -0.058 H15 0FV 35
0FV H16 H16 H 0 1 N N N N N N -21.787 31.647 -1.021 7.657 2.754 -0.707 H16 0FV 36
0FV H17 H17 H 0 1 N N N N N N -31.281 36.805 3.443 -2.083 -1.461 2.034 H17 0FV 37
0FV H18 H18 H 0 1 N N N N N N -29.948 38.490 6.667 -5.315 2.975 0.957 H18 0FV 38
0FV H19 H19 H 0 1 N N N N N N -26.709 39.165 6.293 -4.315 1.938 -1.853 H19 0FV 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
0FV C10 C8 SING N N 1
0FV C8 C9 SING N N 2
0FV C8 C7 DOUB N N 3
0FV C6 C5 SING N N 4
0FV C6 C7 SING N N 5
0FV C5 C3 SING N N 6
0FV C3 C4 SING N N 7
0FV C3 C2 DOUB N Z 8
0FV F2 C2 SING N N 9
0FV O1A PA DOUB N N 10
0FV C2 C1 SING N N 11
0FV PA O1 SING N N 12
0FV PA O2A SING N N 13
0FV PA O3A SING N N 14
0FV O1 C1 SING N N 15
0FV O3A PB SING N N 16
0FV O3B PB DOUB N N 17
0FV PB O2B SING N N 18
0FV PB O1B SING N N 19
0FV C1 H1 SING N N 20
0FV C1 H2 SING N N 21
0FV C4 H3 SING N N 22
0FV C4 H4 SING N N 23
0FV C4 H5 SING N N 24
0FV C5 H6 SING N N 25
0FV C5 H7 SING N N 26
0FV C6 H8 SING N N 27
0FV C6 H9 SING N N 28
0FV C7 H10 SING N N 29
0FV C9 H11 SING N N 30
0FV C9 H12 SING N N 31
0FV C9 H13 SING N N 32
0FV C10 H14 SING N N 33
0FV C10 H15 SING N N 34
0FV C10 H16 SING N N 35
0FV O2A H17 SING N N 36
0FV O1B H18 SING N N 37
0FV O2B H19 SING N N 38
#
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
0FV SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(OCC(\F)=C(/C)CC\C=C(/C)C)O
0FV InChI InChI 1.03 InChI=1S/C10H19FO7P2/c1-8(2)5-4-6-9(3)10(11)7-17-20(15,16)18-19(12,13)14/h5H,4,6-7H2,1-3H3,(H,15,16)(H2,12,13,14)/b10-9-
0FV InChIKey InChI 1.03 BYJNSLXDWGDGAC-KTKRTIGZSA-N
0FV SMILES_CANONICAL CACTVS 3.370 CC(C)=CCCC(/C)=C(F)/CO[P](O)(=O)O[P](O)(O)=O
0FV SMILES CACTVS 3.370 CC(C)=CCCC(C)=C(F)CO[P](O)(=O)O[P](O)(O)=O
0FV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 CC(=CCC/C(=C(/COP(=O)(O)OP(=O)(O)O)\F)/C)C
0FV SMILES "OpenEye OEToolkits" 1.7.6 CC(=CCCC(=C(COP(=O)(O)OP(=O)(O)O)F)C)C
#
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
0FV "SYSTEMATIC NAME" ACDLabs 12.01 "(2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate"
0FV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2Z)-2-fluoranyl-3,7-dimethyl-octa-2,6-dienyl] phosphono hydrogen phosphate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
0FV 'Create component' 2012-01-04 RCSB
0FV 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id 0FV
_pdbx_chem_comp_synonyms.name "2-fluorogeranyl diphosphate"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id 0FV
_pdbe_chem_comp_synonyms.name '2-fluorogeranyl diphosphate'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
0FV C1 C 12.093 0.073 1
0FV O1 O 13.392 -0.677 2
0FV C2 C 10.794 -0.677 3
0FV F2 F 10.794 -2.177 4
0FV C3 C 9.495 0.073 5
0FV C4 C 9.495 1.573 6
0FV C5 C 8.196 -0.677 7
0FV C6 C 6.897 0.073 8
0FV C7 C 5.598 -0.677 9
0FV C8 C 4.299 0.073 10
0FV C9 C 4.299 1.573 11
0FV C10 C 3.000 -0.677 12
0FV PA P 14.691 0.073 13
0FV O1A O 13.941 1.372 14
0FV O2A O 15.441 -1.226 15
0FV O3A O 15.990 0.823 16
0FV PB P 17.290 0.073 17
0FV O1B O 16.540 -1.226 18
0FV O2B O 18.040 1.372 19
0FV O3B O 18.588 -0.677 20
#
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
0FV C10 C8 SINGLE NONE 1
0FV C8 C9 SINGLE NONE 2
0FV C8 C7 DOUBLE NONE 3
0FV C6 C5 SINGLE NONE 4
0FV C6 C7 SINGLE NONE 5
0FV C5 C3 SINGLE ENDUPRIGHT 6
0FV C3 C4 SINGLE ENDUPRIGHT 7
0FV C3 C2 DOUBLE NONE 8
0FV F2 C2 SINGLE ENDUPRIGHT 9
0FV O1A PA DOUBLE NONE 10
0FV C2 C1 SINGLE ENDUPRIGHT 11
0FV PA O1 SINGLE NONE 12
0FV PA O2A SINGLE BEGINWEDGE 13
0FV PA O3A SINGLE NONE 14
0FV O1 C1 SINGLE NONE 15
0FV O3A PB SINGLE NONE 16
0FV O3B PB DOUBLE NONE 17
0FV PB O2B SINGLE NONE 18
0FV PB O1B SINGLE NONE 19
#
_pdbe_chem_comp_substructure.comp_id 0FV
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-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
0FV O1 F1 1
0FV PA F1 1
0FV O1A F1 1
0FV O2A F1 1
0FV O3A F1 1
0FV O3A F1 2
0FV PB F1 2
0FV O3B F1 2
0FV O2B F1 2
0FV O1B F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 0FV
_pdbe_chem_comp_rdkit_properties.exactmw 332.059
_pdbe_chem_comp_rdkit_properties.amw 332.201
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 14
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 10
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 143.474
_pdbe_chem_comp_rdkit_properties.tpsa 113.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP 3.203
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.379
_pdbe_chem_comp_rdkit_properties.chi0v 10.919
_pdbe_chem_comp_rdkit_properties.chi1v 7.025
_pdbe_chem_comp_rdkit_properties.chi2v 2.956
_pdbe_chem_comp_rdkit_properties.chi3v 2.956
_pdbe_chem_comp_rdkit_properties.chi4v 1.802
_pdbe_chem_comp_rdkit_properties.chi0n 28.130
_pdbe_chem_comp_rdkit_properties.chi1n 13.328
_pdbe_chem_comp_rdkit_properties.chi2n 1.042
_pdbe_chem_comp_rdkit_properties.chi3n 1.042
_pdbe_chem_comp_rdkit_properties.chi4n 0.497
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.330
_pdbe_chem_comp_rdkit_properties.kappa1 4.832
_pdbe_chem_comp_rdkit_properties.kappa2 8.195
_pdbe_chem_comp_rdkit_properties.kappa3 10.457
_pdbe_chem_comp_rdkit_properties.Phi 1.980
#
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
0FV UniChem PDBe 0FV
0FV UniChem PubChem 3037771
0FV UniChem ACTor 62163-14-8
0FV UniChem BRENDA 228142
#
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
0FV C1 2.050 0.489 -0.279 ETKDGv3 1
0FV O1 2.181 -0.245 0.915 ETKDGv3 2
0FV C2 0.629 0.969 -0.412 ETKDGv3 3
0FV F2 0.409 2.309 -0.314 ETKDGv3 4
0FV C3 -0.414 0.133 -0.640 ETKDGv3 5
0FV C4 -0.215 -1.359 -0.784 ETKDGv3 6
0FV C5 -1.817 0.694 -0.756 ETKDGv3 7
0FV C6 -2.403 0.984 0.630 ETKDGv3 8
0FV C7 -3.821 1.485 0.516 ETKDGv3 9
0FV C8 -4.912 0.688 0.487 ETKDGv3 10
0FV C9 -6.266 1.331 0.329 ETKDGv3 11
0FV C10 -4.812 -0.813 0.624 ETKDGv3 12
0FV PA 3.740 -0.933 0.951 ETKDGv3 13
0FV O1A 3.922 -1.628 2.283 ETKDGv3 14
0FV O2A 3.869 -2.073 -0.296 ETKDGv3 15
0FV O3A 4.903 0.301 0.784 ETKDGv3 16
0FV PB 6.423 -0.437 0.573 ETKDGv3 17
0FV O1B 6.479 -1.261 -0.904 ETKDGv3 18
0FV O2B 7.608 0.771 0.567 ETKDGv3 19
0FV O3B 6.715 -1.400 1.703 ETKDGv3 20
0FV H1 2.716 1.380 -0.249 ETKDGv3 21
0FV H2 2.308 -0.117 -1.177 ETKDGv3 22
0FV H3 0.446 -1.574 -1.650 ETKDGv3 23
0FV H4 0.236 -1.776 0.140 ETKDGv3 24
0FV H5 -1.179 -1.882 -0.950 ETKDGv3 25
0FV H6 -1.805 1.623 -1.367 ETKDGv3 26
0FV H7 -2.469 -0.025 -1.294 ETKDGv3 27
0FV H8 -1.796 1.773 1.124 ETKDGv3 28
0FV H9 -2.347 0.080 1.274 ETKDGv3 29
0FV H10 -3.953 2.560 0.426 ETKDGv3 30
0FV H11 -7.082 0.578 0.329 ETKDGv3 31
0FV H12 -6.307 1.888 -0.630 ETKDGv3 32
0FV H13 -6.447 2.037 1.167 ETKDGv3 33
0FV H14 -4.169 -1.232 -0.177 ETKDGv3 34
0FV H15 -4.387 -1.075 1.616 ETKDGv3 35
0FV H16 -5.808 -1.296 0.545 ETKDGv3 36
0FV H17 3.082 -2.663 -0.182 ETKDGv3 37
0FV H18 6.245 -0.577 -1.582 ETKDGv3 38
0FV H19 8.451 0.296 0.354 ETKDGv3 39
#