data_F2T
#
_chem_comp.id F2T
_chem_comp.name "2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine"
_chem_comp.type "RNA linking"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C9 H12 F N2 O7 P S"
_chem_comp.mon_nstd_parent_comp_id U
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-05-13
_chem_comp.pdbx_modified_date 2016-07-15
_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 342.238
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code F2T
_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 5JS2
_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
F2T P P1 P 0 1 N N N N N N -25.146 32.037 28.157 -4.096 -0.541 0.367 P F2T 1
F2T SP1 S1 S 0 1 N N N N N N -26.552 32.169 27.596 -3.828 -2.231 -0.885 SP1 F2T 2
F2T OP2 O1 O 0 1 N N N N N N -25.316 30.874 29.146 -5.043 0.400 -0.272 OP2 F2T 3
F2T "O5'" O2 O 0 1 N N N N N N -24.851 33.376 28.852 -2.680 0.192 0.589 "O5'" F2T 4
F2T "C5'" C1 C 0 1 N N N N N N -23.627 33.410 29.501 -1.952 0.818 -0.470 "C5'" F2T 5
F2T "C4'" C2 C 0 1 N N R N N N -23.782 34.102 30.882 -0.657 1.414 0.084 "C4'" F2T 6
F2T "O4'" O3 O 0 1 N N N N N N -24.754 34.923 30.865 0.232 0.369 0.535 "O4'" F2T 7
F2T "C3'" C3 C 0 1 N N R N N N -24.269 33.110 31.883 0.148 2.112 -1.042 "C3'" F2T 8
F2T "O3'" O4 O 0 1 N N N N N N -23.254 32.445 32.415 -0.283 3.463 -1.215 "O3'" F2T 9
F2T "C2'" C4 C 0 1 N N R N N N -24.783 34.005 32.970 1.593 2.060 -0.488 "C2'" F2T 10
F2T "F2'" F1 F 0 1 N N N N N N -23.606 34.515 33.506 1.927 3.273 0.123 "F2'" F2T 11
F2T "C1'" C5 C 0 1 N N R N N N -25.344 34.931 32.354 1.558 0.924 0.553 "C1'" F2T 12
F2T N1 N1 N 0 1 N N N N N N -26.759 34.723 32.332 2.535 -0.108 0.198 N1 F2T 13
F2T C2 C6 C 0 1 N N N N N N -27.506 35.195 33.354 3.578 -0.348 1.013 C2 F2T 14
F2T O2 O5 O 0 1 N N N N N N -27.025 35.773 34.293 3.697 0.296 2.038 O2 F2T 15
F2T N3 N2 N 0 1 N N N N N N -28.827 34.992 33.293 4.490 -1.290 0.711 N3 F2T 16
F2T C4 C7 C 0 1 N N N N N N -29.391 34.339 32.248 4.371 -2.013 -0.421 C4 F2T 17
F2T O4 O6 O 0 1 N N N N N N -30.783 34.169 32.252 5.196 -2.866 -0.696 O4 F2T 18
F2T C5 C8 C 0 1 N N N N N N -28.656 33.831 31.174 3.278 -1.771 -1.288 C5 F2T 19
F2T C6 C9 C 0 1 N N N N N N -27.274 34.061 31.272 2.375 -0.823 -0.958 C6 F2T 20
F2T "H5'" H1 H 0 1 N N N N N N -23.262 32.382 29.646 -1.714 0.078 -1.234 H1 F2T 21
F2T "H5''" H2 H 0 0 N N N N N N -22.905 33.972 28.890 -2.558 1.610 -0.908 H2 F2T 22
F2T "H4'" H3 H 0 1 N N N N N N -22.821 34.535 31.196 -0.872 2.111 0.894 H3 F2T 23
F2T "H3'" H4 H 0 1 N N N N N N -25.067 32.475 31.471 0.070 1.558 -1.977 H4 F2T 24
F2T "HO3'" H5 H 0 0 N Y N N N N -23.583 31.819 33.049 0.191 3.942 -1.908 H5 F2T 25
F2T "H2'" H6 H 0 1 N N N N N N -25.397 33.454 33.698 2.299 1.828 -1.285 H6 F2T 26
F2T "H1'" H7 H 0 1 N N N N N N -25.125 35.918 32.787 1.780 1.322 1.544 H7 F2T 27
F2T H3 H8 H 0 1 N N N N N N -29.409 35.329 34.033 5.236 -1.450 1.310 H8 F2T 28
F2T H5 H9 H 0 1 N N N N N N -29.109 33.309 30.344 3.167 -2.339 -2.200 H9 F2T 29
F2T H6 H10 H 0 1 N N N N N N -26.616 33.705 30.493 1.532 -0.628 -1.605 H10 F2T 30
F2T OP3 O7 O 0 1 N Y N N N N -23.854 31.754 27.351 -4.685 -1.013 1.788 O1 F2T 31
F2T H11 H11 H 0 1 N N N N N N -27.187 31.232 28.236 -5.071 -2.736 -0.982 H11 F2T 32
F2T HOP3 H12 H 0 0 N Y N N N N -23.467 30.938 27.648 -4.115 -1.633 2.264 H12 F2T 33
#
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
F2T P SP1 SING N N 1
F2T P OP2 DOUB N N 2
F2T P "O5'" SING N N 3
F2T "O5'" "C5'" SING N N 4
F2T "C5'" "C4'" SING N N 5
F2T "C4'" "O4'" SING N N 6
F2T "C4'" "C3'" SING N N 7
F2T "O4'" "C1'" SING N N 8
F2T "C3'" "O3'" SING N N 9
F2T "C3'" "C2'" SING N N 10
F2T "C2'" "F2'" SING N N 11
F2T "C2'" "C1'" SING N N 12
F2T "C1'" N1 SING N N 13
F2T N1 C2 SING N N 14
F2T N1 C6 SING N N 15
F2T C2 O2 DOUB N N 16
F2T C2 N3 SING N N 17
F2T N3 C4 SING N N 18
F2T C4 O4 DOUB N N 19
F2T C4 C5 SING N N 20
F2T C5 C6 DOUB N N 21
F2T "C5'" "H5'" SING N N 22
F2T "C5'" "H5''" SING N N 23
F2T "C4'" "H4'" SING N N 24
F2T "C3'" "H3'" SING N N 25
F2T "O3'" "HO3'" SING N N 26
F2T "C2'" "H2'" SING N N 27
F2T "C1'" "H1'" SING N N 28
F2T N3 H3 SING N N 29
F2T C5 H5 SING N N 30
F2T C6 H6 SING N N 31
F2T P OP3 SING N N 32
F2T SP1 H11 SING N N 33
F2T OP3 HOP3 SING N N 34
#
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
F2T SMILES ACDLabs 12.01 P(S)(=O)(OCC1OC(C(C1O)F)N2C(=O)NC(=O)C=C2)O
F2T InChI InChI 1.03 InChI=1S/C9H12FN2O7PS/c10-6-7(14)4(3-18-20(16,17)21)19-8(6)12-2-1-5(13)11-9(12)15/h1-2,4,6-8,14H,3H2,(H,11,13,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1
F2T InChIKey InChI 1.03 GAVMOIRMDKJPDM-XVFCMESISA-N
F2T SMILES_CANONICAL CACTVS 3.385 O[C@H]1[C@@H](F)[C@@H](O[C@@H]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O
F2T SMILES CACTVS 3.385 O[CH]1[CH](F)[CH](O[CH]1CO[P](O)(S)=O)N2C=CC(=O)NC2=O
F2T SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)S)O)F
F2T SMILES "OpenEye OEToolkits" 2.0.4 C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)S)O)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
F2T "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-2'-fluoro-5'-O-thiophosphonouridine"
F2T "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-fluoranyl-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphinic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
F2T 'Create component' 2016-05-13 RCSB
F2T 'Initial release' 2016-07-20 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
F2T P P 9.645 -4.683 1
F2T SP1 S 10.527 -5.896 2
F2T OP2 O 10.859 -3.801 3
F2T "O5'" O 8.764 -3.469 4
F2T "C5'" C 7.272 -3.626 5
F2T "C4'" C 6.390 -2.412 6
F2T "O4'" O 6.854 -0.986 7
F2T "C3'" C 4.890 -2.412 8
F2T "O3'" O 4.008 -3.626 9
F2T "C2'" C 4.427 -0.986 10
F2T "F2'" F 3.000 -0.522 11
F2T "C1'" C 5.640 -0.104 12
F2T N1 N 5.640 1.396 13
F2T C2 C 6.939 2.146 14
F2T O2 O 8.238 1.396 15
F2T N3 N 6.939 3.646 16
F2T C4 C 5.640 4.396 17
F2T O4 O 5.640 5.896 18
F2T C5 C 4.341 3.646 19
F2T C6 C 4.341 2.146 20
F2T OP3 O 8.432 -5.564 21
#
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
F2T P SP1 SINGLE NONE 1
F2T P OP2 DOUBLE NONE 2
F2T P "O5'" SINGLE NONE 3
F2T "O5'" "C5'" SINGLE NONE 4
F2T "C4'" "C5'" SINGLE BEGINDASH 5
F2T "C4'" "O4'" SINGLE NONE 6
F2T "C4'" "C3'" SINGLE NONE 7
F2T "O4'" "C1'" SINGLE NONE 8
F2T "C3'" "O3'" SINGLE BEGINWEDGE 9
F2T "C3'" "C2'" SINGLE NONE 10
F2T "C2'" "F2'" SINGLE BEGINWEDGE 11
F2T "C2'" "C1'" SINGLE NONE 12
F2T "C1'" N1 SINGLE BEGINDASH 13
F2T N1 C2 SINGLE NONE 14
F2T N1 C6 SINGLE NONE 15
F2T C2 O2 DOUBLE NONE 16
F2T C2 N3 SINGLE NONE 17
F2T N3 C4 SINGLE NONE 18
F2T C4 O4 DOUBLE NONE 19
F2T C4 C5 SINGLE NONE 20
F2T C5 C6 DOUBLE NONE 21
F2T P OP3 SINGLE BEGINDASH 22
#
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
F2T MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CCCO2)c(=O)[nH]1' InChI=1S/C8H10N2O3/c11-6-3-4-10(8(12)9-6)7-2-1-5-13-7/h3-4,7H,1-2,5H2,(H,9,11,12)/t7-/m1/s1 CWWIKVUHBBTKHC-SSDOTTSWSA-N
F2T pyrimidine F1 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
F2T "C4'" S1 1
F2T "O4'" S1 1
F2T "C3'" S1 1
F2T "C2'" S1 1
F2T "C1'" S1 1
F2T N1 S1 1
F2T C2 S1 1
F2T O2 S1 1
F2T N3 S1 1
F2T C4 S1 1
F2T O4 S1 1
F2T C5 S1 1
F2T C6 S1 1
F2T C5 F1 1
F2T C4 F1 1
F2T N3 F1 1
F2T C2 F1 1
F2T N1 F1 1
F2T C6 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id F2T
_pdbe_chem_comp_rdkit_properties.exactmw 342.009
_pdbe_chem_comp_rdkit_properties.amw 342.241
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 9
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 12
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.556
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 138.342
_pdbe_chem_comp_rdkit_properties.tpsa 130.850
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.980
_pdbe_chem_comp_rdkit_properties.CrippenMR 71.115
_pdbe_chem_comp_rdkit_properties.chi0v 11.197
_pdbe_chem_comp_rdkit_properties.chi1v 7.318
_pdbe_chem_comp_rdkit_properties.chi2v 2.447
_pdbe_chem_comp_rdkit_properties.chi3v 2.447
_pdbe_chem_comp_rdkit_properties.chi4v 1.453
_pdbe_chem_comp_rdkit_properties.chi0n 21.486
_pdbe_chem_comp_rdkit_properties.chi1n 10.434
_pdbe_chem_comp_rdkit_properties.chi2n 1.908
_pdbe_chem_comp_rdkit_properties.chi3n 1.908
_pdbe_chem_comp_rdkit_properties.chi4n 1.147
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.970
_pdbe_chem_comp_rdkit_properties.kappa1 6.649
_pdbe_chem_comp_rdkit_properties.kappa2 6.030
_pdbe_chem_comp_rdkit_properties.kappa3 3.816
_pdbe_chem_comp_rdkit_properties.Phi 1.909
#
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
F2T UniChem PDBe F2T
F2T UniChem PubChem 138753195
#
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
F2T P 4.473 0.222 0.382 ETKDGv3 1
F2T SP1 3.960 2.135 1.125 ETKDGv3 2
F2T OP2 5.723 0.348 -0.459 ETKDGv3 3
F2T "O5'" 3.210 -0.383 -0.591 ETKDGv3 4
F2T "C5'" 2.122 -0.710 0.241 ETKDGv3 5
F2T "C4'" 0.921 -1.107 -0.623 ETKDGv3 6
F2T "O4'" -0.153 -1.488 0.204 ETKDGv3 7
F2T "C3'" 0.447 0.035 -1.512 ETKDGv3 8
F2T "O3'" 1.138 0.042 -2.734 ETKDGv3 9
F2T "C2'" -1.015 -0.281 -1.690 ETKDGv3 10
F2T "F2'" -1.222 -1.030 -2.840 ETKDGv3 11
F2T "C1'" -1.349 -1.122 -0.456 ETKDGv3 12
F2T N1 -2.223 -0.370 0.460 ETKDGv3 13
F2T C2 -3.657 -0.513 0.390 ETKDGv3 14
F2T O2 -4.188 -1.311 -0.429 ETKDGv3 15
F2T N3 -4.487 0.263 1.256 ETKDGv3 16
F2T C4 -3.882 1.199 2.150 ETKDGv3 17
F2T O4 -4.597 1.890 2.922 ETKDGv3 18
F2T C5 -2.422 1.355 2.159 ETKDGv3 19
F2T C6 -1.656 0.615 1.352 ETKDGv3 20
F2T "H5'" 1.826 0.147 0.888 ETKDGv3 21
F2T "H5''" 2.383 -1.578 0.886 ETKDGv3 22
F2T "H4'" 1.206 -1.982 -1.250 ETKDGv3 23
F2T "H3'" 0.558 1.014 -0.988 ETKDGv3 24
F2T "HO3'" 0.896 0.891 -3.187 ETKDGv3 25
F2T "H2'" -1.620 0.651 -1.751 ETKDGv3 26
F2T "H1'" -1.853 -2.062 -0.770 ETKDGv3 27
F2T H3 -5.526 0.156 1.229 ETKDGv3 28
F2T H5 -1.964 2.081 2.819 ETKDGv3 29
F2T H6 -0.585 0.768 1.378 ETKDGv3 30
F2T OP3 4.781 -0.822 1.679 ETKDGv3 31
F2T H11 3.741 2.636 -0.172 ETKDGv3 32
F2T HOP3 5.016 -1.687 1.258 ETKDGv3 33
#