data_TFF
#
_chem_comp.id TFF
_chem_comp.name "5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl](difluoro)methyl}(hydroxy)phosphoryl]thymidine"
_chem_comp.type "DNA LINKING"
_chem_comp.pdbx_type ATOMN
_chem_comp.formula "C12 H17 F4 N2 O12 P3"
_chem_comp.mon_nstd_parent_comp_id DT
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2010-02-04
_chem_comp.pdbx_modified_date 2011-06-04
_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 550.184
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code TFF
_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 3LK9
_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
TFF N1 N1 N 0 1 N N N 2.243 1.171 3.114 -5.494 0.384 0.464 N1 TFF 1
TFF C2 C2 C 0 1 N N N 2.460 1.385 1.774 -5.497 0.504 -0.876 C2 TFF 2
TFF O2 O2 O 0 1 N N N 2.642 0.455 0.953 -4.826 -0.256 -1.547 O2 TFF 3
TFF N3 N3 N 0 1 N N N 2.495 2.639 1.264 -6.232 1.454 -1.484 N3 TFF 4
TFF C4 C4 C 0 1 N N N 2.308 3.730 2.039 -6.982 2.304 -0.754 C4 TFF 5
TFF O4 O4 O 0 1 N N N 2.372 4.847 1.480 -7.647 3.164 -1.303 O4 TFF 6
TFF C5 C5 C 0 1 N N N 2.061 3.582 3.421 -6.988 2.189 0.657 C5 TFF 7
TFF C6 C6 C 0 1 N N N 2.042 2.261 3.923 -6.241 1.227 1.241 C6 TFF 8
TFF PA PA P 0 1 N N N 1.967 1.862 8.370 0.929 -1.263 -0.512 PA TFF 9
TFF PB PB P 0 1 N N N -0.917 1.446 8.470 3.669 -0.112 -0.330 PB TFF 10
TFF PG PG P 0 1 N N N -3.815 1.342 8.717 6.408 1.038 -0.148 PG TFF 11
TFF "C1'" "C1'" C 0 1 N N R 2.267 -0.179 3.657 -4.689 -0.663 1.097 "C1'" TFF 12
TFF F1A F1A F 0 1 N N N 0.681 1.073 10.400 1.498 1.053 0.624 F1A TFF 13
TFF O1A O1A O 0 1 N N N 1.966 2.993 7.420 0.763 -0.656 -1.851 O1A TFF 14
TFF F1B F1B F 0 1 N N N -2.388 3.316 9.356 4.238 2.204 0.806 F1B TFF 15
TFF O1B O1B O 0 1 N N N -0.927 -0.020 8.294 3.503 0.495 -1.669 O1B TFF 16
TFF O1G O1G O 0 1 N N N -4.959 1.950 9.499 7.394 1.953 0.737 O1G TFF 17
TFF "C2'" "C2'" C 0 1 N N N 3.712 -0.722 3.772 -5.228 -2.051 0.700 "C2'" TFF 18
TFF F2A F2A F 0 1 N N N 0.396 3.185 9.802 2.202 -0.802 1.757 F2A TFF 19
TFF O2A O2A O 0 1 N N N 3.165 1.995 9.283 1.559 -2.737 -0.666 O2A TFF 20
TFF F2B F2B F 0 1 N N N -2.229 1.526 10.660 4.942 0.349 1.939 F2B TFF 21
TFF O2B O2B O 0 1 N N N -0.940 2.099 7.107 4.298 -1.586 -0.484 O2B TFF 22
TFF O2G O2G O 0 1 N N N -3.868 -0.129 8.838 6.987 -0.317 -0.290 O2G TFF 23
TFF "C3'" "C3'" C 0 1 N N S 3.660 -1.626 5.007 -4.023 -2.746 0.020 "C3'" TFF 24
TFF "O3'" "O3'" O 0 1 N N N 3.293 -2.961 4.654 -3.937 -4.117 0.414 "O3'" TFF 25
TFF C3A C3A C 0 1 N N N 0.523 1.906 9.320 2.045 -0.228 0.491 C3A TFF 26
TFF C3B C3B C 0 1 N N N -2.324 1.943 9.354 4.785 0.923 0.673 C3B TFF 27
TFF O3G O3G O 0 1 N N N -3.957 1.740 7.267 6.227 1.699 -1.605 O3G TFF 28
TFF "C4'" "C4'" C 0 1 N N R 2.555 -0.967 5.864 -2.825 -1.935 0.575 "C4'" TFF 29
TFF "O4'" "O4'" O 0 1 N N N 1.642 -0.337 4.948 -3.331 -0.584 0.632 "O4'" TFF 30
TFF "C5'" "C5'" C 0 1 N N N 3.079 0.077 6.889 -1.629 -2.022 -0.375 "C5'" TFF 31
TFF "O5'" "O5'" O 0 1 N N N 2.049 0.549 7.608 -0.505 -1.365 0.213 "O5'" TFF 32
TFF C5M C5M C 0 1 N N N 1.832 4.726 4.334 -7.817 3.127 1.496 C5M TFF 33
TFF HN3 HN3 H 0 1 N N N 2.664 2.761 0.286 -6.222 1.527 -2.451 HN3 TFF 34
TFF H6 H6 H 0 1 N N N 1.864 2.104 4.977 -6.234 1.124 2.316 H6 TFF 35
TFF "H1'" "H1'" H 0 1 N N N 1.675 -0.751 2.928 -4.719 -0.550 2.181 "H1'" TFF 36
TFF "H2'" "H2'" H 0 1 N N N 4.003 -1.285 2.873 -5.540 -2.607 1.584 "H2'" TFF 37
TFF "H2'A" "H2'A" H 0 0 N N N 4.439 0.093 3.900 -6.057 -1.952 -0.001 "H2'A" TFF 38
TFF "H3'" "H3'" H 0 1 N N N 4.628 -1.711 5.522 -4.085 -2.658 -1.064 "H3'" TFF 39
TFF "HO3'" "HO3'" H 0 0 N N N 3.268 -3.500 5.436 -4.708 -4.646 0.168 "HO3'" TFF 40
TFF "H4'" "H4'" H 0 1 N N N 2.077 -1.749 6.472 -2.552 -2.285 1.571 "H4'" TFF 41
TFF "H5'" "H5'" H 0 1 N N N 3.808 -0.401 7.560 -1.385 -3.069 -0.556 "H5'" TFF 42
TFF "H5'A" "H5'A" H 0 0 N N N 3.564 0.906 6.354 -1.879 -1.539 -1.320 "H5'A" TFF 43
TFF H5M H5M H 0 1 N N N 1.663 4.353 5.355 -8.343 3.826 0.847 H5M TFF 44
TFF H5MA H5MA H 0 0 N N N 2.713 5.384 4.325 -8.541 2.553 2.075 H5MA TFF 45
TFF H5MB H5MB H 0 0 N N N 0.949 5.291 4.000 -7.166 3.680 2.174 H5MB TFF 46
TFF H14 H14 H 0 1 N N N -0.956 1.428 6.434 4.435 -2.045 0.356 H14 TFF 47
TFF H15 H15 H 0 1 N N N -4.051 0.961 6.732 5.852 2.590 -1.589 H15 TFF 48
TFF H16 H16 H 0 1 N N N -5.470 1.258 9.903 8.278 2.058 0.360 H16 TFF 49
TFF H17 H17 H 0 1 N N N 3.657 2.774 9.050 1.696 -3.196 0.174 H17 TFF 50
#
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
TFF N1 C2 SING N N 1
TFF N1 C6 SING N N 2
TFF N1 "C1'" SING N N 3
TFF C2 O2 DOUB N N 4
TFF C2 N3 SING N N 5
TFF N3 C4 SING N N 6
TFF N3 HN3 SING N N 7
TFF C4 O4 DOUB N N 8
TFF C4 C5 SING N N 9
TFF C5 C6 DOUB N N 10
TFF C5 C5M SING N N 11
TFF C6 H6 SING N N 12
TFF PA O1A DOUB N N 13
TFF PA O2A SING N N 14
TFF PA C3A SING N N 15
TFF PA "O5'" SING N N 16
TFF PB O1B DOUB N N 17
TFF PB O2B SING N N 18
TFF PB C3A SING N N 19
TFF PB C3B SING N N 20
TFF PG O1G SING N N 21
TFF PG O2G DOUB N N 22
TFF PG C3B SING N N 23
TFF PG O3G SING N N 24
TFF "C1'" "C2'" SING N N 25
TFF "C1'" "O4'" SING N N 26
TFF "C1'" "H1'" SING N N 27
TFF F1A C3A SING N N 28
TFF F1B C3B SING N N 29
TFF "C2'" "C3'" SING N N 30
TFF "C2'" "H2'" SING N N 31
TFF "C2'" "H2'A" SING N N 32
TFF F2A C3A SING N N 33
TFF F2B C3B SING N N 34
TFF "C3'" "O3'" SING N N 35
TFF "C3'" "C4'" SING N N 36
TFF "C3'" "H3'" SING N N 37
TFF "O3'" "HO3'" SING N N 38
TFF "C4'" "O4'" SING N N 39
TFF "C4'" "C5'" SING N N 40
TFF "C4'" "H4'" SING N N 41
TFF "C5'" "O5'" SING N N 42
TFF "C5'" "H5'" SING N N 43
TFF "C5'" "H5'A" SING N N 44
TFF C5M H5M SING N N 45
TFF C5M H5MA SING N N 46
TFF C5M H5MB SING N N 47
TFF O2B H14 SING N N 48
TFF O3G H15 SING N N 49
TFF O1G H16 SING N N 50
TFF O2A H17 SING N N 51
#
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
TFF SMILES_CANONICAL CACTVS 3.352 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)C(F)(F)[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O"
TFF SMILES CACTVS 3.352 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)C(F)(F)[P](O)(=O)C(F)(F)[P](O)(O)=O)O2)C(=O)NC1=O"
TFF SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(C(F)(F)[P@@](=O)(C(F)(F)P(=O)(O)O)O)O)O"
TFF SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(C(F)(F)P(=O)(C(F)(F)P(=O)(O)O)O)O)O"
TFF InChI InChI 1.03 "InChI=1S/C12H17F4N2O12P3/c1-5-3-18(10(21)17-9(5)20)8-2-6(19)7(30-8)4-29-33(27,28)12(15,16)31(22,23)11(13,14)32(24,25)26/h3,6-8,19H,2,4H2,1H3,(H,22,23)(H,27,28)(H,17,20,21)(H2,24,25,26)/t6-,7+,8+/m0/s1"
TFF InChIKey InChI 1.03 HHJYLFURQLSDJT-XLPZGREQSA-N
#
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
TFF "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[[[difluoro-[hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl]methyl]-hydroxy-phosphoryl]-difluoro-methyl]phosphonic 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
TFF "Create component" 2010-02-04 RCSB
TFF "Modify descriptor" 2011-06-04 RCSB
#