data_FDY
#
_chem_comp.id FDY
_chem_comp.name "5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H18 F N2 O13 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-26
_chem_comp.pdbx_modified_date 2018-06-15
_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 498.186
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code FDY
_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 6CTK
_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
FDY C2 C1 C 0 1 N N N 7.769 7.940 9.331 -5.193 -0.414 0.863 C2 FDY 1
FDY C4 C2 C 0 1 N N N 9.664 7.561 10.658 -6.610 -2.269 0.768 C4 FDY 2
FDY C5 C3 C 0 1 N N N 8.857 7.032 11.700 -6.450 -2.305 -0.638 C5 FDY 3
FDY C6 C4 C 0 1 N N N 7.458 6.991 11.452 -5.661 -1.385 -1.233 C6 FDY 4
FDY O4 O1 O 0 1 N N N 10.856 7.617 10.804 -7.316 -3.089 1.327 O4 FDY 5
FDY C7 C5 C 0 1 N N N 9.454 6.507 13.036 -7.151 -3.356 -1.460 C7 FDY 6
FDY N3 N1 N 0 1 N N N 9.079 8.015 9.508 -5.974 -1.319 1.482 N3 FDY 7
FDY O2 O2 O 0 1 N N N 7.275 8.335 8.267 -4.621 0.433 1.521 O2 FDY 8
FDY N1 N2 N 0 1 N N N 6.953 7.449 10.288 -5.032 -0.438 -0.472 N1 FDY 9
FDY "C1'" C6 C 0 1 N N R 5.544 7.351 10.033 -4.177 0.561 -1.118 "C1'" FDY 10
FDY "C2'" C7 C 0 1 N N N 5.261 6.126 9.669 -4.734 1.982 -0.879 "C2'" FDY 11
FDY "C3'" C8 C 0 1 N N S 4.625 5.455 10.836 -3.473 2.854 -0.694 "C3'" FDY 12
FDY "O3'" O3 O 0 1 N N N 3.725 4.392 10.575 -3.406 3.859 -1.707 "O3'" FDY 13
FDY "O4'" O4 O 0 1 N N N 4.687 7.614 11.351 -2.868 0.571 -0.507 "O4'" FDY 14
FDY "C4'" C9 C 0 1 N N R 3.903 6.665 11.503 -2.302 1.857 -0.842 "C4'" FDY 15
FDY "C5'" C10 C 0 1 N N N 3.699 6.367 13.012 -1.174 2.212 0.129 "C5'" FDY 16
FDY "O5'" O5 O 0 1 N N N 5.073 6.102 13.517 -0.057 1.352 -0.104 "O5'" FDY 17
FDY PA P1 P 0 1 N N N 5.287 4.909 14.592 1.311 1.444 0.740 PA FDY 18
FDY O1A O6 O 0 1 N N N 4.302 5.008 15.716 1.021 1.059 2.276 O1A FDY 19
FDY O2A O7 O 0 1 N N N 6.689 5.002 15.102 1.843 2.823 0.669 O2A FDY 20
FDY O3A O8 O 0 1 N N N 5.202 3.506 13.828 2.391 0.420 0.125 O3A FDY 21
FDY PB P2 P 0 1 N N N 3.975 2.592 13.631 3.983 0.242 0.287 PB FDY 22
FDY O2B O9 O 0 1 N N N 3.856 2.264 12.135 4.308 -0.017 1.707 O2B FDY 23
FDY O1B O10 O 0 1 N N N 2.693 3.214 14.139 4.724 1.587 -0.197 O1B FDY 24
FDY C3B C11 C 0 1 N N R 4.369 1.004 14.572 4.544 -1.161 -0.732 C3B FDY 25
FDY F2B F1 F 0 1 N N N 4.040 -0.033 13.801 3.900 -2.330 -0.312 F2B FDY 26
FDY PG P3 P 0 1 N N N 3.499 0.993 16.140 6.347 -1.362 -0.549 PG FDY 27
FDY O3G O11 O 0 1 N N N 2.024 0.707 15.888 7.029 -0.126 -0.993 O3G FDY 28
FDY O2G O12 O 0 1 N N N 4.082 -0.013 17.042 6.701 -1.644 0.996 O2G FDY 29
FDY O1G O13 O 0 1 N N N 3.618 2.374 16.749 6.843 -2.602 -1.448 O1G FDY 30
FDY H1 H1 H 0 1 N N N 6.793 6.589 12.202 -5.527 -1.397 -2.305 H1 FDY 31
FDY H2 H2 H 0 1 N N N 8.642 6.148 13.685 -7.736 -4.001 -0.804 H2 FDY 32
FDY H3 H3 H 0 1 N N N 10.149 5.680 12.827 -7.813 -2.873 -2.179 H3 FDY 33
FDY H4 H4 H 0 1 N N N 9.994 7.321 13.541 -6.411 -3.954 -1.992 H4 FDY 34
FDY H5 H5 H 0 1 N N N 9.650 8.410 8.789 -6.078 -1.288 2.446 H5 FDY 35
FDY H6 H6 H 0 1 N N N 5.243 8.090 9.276 -4.096 0.357 -2.185 H6 FDY 36
FDY H7 H7 H 0 1 N N N 4.566 6.137 8.816 -5.307 2.317 -1.744 H7 FDY 37
FDY H8 H8 H 0 1 N N N 6.182 5.595 9.385 -5.350 2.005 0.020 H8 FDY 38
FDY H9 H9 H 0 1 N N N 5.415 5.113 11.521 -3.464 3.308 0.297 H9 FDY 39
FDY H10 H10 H 0 1 N N N 3.872 3.692 11.200 -4.149 4.477 -1.698 H10 FDY 40
FDY H11 H11 H 0 1 N N N 2.922 6.807 11.026 -1.934 1.854 -1.868 H11 FDY 41
FDY H12 H12 H 0 1 N N N 3.254 7.233 13.525 -0.873 3.248 -0.026 H12 FDY 42
FDY H13 H13 H 0 1 N N N 3.054 5.487 13.153 -1.523 2.084 1.153 H13 FDY 43
FDY H14 H14 H 0 1 N N N 4.768 5.111 16.538 0.670 0.166 2.398 H14 FDY 44
FDY H15 H15 H 0 1 N N N 2.067 3.278 13.427 4.556 1.819 -1.121 H15 FDY 45
FDY H16 H16 H 0 1 N N N 5.444 1.046 14.802 4.305 -0.970 -1.778 H16 FDY 46
FDY H17 H17 H 0 1 N N N 3.415 -0.643 17.287 6.288 -2.441 1.355 H17 FDY 47
FDY H18 H18 H 0 1 N N N 2.753 2.756 16.840 7.795 -2.767 -1.399 H18 FDY 48
#
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
FDY O2 C2 DOUB N N 1
FDY C2 N3 SING N N 2
FDY C2 N1 SING N N 3
FDY N3 C4 SING N N 4
FDY "C2'" "C1'" SING N N 5
FDY "C2'" "C3'" SING N N 6
FDY "C1'" N1 SING N N 7
FDY "C1'" "O4'" SING N N 8
FDY N1 C6 SING N N 9
FDY "O3'" "C3'" SING N N 10
FDY C4 O4 DOUB N N 11
FDY C4 C5 SING N N 12
FDY "C3'" "C4'" SING N N 13
FDY "O4'" "C4'" SING N N 14
FDY C6 C5 DOUB N N 15
FDY "C4'" "C5'" SING N N 16
FDY C5 C7 SING N N 17
FDY O2B PB DOUB N N 18
FDY "C5'" "O5'" SING N N 19
FDY "O5'" PA SING N N 20
FDY PB O3A SING N N 21
FDY PB O1B SING N N 22
FDY PB C3B SING N N 23
FDY F2B C3B SING N N 24
FDY O3A PA SING N N 25
FDY C3B PG SING N N 26
FDY PA O2A DOUB N N 27
FDY PA O1A SING N N 28
FDY O3G PG DOUB N N 29
FDY PG O1G SING N N 30
FDY PG O2G SING N N 31
FDY C6 H1 SING N N 32
FDY C7 H2 SING N N 33
FDY C7 H3 SING N N 34
FDY C7 H4 SING N N 35
FDY N3 H5 SING N N 36
FDY "C1'" H6 SING N N 37
FDY "C2'" H7 SING N N 38
FDY "C2'" H8 SING N N 39
FDY "C3'" H9 SING N N 40
FDY "O3'" H10 SING N N 41
FDY "C4'" H11 SING N N 42
FDY "C5'" H12 SING N N 43
FDY "C5'" H13 SING N N 44
FDY O1A H14 SING N N 45
FDY O1B H15 SING N N 46
FDY C3B H16 SING N N 47
FDY O2G H17 SING N N 48
FDY O1G H18 SING N N 49
#
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
FDY SMILES ACDLabs 12.01 "C1(NC(=O)C(C)=CN1C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)F)=O)=O"
FDY InChI InChI 1.03 "InChI=1S/C11H18FN2O13P3/c1-5-3-14(11(17)13-9(5)16)8-2-6(15)7(26-8)4-25-30(23,24)27-29(21,22)10(12)28(18,19)20/h3,6-8,10,15H,2,4H2,1H3,(H,21,22)(H,23,24)(H,13,16,17)(H2,18,19,20)/t6-,7+,8+,10+/m0/s1"
FDY InChIKey InChI 1.03 XUHVKXPQGWCRQM-OKJYPTKPSA-N
FDY SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](F)[P](O)(O)=O)O2)C(=O)NC1=O"
FDY SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O2)C(=O)NC1=O"
FDY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)OP(=O)([C@H](F)P(=O)(O)O)O)O"
FDY SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(F)P(=O)(O)O)O)O"
#
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
FDY "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
FDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-fluoranyl-[[[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]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
FDY "Create component" 2018-03-26 RCSB
FDY "Initial release" 2018-06-20 RCSB
#