data_FDJ
#
_chem_comp.id FDJ
_chem_comp.name "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H18 Cl 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 514.641
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code FDJ
_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 6CTM
_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
FDJ C2 C1 C 0 1 N N N 55.206 8.991 8.639 -5.298 -0.409 0.865 C2 FDJ 1
FDJ C4 C2 C 0 1 N N N 57.151 8.801 9.863 -6.682 -2.289 0.775 C4 FDJ 2
FDJ C5 C3 C 0 1 N N N 56.438 8.275 10.959 -6.521 -2.326 -0.631 C5 FDJ 3
FDJ C6 C4 C 0 1 N N N 55.046 8.140 10.788 -5.749 -1.394 -1.229 C6 FDJ 4
FDJ C7 C5 C 0 1 N N N 57.143 7.846 12.281 -7.202 -3.393 -1.450 C7 FDJ 5
FDJ O2 O1 O 0 1 N N N 54.679 9.312 7.592 -4.742 0.451 1.521 O2 FDJ 6
FDJ N1 N1 N 0 1 N N N 54.456 8.499 9.622 -5.137 -0.433 -0.470 N1 FDJ 7
FDJ N3 N2 N 0 1 N N N 56.505 9.149 8.737 -6.063 -1.326 1.487 N3 FDJ 8
FDJ O4 O2 O 0 1 N N N 58.359 8.960 9.930 -7.374 -3.120 1.337 O4 FDJ 9
FDJ PA P1 P 0 1 N N N 53.190 6.206 14.118 1.171 1.565 0.737 PA FDJ 10
FDJ PB P2 P 0 1 N N N 52.283 3.548 13.479 3.864 0.410 0.287 PB FDJ 11
FDJ PG P3 P 0 1 N N N 52.622 2.378 16.199 6.257 -1.154 -0.543 PG FDJ 12
FDJ "C1'" C6 C 0 1 N N R 53.138 8.350 9.431 -4.299 0.579 -1.118 "C1'" FDJ 13
FDJ O1A O3 O 0 1 N N N 52.177 6.221 15.218 0.888 1.179 2.274 O1A FDJ 14
FDJ O2B O4 O 0 1 N N N 52.120 2.906 12.117 4.194 0.161 1.709 O2B FDJ 15
FDJ O1G O5 O 0 1 N N N 52.226 3.755 16.633 6.616 -1.426 1.003 O1G FDJ 16
FDJ "C2'" C7 C 0 1 N N N 52.779 6.858 9.098 -4.883 1.990 -0.885 "C2'" FDJ 17
FDJ O2A O6 O 0 1 N N N 54.581 6.430 14.620 1.679 2.953 0.662 O2A FDJ 18
FDJ O1B O7 O 0 1 N N N 50.950 3.848 14.067 4.582 1.766 -0.200 O1B FDJ 19
FDJ CL1 CL1 CL 0 0 N N N 53.441 0.891 13.792 3.648 -2.505 -0.181 CL1 FDJ 20
FDJ O2G O8 O 0 1 N N N 53.646 1.829 17.166 6.775 -2.388 -1.439 O2G FDJ 21
FDJ "C3'" C8 C 0 1 N N S 52.424 6.339 10.212 -3.637 2.885 -0.702 "C3'" FDJ 22
FDJ "O3'" O9 O 0 1 N N N 51.533 5.168 10.126 -3.587 3.888 -1.718 "O3'" FDJ 23
FDJ O3A O10 O 0 1 N N N 53.186 4.839 13.304 2.269 0.558 0.125 O3A FDJ 24
FDJ C3B C9 C 0 1 N N R 53.314 2.484 14.526 4.451 -0.986 -0.727 C3B FDJ 25
FDJ O3G O11 O 0 1 N N N 51.393 1.485 16.171 6.917 0.093 -0.991 O3G FDJ 26
FDJ "C4'" C10 C 0 1 N N R 51.668 7.577 10.954 -2.448 1.909 -0.847 "C4'" FDJ 27
FDJ "O4'" O12 O 0 1 N N N 52.357 8.626 10.726 -2.991 0.614 -0.508 "O4'" FDJ 28
FDJ "C5'" C11 C 0 1 N N N 51.559 7.260 12.448 -1.327 2.287 0.123 "C5'" FDJ 29
FDJ "O5'" O13 O 0 1 N N N 52.856 7.334 13.052 -0.195 1.446 -0.107 "O5'" FDJ 30
FDJ H1 H1 H 0 1 N N N 54.444 7.747 11.594 -5.615 -1.406 -2.300 H1 FDJ 31
FDJ H2 H2 H 0 1 N N N 56.393 7.467 12.991 -7.775 -4.046 -0.791 H2 FDJ 32
FDJ H3 H3 H 0 1 N N N 57.876 7.055 12.065 -7.873 -2.925 -2.170 H3 FDJ 33
FDJ H4 H4 H 0 1 N N N 57.658 8.713 12.720 -6.451 -3.979 -1.980 H4 FDJ 34
FDJ H5 H5 H 0 1 N N N 57.018 9.531 7.968 -6.168 -1.294 2.451 H5 FDJ 35
FDJ H6 H6 H 0 1 N N N 52.755 8.998 8.628 -4.215 0.373 -2.186 H6 FDJ 36
FDJ H7 H7 H 0 1 N N N 52.613 6.373 16.048 0.553 0.281 2.399 H7 FDJ 37
FDJ H8 H8 H 0 1 N N N 51.291 3.779 16.799 6.216 -2.228 1.365 H8 FDJ 38
FDJ H9 H9 H 0 1 N N N 51.954 6.813 8.372 -5.461 2.313 -1.750 H9 FDJ 39
FDJ H10 H10 H 0 1 N N N 53.655 6.333 8.690 -5.499 2.004 0.015 H10 FDJ 40
FDJ H11 H11 H 0 1 N N N 50.269 3.574 13.464 4.409 1.992 -1.124 H11 FDJ 41
FDJ H12 H12 H 0 1 N N N 53.313 1.033 17.563 7.730 -2.536 -1.389 H12 FDJ 42
FDJ H13 H13 H 0 1 N N N 53.293 6.077 10.834 -3.637 3.342 0.288 H13 FDJ 43
FDJ H14 H14 H 0 1 N N N 51.329 4.860 11.001 -4.342 4.493 -1.711 H14 FDJ 44
FDJ H15 H15 H 0 1 N N N 54.318 2.929 14.592 4.208 -0.803 -1.773 H15 FDJ 45
FDJ H16 H16 H 0 1 N N N 50.653 7.641 10.535 -2.079 1.911 -1.872 H16 FDJ 46
FDJ H17 H17 H 0 1 N N N 50.889 7.988 12.929 -1.045 3.328 -0.035 H17 FDJ 47
FDJ H18 H18 H 0 1 N N N 51.152 6.246 12.578 -1.674 2.156 1.148 H18 FDJ 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
FDJ O2 C2 DOUB N N 1
FDJ C2 N3 SING N N 2
FDJ C2 N1 SING N N 3
FDJ N3 C4 SING N N 4
FDJ "C2'" "C1'" SING N N 5
FDJ "C2'" "C3'" SING N N 6
FDJ "C1'" N1 SING N N 7
FDJ "C1'" "O4'" SING N N 8
FDJ N1 C6 SING N N 9
FDJ C4 O4 DOUB N N 10
FDJ C4 C5 SING N N 11
FDJ "O3'" "C3'" SING N N 12
FDJ "C3'" "C4'" SING N N 13
FDJ "O4'" "C4'" SING N N 14
FDJ C6 C5 DOUB N N 15
FDJ "C4'" "C5'" SING N N 16
FDJ C5 C7 SING N N 17
FDJ O2B PB DOUB N N 18
FDJ "C5'" "O5'" SING N N 19
FDJ "O5'" PA SING N N 20
FDJ O3A PB SING N N 21
FDJ O3A PA SING N N 22
FDJ PB O1B SING N N 23
FDJ PB C3B SING N N 24
FDJ CL1 C3B SING N N 25
FDJ PA O2A DOUB N N 26
FDJ PA O1A SING N N 27
FDJ C3B PG SING N N 28
FDJ O3G PG DOUB N N 29
FDJ PG O1G SING N N 30
FDJ PG O2G SING N N 31
FDJ C6 H1 SING N N 32
FDJ C7 H2 SING N N 33
FDJ C7 H3 SING N N 34
FDJ C7 H4 SING N N 35
FDJ N3 H5 SING N N 36
FDJ "C1'" H6 SING N N 37
FDJ O1A H7 SING N N 38
FDJ O1G H8 SING N N 39
FDJ "C2'" H9 SING N N 40
FDJ "C2'" H10 SING N N 41
FDJ O1B H11 SING N N 42
FDJ O2G H12 SING N N 43
FDJ "C3'" H13 SING N N 44
FDJ "O3'" H14 SING N N 45
FDJ C3B H15 SING N N 46
FDJ "C4'" H16 SING N N 47
FDJ "C5'" H17 SING N N 48
FDJ "C5'" 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
FDJ SMILES ACDLabs 12.01 "C1(NC(=O)C(C)=CN1C2OC(C(C2)O)COP(=O)(O)OP(O)(C(P(O)(O)=O)Cl)=O)=O"
FDJ InChI InChI 1.03 "InChI=1S/C11H18ClN2O13P3/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"
FDJ InChIKey InChI 1.03 AEQPCMIHLIQHEG-OKJYPTKPSA-N
FDJ 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](Cl)[P](O)(O)=O)O2)C(=O)NC1=O"
FDJ SMILES CACTVS 3.385 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](Cl)[P](O)(O)=O)O2)C(=O)NC1=O"
FDJ 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](P(=O)(O)O)Cl)O)O"
FDJ SMILES "OpenEye OEToolkits" 2.0.6 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(C(P(=O)(O)O)Cl)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
FDJ "SYSTEMATIC NAME" ACDLabs 12.01 "5'-O-[(R)-{[(R)-[(R)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]thymidine"
FDJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-chloranyl-[[[(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
FDJ "Create component" 2018-03-26 RCSB
FDJ "Initial release" 2018-06-20 RCSB
#