data_FFJ
#
_chem_comp.id FFJ
_chem_comp.name "2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C10 H16 F2 N3 O12 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-27
_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 501.165
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code FFJ
_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 6CTV
_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
FFJ C4 C1 C 0 1 N N N 9.366 7.484 11.016 -6.883 -2.638 0.448 C4 FFJ 1
FFJ N4 N1 N 0 1 N N N 10.804 7.491 11.239 -7.661 -3.623 1.013 N4 FFJ 2
FFJ C5 C2 C 0 1 N N N 8.536 7.114 12.050 -6.690 -2.601 -0.948 C5 FFJ 3
FFJ C6 C3 C 0 1 N N N 7.172 7.118 11.787 -5.920 -1.620 -1.477 C6 FFJ 4
FFJ N3 N2 N 0 1 N N N 8.844 7.839 9.819 -6.316 -1.715 1.214 N3 FFJ 5
FFJ C2 C4 C 0 1 N N N 7.538 7.834 9.633 -5.562 -0.757 0.679 C2 FFJ 6
FFJ O2 O1 O 0 1 N N N 7.108 8.141 8.575 -5.051 0.080 1.405 O2 FFJ 7
FFJ N1 N3 N 0 1 N N N 6.693 7.470 10.590 -5.353 -0.698 -0.649 N1 FFJ 8
FFJ "C1'" C5 C 0 1 N N R 5.371 7.454 10.328 -4.518 0.368 -1.209 "C1'" FFJ 9
FFJ "C2'" C6 C 0 1 N N N 4.897 6.040 9.842 -5.142 1.750 -0.915 "C2'" FFJ 10
FFJ "C3'" C7 C 0 1 N N S 4.490 5.458 10.947 -3.924 2.660 -0.637 "C3'" FFJ 11
FFJ "O3'" O2 O 0 1 N N N 3.601 4.308 10.746 -3.864 3.722 -1.592 "O3'" FFJ 12
FFJ "O4'" O3 O 0 1 N N N 4.478 7.703 11.570 -3.232 0.396 -0.552 "O4'" FFJ 13
FFJ "C4'" C8 C 0 1 N N R 3.710 6.669 11.716 -2.709 1.720 -0.797 "C4'" FFJ 14
FFJ "C5'" C9 C 0 1 N N N 3.508 6.335 13.192 -1.630 2.065 0.232 "C5'" FFJ 15
FFJ "O5'" O4 O 0 1 N N N 4.758 6.221 13.814 -0.471 1.263 -0.006 "O5'" FFJ 16
FFJ PA P1 P 0 1 N N N 4.977 4.973 14.901 0.862 1.362 0.890 PA FFJ 17
FFJ O1A O5 O 0 1 N N N 3.893 4.981 15.923 0.536 0.882 2.392 O1A FFJ 18
FFJ O2A O6 O 0 1 N N N 6.357 5.043 15.494 1.339 2.763 0.913 O2A FFJ 19
FFJ O3A O7 O 0 1 N N N 4.984 3.612 14.039 2.003 0.417 0.261 O3A FFJ 20
FFJ PB P2 P 0 1 N N N 3.794 2.507 13.833 3.595 0.294 0.470 PB FFJ 21
FFJ O1B O8 O 0 1 N N N 2.441 2.983 14.356 4.297 1.691 0.086 O1B FFJ 22
FFJ O2B O9 O 0 1 N N N 3.749 2.173 12.321 3.883 -0.031 1.885 O2B FFJ 23
FFJ C3B C10 C 0 1 N N N 4.409 1.021 14.755 4.249 -1.028 -0.602 C3B FFJ 24
FFJ F3B F1 F 0 1 N N N 5.794 1.161 14.881 3.639 -2.243 -0.268 F3B FFJ 25
FFJ F4B F2 F 0 1 N N N 4.088 -0.106 14.070 3.977 -0.721 -1.939 F4B FFJ 26
FFJ PG P3 P 0 1 N N N 3.687 0.978 16.463 6.051 -1.168 -0.364 PG FFJ 27
FFJ O2G O10 O 0 1 N N N 3.491 2.392 16.964 6.628 -2.335 -1.311 O2G FFJ 28
FFJ O1G O11 O 0 1 N N N 4.666 0.272 17.326 6.752 0.230 -0.748 O1G FFJ 29
FFJ O3G O12 O 0 1 N N N 2.406 0.216 16.471 6.339 -1.492 1.051 O3G FFJ 30
FFJ H1 H1 H 0 1 N N N 11.423 7.761 10.502 -8.077 -4.294 0.449 H1 FFJ 31
FFJ H2 H2 H 0 1 N N N 11.173 7.226 12.130 -7.792 -3.647 1.973 H2 FFJ 32
FFJ H3 H3 H 0 1 N N N 8.926 6.834 13.018 -7.148 -3.342 -1.585 H3 FFJ 33
FFJ H4 H4 H 0 1 N N N 6.483 6.830 12.567 -5.756 -1.570 -2.543 H4 FFJ 34
FFJ H5 H5 H 0 1 N N N 5.106 8.191 9.555 -4.393 0.227 -2.282 H5 FFJ 35
FFJ H6 H6 H 0 1 N N N 4.074 6.128 9.118 -5.698 2.110 -1.780 H6 FFJ 36
FFJ H7 H7 H 0 1 N N N 5.728 5.482 9.386 -5.788 1.699 -0.038 H7 FFJ 37
FFJ H8 H8 H 0 1 N N N 5.335 5.158 11.583 -3.968 3.059 0.376 H8 FFJ 38
FFJ H9 H9 H 0 1 N N N 3.793 3.642 11.395 -4.633 4.308 -1.577 H9 FFJ 39
FFJ H10 H10 H 0 1 N N N 2.728 6.797 11.237 -2.306 1.788 -1.807 H10 FFJ 40
FFJ H11 H11 H 0 1 N N N 2.929 7.136 13.674 -1.368 3.119 0.144 H11 FFJ 41
FFJ H12 H12 H 0 1 N N N 2.964 5.383 13.283 -2.009 1.867 1.235 H12 FFJ 42
FFJ H13 H13 H 0 1 N N N 4.276 5.030 16.791 0.218 -0.029 2.453 H13 FFJ 43
FFJ H14 H14 H 0 1 N N N 1.810 2.987 13.646 4.150 1.967 -0.829 H14 FFJ 44
FFJ H15 H15 H 0 1 N N N 2.578 2.525 17.190 7.583 -2.466 -1.237 H15 FFJ 45
FFJ H16 H16 H 0 1 N N N 4.263 -0.506 17.692 6.605 0.506 -1.663 H16 FFJ 46
#
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
FFJ O2 C2 DOUB N N 1
FFJ C2 N3 SING N N 2
FFJ C2 N1 SING N N 3
FFJ N3 C4 DOUB N N 4
FFJ "C2'" "C1'" SING N N 5
FFJ "C2'" "C3'" SING N N 6
FFJ "C1'" N1 SING N N 7
FFJ "C1'" "O4'" SING N N 8
FFJ N1 C6 SING N N 9
FFJ "O3'" "C3'" SING N N 10
FFJ "C3'" "C4'" SING N N 11
FFJ C4 N4 SING N N 12
FFJ C4 C5 SING N N 13
FFJ "O4'" "C4'" SING N N 14
FFJ "C4'" "C5'" SING N N 15
FFJ C6 C5 DOUB N N 16
FFJ O2B PB DOUB N N 17
FFJ "C5'" "O5'" SING N N 18
FFJ "O5'" PA SING N N 19
FFJ PB O3A SING N N 20
FFJ PB O1B SING N N 21
FFJ PB C3B SING N N 22
FFJ O3A PA SING N N 23
FFJ F4B C3B SING N N 24
FFJ C3B F3B SING N N 25
FFJ C3B PG SING N N 26
FFJ PA O2A DOUB N N 27
FFJ PA O1A SING N N 28
FFJ PG O3G DOUB N N 29
FFJ PG O2G SING N N 30
FFJ PG O1G SING N N 31
FFJ N4 H1 SING N N 32
FFJ N4 H2 SING N N 33
FFJ C5 H3 SING N N 34
FFJ C6 H4 SING N N 35
FFJ "C1'" H5 SING N N 36
FFJ "C2'" H6 SING N N 37
FFJ "C2'" H7 SING N N 38
FFJ "C3'" H8 SING N N 39
FFJ "O3'" H9 SING N N 40
FFJ "C4'" H10 SING N N 41
FFJ "C5'" H11 SING N N 42
FFJ "C5'" H12 SING N N 43
FFJ O1A H13 SING N N 44
FFJ O1B H14 SING N N 45
FFJ O2G H15 SING N N 46
FFJ O1G H16 SING N N 47
#
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
FFJ SMILES ACDLabs 12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(F)(P(=O)(O)O)F)=O"
FFJ InChI InChI 1.03 "InChI=1S/C10H16F2N3O12P3/c11-10(12,28(18,19)20)29(21,22)27-30(23,24)25-4-6-5(16)3-8(26-6)15-2-1-7(13)14-9(15)17/h1-2,5-6,8,16H,3-4H2,(H,21,22)(H,23,24)(H2,13,14,17)(H2,18,19,20)/t5-,6+,8+/m0/s1"
FFJ InChIKey InChI 1.03 FBLKJJQPZBDPCI-SHYZEUOFSA-N
FFJ SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2"
FFJ SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(F)(F)[P](O)(O)=O)O2"
FFJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(F)(F)P(=O)(O)O)O)O"
FFJ SMILES "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(F)(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
FFJ "SYSTEMATIC NAME" ACDLabs 12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"
FFJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[[[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-bis(fluoranyl)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
FFJ "Create component" 2018-03-27 RCSB
FFJ "Initial release" 2018-06-20 RCSB
#