data_EJ8
# 
_chem_comp.id                                    EJ8 
_chem_comp.name                                  "[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H22 N2 O11 P2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2018-03-23 
_chem_comp.pdbx_modified_date                    2018-07-06 
_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                        536.387 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     EJ8 
_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        6G2L 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
EJ8 "C2'" C1  C 0 1 N N N -5.136 27.293 28.264 2.275  1.821  -0.960 "C2'" EJ8 1  
EJ8 "C1'" C2  C 0 1 N N R -3.641 27.690 28.044 1.102  2.333  -1.827 "C1'" EJ8 2  
EJ8 O2    O1  O 0 1 N N N -1.360 28.362 26.705 0.824  4.397  -0.141 O2    EJ8 3  
EJ8 O9    O2  O 0 1 N N N -5.439 20.138 22.740 -3.188 -3.331 0.208  O9    EJ8 4  
EJ8 P2    P1  P 0 1 N N N -4.118 20.029 23.349 -4.433 -2.443 -0.292 P2    EJ8 5  
EJ8 O10   O3  O 0 1 N N N -2.966 20.641 22.682 -4.090 -1.791 -1.576 O10   EJ8 6  
EJ8 O11   O4  O 0 1 N N N -3.910 18.769 24.140 -5.719 -3.389 -0.498 O11   EJ8 7  
EJ8 C18   C3  C 0 1 N N N -4.345 21.139 24.807 -4.811 -1.168 0.955  C18   EJ8 8  
EJ8 S1    S1  S 0 1 N N N -3.027 22.379 25.187 -3.362 -0.101 1.186  S1    EJ8 9  
EJ8 C17   C4  C 0 1 N N N -3.934 23.899 24.718 -3.373 0.932  -0.305 C17   EJ8 10 
EJ8 C5    C5  C 0 1 N N N -3.269 25.032 25.222 -2.210 1.889  -0.262 C5    EJ8 11 
EJ8 C4    C6  C 0 1 N N N -3.755 25.721 26.313 -1.124 1.681  -1.037 C4    EJ8 12 
EJ8 C6    C7  C 0 1 N N N -2.142 25.528 24.615 -2.243 3.021  0.587  C6    EJ8 13 
EJ8 O6    O5  O 0 1 N N N -1.670 24.993 23.617 -3.213 3.232  1.292  O6    EJ8 14 
EJ8 N1    N1  N 0 1 N N N -1.533 26.663 25.134 -1.190 3.863  0.609  N1    EJ8 15 
EJ8 C8    C8  C 0 1 N N N -1.978 27.355 26.275 -0.118 3.628  -0.171 C8    EJ8 16 
EJ8 N9    N2  N 0 1 N N N -3.090 26.909 26.859 -0.076 2.559  -0.986 N9    EJ8 17 
EJ8 "O4'" O6  O 0 1 N N N -2.977 27.563 29.269 0.815  1.326  -2.805 "O4'" EJ8 18 
EJ8 "C3'" C9  C 0 1 N N R -5.167 26.800 29.695 2.908  0.754  -1.882 "C3'" EJ8 19 
EJ8 "O3'" O7  O 0 1 N N N -4.956 25.383 29.628 3.615  -0.221 -1.145 "O3'" EJ8 20 
EJ8 "C4'" C10 C 0 1 N N R -3.972 27.518 30.314 1.661  0.176  -2.582 "C4'" EJ8 21 
EJ8 "C5'" C11 C 0 1 N N N -3.341 26.820 31.455 0.908  -0.757 -1.627 "C5'" EJ8 22 
EJ8 O7    O8  O 0 1 N N N -3.270 25.340 31.229 1.815  -1.673 -1.015 O7    EJ8 23 
EJ8 CAB   C12 C 0 1 N N R -4.485 24.724 30.827 2.835  -1.017 -0.252 CAB   EJ8 24 
EJ8 P     P2  P 0 1 N N N -5.745 24.759 32.211 3.899  -2.260 0.552  P     EJ8 25 
EJ8 OP1   O9  O 0 1 N N N -6.202 26.147 32.530 4.559  -3.208 -0.570 OP1   EJ8 26 
EJ8 OP2   O10 O 0 1 N N N -6.831 23.852 31.842 4.969  -1.577 1.312  OP2   EJ8 27 
EJ8 OP3   O11 O 0 1 N N N -4.915 24.107 33.356 3.014  -3.154 1.557  OP3   EJ8 28 
EJ8 C2    C13 C 0 1 Y N N -4.229 23.353 30.433 2.201  -0.136 0.793  C2    EJ8 29 
EJ8 CAA   C14 C 0 1 Y N N -4.940 22.753 29.388 0.848  -0.238 1.055  CAA   EJ8 30 
EJ8 C9    C15 C 0 1 Y N N -4.722 21.426 29.047 0.266  0.570  2.013  C9    EJ8 31 
EJ8 C10   C16 C 0 1 Y N N -3.781 20.699 29.716 1.038  1.480  2.711  C10   EJ8 32 
EJ8 C11   C17 C 0 1 Y N N -3.018 21.266 30.733 2.392  1.582  2.450  C11   EJ8 33 
EJ8 C12   C18 C 0 1 Y N N -3.273 22.595 31.085 2.974  0.770  1.495  C12   EJ8 34 
EJ8 H1    H1  H 0 1 N N N -5.797 28.163 28.134 2.983  2.623  -0.749 H1    EJ8 35 
EJ8 H2    H2  H 0 1 N N N -5.437 26.497 27.568 1.911  1.372  -0.036 H2    EJ8 36 
EJ8 H3    H3  H 0 1 N N N -3.640 28.752 27.756 1.387  3.261  -2.324 H3    EJ8 37 
EJ8 H4    H4  H 0 1 N N N -5.375 20.629 21.929 -3.342 -3.788 1.046  H4    EJ8 38 
EJ8 H5    H5  H 0 1 N N N -2.995 18.517 24.101 -5.590 -4.093 -1.149 H5    EJ8 39 
EJ8 H6    H6  H 0 1 N N N -5.279 21.697 24.648 -5.654 -0.566 0.615  H6    EJ8 40 
EJ8 H7    H7  H 0 1 N N N -4.449 20.495 25.692 -5.064 -1.648 1.900  H7    EJ8 41 
EJ8 H8    H8  H 0 1 N N N -3.989 23.967 23.621 -3.289 0.297  -1.187 H8    EJ8 42 
EJ8 H9    H9  H 0 1 N N N -4.951 23.859 25.134 -4.305 1.495  -0.350 H9    EJ8 43 
EJ8 H10   H10 H 0 1 N N N -4.662 25.372 26.785 -1.082 0.824  -1.694 H10   EJ8 44 
EJ8 H11   H11 H 0 1 N N N -0.722 27.012 24.664 -1.205 4.641  1.188  H11   EJ8 45 
EJ8 H12   H12 H 0 1 N N N -6.107 27.071 30.199 3.559  1.232  -2.614 H12   EJ8 46 
EJ8 H13   H13 H 0 1 N N N -4.269 28.535 30.610 1.921  -0.317 -3.519 H13   EJ8 47 
EJ8 H14   H14 H 0 1 N N N -2.321 27.209 31.591 0.418  -0.164 -0.855 H14   EJ8 48 
EJ8 H15   H15 H 0 1 N N N -3.932 27.014 32.362 0.157  -1.315 -2.185 H15   EJ8 49 
EJ8 H16   H16 H 0 1 N N N -7.146 26.200 32.435 3.914  -3.688 -1.108 H16   EJ8 50 
EJ8 H17   H17 H 0 1 N N N -5.286 23.260 33.574 3.516  -3.838 2.020  H17   EJ8 51 
EJ8 H18   H18 H 0 1 N N N -5.669 23.331 28.839 0.244  -0.949 0.510  H18   EJ8 52 
EJ8 H19   H19 H 0 1 N N N -5.296 20.970 28.254 -0.792 0.491  2.217  H19   EJ8 53 
EJ8 H20   H20 H 0 1 N N N -3.625 19.664 29.451 0.583  2.112  3.460  H20   EJ8 54 
EJ8 H21   H21 H 0 1 N N N -2.251 20.696 31.236 2.995  2.293  2.995  H21   EJ8 55 
EJ8 H22   H22 H 0 1 N N N -2.707 23.043 31.889 4.032  0.847  1.294  H22   EJ8 56 
# 
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 
EJ8 O10   P2    DOUB N N 1  
EJ8 O9    P2    SING N N 2  
EJ8 P2    O11   SING N N 3  
EJ8 P2    C18   SING N N 4  
EJ8 O6    C6    DOUB N N 5  
EJ8 C6    N1    SING N N 6  
EJ8 C6    C5    SING N N 7  
EJ8 C17   S1    SING N N 8  
EJ8 C17   C5    SING N N 9  
EJ8 C18   S1    SING N N 10 
EJ8 N1    C8    SING N N 11 
EJ8 C5    C4    DOUB N N 12 
EJ8 C8    O2    DOUB N N 13 
EJ8 C8    N9    SING N N 14 
EJ8 C4    N9    SING N N 15 
EJ8 N9    "C1'" SING N N 16 
EJ8 "C1'" "C2'" SING N N 17 
EJ8 "C1'" "O4'" SING N N 18 
EJ8 "C2'" "C3'" SING N N 19 
EJ8 C9    CAA   DOUB Y N 20 
EJ8 C9    C10   SING Y N 21 
EJ8 "O4'" "C4'" SING N N 22 
EJ8 CAA   C2    SING Y N 23 
EJ8 "O3'" "C3'" SING N N 24 
EJ8 "O3'" CAB   SING N N 25 
EJ8 "C3'" "C4'" SING N N 26 
EJ8 C10   C11   DOUB Y N 27 
EJ8 "C4'" "C5'" SING N N 28 
EJ8 C2    CAB   SING N N 29 
EJ8 C2    C12   DOUB Y N 30 
EJ8 C11   C12   SING Y N 31 
EJ8 CAB   O7    SING N N 32 
EJ8 CAB   P     SING N N 33 
EJ8 O7    "C5'" SING N N 34 
EJ8 OP2   P     DOUB N N 35 
EJ8 P     OP1   SING N N 36 
EJ8 P     OP3   SING N N 37 
EJ8 "C2'" H1    SING N N 38 
EJ8 "C2'" H2    SING N N 39 
EJ8 "C1'" H3    SING N N 40 
EJ8 O9    H4    SING N N 41 
EJ8 O11   H5    SING N N 42 
EJ8 C18   H6    SING N N 43 
EJ8 C18   H7    SING N N 44 
EJ8 C17   H8    SING N N 45 
EJ8 C17   H9    SING N N 46 
EJ8 C4    H10   SING N N 47 
EJ8 N1    H11   SING N N 48 
EJ8 "C3'" H12   SING N N 49 
EJ8 "C4'" H13   SING N N 50 
EJ8 "C5'" H14   SING N N 51 
EJ8 "C5'" H15   SING N N 52 
EJ8 OP1   H16   SING N N 53 
EJ8 OP3   H17   SING N N 54 
EJ8 CAA   H18   SING N N 55 
EJ8 C9    H19   SING N N 56 
EJ8 C10   H20   SING N N 57 
EJ8 C11   H21   SING N N 58 
EJ8 C12   H22   SING N N 59 
# 
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 
EJ8 InChI            InChI                1.03  
"InChI=1S/C18H22N2O11P2S/c21-16-11(9-34-10-32(23,24)25)7-20(17(22)19-16)15-6-13-14(30-15)8-29-18(31-13,33(26,27)28)12-4-2-1-3-5-12/h1-5,7,13-15H,6,8-10H2,(H,19,21,22)(H2,23,24,25)(H2,26,27,28)/t13-,14-,15-,18-/m1/s1" 
EJ8 InChIKey         InChI                1.03  KFRRWRABRKBEOD-ATNYBXOESA-N 
EJ8 SMILES_CANONICAL CACTVS               3.385 "O[P](O)(=O)CSCC1=CN([C@H]2C[C@H]3O[C@](OC[C@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O" 
EJ8 SMILES           CACTVS               3.385 "O[P](O)(=O)CSCC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O" 
EJ8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)[C@]2(OC[C@@H]3[C@H](O2)C[C@@H](O3)N4C=C(C(=O)NC4=O)CSCP(=O)(O)O)P(=O)(O)O" 
EJ8 SMILES           "OpenEye OEToolkits" 2.0.6 "c1ccc(cc1)C2(OCC3C(O2)CC(O3)N4C=C(C(=O)NC4=O)CSCP(=O)(O)O)P(=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 
EJ8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(2~{R},4~{a}~{R},6~{R},7~{a}~{R})-6-[2,4-bis(oxidanylidene)-5-(phosphonomethylsulfanylmethyl)pyrimidin-1-yl]-2-phenyl-4~{a},6,7,7~{a}-tetrahydro-4~{H}-furo[3,2-d][1,3]dioxin-2-yl]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 
EJ8 "Create component" 2018-03-23 EBI  
EJ8 "Initial release"  2018-07-11 RCSB 
# 
