data_NE0
# 
_chem_comp.id                                    NE0 
_chem_comp.name                                  "[[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C9 H16 N2 O18 P4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-01-12 
_chem_comp.pdbx_modified_date                    2023-06-30 
_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                        564.121 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     NE0 
_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        8HYK 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
NE0 O01 O1  O 0 1 N N N 4.698  1.406  17.336 -4.259 -5.170 1.114  O01 NE0 1  
NE0 C02 C1  C 0 1 N N N 4.797  0.222  17.468 -3.941 -4.073 0.692  C02 NE0 2  
NE0 C03 C2  C 0 1 N N N 3.814  -0.475 18.195 -4.056 -3.777 -0.688 C03 NE0 3  
NE0 C04 C3  C 0 1 N N N 3.938  -1.859 18.362 -3.697 -2.553 -1.130 C04 NE0 4  
NE0 N05 N1  N 0 1 N N N 5.012  -2.499 17.800 -3.231 -1.622 -0.242 N05 NE0 5  
NE0 C06 C4  C 0 1 N N R 5.172  -3.864 17.873 -2.841 -0.294 -0.722 C06 NE0 6  
NE0 O07 O2  O 0 1 N N N 3.832  -4.673 18.119 -1.497 0.021  -0.296 O07 NE0 7  
NE0 C08 C5  C 0 1 N N R 3.943  -5.319 19.250 -1.402 1.460  -0.369 C08 NE0 8  
NE0 C09 C6  C 0 1 N N N 2.703  -5.163 20.107 -0.256 1.963  0.512  C09 NE0 9  
NE0 O10 O3  O 0 1 N N N 2.608  -3.803 20.560 0.990  1.513  -0.024 O10 NE0 10 
NE0 P11 P1  P 0 1 N N N 1.136  -3.210 21.067 2.410  1.858  0.651  P11 NE0 11 
NE0 O12 O4  O 0 1 N N N 1.240  -1.727 21.379 2.401  1.427  2.067  O12 NE0 12 
NE0 O13 O5  O 0 1 N N N 0.606  -3.931 22.306 2.669  3.445  0.574  O13 NE0 13 
NE0 O14 O6  O 0 1 N N N 0.183  -3.458 19.764 3.581  1.085  -0.138 O14 NE0 14 
NE0 P15 P2  P 0 1 N N N -1.381 -3.809 19.830 5.093  0.670  0.229  P15 NE0 15 
NE0 O16 O7  O 0 1 N N N -1.979 -3.496 21.213 6.036  1.973  0.169  O16 NE0 16 
NE0 O17 O8  O 0 1 N N N -2.124 -3.108 18.706 5.129  0.097  1.594  O17 NE0 17 
NE0 O18 O9  O 0 1 N N N -1.446 -5.383 19.529 5.621  -0.424 -0.826 O18 NE0 18 
NE0 P19 P3  P 0 1 N N N -1.798 -6.621 20.607 6.809  -1.511 -0.811 P19 NE0 19 
NE0 O20 O10 O 0 1 N N N -3.275 -6.805 20.363 6.340  -2.808 0.020  O20 NE0 20 
NE0 O21 O11 O 0 1 N N N -1.503 -6.142 22.088 7.163  -1.940 -2.322 O21 NE0 21 
NE0 O22 O12 O 0 1 N N N -0.879 -7.690 20.039 8.007  -0.922 -0.172 O22 NE0 22 
NE0 C23 C7  C 0 1 N N R 5.262  -4.575 19.961 -2.757 1.973  0.166  C23 NE0 23 
NE0 O24 O13 O 0 1 N N N 5.730  -5.376 21.109 -3.181 3.124  -0.567 O24 NE0 24 
NE0 C25 C8  C 0 1 N N R 6.114  -4.425 18.959 -3.726 0.793  -0.072 C25 NE0 25 
NE0 O26 O14 O 0 1 N N N 6.537  -5.735 18.402 -4.778 1.179  -0.959 O26 NE0 26 
NE0 P27 P4  P 0 1 N N N 7.960  -6.328 18.965 -6.337 1.025  -0.590 P27 NE0 27 
NE0 O28 O15 O 0 1 N N N 8.952  -5.275 18.441 -6.619 -0.380 -0.218 O28 NE0 28 
NE0 O29 O16 O 0 1 N N N 7.821  -6.327 20.487 -6.693 1.990  0.649  O29 NE0 29 
NE0 O30 O17 O 0 1 N N N 8.229  -7.757 18.532 -7.233 1.434  -1.863 O30 NE0 30 
NE0 C31 C9  C 0 1 N N N 5.915  -1.803 17.080 -3.127 -1.915 1.067  C31 NE0 31 
NE0 O32 O18 O 0 1 N N N 6.835  -2.403 16.610 -2.711 -1.072 1.838  O32 NE0 32 
NE0 N33 N2  N 0 1 N N N 5.856  -0.463 16.948 -3.483 -3.126 1.535  N33 NE0 33 
NE0 H1  H1  H 0 1 N N N 2.973  0.053  18.620 -4.425 -4.522 -1.378 H1  NE0 34 
NE0 H2  H2  H 0 1 N N N 3.200  -2.413 18.924 -3.777 -2.310 -2.180 H2  NE0 35 
NE0 H3  H3  H 0 1 N N N 5.565  -4.219 16.909 -2.916 -0.246 -1.808 H3  NE0 36 
NE0 H4  H4  H 0 1 N N N 4.181  -6.385 19.122 -1.256 1.778  -1.401 H4  NE0 37 
NE0 H5  H5  H 0 1 N N N 1.812  -5.416 19.514 -0.269 3.053  0.536  H5  NE0 38 
NE0 H6  H6  H 0 1 N N N 2.769  -5.836 20.975 -0.378 1.575  1.523  H6  NE0 39 
NE0 H7  H7  H 0 1 N N N 0.457  -3.300 23.000 2.687  3.798  -0.326 H7  NE0 40 
NE0 H8  H8  H 0 1 N N N -2.720 -2.909 21.113 6.061  2.401  -0.698 H8  NE0 41 
NE0 H9  H9  H 0 1 N N N -3.417 -7.602 19.866 5.558  -3.246 -0.343 H9  NE0 42 
NE0 H10 H10 H 0 1 N N N -0.754 -6.615 22.431 7.873  -2.594 -2.389 H10 NE0 43 
NE0 H11 H11 H 0 1 N N N 4.910  -3.600 20.329 -2.686 2.204  1.229  H11 NE0 44 
NE0 H12 H12 H 0 1 N N N 5.045  -5.419 21.766 -2.577 3.876  -0.503 H12 NE0 45 
NE0 H13 H13 H 0 1 N N N 6.962  -3.752 19.152 -4.134 0.438  0.875  H13 NE0 46 
NE0 H14 H14 H 0 1 N N N 8.386  -5.659 20.857 -6.533 2.928  0.476  H14 NE0 47 
NE0 H15 H15 H 0 1 N N N 9.002  -7.781 17.980 -8.186 1.364  -1.712 H15 NE0 48 
NE0 H16 H16 H 0 1 N N N 6.585  0.027  16.471 -3.402 -3.320 2.482  H16 NE0 49 
# 
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 
NE0 O32 C31 DOUB N N 1  
NE0 N33 C31 SING N N 2  
NE0 N33 C02 SING N N 3  
NE0 C31 N05 SING N N 4  
NE0 O01 C02 DOUB N N 5  
NE0 C02 C03 SING N N 6  
NE0 N05 C06 SING N N 7  
NE0 N05 C04 SING N N 8  
NE0 C06 O07 SING N N 9  
NE0 C06 C25 SING N N 10 
NE0 O07 C08 SING N N 11 
NE0 C03 C04 DOUB N N 12 
NE0 O26 C25 SING N N 13 
NE0 O26 P27 SING N N 14 
NE0 O28 P27 DOUB N N 15 
NE0 O30 P27 SING N N 16 
NE0 O17 P15 DOUB N N 17 
NE0 C25 C23 SING N N 18 
NE0 P27 O29 SING N N 19 
NE0 C08 C23 SING N N 20 
NE0 C08 C09 SING N N 21 
NE0 O18 P15 SING N N 22 
NE0 O18 P19 SING N N 23 
NE0 O14 P15 SING N N 24 
NE0 O14 P11 SING N N 25 
NE0 P15 O16 SING N N 26 
NE0 C23 O24 SING N N 27 
NE0 O22 P19 DOUB N N 28 
NE0 C09 O10 SING N N 29 
NE0 O20 P19 SING N N 30 
NE0 O10 P11 SING N N 31 
NE0 P19 O21 SING N N 32 
NE0 P11 O12 DOUB N N 33 
NE0 P11 O13 SING N N 34 
NE0 C03 H1  SING N N 35 
NE0 C04 H2  SING N N 36 
NE0 C06 H3  SING N N 37 
NE0 C08 H4  SING N N 38 
NE0 C09 H5  SING N N 39 
NE0 C09 H6  SING N N 40 
NE0 O13 H7  SING N N 41 
NE0 O16 H8  SING N N 42 
NE0 O20 H9  SING N N 43 
NE0 O21 H10 SING N N 44 
NE0 C23 H11 SING N N 45 
NE0 O24 H12 SING N N 46 
NE0 C25 H13 SING N N 47 
NE0 O29 H14 SING N N 48 
NE0 O30 H15 SING N N 49 
NE0 N33 H16 SING N N 50 
# 
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 
NE0 InChI            InChI                1.06  "InChI=1S/C9H16N2O18P4/c12-5-1-2-11(9(14)10-5)8-7(27-30(15,16)17)6(13)4(26-8)3-25-32(21,22)29-33(23,24)28-31(18,19)20/h1-2,4,6-8,13H,3H2,(H,21,22)(H,23,24)(H,10,12,14)(H2,15,16,17)(H2,18,19,20)/t4-,6-,7-,8-/m1/s1" 
NE0 InChIKey         InChI                1.06  OATQDFNIQGUFQP-XVFCMESISA-N                                                                                                                                                                                           
NE0 SMILES_CANONICAL CACTVS               3.385 "O[C@@H]1[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[C@H]([C@@H]1O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                       
NE0 SMILES           CACTVS               3.385 "O[CH]1[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O[CH]([CH]1O[P](O)(O)=O)N2C=CC(=O)NC2=O"                                                                                                                              
NE0 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O"                                                                                                                            
NE0 SMILES           "OpenEye OEToolkits" 2.0.7 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)OP(=O)(O)O"                                                                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           NE0 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[[(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
NE0 "Create component" 2023-01-12 PDBJ 
NE0 "Initial release"  2023-07-05 RCSB 
# 
