data_CVC
# 
_chem_comp.id                                    CVC 
_chem_comp.name                                  "[(1~{R},5~{R},6~{R},8~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,3-bis(oxidanyl)-2,4,7-trioxa-3$l^{4}-vanadabicyclo[3.3.0]octan-8-yl]methyl dihydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H14 N3 O10 P V" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2015-10-19 
_chem_comp.pdbx_modified_date                    2016-02-19 
_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                        406.137 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     CVC 
_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        5EAO 
_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 
CVC O01   O1  O 0 1 N N N 102.534 17.930 -0.600 0.957  -1.847 -1.501 O01   CVC 1  
CVC C02   C1  C 0 1 N N N 99.683  15.907 -1.503 3.333  -3.846 -0.080 C02   CVC 2  
CVC P     P1  P 0 1 N N N 103.022 11.245 0.676  -4.780 -0.622 0.039  P     CVC 3  
CVC "C5'" C2  C 0 1 N N N 104.835 12.741 1.811  -2.323 0.353  -0.349 "C5'" CVC 4  
CVC "O5'" O2  O 0 1 N N N 104.190 12.307 0.642  -3.273 -0.294 0.500  "O5'" CVC 5  
CVC "C4'" C3  C 0 1 N N R 104.803 14.238 1.869  -0.997 0.511  0.398  "C4'" CVC 6  
CVC "O4'" O3  O 0 1 N N N 104.192 14.747 0.646  -0.366 -0.775 0.583  "O4'" CVC 7  
CVC "C3'" C4  C 0 1 N N R 103.971 14.783 3.034  0.009  1.320  -0.455 "C3'" CVC 8  
CVC "O3'" O4  O 0 1 N N N 104.688 15.824 3.679  -0.104 2.715  -0.090 "O3'" CVC 9  
CVC "C2'" C5  C 0 1 N N R 102.709 15.308 2.342  1.360  0.655  -0.180 "C2'" CVC 10 
CVC "O2'" O5  O 0 1 N N N 101.966 16.341 2.980  2.377  1.494  0.414  "O2'" CVC 11 
CVC "C1'" C6  C 0 1 N N R 103.250 15.729 0.981  1.031  -0.486 0.810  "C1'" CVC 12 
CVC C01   C7  C 0 1 N N N 100.050 14.578 -0.678 3.472  -3.225 1.178  C01   CVC 13 
CVC N01   N1  N 0 1 N N N 100.484 16.982 -1.474 2.474  -3.354 -0.963 N01   CVC 14 
CVC O1V   O6  O 0 1 N N N 104.222 18.445 3.116  2.067  4.442  1.241  O1V   CVC 15 
CVC N02   N2  N 0 1 N N N 98.404  15.877 -2.335 4.089  -4.952 -0.393 N02   CVC 16 
CVC O02   O7  O 0 1 N N N 101.836 11.756 1.464  -4.752 -1.696 -1.161 O02   CVC 17 
CVC O2V   O8  O 0 1 N N N 103.147 17.393 5.518  2.313  3.723  -1.706 O2V   CVC 18 
CVC N9    N3  N 0 1 N N N 102.137 15.748 0.047  1.850  -1.666 0.520  N9    CVC 19 
CVC OP1   O9  O 0 1 N N N 103.615 9.965  1.225  -5.602 -1.230 1.283  OP1   CVC 20 
CVC OP2   O10 O 0 1 N N N 102.587 11.233 -0.768 -5.436 0.620  -0.426 OP2   CVC 21 
CVC V     V1  V 0 1 N N N 103.477 17.264 3.937  1.711  3.184  -0.053 V     CVC 22 
CVC C4    C8  C 0 1 N N N 101.765 16.971 -0.661 1.741  -2.280 -0.673 C4    CVC 23 
CVC C8    C9  C 0 1 N N N 101.208 14.579 0.067  2.720  -2.135 1.458  C8    CVC 24 
CVC H1    H1  H 0 1 N N N 104.319 12.328 2.690  -2.166 -0.249 -1.244 H1    CVC 25 
CVC H2    H2  H 0 1 N N N 105.879 12.396 1.804  -2.699 1.336  -0.633 H2    CVC 26 
CVC H3    H3  H 0 1 N N N 105.831 14.619 1.958  -1.158 0.999  1.359  H3    CVC 27 
CVC H4    H4  H 0 1 N N N 103.713 13.971 3.729  -0.234 1.199  -1.511 H4    CVC 28 
CVC H5    H5  H 0 1 N N N 102.044 14.447 2.179  1.743  0.216  -1.102 H5    CVC 29 
CVC H6    H6  H 0 1 N N N 103.713 16.724 1.056  1.189  -0.156 1.836  H6    CVC 30 
CVC H7    H7  H 0 1 N N N 99.408  13.710 -0.707 4.167  -3.614 1.908  H7    CVC 31 
CVC H8    H8  H 0 1 N N N 104.915 18.815 3.651  2.996  4.706  1.288  H8    CVC 32 
CVC H9    H9  H 0 1 N N N 98.143  16.674 -2.879 3.994  -5.374 -1.261 H9    CVC 33 
CVC H10   H10 H 0 1 N N N 97.827  15.060 -2.336 4.717  -5.309 0.254  H10   CVC 34 
CVC H11   H11 H 0 1 N N N 101.118 11.942 0.871  -4.335 -2.536 -0.927 H11   CVC 35 
CVC H12   H12 H 0 1 N N N 103.867 17.830 5.958  3.247  3.973  -1.723 H12   CVC 36 
CVC H13   H13 H 0 1 N N N 103.628 9.304  0.543  -6.520 -1.452 1.077  H13   CVC 37 
CVC H14   H14 H 0 1 N N N 101.448 13.720 0.676  2.809  -1.641 2.415  H14   CVC 38 
# 
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 
CVC N02   C02   SING N N 1  
CVC C02   N01   DOUB N N 2  
CVC C02   C01   SING N N 3  
CVC N01   C4    SING N N 4  
CVC OP2   P     DOUB N N 5  
CVC C01   C8    DOUB N N 6  
CVC C4    O01   DOUB N N 7  
CVC C4    N9    SING N N 8  
CVC N9    C8    SING N N 9  
CVC N9    "C1'" SING N N 10 
CVC "O5'" P     SING N N 11 
CVC "O5'" "C5'" SING N N 12 
CVC "O4'" "C1'" SING N N 13 
CVC "O4'" "C4'" SING N N 14 
CVC P     OP1   SING N N 15 
CVC P     O02   SING N N 16 
CVC "C1'" "C2'" SING N N 17 
CVC "C5'" "C4'" SING N N 18 
CVC "C4'" "C3'" SING N N 19 
CVC "C2'" "O2'" SING N N 20 
CVC "C2'" "C3'" SING N N 21 
CVC "O2'" V     SING N N 22 
CVC "C3'" "O3'" SING N N 23 
CVC O1V   V     SING N N 24 
CVC "O3'" V     SING N N 25 
CVC V     O2V   SING N N 26 
CVC "C5'" H1    SING N N 27 
CVC "C5'" H2    SING N N 28 
CVC "C4'" H3    SING N N 29 
CVC "C3'" H4    SING N N 30 
CVC "C2'" H5    SING N N 31 
CVC "C1'" H6    SING N N 32 
CVC C01   H7    SING N N 33 
CVC O1V   H8    SING N N 34 
CVC N02   H9    SING N N 35 
CVC N02   H10   SING N N 36 
CVC O02   H11   SING N N 37 
CVC O2V   H12   SING N N 38 
CVC OP1   H13   SING N N 39 
CVC C8    H14   SING N N 40 
# 
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 
CVC InChI            InChI                1.03  "InChI=1S/C9H12N3O8P.2H2O.V/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18;;;/h1-2,4,6-8H,3H2,(H2,10,11,15)(H2,16,17,18);2*1H2;/q-2;;;+4/p-2/t4-,6-,7-,8-;;;/m1.../s1" 
CVC InChIKey         InChI                1.03  RQEDDOKDPWKVRD-LLWADOMFSA-L                                                                                                                                                        
CVC SMILES_CANONICAL CACTVS               3.385 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@H]3O[V](O)(O)O[C@@H]23"                                                                                                           
CVC SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH]3O[V](O)(O)O[CH]23"                                                                                                                 
CVC SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C1=CN(C(=O)N=C1N)[C@H]2[C@H]3[C@@H]([C@H](O2)COP(=O)(O)O)O[V](O3)(O)O"                                                                                                            
CVC SMILES           "OpenEye OEToolkits" 2.0.4 "C1=CN(C(=O)N=C1N)C2C3C(C(O2)COP(=O)(O)O)O[V](O3)(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 
CVC "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 "[(1~{R},5~{R},6~{R},8~{R})-6-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,3-bis(oxidanyl)-2,4,7-trioxa-3$l^{4}-vanadabicyclo[3.3.0]octan-8-yl]methyl dihydrogen 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 
CVC "Create component" 2015-10-19 RCSB 
CVC "Create component" 2015-11-16 RCSB 
CVC "Initial release"  2016-02-24 RCSB 
# 
