data_VC9
# 
_chem_comp.id                                    VC9 
_chem_comp.name                                  "2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H16 Br2 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                     2018-03-26 
_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                        622.976 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VC9 
_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        6CTX 
_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 
VC9 C4    C1  C  0 1 N N N 9.320  7.594  11.036 -7.456 -2.728 0.435  C4    VC9 1  
VC9 N4    N1  N  0 1 N N N 10.781 7.611  11.275 -8.197 -3.747 0.987  N4    VC9 2  
VC9 C5    C2  C  0 1 N N N 8.489  7.267  12.066 -7.203 -2.706 -0.952 C5    VC9 3  
VC9 C6    C3  C  0 1 N N N 7.115  7.239  11.771 -6.470 -1.692 -1.470 C6    VC9 4  
VC9 N3    N2  N  0 1 N N N 8.831  7.880  9.831  -6.978 -1.758 1.204  N3    VC9 5  
VC9 C2    C4  C  0 1 N N N 7.534  7.841  9.619  -6.259 -0.767 0.680  C2    VC9 6  
VC9 O2    O1  O  0 1 N N N 7.084  8.103  8.480  -5.830 0.113  1.408  O2    VC9 7  
VC9 N1    N3  N  0 1 N N N 6.674  7.520  10.574 -5.996 -0.721 -0.639 N1    VC9 8  
VC9 "C1'" C5  C  0 1 N N R 5.357  7.475  10.288 -5.201 0.381  -1.186 "C1'" VC9 9  
VC9 "C2'" C6  C  0 1 N N N 4.922  6.031  9.800  -5.918 1.729  -0.950 "C2'" VC9 10 
VC9 "C3'" C7  C  0 1 N N S 4.498  5.466  10.905 -4.769 2.716  -0.641 "C3'" VC9 11 
VC9 "O3'" O2  O  0 1 N N N 3.589  4.299  10.743 -4.730 3.760  -1.615 "O3'" VC9 12 
VC9 "O4'" O3  O  0 1 N N N 4.455  7.692  11.520 -3.949 0.499  -0.476 "O4'" VC9 13 
VC9 "C4'" C8  C  0 1 N N R 3.683  6.661  11.656 -3.495 1.847  -0.727 "C4'" VC9 14 
VC9 "C5'" C9  C  0 1 N N N 3.466  6.294  13.155 -2.484 2.275  0.339  "C5'" VC9 15 
VC9 "O5'" O4  O  0 1 N N N 4.677  6.233  13.817 -1.271 1.541  0.167  "O5'" VC9 16 
VC9 PA    P1  P  0 1 N N N 5.010  4.986  14.840 0.014  1.736  1.117  PA    VC9 17 
VC9 O1A   O5  O  0 1 N N N 3.993  4.909  15.897 -0.348 1.267  2.614  O1A   VC9 18 
VC9 O2A   O6  O  0 1 N N N 6.391  5.111  15.392 0.406  3.163  1.129  O2A   VC9 19 
VC9 O3A   O7  O  0 1 N N N 5.023  3.668  13.950 1.236  0.849  0.558  O3A   VC9 20 
VC9 PB    P2  P  0 1 N N N 3.896  2.403  13.966 2.821  0.826  0.837  PB    VC9 21 
VC9 O1B   O8  O  0 1 N N N 2.553  2.838  14.463 3.455  2.255  0.453  O1B   VC9 22 
VC9 O2B   O9  O  0 1 N N N 3.783  1.945  12.486 3.065  0.547  2.270  O2B   VC9 23 
VC9 C3B   C10 C  0 1 N N N 4.643  1.109  15.022 3.597  -0.476 -0.176 C3B   VC9 24 
VC9 BR1   BR1 BR 0 0 N N N 6.519  1.378  15.335 2.823  -2.221 0.293  BR1   VC9 25 
VC9 BR2   BR2 BR 0 0 N N N 4.707  -0.643 14.210 3.273  -0.105 -2.080 BR2   VC9 26 
VC9 PG    P3  P  0 1 N N N 3.826  0.993  16.680 5.392  -0.503 0.140  PG    VC9 27 
VC9 O2G   O10 O  0 1 N N N 3.732  2.421  17.230 5.658  -0.806 1.699  O2G   VC9 28 
VC9 O1G   O11 O  0 1 N N N 4.758  0.186  17.594 6.078  -1.652 -0.755 O1G   VC9 29 
VC9 O3G   O12 O  0 1 N N N 2.537  0.292  16.580 5.975  0.811  -0.213 O3G   VC9 30 
VC9 H1    H1  H  0 1 N N N 11.407 7.838  10.529 -8.549 -4.452 0.422  H1    VC9 31 
VC9 H2    H2  H  0 1 N N N 11.142 7.395  12.182 -8.369 -3.759 1.942  H2    VC9 32 
VC9 H3    H3  H  0 1 N N N 8.865  7.042  13.053 -7.589 -3.486 -1.592 H3    VC9 33 
VC9 H4    H4  H  0 1 N N N 6.411  6.980  12.548 -6.264 -1.653 -2.529 H4    VC9 34 
VC9 H5    H5  H  0 1 N N N 5.082  8.203  9.510  -5.021 0.227  -2.250 H5    VC9 35 
VC9 H6    H6  H  0 1 N N N 4.118  6.091  9.052  -6.456 2.038  -1.845 H6    VC9 36 
VC9 H7    H7  H  0 1 N N N 5.776  5.482  9.377  -6.597 1.657  -0.101 H7    VC9 37 
VC9 H8    H8  H  0 1 N N N 5.334  5.179  11.560 -4.881 3.131  0.361  H8    VC9 38 
VC9 H9    H9  H  0 1 N N N 3.801  3.639  11.393 -5.532 4.300  -1.646 H9    VC9 39 
VC9 H10   H10 H  0 1 N N N 2.706  6.778  11.165 -3.053 1.919  -1.721 H10   VC9 40 
VC9 H11   H11 H  0 1 N N N 2.833  7.060  13.627 -2.281 3.342  0.238  H11   VC9 41 
VC9 H12   H12 H  0 1 N N N 2.968  5.315  13.220 -2.894 2.075  1.329  H12   VC9 42 
VC9 H13   H13 H  0 1 N N N 4.415  4.954  16.747 -0.615 0.340  2.682  H13   VC9 43 
VC9 H14   H14 H  0 1 N N N 1.912  2.743  13.769 3.332  2.503  -0.474 H14   VC9 44 
VC9 H15   H15 H  0 1 N N N 2.825  2.627  17.423 5.303  -1.653 2.001  H15   VC9 45 
VC9 H16   H16 H  0 1 N N N 4.307  -0.592 17.900 7.035  -1.723 -0.637 H16   VC9 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 
VC9 O2    C2    DOUB N N 1  
VC9 C2    N3    SING N N 2  
VC9 C2    N1    SING N N 3  
VC9 "C2'" "C1'" SING N N 4  
VC9 "C2'" "C3'" SING N N 5  
VC9 N3    C4    DOUB N N 6  
VC9 "C1'" N1    SING N N 7  
VC9 "C1'" "O4'" SING N N 8  
VC9 N1    C6    SING N N 9  
VC9 "O3'" "C3'" SING N N 10 
VC9 "C3'" "C4'" SING N N 11 
VC9 C4    N4    SING N N 12 
VC9 C4    C5    SING N N 13 
VC9 "O4'" "C4'" SING N N 14 
VC9 "C4'" "C5'" SING N N 15 
VC9 C6    C5    DOUB N N 16 
VC9 O2B   PB    DOUB N N 17 
VC9 "C5'" "O5'" SING N N 18 
VC9 "O5'" PA    SING N N 19 
VC9 O3A   PB    SING N N 20 
VC9 O3A   PA    SING N N 21 
VC9 PB    O1B   SING N N 22 
VC9 PB    C3B   SING N N 23 
VC9 BR2   C3B   SING N N 24 
VC9 PA    O2A   DOUB N N 25 
VC9 PA    O1A   SING N N 26 
VC9 C3B   BR1   SING N N 27 
VC9 C3B   PG    SING N N 28 
VC9 O3G   PG    DOUB N N 29 
VC9 PG    O2G   SING N N 30 
VC9 PG    O1G   SING N N 31 
VC9 N4    H1    SING N N 32 
VC9 N4    H2    SING N N 33 
VC9 C5    H3    SING N N 34 
VC9 C6    H4    SING N N 35 
VC9 "C1'" H5    SING N N 36 
VC9 "C2'" H6    SING N N 37 
VC9 "C2'" H7    SING N N 38 
VC9 "C3'" H8    SING N N 39 
VC9 "O3'" H9    SING N N 40 
VC9 "C4'" H10   SING N N 41 
VC9 "C5'" H11   SING N N 42 
VC9 "C5'" H12   SING N N 43 
VC9 O1A   H13   SING N N 44 
VC9 O1B   H14   SING N N 45 
VC9 O2G   H15   SING N N 46 
VC9 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 
VC9 SMILES           ACDLabs              12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Br)(P(O)(O)=O)Br)=O"                                                                                                                              
VC9 InChI            InChI                1.03  "InChI=1S/C10H16Br2N3O12P3/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" 
VC9 InChIKey         InChI                1.03  QBTCYYWCAIICFQ-SHYZEUOFSA-N                                                                                                                                                                          
VC9 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(Br)(Br)[P](O)(O)=O)O2"                                                                                                              
VC9 SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)C(Br)(Br)[P](O)(O)=O)O2"                                                                                                                  
VC9 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(P(=O)(O)O)(Br)Br)O)O"                                                                                                                      
VC9 SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)(Br)Br)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 
VC9 "SYSTEMATIC NAME" ACDLabs              12.01 "2'-deoxy-5'-O-[(R)-{[(R)-[dibromo(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine"                                                                             
VC9 "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(bromanyl)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 
VC9 "Create component" 2018-03-26 RCSB 
VC9 "Initial release"  2018-06-20 RCSB 
# 
