data_DJJ
# 
_chem_comp.id                                    DJJ 
_chem_comp.name                                  "5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H17 Cl 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                     2017-10-26 
_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                        499.629 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DJJ 
_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        6BEM 
_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 
DJJ C4    C1  C  0 1 N N N 9.389  7.658  10.912 -6.904 -2.624 0.483  C4    DJJ 1  
DJJ N4    N1  N  0 1 N N N 10.822 7.727  11.100 -7.697 -3.592 1.055  N4    DJJ 2  
DJJ C5    C2  C  0 1 N N N 8.575  7.232  11.954 -6.694 -2.612 -0.911 C5    DJJ 3  
DJJ C6    C3  C  0 1 N N N 7.199  7.165  11.712 -5.909 -1.648 -1.448 C6    DJJ 4  
DJJ N3    N2  N  0 1 N N N 8.864  7.992  9.749  -6.338 -1.693 1.239  N3    DJJ 5  
DJJ C2    C4  C  0 1 N N N 7.560  7.909  9.566  -5.569 -0.751 0.697  C2    DJJ 6  
DJJ O2    O1  O  0 1 N N N 7.099  8.218  8.512  -5.060 0.095  1.413  O2    DJJ 7  
DJJ N1    N3  N  0 1 N N N 6.737  7.525  10.528 -5.345 -0.716 -0.630 N1    DJJ 8  
DJJ "C1'" C5  C  0 1 N N R 5.315  7.423  10.226 -4.494 0.333  -1.198 "C1'" DJJ 9  
DJJ "C2'" C6  C  0 1 N N N 5.060  6.205  9.822  -5.109 1.725  -0.935 "C2'" DJJ 10 
DJJ "C3'" C7  C  0 1 N N S 4.493  5.464  11.043 -3.887 2.629  -0.659 "C3'" DJJ 11 
DJJ "O3'" O2  O  0 1 N N N 3.673  4.413  10.694 -3.806 3.673  -1.632 "O3'" DJJ 12 
DJJ "O4'" O3  O  0 1 N N N 4.464  7.624  11.555 -3.216 0.361  -0.526 "O4'" DJJ 13 
DJJ "C4'" C8  C  0 1 N N R 3.707  6.599  11.715 -2.678 1.676  -0.787 "C4'" DJJ 14 
DJJ "C5'" C9  C  0 1 N N N 3.530  6.350  13.242 -1.609 2.030  0.248  "C5'" DJJ 15 
DJJ "O5'" O4  O  0 1 N N N 4.798  6.205  13.816 -0.454 1.215  0.038  "O5'" DJJ 16 
DJJ PA    P1  P  0 1 N N N 5.031  4.957  14.874 0.870  1.318  0.948  PA    DJJ 17 
DJJ O1A   O5  O  0 1 N N N 3.950  4.996  15.939 0.522  0.867  2.454  O1A   DJJ 18 
DJJ O2A   O6  O  0 1 N N N 6.410  5.074  15.455 1.358  2.715  0.952  O2A   DJJ 19 
DJJ O3A   O7  O  0 1 N N N 4.974  3.612  13.959 2.010  0.352  0.349  O3A   DJJ 20 
DJJ PB    P2  P  0 1 N N N 3.801  2.486  13.886 3.598  0.219  0.579  PB    DJJ 21 
DJJ O2B   O8  O  0 1 N N N 3.744  2.181  12.420 3.866  -0.083 2.003  O2B   DJJ 22 
DJJ O1B   O9  O  0 1 N N N 2.466  2.998  14.374 4.316  1.604  0.180  O1B   DJJ 23 
DJJ C3B   C10 C  0 1 N N S 4.359  0.975  14.781 4.253  -1.127 -0.461 C3B   DJJ 24 
DJJ CL1   CL1 CL 0 0 N N N 6.131  1.084  14.914 3.926  -0.759 -2.196 CL1   DJJ 25 
DJJ PG    P3  P  0 1 N N N 3.644  0.956  16.484 6.051  -1.277 -0.200 PG    DJJ 26 
DJJ O1G   O10 O  0 1 N N N 3.521  2.393  16.946 6.342  -1.606 1.349  O1G   DJJ 27 
DJJ O2G   O11 O  0 1 N N N 4.588  0.189  17.378 6.629  -2.466 -1.119 O2G   DJJ 28 
DJJ O3G   O12 O  0 1 N N N 2.316  0.286  16.392 6.711  -0.004 -0.567 O3G   DJJ 29 
DJJ H1    H1  H  0 1 N N N 11.411 8.027  10.350 -8.112 -4.270 0.498  H1    DJJ 30 
DJJ H2    H2  H  0 1 N N N 11.224 7.475  11.980 -7.840 -3.598 2.014  H2    DJJ 31 
DJJ H3    H3  H  0 1 N N N 8.989  6.963  12.915 -7.151 -3.361 -1.541 H3    DJJ 32 
DJJ H4    H4  H  0 1 N N N 6.524  6.824  12.483 -5.733 -1.618 -2.513 H4    DJJ 33 
DJJ H5    H5  H  0 1 N N N 5.018  8.190  9.496  -4.357 0.172  -2.267 H5    DJJ 34 
DJJ H6    H6  H  0 1 N N N 4.322  6.219  9.007  -5.652 2.075  -1.814 H6    DJJ 35 
DJJ H7    H7  H  0 1 N N N 5.982  5.717  9.473  -5.766 1.695  -0.066 H7    DJJ 36 
DJJ H8    H8  H  0 1 N N N 5.317  5.145  11.698 -3.940 3.046  0.347  H8    DJJ 37 
DJJ H9    H9  H  0 1 N N N 3.766  3.714  11.330 -4.570 4.267  -1.636 H9    DJJ 38 
DJJ H10   H10 H  0 1 N N N 2.719  6.698  11.242 -2.263 1.723  -1.794 H10   DJJ 39 
DJJ H11   H11 H  0 1 N N N 3.010  7.205  13.700 -1.336 3.080  0.145  H11   DJJ 40 
DJJ H12   H12 H  0 1 N N N 2.942  5.434  13.403 -2.000 1.853  1.250  H12   DJJ 41 
DJJ H13   H13 H  0 1 N N N 4.351  5.089  16.795 0.195  -0.040 2.527  H13   DJJ 42 
DJJ H14   H14 H  0 1 N N N 1.852  3.025  13.649 4.182  1.865  -0.742 H14   DJJ 43 
DJJ H15   H15 H  0 1 N N N 4.058  0.071  14.231 3.767  -2.064 -0.191 H15   DJJ 44 
DJJ H16   H16 H  0 1 N N N 2.606  2.602  17.093 5.939  -2.428 1.659  H16   DJJ 45 
DJJ H17   H17 H  0 1 N N N 4.149  -0.583 17.715 7.582  -2.603 -1.031 H17   DJJ 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 
DJJ O2    C2    DOUB N N 1  
DJJ C2    N3    SING N N 2  
DJJ C2    N1    SING N N 3  
DJJ N3    C4    DOUB N N 4  
DJJ "C2'" "C1'" SING N N 5  
DJJ "C2'" "C3'" SING N N 6  
DJJ "C1'" N1    SING N N 7  
DJJ "C1'" "O4'" SING N N 8  
DJJ N1    C6    SING N N 9  
DJJ "O3'" "C3'" SING N N 10 
DJJ C4    N4    SING N N 11 
DJJ C4    C5    SING N N 12 
DJJ "C3'" "C4'" SING N N 13 
DJJ "O4'" "C4'" SING N N 14 
DJJ C6    C5    DOUB N N 15 
DJJ "C4'" "C5'" SING N N 16 
DJJ O2B   PB    DOUB N N 17 
DJJ "C5'" "O5'" SING N N 18 
DJJ "O5'" PA    SING N N 19 
DJJ PB    O3A   SING N N 20 
DJJ PB    O1B   SING N N 21 
DJJ PB    C3B   SING N N 22 
DJJ O3A   PA    SING N N 23 
DJJ C3B   CL1   SING N N 24 
DJJ C3B   PG    SING N N 25 
DJJ PA    O2A   DOUB N N 26 
DJJ PA    O1A   SING N N 27 
DJJ O3G   PG    DOUB N N 28 
DJJ PG    O1G   SING N N 29 
DJJ PG    O2G   SING N N 30 
DJJ N4    H1    SING N N 31 
DJJ N4    H2    SING N N 32 
DJJ C5    H3    SING N N 33 
DJJ C6    H4    SING N N 34 
DJJ "C1'" H5    SING N N 35 
DJJ "C2'" H6    SING N N 36 
DJJ "C2'" H7    SING N N 37 
DJJ "C3'" H8    SING N N 38 
DJJ "O3'" H9    SING N N 39 
DJJ "C4'" H10   SING N N 40 
DJJ "C5'" H11   SING N N 41 
DJJ "C5'" H12   SING N N 42 
DJJ O1A   H13   SING N N 43 
DJJ O1B   H14   SING N N 44 
DJJ C3B   H15   SING N N 45 
DJJ O1G   H16   SING N N 46 
DJJ O2G   H17   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 
DJJ SMILES           ACDLabs              12.01 "C=1(N)C=CN(C(N=1)=O)C2OC(C(C2)O)COP(=O)(O)OP(O)(C(Cl)P(O)(O)=O)=O"                                                                                                                                   
DJJ InChI            InChI                1.03  "InChI=1S/C10H17ClN3O12P3/c11-9(27(17,18)19)28(20,21)26-29(22,23)24-4-6-5(15)3-8(25-6)14-2-1-7(12)13-10(14)16/h1-2,5-6,8-9,15H,3-4H2,(H,20,21)(H,22,23)(H2,12,13,16)(H2,17,18,19)/t5-,6+,8+,9-/m0/s1" 
DJJ InChIKey         InChI                1.03  DDLGFLMLTFUPNR-LWIVVEGESA-N                                                                                                                                                                           
DJJ 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@@H](Cl)[P](O)(O)=O)O2"                                                                                                              
DJJ SMILES           CACTVS               3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](Cl)[P](O)(O)=O)O2"                                                                                                                    
DJJ 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@H](P(=O)(O)O)Cl)O)O"                                                                                                                       
DJJ SMILES           "OpenEye OEToolkits" 2.0.6 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(O)OP(=O)(C(P(=O)(O)O)Cl)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 
DJJ "SYSTEMATIC NAME" ACDLabs              12.01 "5'-O-[(R)-{[(R)-[(S)-chloro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxycytidine"                                                                              
DJJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{S})-[[[(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]-chloranyl-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 
DJJ "Create component" 2017-10-26 RCSB 
DJJ "Initial release"  2018-06-20 RCSB 
# 
