data_QDM
# 
_chem_comp.id                                    QDM 
_chem_comp.name                                  TDP-3,6-dideoxy-3-N,N-dimethylglucose 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C18 H31 N3 O14 P2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-02-17 
_chem_comp.pdbx_modified_date                    2014-02-21 
_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                        575.398 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     QDM 
_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        4OQD 
_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 
QDM O2A   O2A   O 0 1 N N N 11.761 8.365  17.033 0.384  -3.742 0.073  O2A   QDM 1  
QDM PA    PA    P 0 1 N N N 10.890 9.493  17.455 0.041  -2.436 -0.531 PA    QDM 2  
QDM O1A   O1A   O 0 1 N N N 9.474  9.158  17.993 -0.466 -2.661 -2.043 O1A   QDM 3  
QDM O3A   O3A   O 0 1 N N N 10.523 10.564 16.308 1.343  -1.488 -0.537 O3A   QDM 4  
QDM PB    PB    P 0 1 N N N 9.482  10.675 15.128 2.889  -1.714 -0.926 PB    QDM 5  
QDM O1B   O1B   O 0 1 N N N 8.685  11.936 15.300 3.056  -1.643 -2.525 O1B   QDM 6  
QDM O3B   O3B   O 0 1 N N N 10.553 10.869 13.826 3.787  -0.568 -0.240 O3B   QDM 7  
QDM C1Q   C1Q   C 0 1 N N R 11.274 12.064 13.804 5.215  -0.552 -0.310 C1Q   QDM 8  
QDM C2Q   C2Q   C 0 1 N N R 10.672 13.106 12.857 5.780  0.117  0.946  C2Q   QDM 9  
QDM O2Q   O2Q   O 0 1 N N N 9.364  13.535 13.343 5.321  -0.580 2.106  O2Q   QDM 10 
QDM C3Q   C3Q   C 0 1 N N S 10.499 12.587 11.418 5.301  1.571  1.000  C3Q   QDM 11 
QDM N3Q   N3Q   N 0 1 N N N 9.885  13.603 10.534 5.897  2.242  2.162  N3Q   QDM 12 
QDM C2M   C2M   C 0 1 N N N 9.325  13.007 9.310  7.329  2.493  1.948  C2M   QDM 13 
QDM C1M   C1M   C 0 1 N N N 10.900 14.648 10.221 5.185  3.489  2.473  C1M   QDM 14 
QDM C4Q   C4Q   C 0 1 N N S 11.808 11.937 10.920 5.732  2.287  -0.284 C4Q   QDM 15 
QDM O4Q   O4Q   O 0 1 N N N 11.602 11.297 9.667  5.228  3.624  -0.278 O4Q   QDM 16 
QDM C5Q   C5Q   C 0 1 N N R 12.323 11.006 12.047 5.169  1.534  -1.492 C5Q   QDM 17 
QDM C6Q   C6Q   C 0 1 N N N 13.776 10.568 11.702 5.645  2.208  -2.781 C6Q   QDM 18 
QDM O5Q   O5Q   O 0 1 N N N 12.576 11.636 13.258 5.628  0.180  -1.465 O5Q   QDM 19 
QDM O2B   O2B   O 0 1 N N N 8.857  9.359  14.886 3.330  -3.042 -0.442 O2B   QDM 20 
QDM "O5'" "O5'" O 0 1 N N N 11.599 10.402 18.525 -1.128 -1.737 0.328  "O5'" QDM 21 
QDM "C5'" "C5'" C 0 1 N N N 11.046 11.555 19.150 -2.375 -2.375 0.609  "C5'" QDM 22 
QDM "C4'" "C4'" C 0 1 N N R 11.867 12.777 18.818 -3.251 -1.438 1.443  "C4'" QDM 23 
QDM "C3'" "C3'" C 0 1 N N S 13.255 12.703 19.431 -4.554 -2.153 1.864  "C3'" QDM 24 
QDM "O3'" "O3'" O 0 1 N N N 14.210 13.366 18.572 -4.443 -2.649 3.200  "O3'" QDM 25 
QDM "C2'" "C2'" C 0 1 N N N 13.162 13.382 20.777 -5.631 -1.048 1.785  "C2'" QDM 26 
QDM "C1'" "C1'" C 0 1 N N R 12.122 14.427 20.462 -4.851 0.204  1.325  "C1'" QDM 27 
QDM "O4'" "O4'" O 0 1 N N N 11.251 13.882 19.493 -3.687 -0.315 0.646  "O4'" QDM 28 
QDM N1    N1    N 0 1 N N N 11.289 14.912 21.577 -5.665 1.002  0.404  N1    QDM 29 
QDM C6    C6    C 0 1 N N N 10.201 14.226 21.904 -6.066 2.258  0.769  C6    QDM 30 
QDM C5    C5    C 0 1 N N N 9.489  14.765 22.965 -6.816 2.993  -0.079 C5    QDM 31 
QDM C5M   C5M   C 0 1 N N N 8.277  14.020 23.450 -7.267 4.379  0.305  C5M   QDM 32 
QDM C4    C4    C 0 1 N N N 9.892  15.963 23.532 -7.173 2.446  -1.335 C4    QDM 33 
QDM O4    O4    O 0 1 N N N 9.243  16.584 24.541 -7.848 3.090  -2.117 O4    QDM 34 
QDM N3    N3    N 0 1 N N N 11.025 16.633 23.192 -6.757 1.204  -1.657 N3    QDM 35 
QDM C2    C2    C 0 1 N N N 11.671 16.057 22.155 -6.006 0.495  -0.794 C2    QDM 36 
QDM O2    O2    O 0 1 N N N 12.779 16.752 21.797 -5.635 -0.622 -1.100 O2    QDM 37 
QDM H1    H1    H 0 1 N N N 9.344  8.217  17.980 -0.709 -1.845 -2.502 H1    QDM 38 
QDM H2    H2    H 0 1 N N N 7.759  11.738 15.228 2.785  -0.799 -2.912 H2    QDM 39 
QDM H3    H3    H 0 1 N N N 11.394 12.493 14.810 5.587  -1.575 -0.375 H3    QDM 40 
QDM H4    H4    H 0 1 N N N 11.347 13.974 12.828 6.869  0.092  0.913  H4    QDM 41 
QDM H5    H5    H 0 1 N N N 9.447  13.860 14.232 5.584  -1.510 2.136  H5    QDM 42 
QDM H6    H6    H 0 1 N N N 9.772  11.764 11.488 4.214  1.594  1.083  H6    QDM 43 
QDM H8    H8    H 0 1 N N N 8.582  12.242 9.581  7.454  3.218  1.143  H8    QDM 44 
QDM H9    H9    H 0 1 N N N 8.842  13.791 8.708  7.769  2.888  2.864  H9    QDM 45 
QDM H10   H10   H 0 1 N N N 10.133 12.542 8.726  7.825  1.561  1.679  H10   QDM 46 
QDM H11   H11   H 0 1 N N N 11.295 15.069 11.158 4.127  3.274  2.627  H11   QDM 47 
QDM H12   H12   H 0 1 N N N 11.723 14.199 9.646  5.602  3.930  3.379  H12   QDM 48 
QDM H13   H13   H 0 1 N N N 10.432 15.448 9.628  5.297  4.188  1.644  H13   QDM 49 
QDM H14   H14   H 0 1 N N N 12.548 12.741 10.794 6.820  2.307  -0.343 H14   QDM 50 
QDM H15   H15   H 0 1 N N N 12.415 10.903 9.375  5.464  4.137  -1.063 H15   QDM 51 
QDM H16   H16   H 0 1 N N N 11.671 10.126 12.148 4.079  1.549  -1.455 H16   QDM 52 
QDM H17   H17   H 0 1 N N N 14.157 9.906  12.493 6.734  2.192  -2.818 H17   QDM 53 
QDM H18   H18   H 0 1 N N N 13.779 10.032 10.742 5.244  1.671  -3.641 H18   QDM 54 
QDM H19   H19   H 0 1 N N N 14.419 11.457 11.627 5.295  3.240  -2.801 H19   QDM 55 
QDM H20   H20   H 0 1 N N N 10.016 11.702 18.793 -2.882 -2.609 -0.327 H20   QDM 56 
QDM H21   H21   H 0 1 N N N 11.039 11.408 20.240 -2.195 -3.295 1.165  H21   QDM 57 
QDM H22   H22   H 0 1 N N N 11.925 12.932 17.731 -2.706 -1.092 2.322  H22   QDM 58 
QDM H23   H23   H 0 1 N N N 13.535 11.649 19.572 -4.786 -2.963 1.173  H23   QDM 59 
QDM H24   H24   H 0 1 N N N 15.075 13.316 18.961 -5.234 -3.107 3.516  H24   QDM 60 
QDM H25   H25   H 0 1 N N N 12.823 12.690 21.562 -6.395 -1.312 1.054  H25   QDM 61 
QDM H26   H26   H 0 1 N N N 14.120 13.834 21.075 -6.081 -0.882 2.764  H26   QDM 62 
QDM H27   H27   H 0 1 N N N 12.642 15.292 20.025 -4.555 0.804  2.185  H27   QDM 63 
QDM H28   H28   H 0 1 N N N 9.897  13.327 21.389 -5.785 2.659  1.732  H28   QDM 64 
QDM H29   H29   H 0 1 N N N 7.821  14.566 24.289 -6.521 5.106  -0.017 H29   QDM 65 
QDM H30   H30   H 0 1 N N N 7.548  13.933 22.631 -8.219 4.598  -0.177 H30   QDM 66 
QDM H31   H31   H 0 1 N N N 8.574  13.015 23.785 -7.386 4.436  1.387  H31   QDM 67 
QDM H32   H32   H 0 1 N N N 11.344 17.459 23.657 -6.998 0.822  -2.516 H32   QDM 68 
# 
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 
QDM C2M   N3Q   SING N N 1  
QDM O4Q   C4Q   SING N N 2  
QDM C1M   N3Q   SING N N 3  
QDM N3Q   C3Q   SING N N 4  
QDM C4Q   C3Q   SING N N 5  
QDM C4Q   C5Q   SING N N 6  
QDM C3Q   C2Q   SING N N 7  
QDM C6Q   C5Q   SING N N 8  
QDM C5Q   O5Q   SING N N 9  
QDM C2Q   O2Q   SING N N 10 
QDM C2Q   C1Q   SING N N 11 
QDM O5Q   C1Q   SING N N 12 
QDM C1Q   O3B   SING N N 13 
QDM O3B   PB    SING N N 14 
QDM O2B   PB    DOUB N N 15 
QDM PB    O1B   SING N N 16 
QDM PB    O3A   SING N N 17 
QDM O3A   PA    SING N N 18 
QDM O2A   PA    DOUB N N 19 
QDM PA    O1A   SING N N 20 
QDM PA    "O5'" SING N N 21 
QDM "O5'" "C5'" SING N N 22 
QDM "O3'" "C3'" SING N N 23 
QDM "C4'" "C5'" SING N N 24 
QDM "C4'" "C3'" SING N N 25 
QDM "C4'" "O4'" SING N N 26 
QDM "C3'" "C2'" SING N N 27 
QDM "O4'" "C1'" SING N N 28 
QDM "C1'" "C2'" SING N N 29 
QDM "C1'" N1    SING N N 30 
QDM N1    C6    SING N N 31 
QDM N1    C2    SING N N 32 
QDM O2    C2    DOUB N N 33 
QDM C6    C5    DOUB N N 34 
QDM C2    N3    SING N N 35 
QDM C5    C5M   SING N N 36 
QDM C5    C4    SING N N 37 
QDM N3    C4    SING N N 38 
QDM C4    O4    DOUB N N 39 
QDM O1A   H1    SING N N 40 
QDM O1B   H2    SING N N 41 
QDM C1Q   H3    SING N N 42 
QDM C2Q   H4    SING N N 43 
QDM O2Q   H5    SING N N 44 
QDM C3Q   H6    SING N N 45 
QDM C2M   H8    SING N N 46 
QDM C2M   H9    SING N N 47 
QDM C2M   H10   SING N N 48 
QDM C1M   H11   SING N N 49 
QDM C1M   H12   SING N N 50 
QDM C1M   H13   SING N N 51 
QDM C4Q   H14   SING N N 52 
QDM O4Q   H15   SING N N 53 
QDM C5Q   H16   SING N N 54 
QDM C6Q   H17   SING N N 55 
QDM C6Q   H18   SING N N 56 
QDM C6Q   H19   SING N N 57 
QDM "C5'" H20   SING N N 58 
QDM "C5'" H21   SING N N 59 
QDM "C4'" H22   SING N N 60 
QDM "C3'" H23   SING N N 61 
QDM "O3'" H24   SING N N 62 
QDM "C2'" H25   SING N N 63 
QDM "C2'" H26   SING N N 64 
QDM "C1'" H27   SING N N 65 
QDM C6    H28   SING N N 66 
QDM C5M   H29   SING N N 67 
QDM C5M   H30   SING N N 68 
QDM C5M   H31   SING N N 69 
QDM N3    H32   SING N N 70 
# 
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 
QDM SMILES           ACDLabs              12.01 "O=C1C(=CN(C(=O)N1)C2OC(C(O)C2)COP(=O)(OP(=O)(OC3OC(C(O)C(N(C)C)C3O)C)O)O)C" 
QDM InChI            InChI                1.03  
"InChI=1S/C18H31N3O14P2/c1-8-6-21(18(26)19-16(8)25)12-5-10(22)11(33-12)7-31-36(27,28)35-37(29,30)34-17-15(24)13(20(3)4)14(23)9(2)32-17/h6,9-15,17,22-24H,5,7H2,1-4H3,(H,27,28)(H,29,30)(H,19,25,26)/t9-,10+,11-,12-,13+,14-,15-,17-/m1/s1" 
QDM InChIKey         InChI                1.03  IJJNPDQFXCRKOA-WHRNYZGVSA-N 
QDM SMILES_CANONICAL CACTVS               3.385 "C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H]([C@@H]1O)N(C)C" 
QDM SMILES           CACTVS               3.385 "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH]([CH]1O)N(C)C" 
QDM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N(C)C)O" 
QDM SMILES           "OpenEye OEToolkits" 1.7.6 "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N(C)C)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 
QDM "SYSTEMATIC NAME" ACDLabs              12.01 
"(2R,3R,4S,5S,6R)-4-(dimethylamino)-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" 
QDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 
"[(2R,3R,4S,5S,6R)-4-(dimethylamino)-6-methyl-3,5-bis(oxidanyl)oxan-2-yl] [[(2R,3S,5R)-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 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 
QDM "Create component" 2014-02-17 RCSB 
QDM "Initial release"  2014-02-26 RCSB 
# 
