data_D9D
#

_chem_comp.id                                   D9D
_chem_comp.name                                 "(1S,2S,3S,4R,5R)-2-({[5-(hydroxymethyl)furan-2-yl]methyl}amino)-4-(morpholin-4-yl)-6,8-dioxabicyclo[3.2.1]octan-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H24 N2 O6"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-10-23
_chem_comp.pdbx_modified_date                   2020-04-17
_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                       340.372
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    D9D
_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       5QBL
_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
D9D  O3   O1   O  0  1  N  N  N  -0.219   6.801   9.783  -3.708  -1.199   1.403  O3   D9D   1  
D9D  C4   C1   C  0  1  N  N  N  -0.300   2.865  10.505   0.968  -1.878   0.756  C4   D9D   2  
D9D  C5   C2   C  0  1  N  N  S  -1.556   4.866   9.600  -1.426  -1.527   0.669  C5   D9D   3  
D9D  O4   O2   O  0  1  N  N  N  -3.184  10.193   5.925   0.014   3.791   0.046  O4   D9D   4  
D9D  C6   C3   C  0  1  N  N  S  -2.950   4.385   9.063  -1.838  -1.987  -0.739  C6   D9D   5  
D9D  N1   N1   N  0  1  N  N  N  -2.225   8.425   7.963  -1.451   1.394   0.041  N1   D9D   6  
D9D  C7   C4   C  0  1  N  N  N  -4.068   4.682  10.042  -3.353  -2.297  -0.709  C7   D9D   7  
D9D  C8   C5   C  0  1  N  N  R  -3.695   6.434   8.601  -2.948  -0.080  -1.230  C8   D9D   8  
D9D  C9   C6   C  0  1  N  N  R  -2.415   7.247   8.933  -2.667   0.575   0.131  C9   D9D   9  
D9D  O5   O3   O  0  1  N  N  N  -3.935  -0.052   8.150   6.192  -0.929  -1.211  O5   D9D  10  
D9D  C10  C7   C  0  1  N  N  S  -1.210   6.250   8.918  -2.468  -0.525   1.178  C10  D9D  11  
D9D  C11  C8   C  0  1  N  N  N  -2.351   8.006   6.525  -1.522   2.320  -1.099  C11  D9D  12  
D9D  C12  C9   C  0  1  N  N  N  -2.210   9.208   5.626  -0.213   3.109  -1.191  C12  D9D  13  
D9D  C13  C10  C  0  1  N  N  N  -3.003  10.657   7.255   0.089   2.919   1.178  C13  D9D  14  
D9D  C14  C11  C  0  1  N  N  N  -3.187   9.543   8.256  -1.216   2.128   1.293  C14  D9D  15  
D9D  C15  C12  C  0  1  N  N  N  -3.745  -0.439   9.501   5.227   0.116  -1.069  C15  D9D  16  
D9D  C2   C13  C  0  1  Y  N  N  -3.125   0.657  10.297   4.156  -0.317  -0.101  C2   D9D  17  
D9D  C1   C14  C  0  1  Y  N  N  -3.486   1.281  11.427   4.174  -0.123   1.230  C1   D9D  18  
D9D  O    O4   O  0  1  Y  N  N  -1.924   1.174   9.852   3.020  -0.957  -0.421  O    D9D  19  
D9D  C3   C15  C  0  1  Y  N  N  -1.554   2.143  10.763   2.305  -1.184   0.692  C3   D9D  20  
D9D  C    C16  C  0  1  Y  N  N  -2.485   2.228  11.722   2.981  -0.684   1.742  C    D9D  21  
D9D  N    N2   N  0  1  N  N  N  -0.481   3.846   9.387  -0.106  -0.886   0.612  N    D9D  22  
D9D  O1   O5   O  0  1  N  N  N  -4.383   6.061   9.785  -3.992  -1.055  -1.054  O1   D9D  23  
D9D  O2   O6   O  0  1  N  N  N  -3.336   5.224   7.956  -1.769  -0.827  -1.605  O2   D9D  24  
D9D  H1   H1   H  0  1  N  N  N   0.537   6.226   9.806  -3.657  -1.911   2.056  H1   D9D  25  
D9D  H2   H2   H  0  1  N  N  N   0.483   2.143  10.230   0.899  -2.607  -0.052  H2   D9D  26  
D9D  H3   H3   H  0  1  N  N  N   0.001   3.405  11.415   0.868  -2.386   1.714  H3   D9D  27  
D9D  H4   H4   H  0  1  N  N  N  -1.659   5.046  10.680  -1.387  -2.387   1.338  H4   D9D  28  
D9D  H5   H5   H  0  1  N  N  N  -2.919   3.318   8.797  -1.243  -2.829  -1.095  H5   D9D  29  
D9D  H7   H7   H  0  1  N  N  N  -4.939   4.038   9.851  -3.597  -3.065  -1.443  H7   D9D  30  
D9D  H8   H8   H  0  1  N  N  N  -3.729   4.543  11.079  -3.655  -2.617   0.288  H8   D9D  31  
D9D  H9   H9   H  0  1  N  N  N  -4.342   7.042   7.952  -3.219   0.662  -1.980  H9   D9D  32  
D9D  H10  H10  H  0  1  N  N  N  -2.515   7.648   9.952  -3.511   1.204   0.414  H10  D9D  33  
D9D  H11  H11  H  0  1  N  N  N  -4.331  -0.768   7.668   6.912  -0.719  -1.821  H11  D9D  34  
D9D  H12  H12  H  0  1  N  N  N  -0.845   6.094   7.892  -2.121  -0.082   2.111  H12  D9D  35  
D9D  H13  H13  H  0  1  N  N  N  -3.336   7.544   6.365  -1.670   1.753  -2.019  H13  D9D  36  
D9D  H14  H14  H  0  1  N  N  N  -1.562   7.278   6.287  -2.354   3.009  -0.957  H14  D9D  37  
D9D  H15  H15  H  0  1  N  N  N  -2.332   8.889   4.580  -0.283   3.837  -2.000  H15  D9D  38  
D9D  H16  H16  H  0  1  N  N  N  -1.208   9.642   5.762   0.612   2.425  -1.386  H16  D9D  39  
D9D  H17  H17  H  0  1  N  N  N  -1.987  11.065   7.357   0.924   2.229   1.051  H17  D9D  40  
D9D  H18  H18  H  0  1  N  N  N  -3.738  11.449   7.461   0.238   3.510   2.082  H18  D9D  41  
D9D  H19  H19  H  0  1  N  N  N  -3.000   9.929   9.269  -2.043   2.814   1.474  H19  D9D  42  
D9D  H20  H20  H  0  1  N  N  N  -4.217   9.163   8.193  -1.141   1.422   2.120  H20  D9D  43  
D9D  H21  H21  H  0  1  N  N  N  -4.720  -0.694   9.941   5.717   1.013  -0.692  H21  D9D  44  
D9D  H22  H22  H  0  1  N  N  N  -3.087  -1.320   9.532   4.776   0.328  -2.038  H22  D9D  45  
D9D  H23  H23  H  0  1  N  N  N  -4.379   1.093  12.005   4.950   0.367   1.799  H23  D9D  46  
D9D  H24  H24  H  0  1  N  N  N  -2.471   2.900  12.567   2.672  -0.705   2.776  H24  D9D  47  
D9D  H25  H25  H  0  1  N  N  N  -0.702   3.332   8.558   0.002  -0.356  -0.240  H25  D9D  48  
#   #
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
D9D  C12  O4   SING  N  N   1  
D9D  C12  C11  SING  N  N   2  
D9D  O4   C13  SING  N  N   3  
D9D  C11  N1   SING  N  N   4  
D9D  C13  C14  SING  N  N   5  
D9D  O2   C8   SING  N  N   6  
D9D  O2   C6   SING  N  N   7  
D9D  N1   C14  SING  N  N   8  
D9D  N1   C9   SING  N  N   9  
D9D  O5   C15  SING  N  N  10  
D9D  C8   C9   SING  N  N  11  
D9D  C8   O1   SING  N  N  12  
D9D  C10  C9   SING  N  N  13  
D9D  C10  C5   SING  N  N  14  
D9D  C10  O3   SING  N  N  15  
D9D  C6   C5   SING  N  N  16  
D9D  C6   C7   SING  N  N  17  
D9D  N    C5   SING  N  N  18  
D9D  N    C4   SING  N  N  19  
D9D  C15  C2   SING  N  N  20  
D9D  O1   C7   SING  N  N  21  
D9D  O    C2   SING  Y  N  22  
D9D  O    C3   SING  Y  N  23  
D9D  C2   C1   DOUB  Y  N  24  
D9D  C4   C3   SING  N  N  25  
D9D  C3   C    DOUB  Y  N  26  
D9D  C1   C    SING  Y  N  27  
D9D  O3   H1   SING  N  N  28  
D9D  C4   H2   SING  N  N  29  
D9D  C4   H3   SING  N  N  30  
D9D  C5   H4   SING  N  N  31  
D9D  C6   H5   SING  N  N  32  
D9D  C7   H7   SING  N  N  33  
D9D  C7   H8   SING  N  N  34  
D9D  C8   H9   SING  N  N  35  
D9D  C9   H10  SING  N  N  36  
D9D  O5   H11  SING  N  N  37  
D9D  C10  H12  SING  N  N  38  
D9D  C11  H13  SING  N  N  39  
D9D  C11  H14  SING  N  N  40  
D9D  C12  H15  SING  N  N  41  
D9D  C12  H16  SING  N  N  42  
D9D  C13  H17  SING  N  N  43  
D9D  C13  H18  SING  N  N  44  
D9D  C14  H19  SING  N  N  45  
D9D  C14  H20  SING  N  N  46  
D9D  C15  H21  SING  N  N  47  
D9D  C15  H22  SING  N  N  48  
D9D  C1   H23  SING  N  N  49  
D9D  C    H24  SING  N  N  50  
D9D  N    H25  SING  N  N  51  
#   #
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
D9D  SMILES            ACDLabs               12.01  "OC2C(C3COC(C2N1CCOCC1)O3)NCc4oc(CO)cc4"  
D9D  InChI             InChI                 1.03   "InChI=1S/C16H24N2O6/c19-8-11-2-1-10(23-11)7-17-13-12-9-22-16(24-12)14(15(13)20)18-3-5-21-6-4-18/h1-2,12-17,19-20H,3-9H2/t12-,13-,14-,15+,16-/m1/s1"  
D9D  InChIKey          InChI                 1.03   QPKSUNGYGHKTGL-DGXTUMSLSA-N  
D9D  SMILES_CANONICAL  CACTVS                3.385  "OCc1oc(CN[C@@H]2[C@H]3CO[C@H](O3)[C@@H]([C@H]2O)N4CCOCC4)cc1"  
D9D  SMILES            CACTVS                3.385  "OCc1oc(CN[CH]2[CH]3CO[CH](O3)[CH]([CH]2O)N4CCOCC4)cc1"  
D9D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "c1cc(oc1CN[C@@H]2[C@H]3CO[C@H](O3)[C@@H]([C@H]2O)N4CCOCC4)CO"  
D9D  SMILES            "OpenEye OEToolkits"  2.0.6  "c1cc(oc1CNC2C3COC(O3)C(C2O)N4CCOCC4)CO"  
#   #
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
D9D  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1S,2S,3S,4R,5R)-2-({[5-(hydroxymethyl)furan-2-yl]methyl}amino)-4-(morpholin-4-yl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)"  
D9D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "(1~{S},2~{S},3~{S},4~{R},5~{R})-2-[[5-(hydroxymethyl)furan-2-yl]methylamino]-4-morpholin-4-yl-6,8-dioxabicyclo[3.2.1]octan-3-ol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D9D  "Create component"  2017-10-23  RCSB  
D9D  "Initial release"   2020-04-22  RCSB  
##
