data_TOY
#

_chem_comp.id                                   TOY
_chem_comp.name                                 TOBRAMYCIN
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAD
_chem_comp.formula                              "C18 H37 N5 O9"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2002-04-09
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       467.514
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    TOY
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1LC4
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
TOY  C11   C11   C  0  1  N  N  R  11.840   -7.108   5.575  -1.142  -0.196  -2.574  C11   TOY   1  
TOY  O11   O11   O  0  1  N  N  N  13.055   -7.680   5.183   0.028  -0.989  -2.371  O11   TOY   2  
TOY  C21   C21   C  0  1  N  N  R  10.692   -7.628   4.673  -2.181  -1.012  -3.346  C21   TOY   3  
TOY  N21   N21   N  0  1  N  N  N  10.573   -9.108   4.690  -2.551  -2.200  -2.565  N21   TOY   4  
TOY  C31   C31   C  0  1  N  N  N  10.848   -7.107   3.231  -1.580  -1.445  -4.688  C31   TOY   5  
TOY  C41   C41   C  0  1  N  N  S  10.940   -5.573   3.252  -1.058  -0.200  -5.414  C41   TOY   6  
TOY  O41   O41   O  0  1  N  N  N  11.078   -5.083   1.923  -0.362  -0.593  -6.598  O41   TOY   7  
TOY  C51   C51   C  0  1  N  N  R  12.136   -5.142   4.130  -0.102   0.554  -4.486  C51   TOY   8  
TOY  O51   O51   O  0  1  N  N  N  11.964   -5.655   5.484  -0.799   0.973  -3.315  O51   TOY   9  
TOY  C61   C61   C  0  1  N  N  N  12.296   -3.629   4.239   0.451   1.780  -5.215  C61   TOY  10  
TOY  N61   N61   N  0  1  N  N  N  12.888   -3.046   3.011   1.371   2.503  -4.326  N61   TOY  11  
TOY  C12   C12   C  0  1  N  N  R  16.671   -8.899   7.111   2.642  -0.465   0.915  C12   TOY  12  
TOY  N12   N12   N  0  1  N  N  N  17.844   -8.943   8.018   3.431   0.201   1.959  N12   TOY  13  
TOY  C22   C22   C  0  1  N  N  N  16.702   -7.619   6.265   3.100   0.022  -0.460  C22   TOY  14  
TOY  C32   C32   C  0  1  N  N  S  15.481   -7.595   5.314   2.277  -0.671  -1.547  C32   TOY  15  
TOY  N32   N32   N  0  1  N  N  N  15.602   -6.428   4.401   2.717  -0.203  -2.868  N32   TOY  16  
TOY  C42   C42   C  0  1  N  N  R  14.164   -7.620   6.118   0.796  -0.341  -1.356  C42   TOY  17  
TOY  C52   C52   C  0  1  N  N  S  14.122   -8.865   7.052   0.338  -0.829   0.019  C52   TOY  18  
TOY  O52   O52   O  0  1  N  N  N  12.973   -8.788   7.881  -1.045  -0.520   0.198  O52   TOY  19  
TOY  C62   C62   C  0  1  N  N  S  15.384   -8.933   7.949   1.160  -0.134   1.107  C62   TOY  20  
TOY  O62   O62   O  0  1  N  N  N  15.356  -10.153   8.726   0.732  -0.590   2.392  O62   TOY  21  
TOY  C13   C13   C  0  1  N  N  S  15.424  -10.045  10.116   0.951   0.485   3.306  C13   TOY  22  
TOY  C23   C23   C  0  1  N  N  R  15.972  -11.354  10.714   0.886  -0.043   4.740  C23   TOY  23  
TOY  O23   O23   O  0  1  N  N  N  17.273  -11.609  10.210   1.910  -1.021   4.936  O23   TOY  24  
TOY  C33   C33   C  0  1  N  N  S  15.035  -12.506  10.356  -0.484  -0.683   4.976  C33   TOY  25  
TOY  N33   N33   N  0  1  N  N  N  15.568  -13.807  10.829  -0.621  -1.059   6.389  N33   TOY  26  
TOY  C43   C43   C  0  1  N  N  S  13.653  -12.229  10.970  -1.569   0.334   4.607  C43   TOY  27  
TOY  O43   O43   O  0  1  N  N  N  12.748  -13.280  10.641  -2.854  -0.286   4.677  O43   TOY  28  
TOY  C53   C53   C  0  1  N  N  R  13.107  -10.869  10.470  -1.320   0.835   3.183  C53   TOY  29  
TOY  O53   O53   O  0  1  N  N  N  14.090   -9.783  10.648  -0.050   1.482   3.114  O53   TOY  30  
TOY  C63   C63   C  0  1  N  N  N  11.851  -10.453  11.213  -2.418   1.828   2.795  C63   TOY  31  
TOY  O63   O63   O  0  1  N  N  N  12.112  -10.225  12.594  -2.245   2.221   1.432  O63   TOY  32  
TOY  H11   H11   H  0  1  N  N  N  11.598   -7.392   6.626  -1.554   0.094  -1.608  H11   TOY  33  
TOY  H21   H21   H  0  1  N  N  N   9.743   -7.226   5.099  -3.067  -0.402  -3.523  H21   TOY  34  
TOY  HN21  1HN2  H  0  0  N  N  N  10.475   -9.456   5.644  -3.234  -2.704  -3.111  HN21  TOY  35  
TOY  HN22  2HN2  H  0  0  N  N  N   9.817   -9.450   4.096  -1.729  -2.784  -2.518  HN22  TOY  36  
TOY  H311  1H31  H  0  0  N  N  N  10.036   -7.472   2.560  -0.758  -2.139  -4.514  H311  TOY  37  
TOY  H312  2H31  H  0  0  N  N  N  11.712   -7.575   2.704  -2.347  -1.926  -5.294  H312  TOY  38  
TOY  H41   H41   H  0  1  N  N  N  10.008   -5.142   3.688  -1.895   0.444  -5.680  H41   TOY  39  
TOY  H41O  OH41  H  0  0  N  N  N  11.135   -4.135   1.936  -0.997  -1.071  -7.150  H41O  TOY  40  
TOY  H51   H51   H  0  1  N  N  N  13.043   -5.558   3.633   0.720  -0.101  -4.203  H51   TOY  41  
TOY  H611  1H61  H  0  0  N  N  N  12.882   -3.348   5.145  -0.370   2.436  -5.499  H611  TOY  42  
TOY  H612  2H61  H  0  0  N  N  N  11.329   -3.137   4.496   0.986   1.460  -6.109  H612  TOY  43  
TOY  HN61  1HN6  H  0  0  N  N  N  12.352   -3.303   2.183   1.710   3.299  -4.846  HN61  TOY  44  
TOY  HN62  2HN6  H  0  0  N  N  N  12.995   -2.034   3.084   0.814   2.867  -3.568  HN62  TOY  45  
TOY  H12   H12   H  0  1  N  N  N  16.701   -9.780   6.429   2.785  -1.543   0.984  H12   TOY  46  
TOY  HN11  1HN1  H  0  0  N  N  N  17.910   -8.105   8.597   4.396  -0.043   1.794  HN11  TOY  47  
TOY  HN12  2HN1  H  0  0  N  N  N  17.823   -9.794   8.580   3.352   1.193   1.794  HN12  TOY  48  
TOY  H221  1H22  H  0  0  N  N  N  17.665   -7.501   5.716   4.155  -0.212  -0.596  H221  TOY  49  
TOY  H222  2H22  H  0  0  N  N  N  16.763   -6.700   6.894   2.956   1.101  -0.529  H222  TOY  50  
TOY  H32   H32   H  0  1  N  N  N  15.461   -8.512   4.680   2.421  -1.750  -1.478  H32   TOY  51  
TOY  HN1   1HN   H  0  1  N  N  N  16.488   -6.420   3.896   3.723  -0.277  -2.882  HN1   TOY  52  
TOY  HN2   2HN   H  0  1  N  N  N  14.797   -6.412   3.774   2.368  -0.867  -3.542  HN2   TOY  53  
TOY  H42   H42   H  0  1  N  N  N  14.094   -6.702   6.747   0.653   0.737  -1.425  H42   TOY  54  
TOY  H52   H52   H  0  1  N  N  N  14.086   -9.780   6.416   0.481  -1.907   0.088  H52   TOY  55  
TOY  H52O  OH52  H  0  0  N  N  N  12.947   -9.548   8.451  -1.325  -0.955   1.015  H52O  TOY  56  
TOY  H62   H62   H  0  1  N  N  N  15.379   -8.043   8.621   1.017   0.943   1.037  H62   TOY  57  
TOY  H13   H13   H  0  1  N  N  N  16.105   -9.205  10.389   1.934   0.921   3.124  H13   TOY  58  
TOY  H23   H23   H  0  1  N  N  N  16.031  -11.259  11.823   1.029   0.779   5.440  H23   TOY  59  
TOY  H23O  OH23  H  0  0  N  N  N  17.611  -12.416  10.579   2.754  -0.577   4.778  H23O  TOY  60  
TOY  H33   H33   H  0  1  N  N  N  14.949  -12.573   9.246  -0.587  -1.570   4.350  H33   TOY  61  
TOY  HN31  1HN3  H  0  0  N  N  N  15.769  -13.787  11.829   0.110  -1.726   6.584  HN31  TOY  62  
TOY  HN32  2HN3  H  0  0  N  N  N  14.942  -14.576  10.590  -0.411  -0.233   6.930  HN32  TOY  63  
TOY  H43   H43   H  0  1  N  N  N  13.756  -12.183  12.079  -1.532   1.174   5.301  H43   TOY  64  
TOY  H43O  OH43  H  0  0  N  N  N  11.894  -13.109  11.020  -3.504   0.386   4.432  H43O  TOY  65  
TOY  H53   H53   H  0  1  N  N  N  12.885  -11.022   9.388  -1.335  -0.008   2.494  H53   TOY  66  
TOY  H631  1H63  H  0  0  N  N  N  11.029  -11.193  11.070  -3.393   1.356   2.916  H631  TOY  67  
TOY  H632  2H63  H  0  0  N  N  N  11.371   -9.566  10.737  -2.357   2.707   3.437  H632  TOY  68  
TOY  H63O  OH63  H  0  0  N  N  N  11.326   -9.965  13.059  -2.905   2.903   1.252  H63O  TOY  69  
#   #
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
TOY  C11  O11   SING  N  N   1  
TOY  C11  C21   SING  N  N   2  
TOY  C11  O51   SING  N  N   3  
TOY  C11  H11   SING  N  N   4  
TOY  O11  C42   SING  N  N   5  
TOY  C21  N21   SING  N  N   6  
TOY  C21  C31   SING  N  N   7  
TOY  C21  H21   SING  N  N   8  
TOY  N21  HN21  SING  N  N   9  
TOY  N21  HN22  SING  N  N  10  
TOY  C31  C41   SING  N  N  11  
TOY  C31  H311  SING  N  N  12  
TOY  C31  H312  SING  N  N  13  
TOY  C41  O41   SING  N  N  14  
TOY  C41  C51   SING  N  N  15  
TOY  C41  H41   SING  N  N  16  
TOY  O41  H41O  SING  N  N  17  
TOY  C51  O51   SING  N  N  18  
TOY  C51  C61   SING  N  N  19  
TOY  C51  H51   SING  N  N  20  
TOY  C61  N61   SING  N  N  21  
TOY  C61  H611  SING  N  N  22  
TOY  C61  H612  SING  N  N  23  
TOY  N61  HN61  SING  N  N  24  
TOY  N61  HN62  SING  N  N  25  
TOY  C12  N12   SING  N  N  26  
TOY  C12  C22   SING  N  N  27  
TOY  C12  C62   SING  N  N  28  
TOY  C12  H12   SING  N  N  29  
TOY  N12  HN11  SING  N  N  30  
TOY  N12  HN12  SING  N  N  31  
TOY  C22  C32   SING  N  N  32  
TOY  C22  H221  SING  N  N  33  
TOY  C22  H222  SING  N  N  34  
TOY  C32  N32   SING  N  N  35  
TOY  C32  C42   SING  N  N  36  
TOY  C32  H32   SING  N  N  37  
TOY  N32  HN1   SING  N  N  38  
TOY  N32  HN2   SING  N  N  39  
TOY  C42  C52   SING  N  N  40  
TOY  C42  H42   SING  N  N  41  
TOY  C52  O52   SING  N  N  42  
TOY  C52  C62   SING  N  N  43  
TOY  C52  H52   SING  N  N  44  
TOY  O52  H52O  SING  N  N  45  
TOY  C62  O62   SING  N  N  46  
TOY  C62  H62   SING  N  N  47  
TOY  O62  C13   SING  N  N  48  
TOY  C13  C23   SING  N  N  49  
TOY  C13  O53   SING  N  N  50  
TOY  C13  H13   SING  N  N  51  
TOY  C23  O23   SING  N  N  52  
TOY  C23  C33   SING  N  N  53  
TOY  C23  H23   SING  N  N  54  
TOY  O23  H23O  SING  N  N  55  
TOY  C33  N33   SING  N  N  56  
TOY  C33  C43   SING  N  N  57  
TOY  C33  H33   SING  N  N  58  
TOY  N33  HN31  SING  N  N  59  
TOY  N33  HN32  SING  N  N  60  
TOY  C43  O43   SING  N  N  61  
TOY  C43  C53   SING  N  N  62  
TOY  C43  H43   SING  N  N  63  
TOY  O43  H43O  SING  N  N  64  
TOY  C53  O53   SING  N  N  65  
TOY  C53  C63   SING  N  N  66  
TOY  C53  H53   SING  N  N  67  
TOY  C63  O63   SING  N  N  68  
TOY  C63  H631  SING  N  N  69  
TOY  C63  H632  SING  N  N  70  
TOY  O63  H63O  SING  N  N  71  
#   #
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
TOY  SMILES            ACDLabs               10.04  "O(C2C(O)C(OC1OC(CN)C(O)CC1N)C(N)CC2N)C3OC(C(O)C(N)C3O)CO"  
TOY  SMILES_CANONICAL  CACTVS                3.341  "NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](N)C[C@@H]1O"  
TOY  SMILES            CACTVS                3.341  "NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O)[CH](N)C[CH]1O"  
TOY  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H](C[C@@H]([C@H](O3)CN)O)N)N"  
TOY  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(CC(C(O3)CN)O)N)N"  
TOY  InChI             InChI                 1.03   "InChI=1S/C18H37N5O9/c19-3-9-8(25)2-7(22)17(29-9)31-15-5(20)1-6(21)16(14(15)28)32-18-13(27)11(23)12(26)10(4-24)30-18/h5-18,24-28H,1-4,19-23H2/t5-,6+,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1"  
TOY  InChIKey          InChI                 1.03   NLVFBUXFDBBNBW-PBSUHMDJSA-N  
#   #
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
TOY  "SYSTEMATIC NAME"  ACDLabs               10.04  "(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside"  
TOY  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "(2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxy-oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
TOY  "Create component"   2002-04-09  EBI   
TOY  "Modify descriptor"  2011-06-04  RCSB  
TOY  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     TOY
_pdbx_chem_comp_synonyms.name        "4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
