# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 28 14:19:23 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (2R,3R,4S,5R,6E)-3,4,5-trihydroxy-N-[(3S,6R)-6-hydroxy-2-oxoazepan-3-yl]-2-methoxy-8,8-dimethylnon-6-enamide (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@H]([C@H](O)[C@@H](O)[C@H](O)\C=C\C(C)(C)C)C(=O)N[C@H]1CC[C@@H](O)CNC1=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 TDE  TDE  '(2R,3R,4S,5R,6E)-3,4,5-trihydroxy-N-[(3S,6R)-6-hydroxy-2-oxoazepan-3-yl]-2-methoxy-8,8-dimethylnon-6-enamide (non-preferred name)'  ligand  59  27  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TDE
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 TDE  C2    C  C     0   0.513   0.8396  -0.3453  -4.8231
 TDE  O8    O  O     0  -0.489   1.7558  -0.7641  -5.5159
 TDE  C3    C  CH1   0  -0.172   0.1853  -1.2537  -3.7838
 TDE  C4    C  CH2   0  -0.500  -1.2093  -1.6930  -4.2419
 TDE  C5    C  CH2   0  -0.471  -2.3293  -0.6637  -4.1226
 TDE  C6    C  CH1   0   0.063  -2.1387   0.6299  -4.8986
 TDE  C7    C  CH2   0  -0.333  -0.9031   1.4237  -4.4588
 TDE  N1    N  NH1   0  -0.614   0.3401   0.8928  -4.9789
 TDE  O7    O  OH1   0  -0.672  -3.3054   1.3935  -4.6751
 TDE  N9    N  NH1   0  -0.659   0.1149  -0.6463  -2.4753
 TDE  C10   C  C     0   0.526   1.2044  -0.1694  -1.8485
 TDE  C12   C  CH1   0  -0.053   0.9613   0.4512  -0.4612
 TDE  O21   O  O2    0  -0.482   2.1661   0.9234   0.0505
 TDE  C25   C  CH3   0  -0.405   2.4827   2.2433  -0.3249
 TDE  C13   C  CH1   0  -0.033   0.3564  -0.5458   0.5533
 TDE  O22   O  OH1   0  -0.660  -0.9181  -0.9762   0.1172
 TDE  C14   C  CH1   0  -0.013   0.3640   0.0467   1.9715
 TDE  O23   O  OH1   0  -0.658  -0.1287   1.3646   2.0202
 TDE  C15   C  CH1   0  -0.023  -0.3527  -0.8596   2.9965
 TDE  O24   O  OH1   0  -0.663  -1.7534  -0.7811   2.8668
 TDE  C16   C  C1    0  -0.271   0.1452  -0.5556   4.3818
 TDE  C17   C  C1    0  -0.183  -0.5994  -0.2577   5.4400
 TDE  C18   C  CT    0  -0.134  -0.1127   0.0721   6.8287
 TDE  C21   C  CH3   0  -0.631  -0.5463   1.5080   7.1522
 TDE  C20   C  CH3   0  -0.637  -0.7968  -0.8862   7.8114
 TDE  C19   C  CH3   0  -0.663   1.4017  -0.0463   6.9714
 TDE  O11   O  O     0  -0.471   2.3090  -0.1688  -2.3636
 TDE  H3    H  HCH1  0   0.279   0.8193  -2.1446  -3.7538
 TDE  H41   H  HCH2  0   0.261  -1.1291  -2.0448  -5.2735
 TDE  H42   H  HCH2  0   0.270  -1.4934  -2.5686  -3.6534
 TDE  H51   H  HCH2  0   0.258  -3.2482  -1.1405  -4.4722
 TDE  H52   H  HCH2  0   0.224  -2.5082  -0.4126  -3.0718
 TDE  H6    H  HCH1  0   0.208  -2.0206   0.3945  -5.9670
 TDE  H71   H  HCH2  0   0.269  -0.9807   2.4366  -4.8551
 TDE  H72   H  HCH2  0   0.243  -0.8764   1.5153  -3.3712
 TDE  HN1   H  HNH1  0   0.395   0.7751   1.4301  -5.7139
 TDE  HO7   H  HOH1  0   0.452  -3.2804   2.1678  -5.2464
 TDE  HN9   H  HNH1  0   0.401  -0.7141  -0.7868  -1.9157
 TDE  H12   H  HCH1  0   0.239   0.2338   1.2688  -0.5876
 TDE  H251  H  HCH3  0   0.235   3.4210   2.5056   0.1621
 TDE  H252  H  HCH3  0   0.212   2.6144   2.3537  -1.4048
 TDE  H253  H  HCH3  0   0.211   1.7125   2.9482   0.0054
 TDE  H13   H  HCH1  0   0.261   0.9785  -1.4465   0.5815
 TDE  H22   H  HOH1  0   0.450  -1.5837  -0.3163   0.3394
 TDE  H14   H  HCH1  0   0.260   1.4126   0.1061   2.2686
 TDE  H23   H  HOH1  0   0.437  -1.0884   1.3582   1.9396
 TDE  H15   H  HCH1  0   0.253  -0.0773  -1.8959   2.7652
 TDE  H24   H  HOH1  0   0.453  -2.0779  -0.0341   3.3812
 TDE  H16   H  H     0   0.252   1.2257  -0.5965   4.4772
 TDE  H17   H  H     0   0.225  -1.6846  -0.2354   5.3498
 TDE  H211  H  HCH3  0   0.225  -0.2732   1.7717   8.1763
 TDE  H212  H  HCH3  0   0.227  -0.0702   2.2247   6.4809
 TDE  H213  H  HCH3  0   0.224  -1.6277   1.6263   7.0570
 TDE  H201  H  HCH3  0   0.224  -1.8843  -0.8164   7.7375
 TDE  H202  H  HCH3  0   0.228  -0.5144  -1.9223   7.6167
 TDE  H203  H  HCH3  0   0.227  -0.5181  -0.6495   8.8404
 TDE  H191  H  HCH3  0   0.227   1.9284   0.6364   6.3019
 TDE  H192  H  HCH3  0   0.233   1.7041   0.1970   7.9916
 TDE  H193  H  HCH3  0   0.227   1.7500  -1.0592   6.7590

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 TDE  C2   O8    double  1.223  0.020  1.223
 TDE  C2   C3    single  1.528  0.020  1.528
 TDE  C2   N1    single  1.344  0.020  1.344
 TDE  C3   C4    single  1.532  0.020  1.532
 TDE  C3   N9    single  1.444  0.020  1.444
 TDE  C3   H3    single  0.970  0.020  1.090
 TDE  C4   C5    single  1.526  0.020  1.526
 TDE  C4   H41   single  0.970  0.020  1.090
 TDE  C4   H42   single  0.970  0.020  1.090
 TDE  C5   C6    single  1.520  0.020  1.520
 TDE  C5   H51   single  0.970  0.020  1.090
 TDE  C5   H52   single  0.970  0.020  1.090
 TDE  C6   C7    single  1.533  0.020  1.533
 TDE  C6   O7    single  1.412  0.020  1.412
 TDE  C6   H6    single  0.970  0.020  1.090
 TDE  C7   N1    single  1.448  0.020  1.448
 TDE  C7   H71   single  0.970  0.020  1.090
 TDE  C7   H72   single  0.970  0.020  1.090
 TDE  N1   HN1   single  0.860  0.020  1.020
 TDE  O7   HO7   single  0.850  0.020  0.980
 TDE  N9   C10   single  1.344  0.020  1.344
 TDE  N9   HN9   single  0.860  0.020  1.020
 TDE  C10  C12   single  1.539  0.020  1.539
 TDE  C10  O11   double  1.219  0.020  1.219
 TDE  C12  O21   single  1.392  0.020  1.392
 TDE  C12  C13   single  1.546  0.020  1.546
 TDE  C12  H12   single  0.970  0.020  1.090
 TDE  O21  C25   single  1.408  0.020  1.408
 TDE  C25  H251  single  0.970  0.020  1.090
 TDE  C25  H252  single  0.970  0.020  1.090
 TDE  C25  H253  single  0.970  0.020  1.090
 TDE  C13  O22   single  1.414  0.020  1.414
 TDE  C13  C14   single  1.537  0.020  1.537
 TDE  C13  H13   single  0.970  0.020  1.090
 TDE  O22  H22   single  0.850  0.020  0.980
 TDE  C14  O23   single  1.408  0.020  1.408
 TDE  C14  C15   single  1.545  0.020  1.545
 TDE  C14  H14   single  0.970  0.020  1.090
 TDE  O23  H23   single  0.850  0.020  0.980
 TDE  C15  O24   single  1.409  0.020  1.409
 TDE  C15  C16   single  1.503  0.020  1.503
 TDE  C15  H15   single  0.970  0.020  1.090
 TDE  O24  H24   single  0.850  0.020  0.980
 TDE  C16  C17   double  1.328  0.020  1.328
 TDE  C16  H16   single  0.930  0.020  1.080
 TDE  C17  C18   single  1.508  0.020  1.508
 TDE  C17  H17   single  0.930  0.020  1.080
 TDE  C18  C21   single  1.534  0.020  1.534
 TDE  C18  C20   single  1.534  0.020  1.534
 TDE  C18  C19   single  1.526  0.020  1.526
 TDE  C21  H211  single  0.970  0.020  1.090
 TDE  C21  H212  single  0.970  0.020  1.090
 TDE  C21  H213  single  0.970  0.020  1.090
 TDE  C20  H201  single  0.970  0.020  1.090
 TDE  C20  H202  single  0.970  0.020  1.090
 TDE  C20  H203  single  0.970  0.020  1.090
 TDE  C19  H191  single  0.970  0.020  1.090
 TDE  C19  H192  single  0.970  0.020  1.090
 TDE  C19  H193  single  0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 TDE  N1    C2   C3    117.87  3.000
 TDE  N1    C2   O8    121.89  3.000
 TDE  C3    C2   O8    120.18  3.000
 TDE  H3    C3   N9    110.23  3.000
 TDE  H3    C3   C4    107.60  3.000
 TDE  N9    C3   C4    110.30  3.000
 TDE  H3    C3   C2    104.76  3.000
 TDE  N9    C3   C2    112.78  3.000
 TDE  C4    C3   C2    110.91  3.000
 TDE  H42   C4   H41   105.64  3.000
 TDE  H42   C4   C5    107.92  3.000
 TDE  H41   C4   C5    110.17  3.000
 TDE  H42   C4   C3    107.78  3.000
 TDE  H41   C4   C3    107.92  3.000
 TDE  C5    C4   C3    116.83  3.000
 TDE  H52   C5   H51   105.65  3.000
 TDE  H52   C5   C6    108.37  3.000
 TDE  H51   C5   C6    108.26  3.000
 TDE  H52   C5   C4    110.46  3.000
 TDE  H51   C5   C4    107.33  3.000
 TDE  C6    C5   C4    116.23  3.000
 TDE  H6    C6   O7    110.98  3.000
 TDE  H6    C6   C7    107.62  3.000
 TDE  O7    C6   C7    109.90  3.000
 TDE  H6    C6   C5    109.09  3.000
 TDE  O7    C6   C5    106.00  3.000
 TDE  C7    C6   C5    113.28  3.000
 TDE  H72   C7   H71   106.61  3.000
 TDE  H72   C7   N1    111.55  3.000
 TDE  H71   C7   N1    105.73  3.000
 TDE  H72   C7   C6    110.42  3.000
 TDE  H71   C7   C6    108.62  3.000
 TDE  N1    C7   C6    113.52  3.000
 TDE  HN1   N1   C7    115.87  3.000
 TDE  HN1   N1   C2    114.50  3.000
 TDE  C7    N1   C2    127.95  3.000
 TDE  HO7   O7   C6    108.64  3.000
 TDE  HN9   N9   C10   117.15  3.000
 TDE  HN9   N9   C3    118.91  3.000
 TDE  C10   N9   C3    122.14  3.000
 TDE  O11   C10  C12   121.59  3.000
 TDE  O11   C10  N9    122.52  3.000
 TDE  C12   C10  N9    115.80  3.000
 TDE  H12   C12  C13   107.19  3.000
 TDE  H12   C12  O21   111.23  3.000
 TDE  C13   C12  O21   108.44  3.000
 TDE  H12   C12  C10   107.46  3.000
 TDE  C13   C12  C10   113.16  3.000
 TDE  O21   C12  C10   109.36  3.000
 TDE  C25   O21  C12   114.50  3.000
 TDE  H253  C25  H252  108.52  3.000
 TDE  H253  C25  H251  108.43  3.000
 TDE  H252  C25  H251  108.27  3.000
 TDE  H253  C25  O21   111.39  3.000
 TDE  H252  C25  O21   112.64  3.000
 TDE  H251  C25  O21   107.47  3.000
 TDE  H13   C13  C14   106.89  3.000
 TDE  H13   C13  O22   105.64  3.000
 TDE  C14   C13  O22   113.98  3.000
 TDE  H13   C13  C12   108.97  3.000
 TDE  C14   C13  C12   110.79  3.000
 TDE  O22   C13  C12   110.28  3.000
 TDE  H22   O22  C13   110.06  3.000
 TDE  H14   C14  C15   107.28  3.000
 TDE  H14   C14  O23   106.01  3.000
 TDE  C15   C14  O23   111.34  3.000
 TDE  H14   C14  C13   106.07  3.000
 TDE  C15   C14  C13   112.57  3.000
 TDE  O23   C14  C13   113.02  3.000
 TDE  H23   O23  C14   109.85  3.000
 TDE  H15   C15  C16   107.59  3.000
 TDE  H15   C15  O24   106.43  3.000
 TDE  C16   C15  O24   113.76  3.000
 TDE  H15   C15  C14   107.33  3.000
 TDE  C16   C15  C14   109.83  3.000
 TDE  O24   C15  C14   111.56  3.000
 TDE  H24   O24  C15   109.21  3.000
 TDE  H16   C16  C17   119.77  3.000
 TDE  H16   C16  C15   113.78  3.000
 TDE  C17   C16  C15   126.45  3.000
 TDE  H17   C17  C18   113.16  3.000
 TDE  H17   C17  C16   119.82  3.000
 TDE  C18   C17  C16   127.02  3.000
 TDE  C19   C18  C20   109.53  3.000
 TDE  C19   C18  C21   109.48  3.000
 TDE  C20   C18  C21   108.88  3.000
 TDE  C19   C18  C17   112.92  3.000
 TDE  C20   C18  C17   108.03  3.000
 TDE  C21   C18  C17   107.92  3.000
 TDE  H213  C21  H212  107.89  3.000
 TDE  H213  C21  H211  107.65  3.000
 TDE  H212  C21  H211  108.01  3.000
 TDE  H213  C21  C18   111.27  3.000
 TDE  H212  C21  C18   111.20  3.000
 TDE  H211  C21  C18   110.67  3.000
 TDE  H203  C20  H202  107.93  3.000
 TDE  H203  C20  H201  107.69  3.000
 TDE  H202  C20  H201  107.83  3.000
 TDE  H203  C20  C18   110.77  3.000
 TDE  H202  C20  C18   111.31  3.000
 TDE  H201  C20  C18   111.15  3.000
 TDE  H193  C19  H192  107.47  3.000
 TDE  H193  C19  H191  107.87  3.000
 TDE  H192  C19  H191  107.46  3.000
 TDE  H193  C19  C18   111.75  3.000
 TDE  H192  C19  C18   110.19  3.000
 TDE  H191  C19  C18   111.90  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 TDE  CONST_01  C12   C10  N9   C3    180.00   0.0  0
 TDE  CONST_02  O11   C10  N9   C3      0.00   0.0  0
 TDE  Var_01    C18   C17  C16  C15  -178.88   0.0  2
 TDE  Var_02    C21   C18  C17  C16   117.54  30.0  3
 TDE  Var_03    H251  C25  O21  C12   178.06  30.0  3
 TDE  Var_04    H211  C21  C18  C17   176.27  30.0  3
 TDE  Var_05    H201  C20  C18  C17   -57.13  30.0  3
 TDE  Var_06    H191  C19  C18  C17    60.75  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 TDE  chir_01  C3   C2   C4   N9   positiv
 TDE  chir_02  C6   O7   C5   C7   positiv
 TDE  chir_03  C12  O21  C10  C13  negativ
 TDE  chir_04  C13  O22  C12  C14  negativ
 TDE  chir_05  C14  O23  C13  C15  positiv
 TDE  chir_06  C15  O24  C14  C16  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 TDE  plan-1  C2   0.020
 TDE  plan-1  O8   0.020
 TDE  plan-1  C3   0.020
 TDE  plan-1  C7   0.020
 TDE  plan-1  N1   0.020
 TDE  plan-1  HN1  0.020
 TDE  plan-2  C3   0.020
 TDE  plan-2  N9   0.020
 TDE  plan-2  C10  0.020
 TDE  plan-2  C12  0.020
 TDE  plan-2  O11  0.020
 TDE  plan-2  HN9  0.020
 TDE  plan-3  C15  0.020
 TDE  plan-3  C16  0.020
 TDE  plan-3  C17  0.020
 TDE  plan-3  C18  0.020
 TDE  plan-3  H16  0.020
 TDE  plan-3  H17  0.020

