# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jun 14 15:55:30 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1[C@@H]2CC[C@H]3[C@@]45CO[C@](O)([C@@H](O)[C@@H]4C(C)(C)CC[C@@H]5O)[C@]3([C@@H]2O)C1=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
 ODN  ODN  (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14R,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one  ligand  56  26  .  2021-08-17  2021-08-17  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ODN
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
 ODN  O3   O  O     0  -0.428  -1.8508  -1.6794  -1.5467
 ODN  C17  C  C     0   0.500  -2.1654  -0.8390  -0.7303
 ODN  C10  C  CT    0  -0.305  -1.2440  -0.1987   0.3003
 ODN  C18  C  CT    0   0.517  -0.2806  -1.1501   1.0351
 ODN  O4   O  OH1   0  -0.654  -0.9974  -2.1754   1.6116
 ODN  O1   O  O2    0  -0.512   0.3446  -0.4048   2.0623
 ODN  C8   C  CH2   0  -0.137   0.9798   0.7888   1.6173
 ODN  C19  C  CH1   0  -0.010   0.8745  -1.7017   0.1745
 ODN  O5   O  OH1   0  -0.691   0.4998  -2.6963  -0.7379
 ODN  C6   C  CH1   0  -0.194   1.6654  -0.5326  -0.4436
 ODN  C3   C  CT    0  -0.104   3.2010  -0.7450  -0.3973
 ODN  C5   C  CH3   0  -0.638   3.5543  -1.9630  -1.2570
 ODN  C4   C  CH3   0  -0.667   3.7894  -0.9809   0.9986
 ODN  C2   C  CH2   0  -0.412   3.8557   0.4862  -1.0275
 ODN  C1   C  CH2   0  -0.482   3.4334   1.7672  -0.3380
 ODN  C13  C  CH1   0  -0.341  -3.5242  -0.1958  -0.6570
 ODN  C14  C  CH3   0  -0.668  -4.2535  -0.0800  -1.9827
 ODN  C12  C  CH1   0  -0.301  -3.2305   1.0819   0.1427
 ODN  C11  C  CH1   0   0.084  -2.2498   0.5533   1.2021
 ODN  O2   O  OH1   0  -0.659  -2.8769  -0.3254   2.1019
 ODN  C15  C  CH2   0  -0.437  -2.5460   2.1825  -0.6912
 ODN  C16  C  CH2   0  -0.452  -1.0383   2.2513  -0.4470
 ODN  C9   C  CH1   0  -0.197  -0.3710   0.8718  -0.4655
 ODN  C7   C  CT    0  -0.181   1.0866   0.8088   0.0915
 ODN  C    C  CH1   0   0.084   1.9285   1.9937  -0.4172
 ODN  O    O  OH1   0  -0.669   1.5896   3.1559   0.3123
 ODN  H1   H  HOH1  0   0.456  -0.4155  -2.9308   1.7560
 ODN  H2   H  HCH2  0   0.226   0.4054   1.6516   1.9695
 ODN  H3   H  HCH2  0   0.237   1.9546   0.8492   2.1036
 ODN  H4   H  HCH1  0   0.238   1.5200  -2.2103   0.8997
 ODN  H5   H  HOH1  0   0.449  -0.2706  -2.3798  -1.2403
 ODN  H6   H  HCH1  0   0.237   1.4278  -0.5306  -1.5158
 ODN  H7   H  HCH3  0   0.220   3.1774  -1.8518  -2.2761
 ODN  H8   H  HCH3  0   0.221   4.6392  -2.0774  -1.3143
 ODN  H9   H  HCH3  0   0.234   3.1508  -2.8908  -0.8515
 ODN  H10  H  HCH3  0   0.232   3.3733  -1.8647   1.4841
 ODN  H11  H  HCH3  0   0.232   4.8640  -1.1539   0.9076
 ODN  H12  H  HCH3  0   0.231   3.6613  -0.1433   1.6812
 ODN  H13  H  HCH2  0   0.231   4.9442   0.3834  -0.9997
 ODN  H14  H  HCH2  0   0.221   3.5791   0.5363  -2.0874
 ODN  H15  H  HCH2  0   0.224   3.7546   1.7677   0.7075
 ODN  H16  H  HCH2  0   0.239   3.9303   2.6219  -0.8086
 ODN  H17  H  HCH1  0   0.295  -4.1110  -0.8543  -0.0040
 ODN  H18  H  HCH3  0   0.229  -3.6746   0.4512  -2.7375
 ODN  H19  H  HCH3  0   0.243  -4.4878  -1.0659  -2.3824
 ODN  H20  H  HCH3  0   0.241  -5.1956   0.4520  -1.8472
 ODN  H21  H  HCH1  0   0.258  -4.1433   1.4692   0.6009
 ODN  H22  H  HCH1  0   0.232  -1.7714   1.3684   1.7525
 ODN  H23  H  HOH1  0   0.449  -3.5658   0.1739   2.5531
 ODN  H24  H  HCH2  0   0.235  -2.7408   2.0345  -1.7554
 ODN  H25  H  HCH2  0   0.247  -2.9778   3.1538  -0.4460
 ODN  H26  H  HCH2  0   0.246  -0.5833   2.8772  -1.2144
 ODN  H27  H  HCH2  0   0.237  -0.8512   2.7583   0.4978
 ODN  H28  H  HCH1  0   0.259  -0.3074   0.5672  -1.5158
 ODN  H29  H  HCH1  0   0.204   1.6747   2.1195  -1.4830
 ODN  H30  H  HOH1  0   0.451   2.1121   3.8851  -0.0365

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
 ODN  C14  C13  single  1.518  0.020  1.518
 ODN  C13  C12  single  1.536  0.020  1.536
 ODN  C13  C17  single  1.505  0.020  1.505
 ODN  O2   C11  single  1.405  0.020  1.405
 ODN  C12  C11  single  1.537  0.020  1.537
 ODN  C12  C15  single  1.541  0.020  1.541
 ODN  C11  C10  single  1.546  0.020  1.546
 ODN  C15  C16  single  1.529  0.020  1.529
 ODN  C17  O3   double  1.213  0.020  1.213
 ODN  C17  C10  single  1.524  0.020  1.524
 ODN  O4   C18  single  1.377  0.020  1.377
 ODN  C10  C18  single  1.541  0.020  1.541
 ODN  C10  C9   single  1.579  0.020  1.579
 ODN  C16  C9   single  1.532  0.020  1.532
 ODN  C18  O1   single  1.415  0.020  1.415
 ODN  C18  C19  single  1.542  0.020  1.542
 ODN  O1   C8   single  1.423  0.020  1.423
 ODN  C9   C7   single  1.562  0.020  1.562
 ODN  O5   C19  single  1.401  0.020  1.401
 ODN  C8   C7   single  1.530  0.020  1.530
 ODN  C19  C6   single  1.541  0.020  1.541
 ODN  C7   C6   single  1.556  0.020  1.556
 ODN  C7   C    single  1.540  0.020  1.540
 ODN  C6   C3   single  1.551  0.020  1.551
 ODN  O    C    single  1.413  0.020  1.413
 ODN  C    C1   single  1.524  0.020  1.524
 ODN  C3   C4   single  1.533  0.020  1.533
 ODN  C3   C5   single  1.532  0.020  1.532
 ODN  C3   C2   single  1.530  0.020  1.530
 ODN  C1   C2   single  1.515  0.020  1.515
 ODN  O4   H1   single  0.850  0.020  0.980
 ODN  C8   H2   single  0.970  0.020  1.090
 ODN  C8   H3   single  0.970  0.020  1.090
 ODN  C19  H4   single  0.970  0.020  1.090
 ODN  O5   H5   single  0.850  0.020  0.980
 ODN  C6   H6   single  0.970  0.020  1.090
 ODN  C5   H7   single  0.970  0.020  1.090
 ODN  C5   H8   single  0.970  0.020  1.090
 ODN  C5   H9   single  0.970  0.020  1.090
 ODN  C4   H10  single  0.970  0.020  1.090
 ODN  C4   H11  single  0.970  0.020  1.090
 ODN  C4   H12  single  0.970  0.020  1.090
 ODN  C2   H13  single  0.970  0.020  1.090
 ODN  C2   H14  single  0.970  0.020  1.090
 ODN  C1   H15  single  0.970  0.020  1.090
 ODN  C1   H16  single  0.970  0.020  1.090
 ODN  C13  H17  single  0.970  0.020  1.090
 ODN  C14  H18  single  0.970  0.020  1.090
 ODN  C14  H19  single  0.970  0.020  1.090
 ODN  C14  H20  single  0.970  0.020  1.090
 ODN  C12  H21  single  0.970  0.020  1.090
 ODN  C11  H22  single  0.970  0.020  1.090
 ODN  O2   H23  single  0.850  0.020  0.980
 ODN  C15  H24  single  0.970  0.020  1.090
 ODN  C15  H25  single  0.970  0.020  1.090
 ODN  C16  H26  single  0.970  0.020  1.090
 ODN  C16  H27  single  0.970  0.020  1.090
 ODN  C9   H28  single  0.970  0.020  1.090
 ODN  C    H29  single  0.970  0.020  1.090
 ODN  O    H30  single  0.850  0.020  0.980

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
 ODN  C13  C17  C10  109.48  3.000
 ODN  C10  C17  O3   126.12  3.000
 ODN  C13  C17  O3   124.26  3.000
 ODN  C9   C10  C11  108.22  3.000
 ODN  C9   C10  C18  107.71  3.000
 ODN  C11  C10  C18  115.40  3.000
 ODN  C9   C10  C17  106.93  3.000
 ODN  C18  C10  C17  116.19  3.000
 ODN  C11  C10  C17  101.86  3.000
 ODN  C19  C18  O1   105.22  3.000
 ODN  C19  C18  O4   110.92  3.000
 ODN  O1   C18  O4   108.56  3.000
 ODN  C19  C18  C10  115.03  3.000
 ODN  O1   C18  C10  107.29  3.000
 ODN  O4   C18  C10  109.51  3.000
 ODN  H1   O4   C18  109.37  3.000
 ODN  C8   O1   C18  114.33  3.000
 ODN  H3   C8   H2   106.37  3.000
 ODN  H3   C8   C7   112.42  3.000
 ODN  H2   C8   C7   110.32  3.000
 ODN  H3   C8   O1   107.81  3.000
 ODN  H2   C8   O1   109.04  3.000
 ODN  C7   C8   O1   110.73  3.000
 ODN  H4   C19  C6   108.37  3.000
 ODN  H4   C19  O5   105.02  3.000
 ODN  C6   C19  O5   114.50  3.000
 ODN  H4   C19  C18  103.76  3.000
 ODN  C6   C19  C18  109.69  3.000
 ODN  O5   C19  C18  114.64  3.000
 ODN  H5   O5   C19  108.50  3.000
 ODN  H6   C6   C7   104.70  3.000
 ODN  H6   C6   C3   104.10  3.000
 ODN  C7   C6   C3   118.43  3.000
 ODN  H6   C6   C19  106.38  3.000
 ODN  C3   C6   C19  113.10  3.000
 ODN  C7   C6   C19  108.98  3.000
 ODN  C2   C3   C4   109.55  3.000
 ODN  C2   C3   C5   108.05  3.000
 ODN  C4   C3   C5   107.46  3.000
 ODN  C2   C3   C6   107.53  3.000
 ODN  C5   C3   C6   108.69  3.000
 ODN  C4   C3   C6   115.36  3.000
 ODN  H9   C5   H8   107.33  3.000
 ODN  H9   C5   H7   107.82  3.000
 ODN  H8   C5   H7   107.73  3.000
 ODN  H9   C5   C3   112.49  3.000
 ODN  H8   C5   C3   109.98  3.000
 ODN  H7   C5   C3   111.29  3.000
 ODN  H12  C4   H11  106.86  3.000
 ODN  H12  C4   H10  107.43  3.000
 ODN  H11  C4   H10  106.50  3.000
 ODN  H12  C4   C3   114.05  3.000
 ODN  H11  C4   C3   109.03  3.000
 ODN  H10  C4   C3   112.55  3.000
 ODN  H14  C2   H13  106.26  3.000
 ODN  H14  C2   C1   109.33  3.000
 ODN  H13  C2   C1   110.20  3.000
 ODN  H14  C2   C3   109.08  3.000
 ODN  H13  C2   C3   109.86  3.000
 ODN  C1   C2   C3   111.94  3.000
 ODN  H16  C1   H15  106.10  3.000
 ODN  H16  C1   C    108.05  3.000
 ODN  H15  C1   C    109.85  3.000
 ODN  H16  C1   C2   109.75  3.000
 ODN  H15  C1   C2   110.71  3.000
 ODN  C    C1   C2   112.17  3.000
 ODN  H17  C13  C12  106.96  3.000
 ODN  H17  C13  C14  107.97  3.000
 ODN  C12  C13  C14  118.90  3.000
 ODN  H17  C13  C17  104.80  3.000
 ODN  C12  C13  C17  102.02  3.000
 ODN  C14  C13  C17  115.08  3.000
 ODN  H20  C14  H19  107.54  3.000
 ODN  H20  C14  H18  107.90  3.000
 ODN  H19  C14  H18  107.54  3.000
 ODN  H20  C14  C13  110.12  3.000
 ODN  H19  C14  C13  110.78  3.000
 ODN  H18  C14  C13  112.77  3.000
 ODN  H21  C12  C15  110.18  3.000
 ODN  H21  C12  C11  111.46  3.000
 ODN  C15  C12  C11  109.58  3.000
 ODN  H21  C12  C13  110.71  3.000
 ODN  C15  C12  C13  113.41  3.000
 ODN  C11  C12  C13  101.23  3.000
 ODN  H22  C11  O2   109.81  3.000
 ODN  H22  C11  C12  111.69  3.000
 ODN  O2   C11  C12  111.81  3.000
 ODN  H22  C11  C10  111.81  3.000
 ODN  C12  C11  C10  100.39  3.000
 ODN  O2   C11  C10  111.08  3.000
 ODN  H23  O2   C11  107.15  3.000
 ODN  H25  C15  H24  105.61  3.000
 ODN  H25  C15  C16  108.32  3.000
 ODN  H24  C15  C16  109.74  3.000
 ODN  H25  C15  C12  109.78  3.000
 ODN  H24  C15  C12  110.56  3.000
 ODN  C16  C15  C12  112.56  3.000
 ODN  H27  C16  H26  105.77  3.000
 ODN  H27  C16  C9   110.79  3.000
 ODN  H26  C16  C9   109.07  3.000
 ODN  H27  C16  C15  109.22  3.000
 ODN  H26  C16  C15  108.97  3.000
 ODN  C9   C16  C15  112.77  3.000
 ODN  H28  C9   C7   106.05  3.000
 ODN  H28  C9   C16  106.69  3.000
 ODN  C7   C9   C16  116.01  3.000
 ODN  H28  C9   C10  107.97  3.000
 ODN  C7   C9   C10  108.40  3.000
 ODN  C16  C9   C10  111.32  3.000
 ODN  C    C7   C9   111.19  3.000
 ODN  C    C7   C6   110.26  3.000
 ODN  C9   C7   C6   105.03  3.000
 ODN  C    C7   C8   112.19  3.000
 ODN  C6   C7   C8   110.96  3.000
 ODN  C9   C7   C8   106.92  3.000
 ODN  H29  C    O    110.47  3.000
 ODN  H29  C    C7   106.33  3.000
 ODN  O    C    C7   109.33  3.000
 ODN  H29  C    C1   107.12  3.000
 ODN  O    C    C1   109.40  3.000
 ODN  C7   C    C1   114.11  3.000
 ODN  H30  O    C    107.80  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
 ODN  Var_01  C7   C8   O1   C18  -12.41  30.0  3
 ODN  Var_02  C1   C2   C3   C6    56.30  30.0  1
 ODN  Var_03  C    C1   C2   C3   -60.54  30.0  1
 ODN  Var_04  C9   C16  C15  C12   46.01  30.0  1
 ODN  Var_05  H10  C4   C3   C6    59.97  30.0  3
 ODN  Var_06  H7   C5   C3   C6    55.51  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
 ODN  chir_01  C10  C11  C18  C9   positiv
 ODN  chir_02  C18  O1   C10  C19  negativ
 ODN  chir_03  C19  O5   C18  C6   positiv
 ODN  chir_04  C6   C3   C7   C19  positiv
 ODN  chir_05  C13  C14  C12  C17  positiv
 ODN  chir_06  C12  C15  C11  C13  positiv
 ODN  chir_07  C11  O2   C12  C10  positiv
 ODN  chir_08  C9   C7   C16  C10  positiv
 ODN  chir_09  C7   C6   C    C9   negativ
 ODN  chir_10  C    O    C7   C1   positiv

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
 ODN  plan-1  O3   0.020
 ODN  plan-1  C17  0.020
 ODN  plan-1  C10  0.020
 ODN  plan-1  C13  0.020

