# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 06:55:57 2022
#   Inital geometry file: a 137 line input string
#   Ligand name: (1aR,1bS,4aR,7aS,7bR,8R,9aS)-4a,7b-dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1,1a,1b,4,4a,5,7a,7b,8,9-decahydro-9aH-cyclopropa[3,4]benzo[1,2-e]azulen-9a-yl acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@]2(OC(C)=O)[C@H]([C@@H]3C=C(CO)C[C@@]4(O)[C@@H](C=C(C)C4=O)[C@@]13O)C2(C)C
#
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
 XYV  XYV  "prostratin"
  ligand  58  28  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_XYV
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
 XYV  C10  C  CT    0   0.306  -3.7392   0.7673   1.1198
 XYV  C13  C  CR5   0  -0.010  -2.4087  -2.6662   0.7980
 XYV  C17  C  CH2   0  -0.504  -3.7907  -1.2870   3.8925
 XYV  C26  C  C     0   0.589  -4.5961   4.4497  -0.6044
 XYV  C28  C  CH3   0  -0.770  -4.8131   5.6745  -1.4403
 XYV  C01  C  CH3   0  -0.672  -3.6527   0.8508  -1.4714
 XYV  C02  C  CH1   0  -0.258  -4.5038   0.5768  -0.2305
 XYV  C03  C  CH2   0  -0.518  -5.8322   1.3746  -0.3061
 XYV  C04  C  CT    0   0.318  -5.8521   2.6807   0.4647
 XYV  C05  C  CH1   0  -0.302  -5.2587   2.6082   1.8396
 XYV  C06  C  CT    0  -0.056  -6.7357   2.8798   1.6705
 XYV  C07  C  CH3   0  -0.654  -7.1768   4.2950   1.9803
 XYV  C08  C  CH3   0  -0.683  -7.7995   1.8775   2.0528
 XYV  C09  C  CH1   0  -0.328  -4.7435   1.2321   2.2074
 XYV  C11  C  CR15  0  -0.321  -3.0332  -0.5143   1.6080
 XYV  C12  C  CR15  0  -0.217  -2.3025  -1.3470   0.5971
 XYV  C14  C  CR5   0   0.379  -3.2409  -2.8842   1.9853
 XYV  C16  C  CR5   0   0.097  -3.8680  -1.5401   2.3930
 XYV  C18  C  C     0   0.083  -3.8838   0.1447   4.3526
 XYV  C19  C  C1    0  -0.243  -4.2263   1.2075   3.6193
 XYV  C23  C  CH3   0  -0.724  -1.7636  -3.7802   0.0520
 XYV  O15  O  O     0  -0.397  -3.4436  -3.9374   2.5478
 XYV  O21  O  OH1   0  -0.665  -2.1412   0.0031   5.9776
 XYV  O22  O  OH1   0  -0.652  -5.1916  -1.5990   1.8951
 XYV  O24  O  OH1   0  -0.706  -2.6902   1.7018   1.0028
 XYV  O25  O  O2    0  -0.457  -5.7397   3.8325  -0.3560
 XYV  O27  O  O     0  -0.461  -3.5132   4.0812  -0.2116
 XYV  H2   H  HCH2  0   0.260  -4.5359  -1.8969   4.4188
 XYV  H3   H  HCH2  0   0.204  -3.7011   1.3778   6.0908
 XYV  H4   H  HCH2  0   0.205  -4.1474  -0.2960   6.4171
 XYV  H5   H  HCH3  0   0.263  -3.8690   6.1739  -1.6364
 XYV  H6   H  HCH3  0   0.275  -5.2787   5.4059  -2.3891
 XYV  H7   H  HCH3  0   0.275  -5.4873   6.3654  -0.9337
 XYV  H8   H  HCH3  0   0.231  -2.7122   0.3040  -1.4755
 XYV  H9   H  HCH3  0   0.226  -4.2071   0.5343  -2.3565
 XYV  H10  H  HCH3  0   0.222  -3.4166   1.9051  -1.6051
 XYV  H11  H  HCH1  0   0.243  -4.7914  -0.4750  -0.2806
 XYV  H12  H  HCH2  0   0.260  -6.0760   1.5721  -1.3523
 XYV  H13  H  HCH2  0   0.260  -6.6418   0.7415   0.0558
 XYV  H14  H  HCH1  0   0.271  -4.6760   3.4463   2.2106
 XYV  H15  H  HCH3  0   0.234  -7.4626   4.3627   3.0314
 XYV  H16  H  HCH3  0   0.232  -6.3995   5.0388   1.8114
 XYV  H17  H  HCH3  0   0.230  -8.0478   4.5773   1.3854
 XYV  H18  H  HCH3  0   0.236  -8.0314   1.9715   3.1151
 XYV  H19  H  HCH3  0   0.236  -8.7186   2.0718   1.4967
 XYV  H20  H  HCH3  0   0.233  -7.5275   0.8388   1.8765
 XYV  H21  H  HCH1  0   0.285  -5.5787   0.5344   2.1704
 XYV  H22  H  HCR5  0   0.290  -2.2668  -0.1439   2.3008
 XYV  H23  H  HCR5  0   0.274  -1.6736  -0.9093  -0.1673
 XYV  H25  H  H     0   0.228  -4.1822   2.1723   4.1183
 XYV  H27  H  HCH3  0   0.246  -1.1517  -4.3948   0.7141
 XYV  H28  H  HCH3  0   0.247  -2.5110  -4.4398  -0.3927
 XYV  H29  H  HCH3  0   0.248  -1.1271  -3.4045  -0.7471
 XYV  H30  H  HOH1  0   0.453  -1.9957  -0.1651   6.9129
 XYV  H31  H  HOH1  0   0.455  -5.6885  -2.2326   2.4265
 XYV  H32  H  HOH1  0   0.465  -3.0282   2.5241   0.6113
 XYV  H1   H  HCH2  0   0.256  -2.8251  -1.6666   4.2431
 XYV  C20  C  CH2   0  -0.216  -3.5033   0.3401   5.7952

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
 XYV  C01  C02  single  1.529  0.020  1.529
 XYV  C28  C26  single  1.499  0.020  1.499
 XYV  C03  C02  single  1.551  0.020  1.551
 XYV  C03  C04  single  1.517  0.020  1.517
 XYV  C26  O25  single  1.323  0.020  1.323
 XYV  C26  O27  double  1.210  0.020  1.210
 XYV  C02  C10  single  1.563  0.020  1.563
 XYV  O25  C04  single  1.419  0.020  1.419
 XYV  C23  C13  single  1.488  0.020  1.488
 XYV  C04  C06  single  1.508  0.020  1.508
 XYV  C04  C05  single  1.499  0.020  1.499
 XYV  C12  C13  double  1.339  0.020  1.339
 XYV  C12  C11  single  1.500  0.020  1.500
 XYV  O24  C10  single  1.410  0.020  1.410
 XYV  C10  C11  single  1.543  0.020  1.543
 XYV  C10  C09  single  1.552  0.020  1.552
 XYV  C13  C14  single  1.466  0.020  1.466
 XYV  C06  C08  single  1.511  0.020  1.511
 XYV  C06  C07  single  1.514  0.020  1.514
 XYV  C06  C05  single  1.511  0.020  1.511
 XYV  C11  C16  single  1.538  0.020  1.538
 XYV  C05  C09  single  1.515  0.020  1.515
 XYV  C14  C16  single  1.538  0.020  1.538
 XYV  C14  O15  double  1.211  0.020  1.211
 XYV  C09  C19  single  1.504  0.020  1.504
 XYV  O22  C16  single  1.415  0.020  1.415
 XYV  C16  C17  single  1.523  0.020  1.523
 XYV  C19  C18  double  1.336  0.020  1.336
 XYV  C17  C18  single  1.507  0.020  1.507
 XYV  C18  C20  single  1.505  0.020  1.505
 XYV  C20  O21  single  1.415  0.020  1.415
 XYV  C17  H2   single  0.970  0.020  1.090
 XYV  C20  H3   single  0.970  0.020  1.090
 XYV  C20  H4   single  0.970  0.020  1.090
 XYV  C28  H5   single  0.970  0.020  1.090
 XYV  C28  H6   single  0.970  0.020  1.090
 XYV  C28  H7   single  0.970  0.020  1.090
 XYV  C01  H8   single  0.970  0.020  1.090
 XYV  C01  H9   single  0.970  0.020  1.090
 XYV  C01  H10  single  0.970  0.020  1.090
 XYV  C02  H11  single  0.970  0.020  1.090
 XYV  C03  H12  single  0.970  0.020  1.090
 XYV  C03  H13  single  0.970  0.020  1.090
 XYV  C05  H14  single  0.970  0.020  1.090
 XYV  C07  H15  single  0.970  0.020  1.090
 XYV  C07  H16  single  0.970  0.020  1.090
 XYV  C07  H17  single  0.970  0.020  1.090
 XYV  C08  H18  single  0.970  0.020  1.090
 XYV  C08  H19  single  0.970  0.020  1.090
 XYV  C08  H20  single  0.970  0.020  1.090
 XYV  C09  H21  single  0.970  0.020  1.090
 XYV  C11  H22  single  0.970  0.020  1.090
 XYV  C12  H23  single  0.930  0.020  1.080
 XYV  C19  H25  single  0.930  0.020  1.080
 XYV  C23  H27  single  0.970  0.020  1.090
 XYV  C23  H28  single  0.970  0.020  1.090
 XYV  C23  H29  single  0.970  0.020  1.090
 XYV  O21  H30  single  0.850  0.020  0.980
 XYV  O22  H31  single  0.850  0.020  0.980
 XYV  O24  H32  single  0.850  0.020  0.980
 XYV  C17  H1   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
 XYV  O24  C10  C11  103.68  3.000
 XYV  C11  C10  C09  108.86  3.000
 XYV  O24  C10  C09  109.95  3.000
 XYV  C09  C10  C02  108.99  3.000
 XYV  C11  C10  C02  113.33  3.000
 XYV  O24  C10  C02  111.90  3.000
 XYV  C23  C13  C14  122.74  3.000
 XYV  C14  C13  C12  108.25  3.000
 XYV  C23  C13  C12  128.92  3.000
 XYV  H1   C17  H2   104.63  3.000
 XYV  H1   C17  C18  106.63  3.000
 XYV  H2   C17  C18  109.86  3.000
 XYV  H1   C17  C16  107.60  3.000
 XYV  H2   C17  C16  110.21  3.000
 XYV  C18  C17  C16  117.10  3.000
 XYV  O27  C26  O25  124.80  3.000
 XYV  O27  C26  C28  124.04  3.000
 XYV  O25  C26  C28  111.15  3.000
 XYV  H7   C28  H6   107.24  3.000
 XYV  H7   C28  H5   109.28  3.000
 XYV  H6   C28  H5   109.11  3.000
 XYV  H7   C28  C26  110.38  3.000
 XYV  H6   C28  C26  110.23  3.000
 XYV  H5   C28  C26  110.53  3.000
 XYV  H10  C01  H9   106.95  3.000
 XYV  H10  C01  H8   107.38  3.000
 XYV  H9   C01  H8   106.88  3.000
 XYV  H10  C01  C02  113.19  3.000
 XYV  H9   C01  C02  108.87  3.000
 XYV  H8   C01  C02  113.21  3.000
 XYV  H11  C02  C03  105.52  3.000
 XYV  H11  C02  C01  106.38  3.000
 XYV  C03  C02  C01  110.17  3.000
 XYV  H11  C02  C10  106.62  3.000
 XYV  C03  C02  C10  113.46  3.000
 XYV  C01  C02  C10  114.01  3.000
 XYV  H13  C03  H12  104.91  3.000
 XYV  H13  C03  C04  108.78  3.000
 XYV  H12  C03  C04  109.16  3.000
 XYV  H13  C03  C02  108.74  3.000
 XYV  H12  C03  C02  109.32  3.000
 XYV  C04  C03  C02  115.42  3.000
 XYV  O25  C04  C06  113.69  3.000
 XYV  C06  C04  C05   60.33  3.000
 XYV  O25  C04  C05  122.58  3.000
 XYV  C05  C04  C03  114.79  3.000
 XYV  C06  C04  C03  121.85  3.000
 XYV  O25  C04  C03  113.84  3.000
 XYV  H14  C05  C09  115.82  3.000
 XYV  H14  C05  C06  115.09  3.000
 XYV  C09  C05  C06  121.52  3.000
 XYV  H14  C05  C04  119.23  3.000
 XYV  C09  C05  C04  113.65  3.000
 XYV  C06  C05  C04   60.13  3.000
 XYV  C08  C06  C07  111.29  3.000
 XYV  C07  C06  C05  115.45  3.000
 XYV  C08  C06  C05  122.73  3.000
 XYV  C05  C06  C04   59.54  3.000
 XYV  C07  C06  C04  117.23  3.000
 XYV  C08  C06  C04  121.82  3.000
 XYV  H17  C07  H16  107.96  3.000
 XYV  H17  C07  H15  107.44  3.000
 XYV  H16  C07  H15  107.09  3.000
 XYV  H17  C07  C06  111.25  3.000
 XYV  H16  C07  C06  113.50  3.000
 XYV  H15  C07  C06  109.35  3.000
 XYV  H20  C08  H19  107.33  3.000
 XYV  H20  C08  H18  107.04  3.000
 XYV  H19  C08  H18  107.56  3.000
 XYV  H20  C08  C06  114.60  3.000
 XYV  H19  C08  C06  110.23  3.000
 XYV  H18  C08  C06  109.80  3.000
 XYV  H21  C09  C19  106.57  3.000
 XYV  H21  C09  C05  108.24  3.000
 XYV  C19  C09  C05  111.09  3.000
 XYV  H21  C09  C10  106.30  3.000
 XYV  C19  C09  C10  115.50  3.000
 XYV  C05  C09  C10  108.79  3.000
 XYV  H22  C11  C16  106.38  3.000
 XYV  H22  C11  C12  105.83  3.000
 XYV  C16  C11  C12  103.78  3.000
 XYV  H22  C11  C10  103.83  3.000
 XYV  C16  C11  C10  117.85  3.000
 XYV  C12  C11  C10  118.10  3.000
 XYV  H23  C12  C11  122.32  3.000
 XYV  H23  C12  C13  123.41  3.000
 XYV  C11  C12  C13  114.04  3.000
 XYV  O15  C14  C16  124.65  3.000
 XYV  O15  C14  C13  126.90  3.000
 XYV  C16  C14  C13  108.43  3.000
 XYV  O22  C16  C14  104.57  3.000
 XYV  O22  C16  C11  110.85  3.000
 XYV  C14  C16  C11  103.08  3.000
 XYV  O22  C16  C17  113.63  3.000
 XYV  C14  C16  C17  112.68  3.000
 XYV  C11  C16  C17  111.36  3.000
 XYV  C19  C18  C20  119.20  3.000
 XYV  C20  C18  C17  113.61  3.000
 XYV  C19  C18  C17  127.17  3.000
 XYV  H25  C19  C18  116.34  3.000
 XYV  H25  C19  C09  115.49  3.000
 XYV  C18  C19  C09  128.07  3.000
 XYV  H29  C23  H28  108.05  3.000
 XYV  H29  C23  H27  108.18  3.000
 XYV  H28  C23  H27  106.91  3.000
 XYV  H29  C23  C13  111.29  3.000
 XYV  H28  C23  C13  111.09  3.000
 XYV  H27  C23  C13  111.14  3.000
 XYV  H30  O21  C20  108.23  3.000
 XYV  H31  O22  C16  108.38  3.000
 XYV  H32  O24  C10  109.61  3.000
 XYV  C04  O25  C26  123.76  3.000
 XYV  H4   C20  H3   106.83  3.000
 XYV  H4   C20  O21  110.71  3.000
 XYV  H3   C20  O21  111.36  3.000
 XYV  H4   C20  C18  108.62  3.000
 XYV  H3   C20  C18  109.61  3.000
 XYV  O21  C20  C18  109.64  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
 XYV  Var_01  C06  C04  C03  C02  -113.35  30.0  1
 XYV  Var_02  C05  C04  C03  C02   -44.15  30.0  1
 XYV  Var_03  C05  C06  C04  C03   102.37  30.0  1
 XYV  Var_04  C09  C05  C04  C03     0.05  30.0  1
 XYV  Var_05  C09  C05  C06  C04  -100.98  30.0  1
 XYV  Var_06  C14  C13  C12  C11     0.18  30.0  1
 XYV  Var_07  C16  C14  C13  C12     9.76  30.0  1
 XYV  Var_08  O25  C04  C03  C02   104.32  30.0  1
 XYV  Var_09  C08  C06  C04  C03    -9.55  30.0  1
 XYV  Var_10  C07  C06  C04  C03  -152.68  30.0  1
 XYV  Var_11  C08  C06  C05  C04   110.44  30.0  1
 XYV  Var_12  C07  C06  C05  C04  -107.94  30.0  1
 XYV  Var_13  O25  C04  C06  C05  -115.26  30.0  1
 XYV  Var_14  C09  C05  C06  C07   151.08  30.0  1
 XYV  Var_15  C09  C05  C06  C08     9.46  30.0  1
 XYV  Var_16  O25  C04  C05  C09  -145.36  30.0  1
 XYV  Var_17  C23  C13  C12  C11  -176.24  30.0  1
 XYV  Var_18  O15  C14  C13  C12  -171.95  30.0  1
 XYV  Var_19  C23  C13  C14  C16  -173.55  30.0  1
 XYV  Var_20  H14  C05  C04  C03   142.24  30.0  1
 XYV  Var_21  H14  C05  C06  C04   110.66  30.0  1
 XYV  Var_22  H12  C03  C04  C05  -167.71  30.0  1
 XYV  Var_23  H13  C03  C04  C05    78.35  30.0  1
 XYV  Var_24  H12  C03  C04  C06   123.09  30.0  1
 XYV  Var_25  H13  C03  C04  C06     9.14  30.0  1
 XYV  Var_26  H23  C12  C13  C14   174.75  30.0  1
 XYV  Var_27  C03  C04  O25  C26   -95.31  30.0  3
 XYV  Var_28  C06  C04  O25  C26   119.23  30.0  3
 XYV  Var_29  C05  C04  O25  C26    50.39  30.0  3
 XYV  Var_30  O25  C04  C06  C07   -10.31  30.0  1
 XYV  Var_31  O25  C04  C06  C08   132.82  30.0  1
 XYV  Var_32  O15  C14  C13  C23     4.74  30.0  1
 XYV  Var_33  H18  C08  C06  C04   156.92  30.0  3
 XYV  Var_34  H19  C08  C06  C04   -84.76  30.0  3
 XYV  Var_35  H20  C08  C06  C04    36.44  30.0  3
 XYV  Var_36  H15  C07  C06  C04  -158.41  30.0  3
 XYV  Var_37  H16  C07  C06  C04   -38.92  30.0  3
 XYV  Var_38  H17  C07  C06  C04    83.07  30.0  3
 XYV  Var_39  H18  C08  C06  C05    85.00  30.0  3
 XYV  Var_40  H19  C08  C06  C05  -156.68  30.0  3
 XYV  Var_41  H20  C08  C06  C05   -35.48  30.0  3
 XYV  Var_42  H15  C07  C06  C05   -91.15  30.0  3
 XYV  Var_43  H16  C07  C06  C05    28.34  30.0  3
 XYV  Var_44  H17  C07  C06  C05   150.33  30.0  3
 XYV  Var_45  H14  C05  C06  C07     2.73  30.0  1
 XYV  Var_46  H14  C05  C06  C08  -138.90  30.0  1
 XYV  Var_47  H27  C23  C13  C12   121.12  30.0  3
 XYV  Var_48  H28  C23  C13  C12  -119.97  30.0  3
 XYV  Var_49  H29  C23  C13  C12     0.48  30.0  3
 XYV  Var_50  H27  C23  C13  C14   -54.84  30.0  3
 XYV  Var_51  H28  C23  C13  C14    64.07  30.0  3
 XYV  Var_52  H29  C23  C13  C14  -175.48  30.0  3
 XYV  Var_53  H23  C12  C13  C23    -1.67  30.0  1
 XYV  Var_54  H12  C03  C04  O25   -19.24  30.0  1
 XYV  Var_55  H13  C03  C04  O25  -133.18  30.0  1
 XYV  Var_56  H14  C05  C04  O25    -3.18  30.0  1
 XYV  Var_57  C04  O25  C26  C28  -176.84  30.0  3
 XYV  Var_58  O27  C26  O25  C04     3.11  30.0  1
 XYV  Var_59  H18  C08  C06  C07   -58.01  30.0  3
 XYV  Var_60  H19  C08  C06  C07    60.31  30.0  3
 XYV  Var_61  H20  C08  C06  C07  -178.49  30.0  3
 XYV  Var_62  H15  C07  C06  C08    54.76  30.0  3
 XYV  Var_63  H16  C07  C06  C08   174.25  30.0  3
 XYV  Var_64  H17  C07  C06  C08   -63.76  30.0  3
 XYV  Var_65  H5   C28  C26  O25   179.89  30.0  3
 XYV  Var_66  H6   C28  C26  O25   -59.40  30.0  3
 XYV  Var_67  H7   C28  C26  O25    58.88  30.0  3
 XYV  Var_68  H5   C28  C26  O27    -0.07  30.0  3
 XYV  Var_69  H6   C28  C26  O27   120.64  30.0  3
 XYV  Var_70  H7   C28  C26  O27  -121.08  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
 XYV  chir_01  C10  C02  C11  C09  positiv
 XYV  chir_02  C02  C01  C03  C10  positiv
 XYV  chir_05  C09  C10  C05  C19  positiv
 XYV  chir_06  C11  C16  C10  C12  positiv
 XYV  chir_07  C16  C17  C14  C11  positiv
 XYV  chir_08  C04  O25  C06  C05  both
 XYV  chir_09  C05  C04  C06  C09  both

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
 XYV  plan-1  C13  0.020
 XYV  plan-1  C14  0.020
 XYV  plan-1  C16  0.020
 XYV  plan-1  O15  0.020
 XYV  plan-2  C26  0.020
 XYV  plan-2  C28  0.020
 XYV  plan-2  O25  0.020
 XYV  plan-2  O27  0.020

