# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 21:07:06 2022
#   Inital geometry file: a 138 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@]12CC[C@H](O)C[C@H]1CC[C@@H]3[C@@H]2CC[C@]4(C)[C@H](C[C@H]5O[C@@]345)C6=COC(=O)C=C6
#
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
 6JI  6JI  "5-[(1R,2S,4R,6R,7R,10S,11S,14S,16R)-14-hydroxy-7,11-dimethyl-3-oxapentacyclo[8.8.0.02,4.02,7.011,16]octadecan-6-yl]pyran-2-one"
  ligand  60  28  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6JI
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
 6JI  O4   O  O2    0  -0.504  27.8009  37.1756  43.9874
 6JI  C4   C  C     0  -0.479  29.8938  30.1788  45.9313
 6JI  C3   C  C     0  -0.436  29.1729  31.5071  46.1695
 6JI  O3   O  O2    0  -0.425  29.5415  40.5487  48.8577
 6JI  C2   C  CR6   0  -0.040  29.5927  32.6213  45.2023
 6JI  O2   O  O     0  -0.443  29.8298  42.7041  48.5163
 6JI  C1   C  CH3   0  -0.688  31.0978  32.8784  45.3289
 6JI  O1   O  OH1   0  -0.672  31.2769  29.8923  43.8933
 6JI  C10  C  CH1   0  -0.304  28.8786  34.9091  44.3723
 6JI  C11  C  CH1   0  -0.187  28.7961  33.9079  45.5387
 6JI  C12  C  CH2   0  -0.468  29.1707  34.5788  46.8814
 6JI  C13  C  CH2   0  -0.449  30.0290  35.8266  46.7075
 6JI  C14  C  CT    0  -0.047  29.2886  36.9234  45.9220
 6JI  C15  C  CH3   0  -0.667  30.3193  37.8338  45.2611
 6JI  C16  C  CH1   0  -0.338  28.2650  37.6656  46.8595
 6JI  C17  C  C     0   0.008  28.6531  39.0600  47.2477
 6JI  C18  C  C1    0  -0.127  28.5169  40.1832  46.3692
 6JI  C19  C  C1    0  -0.471  28.8944  41.4219  46.7511
 6JI  C20  C  C     0   0.544  29.4487  41.6534  48.0600
 6JI  C21  C  C1    0   0.039  29.1606  39.3240  48.4646
 6JI  C22  C  CH2   0  -0.457  26.8584  37.5589  46.2191
 6JI  C23  C  CH1   0  -0.058  27.0156  36.6326  45.0474
 6JI  C24  C  CT    0   0.330  28.4088  36.2476  44.8734
 6JI  C5   C  CR16  0   0.055  29.9738  29.7789  44.4425
 6JI  C6   C  C     0  -0.457  29.0406  30.6458  43.6208
 6JI  C7   C  CR16  0  -0.202  29.2634  32.1614  43.7387
 6JI  C8   C  CH2   0  -0.445  28.0257  32.8557  43.1714
 6JI  C9   C  CH2   0  -0.420  28.1332  34.3781  43.1423
 6JI  H1   H  H     0   0.232  29.3707  29.3979  46.4880
 6JI  H2   H  H     0   0.229  30.9016  30.2180  46.3535
 6JI  H3   H  H     0   0.232  29.3397  31.8193  47.2038
 6JI  H4   H  H     0   0.218  28.0917  31.3552  46.0773
 6JI  H5   H  HCH3  0   0.220  31.3930  33.0792  46.3611
 6JI  H6   H  HCH3  0   0.243  31.6737  32.0225  44.9843
 6JI  H7   H  HCH3  0   0.224  31.4105  33.7321  44.7242
 6JI  H8   H  HOH1  0   0.442  31.8758  29.3661  44.4320
 6JI  H9   H  HCH1  0   0.237  29.9337  35.0291  44.0949
 6JI  H10  H  HCH1  0   0.224  27.7431  33.6135  45.6238
 6JI  H11  H  HCH2  0   0.235  28.2517  34.8559  47.4068
 6JI  H12  H  HCH2  0   0.239  29.6776  33.8755  47.5446
 6JI  H13  H  HCH2  0   0.236  30.9525  35.5646  46.1846
 6JI  H14  H  HCH2  0   0.238  30.3359  36.2208  47.6808
 6JI  H15  H  HCH3  0   0.233  30.9818  38.2802  46.0050
 6JI  H16  H  HCH3  0   0.237  30.9452  37.2540  44.5789
 6JI  H17  H  HCH3  0   0.234  29.8729  38.6425  44.6843
 6JI  H18  H  HCH1  0   0.270  28.2304  37.0917  47.7890
 6JI  H19  H  H     0   0.286  28.1013  40.0359  45.3797
 6JI  H20  H  H     0   0.286  28.7950  42.2745  46.0944
 6JI  H21  H  H     0   0.296  29.3095  38.5816  49.2386
 6JI  H22  H  HCH2  0   0.249  26.4500  38.5227  45.9055
 6JI  H23  H  HCH2  0   0.253  26.1485  37.1424  46.9349
 6JI  H24  H  HCH1  0   0.244  26.1839  36.0028  44.7397
 6JI  H25  H  HCR6  0   0.206  29.6385  28.7372  44.3437
 6JI  H26  H  H     0   0.218  28.0212  30.4151  43.9476
 6JI  H27  H  H     0   0.234  29.0876  30.3507  42.5685
 6JI  H28  H  HCR6  0   0.220  30.1134  32.4340  43.1025
 6JI  H29  H  HCH2  0   0.214  27.1535  32.5569  43.7622
 6JI  H30  H  HCH2  0   0.228  27.8345  32.4824  42.1615
 6JI  H31  H  HCH2  0   0.225  28.6538  34.6992  42.2376
 6JI  H32  H  HCH2  0   0.228  27.1258  34.7950  43.0738

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
 6JI  C9   C8   single  1.526  0.020  1.526
 6JI  C9   C10  single  1.533  0.020  1.533
 6JI  C8   C7   single  1.528  0.020  1.528
 6JI  O1   C5   single  1.419  0.020  1.419
 6JI  C7   C6   single  1.536  0.020  1.536
 6JI  C7   C2   single  1.569  0.020  1.569
 6JI  C6   C5   single  1.516  0.020  1.516
 6JI  O4   C23  single  1.427  0.020  1.427
 6JI  O4   C24  single  1.420  0.020  1.420
 6JI  C5   C4   single  1.544  0.020  1.544
 6JI  C10  C24  single  1.504  0.020  1.504
 6JI  C10  C11  single  1.539  0.020  1.539
 6JI  C23  C24  single  1.456  0.020  1.456
 6JI  C23  C22  single  1.502  0.020  1.502
 6JI  C1   C2   single  1.532  0.020  1.532
 6JI  C24  C14  single  1.527  0.020  1.527
 6JI  C2   C11  single  1.550  0.020  1.550
 6JI  C2   C3   single  1.534  0.020  1.534
 6JI  C11  C12  single  1.547  0.020  1.547
 6JI  C15  C14  single  1.526  0.020  1.526
 6JI  C4   C3   single  1.530  0.020  1.530
 6JI  C22  C16  single  1.549  0.020  1.549
 6JI  C18  C19  double  1.350  0.020  1.350
 6JI  C18  C17  single  1.432  0.020  1.432
 6JI  C14  C16  single  1.574  0.020  1.574
 6JI  C14  C13  single  1.539  0.020  1.539
 6JI  C19  C20  single  1.440  0.020  1.440
 6JI  C16  C17  single  1.499  0.020  1.499
 6JI  C12  C13  single  1.524  0.020  1.524
 6JI  C17  C21  double  1.345  0.020  1.345
 6JI  C20  O2   double  1.207  0.020  1.207
 6JI  C20  O3   single  1.366  0.020  1.366
 6JI  C21  O3   single  1.341  0.020  1.341
 6JI  C4   H1   single  0.970  0.020  1.090
 6JI  C4   H2   single  0.970  0.020  1.090
 6JI  C3   H3   single  0.970  0.020  1.090
 6JI  C3   H4   single  0.970  0.020  1.090
 6JI  C1   H5   single  0.970  0.020  1.090
 6JI  C1   H6   single  0.970  0.020  1.090
 6JI  C1   H7   single  0.970  0.020  1.090
 6JI  O1   H8   single  0.850  0.020  0.980
 6JI  C10  H9   single  0.970  0.020  1.090
 6JI  C11  H10  single  0.970  0.020  1.090
 6JI  C12  H11  single  0.970  0.020  1.090
 6JI  C12  H12  single  0.970  0.020  1.090
 6JI  C13  H13  single  0.970  0.020  1.090
 6JI  C13  H14  single  0.970  0.020  1.090
 6JI  C15  H15  single  0.970  0.020  1.090
 6JI  C15  H16  single  0.970  0.020  1.090
 6JI  C15  H17  single  0.970  0.020  1.090
 6JI  C16  H18  single  0.970  0.020  1.090
 6JI  C18  H19  single  0.930  0.020  1.080
 6JI  C19  H20  single  0.930  0.020  1.080
 6JI  C21  H21  single  0.930  0.020  1.080
 6JI  C22  H22  single  0.970  0.020  1.090
 6JI  C22  H23  single  0.970  0.020  1.090
 6JI  C23  H24  single  0.970  0.020  1.090
 6JI  C5   H25  single  0.970  0.020  1.090
 6JI  C6   H26  single  0.970  0.020  1.090
 6JI  C6   H27  single  0.970  0.020  1.090
 6JI  C7   H28  single  0.970  0.020  1.090
 6JI  C8   H29  single  0.970  0.020  1.090
 6JI  C8   H30  single  0.970  0.020  1.090
 6JI  C9   H31  single  0.970  0.020  1.090
 6JI  C9   H32  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
 6JI  C24  O4   C23   61.52  3.000
 6JI  H2   C4   H1   105.68  3.000
 6JI  H2   C4   C5   109.51  3.000
 6JI  H1   C4   C5   109.34  3.000
 6JI  H2   C4   C3   110.06  3.000
 6JI  H1   C4   C3   108.40  3.000
 6JI  C5   C4   C3   113.55  3.000
 6JI  H4   C3   H3   105.65  3.000
 6JI  H4   C3   C2   108.52  3.000
 6JI  H3   C3   C2   110.33  3.000
 6JI  H4   C3   C4   109.36  3.000
 6JI  H3   C3   C4   108.87  3.000
 6JI  C2   C3   C4   113.79  3.000
 6JI  C21  O3   C20  123.23  3.000
 6JI  C7   C2   C11  109.74  3.000
 6JI  C11  C2   C1   110.34  3.000
 6JI  C7   C2   C1   109.42  3.000
 6JI  C11  C2   C3   108.99  3.000
 6JI  C1   C2   C3   109.80  3.000
 6JI  C7   C2   C3   108.53  3.000
 6JI  H7   C1   H6   106.75  3.000
 6JI  H7   C1   H5   107.59  3.000
 6JI  H6   C1   H5   107.52  3.000
 6JI  H7   C1   C2   111.51  3.000
 6JI  H6   C1   C2   111.21  3.000
 6JI  H5   C1   C2   111.99  3.000
 6JI  H8   O1   C5   108.14  3.000
 6JI  H9   C10  C9   107.61  3.000
 6JI  H9   C10  C24  106.69  3.000
 6JI  C9   C10  C24  115.06  3.000
 6JI  H9   C10  C11  108.31  3.000
 6JI  C24  C10  C11  108.03  3.000
 6JI  C9   C10  C11  110.89  3.000
 6JI  H10  C11  C12  106.36  3.000
 6JI  H10  C11  C10  106.55  3.000
 6JI  C12  C11  C10  111.26  3.000
 6JI  H10  C11  C2   106.70  3.000
 6JI  C12  C11  C2   115.08  3.000
 6JI  C10  C11  C2   110.35  3.000
 6JI  H12  C12  H11  105.16  3.000
 6JI  H12  C12  C13  109.59  3.000
 6JI  H11  C12  C13  108.69  3.000
 6JI  H12  C12  C11  111.12  3.000
 6JI  H11  C12  C11  108.86  3.000
 6JI  C13  C12  C11  113.10  3.000
 6JI  H14  C13  H13  105.96  3.000
 6JI  H14  C13  C14  109.40  3.000
 6JI  H13  C13  C14  109.46  3.000
 6JI  H14  C13  C12  110.57  3.000
 6JI  H13  C13  C12  109.52  3.000
 6JI  C14  C13  C12  111.76  3.000
 6JI  C24  C14  C16  104.07  3.000
 6JI  C16  C14  C15  114.58  3.000
 6JI  C24  C14  C15  110.85  3.000
 6JI  C16  C14  C13  110.18  3.000
 6JI  C15  C14  C13  108.75  3.000
 6JI  C24  C14  C13  108.20  3.000
 6JI  H17  C15  H16  107.36  3.000
 6JI  H17  C15  H15  107.82  3.000
 6JI  H16  C15  H15  107.15  3.000
 6JI  H17  C15  C14  113.30  3.000
 6JI  H16  C15  C14  109.92  3.000
 6JI  H15  C15  C14  111.03  3.000
 6JI  H18  C16  C22  106.66  3.000
 6JI  H18  C16  C17  106.05  3.000
 6JI  C22  C16  C17  113.97  3.000
 6JI  H18  C16  C14  106.23  3.000
 6JI  C17  C16  C14  115.13  3.000
 6JI  C22  C16  C14  108.17  3.000
 6JI  C21  C17  C18  115.91  3.000
 6JI  C21  C17  C16  120.99  3.000
 6JI  C18  C17  C16  123.10  3.000
 6JI  H19  C18  C19  119.36  3.000
 6JI  H19  C18  C17  119.35  3.000
 6JI  C19  C18  C17  121.29  3.000
 6JI  H20  C19  C20  117.44  3.000
 6JI  H20  C19  C18  121.75  3.000
 6JI  C20  C19  C18  120.81  3.000
 6JI  C19  C20  O2   127.23  3.000
 6JI  O2   C20  O3   117.50  3.000
 6JI  C19  C20  O3   115.27  3.000
 6JI  H21  C21  C17  124.34  3.000
 6JI  H21  C21  O3   112.18  3.000
 6JI  C17  C21  O3   123.48  3.000
 6JI  H23  C22  H22  106.37  3.000
 6JI  H23  C22  C23  110.15  3.000
 6JI  H22  C22  C23  111.05  3.000
 6JI  H23  C22  C16  110.24  3.000
 6JI  H22  C22  C16  113.41  3.000
 6JI  C23  C22  C16  105.66  3.000
 6JI  H24  C23  C24  123.01  3.000
 6JI  H24  C23  C22  119.86  3.000
 6JI  C24  C23  C22  110.89  3.000
 6JI  H24  C23  O4   115.54  3.000
 6JI  C22  C23  O4   113.74  3.000
 6JI  C24  C23  O4    59.01  3.000
 6JI  C23  C24  C14  110.63  3.000
 6JI  C14  C24  C10  116.27  3.000
 6JI  C23  C24  C10  125.03  3.000
 6JI  C14  C24  O4   112.71  3.000
 6JI  C23  C24  O4    59.47  3.000
 6JI  C10  C24  O4   120.49  3.000
 6JI  H25  C5   C6   107.80  3.000
 6JI  H25  C5   O1   108.74  3.000
 6JI  C6   C5   O1   108.06  3.000
 6JI  H25  C5   C4   108.45  3.000
 6JI  C6   C5   C4   110.05  3.000
 6JI  O1   C5   C4   113.60  3.000
 6JI  H27  C6   H26  105.67  3.000
 6JI  H27  C6   C7   109.50  3.000
 6JI  H26  C6   C7   108.66  3.000
 6JI  H27  C6   C5   109.93  3.000
 6JI  H26  C6   C5   106.90  3.000
 6JI  C7   C6   C5   115.68  3.000
 6JI  H28  C7   C8   107.43  3.000
 6JI  H28  C7   C6   108.25  3.000
 6JI  C8   C7   C6   107.59  3.000
 6JI  H28  C7   C2   107.80  3.000
 6JI  C6   C7   C2   113.03  3.000
 6JI  C8   C7   C2   112.52  3.000
 6JI  H30  C8   H29  105.41  3.000
 6JI  H30  C8   C9   109.58  3.000
 6JI  H29  C8   C9   109.79  3.000
 6JI  H30  C8   C7   109.23  3.000
 6JI  H29  C8   C7   108.71  3.000
 6JI  C9   C8   C7   113.78  3.000
 6JI  H32  C9   H31  105.99  3.000
 6JI  H32  C9   C8   108.48  3.000
 6JI  H31  C9   C8   110.04  3.000
 6JI  H32  C9   C10  111.50  3.000
 6JI  H31  C9   C10  109.32  3.000
 6JI  C8   C9   C10  111.37  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
 6JI  Var_01  C10  C24  C23  O4   -107.82  30.0  1
 6JI  Var_02  C14  C24  C23  O4    104.88  30.0  1
 6JI  Var_03  C16  C22  C23  O4    -68.18  30.0  1
 6JI  Var_04  C22  C23  C24  O4   -105.87  30.0  1
 6JI  Var_05  C18  C19  C20  O3     -0.65  30.0  1
 6JI  Var_06  C18  C17  C21  O3     -0.82  30.0  1
 6JI  Var_07  C16  C17  C21  O3    179.05  30.0  1
 6JI  Var_08  C5   C4   C3   C2    -44.79  30.0  1
 6JI  Var_09  C7   C8   C9   C10   -36.95  30.0  1
 6JI  Var_10  C22  C23  C24  C10   146.32  30.0  1
 6JI  Var_11  C14  C13  C12  C11    62.40  30.0  1
 6JI  Var_12  C22  C23  C24  C14    -0.99  30.0  1
 6JI  Var_13  C24  C23  C22  C16    -3.92  30.0  1
 6JI  Var_14  C19  C18  C17  C16  -179.13  30.0  1
 6JI  Var_15  C20  C19  C18  C17     0.00  30.0  1
 6JI  Var_16  C20  O3   C21  C17     0.15  30.0  1
 6JI  Var_17  C21  C17  C18  C19     0.72  30.0  1
 6JI  Var_18  C21  O3   C20  C19     0.60  30.0  1
 6JI  Var_19  C18  C19  C20  O2    179.50  30.0  1
 6JI  Var_20  C21  O3   C20  O2   -179.54  30.0  1
 6JI  Var_21  H22  C22  C23  O4     55.18  30.0  1
 6JI  Var_22  H23  C22  C23  O4    172.76  30.0  1
 6JI  Var_23  H24  C23  C24  O4    102.09  30.0  1
 6JI  Var_24  H20  C19  C20  O3    179.35  30.0  1
 6JI  Var_25  H1   C4   C3   C2   -166.50  30.0  1
 6JI  Var_26  H2   C4   C3   C2     78.37  30.0  1
 6JI  Var_27  H29  C8   C9   C10    85.13  30.0  1
 6JI  Var_28  H30  C8   C9   C10  -159.54  30.0  1
 6JI  Var_29  H24  C23  C24  C10    -5.72  30.0  1
 6JI  Var_30  H13  C13  C12  C11   -59.07  30.0  1
 6JI  Var_31  H14  C13  C12  C11  -175.47  30.0  1
 6JI  Var_32  H24  C23  C24  C14  -153.03  30.0  1
 6JI  Var_33  H11  C12  C13  C14   -58.61  30.0  1
 6JI  Var_34  H12  C12  C13  C14  -173.03  30.0  1
 6JI  Var_35  H24  C23  C22  C16   149.12  30.0  1
 6JI  Var_36  H19  C18  C17  C16     0.96  30.0  1
 6JI  Var_37  H21  C21  C17  C16    -0.99  30.0  1
 6JI  Var_38  H20  C19  C18  C17   180.00  30.0  1
 6JI  Var_39  H21  C21  C17  C18   179.15  30.0  1
 6JI  Var_40  H19  C18  C19  C20   179.91  30.0  1
 6JI  Var_41  H21  C21  O3   C20  -179.81  30.0  1
 6JI  Var_42  H19  C18  C17  C21  -179.18  30.0  1
 6JI  Var_43  H22  C22  C23  C24   119.44  30.0  1
 6JI  Var_44  H23  C22  C23  C24  -122.98  30.0  1
 6JI  Var_45  H3   C3   C4   C5   -168.28  30.0  1
 6JI  Var_46  H4   C3   C4   C5     76.74  30.0  1
 6JI  Var_47  H31  C9   C8   C7     84.45  30.0  1
 6JI  Var_48  H32  C9   C8   C7   -160.02  30.0  1
 6JI  Var_49  H20  C19  C20  O2     -0.49  30.0  1

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
 6JI  chir_01  C2   C7   C11  C3   negativ
 6JI  chir_02  C10  C11  C24  C9   positiv
 6JI  chir_03  C11  C12  C2   C10  positiv
 6JI  chir_04  C14  C16  C13  C24  negativ
 6JI  chir_05  C16  C22  C14  C17  negativ
 6JI  chir_08  C5   O1   C6   C4   positiv
 6JI  chir_09  C7   C2   C6   C8   negativ
 6JI  chir_10  C23  O4   C24  C22  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
 6JI  plan-1  O3   0.020
 6JI  plan-1  O2   0.020
 6JI  plan-1  C19  0.020
 6JI  plan-1  C20  0.020

