# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:57:18 2022
#   Inital geometry file: a 146 line input string
#   Ligand name: (2~{S})-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-(phenylmethyl)-2,3-dihydroinden-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(C[C@H]2Cc3c(Cc4ccccc4)cc(cc3C2=O)c5ccc(O)cc5)cc1
#
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
 J2U  J2U  (2~{S})-6-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-(phenylmethyl)-2,3-dihydroinden-1-one  ligand  56  32  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J2U
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
 J2U  C17  C  CR16  0  -0.238  26.0964  -33.4320  26.6349
 J2U  C12  C  CH2   0  -0.503  27.1151  -29.1772  24.4051
 J2U  C13  C  CR6   0   0.135  29.1241  -30.6034  25.2655
 J2U  C14  C  CH2   0  -0.596  28.6553  -30.6202  26.6944
 J2U  C15  C  CR6   0   0.134  27.3746  -31.3960  26.8914
 J2U  C16  C  CR16  0  -0.285  27.2630  -32.7083  26.4353
 J2U  C19  C  CR16  0  -0.239  25.1192  -31.5471  27.7521
 J2U  C20  C  CR16  0  -0.320  26.2893  -30.8256  27.5490
 J2U  C21  C  CR16  0  -0.393  30.2944  -31.2440  24.8814
 J2U  C22  C  CR6   0   0.114  30.7697  -31.2483  23.5588
 J2U  C23  C  CR16  0  -0.376  30.0377  -30.5692  22.5927
 J2U  C24  C  CR6   0   0.064  32.0246  -31.9448  23.2157
 J2U  C10  C  CR56  0   0.014  28.8762  -29.9122  22.9755
 J2U  C11  C  CR56  0   0.041  28.4066  -29.9291  24.2786
 J2U  C18  C  CR16  0  -0.270  25.0189  -32.8533  27.2950
 J2U  C01  C  CR5   0   0.376  27.9731  -29.1100  22.1335
 J2U  C02  C  CR15  0  -0.390  26.9427  -28.4653  23.0525
 J2U  C03  C  CH2   0  -0.521  25.5069  -28.4960  22.5238
 J2U  C04  C  CR6   0   0.142  25.2621  -27.6551  21.3007
 J2U  C05  C  CR16  0  -0.297  25.3911  -26.2676  21.3452
 J2U  C06  C  CR16  0  -0.321  25.1601  -25.4786  20.2302
 J2U  C07  C  CR6   0   0.334  24.7843  -26.0693  19.0251
 J2U  C08  C  CR16  0  -0.368  24.6407  -27.4518  18.9651
 J2U  C09  C  CR16  0  -0.305  24.8804  -28.2251  20.0926
 J2U  C25  C  CR16  0  -0.295  32.9049  -31.4179  22.2675
 J2U  C26  C  CR16  0  -0.321  34.0858  -32.0587  21.9393
 J2U  C27  C  CR6   0   0.345  34.4243  -33.2601  22.5592
 J2U  C28  C  CR16  0  -0.367  33.5578  -33.8030  23.5050
 J2U  C29  C  CR16  0  -0.295  32.3779  -33.1495  23.8228
 J2U  O01  O  O     0  -0.384  28.0556  -28.9752  20.9342
 J2U  O02  O  OH1   0  -0.633  24.5731  -25.2629  17.9628
 J2U  O03  O  OH1   0  -0.626  35.5869  -33.8417  22.2099
 J2U  H1   H  HCR6  0   0.252  26.0271  -34.4504  26.2741
 J2U  H3   H  HCH2  0   0.265  27.1182  -28.4829  25.2473
 J2U  H4   H  HCH2  0   0.275  29.4389  -31.0490  27.3245
 J2U  H5   H  HCH2  0   0.268  28.5102  -29.5943  27.0446
 J2U  H6   H  HCR6  0   0.248  28.0961  -33.1703  25.9180
 J2U  H7   H  HCR6  0   0.252  24.2852  -31.0852  28.2651
 J2U  H8   H  HCR6  0   0.248  26.3580  -29.8040  27.9046
 J2U  H9   H  HCR6  0   0.254  30.8763  -31.7462  25.6463
 J2U  H10  H  HCR6  0   0.256  30.3570  -30.5533  21.5575
 J2U  H12  H  HCR6  0   0.252  24.1078  -33.4169  27.4496
 J2U  H15  H  HCR5  0   0.298  27.2562  -27.4205  23.1673
 J2U  H16  H  HCH2  0   0.252  25.2215  -29.5327  22.3270
 J2U  H17  H  HCH2  0   0.259  24.8567  -28.1539  23.3344
 J2U  H18  H  HCR6  0   0.246  25.6764  -25.7830  22.2727
 J2U  H19  H  HCR6  0   0.256  25.2678  -24.4024  20.2909
 J2U  H20  H  HCR6  0   0.264  24.3440  -27.9302  18.0380
 J2U  H21  H  HCR6  0   0.246  24.7665  -29.3004  20.0214
 J2U  H22  H  HCR6  0   0.254  32.6773  -30.4746  21.7866
 J2U  H23  H  HCR6  0   0.263  34.7552  -31.6239  21.2076
 J2U  H24  H  HCR6  0   0.271  33.7985  -34.7422  23.9908
 J2U  H25  H  HCR6  0   0.257  31.7152  -33.6064  24.5475
 J2U  H27  H  HOH1  0   0.470  24.3235  -25.7830  17.1905
 J2U  H28  H  HOH1  0   0.474  35.7178  -34.6591  22.7041
 J2U  H2   H  HCH2  0   0.268  26.2919  -29.8757  24.5856

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
 J2U  C17  C16  aromatic  1.387  0.020  1.387
 J2U  C17  C18  aromatic  1.390  0.020  1.390
 J2U  C12  C11  single    1.500  0.020  1.500
 J2U  C12  C02  single    1.538  0.020  1.538
 J2U  C13  C14  single    1.504  0.020  1.504
 J2U  C13  C21  aromatic  1.388  0.020  1.388
 J2U  C13  C11  aromatic  1.394  0.020  1.394
 J2U  C14  C15  single    1.510  0.020  1.510
 J2U  C15  C16  aromatic  1.394  0.020  1.394
 J2U  C15  C20  aromatic  1.391  0.020  1.391
 J2U  C19  C20  aromatic  1.390  0.020  1.390
 J2U  C19  C18  aromatic  1.387  0.020  1.387
 J2U  C21  C22  aromatic  1.405  0.020  1.405
 J2U  C22  C23  aromatic  1.389  0.020  1.389
 J2U  C22  C24  single    1.476  0.020  1.476
 J2U  C23  C10  aromatic  1.388  0.020  1.388
 J2U  C24  C25  aromatic  1.397  0.020  1.397
 J2U  C24  C29  aromatic  1.395  0.020  1.395
 J2U  C10  C11  aromatic  1.385  0.020  1.385
 J2U  C01  C02  single    1.524  0.020  1.524
 J2U  C01  O01  double    1.210  0.020  1.210
 J2U  C02  C03  single    1.530  0.020  1.530
 J2U  C03  C04  single    1.504  0.020  1.504
 J2U  C04  C05  aromatic  1.394  0.020  1.394
 J2U  C04  C09  aromatic  1.389  0.020  1.389
 J2U  C05  C06  aromatic  1.385  0.020  1.385
 J2U  C06  C07  aromatic  1.394  0.020  1.394
 J2U  C07  C08  aromatic  1.391  0.020  1.391
 J2U  C07  O02  single    1.350  0.020  1.350
 J2U  C08  C09  aromatic  1.388  0.020  1.388
 J2U  C25  C26  aromatic  1.383  0.020  1.383
 J2U  C26  C27  aromatic  1.394  0.020  1.394
 J2U  C27  C28  aromatic  1.393  0.020  1.393
 J2U  C27  O03  single    1.346  0.020  1.346
 J2U  C28  C29  aromatic  1.386  0.020  1.386
 J2U  C17  H1   single    0.930  0.020  1.080
 J2U  C12  H2   single    0.970  0.020  1.090
 J2U  C12  H3   single    0.970  0.020  1.090
 J2U  C14  H4   single    0.970  0.020  1.090
 J2U  C14  H5   single    0.970  0.020  1.090
 J2U  C16  H6   single    0.930  0.020  1.080
 J2U  C19  H7   single    0.930  0.020  1.080
 J2U  C20  H8   single    0.930  0.020  1.080
 J2U  C21  H9   single    0.930  0.020  1.080
 J2U  C23  H10  single    0.930  0.020  1.080
 J2U  C18  H12  single    0.930  0.020  1.080
 J2U  C02  H15  single    0.970  0.020  1.090
 J2U  C03  H16  single    0.970  0.020  1.090
 J2U  C03  H17  single    0.970  0.020  1.090
 J2U  C05  H18  single    0.930  0.020  1.080
 J2U  C06  H19  single    0.930  0.020  1.080
 J2U  C08  H20  single    0.930  0.020  1.080
 J2U  C09  H21  single    0.930  0.020  1.080
 J2U  C25  H22  single    0.930  0.020  1.080
 J2U  C26  H23  single    0.930  0.020  1.080
 J2U  C28  H24  single    0.930  0.020  1.080
 J2U  C29  H25  single    0.930  0.020  1.080
 J2U  O02  H27  single    0.850  0.020  0.980
 J2U  O03  H28  single    0.850  0.020  0.980
 J2U  C01  C10  single    1.472  0.020  1.472

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
 J2U  H1   C17  C18  120.02  3.000
 J2U  H1   C17  C16  119.77  3.000
 J2U  C18  C17  C16  120.20  3.000
 J2U  H3   C12  H2   106.31  3.000
 J2U  H3   C12  C02  112.61  3.000
 J2U  H2   C12  C02  110.86  3.000
 J2U  H3   C12  C11  112.43  3.000
 J2U  H2   C12  C11  109.97  3.000
 J2U  C02  C12  C11  104.73  3.000
 J2U  C11  C13  C21  117.46  3.000
 J2U  C11  C13  C14  121.17  3.000
 J2U  C21  C13  C14  121.37  3.000
 J2U  H5   C14  H4   106.17  3.000
 J2U  H5   C14  C15  109.13  3.000
 J2U  H4   C14  C15  109.34  3.000
 J2U  H5   C14  C13  109.58  3.000
 J2U  H4   C14  C13  109.18  3.000
 J2U  C15  C14  C13  113.20  3.000
 J2U  C20  C15  C16  118.56  3.000
 J2U  C20  C15  C14  120.83  3.000
 J2U  C16  C15  C14  120.59  3.000
 J2U  H6   C16  C15  119.73  3.000
 J2U  H6   C16  C17  119.51  3.000
 J2U  C15  C16  C17  120.76  3.000
 J2U  H7   C19  C18  120.14  3.000
 J2U  H7   C19  C20  119.76  3.000
 J2U  C18  C19  C20  120.10  3.000
 J2U  H8   C20  C19  119.66  3.000
 J2U  H8   C20  C15  119.47  3.000
 J2U  C19  C20  C15  120.87  3.000
 J2U  H9   C21  C22  118.75  3.000
 J2U  H9   C21  C13  118.09  3.000
 J2U  C22  C21  C13  123.15  3.000
 J2U  C24  C22  C23  121.13  3.000
 J2U  C24  C22  C21  120.52  3.000
 J2U  C23  C22  C21  118.34  3.000
 J2U  H10  C23  C10  120.20  3.000
 J2U  H10  C23  C22  121.09  3.000
 J2U  C10  C23  C22  118.71  3.000
 J2U  C29  C24  C25  117.49  3.000
 J2U  C29  C24  C22  121.46  3.000
 J2U  C25  C24  C22  121.04  3.000
 J2U  C01  C10  C11  109.67  3.000
 J2U  C01  C10  C23  127.83  3.000
 J2U  C11  C10  C23  122.50  3.000
 J2U  C10  C11  C13  119.83  3.000
 J2U  C10  C11  C12  111.42  3.000
 J2U  C13  C11  C12  128.75  3.000
 J2U  H12  C18  C19  120.26  3.000
 J2U  H12  C18  C17  120.24  3.000
 J2U  C19  C18  C17  119.50  3.000
 J2U  O01  C01  C02  126.65  3.000
 J2U  O01  C01  C10  125.86  3.000
 J2U  C02  C01  C10  107.48  3.000
 J2U  H15  C02  C03  108.87  3.000
 J2U  H15  C02  C01  105.84  3.000
 J2U  C03  C02  C01  114.68  3.000
 J2U  H15  C02  C12  108.47  3.000
 J2U  C03  C02  C12  113.56  3.000
 J2U  C01  C02  C12  105.00  3.000
 J2U  H17  C03  H16  105.94  3.000
 J2U  H17  C03  C04  109.33  3.000
 J2U  H16  C03  C04  109.96  3.000
 J2U  H17  C03  C02  107.18  3.000
 J2U  H16  C03  C02  109.04  3.000
 J2U  C04  C03  C02  114.99  3.000
 J2U  C09  C04  C05  117.48  3.000
 J2U  C09  C04  C03  121.49  3.000
 J2U  C05  C04  C03  121.02  3.000
 J2U  H18  C05  C06  118.53  3.000
 J2U  H18  C05  C04  119.75  3.000
 J2U  C06  C05  C04  121.72  3.000
 J2U  H19  C06  C07  119.76  3.000
 J2U  H19  C06  C05  120.27  3.000
 J2U  C07  C06  C05  119.97  3.000
 J2U  O02  C07  C08  122.91  3.000
 J2U  O02  C07  C06  117.99  3.000
 J2U  C08  C07  C06  119.09  3.000
 J2U  H20  C08  C09  119.72  3.000
 J2U  H20  C08  C07  120.22  3.000
 J2U  C09  C08  C07  120.06  3.000
 J2U  H21  C09  C08  118.77  3.000
 J2U  H21  C09  C04  119.55  3.000
 J2U  C08  C09  C04  121.68  3.000
 J2U  H22  C25  C26  118.52  3.000
 J2U  H22  C25  C24  119.84  3.000
 J2U  C26  C25  C24  121.63  3.000
 J2U  H23  C26  C27  119.78  3.000
 J2U  H23  C26  C25  120.14  3.000
 J2U  C27  C26  C25  120.08  3.000
 J2U  O03  C27  C28  123.03  3.000
 J2U  O03  C27  C26  117.83  3.000
 J2U  C28  C27  C26  119.14  3.000
 J2U  H24  C28  C29  119.65  3.000
 J2U  H24  C28  C27  120.24  3.000
 J2U  C29  C28  C27  120.10  3.000
 J2U  H25  C29  C28  118.39  3.000
 J2U  H25  C29  C24  120.05  3.000
 J2U  C28  C29  C24  121.55  3.000
 J2U  H27  O02  C07  110.40  3.000
 J2U  H28  O03  C27  110.53  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
 J2U  CONST_01  C20  C15  C16  C17     0.00   0.0  0
 J2U  CONST_02  C20  C19  C18  C17     0.00   0.0  0
 J2U  CONST_03  C23  C22  C21  C13     0.00   0.0  0
 J2U  CONST_04  C24  C22  C21  C13   180.00   0.0  0
 J2U  CONST_05  C23  C10  C11  C13     0.00   0.0  0
 J2U  CONST_06  C18  C17  C16  C15     0.00   0.0  0
 J2U  CONST_07  C18  C19  C20  C15     0.00   0.0  0
 J2U  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 J2U  CONST_09  C19  C20  C15  C16     0.00   0.0  0
 J2U  CONST_10  C10  C11  C13  C21     0.00   0.0  0
 J2U  CONST_11  C10  C23  C22  C21     0.00   0.0  0
 J2U  CONST_14  C11  C13  C21  C22     0.00   0.0  0
 J2U  CONST_15  C11  C10  C23  C22     0.00   0.0  0
 J2U  CONST_16  C26  C25  C24  C22   180.00   0.0  0
 J2U  CONST_17  C28  C29  C24  C22   180.00   0.0  0
 J2U  CONST_20  C10  C23  C22  C24   180.00   0.0  0
 J2U  CONST_21  C27  C26  C25  C24     0.00   0.0  0
 J2U  CONST_22  C27  C28  C29  C24     0.00   0.0  0
 J2U  CONST_23  C07  C06  C05  C04     0.00   0.0  0
 J2U  CONST_24  C07  C08  C09  C04     0.00   0.0  0
 J2U  CONST_25  C08  C09  C04  C05     0.00   0.0  0
 J2U  CONST_26  C08  C07  C06  C05     0.00   0.0  0
 J2U  CONST_27  C09  C04  C05  C06     0.00   0.0  0
 J2U  CONST_28  C09  C08  C07  C06     0.00   0.0  0
 J2U  CONST_29  C28  C29  C24  C25     0.00   0.0  0
 J2U  CONST_30  C28  C27  C26  C25     0.00   0.0  0
 J2U  CONST_31  C29  C24  C25  C26     0.00   0.0  0
 J2U  CONST_32  C29  C28  C27  C26     0.00   0.0  0
 J2U  CONST_33  C14  C15  C16  C17   180.00   0.0  0
 J2U  CONST_34  C14  C13  C11  C12     0.00   0.0  0
 J2U  CONST_35  C22  C21  C13  C14   180.00   0.0  0
 J2U  CONST_36  C10  C11  C13  C14   180.00   0.0  0
 J2U  CONST_37  C19  C20  C15  C14   180.00   0.0  0
 J2U  CONST_38  C06  C05  C04  C03   180.00   0.0  0
 J2U  CONST_39  C08  C09  C04  C03   180.00   0.0  0
 J2U  CONST_40  O02  C07  C06  C05   180.00   0.0  0
 J2U  CONST_41  O02  C07  C08  C09   180.00   0.0  0
 J2U  CONST_42  O03  C27  C26  C25   180.00   0.0  0
 J2U  CONST_43  O03  C27  C28  C29   180.00   0.0  0
 J2U  CONST_44  H7   C19  C18  C17   180.00   0.0  0
 J2U  CONST_45  H1   C17  C16  C15   180.00   0.0  0
 J2U  CONST_46  H12  C18  C17  C16   180.00   0.0  0
 J2U  CONST_47  H8   C20  C15  C16   180.00   0.0  0
 J2U  CONST_48  H6   C16  C15  C20   180.00   0.0  0
 J2U  CONST_49  H10  C23  C22  C21   180.00   0.0  0
 J2U  CONST_50  H22  C25  C24  C22     0.00   0.0  0
 J2U  CONST_51  H25  C29  C24  C22     0.00   0.0  0
 J2U  CONST_52  H9   C21  C22  C23   180.00   0.0  0
 J2U  CONST_53  H23  C26  C25  C24   180.00   0.0  0
 J2U  CONST_54  H24  C28  C29  C24   180.00   0.0  0
 J2U  CONST_55  H19  C06  C05  C04   180.00   0.0  0
 J2U  CONST_56  H20  C08  C09  C04   180.00   0.0  0
 J2U  CONST_57  H21  C09  C04  C05   180.00   0.0  0
 J2U  CONST_58  H18  C05  C06  C07   180.00   0.0  0
 J2U  Var_01    C02  C12  C11  C13   170.96  30.0  1
 J2U  Var_02    C02  C01  C10  C23  -173.20  30.0  1
 J2U  Var_03    C16  C15  C14  C13    53.02  30.0  2
 J2U  Var_04    C21  C13  C14  C15  -113.17  30.0  2
 J2U  Var_05    C05  C04  C03  C02   -64.42  30.0  2

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
 J2U  chir_01  C02  C12  C01  C03  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
 J2U  plan-1  C17  0.020
 J2U  plan-1  C14  0.020
 J2U  plan-1  C15  0.020
 J2U  plan-1  C16  0.020
 J2U  plan-1  C19  0.020
 J2U  plan-1  C20  0.020
 J2U  plan-1  C18  0.020
 J2U  plan-1  H1   0.020
 J2U  plan-1  H6   0.020
 J2U  plan-1  H7   0.020
 J2U  plan-1  H8   0.020
 J2U  plan-1  H12  0.020
 J2U  plan-2  C22  0.020
 J2U  plan-2  C24  0.020
 J2U  plan-2  C25  0.020
 J2U  plan-2  C26  0.020
 J2U  plan-2  C27  0.020
 J2U  plan-2  C28  0.020
 J2U  plan-2  C29  0.020
 J2U  plan-2  O03  0.020
 J2U  plan-2  H22  0.020
 J2U  plan-2  H23  0.020
 J2U  plan-2  H24  0.020
 J2U  plan-2  H25  0.020
 J2U  plan-3  C12  0.020
 J2U  plan-3  C13  0.020
 J2U  plan-3  C14  0.020
 J2U  plan-3  C21  0.020
 J2U  plan-3  C22  0.020
 J2U  plan-3  C23  0.020
 J2U  plan-3  C24  0.020
 J2U  plan-3  C10  0.020
 J2U  plan-3  C11  0.020
 J2U  plan-3  C01  0.020
 J2U  plan-3  H9   0.020
 J2U  plan-3  H10  0.020
 J2U  plan-4  C03  0.020
 J2U  plan-4  C04  0.020
 J2U  plan-4  C05  0.020
 J2U  plan-4  C06  0.020
 J2U  plan-4  C07  0.020
 J2U  plan-4  C08  0.020
 J2U  plan-4  C09  0.020
 J2U  plan-4  O02  0.020
 J2U  plan-4  H18  0.020
 J2U  plan-4  H19  0.020
 J2U  plan-4  H20  0.020
 J2U  plan-4  H21  0.020
 J2U  plan-5  C10  0.020
 J2U  plan-5  C01  0.020
 J2U  plan-5  C02  0.020
 J2U  plan-5  O01  0.020

