# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 03:51:45 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-(1,3-thiazol-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(F)cc1[C@@H](N2Cc3ccccc3C2=O)C(=O)Nc4sccn4
#
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
 9LL  9LL  (2R)-2-(5-fluoro-2-hydroxyphenyl)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-N-(1,3-thiazol-2-yl)acetamide  ligand  41  27  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9LL
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
 9LL  C10  C  C     0   0.570  -0.9489  -0.7593  -0.3973
 9LL  C15  C  CR15  0  -0.513  -4.9990  -2.7864   0.0712
 9LL  C20  C  CR56  0  -0.072   3.2165  -0.9996   0.7093
 9LL  C21  C  CR16  0  -0.299   4.1158  -1.2965   1.7205
 9LL  C22  C  CR16  0  -0.259   5.3057  -1.9148   1.3655
 9LL  C24  C  CR16  0  -0.318   4.6624  -1.9233  -0.9757
 9LL  C26  C  CH2   0  -0.277   2.3168  -0.8771  -1.4555
 9LL  C02  C  CR6   0   0.347   0.4563   2.6888  -1.1472
 9LL  C03  C  CR16  0  -0.363   0.2705   4.0136  -0.7631
 9LL  C04  C  CR16  0  -0.402  -0.4556   4.3205   0.3763
 9LL  C05  C  CR6   0   0.516  -0.9875   3.2883   1.1211
 9LL  C07  C  CR16  0  -0.416  -0.8162   1.9687   0.7605
 9LL  C08  C  CR6   0   0.008  -0.0995   1.6542  -0.3878
 9LL  C09  C  CH1   0  -0.273   0.1371   0.2250  -0.8331
 9LL  C12  C  CR5   0   0.299  -3.3350  -1.1475  -0.5080
 9LL  C14  C  CR15  0  -0.021  -5.4575  -1.6650  -0.5321
 9LL  C19  C  CR5   0   0.578   1.8893  -0.3581   0.8000
 9LL  C23  C  CR16  0  -0.241   5.5732  -2.2227   0.0309
 9LL  C25  C  CR56  0   0.081   3.4762  -1.3075  -0.6158
 9LL  F06  F  F     0  -0.321  -1.6871   3.5721   2.2354
 9LL  N11  N  NH1   0  -0.689  -2.2109  -0.3871  -0.7343
 9LL  N13  N  N     0  -0.421  -4.5096  -0.7358  -0.8588
 9LL  N18  N  NR5   0  -0.512   1.4374  -0.2633  -0.4790
 9LL  O01  O  OH1   0  -0.624   1.1668   2.3480  -2.2394
 9LL  O17  O  O     0  -0.423  -0.7126  -1.8170   0.1440
 9LL  O27  O  O     0  -0.466   1.3073   0.0176   1.8001
 9LL  S16  S  S2    0   0.230  -3.2870  -2.7011   0.2501
 9LL  H2   H  HCR6  0   0.261   3.8967  -1.0541   2.7526
 9LL  H3   H  HCR6  0   0.264   6.0340  -2.1622   2.1265
 9LL  H4   H  HCR6  0   0.262   4.8813  -2.1677  -2.0072
 9LL  H5   H  HCH2  0   0.278   2.6018  -0.1649  -2.2332
 9LL  H6   H  HCH2  0   0.277   1.8328  -1.7280  -1.9447
 9LL  H7   H  HCR6  0   0.285   0.6949   4.8153  -1.3560
 9LL  H8   H  HCR6  0   0.287  -0.5992   5.3504   0.6751
 9LL  H9   H  HCR6  0   0.278  -1.2387   1.1912   1.3828
 9LL  H10  H  HCH1  0   0.332   0.0911   0.2106  -1.9277
 9LL  H11  H  HCR5  0   0.274  -6.4941  -1.4659  -0.7622
 9LL  H12  H  HCR6  0   0.266   6.5073  -2.7056  -0.2252
 9LL  H13  H  HNH1  0   0.431  -2.3709   0.4945  -1.2042
 9LL  H14  H  HOH1  0   0.482   1.4625   3.1332  -2.7138
 9LL  H1   H  HCR5  0   0.304  -5.5582  -3.6415   0.4153

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
 9LL  O01  C02  single    1.347  0.020  1.347
 9LL  C03  C02  aromatic  1.392  0.020  1.392
 9LL  C03  C04  aromatic  1.386  0.020  1.386
 9LL  C02  C08  aromatic  1.399  0.020  1.399
 9LL  O27  C19  double    1.217  0.020  1.217
 9LL  C04  C05  aromatic  1.380  0.020  1.380
 9LL  C19  N18  single    1.360  0.020  1.360
 9LL  C19  C20  single    1.477  0.020  1.477
 9LL  C08  C09  single    1.516  0.020  1.516
 9LL  C08  C07  aromatic  1.390  0.020  1.390
 9LL  C09  N18  single    1.433  0.020  1.433
 9LL  C09  C10  single    1.529  0.020  1.529
 9LL  C21  C20  aromatic  1.385  0.020  1.385
 9LL  C21  C22  aromatic  1.387  0.020  1.387
 9LL  N18  C26  single    1.450  0.020  1.450
 9LL  C20  C25  aromatic  1.385  0.020  1.385
 9LL  C22  C23  aromatic  1.396  0.020  1.396
 9LL  C26  C25  single    1.495  0.020  1.495
 9LL  C25  C24  aromatic  1.384  0.020  1.384
 9LL  C05  C07  aromatic  1.379  0.020  1.379
 9LL  C05  F06  single    1.346  0.020  1.346
 9LL  C23  C24  aromatic  1.390  0.020  1.390
 9LL  N11  C10  single    1.358  0.020  1.358
 9LL  N11  C12  single    1.376  0.020  1.376
 9LL  C10  O17  double    1.211  0.020  1.211
 9LL  C12  N13  aromatic  1.293  0.020  1.293
 9LL  C12  S16  aromatic  1.729  0.020  1.729
 9LL  N13  C14  aromatic  1.367  0.020  1.367
 9LL  C14  C15  aromatic  1.353  0.020  1.353
 9LL  S16  C15  aromatic  1.723  0.020  1.723
 9LL  C15  H1   single    0.930  0.020  1.080
 9LL  C21  H2   single    0.930  0.020  1.080
 9LL  C22  H3   single    0.930  0.020  1.080
 9LL  C24  H4   single    0.930  0.020  1.080
 9LL  C26  H5   single    0.970  0.020  1.090
 9LL  C26  H6   single    0.970  0.020  1.090
 9LL  C03  H7   single    0.930  0.020  1.080
 9LL  C04  H8   single    0.930  0.020  1.080
 9LL  C07  H9   single    0.930  0.020  1.080
 9LL  C09  H10  single    0.970  0.020  1.090
 9LL  C14  H11  single    0.930  0.020  1.080
 9LL  C23  H12  single    0.930  0.020  1.080
 9LL  N11  H13  single    0.860  0.020  1.020
 9LL  O01  H14  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
 9LL  O17  C10  N11  122.10  3.000
 9LL  O17  C10  C09  123.42  3.000
 9LL  N11  C10  C09  114.38  3.000
 9LL  H1   C15  S16  121.42  3.000
 9LL  H1   C15  C14  128.59  3.000
 9LL  S16  C15  C14  109.99  3.000
 9LL  C25  C20  C19  108.90  3.000
 9LL  C25  C20  C21  121.93  3.000
 9LL  C19  C20  C21  129.17  3.000
 9LL  H2   C21  C22  121.15  3.000
 9LL  H2   C21  C20  121.10  3.000
 9LL  C22  C21  C20  117.75  3.000
 9LL  H3   C22  C23  119.55  3.000
 9LL  H3   C22  C21  119.96  3.000
 9LL  C23  C22  C21  120.50  3.000
 9LL  H4   C24  C25  121.43  3.000
 9LL  H4   C24  C23  120.60  3.000
 9LL  C25  C24  C23  117.97  3.000
 9LL  H6   C26  H5   107.70  3.000
 9LL  H6   C26  N18  111.22  3.000
 9LL  H5   C26  N18  111.20  3.000
 9LL  H6   C26  C25  111.73  3.000
 9LL  H5   C26  C25  112.66  3.000
 9LL  N18  C26  C25  102.35  3.000
 9LL  O01  C02  C08  117.57  3.000
 9LL  C08  C02  C03  120.08  3.000
 9LL  O01  C02  C03  122.35  3.000
 9LL  H7   C03  C04  119.42  3.000
 9LL  H7   C03  C02  120.06  3.000
 9LL  C04  C03  C02  120.52  3.000
 9LL  H8   C04  C05  120.80  3.000
 9LL  H8   C04  C03  120.50  3.000
 9LL  C05  C04  C03  118.70  3.000
 9LL  F06  C05  C07  118.88  3.000
 9LL  F06  C05  C04  119.31  3.000
 9LL  C07  C05  C04  121.81  3.000
 9LL  H9   C07  C08  120.94  3.000
 9LL  H9   C07  C05  119.27  3.000
 9LL  C08  C07  C05  119.79  3.000
 9LL  C09  C08  C07  122.46  3.000
 9LL  C07  C08  C02  119.09  3.000
 9LL  C09  C08  C02  118.42  3.000
 9LL  H10  C09  N18  106.29  3.000
 9LL  H10  C09  C08  107.42  3.000
 9LL  N18  C09  C08  112.97  3.000
 9LL  H10  C09  C10  104.26  3.000
 9LL  N18  C09  C10  110.77  3.000
 9LL  C08  C09  C10  114.35  3.000
 9LL  S16  C12  N13  115.47  3.000
 9LL  S16  C12  N11  123.09  3.000
 9LL  N13  C12  N11  121.44  3.000
 9LL  H11  C14  N13  119.28  3.000
 9LL  H11  C14  C15  124.94  3.000
 9LL  N13  C14  C15  115.77  3.000
 9LL  O27  C19  N18  126.35  3.000
 9LL  N18  C19  C20  105.73  3.000
 9LL  O27  C19  C20  127.92  3.000
 9LL  H12  C23  C24  119.36  3.000
 9LL  H12  C23  C22  119.35  3.000
 9LL  C24  C23  C22  121.29  3.000
 9LL  C26  C25  C24  130.30  3.000
 9LL  C24  C25  C20  120.56  3.000
 9LL  C26  C25  C20  109.15  3.000
 9LL  H13  N11  C12  115.38  3.000
 9LL  H13  N11  C10  120.07  3.000
 9LL  C12  N11  C10  124.54  3.000
 9LL  C14  N13  C12  110.40  3.000
 9LL  C19  N18  C09  123.89  3.000
 9LL  C09  N18  C26  121.86  3.000
 9LL  C19  N18  C26  113.72  3.000
 9LL  H14  O01  C02  110.78  3.000
 9LL  C12  S16  C15   88.36  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
 9LL  CONST_01  C12  N13  C14  C15    0.00   0.0  0
 9LL  CONST_02  N13  C12  S16  C15    0.00   0.0  0
 9LL  CONST_03  C23  C22  C21  C20    0.00   0.0  0
 9LL  CONST_04  C23  C24  C25  C20    0.00   0.0  0
 9LL  CONST_05  C24  C25  C20  C21    0.00   0.0  0
 9LL  CONST_06  C24  C23  C22  C21    0.00   0.0  0
 9LL  CONST_07  C25  C20  C21  C22    0.00   0.0  0
 9LL  CONST_08  C25  C24  C23  C22    0.00   0.0  0
 9LL  CONST_09  C05  C04  C03  C02    0.00   0.0  0
 9LL  CONST_10  C05  C07  C08  C02    0.00   0.0  0
 9LL  CONST_11  C07  C08  C02  C03    0.00   0.0  0
 9LL  CONST_12  C07  C05  C04  C03    0.00   0.0  0
 9LL  CONST_13  C08  C02  C03  C04    0.00   0.0  0
 9LL  CONST_14  C08  C07  C05  C04    0.00   0.0  0
 9LL  CONST_15  C14  C15  S16  C12    0.00   0.0  0
 9LL  CONST_16  S16  C12  N13  C14    0.00   0.0  0
 9LL  CONST_17  S16  C15  C14  N13    0.00   0.0  0
 9LL  CONST_18  C26  N18  C19  C20    0.00   0.0  0
 9LL  CONST_19  N11  C12  S16  C15  180.00   0.0  0
 9LL  CONST_20  C09  C08  C02  C03  180.00   0.0  0
 9LL  CONST_21  F06  C05  C04  C03  180.00   0.0  0
 9LL  CONST_22  O01  C02  C03  C04  180.00   0.0  0
 9LL  CONST_23  C09  C08  C07  C05  180.00   0.0  0
 9LL  CONST_24  O01  C02  C08  C07  180.00   0.0  0
 9LL  CONST_25  F06  C05  C07  C08  180.00   0.0  0
 9LL  CONST_26  N11  C12  N13  C14  180.00   0.0  0
 9LL  CONST_27  C09  N18  C19  C20  180.00   0.0  0
 9LL  CONST_28  O27  C19  N18  C26  180.00   0.0  0
 9LL  CONST_29  H3   C22  C21  C20  180.00   0.0  0
 9LL  CONST_30  H4   C24  C25  C20  180.00   0.0  0
 9LL  CONST_31  H12  C23  C22  C21  180.00   0.0  0
 9LL  CONST_32  H8   C04  C03  C02  180.00   0.0  0
 9LL  CONST_33  H9   C07  C08  C02  180.00   0.0  0
 9LL  CONST_34  H7   C03  C04  C05  180.00   0.0  0
 9LL  CONST_35  H11  C14  N13  C12  180.00   0.0  0
 9LL  CONST_36  H1   C15  S16  C12  180.00   0.0  0
 9LL  CONST_37  H2   C21  C20  C19    0.00   0.0  0
 9LL  CONST_38  N13  C12  N11  C10  180.00   0.0  0
 9LL  CONST_39  S16  C12  N11  C10    0.00   0.0  0
 9LL  CONST_40  O27  C19  N18  C09    0.00   0.0  0
 9LL  CONST_41  H13  N11  C12  N13    0.00   0.0  0
 9LL  CONST_42  C12  N11  C10  C09  180.00   0.0  0
 9LL  CONST_43  O17  C10  N11  C12    0.00   0.0  0
 9LL  Var_01    H5   C26  C25  C20  121.76  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
 9LL  chir_01  C09  C08  N18  C10  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
 9LL  plan-1  C15  0.020
 9LL  plan-1  C12  0.020
 9LL  plan-1  C14  0.020
 9LL  plan-1  N11  0.020
 9LL  plan-1  N13  0.020
 9LL  plan-1  S16  0.020
 9LL  plan-1  H11  0.020
 9LL  plan-1  H1   0.020
 9LL  plan-2  C02  0.020
 9LL  plan-2  C03  0.020
 9LL  plan-2  C04  0.020
 9LL  plan-2  C05  0.020
 9LL  plan-2  C07  0.020
 9LL  plan-2  C08  0.020
 9LL  plan-2  C09  0.020
 9LL  plan-2  F06  0.020
 9LL  plan-2  O01  0.020
 9LL  plan-2  H7   0.020
 9LL  plan-2  H8   0.020
 9LL  plan-2  H9   0.020
 9LL  plan-3  C10  0.020
 9LL  plan-3  C09  0.020
 9LL  plan-3  C12  0.020
 9LL  plan-3  N11  0.020
 9LL  plan-3  O17  0.020
 9LL  plan-3  H13  0.020
 9LL  plan-4  C20  0.020
 9LL  plan-4  C21  0.020
 9LL  plan-4  C22  0.020
 9LL  plan-4  C24  0.020
 9LL  plan-4  C26  0.020
 9LL  plan-4  C09  0.020
 9LL  plan-4  C19  0.020
 9LL  plan-4  C23  0.020
 9LL  plan-4  C25  0.020
 9LL  plan-4  N18  0.020
 9LL  plan-4  O27  0.020
 9LL  plan-4  H2   0.020
 9LL  plan-4  H3   0.020
 9LL  plan-4  H4   0.020
 9LL  plan-4  H12  0.020

