# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 22:57:26 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 5-[4-phenyl-5-(trifluoromethyl)thiophen-2-yl]-3-[3-(trifluoromethyl)phenyl]-1,2,4-oxadiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(c1)c2noc(n2)c3sc(c(c3)c4ccccc4)C(F)(F)F
#
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
 JEX  JEX  "5-[4-phenyl-5-(trifluoromethyl)thiophen-2-yl]-3-[3-(trifluoromethyl)phenyl]-1,2,4-oxadiazole"
  ligand  40  30  .  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_JEX
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
 JEX  C02  C  CT    0   1.084  104.6101  103.3446  76.7602
 JEX  C03  C  CR5   0  -0.609  105.8429  102.5147  76.8680
 JEX  C05  C  CR5   0  -0.325  107.9463  101.3850  76.3794
 JEX  C06  C  CR15  0  -0.219  107.5684  101.2337  77.6842
 JEX  C07  C  CR5   0   0.278  106.3430  101.8823  77.9789
 JEX  C08  C  CR6   0   0.040  105.7413  101.8800  79.3244
 JEX  C09  C  CR16  0  -0.292  106.5026  102.3044  80.4126
 JEX  C10  C  CR16  0  -0.237  105.9561  102.3218  81.6872
 JEX  C11  C  CR16  0  -0.255  104.6455  101.9095  81.8894
 JEX  C12  C  CR16  0  -0.237  103.8888  101.4679  80.8124
 JEX  C13  C  CR16  0  -0.297  104.4328  101.4508  79.5365
 JEX  C14  C  CR5   0   0.599  109.1274  100.8895  75.7244
 JEX  C17  C  CR5   0   0.346  110.6820  100.4354  74.4337
 JEX  C19  C  CR6   0   0.017  111.5067  100.4073  73.2261
 JEX  C20  C  CR16  0  -0.277  111.0079  100.9482  72.0462
 JEX  C21  C  CR16  0  -0.225  111.7810  100.9363  70.8950
 JEX  C22  C  CR16  0  -0.260  113.0529  100.3929  70.9157
 JEX  C23  C  CR6   0  -0.173  113.5556   99.8551  72.0986
 JEX  C24  C  CR16  0  -0.328  112.7886   99.8572  73.2509
 JEX  C25  C  CT    0   1.059  114.9385   99.2786  72.0811
 JEX  F01  F  F     0  -0.305  104.6681  104.1315  75.6802
 JEX  F26  F  F     0  -0.312  115.0238   98.2428  71.2357
 JEX  F27  F  F     0  -0.299  115.3363   98.8429  73.2781
 JEX  F28  F  F     0  -0.312  115.8405  100.1801  71.6692
 JEX  F29  F  F     0  -0.296  104.4445  104.1260  77.8267
 JEX  F30  F  F     0  -0.305  103.5022  102.6046  76.6369
 JEX  N16  N  N     0  -0.143  111.0103   99.8402  75.5429
 JEX  N18  N  N     0  -0.469  109.4966  101.1052  74.5054
 JEX  O15  O  O     0  -0.323  109.9860  100.1378  76.3967
 JEX  S04  S  S2    0   0.372  106.8306  102.3259  75.4842
 JEX  H1   H  HCR5  0   0.291  108.1335  100.6749  78.4172
 JEX  H2   H  HCR6  0   0.260  107.5218  102.6378  80.2596
 JEX  H3   H  HCR6  0   0.261  106.5536  102.6642  82.5219
 JEX  H4   H  HCR6  0   0.261  104.2175  101.9271  82.8830
 JEX  H5   H  HCR6  0   0.261  102.8712  101.1323  80.9641
 JEX  H6   H  HCR6  0   0.258  103.8402  101.0800  78.7110
 JEX  H7   H  HCR6  0   0.274  110.0156  101.3779  72.0246
 JEX  H8   H  HCR6  0   0.277  111.3891  101.3548  69.9785
 JEX  H9   H  HCR6  0   0.284  113.6468  100.3926  70.0104
 JEX  H10  H  HCR6  0   0.276  113.1737   99.4444  74.1737

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
 JEX  F26  C25  single    1.340  0.020  1.340
 JEX  C22  C21  aromatic  1.383  0.020  1.383
 JEX  C22  C23  aromatic  1.393  0.020  1.393
 JEX  C21  C20  aromatic  1.387  0.020  1.387
 JEX  F28  C25  single    1.340  0.020  1.340
 JEX  C25  C23  single    1.498  0.020  1.498
 JEX  C25  F27  single    1.334  0.020  1.334
 JEX  C23  C24  aromatic  1.384  0.020  1.384
 JEX  C20  C19  aromatic  1.391  0.020  1.391
 JEX  C24  C19  aromatic  1.395  0.020  1.395
 JEX  C19  C17  single    1.463  0.020  1.463
 JEX  C17  N18  aromatic  1.363  0.020  1.363
 JEX  C17  N16  aromatic  1.301  0.020  1.301
 JEX  N18  C14  aromatic  1.292  0.020  1.292
 JEX  N16  O15  aromatic  1.366  0.020  1.366
 JEX  S04  C05  aromatic  1.712  0.020  1.712
 JEX  S04  C03  aromatic  1.711  0.020  1.711
 JEX  F01  C02  single    1.338  0.020  1.338
 JEX  C14  O15  aromatic  1.324  0.020  1.324
 JEX  C14  C05  single    1.439  0.020  1.439
 JEX  C05  C06  aromatic  1.367  0.020  1.367
 JEX  F30  C02  single    1.338  0.020  1.338
 JEX  C02  C03  single    1.490  0.020  1.490
 JEX  C02  F29  single    1.332  0.020  1.332
 JEX  C03  C07  aromatic  1.373  0.020  1.373
 JEX  C06  C07  aromatic  1.417  0.020  1.417
 JEX  C07  C08  single    1.474  0.020  1.474
 JEX  C08  C13  aromatic  1.393  0.020  1.393
 JEX  C08  C09  aromatic  1.394  0.020  1.394
 JEX  C13  C12  aromatic  1.387  0.020  1.387
 JEX  C09  C10  aromatic  1.387  0.020  1.387
 JEX  C12  C11  aromatic  1.388  0.020  1.388
 JEX  C10  C11  aromatic  1.389  0.020  1.389
 JEX  C06  H1   single    0.930  0.020  1.080
 JEX  C09  H2   single    0.930  0.020  1.080
 JEX  C10  H3   single    0.930  0.020  1.080
 JEX  C11  H4   single    0.930  0.020  1.080
 JEX  C12  H5   single    0.930  0.020  1.080
 JEX  C13  H6   single    0.930  0.020  1.080
 JEX  C20  H7   single    0.930  0.020  1.080
 JEX  C21  H8   single    0.930  0.020  1.080
 JEX  C22  H9   single    0.930  0.020  1.080
 JEX  C24  H10  single    0.930  0.020  1.080

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
 JEX  F30  C02  F29  107.17  3.000
 JEX  F29  C02  F01  107.86  3.000
 JEX  F30  C02  F01  106.67  3.000
 JEX  F29  C02  C03  111.81  3.000
 JEX  F30  C02  C03  112.57  3.000
 JEX  F01  C02  C03  110.50  3.000
 JEX  S04  C03  C07  113.17  3.000
 JEX  C07  C03  C02  128.06  3.000
 JEX  S04  C03  C02  118.73  3.000
 JEX  S04  C05  C14  119.09  3.000
 JEX  C14  C05  C06  128.57  3.000
 JEX  S04  C05  C06  112.32  3.000
 JEX  H1   C06  C07  123.19  3.000
 JEX  H1   C06  C05  124.05  3.000
 JEX  C07  C06  C05  112.76  3.000
 JEX  C08  C07  C06  122.82  3.000
 JEX  C08  C07  C03  126.22  3.000
 JEX  C06  C07  C03  110.95  3.000
 JEX  C13  C08  C09  119.19  3.000
 JEX  C09  C08  C07  119.29  3.000
 JEX  C13  C08  C07  121.52  3.000
 JEX  H2   C09  C10  119.79  3.000
 JEX  H2   C09  C08  119.81  3.000
 JEX  C10  C09  C08  120.39  3.000
 JEX  H3   C10  C11  120.18  3.000
 JEX  H3   C10  C09  119.69  3.000
 JEX  C11  C10  C09  120.13  3.000
 JEX  H4   C11  C12  120.13  3.000
 JEX  H4   C11  C10  120.14  3.000
 JEX  C12  C11  C10  119.73  3.000
 JEX  H5   C12  C13  119.59  3.000
 JEX  H5   C12  C11  120.16  3.000
 JEX  C13  C12  C11  120.24  3.000
 JEX  H6   C13  C12  119.43  3.000
 JEX  H6   C13  C08  120.25  3.000
 JEX  C12  C13  C08  120.30  3.000
 JEX  O15  C14  N18  112.86  3.000
 JEX  O15  C14  C05  119.78  3.000
 JEX  N18  C14  C05  127.36  3.000
 JEX  N18  C17  N16  113.53  3.000
 JEX  N16  C17  C19  123.56  3.000
 JEX  N18  C17  C19  122.90  3.000
 JEX  C24  C19  C20  119.87  3.000
 JEX  C24  C19  C17  120.73  3.000
 JEX  C20  C19  C17  119.39  3.000
 JEX  H7   C20  C21  119.88  3.000
 JEX  H7   C20  C19  120.04  3.000
 JEX  C21  C20  C19  120.07  3.000
 JEX  H8   C21  C22  119.87  3.000
 JEX  H8   C21  C20  119.89  3.000
 JEX  C22  C21  C20  120.23  3.000
 JEX  H9   C22  C23  120.79  3.000
 JEX  H9   C22  C21  119.47  3.000
 JEX  C23  C22  C21  119.74  3.000
 JEX  C25  C23  C24  121.44  3.000
 JEX  C24  C23  C22  120.41  3.000
 JEX  C25  C23  C22  118.14  3.000
 JEX  H10  C24  C23  120.81  3.000
 JEX  H10  C24  C19  119.52  3.000
 JEX  C23  C24  C19  119.66  3.000
 JEX  F28  C25  F27  107.14  3.000
 JEX  F27  C25  F26  107.14  3.000
 JEX  F28  C25  F26  106.46  3.000
 JEX  F27  C25  C23  112.97  3.000
 JEX  F28  C25  C23  111.46  3.000
 JEX  F26  C25  C23  111.32  3.000
 JEX  O15  N16  C17  104.12  3.000
 JEX  C17  N18  C14  102.48  3.000
 JEX  N16  O15  C14  107.00  3.000
 JEX  C05  S04  C03   90.80  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
 JEX  CONST_01  C14  C05  S04  C03   180.00   0.0  0
 JEX  CONST_02  C06  C05  S04  C03     0.00   0.0  0
 JEX  CONST_03  C05  C06  C07  C03     0.00   0.0  0
 JEX  CONST_06  C07  C03  S04  C05     0.00   0.0  0
 JEX  CONST_07  C17  N18  C14  C05   180.00   0.0  0
 JEX  CONST_08  N16  O15  C14  C05   180.00   0.0  0
 JEX  CONST_09  C08  C07  C06  C05   180.00   0.0  0
 JEX  CONST_10  N18  C14  C05  C06   180.00   0.0  0
 JEX  CONST_11  O15  C14  C05  C06     0.00   0.0  0
 JEX  CONST_12  S04  C03  C07  C06     0.00   0.0  0
 JEX  CONST_15  S04  C05  C06  C07     0.00   0.0  0
 JEX  CONST_16  C14  C05  C06  C07   180.00   0.0  0
 JEX  CONST_17  C12  C13  C08  C07   180.00   0.0  0
 JEX  CONST_18  C10  C09  C08  C07   180.00   0.0  0
 JEX  CONST_19  S04  C03  C07  C08   180.00   0.0  0
 JEX  CONST_20  C11  C12  C13  C08     0.00   0.0  0
 JEX  CONST_21  C11  C10  C09  C08     0.00   0.0  0
 JEX  CONST_22  C12  C13  C08  C09     0.00   0.0  0
 JEX  CONST_23  C12  C11  C10  C09     0.00   0.0  0
 JEX  CONST_24  C13  C08  C09  C10     0.00   0.0  0
 JEX  CONST_25  C13  C12  C11  C10     0.00   0.0  0
 JEX  CONST_26  C19  C17  N18  C14   180.00   0.0  0
 JEX  CONST_27  N16  C17  N18  C14     0.00   0.0  0
 JEX  CONST_28  C17  N16  O15  C14     0.00   0.0  0
 JEX  CONST_29  C21  C20  C19  C17   180.00   0.0  0
 JEX  CONST_30  C23  C24  C19  C17   180.00   0.0  0
 JEX  CONST_31  O15  C14  N18  C17     0.00   0.0  0
 JEX  CONST_32  C22  C21  C20  C19     0.00   0.0  0
 JEX  CONST_33  C22  C23  C24  C19     0.00   0.0  0
 JEX  CONST_34  O15  N16  C17  C19   180.00   0.0  0
 JEX  CONST_35  C23  C22  C21  C20     0.00   0.0  0
 JEX  CONST_36  C23  C24  C19  C20     0.00   0.0  0
 JEX  CONST_37  N18  C17  C19  C20     0.00   0.0  0
 JEX  CONST_38  N16  C17  C19  C20   180.00   0.0  0
 JEX  CONST_39  C24  C23  C22  C21     0.00   0.0  0
 JEX  CONST_40  C24  C19  C20  C21     0.00   0.0  0
 JEX  CONST_41  N18  C17  C19  C24   180.00   0.0  0
 JEX  CONST_42  N16  C17  C19  C24     0.00   0.0  0
 JEX  CONST_43  N18  C14  O15  N16     0.00   0.0  0
 JEX  CONST_44  O15  N16  C17  N18     0.00   0.0  0
 JEX  CONST_45  S04  C05  C14  N18     0.00   0.0  0
 JEX  CONST_46  S04  C05  C14  O15   180.00   0.0  0
 JEX  CONST_47  C05  S04  C03  C02   180.00   0.0  0
 JEX  CONST_48  C06  C07  C03  C02   180.00   0.0  0
 JEX  CONST_49  C08  C07  C03  C02     0.00   0.0  0
 JEX  CONST_50  C25  C23  C24  C19   180.00   0.0  0
 JEX  CONST_51  C25  C23  C22  C21   180.00   0.0  0
 JEX  CONST_52  H1   C06  C07  C03   180.00   0.0  0
 JEX  CONST_53  H6   C13  C08  C07     0.00   0.0  0
 JEX  CONST_54  H2   C09  C08  C07     0.00   0.0  0
 JEX  CONST_55  H1   C06  C07  C08     0.00   0.0  0
 JEX  CONST_56  H5   C12  C13  C08   180.00   0.0  0
 JEX  CONST_57  H3   C10  C09  C08   180.00   0.0  0
 JEX  CONST_58  H6   C13  C08  C09   180.00   0.0  0
 JEX  CONST_59  H4   C11  C10  C09   180.00   0.0  0
 JEX  CONST_60  H5   C12  C11  C10   180.00   0.0  0
 JEX  CONST_61  H6   C13  C12  C11   180.00   0.0  0
 JEX  CONST_62  H2   C09  C10  C11   180.00   0.0  0
 JEX  CONST_63  H3   C10  C11  C12   180.00   0.0  0
 JEX  CONST_64  H2   C09  C08  C13   180.00   0.0  0
 JEX  CONST_65  H4   C11  C12  C13   180.00   0.0  0
 JEX  CONST_66  H1   C06  C05  C14     0.00   0.0  0
 JEX  CONST_67  H7   C20  C19  C17     0.00   0.0  0
 JEX  CONST_68  H10  C24  C19  C17     0.00   0.0  0
 JEX  CONST_69  H8   C21  C20  C19   180.00   0.0  0
 JEX  CONST_70  H9   C22  C21  C20   180.00   0.0  0
 JEX  CONST_71  H10  C24  C19  C20   180.00   0.0  0
 JEX  CONST_72  H7   C20  C21  C22   180.00   0.0  0
 JEX  CONST_73  H10  C24  C23  C22   180.00   0.0  0
 JEX  CONST_74  H8   C21  C22  C23   180.00   0.0  0
 JEX  CONST_75  H9   C22  C23  C24   180.00   0.0  0
 JEX  CONST_76  H7   C20  C19  C24   180.00   0.0  0
 JEX  CONST_77  H1   C06  C05  S04   180.00   0.0  0
 JEX  Var_01    F01  C02  C03  C07   159.97  30.0  3
 JEX  Var_02    F30  C02  C03  C07   -80.88  30.0  3
 JEX  Var_03    F29  C02  C03  C07    39.82  30.0  3
 JEX  Var_04    F26  C25  C23  C22   -61.98  30.0  2
 JEX  Var_05    F28  C25  C23  C22    56.72  30.0  2
 JEX  Var_06    F27  C25  C23  C22   177.42  30.0  2
 JEX  Var_07    F26  C25  C23  C24   117.91  30.0  2
 JEX  Var_08    F28  C25  C23  C24  -123.39  30.0  2
 JEX  Var_09    F27  C25  C23  C24    -2.68  30.0  2
 JEX  Var_10    S04  C03  C02  F01   -17.89  30.0  2
 JEX  Var_11    S04  C03  C02  F29  -138.04  30.0  2
 JEX  Var_12    S04  C03  C02  F30   101.26  30.0  2

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
 JEX  plan-1  C05  0.020
 JEX  plan-1  C14  0.020
 JEX  plan-1  C17  0.020
 JEX  plan-1  C19  0.020
 JEX  plan-1  N16  0.020
 JEX  plan-1  N18  0.020
 JEX  plan-1  O15  0.020
 JEX  plan-2  C02  0.020
 JEX  plan-2  C03  0.020
 JEX  plan-2  C05  0.020
 JEX  plan-2  C06  0.020
 JEX  plan-2  C07  0.020
 JEX  plan-2  C08  0.020
 JEX  plan-2  C14  0.020
 JEX  plan-2  S04  0.020
 JEX  plan-2  H1   0.020
 JEX  plan-3  C07  0.020
 JEX  plan-3  C08  0.020
 JEX  plan-3  C09  0.020
 JEX  plan-3  C10  0.020
 JEX  plan-3  C11  0.020
 JEX  plan-3  C12  0.020
 JEX  plan-3  C13  0.020
 JEX  plan-3  H2   0.020
 JEX  plan-3  H3   0.020
 JEX  plan-3  H4   0.020
 JEX  plan-3  H5   0.020
 JEX  plan-3  H6   0.020
 JEX  plan-4  C17  0.020
 JEX  plan-4  C19  0.020
 JEX  plan-4  C20  0.020
 JEX  plan-4  C21  0.020
 JEX  plan-4  C22  0.020
 JEX  plan-4  C23  0.020
 JEX  plan-4  C24  0.020
 JEX  plan-4  C25  0.020
 JEX  plan-4  H7   0.020
 JEX  plan-4  H8   0.020
 JEX  plan-4  H9   0.020
 JEX  plan-4  H10  0.020

