# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 16:23:34 2022
#   Inital geometry file: a 107 line input string
#   Ligand name: a 2 line input string
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1sccc1C(=O)Nc2c(F)cc(cc2F)c3cccc(OC(F)(F)F)c3
#
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
 ILF  ILF  '3-{[3,5-difluoro-3'-(trifluoromethoxy)biphenyl-4-yl]carbamoyl}thiophene-2-carboxylic acid'  ligand  39  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ILF
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
 ILF  C1    C  CR16   0  -0.306  55.6154  48.1430  -0.6472
 ILF  C2    C  CR6    0   0.338  55.2144  47.8967  -1.9487
 ILF  C8    C  CR16   0  -0.361  54.2333  46.9706  -2.2485
 ILF  C9    C  CR6    0   0.097  53.6354  46.2428  -1.2201
 ILF  C10   C  CR6    0   0.115  52.6156  45.2221  -1.5298
 ILF  C11   C  CR16   0  -0.300  54.0358  46.4816   0.0943
 ILF  C12   C  CR16   0  -0.237  55.0097  47.4272   0.3754
 ILF  C13   C  CR16   0  -0.507  51.5229  45.0257  -0.6858
 ILF  C14   C  CR6    0   0.571  50.5987  44.0502  -0.9913
 ILF  C16   C  CR6    0  -0.031  50.7091  43.2213  -2.1024
 ILF  C20   C  CR16   0  -0.504  52.7409  44.4342  -2.6723
 ILF  C21   C  C      0   0.500  49.6436  41.1617  -1.5509
 ILF  C22   C  CR5    0   0.053  48.6464  40.1252  -1.9469
 ILF  C24   C  CR15   0  -0.180  48.4321  39.0363  -1.0504
 ILF  C27   C  CR5    0  -0.423  47.8591  40.0265  -3.0778
 ILF  O3    O  O2     0  -0.523  55.7768  48.6441  -2.9784
 ILF  C4    C  CT     0   1.073  56.8194  48.1140  -3.6301
 ILF  F5    F  F      0  -0.298  57.8123  47.7679  -2.8105
 ILF  F6    F  F      0  -0.299  56.4948  47.0211  -4.3252
 ILF  F7    F  F      0  -0.276  57.2709  49.0221  -4.4803
 ILF  F15   F  F      0  -0.298  49.5334  43.8999  -0.2022
 ILF  N17   N  NH1    0  -0.780  49.7860  42.2139  -2.3811
 ILF  C18   C  CR6    0   0.556  51.7995  43.4603  -2.9285
 ILF  F19   F  F      0  -0.298  51.9421  42.6937  -4.0137
 ILF  O23   O  O      0  -0.473  50.2854  41.0301  -0.5185
 ILF  C25   C  CR15   0  -0.468  47.5073  38.1495  -1.5004
 ILF  S26   S  S2     0   0.252  46.8806  38.6162  -3.0175
 ILF  C28   C  C      0   0.460  47.6600  40.8412  -4.3379
 ILF  O29   O  OC    -1  -0.574  48.3381  41.8866  -4.4912
 ILF  O30   O  O      0  -0.547  46.8242  40.3845  -5.1253
 ILF  H1    H  HCR6   0   0.282  56.3745  48.8837  -0.4332
 ILF  H8    H  HCR6   0   0.282  53.9128  46.8379  -3.2738
 ILF  H11   H  HCR6   0   0.267  53.5994  45.9136   0.9057
 ILF  H12   H  HCR6   0   0.272  55.3119  47.5991   1.3997
 ILF  H13   H  HCR6   0   0.282  51.3716  45.6450   0.1890
 ILF  H20   H  HCR6   0   0.284  53.5853  44.5416  -3.3408
 ILF  H24   H  HCR5   0   0.266  48.9517  38.9317  -0.1099
 ILF  HN17  H  HNH1   0   0.442  49.2570  42.1917  -3.2945
 ILF  H25   H  HCR5   0   0.293  47.1683  37.2492  -1.0106

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
 ILF  C1   C2    aromatic  1.384  0.020  1.384
 ILF  C1   C12   aromatic  1.387  0.020  1.387
 ILF  C1   H1    single    0.930  0.020  1.080
 ILF  C2   C8    aromatic  1.382  0.020  1.382
 ILF  C2   O3    single    1.391  0.020  1.391
 ILF  C8   C9    aromatic  1.395  0.020  1.395
 ILF  C8   H8    single    0.930  0.020  1.080
 ILF  C9   C10   single    1.476  0.020  1.476
 ILF  C9   C11   aromatic  1.395  0.020  1.395
 ILF  C10  C13   aromatic  1.395  0.020  1.395
 ILF  C10  C20   aromatic  1.393  0.020  1.393
 ILF  C11  C12   aromatic  1.386  0.020  1.386
 ILF  C11  H11   single    0.930  0.020  1.080
 ILF  C12  H12   single    0.930  0.020  1.080
 ILF  C13  C14   aromatic  1.378  0.020  1.378
 ILF  C13  H13   single    0.930  0.020  1.080
 ILF  C14  C16   aromatic  1.391  0.020  1.391
 ILF  C14  F15   single    1.334  0.020  1.334
 ILF  C16  N17   single    1.394  0.020  1.394
 ILF  C16  C18   aromatic  1.389  0.020  1.389
 ILF  C20  C18   aromatic  1.379  0.020  1.379
 ILF  C20  H20   single    0.930  0.020  1.080
 ILF  C21  C22   single    1.492  0.020  1.492
 ILF  C21  N17   single    1.348  0.020  1.348
 ILF  C21  O23   double    1.223  0.020  1.223
 ILF  C22  C24   aromatic  1.427  0.020  1.427
 ILF  C22  C27   aromatic  1.382  0.020  1.382
 ILF  C24  C25   aromatic  1.358  0.020  1.358
 ILF  C24  H24   single    0.930  0.020  1.080
 ILF  C27  S26   aromatic  1.718  0.020  1.718
 ILF  C27  C28   single    1.514  0.020  1.514
 ILF  O3   C4    single    1.339  0.020  1.339
 ILF  C4   F5    single    1.333  0.020  1.333
 ILF  C4   F6    single    1.335  0.020  1.335
 ILF  C4   F7    single    1.323  0.020  1.323
 ILF  N17  HN17  single    0.860  0.020  1.020
 ILF  C18  F19   single    1.336  0.020  1.336
 ILF  C25  S26   aromatic  1.707  0.020  1.707
 ILF  C25  H25   single    0.930  0.020  1.080
 ILF  C28  O29   deloc     1.255  0.020  1.255
 ILF  C28  O30   deloc     1.236  0.020  1.236

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
 ILF  H1    C1   C12  120.91  3.000
 ILF  H1    C1   C2   120.74  3.000
 ILF  C12   C1   C2   118.35  3.000
 ILF  O3    C2   C8   119.11  3.000
 ILF  O3    C2   C1   118.91  3.000
 ILF  C8    C2   C1   121.93  3.000
 ILF  H8    C8   C9   120.51  3.000
 ILF  H8    C8   C2   119.85  3.000
 ILF  C9    C8   C2   119.61  3.000
 ILF  C11   C9   C10  120.98  3.000
 ILF  C11   C9   C8   118.85  3.000
 ILF  C10   C9   C8   120.17  3.000
 ILF  C20   C10  C13  119.15  3.000
 ILF  C20   C10  C9   120.07  3.000
 ILF  C13   C10  C9   120.79  3.000
 ILF  H11   C11  C12  119.29  3.000
 ILF  H11   C11  C9   120.06  3.000
 ILF  C12   C11  C9   120.64  3.000
 ILF  H12   C12  C11  119.78  3.000
 ILF  H12   C12  C1   119.61  3.000
 ILF  C11   C12  C1   120.61  3.000
 ILF  H13   C13  C14  119.37  3.000
 ILF  H13   C13  C10  121.20  3.000
 ILF  C14   C13  C10  119.40  3.000
 ILF  F15   C14  C16  117.95  3.000
 ILF  F15   C14  C13  118.95  3.000
 ILF  C16   C14  C13  123.08  3.000
 ILF  C18   C16  N17  121.68  3.000
 ILF  C18   C16  C14  115.79  3.000
 ILF  N17   C16  C14  122.54  3.000
 ILF  H20   C20  C18  119.21  3.000
 ILF  H20   C20  C10  121.36  3.000
 ILF  C18   C20  C10  119.37  3.000
 ILF  O23   C21  N17  123.27  3.000
 ILF  O23   C21  C22  120.02  3.000
 ILF  N17   C21  C22  116.71  3.000
 ILF  C27   C22  C24  111.98  3.000
 ILF  C27   C22  C21  130.38  3.000
 ILF  C24   C22  C21  117.64  3.000
 ILF  H24   C24  C25  123.59  3.000
 ILF  H24   C24  C22  123.31  3.000
 ILF  C25   C24  C22  113.10  3.000
 ILF  C28   C27  S26  113.34  3.000
 ILF  C28   C27  C22  135.89  3.000
 ILF  S26   C27  C22  110.77  3.000
 ILF  C4    O3   C2   117.54  3.000
 ILF  F7    C4   F6   108.07  3.000
 ILF  F7    C4   F5   108.60  3.000
 ILF  F6    C4   F5   106.77  3.000
 ILF  F7    C4   O3   107.86  3.000
 ILF  F6    C4   O3   112.84  3.000
 ILF  F5    C4   O3   112.55  3.000
 ILF  HN17  N17  C21  117.61  3.000
 ILF  HN17  N17  C16  121.32  3.000
 ILF  C21   N17  C16  120.72  3.000
 ILF  F19   C18  C20  118.91  3.000
 ILF  F19   C18  C16  117.91  3.000
 ILF  C20   C18  C16  123.18  3.000
 ILF  H25   C25  S26  121.07  3.000
 ILF  H25   C25  C24  127.45  3.000
 ILF  S26   C25  C24  111.48  3.000
 ILF  C25   S26  C27   92.67  3.000
 ILF  O30   C28  O29  126.53  3.000
 ILF  O30   C28  C27  114.87  3.000
 ILF  O29   C28  C27  118.60  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
 ILF  CONST_01  C9   C8   C2   C1      0.00   0.0  0
 ILF  CONST_02  C9   C11  C12  C1      0.00   0.0  0
 ILF  CONST_03  C11  C12  C1   C2      0.00   0.0  0
 ILF  CONST_04  C10  C9   C8   C2    180.00   0.0  0
 ILF  CONST_05  C11  C9   C8   C2      0.00   0.0  0
 ILF  CONST_06  C12  C1   C2   C8      0.00   0.0  0
 ILF  CONST_09  C12  C11  C9   C8      0.00   0.0  0
 ILF  CONST_10  C14  C13  C10  C9    180.00   0.0  0
 ILF  CONST_11  C18  C20  C10  C9    180.00   0.0  0
 ILF  CONST_12  C12  C11  C9   C10   180.00   0.0  0
 ILF  CONST_13  C16  C14  C13  C10     0.00   0.0  0
 ILF  CONST_14  C16  C18  C20  C10     0.00   0.0  0
 ILF  CONST_17  C18  C20  C10  C13     0.00   0.0  0
 ILF  CONST_18  C18  C16  C14  C13     0.00   0.0  0
 ILF  CONST_19  C20  C10  C13  C14     0.00   0.0  0
 ILF  CONST_20  C20  C18  C16  C14     0.00   0.0  0
 ILF  CONST_21  S26  C25  C24  C22     0.00   0.0  0
 ILF  CONST_22  C25  S26  C27  C22     0.00   0.0  0
 ILF  CONST_23  S26  C27  C22  C24     0.00   0.0  0
 ILF  CONST_24  C27  S26  C25  C24     0.00   0.0  0
 ILF  CONST_25  C25  C24  C22  C27     0.00   0.0  0
 ILF  CONST_26  O3   C2   C8   C9    180.00   0.0  0
 ILF  CONST_27  F15  C14  C13  C10   180.00   0.0  0
 ILF  CONST_28  F19  C18  C20  C10   180.00   0.0  0
 ILF  CONST_29  O3   C2   C1   C12   180.00   0.0  0
 ILF  CONST_30  N17  C16  C14  C13   180.00   0.0  0
 ILF  CONST_31  F19  C18  C16  C14   180.00   0.0  0
 ILF  CONST_32  N17  C16  C18  C20   180.00   0.0  0
 ILF  CONST_33  C25  C24  C22  C21   180.00   0.0  0
 ILF  CONST_34  S26  C27  C22  C21   180.00   0.0  0
 ILF  CONST_35  C28  C27  C22  C24   180.00   0.0  0
 ILF  CONST_36  C18  C16  C14  F15   180.00   0.0  0
 ILF  CONST_37  C28  C27  S26  C25   180.00   0.0  0
 ILF  CONST_38  H8   C8   C2   C1    180.00   0.0  0
 ILF  CONST_39  H11  C11  C12  C1    180.00   0.0  0
 ILF  CONST_40  H12  C12  C1   C2    180.00   0.0  0
 ILF  CONST_41  H1   C1   C2   C8    180.00   0.0  0
 ILF  CONST_42  H13  C13  C10  C9      0.00   0.0  0
 ILF  CONST_43  H20  C20  C10  C9      0.00   0.0  0
 ILF  CONST_44  H25  C25  C24  C22   180.00   0.0  0
 ILF  CONST_45  H24  C24  C22  C27   180.00   0.0  0
 ILF  CONST_46  C22  C21  N17  C16   180.00   0.0  0
 ILF  CONST_50  O23  C21  N17  C16     0.00   0.0  0
 ILF  Var_01    O29  C28  C27  C22     0.31  30.0  2
 ILF  Var_02    N17  C21  C22  C24  -176.99  30.0  2
 ILF  Var_03    F5   C4   O3   C2    -54.91  30.0  3

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
 ILF  plan-1  C21   0.020
 ILF  plan-1  C22   0.020
 ILF  plan-1  C24   0.020
 ILF  plan-1  C27   0.020
 ILF  plan-1  C25   0.020
 ILF  plan-1  S26   0.020
 ILF  plan-1  C28   0.020
 ILF  plan-1  H24   0.020
 ILF  plan-1  H25   0.020
 ILF  plan-2  C1    0.020
 ILF  plan-2  C2    0.020
 ILF  plan-2  C8    0.020
 ILF  plan-2  C9    0.020
 ILF  plan-2  C10   0.020
 ILF  plan-2  C11   0.020
 ILF  plan-2  C12   0.020
 ILF  plan-2  O3    0.020
 ILF  plan-2  H1    0.020
 ILF  plan-2  H8    0.020
 ILF  plan-2  H11   0.020
 ILF  plan-2  H12   0.020
 ILF  plan-3  C9    0.020
 ILF  plan-3  C10   0.020
 ILF  plan-3  C13   0.020
 ILF  plan-3  C14   0.020
 ILF  plan-3  C16   0.020
 ILF  plan-3  C20   0.020
 ILF  plan-3  F15   0.020
 ILF  plan-3  N17   0.020
 ILF  plan-3  C18   0.020
 ILF  plan-3  F19   0.020
 ILF  plan-3  H13   0.020
 ILF  plan-3  H20   0.020
 ILF  plan-4  C16   0.020
 ILF  plan-4  C21   0.020
 ILF  plan-4  C22   0.020
 ILF  plan-4  N17   0.020
 ILF  plan-4  O23   0.020
 ILF  plan-4  HN17  0.020
 ILF  plan-5  C27   0.020
 ILF  plan-5  C28   0.020
 ILF  plan-5  O29   0.020
 ILF  plan-5  O30   0.020

