# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 18:59:05 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-{[3,5-difluoro-3'-(trifluoromethoxy)biphenyl-4-yl]carbamoyl}cyclopent-1-ene-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(CCC1)C(=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
 ILB  ILB  '2-{[3,5-difluoro-3'-(trifluoromethoxy)biphenyl-4-yl]carbamoyl}cyclopent-1-ene-1-carboxylic acid'  ligand  43  30  .  2021-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_ILB
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
 ILB  C1    C  CR16   0  -0.238   4.6147  -0.5263  -2.4664
 ILB  C2    C  CR16   0  -0.308   5.4969  -0.2367  -1.4357
 ILB  C3    C  CR6    0   0.339   4.9795   0.2272  -0.2387
 ILB  C7    C  CR16   0  -0.298   3.2503  -0.3530  -2.2968
 ILB  C8    C  CR16   0  -0.499   0.8116   1.4410  -0.2192
 ILB  C9    C  CR6    0   0.562  -0.5492   1.6103  -0.0773
 ILB  C11   C  CR6    0  -0.024  -1.4829   0.7343  -0.6152
 ILB  C13   C  CR6    0   0.575  -0.9704  -0.3537  -1.3113
 ILB  C15   C  CR16   0  -0.503   0.3817  -0.5739  -1.4618
 ILB  C16   C  C      0   0.506  -3.6581   0.0858   0.2258
 ILB  C19   C  CR5    0  -0.009  -6.0241  -0.3151   0.8138
 ILB  C20   C  CH2    0  -0.485  -7.3848   0.2886   0.6085
 ILB  C21   C  CH2    0  -0.455  -7.0886   1.7334   0.1871
 ILB  C22   C  CH2    0  -0.506  -5.6577   1.7025  -0.3698
 ILB  C27   C  CT     0   1.074   6.1975  -0.3942   1.6570
 ILB  C4    C  CR16   0  -0.357   3.6227   0.4161  -0.0518
 ILB  C5    C  CR6    0   0.091   2.7398   0.1266  -1.0908
 ILB  C6    C  CR6    0   0.115   1.2887   0.3332  -0.9166
 ILB  F14   F  F      0  -0.295  -1.8299  -1.2136  -1.8579
 ILB  C17   C  CR5    0  -0.094  -5.0754   0.4618   0.2696
 ILB  O18   O  O      0  -0.472  -3.2004  -0.9152   0.7525
 ILB  O24   O  OC    -1  -0.600  -5.7300  -1.6042   2.7350
 ILB  O25   O  O      0  -0.601  -6.0642  -2.6468   0.7838
 ILB  O26   O  O2     0  -0.524   5.8499   0.5664   0.7913
 ILB  F28   F  F      0  -0.299   6.8034  -1.4265   1.0675
 ILB  F29   F  F      0  -0.276   7.0359   0.1366   2.5320
 ILB  F30   F  F      0  -0.299   5.1530  -0.8911   2.3222
 ILB  H1    H  HCR6   0   0.275   4.9977  -0.8831  -3.4126
 ILB  H2    H  HCR6   0   0.284   6.5637  -0.3539  -1.5713
 ILB  H7    H  HCR6   0   0.268   2.5822  -0.5652  -3.1214
 ILB  H8    H  HCR6   0   0.287   1.4850   2.1768   0.2009
 ILB  H15   H  HCR6   0   0.285   0.7195  -1.4540  -1.9929
 ILB  H201  H  HCH2   0   0.251  -7.9076  -0.2719  -0.1741
 ILB  H202  H  HCH2   0   0.249  -8.0108   0.2245   1.5012
 ILB  H211  H  HCH2   0   0.239  -7.1201   2.3791   1.0660
 ILB  H212  H  HCH2   0   0.238  -7.8106   2.1246  -0.5290
 ILB  H221  H  HCH2   0   0.239  -5.1150   2.6178  -0.1163
 ILB  H222  H  HCH2   0   0.244  -5.6480   1.6223  -1.4625
 ILB  H4    H  HCR6   0   0.282   3.2545   0.7820   0.8982
 ILB  HN12  H  HNH1   0   0.418  -3.2353   1.8163  -0.8168
 ILB  F10   F  F      0  -0.297  -1.0065   2.6727   0.5909
 ILB  N12   N  NH1    0  -0.752  -2.8565   0.9478  -0.4728
 ILB  C23   C  C      0   0.369  -5.8990  -1.6483   1.5050

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
 ILB  C1   C2    aromatic  1.387  0.020  1.387
 ILB  C1   C7    aromatic  1.386  0.020  1.386
 ILB  C1   H1    single    0.930  0.020  1.080
 ILB  C2   C3    aromatic  1.384  0.020  1.384
 ILB  C2   H2    single    0.930  0.020  1.080
 ILB  C3   C4    aromatic  1.383  0.020  1.383
 ILB  C3   O26   single    1.391  0.020  1.391
 ILB  C7   C5    aromatic  1.395  0.020  1.395
 ILB  C7   H7    single    0.930  0.020  1.080
 ILB  C8   C9    aromatic  1.379  0.020  1.379
 ILB  C8   C6    aromatic  1.393  0.020  1.393
 ILB  C8   H8    single    0.930  0.020  1.080
 ILB  C9   C11   aromatic  1.389  0.020  1.389
 ILB  C9   F10   single    1.336  0.020  1.336
 ILB  C11  C13   aromatic  1.390  0.020  1.390
 ILB  C11  N12   single    1.397  0.020  1.397
 ILB  C13  C15   aromatic  1.378  0.020  1.378
 ILB  C13  F14   single    1.333  0.020  1.333
 ILB  C15  C6    aromatic  1.394  0.020  1.394
 ILB  C15  H15   single    0.930  0.020  1.080
 ILB  C16  N12   single    1.369  0.020  1.369
 ILB  C16  C17   single    1.467  0.020  1.467
 ILB  C16  O18   double    1.220  0.020  1.220
 ILB  C19  C20   single    1.503  0.020  1.503
 ILB  C19  C17   double    1.342  0.020  1.342
 ILB  C19  C23   single    1.507  0.020  1.507
 ILB  C20  C21   single    1.534  0.020  1.534
 ILB  C20  H201  single    0.970  0.020  1.090
 ILB  C20  H202  single    0.970  0.020  1.090
 ILB  C21  C22   single    1.536  0.020  1.536
 ILB  C21  H211  single    0.970  0.020  1.090
 ILB  C21  H212  single    0.970  0.020  1.090
 ILB  C22  C17   single    1.512  0.020  1.512
 ILB  C22  H221  single    0.970  0.020  1.090
 ILB  C22  H222  single    0.970  0.020  1.090
 ILB  C27  O26   single    1.339  0.020  1.339
 ILB  C27  F28   single    1.334  0.020  1.334
 ILB  C27  F29   single    1.323  0.020  1.323
 ILB  C27  F30   single    1.334  0.020  1.334
 ILB  C4   C5    aromatic  1.394  0.020  1.394
 ILB  C4   H4    single    0.930  0.020  1.080
 ILB  C5   C6    single    1.476  0.020  1.476
 ILB  N12  HN12  single    0.860  0.020  1.020
 ILB  C23  O24   deloc     1.242  0.020  1.242
 ILB  C23  O25   deloc     1.243  0.020  1.243

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
 ILB  H1    C1   C7    119.81  3.000
 ILB  H1    C1   C2    119.59  3.000
 ILB  C7    C1   C2    120.60  3.000
 ILB  H2    C2   C3    120.89  3.000
 ILB  H2    C2   C1    120.75  3.000
 ILB  C3    C2   C1    118.35  3.000
 ILB  O26   C3   C4    118.74  3.000
 ILB  O26   C3   C2    119.23  3.000
 ILB  C4    C3   C2    121.97  3.000
 ILB  H7    C7   C5    120.02  3.000
 ILB  H7    C7   C1    119.34  3.000
 ILB  C5    C7   C1    120.61  3.000
 ILB  H8    C8   C6    121.45  3.000
 ILB  H8    C8   C9    119.39  3.000
 ILB  C6    C8   C9    119.16  3.000
 ILB  F10   C9   C11   117.73  3.000
 ILB  F10   C9   C8    119.15  3.000
 ILB  C11   C9   C8    123.12  3.000
 ILB  N12   C11  C13   122.23  3.000
 ILB  N12   C11  C9    121.67  3.000
 ILB  C13   C11  C9    116.10  3.000
 ILB  F14   C13  C15   119.00  3.000
 ILB  F14   C13  C11   118.20  3.000
 ILB  C15   C13  C11   122.80  3.000
 ILB  H15   C15  C6    121.21  3.000
 ILB  H15   C15  C13   119.33  3.000
 ILB  C6    C15  C13   119.45  3.000
 ILB  O18   C16  C17   124.04  3.000
 ILB  O18   C16  N12   121.15  3.000
 ILB  C17   C16  N12   114.81  3.000
 ILB  C23   C19  C17   129.77  3.000
 ILB  C23   C19  C20   119.56  3.000
 ILB  C17   C19  C20   110.62  3.000
 ILB  H202  C20  H201  106.28  3.000
 ILB  H202  C20  C21   112.99  3.000
 ILB  H201  C20  C21   112.20  3.000
 ILB  H202  C20  C19   112.57  3.000
 ILB  H201  C20  C19   108.92  3.000
 ILB  C21   C20  C19   103.96  3.000
 ILB  H212  C21  H211  107.33  3.000
 ILB  H212  C21  C22   112.72  3.000
 ILB  H211  C21  C22   109.32  3.000
 ILB  H212  C21  C20   113.01  3.000
 ILB  H211  C21  C20   109.30  3.000
 ILB  C22   C21  C20   105.10  3.000
 ILB  H222  C22  H221  106.73  3.000
 ILB  H222  C22  C17   111.00  3.000
 ILB  H221  C22  C17   113.42  3.000
 ILB  H222  C22  C21   111.80  3.000
 ILB  H221  C22  C21   111.18  3.000
 ILB  C17   C22  C21   102.82  3.000
 ILB  F30   C27  F29   108.40  3.000
 ILB  F30   C27  F28   106.71  3.000
 ILB  F29   C27  F28   108.35  3.000
 ILB  F30   C27  O26   112.72  3.000
 ILB  F29   C27  O26   107.72  3.000
 ILB  F28   C27  O26   112.79  3.000
 ILB  H4    C4   C5    120.59  3.000
 ILB  H4    C4   C3    119.90  3.000
 ILB  C5    C4   C3    119.50  3.000
 ILB  C6    C5   C4    120.38  3.000
 ILB  C6    C5   C7    120.67  3.000
 ILB  C4    C5   C7    118.96  3.000
 ILB  C5    C6   C15   120.16  3.000
 ILB  C5    C6   C8    120.47  3.000
 ILB  C15   C6   C8    119.37  3.000
 ILB  C22   C17  C19   111.99  3.000
 ILB  C22   C17  C16   124.72  3.000
 ILB  C19   C17  C16   123.15  3.000
 ILB  C27   O26  C3    117.80  3.000
 ILB  HN12  N12  C16   119.78  3.000
 ILB  HN12  N12  C11   117.79  3.000
 ILB  C16   N12  C11   122.10  3.000
 ILB  O25   C23  O24   128.40  3.000
 ILB  O25   C23  C19   115.70  3.000
 ILB  O24   C23  C19   115.72  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
 ILB  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 ILB  CONST_02  C4   C5   C7   C1     0.00   0.0  0
 ILB  CONST_03  C6   C5   C7   C1   180.00   0.0  0
 ILB  CONST_04  C5   C7   C1   C2     0.00   0.0  0
 ILB  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 ILB  CONST_06  C7   C1   C2   C3     0.00   0.0  0
 ILB  CONST_07  C7   C5   C4   C3     0.00   0.0  0
 ILB  CONST_08  C6   C5   C4   C3   180.00   0.0  0
 ILB  CONST_11  C13  C11  C9   C8     0.00   0.0  0
 ILB  CONST_12  C13  C15  C6   C8     0.00   0.0  0
 ILB  CONST_14  C15  C6   C8   C9     0.00   0.0  0
 ILB  CONST_15  C5   C6   C8   C9   180.00   0.0  0
 ILB  CONST_16  C15  C13  C11  C9     0.00   0.0  0
 ILB  CONST_17  C6   C8   C9   C11    0.00   0.0  0
 ILB  CONST_18  C6   C15  C13  C11    0.00   0.0  0
 ILB  CONST_19  C5   C6   C15  C13  180.00   0.0  0
 ILB  CONST_21  O26  C3   C2   C1   180.00   0.0  0
 ILB  CONST_22  N12  C11  C9   C8   180.00   0.0  0
 ILB  CONST_23  F14  C13  C11  C9   180.00   0.0  0
 ILB  CONST_24  F10  C9   C11  C13  180.00   0.0  0
 ILB  CONST_25  N12  C11  C13  C15  180.00   0.0  0
 ILB  CONST_26  O26  C3   C4   C5   180.00   0.0  0
 ILB  CONST_27  F10  C9   C8   C6   180.00   0.0  0
 ILB  CONST_28  F14  C13  C15  C6   180.00   0.0  0
 ILB  CONST_29  H7   C7   C1   C2   180.00   0.0  0
 ILB  CONST_30  H4   C4   C3   C2   180.00   0.0  0
 ILB  CONST_31  H1   C1   C2   C3   180.00   0.0  0
 ILB  CONST_32  H2   C2   C1   C7   180.00   0.0  0
 ILB  CONST_33  H15  C15  C6   C8   180.00   0.0  0
 ILB  CONST_34  H8   C8   C9   C11  180.00   0.0  0
 ILB  CONST_35  C17  C16  N12  C11  180.00   0.0  0
 ILB  CONST_39  O18  C16  N12  C11    0.00   0.0  0
 ILB  Var_01    C22  C21  C20  C19   22.59  30.0  1
 ILB  Var_02    C21  C22  C17  C19   13.98  30.0  1
 ILB  Var_03    C22  C17  C19  C20    0.42  30.0  1
 ILB  Var_04    C17  C22  C21  C20  -22.07  30.0  1
 ILB  Var_05    C17  C19  C20  C21  -14.73  30.0  1
 ILB  Var_06    N12  C16  C17  C19  174.44  30.0  2
 ILB  Var_07    O24  C23  C19  C20  -92.19  30.0  2
 ILB  Var_08    C4   C3   O26  C27   93.05  30.0  3
 ILB  Var_09    F28  C27  O26  C3    59.63  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
 ILB  plan-1  C1    0.020
 ILB  plan-1  C2    0.020
 ILB  plan-1  C3    0.020
 ILB  plan-1  C7    0.020
 ILB  plan-1  C4    0.020
 ILB  plan-1  C5    0.020
 ILB  plan-1  C6    0.020
 ILB  plan-1  O26   0.020
 ILB  plan-1  H1    0.020
 ILB  plan-1  H2    0.020
 ILB  plan-1  H7    0.020
 ILB  plan-1  H4    0.020
 ILB  plan-2  C8    0.020
 ILB  plan-2  C9    0.020
 ILB  plan-2  C11   0.020
 ILB  plan-2  C13   0.020
 ILB  plan-2  C15   0.020
 ILB  plan-2  C5    0.020
 ILB  plan-2  C6    0.020
 ILB  plan-2  F14   0.020
 ILB  plan-2  H8    0.020
 ILB  plan-2  H15   0.020
 ILB  plan-2  F10   0.020
 ILB  plan-2  N12   0.020
 ILB  plan-3  C11   0.020
 ILB  plan-3  C16   0.020
 ILB  plan-3  C17   0.020
 ILB  plan-3  O18   0.020
 ILB  plan-3  HN12  0.020
 ILB  plan-3  N12   0.020
 ILB  plan-4  C19   0.020
 ILB  plan-4  O24   0.020
 ILB  plan-4  O25   0.020
 ILB  plan-4  C23   0.020

