# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 18:45:36 2022
#   Inital geometry file: a 87 line input string
#   Ligand name: (1R)-4-(3,5-difluorophenoxy)-7-(trifluoromethyl)-2,3-dihydro-1H-inden-1-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCc2c(Oc3cc(F)cc(F)c3)ccc(c12)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
 ULG  ULG  (1R)-4-(3,5-difluorophenoxy)-7-(trifluoromethyl)-2,3-dihydro-1H-inden-1-ol  ligand  34  23  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ULG
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
 ULG  F4   F  F     0  -0.319  28.5129   0.1265   -9.4206
 ULG  C15  C  CT    0   1.058  27.6080  -0.7823   -9.0154
 ULG  F2   F  F     0  -0.311  27.8761  -1.9075   -9.6934
 ULG  F3   F  F     0  -0.296  27.8665  -1.0316   -7.7313
 ULG  C3   C  CR6   0  -0.266  26.2035  -0.3158   -9.2427
 ULG  C2   C  CR16  0  -0.311  25.3097  -0.2302   -8.1798
 ULG  C1   C  CR16  0  -0.303  24.0005   0.1778   -8.3898
 ULG  C12  C  CR56  0   0.112  25.7663   0.0107  -10.5234
 ULG  C11  C  CR15  0  -0.065  26.5314   0.0902  -11.8360
 ULG  O1   O  OH1   0  -0.655  27.1633   1.3459  -11.9717
 ULG  C13  C  CR56  0   0.043  24.4512   0.4063  -10.7383
 ULG  C14  C  CH2   0  -0.484  24.1936   0.6826  -12.1905
 ULG  C10  C  CH2   0  -0.474  25.4012   0.0161  -12.8612
 ULG  C    C  CR6   0   0.256  23.5769   0.4998   -9.6686
 ULG  O    O  O2    0  -0.499  22.2942   0.9445   -9.8608
 ULG  C7   C  CR6   0   0.404  21.3639   0.0988  -10.3683
 ULG  C6   C  CR16  0  -0.498  20.1372   0.6710  -10.6938
 ULG  C5   C  CR6   0   0.554  19.1545  -0.1527  -11.2001
 ULG  F    F  F     0  -0.305  17.9690   0.3816  -11.5106
 ULG  C8   C  CR16  0  -0.504  21.5965  -1.2594  -10.5517
 ULG  C9   C  CR6   0   0.562  20.5668  -2.0217  -11.0710
 ULG  F1   F  F     0  -0.305  20.7816  -3.3284  -11.2531
 ULG  C4   C  CR16  0  -0.576  19.3318  -1.5084  -11.4085
 ULG  H1   H  HCR6  0   0.277  25.6133  -0.4863   -7.1745
 ULG  H2   H  HCR6  0   0.283  23.3117   0.2408   -7.5575
 ULG  H3   H  HCR5  0   0.236  27.2444  -0.7293  -11.9695
 ULG  H4   H  HOH1  0   0.446  27.9043   1.3949  -11.3609
 ULG  H5   H  HCH2  0   0.267  24.1648   1.7599  -12.3733
 ULG  H6   H  HCH2  0   0.260  23.2466   0.2732  -12.5425
 ULG  H7   H  HCH2  0   0.254  25.1720  -1.0337  -13.0520
 ULG  H8   H  HCH2  0   0.253  25.6827   0.4715  -13.8103
 ULG  H9   H  HCR6  0   0.297  19.9617   1.7292  -10.5518
 ULG  H10  H  HCR6  0   0.307  22.5390  -1.7273  -10.2999
 ULG  H11  H  HCR6  0   0.302  18.5449  -2.1308  -11.8124

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
 ULG  C10  C14  single    1.534  0.020  1.534
 ULG  C10  C11  single    1.528  0.020  1.528
 ULG  C14  C13  single    1.500  0.020  1.500
 ULG  C11  O1   single    1.412  0.020  1.412
 ULG  C11  C12  single    1.521  0.020  1.521
 ULG  O    C7   single    1.356  0.020  1.356
 ULG  O    C    single    1.371  0.020  1.371
 ULG  C13  C12  aromatic  1.390  0.020  1.390
 ULG  C13  C    aromatic  1.385  0.020  1.385
 ULG  C8   C7   aromatic  1.390  0.020  1.390
 ULG  C8   C9   aromatic  1.382  0.020  1.382
 ULG  C7   C6   aromatic  1.392  0.020  1.392
 ULG  F1   C9   single    1.337  0.020  1.337
 ULG  C12  C3   aromatic  1.392  0.020  1.392
 ULG  C9   C4   aromatic  1.379  0.020  1.379
 ULG  C    C1   aromatic  1.385  0.020  1.385
 ULG  C6   C5   aromatic  1.379  0.020  1.379
 ULG  C4   C5   aromatic  1.383  0.020  1.383
 ULG  C5   F    single    1.337  0.020  1.337
 ULG  C1   C2   aromatic  1.387  0.020  1.387
 ULG  C3   C2   aromatic  1.391  0.020  1.391
 ULG  C3   C15  single    1.497  0.020  1.497
 ULG  F2   C15  single    1.341  0.020  1.341
 ULG  F4   C15  single    1.345  0.020  1.345
 ULG  C15  F3   single    1.333  0.020  1.333
 ULG  C2   H1   single    0.930  0.020  1.080
 ULG  C1   H2   single    0.930  0.020  1.080
 ULG  C11  H3   single    0.970  0.020  1.090
 ULG  O1   H4   single    0.850  0.020  0.980
 ULG  C14  H5   single    0.970  0.020  1.090
 ULG  C14  H6   single    0.970  0.020  1.090
 ULG  C10  H7   single    0.970  0.020  1.090
 ULG  C10  H8   single    0.970  0.020  1.090
 ULG  C6   H9   single    0.930  0.020  1.080
 ULG  C8   H10  single    0.930  0.020  1.080
 ULG  C4   H11  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
 ULG  C3   C15  F3   112.72  3.000
 ULG  F3   C15  F2   106.93  3.000
 ULG  C3   C15  F2   111.86  3.000
 ULG  F3   C15  F4   106.62  3.000
 ULG  F2   C15  F4   106.27  3.000
 ULG  C3   C15  F4   112.02  3.000
 ULG  C12  C3   C2   119.12  3.000
 ULG  C2   C3   C15  120.38  3.000
 ULG  C12  C3   C15  120.49  3.000
 ULG  H1   C2   C1   118.40  3.000
 ULG  H1   C2   C3   121.03  3.000
 ULG  C1   C2   C3   120.58  3.000
 ULG  H2   C1   C    120.12  3.000
 ULG  H2   C1   C2   120.09  3.000
 ULG  C    C1   C2   119.79  3.000
 ULG  C13  C12  C11  109.12  3.000
 ULG  C13  C12  C3   120.41  3.000
 ULG  C11  C12  C3   130.39  3.000
 ULG  H3   C11  C10  111.34  3.000
 ULG  H3   C11  O1   111.25  3.000
 ULG  C10  C11  O1   108.04  3.000
 ULG  H3   C11  C12  113.19  3.000
 ULG  O1   C11  C12  110.76  3.000
 ULG  C10  C11  C12  101.80  3.000
 ULG  H4   O1   C11  109.21  3.000
 ULG  C    C13  C14  128.81  3.000
 ULG  C    C13  C12  119.81  3.000
 ULG  C14  C13  C12  111.38  3.000
 ULG  H6   C14  H5   107.06  3.000
 ULG  H6   C14  C10  112.31  3.000
 ULG  H5   C14  C10  112.08  3.000
 ULG  H6   C14  C13  113.11  3.000
 ULG  H5   C14  C13  110.36  3.000
 ULG  C10  C14  C13  102.01  3.000
 ULG  H8   C10  H7   107.69  3.000
 ULG  H8   C10  C14  113.75  3.000
 ULG  H7   C10  C14  109.22  3.000
 ULG  H8   C10  C11  111.91  3.000
 ULG  H7   C10  C11  108.62  3.000
 ULG  C14  C10  C11  105.54  3.000
 ULG  O    C    C13  120.29  3.000
 ULG  C13  C    C1   120.29  3.000
 ULG  O    C    C1   119.40  3.000
 ULG  C7   O    C    119.47  3.000
 ULG  C8   C7   C6   121.21  3.000
 ULG  C6   C7   O    115.83  3.000
 ULG  C8   C7   O    122.96  3.000
 ULG  H9   C6   C5   121.13  3.000
 ULG  H9   C6   C7   120.95  3.000
 ULG  C5   C6   C7   117.93  3.000
 ULG  C4   C5   F    118.06  3.000
 ULG  F    C5   C6   118.59  3.000
 ULG  C4   C5   C6   123.34  3.000
 ULG  H10  C8   C9   119.86  3.000
 ULG  H10  C8   C7   122.52  3.000
 ULG  C9   C8   C7   117.62  3.000
 ULG  C4   C9   F1   118.32  3.000
 ULG  C4   C9   C8   123.62  3.000
 ULG  F1   C9   C8   118.06  3.000
 ULG  H11  C4   C9   121.91  3.000
 ULG  H11  C4   C5   121.81  3.000
 ULG  C9   C4   C5   116.27  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
 ULG  CONST_01  C    C13  C12  C3     0.00   0.0  0
 ULG  CONST_02  C    C1   C2   C3     0.00   0.0  0
 ULG  CONST_03  C13  C    C1   C2     0.00   0.0  0
 ULG  CONST_04  C13  C12  C3   C2     0.00   0.0  0
 ULG  CONST_05  C12  C13  C    C1     0.00   0.0  0
 ULG  CONST_06  C12  C3   C2   C1     0.00   0.0  0
 ULG  CONST_07  C4   C9   C8   C7     0.00   0.0  0
 ULG  CONST_08  C4   C5   C6   C7     0.00   0.0  0
 ULG  CONST_09  C9   C8   C7   C6     0.00   0.0  0
 ULG  CONST_10  C9   C4   C5   C6     0.00   0.0  0
 ULG  CONST_11  C8   C7   C6   C5     0.00   0.0  0
 ULG  CONST_12  C8   C9   C4   C5     0.00   0.0  0
 ULG  CONST_13  C11  C12  C3   C15    0.00   0.0  0
 ULG  CONST_14  C13  C12  C3   C15  180.00   0.0  0
 ULG  CONST_15  C1   C2   C3   C15  180.00   0.0  0
 ULG  CONST_16  O    C    C1   C2   180.00   0.0  0
 ULG  CONST_17  O    C    C13  C12  180.00   0.0  0
 ULG  CONST_18  O    C    C13  C14    0.00   0.0  0
 ULG  CONST_19  C9   C8   C7   O    180.00   0.0  0
 ULG  CONST_20  C5   C6   C7   O    180.00   0.0  0
 ULG  CONST_21  F1   C9   C8   C7   180.00   0.0  0
 ULG  CONST_22  F    C5   C6   C7   180.00   0.0  0
 ULG  CONST_23  F1   C9   C4   C5   180.00   0.0  0
 ULG  CONST_24  C9   C4   C5   F    180.00   0.0  0
 ULG  CONST_25  H2   C1   C2   C3   180.00   0.0  0
 ULG  CONST_26  H1   C2   C3   C12  180.00   0.0  0
 ULG  CONST_27  H10  C8   C7   C6   180.00   0.0  0
 ULG  CONST_28  H11  C4   C5   C6   180.00   0.0  0
 ULG  CONST_29  H9   C6   C7   C8   180.00   0.0  0
 ULG  Var_01    C10  C14  C13  C12   15.71  30.0  1
 ULG  Var_02    C13  C14  C10  C11  -29.12  30.0  1
 ULG  Var_03    C8   C7   O    C      8.42  30.0  2
 ULG  Var_04    C12  C3   C15  F4    58.75  30.0  3

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
 ULG  chir_01  C11  C10  O1  C12  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
 ULG  plan-1  O    0.020
 ULG  plan-1  C7   0.020
 ULG  plan-1  C6   0.020
 ULG  plan-1  C5   0.020
 ULG  plan-1  F    0.020
 ULG  plan-1  C8   0.020
 ULG  plan-1  C9   0.020
 ULG  plan-1  F1   0.020
 ULG  plan-1  C4   0.020
 ULG  plan-1  H9   0.020
 ULG  plan-1  H10  0.020
 ULG  plan-1  H11  0.020
 ULG  plan-2  C15  0.020
 ULG  plan-2  C3   0.020
 ULG  plan-2  C2   0.020
 ULG  plan-2  C1   0.020
 ULG  plan-2  C12  0.020
 ULG  plan-2  C11  0.020
 ULG  plan-2  C13  0.020
 ULG  plan-2  C14  0.020
 ULG  plan-2  C    0.020
 ULG  plan-2  O    0.020
 ULG  plan-2  H1   0.020
 ULG  plan-2  H2   0.020

