# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 11:18:49 2022
#   Inital geometry file: a 91 line input string
#   Ligand name: 3-fluoro-5-{[(7R)-7-hydroxy-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl]oxy}benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CCc2c(Oc3cc(F)cc(c3)C#N)cnc(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
 ULS  ULS  3-fluoro-5-{[(7R)-7-hydroxy-1-(trifluoromethyl)-6,7-dihydro-5H-cyclopenta[c]pyridin-4-yl]oxy}benzonitrile  ligand  34  24  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_ULS
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
 ULS  N2   N  NS    0  -0.233  18.2549   2.0168   -8.6292
 ULS  C16  C  CSP   0   0.067  18.8309   1.1825   -9.1746
 ULS  C15  C  CR6   0   0.026  19.5484   0.1484   -9.8508
 ULS  C10  C  CR16  0  -0.402  18.9768  -1.1170   -9.9618
 ULS  C14  C  CR16  0  -0.296  20.8005   0.4334  -10.3879
 ULS  C13  C  CR6   0   0.335  21.4774  -0.5774  -11.0481
 ULS  C12  C  CR16  0  -0.436  20.9406  -1.8488  -11.1773
 ULS  C11  C  CR6   0   0.561  19.6944  -2.0881  -10.6287
 ULS  F4   F  F     0  -0.296  19.1677  -3.3074  -10.7474
 ULS  O2   O  O2    0  -0.497  22.6856  -0.3032  -11.6281
 ULS  C2   C  CR6   0   0.236  23.8143  -0.3769  -10.8824
 ULS  C3   C  CR16  0  -0.160  23.8759  -0.8994   -9.5925
 ULS  N1   N  N     0  -0.409  25.0099  -0.9792   -8.9143
 ULS  C8   C  CR56  0   0.134  24.9875   0.0800  -11.4595
 ULS  C9   C  CH2   0  -0.485  25.2119   0.6559  -12.8230
 ULS  C5   C  CH2   0  -0.479  26.7398   0.5824  -12.9545
 ULS  C7   C  CR56  0   0.063  26.1660   0.0167  -10.7331
 ULS  C6   C  CR15  0  -0.060  27.2860   0.6688  -11.5279
 ULS  O1   O  OH1   0  -0.652  27.4072   2.0321  -11.1844
 ULS  C1   C  CR6   0  -0.108  26.1282  -0.5329   -9.4590
 ULS  C4   C  CT    0   1.045  27.3787  -0.7088   -8.6412
 ULS  F1   F  F     0  -0.293  27.1239  -1.0997   -7.3984
 ULS  F2   F  F     0  -0.312  28.1952  -1.6218   -9.1871
 ULS  F3   F  F     0  -0.317  28.0828   0.4330   -8.5645
 ULS  H1   H  HCR6  0   0.310  18.0025  -1.3341   -9.5451
 ULS  H2   H  HCR6  0   0.307  21.2316   1.4217  -10.3005
 ULS  H3   H  HCR6  0   0.316  21.4785  -2.6318  -11.6969
 ULS  H4   H  HCR6  0   0.293  22.9906  -1.2771   -9.0936
 ULS  H5   H  HCH2  0   0.272  24.8435   1.6844  -12.8651
 ULS  H6   H  HCH2  0   0.269  24.6951   0.0989  -13.6045
 ULS  H7   H  HCH2  0   0.258  27.0189  -0.3842  -13.3768
 ULS  H8   H  HCH2  0   0.257  27.1593   1.3566  -13.5961
 ULS  H9   H  HCR5  0   0.241  28.2418   0.1444  -11.4319
 ULS  H10  H  HOH1  0   0.448  27.8053   2.1050  -10.3118

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
 ULS  C5   C9   single    1.535  0.020  1.535
 ULS  C5   C6   single    1.530  0.020  1.530
 ULS  C9   C8   single    1.497  0.020  1.497
 ULS  C6   O1   single    1.411  0.020  1.411
 ULS  C6   C7   single    1.520  0.020  1.520
 ULS  O2   C13  single    1.368  0.020  1.368
 ULS  O2   C2   single    1.355  0.020  1.355
 ULS  C8   C2   aromatic  1.385  0.020  1.385
 ULS  C8   C7   aromatic  1.386  0.020  1.386
 ULS  C12  C13  aromatic  1.386  0.020  1.386
 ULS  C12  C11  aromatic  1.382  0.020  1.382
 ULS  C13  C14  aromatic  1.384  0.020  1.384
 ULS  F4   C11  single    1.334  0.020  1.334
 ULS  C2   C3   aromatic  1.393  0.020  1.393
 ULS  C11  C10  aromatic  1.379  0.020  1.379
 ULS  C7   C1   aromatic  1.388  0.020  1.388
 ULS  C14  C15  aromatic  1.392  0.020  1.392
 ULS  C10  C15  aromatic  1.393  0.020  1.393
 ULS  C15  C16  single    1.429  0.020  1.429
 ULS  C3   N1   aromatic  1.324  0.020  1.324
 ULS  C1   N1   aromatic  1.322  0.020  1.322
 ULS  C1   C4   single    1.505  0.020  1.505
 ULS  C16  N2   triple    1.151  0.020  1.151
 ULS  F2   C4   single    1.341  0.020  1.341
 ULS  C4   F3   single    1.344  0.020  1.344
 ULS  C4   F1   single    1.327  0.020  1.327
 ULS  C10  H1   single    0.930  0.020  1.080
 ULS  C14  H2   single    0.930  0.020  1.080
 ULS  C12  H3   single    0.930  0.020  1.080
 ULS  C3   H4   single    0.930  0.020  1.080
 ULS  C9   H5   single    0.970  0.020  1.090
 ULS  C9   H6   single    0.970  0.020  1.090
 ULS  C5   H7   single    0.970  0.020  1.090
 ULS  C5   H8   single    0.970  0.020  1.090
 ULS  C6   H9   single    0.970  0.020  1.090
 ULS  O1   H10  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
 ULS  C15  C16  N2   180.00  3.000
 ULS  C14  C15  C10  121.63  3.000
 ULS  C10  C15  C16  119.29  3.000
 ULS  C14  C15  C16  119.09  3.000
 ULS  H1   C10  C11  120.90  3.000
 ULS  H1   C10  C15  121.42  3.000
 ULS  C11  C10  C15  117.69  3.000
 ULS  H2   C14  C13  120.72  3.000
 ULS  H2   C14  C15  120.95  3.000
 ULS  C13  C14  C15  118.32  3.000
 ULS  O2   C13  C12  119.10  3.000
 ULS  C12  C13  C14  121.66  3.000
 ULS  O2   C13  C14  119.20  3.000
 ULS  H3   C12  C11  120.87  3.000
 ULS  H3   C12  C13  121.03  3.000
 ULS  C11  C12  C13  118.09  3.000
 ULS  F4   C11  C12  118.62  3.000
 ULS  F4   C11  C10  118.77  3.000
 ULS  C12  C11  C10  122.61  3.000
 ULS  C2   O2   C13  119.44  3.000
 ULS  C8   C2   C3   118.17  3.000
 ULS  C3   C2   O2   124.53  3.000
 ULS  C8   C2   O2   117.28  3.000
 ULS  H4   C3   N1   116.28  3.000
 ULS  H4   C3   C2   121.38  3.000
 ULS  N1   C3   C2   122.33  3.000
 ULS  C1   N1   C3   119.57  3.000
 ULS  C7   C8   C9   111.56  3.000
 ULS  C7   C8   C2   119.13  3.000
 ULS  C9   C8   C2   129.30  3.000
 ULS  H6   C9   H5   107.06  3.000
 ULS  H6   C9   C5   112.70  3.000
 ULS  H5   C9   C5   112.15  3.000
 ULS  H6   C9   C8   112.67  3.000
 ULS  H5   C9   C8   110.28  3.000
 ULS  C5   C9   C8   102.05  3.000
 ULS  H8   C5   H7   107.64  3.000
 ULS  H8   C5   C6   111.81  3.000
 ULS  H7   C5   C6   108.64  3.000
 ULS  H8   C5   C9   113.56  3.000
 ULS  H7   C5   C9   109.28  3.000
 ULS  C6   C5   C9   105.82  3.000
 ULS  C1   C7   C6   132.05  3.000
 ULS  C1   C7   C8   118.43  3.000
 ULS  C6   C7   C8   109.44  3.000
 ULS  H9   C6   O1   111.51  3.000
 ULS  H9   C6   C7   113.07  3.000
 ULS  O1   C6   C7   110.51  3.000
 ULS  H9   C6   C5   111.50  3.000
 ULS  C7   C6   C5   101.55  3.000
 ULS  O1   C6   C5   108.19  3.000
 ULS  H10  O1   C6   109.25  3.000
 ULS  C4   C1   C7   121.50  3.000
 ULS  C4   C1   N1   116.10  3.000
 ULS  C7   C1   N1   122.35  3.000
 ULS  F3   C4   F2   106.42  3.000
 ULS  F3   C4   F1   107.31  3.000
 ULS  F2   C4   F1   107.31  3.000
 ULS  F1   C4   C1   112.57  3.000
 ULS  F3   C4   C1   111.54  3.000
 ULS  F2   C4   C1   111.37  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
 ULS  CONST_01  C12  C13  C14  C15     0.00   0.0  0
 ULS  CONST_02  C12  C11  C10  C15     0.00   0.0  0
 ULS  CONST_03  C13  C12  C11  C10     0.00   0.0  0
 ULS  CONST_04  C13  C14  C15  C10     0.00   0.0  0
 ULS  CONST_05  C11  C12  C13  C14     0.00   0.0  0
 ULS  CONST_06  C11  C10  C15  C14     0.00   0.0  0
 ULS  CONST_07  C1   C7   C8   C2      0.00   0.0  0
 ULS  CONST_08  C1   N1   C3   C2      0.00   0.0  0
 ULS  CONST_09  C7   C8   C2   C3      0.00   0.0  0
 ULS  CONST_10  C7   C1   N1   C3      0.00   0.0  0
 ULS  CONST_11  C8   C2   C3   N1      0.00   0.0  0
 ULS  CONST_12  C8   C7   C1   N1      0.00   0.0  0
 ULS  CONST_13  C13  C14  C15  C16   180.00   0.0  0
 ULS  CONST_14  C11  C10  C15  C16   180.00   0.0  0
 ULS  CONST_15  O2   C13  C14  C15   180.00   0.0  0
 ULS  CONST_16  F4   C11  C10  C15   180.00   0.0  0
 ULS  CONST_17  F4   C11  C12  C13   180.00   0.0  0
 ULS  CONST_18  O2   C13  C12  C11   180.00   0.0  0
 ULS  CONST_19  C9   C8   C2   O2      0.00   0.0  0
 ULS  CONST_20  C7   C8   C2   O2    180.00   0.0  0
 ULS  CONST_21  N1   C3   C2   O2    180.00   0.0  0
 ULS  CONST_22  C4   C1   N1   C3    180.00   0.0  0
 ULS  CONST_23  C4   C1   C7   C8    180.00   0.0  0
 ULS  CONST_24  C4   C1   C7   C6      0.00   0.0  0
 ULS  CONST_25  H3   C12  C11  C10   180.00   0.0  0
 ULS  CONST_26  H2   C14  C15  C10   180.00   0.0  0
 ULS  CONST_27  H1   C10  C15  C14   180.00   0.0  0
 ULS  CONST_28  H4   C3   C2   C8    180.00   0.0  0
 ULS  Var_01    C5   C9   C8   C2   -164.91  30.0  1
 ULS  Var_02    C6   C5   C9   C8    -27.98  30.0  1
 ULS  Var_03    C8   C2   O2   C13  -171.58  30.0  2
 ULS  Var_04    F2   C4   C1   N1    110.50  30.0  2

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
 ULS  chir_01  C6  C5  O1  C7  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
 ULS  plan-1  N2   0.020
 ULS  plan-1  C16  0.020
 ULS  plan-1  C15  0.020
 ULS  plan-1  C10  0.020
 ULS  plan-1  C14  0.020
 ULS  plan-1  C13  0.020
 ULS  plan-1  C12  0.020
 ULS  plan-1  C11  0.020
 ULS  plan-1  F4   0.020
 ULS  plan-1  O2   0.020
 ULS  plan-1  H1   0.020
 ULS  plan-1  H2   0.020
 ULS  plan-1  H3   0.020
 ULS  plan-2  O2   0.020
 ULS  plan-2  C2   0.020
 ULS  plan-2  C3   0.020
 ULS  plan-2  N1   0.020
 ULS  plan-2  C8   0.020
 ULS  plan-2  C9   0.020
 ULS  plan-2  C7   0.020
 ULS  plan-2  C6   0.020
 ULS  plan-2  C1   0.020
 ULS  plan-2  C4   0.020
 ULS  plan-2  H4   0.020

