# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 20:14:19 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 4-(trifluoromethyl)-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)C1=CC(=O)NC2=C1CCC2
#
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
 JKZ  JKZ  4-(trifluoromethyl)-1,5,6,7-tetrahydro-2H-cyclopenta[b]pyridin-2-one  ligand  22  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_JKZ
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
 JKZ  F1    F  F     0  -0.295  -2.7843  -0.9645  -0.0164
 JKZ  C2    C  CT    0   1.066  -1.9645   0.0846   0.0425
 JKZ  F3    F  F     0  -0.310  -2.2733   0.8861  -0.9838
 JKZ  F4    F  F     0  -0.310  -2.2576   0.7529   1.1652
 JKZ  C5    C  CR6   0  -0.085  -0.5130  -0.2976   0.0113
 JKZ  C6    C  CR56  0  -0.024   0.4612   0.7271  -0.0215
 JKZ  C7    C  CR56  0   0.367   1.7676   0.3479  -0.0416
 JKZ  N8    N  NR16  0  -0.715   2.1342  -0.9479  -0.0246
 JKZ  C9    C  CR6   0   0.541   1.2451  -2.0055   0.0176
 JKZ  C10   C  CR16  0  -0.536  -0.1426  -1.6080   0.0363
 JKZ  O12   O  O     0  -0.500   1.6455  -3.1646   0.0385
 JKZ  C14   C  CH2   0  -0.497   2.7055   1.5054  -0.1255
 JKZ  C17   C  CH2   0  -0.463   1.7849   2.6856   0.2277
 JKZ  C20   C  CH2   0  -0.498   0.3530   2.2266  -0.1088
 JKZ  HN8   H  HNR6  0   0.422   3.1200  -1.1805  -0.0379
 JKZ  H10   H  HCR6  0   0.285  -0.8681  -2.4078   0.0704
 JKZ  H14   H  HCH2  0   0.274   3.5570   1.4101   0.5501
 JKZ  H14A  H  HCH2  0   0.274   3.1056   1.5822  -1.1412
 JKZ  H17   H  HCH2  0   0.251   1.8577   2.8872   1.2970
 JKZ  H17A  H  HCH2  0   0.250   2.0634   3.5975  -0.2976
 JKZ  H20   H  HCH2  0   0.253   0.0650   2.5341  -1.1180
 JKZ  H20A  H  HCH2  0   0.251  -0.3785   2.6567   0.5756

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
 JKZ  F1   C2    single  1.333  0.020  1.333
 JKZ  C2   F3    single  1.338  0.020  1.338
 JKZ  C2   F4    single  1.339  0.020  1.339
 JKZ  C2   C5    single  1.501  0.020  1.501
 JKZ  C5   C6    single  1.414  0.020  1.414
 JKZ  C5   C10   double  1.362  0.020  1.362
 JKZ  C6   C7    double  1.360  0.020  1.360
 JKZ  C6   C20   single  1.506  0.020  1.506
 JKZ  C7   N8    single  1.347  0.020  1.347
 JKZ  C7   C14   single  1.492  0.020  1.492
 JKZ  N8   C9    single  1.382  0.020  1.382
 JKZ  C9   C10   single  1.444  0.020  1.444
 JKZ  C9   O12   double  1.226  0.020  1.226
 JKZ  C14  C17   single  1.538  0.020  1.538
 JKZ  C17  C20   single  1.541  0.020  1.541
 JKZ  N8   HN8   single  0.860  0.020  1.020
 JKZ  C10  H10   single  0.930  0.020  1.080
 JKZ  C14  H14   single  0.970  0.020  1.090
 JKZ  C14  H14A  single  0.970  0.020  1.090
 JKZ  C17  H17   single  0.970  0.020  1.090
 JKZ  C17  H17A  single  0.970  0.020  1.090
 JKZ  C20  H20   single  0.970  0.020  1.090
 JKZ  C20  H20A  single  0.970  0.020  1.090

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
 JKZ  C5    C2   F4   110.86  3.000
 JKZ  C5    C2   F3   111.08  3.000
 JKZ  F4    C2   F3   107.07  3.000
 JKZ  C5    C2   F1   113.17  3.000
 JKZ  F4    C2   F1   107.17  3.000
 JKZ  F3    C2   F1   107.19  3.000
 JKZ  C10   C5   C6   120.68  3.000
 JKZ  C10   C5   C2   120.49  3.000
 JKZ  C6    C5   C2   118.82  3.000
 JKZ  C20   C6   C7   110.22  3.000
 JKZ  C20   C6   C5   132.32  3.000
 JKZ  C7    C6   C5   117.38  3.000
 JKZ  C14   C7   N8   125.17  3.000
 JKZ  C14   C7   C6   112.84  3.000
 JKZ  N8    C7   C6   121.96  3.000
 JKZ  HN8   N8   C9   116.78  3.000
 JKZ  HN8   N8   C7   119.06  3.000
 JKZ  C9    N8   C7   124.16  3.000
 JKZ  O12   C9   C10  125.02  3.000
 JKZ  O12   C9   N8   120.91  3.000
 JKZ  C10   C9   N8   114.08  3.000
 JKZ  H10   C10  C9   116.23  3.000
 JKZ  H10   C10  C5   122.03  3.000
 JKZ  C9    C10  C5   121.74  3.000
 JKZ  H14A  C14  H14  107.19  3.000
 JKZ  H14A  C14  C17  112.22  3.000
 JKZ  H14   C14  C17  113.08  3.000
 JKZ  H14A  C14  C7   109.66  3.000
 JKZ  H14   C14  C7   112.82  3.000
 JKZ  C17   C14  C7   101.89  3.000
 JKZ  H17A  C17  H17  107.53  3.000
 JKZ  H17A  C17  C20  112.45  3.000
 JKZ  H17   C17  C20  109.35  3.000
 JKZ  H17A  C17  C14  112.26  3.000
 JKZ  H17   C17  C14  109.09  3.000
 JKZ  C20   C17  C14  106.11  3.000
 JKZ  H20A  C20  H20  106.96  3.000
 JKZ  H20A  C20  C17  111.65  3.000
 JKZ  H20   C20  C17  111.25  3.000
 JKZ  H20A  C20  C6   113.87  3.000
 JKZ  H20   C20  C6   110.64  3.000
 JKZ  C17   C20  C6   102.54  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
 JKZ  CONST_01  C10  C9   N8   C7     0.00   0.0  0
 JKZ  CONST_02  O12  C9   N8   C7   180.00   0.0  0
 JKZ  CONST_03  HN8  N8   C9   C10  180.00   0.0  0
 JKZ  Var_01    C17  C20  C6   C5   167.52  30.0  1
 JKZ  Var_02    C17  C14  C7   C6    14.74  30.0  1
 JKZ  Var_03    C14  C17  C20  C6    24.40  30.0  1
 JKZ  Var_04    C20  C17  C14  C7   -23.81  30.0  1
 JKZ  Var_05    C6   C5   C2   F1   175.88  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
 JKZ  plan-1  C2   0.020
 JKZ  plan-1  C5   0.020
 JKZ  plan-1  C6   0.020
 JKZ  plan-1  C7   0.020
 JKZ  plan-1  N8   0.020
 JKZ  plan-1  C9   0.020
 JKZ  plan-1  C10  0.020
 JKZ  plan-1  O12  0.020
 JKZ  plan-1  C14  0.020
 JKZ  plan-1  C20  0.020
 JKZ  plan-1  HN8  0.020
 JKZ  plan-1  H10  0.020

