# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 05:42:36 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (4-{[2-(3-chlorophenyl)-6-(trifluoromethyl)pyridin-4-yl]methyl}phenyl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1ccc(Cc2cc(nc(c2)C(F)(F)F)c3cccc(Cl)c3)cc1
#
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
 KR7  KR7  '(4-{[2-(3-chlorophenyl)-6-(trifluoromethyl)pyridin-4-yl]methyl}phenyl)acetic acid'  ligand  42  28  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KR7
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
 KR7  C8   C   CH2    0  -0.631   1.1130  -0.6046   2.1754
 KR7  C9   C   CR6    0   0.288  -0.1050  -0.9255   1.3541
 KR7  C10  C   CR16   0  -0.387  -0.3195  -2.2124   0.8658
 KR7  C11  C   CR6    0  -0.005  -1.4394  -2.4304   0.0879
 KR7  C12  C   CT     0   1.056  -1.7689  -3.7863  -0.4762
 KR7  C7   C   CR6    0   0.133   2.2471  -0.1647   1.2809
 KR7  C2   C   CR6    0   0.160   4.3097   0.6368  -0.4718
 KR7  C3   C   CR16   0  -0.284   4.1747  -0.6934  -0.0780
 KR7  C6   C   CR16   0  -0.292   2.3784   1.1645   0.8956
 KR7  C4   C   CR16   0  -0.301   3.1599  -1.0891   0.7793
 KR7  C5   C   CR16   0  -0.301   3.3929   1.5558   0.0317
 KR7  O1   O   O      0  -0.596   6.9668   0.6184   0.3797
 KR7  C13  C   CR6    0   0.251  -2.1181  -0.2615   0.2133
 KR7  C14  C   C      0   0.064  -3.1228   0.7519  -0.1735
 KR7  C1   C   CH2    0  -0.688   5.4118   1.0654  -1.3870
 KR7  C15  C   C1     0  -0.274  -4.4232   0.3607  -0.4910
 KR7  C16  C   C1     0  -0.245  -5.3711   1.3060  -0.8472
 KR7  C18  C   C      0  -0.021  -3.7451   3.0319  -0.6002
 KR7  C20  C   CR16   0  -0.396  -1.0284   0.0534   1.0258
 KR7  C17  C   C1     0  -0.221  -5.0425   2.6532  -0.9059
 KR7  C19  C   C1     0  -0.271  -2.7855   2.1027  -0.2355
 KR7  C    C   C      0   0.420   6.8041   1.1869  -0.7136
 KR7  O    O   OC    -1  -0.622   7.6531   1.8320  -1.3593
 KR7  N    N   N      0  -0.452  -2.3135  -1.4942  -0.2375
 KR7  F2   F   F      0  -0.300  -0.8863  -4.7180  -0.1092
 KR7  F1   F   F      0  -0.310  -2.9755  -4.1983  -0.0746
 KR7  F    F   F      0  -0.311  -1.7903  -3.7613  -1.8134
 KR7  CL   CL  CL     0  -0.123  -3.3047   4.7062  -0.6842
 KR7  H1   H   HCH2   0   0.283   0.8756   0.1818   2.8937
 KR7  H2   H   HCH2   0   0.281   1.4101  -1.4853   2.7468
 KR7  H3   H   HCR6   0   0.278   0.3725  -3.0087   1.1039
 KR7  H4   H   HCR6   0   0.239   4.8696  -1.4350  -0.4536
 KR7  H5   H   HCR6   0   0.241   1.6828   1.9070   1.2707
 KR7  H6   H   HCR6   0   0.241   3.0803  -2.1314   1.0672
 KR7  H7   H   HCR6   0   0.242   3.4709   2.5986  -0.2547
 KR7  H8   H   HCH2   0   0.249   5.5145   0.3416  -2.2030
 KR7  H9   H   HCH2   0   0.237   5.1609   2.0172  -1.8608
 KR7  H10  H   H      0   0.263  -4.6926  -0.6857  -0.4512
 KR7  H11  H   H      0   0.273  -6.3798   0.9953  -1.0834
 KR7  H12  H   HCR6   0   0.272  -0.9111   1.0536   1.4223
 KR7  H13  H   H      0   0.284  -5.7819   3.3911  -1.1859
 KR7  H14  H   H      0   0.275  -1.7780   2.4358  -0.0244

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
 KR7  O1   C    deloc     1.243  0.020  1.243
 KR7  O    C    deloc     1.247  0.020  1.247
 KR7  C    C1   single    1.551  0.020  1.551
 KR7  C1   C2   single    1.495  0.020  1.495
 KR7  C3   C2   aromatic  1.394  0.020  1.394
 KR7  C3   C4   aromatic  1.386  0.020  1.386
 KR7  C2   C5   aromatic  1.392  0.020  1.392
 KR7  C4   C7   aromatic  1.393  0.020  1.393
 KR7  C5   C6   aromatic  1.389  0.020  1.389
 KR7  C7   C6   aromatic  1.390  0.020  1.390
 KR7  C7   C8   single    1.510  0.020  1.510
 KR7  C8   C9   single    1.504  0.020  1.504
 KR7  C9   C10  aromatic  1.393  0.020  1.393
 KR7  C9   C20  aromatic  1.385  0.020  1.385
 KR7  C10  C11  aromatic  1.381  0.020  1.381
 KR7  C20  C13  aromatic  1.395  0.020  1.395
 KR7  F2   C12  single    1.335  0.020  1.335
 KR7  C11  C12  single    1.505  0.020  1.505
 KR7  C11  N    aromatic  1.322  0.020  1.322
 KR7  C13  N    aromatic  1.327  0.020  1.327
 KR7  C13  C14  single    1.478  0.020  1.478
 KR7  F    C12  single    1.338  0.020  1.338
 KR7  C12  F1   single    1.337  0.020  1.337
 KR7  C19  C14  aromatic  1.394  0.020  1.394
 KR7  C19  C18  aromatic  1.385  0.020  1.385
 KR7  C14  C15  aromatic  1.395  0.020  1.395
 KR7  CL   C18  single    1.733  0.020  1.733
 KR7  C18  C17  aromatic  1.386  0.020  1.386
 KR7  C15  C16  aromatic  1.385  0.020  1.385
 KR7  C17  C16  aromatic  1.388  0.020  1.388
 KR7  C8   H1   single    0.970  0.020  1.090
 KR7  C8   H2   single    0.970  0.020  1.090
 KR7  C10  H3   single    0.930  0.020  1.080
 KR7  C3   H4   single    0.930  0.020  1.080
 KR7  C6   H5   single    0.930  0.020  1.080
 KR7  C4   H6   single    0.930  0.020  1.080
 KR7  C5   H7   single    0.930  0.020  1.080
 KR7  C1   H8   single    0.970  0.020  1.090
 KR7  C1   H9   single    0.970  0.020  1.090
 KR7  C15  H10  single    0.930  0.020  1.080
 KR7  C16  H11  single    0.930  0.020  1.080
 KR7  C20  H12  single    0.930  0.020  1.080
 KR7  C17  H13  single    0.930  0.020  1.080
 KR7  C19  H14  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
 KR7  H2   C8   H1   107.23  3.000
 KR7  H2   C8   C7   109.94  3.000
 KR7  H1   C8   C7   110.09  3.000
 KR7  H2   C8   C9   109.53  3.000
 KR7  H1   C8   C9   109.70  3.000
 KR7  C7   C8   C9   110.30  3.000
 KR7  C20  C9   C10  117.85  3.000
 KR7  C20  C9   C8   121.24  3.000
 KR7  C10  C9   C8   120.88  3.000
 KR7  H3   C10  C11  121.79  3.000
 KR7  H3   C10  C9   120.30  3.000
 KR7  C11  C10  C9   117.91  3.000
 KR7  N    C11  C12  113.65  3.000
 KR7  N    C11  C10  124.29  3.000
 KR7  C12  C11  C10  122.06  3.000
 KR7  F    C12  F1   106.95  3.000
 KR7  F1   C12  F2   107.40  3.000
 KR7  F    C12  F2   107.37  3.000
 KR7  F1   C12  C11  111.27  3.000
 KR7  F    C12  C11  111.18  3.000
 KR7  F2   C12  C11  112.40  3.000
 KR7  C4   C7   C6   118.23  3.000
 KR7  C6   C7   C8   120.91  3.000
 KR7  C4   C7   C8   120.82  3.000
 KR7  C1   C2   C5   121.16  3.000
 KR7  C5   C2   C3   117.64  3.000
 KR7  C1   C2   C3   121.19  3.000
 KR7  H4   C3   C4   119.25  3.000
 KR7  H4   C3   C2   119.55  3.000
 KR7  C4   C3   C2   121.20  3.000
 KR7  H5   C6   C5   119.40  3.000
 KR7  H5   C6   C7   119.88  3.000
 KR7  C5   C6   C7   120.72  3.000
 KR7  H6   C4   C3   119.50  3.000
 KR7  H6   C4   C7   119.63  3.000
 KR7  C3   C4   C7   120.87  3.000
 KR7  H7   C5   C6   119.20  3.000
 KR7  H7   C5   C2   119.47  3.000
 KR7  C6   C5   C2   121.33  3.000
 KR7  N    C13  C20  121.50  3.000
 KR7  N    C13  C14  116.60  3.000
 KR7  C20  C13  C14  121.89  3.000
 KR7  C19  C14  C15  119.17  3.000
 KR7  C15  C14  C13  120.06  3.000
 KR7  C19  C14  C13  120.77  3.000
 KR7  H9   C1   H8   105.91  3.000
 KR7  H9   C1   C    109.04  3.000
 KR7  H8   C1   C    106.91  3.000
 KR7  H9   C1   C2   110.24  3.000
 KR7  H8   C1   C2   109.61  3.000
 KR7  C    C1   C2   114.72  3.000
 KR7  H10  C15  C16  119.96  3.000
 KR7  H10  C15  C14  119.69  3.000
 KR7  C16  C15  C14  120.34  3.000
 KR7  H11  C16  C17  119.36  3.000
 KR7  H11  C16  C15  119.89  3.000
 KR7  C17  C16  C15  120.75  3.000
 KR7  CL   C18  C19  119.00  3.000
 KR7  CL   C18  C17  119.42  3.000
 KR7  C19  C18  C17  121.58  3.000
 KR7  H12  C20  C13  120.43  3.000
 KR7  H12  C20  C9   119.61  3.000
 KR7  C13  C20  C9   119.94  3.000
 KR7  H13  C17  C18  120.72  3.000
 KR7  H13  C17  C16  120.75  3.000
 KR7  C18  C17  C16  118.53  3.000
 KR7  H14  C19  C18  119.35  3.000
 KR7  H14  C19  C14  121.01  3.000
 KR7  C18  C19  C14  119.63  3.000
 KR7  O    C    C1   115.27  3.000
 KR7  C1   C    O1   117.61  3.000
 KR7  O    C    O1   127.10  3.000
 KR7  C13  N    C11  118.49  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
 KR7  CONST_01  N    C11  C10  C9     0.00   0.0  0
 KR7  CONST_02  N    C13  C20  C9     0.00   0.0  0
 KR7  CONST_03  C14  C13  C20  C9   180.00   0.0  0
 KR7  CONST_04  C13  C20  C9   C10    0.00   0.0  0
 KR7  CONST_05  C13  N    C11  C10    0.00   0.0  0
 KR7  CONST_06  C20  C9   C10  C11    0.00   0.0  0
 KR7  CONST_07  C20  C13  N    C11    0.00   0.0  0
 KR7  CONST_08  C14  C13  N    C11  180.00   0.0  0
 KR7  CONST_09  C2   C3   C4   C7     0.00   0.0  0
 KR7  CONST_10  C2   C5   C6   C7     0.00   0.0  0
 KR7  CONST_11  C6   C5   C2   C3     0.00   0.0  0
 KR7  CONST_12  C6   C7   C4   C3     0.00   0.0  0
 KR7  CONST_13  C5   C2   C3   C4     0.00   0.0  0
 KR7  CONST_14  C5   C6   C7   C4     0.00   0.0  0
 KR7  CONST_15  C18  C19  C14  C13  180.00   0.0  0
 KR7  CONST_16  C16  C15  C14  C13  180.00   0.0  0
 KR7  CONST_17  C17  C18  C19  C14    0.00   0.0  0
 KR7  CONST_18  C17  C16  C15  C14    0.00   0.0  0
 KR7  CONST_21  C18  C19  C14  C15    0.00   0.0  0
 KR7  CONST_22  C18  C17  C16  C15    0.00   0.0  0
 KR7  CONST_23  C19  C14  C15  C16    0.00   0.0  0
 KR7  CONST_24  C19  C18  C17  C16    0.00   0.0  0
 KR7  CONST_27  C3   C4   C7   C8   180.00   0.0  0
 KR7  CONST_28  C5   C6   C7   C8   180.00   0.0  0
 KR7  CONST_29  C11  C10  C9   C8   180.00   0.0  0
 KR7  CONST_30  C13  C20  C9   C8   180.00   0.0  0
 KR7  CONST_31  C12  C11  C10  C9   180.00   0.0  0
 KR7  CONST_32  C13  N    C11  C12  180.00   0.0  0
 KR7  CONST_33  C1   C2   C5   C6   180.00   0.0  0
 KR7  CONST_34  C1   C2   C3   C4   180.00   0.0  0
 KR7  CONST_35  CL   C18  C19  C14  180.00   0.0  0
 KR7  CONST_36  CL   C18  C17  C16  180.00   0.0  0
 KR7  CONST_37  H12  C20  C9   C10  180.00   0.0  0
 KR7  CONST_38  H4   C3   C4   C7   180.00   0.0  0
 KR7  CONST_39  H7   C5   C6   C7   180.00   0.0  0
 KR7  CONST_40  H6   C4   C3   C2   180.00   0.0  0
 KR7  CONST_41  H5   C6   C5   C2   180.00   0.0  0
 KR7  CONST_42  H14  C19  C14  C13    0.00   0.0  0
 KR7  CONST_43  H10  C15  C14  C13    0.00   0.0  0
 KR7  CONST_44  H11  C16  C15  C14  180.00   0.0  0
 KR7  CONST_45  H13  C17  C16  C15  180.00   0.0  0
 KR7  CONST_46  H3   C10  C9   C20  180.00   0.0  0
 KR7  Var_01    C4   C7   C8   C9   -91.06  30.0  2
 KR7  Var_02    C7   C8   C9   C10   89.93  30.0  2
 KR7  Var_03    F2   C12  C11  C10    1.54  30.0  2
 KR7  Var_04    C    C1   C2   C3   -76.79  30.0  2
 KR7  Var_05    O1   C    C1   C2    17.69  30.0  2

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
 KR7  plan-1  C8   0.020
 KR7  plan-1  C9   0.020
 KR7  plan-1  C10  0.020
 KR7  plan-1  C11  0.020
 KR7  plan-1  C12  0.020
 KR7  plan-1  C13  0.020
 KR7  plan-1  C14  0.020
 KR7  plan-1  C20  0.020
 KR7  plan-1  N    0.020
 KR7  plan-1  H3   0.020
 KR7  plan-1  H12  0.020
 KR7  plan-2  C8   0.020
 KR7  plan-2  C7   0.020
 KR7  plan-2  C2   0.020
 KR7  plan-2  C3   0.020
 KR7  plan-2  C6   0.020
 KR7  plan-2  C4   0.020
 KR7  plan-2  C5   0.020
 KR7  plan-2  C1   0.020
 KR7  plan-2  H4   0.020
 KR7  plan-2  H5   0.020
 KR7  plan-2  H6   0.020
 KR7  plan-2  H7   0.020
 KR7  plan-3  C13  0.020
 KR7  plan-3  C14  0.020
 KR7  plan-3  C15  0.020
 KR7  plan-3  C16  0.020
 KR7  plan-3  C18  0.020
 KR7  plan-3  C17  0.020
 KR7  plan-3  C19  0.020
 KR7  plan-3  CL   0.020
 KR7  plan-3  H10  0.020
 KR7  plan-3  H11  0.020
 KR7  plan-3  H13  0.020
 KR7  plan-3  H14  0.020
 KR7  plan-4  O1   0.020
 KR7  plan-4  C1   0.020
 KR7  plan-4  C    0.020
 KR7  plan-4  O    0.020

