# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 00:54:15 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: (2~{R})-2-[[4-[[4-methoxy-2-(trifluoromethyl)phenyl]methylcarbamoyl]phenyl]methyl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](Cc1ccc(cc1)C(=O)NCc2ccc(OC)cc2C(F)(F)F)C(O)=O
#
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
 TK9  TK9  '(2~{R})-2-[[4-[[4-methoxy-2-(trifluoromethyl)phenyl]methylcarbamoyl]phenyl]methyl]butanoic acid'  ligand  50  29  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TK9
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
 TK9  F2   F  F      0  -0.296   0.9506  -1.2911  -17.2012
 TK9  C15  C  CT     0   1.057  -0.1662  -0.9170  -17.8299
 TK9  F    F  F      0  -0.313  -0.2582   0.4131  -17.6798
 TK9  F1   F  F      0  -0.316   0.0410  -1.1441  -19.1366
 TK9  C14  C  CR6    0  -0.227  -1.3926  -1.6224  -17.3232
 TK9  C16  C  CR16   0  -0.426  -1.2537  -2.4598  -16.2180
 TK9  C17  C  CR6    0   0.406  -2.3594  -3.1256  -15.7008
 TK9  O3   O  O2     0  -0.464  -2.3196  -3.9508  -14.6439
 TK9  C18  C  CH3    0  -0.442  -1.0947  -4.1306  -13.9603
 TK9  C19  C  CR16   0  -0.320  -3.6037  -2.9401  -16.3009
 TK9  C20  C  CR16   0  -0.275  -3.7242  -2.1027  -17.3895
 TK9  C13  C  CR6    0   0.120  -2.6333  -1.4220  -17.9312
 TK9  C12  C  CH2    0  -0.429  -2.8838  -0.5442  -19.1398
 TK9  N    N  NH1    0  -0.636  -2.8684  -1.2748  -20.3887
 TK9  C    C  C      0   0.536  -3.9763  -1.7427  -20.9946
 TK9  O    O  O      0  -0.483  -5.0970  -1.6305  -20.5149
 TK9  C1   C  CR6    0  -0.052  -3.7666  -2.4121  -22.3136
 TK9  C11  C  CR16   0  -0.253  -4.7339  -3.3078  -22.7618
 TK9  C10  C  CR16   0  -0.301  -4.5990  -3.9378  -23.9886
 TK9  C4   C  CR6    0   0.137  -3.5071  -3.6811  -24.8146
 TK9  C3   C  CR16   0  -0.288  -2.5491  -2.7732  -24.3656
 TK9  C2   C  CR16   0  -0.278  -2.6715  -2.1480  -23.1362
 TK9  C5   C  CH2    0  -0.510  -3.3466  -4.3637  -26.1415
 TK9  C6   C  CH1    0  -0.315  -2.2713  -5.4648  -26.1301
 TK9  C8   C  CH2    0  -0.407  -2.6659  -6.6154  -25.2075
 TK9  C9   C  CH3    0  -0.664  -1.6210  -7.7212  -25.1355
 TK9  C7   C  C      0   0.400  -2.0221  -5.9564  -27.5745
 TK9  O2   O  OC    -1  -0.612  -2.9826  -6.5250  -28.1362
 TK9  O1   O  O      0  -0.605  -0.8959  -5.7412  -28.0663
 TK9  H1   H  HCR6   0   0.294  -0.2824  -2.5902  -15.7641
 TK9  H2   H  HCH3   0   0.263  -1.2992  -4.8114  -13.1380
 TK9  H3   H  HCH3   0   0.232  -0.3299  -4.5749  -14.6024
 TK9  H4   H  HCH3   0   0.232  -0.7131  -3.1906  -13.5531
 TK9  H5   H  HCR6   0   0.271  -4.4726  -3.4494  -15.9033
 TK9  H6   H  HCR6   0   0.264  -4.6992  -1.9658  -17.8391
 TK9  H7   H  HCH2   0   0.275  -2.1732   0.2755  -19.2179
 TK9  H8   H  HCH2   0   0.280  -3.8621  -0.0795  -19.0334
 TK9  H9   H  HNH1   0   0.403  -1.9676  -1.5124  -20.7687
 TK9  H10  H  HCR6   0   0.253  -5.5981  -3.5177  -22.1454
 TK9  H11  H  HCR6   0   0.250  -5.3607  -4.6368  -24.3131
 TK9  H12  H  HCR6   0   0.250  -1.6982  -2.5403  -24.9951
 TK9  H13  H  HCR6   0   0.253  -1.9145  -1.4283  -22.8492
 TK9  H14  H  HCH2   0   0.242  -3.0791  -3.6136  -26.8922
 TK9  H15  H  HCH2   0   0.233  -4.3010  -4.7953  -26.4514
 TK9  H16  H  HCH1   0   0.196  -1.3422  -5.0231  -25.7512
 TK9  H17  H  HCH2   0   0.213  -2.8413  -6.2304  -24.1987
 TK9  H18  H  HCH2   0   0.203  -3.6207  -7.0320  -25.5420
 TK9  H19  H  HCH3   0   0.222  -1.9065  -8.4868  -24.4127
 TK9  H20  H  HCH3   0   0.218  -1.4895  -8.2174  -26.0982
 TK9  H21  H  HCH3   0   0.212  -0.6492  -7.3278  -24.8308

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
 TK9  O1   C7   deloc     1.248  0.020  1.248
 TK9  C7   O2   deloc     1.250  0.020  1.250
 TK9  C7   C6   single    1.546  0.020  1.546
 TK9  C5   C6   single    1.539  0.020  1.539
 TK9  C5   C4   single    1.501  0.020  1.501
 TK9  C6   C8   single    1.527  0.020  1.527
 TK9  C4   C3   aromatic  1.394  0.020  1.394
 TK9  C4   C10  aromatic  1.393  0.020  1.393
 TK9  C8   C9   single    1.523  0.020  1.523
 TK9  C3   C2   aromatic  1.385  0.020  1.385
 TK9  C10  C11  aromatic  1.386  0.020  1.386
 TK9  C2   C1   aromatic  1.395  0.020  1.395
 TK9  C11  C1   aromatic  1.392  0.020  1.392
 TK9  C1   C    single    1.494  0.020  1.494
 TK9  C    O    double    1.224  0.020  1.224
 TK9  C    N    single    1.347  0.020  1.347
 TK9  N    C12  single    1.447  0.020  1.447
 TK9  F1   C15  single    1.342  0.020  1.342
 TK9  C12  C13  single    1.515  0.020  1.515
 TK9  C15  F2   single    1.335  0.020  1.335
 TK9  C15  F    single    1.342  0.020  1.342
 TK9  C15  C14  single    1.503  0.020  1.503
 TK9  C13  C14  aromatic  1.396  0.020  1.396
 TK9  C13  C20  aromatic  1.395  0.020  1.395
 TK9  C14  C16  aromatic  1.394  0.020  1.394
 TK9  C20  C19  aromatic  1.379  0.020  1.379
 TK9  C19  C17  aromatic  1.394  0.020  1.394
 TK9  C16  C17  aromatic  1.390  0.020  1.390
 TK9  C17  O3   single    1.341  0.020  1.341
 TK9  O3   C18  single    1.414  0.020  1.414
 TK9  C16  H1   single    0.930  0.020  1.080
 TK9  C18  H2   single    0.970  0.020  1.090
 TK9  C18  H3   single    0.970  0.020  1.090
 TK9  C18  H4   single    0.970  0.020  1.090
 TK9  C19  H5   single    0.930  0.020  1.080
 TK9  C20  H6   single    0.930  0.020  1.080
 TK9  C12  H7   single    0.970  0.020  1.090
 TK9  C12  H8   single    0.970  0.020  1.090
 TK9  N    H9   single    0.860  0.020  1.020
 TK9  C11  H10  single    0.930  0.020  1.080
 TK9  C10  H11  single    0.930  0.020  1.080
 TK9  C3   H12  single    0.930  0.020  1.080
 TK9  C2   H13  single    0.930  0.020  1.080
 TK9  C5   H14  single    0.970  0.020  1.090
 TK9  C5   H15  single    0.970  0.020  1.090
 TK9  C6   H16  single    0.970  0.020  1.090
 TK9  C8   H17  single    0.970  0.020  1.090
 TK9  C8   H18  single    0.970  0.020  1.090
 TK9  C9   H19  single    0.970  0.020  1.090
 TK9  C9   H20  single    0.970  0.020  1.090
 TK9  C9   H21  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
 TK9  C14  C15  F1   112.01  3.000
 TK9  C14  C15  F    111.82  3.000
 TK9  F1   C15  F    106.69  3.000
 TK9  C14  C15  F2   113.10  3.000
 TK9  F    C15  F2   106.40  3.000
 TK9  F1   C15  F2   106.37  3.000
 TK9  C13  C14  C16  121.34  3.000
 TK9  C16  C14  C15  117.91  3.000
 TK9  C13  C14  C15  120.74  3.000
 TK9  H1   C16  C17  120.07  3.000
 TK9  H1   C16  C14  119.71  3.000
 TK9  C17  C16  C14  120.23  3.000
 TK9  C19  C17  O3   116.59  3.000
 TK9  O3   C17  C16  124.33  3.000
 TK9  C19  C17  C16  119.08  3.000
 TK9  C18  O3   C17  119.00  3.000
 TK9  H4   C18  H3   108.91  3.000
 TK9  H4   C18  H2   108.81  3.000
 TK9  H3   C18  H2   108.75  3.000
 TK9  H4   C18  O3   111.90  3.000
 TK9  H3   C18  O3   111.95  3.000
 TK9  H2   C18  O3   106.40  3.000
 TK9  H5   C19  C20  120.37  3.000
 TK9  H5   C19  C17  119.71  3.000
 TK9  C20  C19  C17  119.92  3.000
 TK9  H6   C20  C13  118.78  3.000
 TK9  H6   C20  C19  118.91  3.000
 TK9  C13  C20  C19  122.31  3.000
 TK9  C12  C13  C20  117.60  3.000
 TK9  C20  C13  C14  117.11  3.000
 TK9  C12  C13  C14  125.28  3.000
 TK9  H8   C12  H7   105.81  3.000
 TK9  H8   C12  N    108.04  3.000
 TK9  H7   C12  N    108.16  3.000
 TK9  H8   C12  C13  108.54  3.000
 TK9  H7   C12  C13  112.71  3.000
 TK9  N    C12  C13  113.22  3.000
 TK9  H9   N    C    118.98  3.000
 TK9  H9   N    C12  117.05  3.000
 TK9  C    N    C12  123.71  3.000
 TK9  C1   C    O    121.03  3.000
 TK9  O    C    N    123.02  3.000
 TK9  C1   C    N    115.94  3.000
 TK9  C2   C1   C11  118.52  3.000
 TK9  C11  C1   C    118.36  3.000
 TK9  C2   C1   C    123.09  3.000
 TK9  H10  C11  C10  119.59  3.000
 TK9  H10  C11  C1   119.75  3.000
 TK9  C10  C11  C1   120.65  3.000
 TK9  H11  C10  C4   119.50  3.000
 TK9  H11  C10  C11  119.34  3.000
 TK9  C4   C10  C11  121.16  3.000
 TK9  C5   C4   C3   120.50  3.000
 TK9  C3   C4   C10  117.89  3.000
 TK9  C5   C4   C10  121.62  3.000
 TK9  H12  C3   C2   119.21  3.000
 TK9  H12  C3   C4   119.50  3.000
 TK9  C2   C3   C4   121.28  3.000
 TK9  H13  C2   C3   118.26  3.000
 TK9  H13  C2   C1   121.21  3.000
 TK9  C3   C2   C1   120.49  3.000
 TK9  H15  C5   H14  106.85  3.000
 TK9  H15  C5   C6   109.26  3.000
 TK9  H14  C5   C6   108.94  3.000
 TK9  H15  C5   C4   109.70  3.000
 TK9  H14  C5   C4   108.71  3.000
 TK9  C6   C5   C4   113.17  3.000
 TK9  H16  C6   C7   108.33  3.000
 TK9  H16  C6   C8   108.29  3.000
 TK9  C7   C6   C8   111.51  3.000
 TK9  H16  C6   C5   107.84  3.000
 TK9  C8   C6   C5   111.29  3.000
 TK9  C7   C6   C5   109.46  3.000
 TK9  H18  C8   H17  106.02  3.000
 TK9  H18  C8   C9   109.68  3.000
 TK9  H17  C8   C9   108.79  3.000
 TK9  H18  C8   C6   109.13  3.000
 TK9  H17  C8   C6   109.48  3.000
 TK9  C9   C8   C6   113.48  3.000
 TK9  H21  C9   H20  107.63  3.000
 TK9  H21  C9   H19  107.51  3.000
 TK9  H20  C9   H19  107.28  3.000
 TK9  H21  C9   C8   111.23  3.000
 TK9  H20  C9   C8   111.79  3.000
 TK9  H19  C9   C8   111.18  3.000
 TK9  O1   C7   O2   126.53  3.000
 TK9  O2   C7   C6   116.15  3.000
 TK9  O1   C7   C6   117.32  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
 TK9  CONST_01  C19  C20  C13  C14     0.00   0.0  0
 TK9  CONST_02  C19  C17  C16  C14     0.00   0.0  0
 TK9  CONST_03  C20  C13  C14  C16     0.00   0.0  0
 TK9  CONST_04  C20  C19  C17  C16     0.00   0.0  0
 TK9  CONST_05  C13  C20  C19  C17     0.00   0.0  0
 TK9  CONST_06  C13  C14  C16  C17     0.00   0.0  0
 TK9  CONST_07  C4   C3   C2   C1      0.00   0.0  0
 TK9  CONST_08  C4   C10  C11  C1      0.00   0.0  0
 TK9  CONST_09  C3   C4   C10  C11     0.00   0.0  0
 TK9  CONST_10  C3   C2   C1   C11     0.00   0.0  0
 TK9  CONST_11  C2   C3   C4   C10     0.00   0.0  0
 TK9  CONST_12  C2   C1   C11  C10     0.00   0.0  0
 TK9  CONST_13  C20  C13  C14  C15   180.00   0.0  0
 TK9  CONST_14  C17  C16  C14  C15   180.00   0.0  0
 TK9  CONST_15  O3   C17  C16  C14   180.00   0.0  0
 TK9  CONST_16  C12  C13  C14  C16   180.00   0.0  0
 TK9  CONST_17  C20  C19  C17  O3    180.00   0.0  0
 TK9  CONST_18  C12  C13  C20  C19   180.00   0.0  0
 TK9  CONST_19  C3   C2   C1   C     180.00   0.0  0
 TK9  CONST_20  C10  C11  C1   C     180.00   0.0  0
 TK9  CONST_21  C5   C4   C10  C11   180.00   0.0  0
 TK9  CONST_22  C5   C4   C3   C2    180.00   0.0  0
 TK9  CONST_23  H6   C20  C13  C14   180.00   0.0  0
 TK9  CONST_24  H5   C19  C17  C16   180.00   0.0  0
 TK9  CONST_25  H1   C16  C17  C19   180.00   0.0  0
 TK9  CONST_26  H12  C3   C2   C1    180.00   0.0  0
 TK9  CONST_27  H11  C10  C11  C1    180.00   0.0  0
 TK9  CONST_28  H13  C2   C1   C11   180.00   0.0  0
 TK9  CONST_29  H10  C11  C10  C4    180.00   0.0  0
 TK9  CONST_30  C1   C    N    C12   180.00   0.0  0
 TK9  CONST_31  H9   N    C    C1      0.00   0.0  0
 TK9  CONST_32  O    C    N    C12     0.00   0.0  0
 TK9  Var_01    C13  C14  C15  F2   -175.47  30.0  2
 TK9  Var_02    N    C12  C13  C14    95.06  30.0  1
 TK9  Var_03    C19  C17  O3   C18  -177.28  30.0  2
 TK9  Var_04    C2   C1   C    N     -24.56  30.0  2
 TK9  Var_05    C6   C5   C4   C10  -105.19  30.0  2
 TK9  Var_06    C    N    C12  C13    95.62  30.0  1
 TK9  Var_07    H2   C18  O3   C17   178.71  30.0  3
 TK9  Var_08    H19  C9   C8   C6    175.85  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
 TK9  chir_01  C6  C7  C5  C8  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
 TK9  plan-1  C15  0.020
 TK9  plan-1  C14  0.020
 TK9  plan-1  C16  0.020
 TK9  plan-1  C17  0.020
 TK9  plan-1  O3   0.020
 TK9  plan-1  C19  0.020
 TK9  plan-1  C20  0.020
 TK9  plan-1  C13  0.020
 TK9  plan-1  C12  0.020
 TK9  plan-1  H1   0.020
 TK9  plan-1  H5   0.020
 TK9  plan-1  H6   0.020
 TK9  plan-2  C    0.020
 TK9  plan-2  C1   0.020
 TK9  plan-2  C11  0.020
 TK9  plan-2  C10  0.020
 TK9  plan-2  C4   0.020
 TK9  plan-2  C3   0.020
 TK9  plan-2  C2   0.020
 TK9  plan-2  C5   0.020
 TK9  plan-2  H10  0.020
 TK9  plan-2  H11  0.020
 TK9  plan-2  H12  0.020
 TK9  plan-2  H13  0.020
 TK9  plan-3  C12  0.020
 TK9  plan-3  N    0.020
 TK9  plan-3  C    0.020
 TK9  plan-3  O    0.020
 TK9  plan-3  C1   0.020
 TK9  plan-3  H9   0.020
 TK9  plan-4  C6   0.020
 TK9  plan-4  C7   0.020
 TK9  plan-4  O2   0.020
 TK9  plan-4  O1   0.020

