# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:18:42 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 6-({(2S)-3-cyclopentyl-2-[4-(trifluoromethyl)-1H-imidazol-1-yl]propanoyl}amino)pyridine-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccc(NC(=O)[C@H](CC2CCCC2)n3cnc(c3)C(F)(F)F)nc1
#
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
 0H6  0H6  '6-({(2S)-3-cyclopentyl-2-[4-(trifluoromethyl)-1H-imidazol-1-yl]propanoyl}amino)pyridine-3-carboxylic acid'  ligand  47  28  .  2022-07-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_0H6
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
 0H6  C4   C  CH2   0  -0.443   0.9719   1.9108  -0.8817
 0H6  C7   C  CH2   0  -0.451   3.5477   4.6969  -0.7594
 0H6  C6   C  CH2   0  -0.424   2.4158   3.9290  -1.4480
 0H6  C9   C  CH2   0  -0.446   2.3913   3.2070   0.8257
 0H6  C13  C  CR16  0  -0.356  -3.4458  -0.8179  -0.6880
 0H6  C21  C  CR15  0  -0.063   2.4859  -0.8977   0.9292
 0H6  C8   C  CH2   0  -0.443   3.4669   4.3033   0.7346
 0H6  C16  C  CR16  0  -0.042  -5.0134   0.5607   1.0656
 0H6  N1   N  NR5   0  -0.404   1.8765  -0.2551  -0.1059
 0H6  C2   C  CH1   0  -0.275   0.7810   0.6816   0.0141
 0H6  C3   C  C     0   0.596  -0.5269  -0.0260  -0.3425
 0H6  C5   C  CH1   0  -0.239   2.2610   2.6681  -0.6003
 0H6  N10  N  NH1   0  -0.712  -1.6005   0.4610   0.3312
 0H6  O11  O  O     0  -0.426  -0.5676  -0.9013  -1.1782
 0H6  C12  C  CR6   0   0.513  -2.9405   0.1212   0.2150
 0H6  C14  C  CR16  0  -0.137  -4.8058  -1.0438  -0.6759
 0H6  C15  C  CR6   0  -0.179  -5.6256  -0.3515   0.2121
 0H6  N17  N  N     0  -0.448  -3.7126   0.7887   1.0656
 0H6  O19  O  O     0  -0.437  -7.6184  -1.3982  -0.5261
 0H6  O20  O  OH1   0  -0.595  -7.7329   0.1177   1.1083
 0H6  C22  C  CR5   0  -0.190   3.4103  -1.7095   0.3430
 0H6  N23  N  N     0  -0.448   3.3796  -1.5841  -1.0133
 0H6  C24  C  CR15  0   0.112   2.4442  -0.7074  -1.2502
 0H6  F26  F  F     0  -0.317   4.2649  -3.8765   0.5633
 0H6  F27  F  F     0  -0.318   5.6447  -2.2518   0.7893
 0H6  F28  F  F     0  -0.307   4.1846  -2.6370   2.3296
 0H6  H1   H  HCH2  0   0.260   0.9271   1.6113  -1.9325
 0H6  H2   H  HCH2  0   0.264   0.1197   2.5772  -0.7196
 0H6  H3   H  HCH2  0   0.226   4.5090   4.3931  -1.1784
 0H6  H4   H  HCH2  0   0.230   3.4654   5.7734  -0.9122
 0H6  H5   H  HCH2  0   0.217   1.4854   4.5054  -1.4145
 0H6  H6   H  HCH2  0   0.235   2.6251   3.7112  -2.4967
 0H6  H7   H  HCH2  0   0.235   2.6441   2.4346   1.5551
 0H6  H8   H  HCH2  0   0.223   1.4333   3.6372   1.1358
 0H6  H9   H  HCR6  0   0.299  -2.8075  -1.3519  -1.3706
 0H6  H10  H  HCR5  0   0.320   2.2184  -0.7184   1.9572
 0H6  H11  H  HCH2  0   0.229   4.4300   3.9294   1.0839
 0H6  H12  H  HCH2  0   0.230   3.2155   5.1546   1.3676
 0H6  H13  H  HCR6  0   0.284  -5.5900   1.1336   1.7812
 0H6  H14  H  HCH1  0   0.314   0.7577   1.0057   1.0566
 0H6  H15  H  HCH1  0   0.236   3.1175   2.0138  -0.8053
 0H6  H16  H  HNH1  0   0.421  -1.4322   1.1569   1.0453
 0H6  H17  H  HCR6  0   0.284  -5.2295  -1.7659  -1.3610
 0H6  H18  H  HOH1  0   0.490  -8.6798  -0.0851   1.0762
 0H6  H19  H  HCR5  0   0.297   2.1465  -0.3612  -2.2270
 0H6  C25  C  CT    0   1.054   4.3711  -2.6157   1.0049
 0H6  C18  C  C     0   0.531  -7.0806  -0.6089   0.2127

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
 0H6  F28  C25  single    1.338  0.020  1.338
 0H6  F26  C25  single    1.340  0.020  1.340
 0H6  F27  C25  single    1.342  0.020  1.342
 0H6  C25  C22  single    1.477  0.020  1.477
 0H6  C22  C21  aromatic  1.363  0.020  1.363
 0H6  C22  N23  aromatic  1.362  0.020  1.362
 0H6  C21  N1   aromatic  1.362  0.020  1.362
 0H6  N23  C24  aromatic  1.304  0.020  1.304
 0H6  C6   C5   single    1.527  0.020  1.527
 0H6  C6   C7   single    1.531  0.020  1.531
 0H6  O11  C3   double    1.211  0.020  1.211
 0H6  N1   C24  aromatic  1.355  0.020  1.355
 0H6  N1   C2   single    1.446  0.020  1.446
 0H6  C5   C4   single    1.521  0.020  1.521
 0H6  C5   C9   single    1.530  0.020  1.530
 0H6  C4   C2   single    1.533  0.020  1.533
 0H6  C7   C8   single    1.547  0.020  1.547
 0H6  C3   C2   single    1.529  0.020  1.529
 0H6  C3   N10  single    1.358  0.020  1.358
 0H6  C13  C14  aromatic  1.379  0.020  1.379
 0H6  C13  C12  aromatic  1.397  0.020  1.397
 0H6  C8   C9   single    1.538  0.020  1.538
 0H6  C14  C15  aromatic  1.393  0.020  1.393
 0H6  N10  C12  single    1.387  0.020  1.387
 0H6  C12  N17  aromatic  1.329  0.020  1.329
 0H6  O19  C18  double    1.208  0.020  1.208
 0H6  C15  C18  single    1.478  0.020  1.478
 0H6  C15  C16  aromatic  1.391  0.020  1.391
 0H6  N17  C16  aromatic  1.321  0.020  1.321
 0H6  C18  O20  single    1.325  0.020  1.325
 0H6  C4   H1   single    0.970  0.020  1.090
 0H6  C4   H2   single    0.970  0.020  1.090
 0H6  C7   H3   single    0.970  0.020  1.090
 0H6  C7   H4   single    0.970  0.020  1.090
 0H6  C6   H5   single    0.970  0.020  1.090
 0H6  C6   H6   single    0.970  0.020  1.090
 0H6  C9   H7   single    0.970  0.020  1.090
 0H6  C9   H8   single    0.970  0.020  1.090
 0H6  C13  H9   single    0.930  0.020  1.080
 0H6  C21  H10  single    0.930  0.020  1.080
 0H6  C8   H11  single    0.970  0.020  1.090
 0H6  C8   H12  single    0.970  0.020  1.090
 0H6  C16  H13  single    0.930  0.020  1.080
 0H6  C2   H14  single    0.970  0.020  1.090
 0H6  C5   H15  single    0.970  0.020  1.090
 0H6  N10  H16  single    0.860  0.020  1.020
 0H6  C14  H17  single    0.930  0.020  1.080
 0H6  O20  H18  single    0.850  0.020  0.980
 0H6  C24  H19  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
 0H6  H2   C4   H1   106.10  3.000
 0H6  H2   C4   C5   109.24  3.000
 0H6  H1   C4   C5   110.42  3.000
 0H6  H2   C4   C2   107.75  3.000
 0H6  H1   C4   C2   109.68  3.000
 0H6  C5   C4   C2   113.36  3.000
 0H6  H4   C7   H3   106.70  3.000
 0H6  H4   C7   C8   112.49  3.000
 0H6  H3   C7   C8   110.23  3.000
 0H6  H4   C7   C6   112.10  3.000
 0H6  H3   C7   C6   109.80  3.000
 0H6  C8   C7   C6   105.55  3.000
 0H6  H6   C6   H5   107.30  3.000
 0H6  H6   C6   C5   112.83  3.000
 0H6  H5   C6   C5   109.36  3.000
 0H6  H6   C6   C7   112.98  3.000
 0H6  H5   C6   C7   110.51  3.000
 0H6  C5   C6   C7   103.85  3.000
 0H6  H8   C9   H7   106.93  3.000
 0H6  H8   C9   C5   109.14  3.000
 0H6  H7   C9   C5   113.15  3.000
 0H6  H8   C9   C8   110.39  3.000
 0H6  H7   C9   C8   112.44  3.000
 0H6  C5   C9   C8   104.79  3.000
 0H6  H9   C13  C14  120.62  3.000
 0H6  H9   C13  C12  121.92  3.000
 0H6  C14  C13  C12  117.46  3.000
 0H6  H10  C21  C22  132.69  3.000
 0H6  H10  C21  N1   122.38  3.000
 0H6  C22  C21  N1   104.93  3.000
 0H6  H12  C8   H11  106.58  3.000
 0H6  H12  C8   C9   111.15  3.000
 0H6  H11  C8   C9   110.74  3.000
 0H6  H12  C8   C7   111.97  3.000
 0H6  H11  C8   C7   110.51  3.000
 0H6  C9   C8   C7   105.96  3.000
 0H6  H13  C16  N17  115.66  3.000
 0H6  H13  C16  C15  121.19  3.000
 0H6  N17  C16  C15  123.14  3.000
 0H6  C24  N1   C2   127.13  3.000
 0H6  C2   N1   C21  125.54  3.000
 0H6  C24  N1   C21  107.27  3.000
 0H6  H14  C2   C3   109.98  3.000
 0H6  H14  C2   N1   106.72  3.000
 0H6  C3   C2   N1   109.20  3.000
 0H6  H14  C2   C4   108.82  3.000
 0H6  C3   C2   C4   109.95  3.000
 0H6  N1   C2   C4   112.12  3.000
 0H6  O11  C3   N10  125.11  3.000
 0H6  N10  C3   C2   113.24  3.000
 0H6  O11  C3   C2   121.61  3.000
 0H6  H15  C5   C9   108.53  3.000
 0H6  H15  C5   C6   108.03  3.000
 0H6  C9   C5   C6   102.58  3.000
 0H6  H15  C5   C4   109.28  3.000
 0H6  C9   C5   C4   114.83  3.000
 0H6  C6   C5   C4   113.21  3.000
 0H6  H16  N10  C12  112.87  3.000
 0H6  H16  N10  C3   117.75  3.000
 0H6  C12  N10  C3   129.37  3.000
 0H6  N17  C12  N10  112.62  3.000
 0H6  N17  C12  C13  122.76  3.000
 0H6  N10  C12  C13  124.62  3.000
 0H6  H17  C14  C15  120.33  3.000
 0H6  H17  C14  C13  119.35  3.000
 0H6  C15  C14  C13  120.32  3.000
 0H6  C14  C15  C16  117.26  3.000
 0H6  C16  C15  C18  123.19  3.000
 0H6  C14  C15  C18  119.56  3.000
 0H6  C12  N17  C16  119.05  3.000
 0H6  H18  O20  C18  110.12  3.000
 0H6  C25  C22  N23  121.14  3.000
 0H6  N23  C22  C21  110.98  3.000
 0H6  C25  C22  C21  127.87  3.000
 0H6  C24  N23  C22  105.01  3.000
 0H6  H19  C24  N23  125.35  3.000
 0H6  H19  C24  N1   122.83  3.000
 0H6  N23  C24  N1   111.81  3.000
 0H6  F28  C25  F27  107.20  3.000
 0H6  F27  C25  F26  106.10  3.000
 0H6  F28  C25  F26  107.47  3.000
 0H6  F27  C25  C22  112.27  3.000
 0H6  F26  C25  C22  112.20  3.000
 0H6  F28  C25  C22  111.27  3.000
 0H6  O20  C18  O19  123.56  3.000
 0H6  O20  C18  C15  112.92  3.000
 0H6  O19  C18  C15  123.52  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
 0H6  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 0H6  CONST_02  C16  N17  C12  C13    0.00   0.0  0
 0H6  CONST_03  C24  N23  C22  C21    0.00   0.0  0
 0H6  CONST_04  N23  C24  N1   C21    0.00   0.0  0
 0H6  CONST_05  N23  C22  C21  N1     0.00   0.0  0
 0H6  CONST_06  C22  N23  C24  N1     0.00   0.0  0
 0H6  CONST_07  C15  C14  C13  C12    0.00   0.0  0
 0H6  CONST_08  C15  C16  N17  C12    0.00   0.0  0
 0H6  CONST_09  N17  C12  C13  C14    0.00   0.0  0
 0H6  CONST_10  N17  C16  C15  C14    0.00   0.0  0
 0H6  CONST_11  C24  N1   C21  C22    0.00   0.0  0
 0H6  CONST_12  C18  C15  C14  C13  180.00   0.0  0
 0H6  CONST_13  N17  C16  C15  C18  180.00   0.0  0
 0H6  CONST_14  N10  C12  N17  C16  180.00   0.0  0
 0H6  CONST_15  C25  C22  C21  N1   180.00   0.0  0
 0H6  CONST_16  C22  C21  N1   C2   180.00   0.0  0
 0H6  CONST_17  N23  C24  N1   C2   180.00   0.0  0
 0H6  CONST_18  C14  C13  C12  N10  180.00   0.0  0
 0H6  CONST_19  C25  C22  N23  C24  180.00   0.0  0
 0H6  CONST_20  H19  C24  N1   C21  180.00   0.0  0
 0H6  CONST_21  H17  C14  C15  C16  180.00   0.0  0
 0H6  CONST_22  H13  C16  N17  C12  180.00   0.0  0
 0H6  CONST_23  H9   C13  C14  C15  180.00   0.0  0
 0H6  CONST_24  H10  C21  C22  N23  180.00   0.0  0
 0H6  CONST_25  C3   N10  C12  C13    0.00   0.0  0
 0H6  CONST_26  N17  C12  N10  C3   180.00   0.0  0
 0H6  CONST_27  H16  N10  C12  C13  180.00   0.0  0
 0H6  CONST_28  C12  N10  C3   C2   180.00   0.0  0
 0H6  CONST_29  C12  N10  C3   O11    0.00   0.0  0
 0H6  CONST_30  H18  O20  C18  C15  180.00   0.0  0
 0H6  Var_01    C5   C9   C8   C7    19.51  30.0  1
 0H6  Var_02    C9   C8   C7   C6     6.03  30.0  1
 0H6  Var_03    C5   C6   C7   C8   -29.33  30.0  1
 0H6  Var_04    F28  C25  C22  C21    4.28  30.0  3
 0H6  Var_05    O19  C18  C15  C16  179.93  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
 0H6  chir_01  C2  N1  C4  C3  negativ
 0H6  chir_02  C5  C6  C4  C9  positiv

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
 0H6  plan-1  C21  0.020
 0H6  plan-1  N1   0.020
 0H6  plan-1  C2   0.020
 0H6  plan-1  C22  0.020
 0H6  plan-1  N23  0.020
 0H6  plan-1  C24  0.020
 0H6  plan-1  H10  0.020
 0H6  plan-1  H19  0.020
 0H6  plan-1  C25  0.020
 0H6  plan-2  C13  0.020
 0H6  plan-2  C16  0.020
 0H6  plan-2  N10  0.020
 0H6  plan-2  C12  0.020
 0H6  plan-2  C14  0.020
 0H6  plan-2  C15  0.020
 0H6  plan-2  N17  0.020
 0H6  plan-2  H9   0.020
 0H6  plan-2  H13  0.020
 0H6  plan-2  H17  0.020
 0H6  plan-2  C18  0.020
 0H6  plan-3  C2   0.020
 0H6  plan-3  C3   0.020
 0H6  plan-3  N10  0.020
 0H6  plan-3  O11  0.020
 0H6  plan-3  C12  0.020
 0H6  plan-3  H16  0.020
 0H6  plan-4  C15  0.020
 0H6  plan-4  O19  0.020
 0H6  plan-4  O20  0.020
 0H6  plan-4  H18  0.020
 0H6  plan-4  C18  0.020

