# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 00:35:40 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 4-(3-{[5-(trifluoromethyl)pyridin-2-yl]oxy}benzyl)piperidine-1-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)N1CCC(CC1)Cc2cccc(Oc3ccc(cn3)C(F)(F)F)c2
#
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
 PIX  PIX  '4-(3-{[5-(trifluoromethyl)pyridin-2-yl]oxy}benzyl)piperidine-1-carboxylic acid'  ligand  45  27  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PIX
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
 PIX  O9    O  O      0  -0.646  -7.3086  -1.4992   1.6186
 PIX  C8    C  C      0   0.518  -6.6456  -1.6002   0.5639
 PIX  N3    N  NT     0  -0.473  -6.2781  -0.3940  -0.0785
 PIX  C2    C  CH2    0  -0.299  -6.3013   0.8408   0.6739
 PIX  C1    C  CH2    0  -0.421  -4.9755   1.0925   1.3886
 PIX  C4    C  CH2    0  -0.296  -5.2181  -0.4089  -1.0620
 PIX  C5    C  CH2    0  -0.414  -3.8437  -0.2010  -0.4287
 PIX  C6    C  CH1    0  -0.230  -3.8132   1.0844   0.3963
 PIX  C7    C  CH2    0  -0.502  -2.4748   1.2995   1.1130
 PIX  C12   C  CR6    0   0.146  -1.3198   1.4632   0.1659
 PIX  C13   C  CR16   0  -0.311  -1.1472   2.6585  -0.5298
 PIX  C14   C  CR16   0  -0.241  -0.1127   2.8084  -1.4418
 PIX  C15   C  CR16   0  -0.324   0.7765   1.7689  -1.6753
 PIX  C17   C  CR16   0  -0.378  -0.4209   0.4252  -0.0631
 PIX  C16   C  CR6    0   0.374   0.6080   0.5865  -0.9755
 PIX  O18   O  O2     0  -0.513   1.4346  -0.4894  -1.2342
 PIX  C19   C  CR6    0   0.534   2.6822  -0.4960  -0.7400
 PIX  C20   C  CR16   0  -0.376   3.5246  -1.5252  -1.1675
 PIX  C21   C  CR16   0  -0.148   4.8061  -1.5465  -0.6701
 PIX  N24   N  N      0  -0.440   3.0444   0.4377   0.1098
 PIX  C23   C  CR16   0  -0.050   4.2828   0.4080   0.5875
 PIX  C24   C  CR6    0  -0.326   5.2057  -0.5600   0.2330
 PIX  C25   C  CT     0   1.065   6.5995  -0.5170   0.7607
 PIX  F28   F  F      0  -0.313   7.4081   0.2164  -0.0204
 PIX  F26   F  F      0  -0.307   6.6592   0.0207   1.9843
 PIX  F27   F  F      0  -0.307   7.1436  -1.7370   0.8361
 PIX  OXT   O  OC    -1  -0.647  -6.3104  -2.6653   0.0024
 PIX  H21C  H  HCH2   0   0.203  -6.4913   1.6709  -0.0183
 PIX  H22C  H  HCH2   0   0.233  -7.1250   0.8189   1.3822
 PIX  H41C  H  HCH2   0   0.233  -5.2488  -1.3449  -1.6139
 PIX  H42C  H  HCH2   0   0.203  -5.3976   0.3956  -1.7864
 PIX  H11C  H  HCH2   0   0.218  -5.0090   2.0488   1.9203
 PIX  H12C  H  HCH2   0   0.210  -4.8228   0.3118   2.1421
 PIX  H6    H  HCH1   0   0.213  -3.9642   1.9258  -0.2945
 PIX  H51C  H  HCH2   0   0.206  -3.6165  -1.0586   0.2151
 PIX  H52C  H  HCH2   0   0.223  -3.0770  -0.1769  -1.2082
 PIX  H71C  H  HCH2   0   0.244  -2.5545   2.1926   1.7404
 PIX  H72C  H  HCH2   0   0.236  -2.2912   0.4605   1.7910
 PIX  H13   H  HCR6   0   0.249  -1.8325   3.4801  -0.3572
 PIX  H17   H  HCR6   0   0.259  -0.5253  -0.5151   0.4658
 PIX  H14   H  HCR6   0   0.260   0.0053   3.7418  -1.9768
 PIX  H15   H  HCR6   0   0.269   1.5810   1.8778  -2.3913
 PIX  H20   H  HCR6   0   0.292   3.1793  -2.2740  -1.8665
 PIX  H21   H  HCR6   0   0.291   5.4846  -2.3265  -0.9889
 PIX  H23   H  HCR6   0   0.285   4.5350   1.1982   1.2851

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
 PIX  O9   C8    deloc     1.250  0.020  1.250
 PIX  C8   N3    single    1.415  0.020  1.415
 PIX  C8   OXT   deloc     1.250  0.020  1.250
 PIX  N3   C2    single    1.446  0.020  1.446
 PIX  N3   C4    single    1.446  0.020  1.446
 PIX  C2   C1    single    1.527  0.020  1.527
 PIX  C1   C6    single    1.528  0.020  1.528
 PIX  C4   C5    single    1.528  0.020  1.528
 PIX  C5   C6    single    1.528  0.020  1.528
 PIX  C6   C7    single    1.533  0.020  1.533
 PIX  C7   C12   single    1.503  0.020  1.503
 PIX  C12  C13   aromatic  1.394  0.020  1.394
 PIX  C12  C17   aromatic  1.392  0.020  1.392
 PIX  C13  C14   aromatic  1.387  0.020  1.387
 PIX  C14  C15   aromatic  1.388  0.020  1.388
 PIX  C15  C16   aromatic  1.384  0.020  1.384
 PIX  C17  C16   aromatic  1.385  0.020  1.385
 PIX  C16  O18   single    1.381  0.020  1.381
 PIX  O18  C19   single    1.342  0.020  1.342
 PIX  C19  C20   aromatic  1.397  0.020  1.397
 PIX  C19  N24   aromatic  1.313  0.020  1.313
 PIX  C20  C21   aromatic  1.375  0.020  1.375
 PIX  C21  C24   aromatic  1.396  0.020  1.396
 PIX  N24  C23   aromatic  1.328  0.020  1.328
 PIX  C23  C24   aromatic  1.384  0.020  1.384
 PIX  C24  C25   single    1.491  0.020  1.491
 PIX  C25  F28   single    1.342  0.020  1.342
 PIX  C25  F26   single    1.338  0.020  1.338
 PIX  C25  F27   single    1.338  0.020  1.338
 PIX  C2   H21C  single    0.970  0.020  1.090
 PIX  C2   H22C  single    0.970  0.020  1.090
 PIX  C4   H41C  single    0.970  0.020  1.090
 PIX  C4   H42C  single    0.970  0.020  1.090
 PIX  C1   H11C  single    0.970  0.020  1.090
 PIX  C1   H12C  single    0.970  0.020  1.090
 PIX  C6   H6    single    0.970  0.020  1.090
 PIX  C5   H51C  single    0.970  0.020  1.090
 PIX  C5   H52C  single    0.970  0.020  1.090
 PIX  C7   H71C  single    0.970  0.020  1.090
 PIX  C7   H72C  single    0.970  0.020  1.090
 PIX  C13  H13   single    0.930  0.020  1.080
 PIX  C17  H17   single    0.930  0.020  1.080
 PIX  C14  H14   single    0.930  0.020  1.080
 PIX  C15  H15   single    0.930  0.020  1.080
 PIX  C20  H20   single    0.930  0.020  1.080
 PIX  C21  H21   single    0.930  0.020  1.080
 PIX  C23  H23   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
 PIX  OXT   C8   N3    116.93  3.000
 PIX  OXT   C8   O9    126.17  3.000
 PIX  N3    C8   O9    116.87  3.000
 PIX  C4    N3   C2    111.99  3.000
 PIX  C4    N3   C8    119.36  3.000
 PIX  C2    N3   C8    119.17  3.000
 PIX  H22C  C2   H21C  107.17  3.000
 PIX  H22C  C2   C1    110.88  3.000
 PIX  H21C  C2   C1    108.71  3.000
 PIX  H22C  C2   N3    109.51  3.000
 PIX  H21C  C2   N3    108.69  3.000
 PIX  C1    C2   N3    111.74  3.000
 PIX  H12C  C1   H11C  107.02  3.000
 PIX  H12C  C1   C6    109.68  3.000
 PIX  H11C  C1   C6    110.08  3.000
 PIX  H12C  C1   C2    108.99  3.000
 PIX  H11C  C1   C2    110.17  3.000
 PIX  C6    C1   C2    110.82  3.000
 PIX  H42C  C4   H41C  106.94  3.000
 PIX  H42C  C4   C5    108.73  3.000
 PIX  H41C  C4   C5    110.68  3.000
 PIX  H42C  C4   N3    108.76  3.000
 PIX  H41C  C4   N3    109.48  3.000
 PIX  C5    C4   N3    112.10  3.000
 PIX  H52C  C5   H51C  106.90  3.000
 PIX  H52C  C5   C6    110.63  3.000
 PIX  H51C  C5   C6    109.69  3.000
 PIX  H52C  C5   C4    109.77  3.000
 PIX  H51C  C5   C4    108.87  3.000
 PIX  C6    C5   C4    110.88  3.000
 PIX  H6    C6   C7    107.83  3.000
 PIX  H6    C6   C5    107.58  3.000
 PIX  C7    C6   C5    112.82  3.000
 PIX  H6    C6   C1    107.43  3.000
 PIX  C7    C6   C1    111.08  3.000
 PIX  C5    C6   C1    109.87  3.000
 PIX  H72C  C7   H71C  106.42  3.000
 PIX  H72C  C7   C12   110.19  3.000
 PIX  H71C  C7   C12   109.17  3.000
 PIX  H72C  C7   C6    109.18  3.000
 PIX  H71C  C7   C6    108.59  3.000
 PIX  C12   C7   C6    113.06  3.000
 PIX  C17   C12  C13   118.52  3.000
 PIX  C17   C12  C7    121.25  3.000
 PIX  C13   C12  C7    120.22  3.000
 PIX  H13   C13  C14   119.63  3.000
 PIX  H13   C13  C12   119.50  3.000
 PIX  C14   C13  C12   120.87  3.000
 PIX  H14   C14  C15   119.54  3.000
 PIX  H14   C14  C13   119.96  3.000
 PIX  C15   C14  C13   120.50  3.000
 PIX  H15   C15  C16   120.71  3.000
 PIX  H15   C15  C14   120.81  3.000
 PIX  C16   C15  C14   118.48  3.000
 PIX  H17   C17  C16   119.62  3.000
 PIX  H17   C17  C12   120.29  3.000
 PIX  C16   C17  C12   120.09  3.000
 PIX  O18   C16  C17   118.52  3.000
 PIX  O18   C16  C15   119.86  3.000
 PIX  C17   C16  C15   121.54  3.000
 PIX  C19   O18  C16   119.42  3.000
 PIX  N24   C19  C20   123.74  3.000
 PIX  N24   C19  O18   119.42  3.000
 PIX  C20   C19  O18   116.84  3.000
 PIX  H20   C20  C21   121.39  3.000
 PIX  H20   C20  C19   121.04  3.000
 PIX  C21   C20  C19   117.57  3.000
 PIX  H21   C21  C24   121.37  3.000
 PIX  H21   C21  C20   119.29  3.000
 PIX  C24   C21  C20   119.34  3.000
 PIX  C23   N24  C19   118.30  3.000
 PIX  H23   C23  C24   121.31  3.000
 PIX  H23   C23  N24   115.62  3.000
 PIX  C24   C23  N24   123.07  3.000
 PIX  C25   C24  C23   120.84  3.000
 PIX  C25   C24  C21   121.13  3.000
 PIX  C23   C24  C21   117.99  3.000
 PIX  F27   C25  F26   107.26  3.000
 PIX  F27   C25  F28   106.62  3.000
 PIX  F26   C25  F28   106.61  3.000
 PIX  F27   C25  C24   111.95  3.000
 PIX  F26   C25  C24   112.15  3.000
 PIX  F28   C25  C24   111.90  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
 PIX  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 PIX  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 PIX  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 PIX  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 PIX  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 PIX  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 PIX  CONST_07  C24  C21  C20  C19     0.00   0.0  0
 PIX  CONST_08  C24  C23  N24  C19     0.00   0.0  0
 PIX  CONST_09  C23  N24  C19  C20     0.00   0.0  0
 PIX  CONST_10  C23  C24  C21  C20     0.00   0.0  0
 PIX  CONST_11  N24  C19  C20  C21     0.00   0.0  0
 PIX  CONST_12  N24  C23  C24  C21     0.00   0.0  0
 PIX  CONST_13  C14  C13  C12  C7    180.00   0.0  0
 PIX  CONST_14  C16  C17  C12  C7    180.00   0.0  0
 PIX  CONST_15  O18  C16  C17  C12   180.00   0.0  0
 PIX  CONST_16  O18  C16  C15  C14   180.00   0.0  0
 PIX  CONST_17  C21  C20  C19  O18   180.00   0.0  0
 PIX  CONST_18  C23  N24  C19  O18   180.00   0.0  0
 PIX  CONST_19  C25  C24  C21  C20   180.00   0.0  0
 PIX  CONST_20  C25  C24  C23  N24   180.00   0.0  0
 PIX  CONST_21  H14  C14  C13  C12   180.00   0.0  0
 PIX  CONST_22  H17  C17  C12  C13   180.00   0.0  0
 PIX  CONST_23  H15  C15  C14  C13   180.00   0.0  0
 PIX  CONST_24  H13  C13  C14  C15   180.00   0.0  0
 PIX  CONST_25  H21  C21  C20  C19   180.00   0.0  0
 PIX  CONST_26  H23  C23  N24  C19   180.00   0.0  0
 PIX  CONST_27  H20  C20  C19  N24   180.00   0.0  0
 PIX  Var_01    C6   C1   C2   N3     55.94  30.0  1
 PIX  Var_02    C6   C5   C4   N3    -55.09  30.0  1
 PIX  Var_03    C5   C4   N3   C2     57.76  30.0  1
 PIX  Var_04    C4   N3   C2   C1    -58.11  30.0  1
 PIX  Var_05    C13  C12  C7   C6     75.28  30.0  2
 PIX  Var_06    C20  C19  O18  C16  -172.34  30.0  2
 PIX  Var_07    C2   N3   C8   O9     18.92  30.0  2
 PIX  Var_08    F28  C25  C24  C21    89.22  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
 PIX  chir_01  C6  C1  C5  C7  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
 PIX  plan-1  C7   0.020
 PIX  plan-1  C12  0.020
 PIX  plan-1  C13  0.020
 PIX  plan-1  C14  0.020
 PIX  plan-1  C15  0.020
 PIX  plan-1  C17  0.020
 PIX  plan-1  C16  0.020
 PIX  plan-1  O18  0.020
 PIX  plan-1  H13  0.020
 PIX  plan-1  H17  0.020
 PIX  plan-1  H14  0.020
 PIX  plan-1  H15  0.020
 PIX  plan-2  O18  0.020
 PIX  plan-2  C19  0.020
 PIX  plan-2  C20  0.020
 PIX  plan-2  C21  0.020
 PIX  plan-2  N24  0.020
 PIX  plan-2  C23  0.020
 PIX  plan-2  C24  0.020
 PIX  plan-2  C25  0.020
 PIX  plan-2  H20  0.020
 PIX  plan-2  H21  0.020
 PIX  plan-2  H23  0.020
 PIX  plan-3  O9   0.020
 PIX  plan-3  C8   0.020
 PIX  plan-3  N3   0.020
 PIX  plan-3  OXT  0.020

