# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 11:08:22 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (~{R})-[2,8-bis(trifluoromethyl)quinolin-4-yl]-[(2~{S})-piperidin-2-yl]methanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]([C@@H]1CCCCN1)c2cc(nc3c2cccc3C(F)(F)F)C(F)(F)F
#
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
 YMZ  YMZ  (~{R})-[2,8-bis(trifluoromethyl)quinolin-4-yl]-[(2~{S})-piperidin-2-yl]methanol  ligand  42  26  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YMZ
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
 YMZ  FAE  F  F     0  -0.305   4.0555  -2.9249  -0.0886
 YMZ  CAZ  C  CT    0   1.081   3.4202  -1.7463  -0.1396
 YMZ  FAF  F  F     0  -0.311   4.1499  -0.8921   0.5862
 YMZ  FAG  F  F     0  -0.310   3.4773  -1.3401  -1.4125
 YMZ  CAT  C  CR6   0  -0.258   2.0104  -1.8574   0.3614
 YMZ  CAI  C  CR16  0  -0.315   1.5235  -3.0527   0.8132
 YMZ  CAH  C  CR16  0  -0.231   0.2038  -3.1465   1.2930
 YMZ  CAJ  C  CR16  0  -0.350  -0.6134  -2.0535   1.3038
 YMZ  CAU  C  CR66  0   0.101  -0.1555  -0.8009   0.8334
 YMZ  CAV  C  CR66  0   0.219   1.1805  -0.7029   0.3654
 YMZ  NAP  N  N     0  -0.450   1.7062   0.4535  -0.0834
 YMZ  CAR  C  CR6   0  -0.019   0.9499   1.5082  -0.0805
 YMZ  CAY  C  CT    0   1.046   1.5684   2.7912  -0.5779
 YMZ  FAC  F  F     0  -0.314   0.8825   3.2795  -1.6201
 YMZ  FAD  F  F     0  -0.314   1.5443   3.7316   0.3764
 YMZ  FAB  F  F     0  -0.291   2.8286   2.6365  -0.9603
 YMZ  CAK  C  CR16  0  -0.399  -0.3840   1.5296   0.3553
 YMZ  CAS  C  CR6   0   0.282  -0.9570   0.3724   0.8108
 YMZ  CAW  C  CH1   0  -0.058  -2.4044   0.3933   1.2665
 YMZ  OAA  O  OH1   0  -0.651  -2.6938   1.5565   1.9997
 YMZ  CAX  C  CH1   0  -0.134  -3.3483   0.2226   0.0647
 YMZ  CAO  C  CH2   0  -0.426  -4.8227   0.2568   0.4723
 YMZ  CAM  C  CH2   0  -0.443  -5.7131   0.0741  -0.7554
 YMZ  CAL  C  CH2   0  -0.439  -5.3198  -1.1651  -1.5527
 YMZ  CAN  C  CH2   0  -0.312  -3.8253  -1.1515  -1.8578
 YMZ  NAQ  N  NH1   0  -0.579  -2.9955  -0.9789  -0.6724
 YMZ  H1   H  HCR6  0   0.284   2.1388  -3.9412   0.8154
 YMZ  H2   H  HCR6  0   0.280  -0.1596  -4.0982   1.6544
 YMZ  H3   H  HCR6  0   0.265  -1.6170  -2.1591   1.6884
 YMZ  H4   H  HCR6  0   0.273  -0.9440   2.4550   0.3284
 YMZ  H5   H  HCH1  0   0.254  -2.5761  -0.4300   1.9651
 YMZ  H6   H  HOH1  0   0.455  -2.9094   2.2759   1.3970
 YMZ  H7   H  HCH1  0   0.232  -3.1625   1.0687  -0.6158
 YMZ  H8   H  HCH2  0   0.218  -5.0102  -0.5449   1.1962
 YMZ  H9   H  HCH2  0   0.231  -5.0719   1.1970   0.9681
 YMZ  H10  H  HCH2  0   0.234  -6.7608   0.0196  -0.4519
 YMZ  H11  H  HCH2  0   0.216  -5.6222   0.9581  -1.3958
 YMZ  H12  H  HCH2  0   0.215  -5.5652  -2.0677  -0.9828
 YMZ  H13  H  HCH2  0   0.228  -5.8918  -1.2185  -2.4826
 YMZ  H14  H  HCH2  0   0.237  -3.5235  -2.0748  -2.3560
 YMZ  H15  H  HCH2  0   0.218  -3.6002  -0.3322  -2.5490
 YMZ  H16  H  HNH1  0   0.338  -3.1338  -1.7880  -0.0744

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
 YMZ  CAM  CAL  single    1.525  0.020  1.525
 YMZ  CAM  CAO  single    1.528  0.020  1.528
 YMZ  CAL  CAN  single    1.525  0.020  1.525
 YMZ  CAO  CAX  single    1.530  0.020  1.530
 YMZ  CAN  NAQ  single    1.457  0.020  1.457
 YMZ  CAX  NAQ  single    1.453  0.020  1.453
 YMZ  CAX  CAW  single    1.538  0.020  1.538
 YMZ  CAW  OAA  single    1.405  0.020  1.405
 YMZ  CAW  CAS  single    1.518  0.020  1.518
 YMZ  CAS  CAU  aromatic  1.421  0.020  1.421
 YMZ  CAS  CAK  aromatic  1.369  0.020  1.369
 YMZ  CAJ  CAU  aromatic  1.414  0.020  1.414
 YMZ  CAJ  CAH  aromatic  1.365  0.020  1.365
 YMZ  CAU  CAV  aromatic  1.419  0.020  1.419
 YMZ  CAH  CAI  aromatic  1.407  0.020  1.407
 YMZ  CAK  CAR  aromatic  1.403  0.020  1.403
 YMZ  CAV  NAP  aromatic  1.347  0.020  1.347
 YMZ  CAV  CAT  aromatic  1.422  0.020  1.422
 YMZ  CAI  CAT  aromatic  1.367  0.020  1.367
 YMZ  CAR  NAP  aromatic  1.298  0.020  1.298
 YMZ  CAR  CAY  single    1.509  0.020  1.509
 YMZ  FAC  CAY  single    1.340  0.020  1.340
 YMZ  FAD  CAY  single    1.340  0.020  1.340
 YMZ  CAT  CAZ  single    1.500  0.020  1.500
 YMZ  CAY  FAB  single    1.326  0.020  1.326
 YMZ  CAZ  FAE  single    1.340  0.020  1.340
 YMZ  CAZ  FAF  single    1.338  0.020  1.338
 YMZ  CAZ  FAG  single    1.337  0.020  1.337
 YMZ  CAI  H1   single    0.930  0.020  1.080
 YMZ  CAH  H2   single    0.930  0.020  1.080
 YMZ  CAJ  H3   single    0.930  0.020  1.080
 YMZ  CAK  H4   single    0.930  0.020  1.080
 YMZ  CAW  H5   single    0.970  0.020  1.090
 YMZ  OAA  H6   single    0.850  0.020  0.980
 YMZ  CAX  H7   single    0.970  0.020  1.090
 YMZ  CAO  H8   single    0.970  0.020  1.090
 YMZ  CAO  H9   single    0.970  0.020  1.090
 YMZ  CAM  H10  single    0.970  0.020  1.090
 YMZ  CAM  H11  single    0.970  0.020  1.090
 YMZ  CAL  H12  single    0.970  0.020  1.090
 YMZ  CAL  H13  single    0.970  0.020  1.090
 YMZ  CAN  H14  single    0.970  0.020  1.090
 YMZ  CAN  H15  single    0.970  0.020  1.090
 YMZ  NAQ  H16  single    0.890  0.020  1.040

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
 YMZ  CAT  CAZ  FAG  112.36  3.000
 YMZ  FAG  CAZ  FAF  107.41  3.000
 YMZ  CAT  CAZ  FAF  112.25  3.000
 YMZ  FAG  CAZ  FAE  106.45  3.000
 YMZ  FAF  CAZ  FAE  106.41  3.000
 YMZ  CAT  CAZ  FAE  111.58  3.000
 YMZ  CAV  CAT  CAI  120.07  3.000
 YMZ  CAI  CAT  CAZ  120.63  3.000
 YMZ  CAV  CAT  CAZ  119.30  3.000
 YMZ  H1   CAI  CAH  118.58  3.000
 YMZ  H1   CAI  CAT  121.11  3.000
 YMZ  CAH  CAI  CAT  120.31  3.000
 YMZ  H2   CAH  CAJ  120.08  3.000
 YMZ  H2   CAH  CAI  119.20  3.000
 YMZ  CAJ  CAH  CAI  120.72  3.000
 YMZ  H3   CAJ  CAU  120.39  3.000
 YMZ  H3   CAJ  CAH  118.75  3.000
 YMZ  CAU  CAJ  CAH  120.85  3.000
 YMZ  CAS  CAU  CAV  117.95  3.000
 YMZ  CAV  CAU  CAJ  118.41  3.000
 YMZ  CAS  CAU  CAJ  123.64  3.000
 YMZ  NAP  CAV  CAU  122.44  3.000
 YMZ  NAP  CAV  CAT  117.92  3.000
 YMZ  CAU  CAV  CAT  119.63  3.000
 YMZ  CAR  NAP  CAV  118.00  3.000
 YMZ  CAK  CAR  CAY  118.63  3.000
 YMZ  CAY  CAR  NAP  116.83  3.000
 YMZ  CAK  CAR  NAP  124.54  3.000
 YMZ  FAB  CAY  FAD  107.72  3.000
 YMZ  FAB  CAY  FAC  107.74  3.000
 YMZ  FAD  CAY  FAC  106.80  3.000
 YMZ  FAB  CAY  CAR  112.68  3.000
 YMZ  FAD  CAY  CAR  110.77  3.000
 YMZ  FAC  CAY  CAR  110.89  3.000
 YMZ  H4   CAK  CAS  120.97  3.000
 YMZ  H4   CAK  CAR  119.81  3.000
 YMZ  CAS  CAK  CAR  119.22  3.000
 YMZ  CAW  CAS  CAK  119.16  3.000
 YMZ  CAK  CAS  CAU  117.84  3.000
 YMZ  CAW  CAS  CAU  122.99  3.000
 YMZ  H5   CAW  CAX  108.63  3.000
 YMZ  H5   CAW  OAA  104.93  3.000
 YMZ  CAX  CAW  OAA  111.92  3.000
 YMZ  H5   CAW  CAS  109.35  3.000
 YMZ  OAA  CAW  CAS  111.38  3.000
 YMZ  CAX  CAW  CAS  110.44  3.000
 YMZ  H6   OAA  CAW  109.75  3.000
 YMZ  H7   CAX  NAQ  106.31  3.000
 YMZ  H7   CAX  CAO  108.06  3.000
 YMZ  NAQ  CAX  CAO  112.80  3.000
 YMZ  H7   CAX  CAW  107.10  3.000
 YMZ  NAQ  CAX  CAW  109.83  3.000
 YMZ  CAO  CAX  CAW  112.38  3.000
 YMZ  H9   CAO  H8   106.91  3.000
 YMZ  H9   CAO  CAM  109.57  3.000
 YMZ  H8   CAO  CAM  110.09  3.000
 YMZ  H9   CAO  CAX  111.11  3.000
 YMZ  H8   CAO  CAX  108.93  3.000
 YMZ  CAM  CAO  CAX  110.17  3.000
 YMZ  H11  CAM  H10  106.40  3.000
 YMZ  H11  CAM  CAL  109.19  3.000
 YMZ  H10  CAM  CAL  110.61  3.000
 YMZ  H11  CAM  CAO  108.97  3.000
 YMZ  H10  CAM  CAO  109.99  3.000
 YMZ  CAL  CAM  CAO  111.53  3.000
 YMZ  H13  CAL  H12  106.57  3.000
 YMZ  H13  CAL  CAN  110.06  3.000
 YMZ  H12  CAL  CAN  109.33  3.000
 YMZ  H13  CAL  CAM  110.45  3.000
 YMZ  H12  CAL  CAM  109.86  3.000
 YMZ  CAN  CAL  CAM  110.48  3.000
 YMZ  H15  CAN  H14  106.72  3.000
 YMZ  H15  CAN  NAQ  107.92  3.000
 YMZ  H14  CAN  NAQ  108.30  3.000
 YMZ  H15  CAN  CAL  109.53  3.000
 YMZ  H14  CAN  CAL  110.77  3.000
 YMZ  NAQ  CAN  CAL  113.35  3.000
 YMZ  H16  NAQ  CAN  107.88  3.000
 YMZ  H16  NAQ  CAX  109.09  3.000
 YMZ  CAN  NAQ  CAX  111.86  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
 YMZ  CONST_01  CAS  CAU  CAV  CAT   180.00   0.0  0
 YMZ  CONST_02  CAJ  CAU  CAV  CAT     0.00   0.0  0
 YMZ  CONST_03  CAR  NAP  CAV  CAT   180.00   0.0  0
 YMZ  CONST_04  CAJ  CAH  CAI  CAT     0.00   0.0  0
 YMZ  CONST_05  CAU  CAJ  CAH  CAI     0.00   0.0  0
 YMZ  CONST_06  CAU  CAV  CAT  CAI     0.00   0.0  0
 YMZ  CONST_07  NAP  CAV  CAT  CAI   180.00   0.0  0
 YMZ  CONST_08  CAS  CAU  CAJ  CAH   180.00   0.0  0
 YMZ  CONST_09  CAV  CAU  CAJ  CAH     0.00   0.0  0
 YMZ  CONST_10  CAV  CAT  CAI  CAH     0.00   0.0  0
 YMZ  CONST_11  CAK  CAS  CAU  CAJ   180.00   0.0  0
 YMZ  CONST_12  NAP  CAV  CAU  CAJ   180.00   0.0  0
 YMZ  CONST_13  CAR  CAK  CAS  CAU     0.00   0.0  0
 YMZ  CONST_14  CAR  NAP  CAV  CAU     0.00   0.0  0
 YMZ  CONST_15  CAK  CAS  CAU  CAV     0.00   0.0  0
 YMZ  CONST_16  CAK  CAR  NAP  CAV     0.00   0.0  0
 YMZ  CONST_17  CAS  CAU  CAV  NAP     0.00   0.0  0
 YMZ  CONST_18  CAS  CAK  CAR  NAP     0.00   0.0  0
 YMZ  CONST_19  CAU  CAV  CAT  CAZ   180.00   0.0  0
 YMZ  CONST_20  NAP  CAV  CAT  CAZ     0.00   0.0  0
 YMZ  CONST_21  CAH  CAI  CAT  CAZ   180.00   0.0  0
 YMZ  CONST_22  CAW  CAS  CAU  CAJ     0.00   0.0  0
 YMZ  CONST_23  CAW  CAS  CAU  CAV   180.00   0.0  0
 YMZ  CONST_24  CAY  CAR  NAP  CAV   180.00   0.0  0
 YMZ  CONST_25  CAW  CAS  CAK  CAR   180.00   0.0  0
 YMZ  CONST_26  CAS  CAK  CAR  CAY   180.00   0.0  0
 YMZ  CONST_27  H2   CAH  CAI  CAT   180.00   0.0  0
 YMZ  CONST_28  H3   CAJ  CAH  CAI   180.00   0.0  0
 YMZ  CONST_29  H1   CAI  CAH  CAJ   180.00   0.0  0
 YMZ  CONST_30  H4   CAK  CAS  CAU   180.00   0.0  0
 YMZ  Var_01    CAL  CAM  CAO  CAX    52.42  30.0  1
 YMZ  Var_02    CAL  CAN  NAQ  CAX   -55.76  30.0  1
 YMZ  Var_03    CAN  CAL  CAM  CAO   -51.72  30.0  1
 YMZ  Var_04    NAQ  CAN  CAL  CAM    53.36  30.0  1
 YMZ  Var_05    CAV  CAT  CAZ  FAE  -179.31  30.0  3
 YMZ  Var_06    FAC  CAY  CAR  NAP   121.19  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
 YMZ  chir_01  CAW  CAX  OAA  CAS  positiv
 YMZ  chir_02  CAX  NAQ  CAO  CAW  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
 YMZ  plan-1  CAZ  0.020
 YMZ  plan-1  CAT  0.020
 YMZ  plan-1  CAI  0.020
 YMZ  plan-1  CAH  0.020
 YMZ  plan-1  CAJ  0.020
 YMZ  plan-1  CAU  0.020
 YMZ  plan-1  CAV  0.020
 YMZ  plan-1  NAP  0.020
 YMZ  plan-1  CAR  0.020
 YMZ  plan-1  CAY  0.020
 YMZ  plan-1  CAK  0.020
 YMZ  plan-1  CAS  0.020
 YMZ  plan-1  CAW  0.020
 YMZ  plan-1  H1   0.020
 YMZ  plan-1  H2   0.020
 YMZ  plan-1  H3   0.020
 YMZ  plan-1  H4   0.020

