# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 11 08:46:07 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 4-[(quinolin-3-yl)methyl]-N-[4-(trifluoromethoxy)phenyl]piperidine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)Oc1ccc(NC(=O)N2CCC(CC2)Cc3cnc4ccccc4c3)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
 KDS  KDS  4-[(quinolin-3-yl)methyl]-N-[4-(trifluoromethoxy)phenyl]piperidine-1-carboxamide  ligand  53  31  .  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_KDS
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
 KDS  C13  C  CR16  0  -0.292   4.1278  -1.2392  -0.5822
 KDS  C17  C  CH2   0  -0.423  -1.9709   3.1397  -0.8111
 KDS  C20  C  CR6   0   0.052  -4.8388   0.5458  -0.8622
 KDS  C21  C  CR16  0  -0.112  -6.0014   1.0139  -0.1991
 KDS  C24  C  CR16  0  -0.291  -7.8044  -1.9320   0.7112
 KDS  C26  C  CR16  0  -0.256  -6.5809  -3.8744  -0.0370
 KDS  C28  C  CR66  0   0.089  -5.6835  -1.6760  -0.4663
 KDS  O01  O  O     0  -0.518   1.6819   3.0924  -0.1980
 KDS  C02  C  C     0   0.710   0.9898   2.2600   0.3702
 KDS  N03  N  NH1   0  -0.790   1.4535   0.9832   0.6161
 KDS  C04  C  CR6   0   0.384   2.7333   0.5431   0.2717
 KDS  C05  C  CR16  0  -0.289   3.8736   1.3181   0.4864
 KDS  C06  C  CR16  0  -0.298   5.1247   0.8234   0.1575
 KDS  C07  C  CR6   0   0.296   5.2435  -0.4491  -0.3740
 KDS  O08  O  O2    0  -0.523   6.4989  -0.9125  -0.7597
 KDS  C09  C  CT    0   1.071   7.2053  -1.6141   0.1328
 KDS  F10  F  F     0  -0.300   7.4512  -0.9306   1.2525
 KDS  F11  F  F     0  -0.300   6.5986  -2.7457   0.4993
 KDS  F12  F  F     0  -0.278   8.3638  -1.9275  -0.4266
 KDS  C14  C  CR16  0  -0.335   2.8770  -0.7362  -0.2637
 KDS  N15  N  NT    0  -0.474  -0.2632   2.5326   0.8241
 KDS  C16  C  CH2   0  -0.325  -0.9953   3.6477   0.2451
 KDS  C18  C  CH1   0  -0.240  -2.9182   2.0786  -0.2478
 KDS  C19  C  CH2   0  -0.510  -3.8150   1.5209  -1.3598
 KDS  N22  N  N     0  -0.428  -6.9363   0.2516   0.2968
 KDS  C23  C  CR66  0   0.196  -6.8005  -1.0920   0.1790
 KDS  C25  C  CR16  0  -0.261  -7.6948  -3.2925   0.6048
 KDS  C27  C  CR16  0  -0.313  -5.5955  -3.0830  -0.5623
 KDS  C29  C  CR16  0  -0.251  -4.6985  -0.8091  -0.9876
 KDS  C30  C  CH2   0  -0.412  -2.1306   0.9780   0.4638
 KDS  C31  C  CH2   0  -0.365  -1.1495   1.5763   1.4648
 KDS  H1   H  HCR6  0   0.281   4.2181  -2.2267  -1.0152
 KDS  H2   H  HCH2  0   0.242  -2.5451   3.9801  -1.2097
 KDS  H3   H  HCH2  0   0.224  -1.4018   2.7187  -1.6475
 KDS  H4   H  HCR6  0   0.257  -6.1454   2.0863  -0.0919
 KDS  H5   H  HCR6  0   0.260  -8.6560  -1.4757   1.1994
 KDS  H6   H  HCR6  0   0.262  -6.5101  -4.9514  -0.1129
 KDS  H7   H  HNH1  0   0.415   0.7765   0.2484   0.7452
 KDS  H8   H  HCR6  0   0.274   3.7989   2.3027   0.9220
 KDS  H9   H  HCR6  0   0.280   6.0022   1.4368   0.3139
 KDS  H10  H  HCR6  0   0.276   2.0006  -1.3467  -0.4425
 KDS  H11  H  HCH2  0   0.266  -0.3019   4.3695  -0.1771
 KDS  H12  H  HCH2  0   0.241  -1.5401   4.1517   1.0487
 KDS  H13  H  HCH1  0   0.232  -3.5607   2.5664   0.4979
 KDS  H14  H  HCH2  0   0.246  -3.1882   1.0399  -2.1162
 KDS  H15  H  HCH2  0   0.254  -4.3167   2.3577  -1.8547
 KDS  H16  H  HCR6  0   0.262  -8.4675  -3.9302   1.0138
 KDS  H17  H  HCR6  0   0.261  -4.7381  -3.5246  -1.0553
 KDS  H18  H  HCR6  0   0.262  -3.8310  -1.2301  -1.4845
 KDS  H19  H  HCH2  0   0.246  -2.8064   0.3013   0.9912
 KDS  H20  H  HCH2  0   0.223  -1.5885   0.3722  -0.2727
 KDS  H21  H  HCH2  0   0.266  -0.5873   0.8096   1.9948
 KDS  H22  H  HCH2  0   0.261  -1.7026   2.1171   2.2384

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
 KDS  C26  C25  aromatic  1.411  0.020  1.411
 KDS  C26  C27  aromatic  1.369  0.020  1.369
 KDS  C25  C24  aromatic  1.369  0.020  1.369
 KDS  C27  C28  aromatic  1.413  0.020  1.413
 KDS  C24  C23  aromatic  1.413  0.020  1.413
 KDS  C28  C23  aromatic  1.416  0.020  1.416
 KDS  C28  C29  aromatic  1.412  0.020  1.412
 KDS  C23  N22  aromatic  1.356  0.020  1.356
 KDS  C29  C20  aromatic  1.368  0.020  1.368
 KDS  N22  C21  aromatic  1.304  0.020  1.304
 KDS  C20  C21  aromatic  1.418  0.020  1.418
 KDS  C20  C19  single    1.499  0.020  1.499
 KDS  C19  C18  single    1.534  0.020  1.534
 KDS  C17  C18  single    1.530  0.020  1.530
 KDS  C17  C16  single    1.525  0.020  1.525
 KDS  C18  C30  single    1.529  0.020  1.529
 KDS  C30  C31  single    1.524  0.020  1.524
 KDS  C16  N15  single    1.454  0.020  1.454
 KDS  C31  N15  single    1.453  0.020  1.453
 KDS  N15  C02  single    1.360  0.020  1.360
 KDS  C02  N03  single    1.380  0.020  1.380
 KDS  C02  O01  double    1.223  0.020  1.223
 KDS  N03  C04  single    1.397  0.020  1.397
 KDS  C05  C04  aromatic  1.395  0.020  1.395
 KDS  C05  C06  aromatic  1.385  0.020  1.385
 KDS  C04  C14  aromatic  1.394  0.020  1.394
 KDS  C06  C07  aromatic  1.384  0.020  1.384
 KDS  F10  C09  single    1.335  0.020  1.335
 KDS  C14  C13  aromatic  1.385  0.020  1.385
 KDS  C07  C13  aromatic  1.383  0.020  1.383
 KDS  C07  O08  single    1.393  0.020  1.393
 KDS  F12  C09  single    1.324  0.020  1.324
 KDS  C09  O08  single    1.337  0.020  1.337
 KDS  C09  F11  single    1.335  0.020  1.335
 KDS  C13  H1   single    0.930  0.020  1.080
 KDS  C17  H2   single    0.970  0.020  1.090
 KDS  C17  H3   single    0.970  0.020  1.090
 KDS  C21  H4   single    0.930  0.020  1.080
 KDS  C24  H5   single    0.930  0.020  1.080
 KDS  C26  H6   single    0.930  0.020  1.080
 KDS  N03  H7   single    0.890  0.020  1.040
 KDS  C05  H8   single    0.930  0.020  1.080
 KDS  C06  H9   single    0.930  0.020  1.080
 KDS  C14  H10  single    0.930  0.020  1.080
 KDS  C16  H11  single    0.970  0.020  1.090
 KDS  C16  H12  single    0.970  0.020  1.090
 KDS  C18  H13  single    0.970  0.020  1.090
 KDS  C19  H14  single    0.970  0.020  1.090
 KDS  C19  H15  single    0.970  0.020  1.090
 KDS  C25  H16  single    0.930  0.020  1.080
 KDS  C27  H17  single    0.930  0.020  1.080
 KDS  C29  H18  single    0.930  0.020  1.080
 KDS  C30  H19  single    0.970  0.020  1.090
 KDS  C30  H20  single    0.970  0.020  1.090
 KDS  C31  H21  single    0.970  0.020  1.090
 KDS  C31  H22  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
 KDS  H1   C13  C14  119.92  3.000
 KDS  H1   C13  C07  120.96  3.000
 KDS  C14  C13  C07  119.10  3.000
 KDS  H3   C17  H2   106.85  3.000
 KDS  H3   C17  C18  109.64  3.000
 KDS  H2   C17  C18  110.01  3.000
 KDS  H3   C17  C16  108.93  3.000
 KDS  H2   C17  C16  109.42  3.000
 KDS  C18  C17  C16  111.85  3.000
 KDS  C29  C20  C19  122.94  3.000
 KDS  C19  C20  C21  120.04  3.000
 KDS  C29  C20  C21  117.00  3.000
 KDS  H4   C21  N22  116.36  3.000
 KDS  H4   C21  C20  118.70  3.000
 KDS  N22  C21  C20  124.94  3.000
 KDS  H5   C24  C25  121.13  3.000
 KDS  H5   C24  C23  118.57  3.000
 KDS  C25  C24  C23  120.30  3.000
 KDS  H6   C26  C27  120.10  3.000
 KDS  H6   C26  C25  119.60  3.000
 KDS  C27  C26  C25  120.30  3.000
 KDS  C29  C28  C27  122.88  3.000
 KDS  C29  C28  C23  117.74  3.000
 KDS  C27  C28  C23  119.39  3.000
 KDS  N15  C02  N03  115.80  3.000
 KDS  N03  C02  O01  121.49  3.000
 KDS  N15  C02  O01  122.69  3.000
 KDS  H7   N03  C04  114.68  3.000
 KDS  H7   N03  C02  118.15  3.000
 KDS  C04  N03  C02  123.73  3.000
 KDS  C14  C04  C05  118.98  3.000
 KDS  C14  C04  N03  118.58  3.000
 KDS  C05  C04  N03  122.41  3.000
 KDS  H8   C05  C06  118.97  3.000
 KDS  H8   C05  C04  120.81  3.000
 KDS  C06  C05  C04  120.21  3.000
 KDS  H9   C06  C07  120.47  3.000
 KDS  H9   C06  C05  119.72  3.000
 KDS  C07  C06  C05  119.81  3.000
 KDS  O08  C07  C06  119.32  3.000
 KDS  O08  C07  C13  119.70  3.000
 KDS  C06  C07  C13  120.92  3.000
 KDS  C09  O08  C07  117.78  3.000
 KDS  F12  C09  F11  108.24  3.000
 KDS  F11  C09  F10  106.70  3.000
 KDS  F12  C09  F10  108.33  3.000
 KDS  F11  C09  O08  112.82  3.000
 KDS  F12  C09  O08  107.72  3.000
 KDS  F10  C09  O08  112.87  3.000
 KDS  H10  C14  C04  119.82  3.000
 KDS  H10  C14  C13  119.21  3.000
 KDS  C04  C14  C13  120.97  3.000
 KDS  C31  N15  C16  111.92  3.000
 KDS  C31  N15  C02  125.25  3.000
 KDS  C16  N15  C02  118.98  3.000
 KDS  H12  C16  H11  107.29  3.000
 KDS  H12  C16  N15  108.15  3.000
 KDS  H11  C16  N15  110.05  3.000
 KDS  H12  C16  C17  110.10  3.000
 KDS  H11  C16  C17  111.13  3.000
 KDS  N15  C16  C17  110.02  3.000
 KDS  H13  C18  C30  107.76  3.000
 KDS  H13  C18  C19  108.16  3.000
 KDS  C30  C18  C19  112.14  3.000
 KDS  H13  C18  C17  107.70  3.000
 KDS  C30  C18  C17  110.59  3.000
 KDS  C19  C18  C17  110.32  3.000
 KDS  H15  C19  H14  106.64  3.000
 KDS  H15  C19  C18  108.54  3.000
 KDS  H14  C19  C18  109.04  3.000
 KDS  H15  C19  C20  109.54  3.000
 KDS  H14  C19  C20  109.57  3.000
 KDS  C18  C19  C20  113.28  3.000
 KDS  C23  N22  C21  118.32  3.000
 KDS  N22  C23  C28  121.83  3.000
 KDS  N22  C23  C24  119.03  3.000
 KDS  C28  C23  C24  119.14  3.000
 KDS  H16  C25  C26  119.51  3.000
 KDS  H16  C25  C24  119.93  3.000
 KDS  C26  C25  C24  120.55  3.000
 KDS  H17  C27  C28  119.09  3.000
 KDS  H17  C27  C26  120.59  3.000
 KDS  C28  C27  C26  120.32  3.000
 KDS  H18  C29  C28  119.26  3.000
 KDS  H18  C29  C20  120.57  3.000
 KDS  C28  C29  C20  120.18  3.000
 KDS  H20  C30  H19  106.73  3.000
 KDS  H20  C30  C31  109.86  3.000
 KDS  H19  C30  C31  108.93  3.000
 KDS  H20  C30  C18  109.85  3.000
 KDS  H19  C30  C18  110.61  3.000
 KDS  C31  C30  C18  110.78  3.000
 KDS  H22  C31  H21  105.37  3.000
 KDS  H22  C31  C30  109.45  3.000
 KDS  H21  C31  C30  112.07  3.000
 KDS  H22  C31  N15  107.15  3.000
 KDS  H21  C31  N15  111.31  3.000
 KDS  C30  C31  N15  111.19  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
 KDS  CONST_01  C05  C04  C14  C13    0.00   0.0  0
 KDS  CONST_02  C05  C06  C07  C13    0.00   0.0  0
 KDS  CONST_03  C27  C28  C29  C20  180.00   0.0  0
 KDS  CONST_04  C23  C28  C29  C20    0.00   0.0  0
 KDS  CONST_05  C23  N22  C21  C20    0.00   0.0  0
 KDS  CONST_06  C24  C23  N22  C21  180.00   0.0  0
 KDS  CONST_07  C28  C23  N22  C21    0.00   0.0  0
 KDS  CONST_08  C28  C29  C20  C21    0.00   0.0  0
 KDS  CONST_09  C27  C26  C25  C24    0.00   0.0  0
 KDS  CONST_10  C27  C28  C23  C24    0.00   0.0  0
 KDS  CONST_11  C29  C28  C23  C24  180.00   0.0  0
 KDS  CONST_12  C23  C24  C25  C26    0.00   0.0  0
 KDS  CONST_13  C23  C28  C27  C26    0.00   0.0  0
 KDS  CONST_14  C29  C28  C27  C26  180.00   0.0  0
 KDS  CONST_15  C25  C26  C27  C28    0.00   0.0  0
 KDS  CONST_16  C25  C24  C23  C28    0.00   0.0  0
 KDS  CONST_17  C07  C06  C05  C04    0.00   0.0  0
 KDS  CONST_18  C07  C13  C14  C04    0.00   0.0  0
 KDS  CONST_19  C14  C04  C05  C06    0.00   0.0  0
 KDS  CONST_20  C14  C13  C07  C06    0.00   0.0  0
 KDS  CONST_21  C25  C24  C23  N22  180.00   0.0  0
 KDS  CONST_22  C27  C28  C23  N22  180.00   0.0  0
 KDS  CONST_23  C29  C28  C23  N22    0.00   0.0  0
 KDS  CONST_24  C29  C20  C21  N22    0.00   0.0  0
 KDS  CONST_25  N03  C04  C14  C13  180.00   0.0  0
 KDS  CONST_26  C19  C20  C29  C28  180.00   0.0  0
 KDS  CONST_27  C06  C05  C04  N03  180.00   0.0  0
 KDS  CONST_28  O08  C07  C06  C05  180.00   0.0  0
 KDS  CONST_29  C14  C13  C07  O08  180.00   0.0  0
 KDS  CONST_30  N22  C21  C20  C19  180.00   0.0  0
 KDS  CONST_31  H9   C06  C07  C13  180.00   0.0  0
 KDS  CONST_32  H18  C29  C20  C21  180.00   0.0  0
 KDS  CONST_33  H6   C26  C25  C24  180.00   0.0  0
 KDS  CONST_34  H5   C24  C25  C26  180.00   0.0  0
 KDS  CONST_35  H1   C13  C14  C04  180.00   0.0  0
 KDS  CONST_36  H10  C14  C04  C05  180.00   0.0  0
 KDS  CONST_37  H8   C05  C06  C07  180.00   0.0  0
 KDS  CONST_38  H16  C25  C24  C23  180.00   0.0  0
 KDS  CONST_39  H17  C27  C28  C23  180.00   0.0  0
 KDS  CONST_40  H4   C21  N22  C23  180.00   0.0  0
 KDS  CONST_42  C31  N15  C02  O01  180.00   0.0  0
 KDS  CONST_45  N15  C02  N03  C04  180.00   0.0  0
 KDS  CONST_47  C31  N15  C02  N03    0.00   0.0  0
 KDS  CONST_49  C04  N03  C02  O01    0.00   0.0  0
 KDS  Var_01    C31  N15  C16  C17  -60.29  30.0  1
 KDS  Var_02    C18  C17  C16  N15   55.48  30.0  1
 KDS  Var_03    C18  C30  C31  N15  -55.55  30.0  1
 KDS  Var_04    C30  C31  N15  C16   60.99  30.0  1
 KDS  Var_05    C18  C19  C20  C21   77.10  30.0  2
 KDS  Var_06    F10  C09  O08  C07  -59.17  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
 KDS  chir_01  C18  C19  C17  C30  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
 KDS  plan-1  C13  0.020
 KDS  plan-1  N03  0.020
 KDS  plan-1  C04  0.020
 KDS  plan-1  C05  0.020
 KDS  plan-1  C06  0.020
 KDS  plan-1  C07  0.020
 KDS  plan-1  O08  0.020
 KDS  plan-1  C14  0.020
 KDS  plan-1  H1   0.020
 KDS  plan-1  H8   0.020
 KDS  plan-1  H9   0.020
 KDS  plan-1  H10  0.020
 KDS  plan-2  C20  0.020
 KDS  plan-2  C21  0.020
 KDS  plan-2  C24  0.020
 KDS  plan-2  C26  0.020
 KDS  plan-2  C28  0.020
 KDS  plan-2  C19  0.020
 KDS  plan-2  N22  0.020
 KDS  plan-2  C23  0.020
 KDS  plan-2  C25  0.020
 KDS  plan-2  C27  0.020
 KDS  plan-2  C29  0.020
 KDS  plan-2  H4   0.020
 KDS  plan-2  H5   0.020
 KDS  plan-2  H6   0.020
 KDS  plan-2  H16  0.020
 KDS  plan-2  H17  0.020
 KDS  plan-2  H18  0.020
 KDS  plan-3  O01  0.020
 KDS  plan-3  C02  0.020
 KDS  plan-3  N03  0.020
 KDS  plan-3  C04  0.020
 KDS  plan-3  N15  0.020
 KDS  plan-3  C16  0.020
 KDS  plan-3  C31  0.020
 KDS  plan-3  H7   0.020

