# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 21:59:19 2021
#   Inital geometry file: a 137 line input string
#   Ligand name: [(2~{S})-2-(phenylcarbamoyloxy)-3-piperidin-1-yl-propyl] ~{N}-phenylcarbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccccc1)OC[C@H](CN2CCCCC2)OC(=O)Nc3ccccc3
#
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
 QKT  QKT  '[(2~{S})-2-(phenylcarbamoyloxy)-3-piperidin-1-yl-propyl] ~{N}-phenylcarbamate'  ligand  56  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 OK
;

data_comp_QKT
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
 QKT  C2   C  CR6   0   0.355  16.9546  -15.2971   9.0575
 QKT  C3   C  CR16  0  -0.328  16.0661  -14.5148   9.7954
 QKT  C4   C  CR16  0  -0.248  15.9911  -14.6472  11.1729
 QKT  C5   C  CR16  0  -0.270  16.7934  -15.5667  11.8352
 QKT  C11  C  CH2   0  -0.213  17.7737  -16.2014   4.4132
 QKT  C12  C  CH1   0  -0.010  19.2308  -15.8448   4.1658
 QKT  C17  C  CR6   0   0.361  21.2699  -18.2121   7.8455
 QKT  C18  C  CR16  0  -0.338  21.3588  -17.8798   9.1993
 QKT  C19  C  CR16  0  -0.247  21.6577  -18.8463  10.1454
 QKT  C20  C  CR16  0  -0.272  21.8687  -20.1637   9.7601
 QKT  C21  C  CR16  0  -0.249  21.7885  -20.4920   8.4143
 QKT  C22  C  CR16  0  -0.304  21.4997  -19.5311   7.4543
 QKT  C23  C  CH2   0  -0.314  19.7596  -16.5076   2.8930
 QKT  C25  C  CH2   0  -0.286  21.9584  -17.3666   2.1624
 QKT  C26  C  CH2   0  -0.469  22.1977  -17.2576   0.6441
 QKT  C27  C  CH2   0  -0.439  21.1009  -16.4299  -0.0133
 QKT  C28  C  CH2   0  -0.459  21.0862  -15.0082   0.5635
 QKT  C29  C  CH2   0  -0.328  21.4835  -15.0193   2.0529
 QKT  C6   C  CR16  0  -0.249  17.6812  -16.3404  11.1005
 QKT  C7   C  CR16  0  -0.301  17.7740  -16.2100   9.7220
 QKT  C8   C  C     0   0.748  17.3516  -16.0043   6.7380
 QKT  N1   N  NH1   0  -0.761  17.0114  -15.0846   7.6743
 QKT  N16  N  NH1   0  -0.764  20.9862  -17.1766   6.9503
 QKT  N24  N  NT    0  -0.417  21.1738  -16.2706   2.7162
 QKT  O10  O  O2    0  -0.484  17.2580  -15.4627   5.5188
 QKT  O13  O  O2    0  -0.495  20.0287  -16.0582   5.3308
 QKT  O15  O  O     0  -0.485  20.0319  -18.3182   5.2138
 QKT  O9   O  O     0  -0.488  17.6782  -17.1467   6.9618
 QKT  H1   H  HCR6  0   0.269  15.4286  -13.8009   9.2870
 QKT  H2   H  HCR6  0   0.260  15.2952  -14.0322  11.7283
 QKT  H3   H  HCR6  0   0.256  16.7297  -15.6766  12.9095
 QKT  H4   H  HCH2  0   0.268  17.1885  -15.8894   3.5483
 QKT  H5   H  HCH2  0   0.257  17.6287  -17.2727   4.5509
 QKT  H6   H  HCH1  0   0.263  19.2911  -14.7606   4.0419
 QKT  H7   H  HCR6  0   0.267  21.1871  -16.8564   9.5138
 QKT  H8   H  HCR6  0   0.259  21.7197  -18.5659  11.1889
 QKT  H9   H  HCR6  0   0.255  22.0970  -20.9219  10.4973
 QKT  H10  H  HCR6  0   0.258  21.9630  -21.5120   8.0965
 QKT  H11  H  HCR6  0   0.269  21.4644  -19.8152   6.4145
 QKT  H12  H  HCH2  0   0.228  19.1443  -16.1185   2.0678
 QKT  H13  H  HCH2  0   0.254  19.5727  -17.5785   2.9284
 QKT  H14  H  HCH2  0   0.227  21.4515  -18.3033   2.3991
 QKT  H15  H  HCH2  0   0.234  22.2519  -18.2562   0.2056
 QKT  H16  H  HCH2  0   0.218  20.1329  -16.9115   0.1544
 QKT  H17  H  HCH2  0   0.234  21.2352  -16.3982  -1.0963
 QKT  H18  H  HCH2  0   0.228  21.7899  -14.3751   0.0171
 QKT  H19  H  HCH2  0   0.226  20.0996  -14.5610   0.4218
 QKT  H20  H  HCH2  0   0.232  22.5606  -14.8518   2.1473
 QKT  H21  H  HCH2  0   0.240  21.0085  -14.1905   2.5825
 QKT  H22  H  HCR6  0   0.256  18.3203  -17.0545  11.6044
 QKT  H23  H  HCR6  0   0.271  18.4859  -16.8121   9.1788
 QKT  H24  H  HNH1  0   0.415  16.6530  -14.2019   7.3413
 QKT  H25  H  HNH1  0   0.409  21.0734  -16.2439   7.3252
 QKT  H26  H  HCH2  0   0.219  22.9239  -17.4110   2.6786
 QKT  H27  H  HCH2  0   0.218  23.1655  -16.7868   0.4469
 QKT  C14  C  C     0   0.766  20.3121  -17.2849   5.7715

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
 QKT  C28  C27  single    1.534  0.020  1.534
 QKT  C28  C29  single    1.542  0.020  1.542
 QKT  C27  C26  single    1.523  0.020  1.523
 QKT  C29  N24  single    1.450  0.020  1.450
 QKT  C26  C25  single    1.541  0.020  1.541
 QKT  N24  C23  single    1.445  0.020  1.445
 QKT  N24  C25  single    1.457  0.020  1.457
 QKT  C23  C12  single    1.529  0.020  1.529
 QKT  C12  C11  single    1.520  0.020  1.520
 QKT  C12  O13  single    1.428  0.020  1.428
 QKT  C11  O10  single    1.426  0.020  1.426
 QKT  O13  C14  single    1.334  0.020  1.334
 QKT  O15  C14  double    1.207  0.020  1.207
 QKT  O10  C8   single    1.337  0.020  1.337
 QKT  C14  N16  single    1.362  0.020  1.362
 QKT  C8   O9   double    1.209  0.020  1.209
 QKT  C8   N1   single    1.356  0.020  1.356
 QKT  N16  C17  single    1.398  0.020  1.398
 QKT  C22  C17  aromatic  1.395  0.020  1.395
 QKT  C22  C21  aromatic  1.389  0.020  1.389
 QKT  N1   C2   single    1.401  0.020  1.401
 QKT  C17  C18  aromatic  1.397  0.020  1.397
 QKT  C21  C20  aromatic  1.388  0.020  1.388
 QKT  C2   C7   aromatic  1.395  0.020  1.395
 QKT  C2   C3   aromatic  1.395  0.020  1.395
 QKT  C18  C19  aromatic  1.385  0.020  1.385
 QKT  C20  C19  aromatic  1.389  0.020  1.389
 QKT  C7   C6   aromatic  1.388  0.020  1.388
 QKT  C3   C4   aromatic  1.386  0.020  1.386
 QKT  C6   C5   aromatic  1.388  0.020  1.388
 QKT  C4   C5   aromatic  1.388  0.020  1.388
 QKT  C3   H1   single    0.930  0.020  1.080
 QKT  C4   H2   single    0.930  0.020  1.080
 QKT  C5   H3   single    0.930  0.020  1.080
 QKT  C11  H4   single    0.970  0.020  1.090
 QKT  C11  H5   single    0.970  0.020  1.090
 QKT  C12  H6   single    0.970  0.020  1.090
 QKT  C18  H7   single    0.930  0.020  1.080
 QKT  C19  H8   single    0.930  0.020  1.080
 QKT  C20  H9   single    0.930  0.020  1.080
 QKT  C21  H10  single    0.930  0.020  1.080
 QKT  C22  H11  single    0.930  0.020  1.080
 QKT  C23  H12  single    0.970  0.020  1.090
 QKT  C23  H13  single    0.970  0.020  1.090
 QKT  C25  H14  single    0.970  0.020  1.090
 QKT  C26  H15  single    0.970  0.020  1.090
 QKT  C27  H16  single    0.970  0.020  1.090
 QKT  C27  H17  single    0.970  0.020  1.090
 QKT  C28  H18  single    0.970  0.020  1.090
 QKT  C28  H19  single    0.970  0.020  1.090
 QKT  C29  H20  single    0.970  0.020  1.090
 QKT  C29  H21  single    0.970  0.020  1.090
 QKT  C6   H22  single    0.930  0.020  1.080
 QKT  C7   H23  single    0.930  0.020  1.080
 QKT  N1   H24  single    0.860  0.020  1.020
 QKT  N16  H25  single    0.860  0.020  1.020
 QKT  C25  H26  single    0.970  0.020  1.090
 QKT  C26  H27  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
 QKT  N1   C2   C7   123.08  3.000
 QKT  C7   C2   C3   119.28  3.000
 QKT  N1   C2   C3   117.59  3.000
 QKT  H1   C3   C4   119.83  3.000
 QKT  H1   C3   C2   119.73  3.000
 QKT  C4   C3   C2   120.44  3.000
 QKT  H2   C4   C5   120.20  3.000
 QKT  H2   C4   C3   119.39  3.000
 QKT  C5   C4   C3   120.41  3.000
 QKT  H3   C5   C6   120.44  3.000
 QKT  H3   C5   C4   120.46  3.000
 QKT  C6   C5   C4   119.09  3.000
 QKT  H5   C11  H4   108.08  3.000
 QKT  H5   C11  O10  111.29  3.000
 QKT  H4   C11  O10  105.83  3.000
 QKT  H5   C11  C12  112.25  3.000
 QKT  H4   C11  C12  108.56  3.000
 QKT  O10  C11  C12  110.56  3.000
 QKT  H6   C12  O13  102.12  3.000
 QKT  H6   C12  C23  108.45  3.000
 QKT  O13  C12  C23  114.90  3.000
 QKT  H6   C12  C11  107.70  3.000
 QKT  O13  C12  C11  111.57  3.000
 QKT  C23  C12  C11  111.42  3.000
 QKT  N16  C17  C22  123.66  3.000
 QKT  C22  C17  C18  119.10  3.000
 QKT  N16  C17  C18  117.22  3.000
 QKT  H7   C18  C19  119.64  3.000
 QKT  H7   C18  C17  119.71  3.000
 QKT  C19  C18  C17  120.64  3.000
 QKT  H8   C19  C20  120.30  3.000
 QKT  H8   C19  C18  119.35  3.000
 QKT  C20  C19  C18  120.35  3.000
 QKT  H9   C20  C21  120.49  3.000
 QKT  H9   C20  C19  120.52  3.000
 QKT  C21  C20  C19  119.00  3.000
 QKT  H10  C21  C22  118.85  3.000
 QKT  H10  C21  C20  119.89  3.000
 QKT  C22  C21  C20  121.25  3.000
 QKT  H11  C22  C21  119.41  3.000
 QKT  H11  C22  C17  120.94  3.000
 QKT  C21  C22  C17  119.65  3.000
 QKT  H13  C23  H12  106.05  3.000
 QKT  H13  C23  N24  109.49  3.000
 QKT  H12  C23  N24  113.42  3.000
 QKT  H13  C23  C12  109.89  3.000
 QKT  H12  C23  C12  106.11  3.000
 QKT  N24  C23  C12  111.67  3.000
 QKT  H26  C25  H14  105.81  3.000
 QKT  H26  C25  N24  109.01  3.000
 QKT  H14  C25  N24  108.25  3.000
 QKT  H26  C25  C26  109.28  3.000
 QKT  H14  C25  C26  110.29  3.000
 QKT  N24  C25  C26  113.88  3.000
 QKT  H27  C26  H15  106.10  3.000
 QKT  H27  C26  C27  108.99  3.000
 QKT  H15  C26  C27  111.06  3.000
 QKT  H27  C26  C25  110.20  3.000
 QKT  H15  C26  C25  109.80  3.000
 QKT  C27  C26  C25  110.60  3.000
 QKT  H17  C27  H16  105.88  3.000
 QKT  H17  C27  C28  110.32  3.000
 QKT  H16  C27  C28  109.98  3.000
 QKT  H17  C27  C26  110.81  3.000
 QKT  H16  C27  C26  109.38  3.000
 QKT  C28  C27  C26  110.37  3.000
 QKT  H19  C28  H18  106.23  3.000
 QKT  H19  C28  C29  111.16  3.000
 QKT  H18  C28  C29  108.74  3.000
 QKT  H19  C28  C27  109.83  3.000
 QKT  H18  C28  C27  110.04  3.000
 QKT  C29  C28  C27  110.73  3.000
 QKT  H21  C29  H20  105.67  3.000
 QKT  H21  C29  N24  109.89  3.000
 QKT  H20  C29  N24  107.64  3.000
 QKT  H21  C29  C28  110.54  3.000
 QKT  H20  C29  C28  109.63  3.000
 QKT  N24  C29  C28  113.16  3.000
 QKT  H22  C6   C7   119.00  3.000
 QKT  H22  C6   C5   119.93  3.000
 QKT  C7   C6   C5   121.08  3.000
 QKT  H23  C7   C6   119.45  3.000
 QKT  H23  C7   C2   120.85  3.000
 QKT  C6   C7   C2   119.69  3.000
 QKT  O9   C8   O10  124.77  3.000
 QKT  O9   C8   N1   125.51  3.000
 QKT  O10  C8   N1   109.71  3.000
 QKT  H24  N1   C8   117.03  3.000
 QKT  H24  N1   C2   116.37  3.000
 QKT  C8   N1   C2   126.10  3.000
 QKT  H25  N16  C17  115.42  3.000
 QKT  H25  N16  C14  115.96  3.000
 QKT  C17  N16  C14  126.57  3.000
 QKT  C29  N24  C25  111.12  3.000
 QKT  C25  N24  C23  116.75  3.000
 QKT  C29  N24  C23  114.00  3.000
 QKT  C8   O10  C11  118.14  3.000
 QKT  C14  O13  C12  121.71  3.000
 QKT  O15  C14  O13  125.82  3.000
 QKT  O15  C14  N16  125.64  3.000
 QKT  O13  C14  N16  108.54  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
 QKT  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 QKT  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 QKT  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 QKT  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 QKT  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 QKT  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 QKT  CONST_07  C20  C21  C22  C17    0.00   0.0  0
 QKT  CONST_08  C20  C19  C18  C17    0.00   0.0  0
 QKT  CONST_09  C21  C22  C17  C18    0.00   0.0  0
 QKT  CONST_10  C21  C20  C19  C18    0.00   0.0  0
 QKT  CONST_11  C22  C17  C18  C19    0.00   0.0  0
 QKT  CONST_12  C22  C21  C20  C19    0.00   0.0  0
 QKT  CONST_13  N1   C2   C3   C4   180.00   0.0  0
 QKT  CONST_14  N16  C17  C18  C19  180.00   0.0  0
 QKT  CONST_15  N16  C17  C22  C21  180.00   0.0  0
 QKT  CONST_16  N1   C2   C7   C6   180.00   0.0  0
 QKT  CONST_17  H22  C6   C7   C2   180.00   0.0  0
 QKT  CONST_18  H2   C4   C3   C2   180.00   0.0  0
 QKT  CONST_19  H23  C7   C2   C3   180.00   0.0  0
 QKT  CONST_20  H3   C5   C4   C3   180.00   0.0  0
 QKT  CONST_21  H1   C3   C4   C5   180.00   0.0  0
 QKT  CONST_22  H10  C21  C22  C17  180.00   0.0  0
 QKT  CONST_23  H8   C19  C18  C17  180.00   0.0  0
 QKT  CONST_24  H11  C22  C17  C18  180.00   0.0  0
 QKT  CONST_25  H9   C20  C19  C18  180.00   0.0  0
 QKT  CONST_26  H7   C18  C19  C20  180.00   0.0  0
 QKT  CONST_32  H25  N16  C17  C18    0.00   0.0  0
 QKT  CONST_33  O10  C8   N1   C2   180.00   0.0  0
 QKT  CONST_34  O9   C8   N1   C2     0.00   0.0  0
 QKT  CONST_35  O13  C14  N16  C17  180.00   0.0  0
 QKT  CONST_36  O15  C14  N16  C17    0.00   0.0  0
 QKT  Var_01    C28  C27  C26  C25   60.74  30.0  1
 QKT  Var_02    C28  C29  N24  C25   64.84  30.0  1
 QKT  Var_03    C29  C28  C27  C26  -33.66  30.0  1
 QKT  Var_04    C29  N24  C25  C26  -35.90  30.0  1
 QKT  Var_05    N24  C29  C28  C27  -27.17  30.0  1
 QKT  Var_06    N24  C25  C26  C27  -25.14  30.0  1
 QKT  Var_07    H4   C11  O10  C8   151.90  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
 QKT  chir_01  C12  C23  C11  O13  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
 QKT  plan-1  C2   0.020
 QKT  plan-1  C3   0.020
 QKT  plan-1  C4   0.020
 QKT  plan-1  C5   0.020
 QKT  plan-1  C6   0.020
 QKT  plan-1  C7   0.020
 QKT  plan-1  N1   0.020
 QKT  plan-1  H1   0.020
 QKT  plan-1  H2   0.020
 QKT  plan-1  H3   0.020
 QKT  plan-1  H22  0.020
 QKT  plan-1  H23  0.020
 QKT  plan-2  C17  0.020
 QKT  plan-2  C18  0.020
 QKT  plan-2  C19  0.020
 QKT  plan-2  C20  0.020
 QKT  plan-2  C21  0.020
 QKT  plan-2  C22  0.020
 QKT  plan-2  N16  0.020
 QKT  plan-2  H7   0.020
 QKT  plan-2  H8   0.020
 QKT  plan-2  H9   0.020
 QKT  plan-2  H10  0.020
 QKT  plan-2  H11  0.020
 QKT  plan-3  C2   0.020
 QKT  plan-3  C8   0.020
 QKT  plan-3  N1   0.020
 QKT  plan-3  H24  0.020
 QKT  plan-4  C17  0.020
 QKT  plan-4  N16  0.020
 QKT  plan-4  H25  0.020
 QKT  plan-4  C14  0.020
 QKT  plan-5  N16  0.020
 QKT  plan-5  O13  0.020
 QKT  plan-5  O15  0.020
 QKT  plan-5  C14  0.020
 QKT  plan-6  C8   0.020
 QKT  plan-6  N1   0.020
 QKT  plan-6  O10  0.020
 QKT  plan-6  O9   0.020

