# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 18:05:13 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H](O)c1ccc(O)cc1)N2CC[C@@H](CC2)Cc3ccccc3
#
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
 QEL  QEL  4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol  ligand  51  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QEL
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
 QEL  C1    C  CR16  0  -0.275  -7.2322   1.3925  -0.3188
 QEL  N1    N  NT    0  -0.458   0.1291  -0.2112  -0.1054
 QEL  O1    O  OH1   0  -0.679   1.9608   0.0415   1.8376
 QEL  C2    C  CR16  0  -0.325   5.9227  -0.7699  -0.7548
 QEL  C3    C  CR16  0  -0.371   5.8840   1.0363   0.8282
 QEL  C4    C  CR6   0   0.143  -5.1308  -0.3255   0.3859
 QEL  C5    C  CR16  0  -0.309  -5.7913  -0.4659  -0.8345
 QEL  C6    C  CR16  0  -0.240  -6.8308   0.3835  -1.1863
 QEL  C7    C  CH2   0  -0.500  -3.9848  -1.2307   0.7427
 QEL  C8    C  CH1   0  -0.235  -2.7036  -0.9277  -0.0401
 QEL  C9    C  CH2   0  -0.410  -2.1959   0.4900   0.1924
 QEL  C01   C  CR16  0  -0.241  -6.5857   1.5410   0.9005
 QEL  C02   C  CR16  0  -0.316  -5.5441   0.6885   1.2461
 QEL  C10   C  CH2   0  -0.280  -0.8808   0.7466  -0.5280
 QEL  C11   C  CH2   0  -0.290  -0.3039  -1.5685  -0.4078
 QEL  C12   C  CH2   0  -0.419  -1.5962  -1.9142   0.3130
 QEL  C13   C  CH1   0  -0.081   1.5153   0.0237  -0.5284
 QEL  C14   C  CH1   0   0.021   2.4046  -0.5127   0.6290
 QEL  C15   C  CR6   0   0.055   3.8675  -0.2364   0.4181
 QEL  C16   C  CR16  0  -0.288   4.5848  -1.0107  -0.4915
 QEL  C18   C  CR6   0   0.338   6.5837   0.2615  -0.0913
 QEL  C19   C  CR16  0  -0.287   4.5405   0.7868   1.0749
 QEL  C24   C  CH3   0  -0.704   1.8237   1.4797  -0.8456
 QEL  H1    H  HCR6  0   0.252  -8.0446   2.0543  -0.5902
 QEL  HO2   H  HOH1  0   0.472   8.2353   1.1930   0.1490
 QEL  H3    H  HCR6  0   0.266   6.3852   1.8400   1.3565
 QEL  H5    H  HCR6  0   0.244  -5.4897  -1.2508  -1.5192
 QEL  H6    H  HCR6  0   0.251  -7.3304   0.2565  -2.1384
 QEL  H7    H  HCH2  0   0.234  -3.7742  -1.1504   1.8136
 QEL  H7A   H  HCH2  0   0.243  -4.2695  -2.2714   0.5585
 QEL  H8    H  HCH1  0   0.218  -2.9203  -1.0388  -1.1113
 QEL  H9    H  HCH2  0   0.234  -2.9319   1.2232  -0.1453
 QEL  H9A   H  HCH2  0   0.211  -2.0505   0.6533   1.2663
 QEL  H01   H  HCR6  0   0.251  -6.8940   2.3196   1.5868
 QEL  H02   H  HCR6  0   0.244  -5.0474   0.8113   2.2017
 QEL  H10   H  HCH2  0   0.247  -0.5492   1.7565  -0.2934
 QEL  H10A  H  HCH2  0   0.192  -1.0486   0.7067  -1.6177
 QEL  H11   H  HCH2  0   0.200  -0.4462  -1.6943  -1.4949
 QEL  H11A  H  HCH2  0   0.241   0.4746  -2.2742  -0.1147
 QEL  H12   H  HCH2  0   0.215  -1.4198  -1.8985   1.3938
 QEL  H12A  H  HCH2  0   0.231  -1.8936  -2.9332   0.0511
 QEL  H13   H  HCH1  0   0.215   1.7481  -0.5610  -1.4316
 QEL  H16   H  HCR6  0   0.247   4.0899  -1.8256  -1.0083
 QEL  H19   H  HCR6  0   0.250   4.0199   1.4091   1.7906
 QEL  H24   H  HCH3  0   0.227   1.6674   2.1374   0.0103
 QEL  H24A  H  HCH3  0   0.253   2.8656   1.5746  -1.1461
 QEL  H24B  H  HCH3  0   0.245   1.2186   1.8452  -1.6741
 QEL  H26   H  HOH1  0   0.434   0.9950   0.0850   1.7223
 QEL  H27   H  HCH1  0   0.211   2.2864  -1.6079   0.6506
 QEL  H2    H  HCR6  0   0.260   6.4606  -1.3840  -1.4667
 QEL  O2    O  OH1   0  -0.636   7.8896   0.4594  -0.3711

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
 QEL  C1   C6    aromatic  1.390  0.020  1.390
 QEL  C1   C01   aromatic  1.388  0.020  1.388
 QEL  C1   H1    single    0.930  0.020  1.080
 QEL  N1   C11   single    1.456  0.020  1.456
 QEL  C2   H2    single    0.930  0.020  1.080
 QEL  O2   HO2   single    0.850  0.020  0.980
 QEL  C3   C18   aromatic  1.391  0.020  1.391
 QEL  C3   H3    single    0.930  0.020  1.080
 QEL  C4   C7    single    1.503  0.020  1.503
 QEL  C5   C4    aromatic  1.395  0.020  1.395
 QEL  C5   H5    single    0.930  0.020  1.080
 QEL  C6   C5    aromatic  1.388  0.020  1.388
 QEL  C6   H6    single    0.930  0.020  1.080
 QEL  C7   H7    single    0.970  0.020  1.090
 QEL  C7   H7A   single    0.970  0.020  1.090
 QEL  C8   C7    single    1.532  0.020  1.532
 QEL  C8   C12   single    1.524  0.020  1.524
 QEL  C8   H8    single    0.970  0.020  1.090
 QEL  C9   C8    single    1.524  0.020  1.524
 QEL  C9   H9    single    0.970  0.020  1.090
 QEL  C9   H9A   single    0.970  0.020  1.090
 QEL  C01  C02   aromatic  1.390  0.020  1.390
 QEL  C01  H01   single    0.930  0.020  1.080
 QEL  C02  C4    aromatic  1.392  0.020  1.392
 QEL  C02  H02   single    0.930  0.020  1.080
 QEL  C10  N1    single    1.455  0.020  1.455
 QEL  C10  C9    single    1.521  0.020  1.521
 QEL  C10  H10   single    0.970  0.020  1.090
 QEL  C10  H10A  single    0.970  0.020  1.090
 QEL  C11  C12   single    1.520  0.020  1.520
 QEL  C11  H11   single    0.970  0.020  1.090
 QEL  C11  H11A  single    0.970  0.020  1.090
 QEL  C12  H12   single    0.970  0.020  1.090
 QEL  C12  H12A  single    0.970  0.020  1.090
 QEL  C13  N1    single    1.468  0.020  1.468
 QEL  C13  C14   single    1.555  0.020  1.555
 QEL  C13  H13   single    0.970  0.020  1.090
 QEL  C14  O1    single    1.402  0.020  1.402
 QEL  C14  C15   single    1.504  0.020  1.504
 QEL  C15  C16   aromatic  1.393  0.020  1.393
 QEL  C16  C2    aromatic  1.385  0.020  1.385
 QEL  C16  H16   single    0.930  0.020  1.080
 QEL  C18  C2    aromatic  1.393  0.020  1.393
 QEL  C18  O2    single    1.350  0.020  1.350
 QEL  C19  C3    aromatic  1.389  0.020  1.389
 QEL  C19  C15   aromatic  1.390  0.020  1.390
 QEL  C19  H19   single    0.930  0.020  1.080
 QEL  C24  C13   single    1.522  0.020  1.522
 QEL  C24  H24   single    0.970  0.020  1.090
 QEL  C24  H24A  single    0.970  0.020  1.090
 QEL  C24  H24B  single    0.970  0.020  1.090
 QEL  O1   H26   single    0.850  0.020  0.980
 QEL  C14  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
 QEL  H1    C1   C01   120.29  3.000
 QEL  H1    C1   C6    120.27  3.000
 QEL  C01   C1   C6    119.44  3.000
 QEL  C13   N1   C11   111.72  3.000
 QEL  C13   N1   C10   117.80  3.000
 QEL  C11   N1   C10   110.30  3.000
 QEL  H26   O1   C14   103.27  3.000
 QEL  H2    C2   C18   119.81  3.000
 QEL  C18   C2   C16   119.77  3.000
 QEL  H2    C2   C16   120.41  3.000
 QEL  H3    C3   C19   119.59  3.000
 QEL  C19   C3   C18   120.27  3.000
 QEL  H3    C3   C18   120.15  3.000
 QEL  C02   C4   C7    121.21  3.000
 QEL  C02   C4   C5    118.25  3.000
 QEL  C7    C4   C5    120.53  3.000
 QEL  H5    C5   C6    119.43  3.000
 QEL  C6    C5   C4    120.99  3.000
 QEL  H5    C5   C4    119.58  3.000
 QEL  H6    C6   C5    119.79  3.000
 QEL  H6    C6   C1    120.05  3.000
 QEL  C5    C6   C1    120.16  3.000
 QEL  H7A   C7   H7    106.52  3.000
 QEL  H7A   C7   C8    108.64  3.000
 QEL  H7    C7   C8    108.94  3.000
 QEL  C8    C7   C4    113.41  3.000
 QEL  H7A   C7   C4    109.53  3.000
 QEL  H7    C7   C4    109.56  3.000
 QEL  H8    C8   C12   107.68  3.000
 QEL  H8    C8   C9    107.97  3.000
 QEL  C12   C8   C9    108.95  3.000
 QEL  C9    C8   C7    112.63  3.000
 QEL  H8    C8   C7    108.26  3.000
 QEL  C12   C8   C7    111.18  3.000
 QEL  H9A   C9   H9    106.99  3.000
 QEL  H9A   C9   C10   108.91  3.000
 QEL  H9    C9   C10   108.83  3.000
 QEL  C10   C9   C8    111.88  3.000
 QEL  H9A   C9   C8    109.42  3.000
 QEL  H9    C9   C8    110.66  3.000
 QEL  H01   C01  C02   119.79  3.000
 QEL  H01   C01  C1    120.08  3.000
 QEL  C02   C01  C1    120.13  3.000
 QEL  H02   C02  C01   119.55  3.000
 QEL  H02   C02  C4    119.41  3.000
 QEL  C01   C02  C4    121.03  3.000
 QEL  H10A  C10  H10   107.02  3.000
 QEL  H10A  C10  C9    109.27  3.000
 QEL  H10   C10  C9    108.53  3.000
 QEL  H10A  C10  N1    111.64  3.000
 QEL  H10   C10  N1    109.68  3.000
 QEL  C9    C10  N1    110.58  3.000
 QEL  H11A  C11  H11   106.44  3.000
 QEL  H11A  C11  C12   109.41  3.000
 QEL  H11   C11  C12   109.37  3.000
 QEL  H11A  C11  N1    109.56  3.000
 QEL  H11   C11  N1    110.44  3.000
 QEL  C12   C11  N1    111.49  3.000
 QEL  H12A  C12  H12   107.07  3.000
 QEL  H12A  C12  C11   109.25  3.000
 QEL  H12   C12  C11   109.14  3.000
 QEL  H12A  C12  C8    110.49  3.000
 QEL  H12   C12  C8    109.65  3.000
 QEL  C11   C12  C8    111.14  3.000
 QEL  H13   C13  C24   107.12  3.000
 QEL  C24   C13  C14   111.67  3.000
 QEL  H13   C13  C14   107.85  3.000
 QEL  C24   C13  N1    113.86  3.000
 QEL  H13   C13  N1    110.55  3.000
 QEL  C14   C13  N1    105.68  3.000
 QEL  H27   C14  C15   106.84  3.000
 QEL  H27   C14  C13   107.23  3.000
 QEL  C15   C14  C13   112.87  3.000
 QEL  H27   C14  O1    110.01  3.000
 QEL  C15   C14  O1    110.87  3.000
 QEL  C13   C14  O1    108.92  3.000
 QEL  C19   C15  C16   117.92  3.000
 QEL  C19   C15  C14   122.69  3.000
 QEL  C16   C15  C14   119.37  3.000
 QEL  H16   C16  C15   119.58  3.000
 QEL  H16   C16  C2    118.75  3.000
 QEL  C15   C16  C2    121.67  3.000
 QEL  C3    C18  O2    122.81  3.000
 QEL  O2    C18  C2    117.95  3.000
 QEL  C3    C18  C2    119.24  3.000
 QEL  H19   C19  C15   120.20  3.000
 QEL  H19   C19  C3    118.67  3.000
 QEL  C15   C19  C3    121.12  3.000
 QEL  H24B  C24  H24A  107.01  3.000
 QEL  H24B  C24  H24   108.36  3.000
 QEL  H24A  C24  H24   107.53  3.000
 QEL  H24B  C24  C13   111.54  3.000
 QEL  H24A  C24  C13   109.56  3.000
 QEL  H24   C24  C13   112.60  3.000
 QEL  HO2   O2   C18   110.29  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
 QEL  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 QEL  CONST_02  C4   C02  C01  C1     0.00   0.0  0
 QEL  CONST_03  C19  C15  C16  C2     0.00   0.0  0
 QEL  CONST_04  C19  C3   C18  C2     0.00   0.0  0
 QEL  CONST_05  C16  C2   C18  C3     0.00   0.0  0
 QEL  CONST_06  C16  C15  C19  C3     0.00   0.0  0
 QEL  CONST_07  C01  C02  C4   C5     0.00   0.0  0
 QEL  CONST_08  C01  C1   C6   C5     0.00   0.0  0
 QEL  CONST_09  C02  C01  C1   C6     0.00   0.0  0
 QEL  CONST_10  C02  C4   C5   C6     0.00   0.0  0
 QEL  CONST_11  C18  C2   C16  C15    0.00   0.0  0
 QEL  CONST_12  C18  C3   C19  C15    0.00   0.0  0
 QEL  CONST_13  C14  C15  C16  C2   180.00   0.0  0
 QEL  CONST_14  C19  C3   C18  O2   180.00   0.0  0
 QEL  CONST_15  C16  C2   C18  O2   180.00   0.0  0
 QEL  CONST_16  C14  C15  C19  C3   180.00   0.0  0
 QEL  CONST_17  C7   C4   C5   C6   180.00   0.0  0
 QEL  CONST_18  C01  C02  C4   C7   180.00   0.0  0
 QEL  CONST_19  H5   C5   C6   C1   180.00   0.0  0
 QEL  CONST_20  H02  C02  C01  C1   180.00   0.0  0
 QEL  CONST_21  H3   C3   C18  C2   180.00   0.0  0
 QEL  CONST_22  H2   C2   C18  C3   180.00   0.0  0
 QEL  CONST_23  H6   C6   C5   C4   180.00   0.0  0
 QEL  CONST_24  H01  C01  C02  C4   180.00   0.0  0
 QEL  CONST_25  H1   C1   C6   C5   180.00   0.0  0
 QEL  CONST_26  H19  C19  C15  C16  180.00   0.0  0
 QEL  CONST_27  H16  C16  C2   C18  180.00   0.0  0
 QEL  Var_01    C8   C12  C11  N1    57.13  30.0  1
 QEL  Var_02    C8   C9   C10  N1   -57.40  30.0  1
 QEL  Var_03    C11  N1   C10  C9    60.09  30.0  1
 QEL  Var_04    C12  C11  N1   C10  -60.49  30.0  1
 QEL  Var_05    C8   C7   C4   C5    72.86  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
 QEL  chir_01  C8   C7  C12  C9   positiv
 QEL  chir_02  C13  N1  C14  C24  positiv
 QEL  chir_03  C14  O1  C13  C15  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
 QEL  plan-1  C1   0.020
 QEL  plan-1  C4   0.020
 QEL  plan-1  C5   0.020
 QEL  plan-1  C6   0.020
 QEL  plan-1  C7   0.020
 QEL  plan-1  C01  0.020
 QEL  plan-1  C02  0.020
 QEL  plan-1  H1   0.020
 QEL  plan-1  H5   0.020
 QEL  plan-1  H6   0.020
 QEL  plan-1  H01  0.020
 QEL  plan-1  H02  0.020
 QEL  plan-2  C2   0.020
 QEL  plan-2  C3   0.020
 QEL  plan-2  C14  0.020
 QEL  plan-2  C15  0.020
 QEL  plan-2  C16  0.020
 QEL  plan-2  C18  0.020
 QEL  plan-2  C19  0.020
 QEL  plan-2  H3   0.020
 QEL  plan-2  H16  0.020
 QEL  plan-2  H19  0.020
 QEL  plan-2  H2   0.020
 QEL  plan-2  O2   0.020

