# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 01:14:13 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: (3~{R},4~{S})-1-[(2-methoxyphenyl)methyl]-~{N},~{N}-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccccc1CN2C[C@@H]([C@H](C2)c3cn(C)c4ccccc34)N(C)C
#
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
 LQD  LQD  (3~{R},4~{S})-1-[(2-methoxyphenyl)methyl]-~{N},~{N}-dimethyl-4-(1-methylindol-3-yl)pyrrolidin-3-amine  ligand  56  27  .  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_LQD
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
 LQD  C1   C  CR5   0   0.059   2.1490   0.1044   0.0896
 LQD  C2   C  CR15  0  -0.398   1.1360  -0.9038   0.5250
 LQD  C3   C  CR15  0  -0.092   1.9841   1.1355  -0.7932
 LQD  C11  C  CH2   0  -0.291  -1.1948  -1.1885  -0.0744
 LQD  C14  C  CR6   0   0.351  -4.4663   0.0717   0.4251
 LQD  C16  C  CR16  0  -0.379   4.2633  -0.5242   1.4745
 LQD  C18  C  CR16  0  -0.315   5.3982   1.7120   0.1513
 LQD  C19  C  CR16  0  -0.268  -3.1561   2.0389   0.0222
 LQD  C20  C  CH3   0  -0.528  -0.4919  -3.2879  -1.9373
 LQD  C21  C  CH3   0  -0.522   1.8204  -2.9167  -1.5537
 LQD  C22  C  CR16  0  -0.384  -5.4495   0.5676  -0.4319
 LQD  C23  C  CH3   0  -0.435  -5.7182  -1.9052   0.8421
 LQD  C24  C  CR16  0  -0.270   5.5706  -0.1437   1.7097
 LQD  C25  C  CR16  0  -0.284   6.1322   0.9639   1.0529
 LQD  C26  C  CR16  0  -0.276  -4.1281   2.5408  -0.8326
 LQD  C27  C  CR16  0  -0.253  -5.2758   1.7966  -1.0546
 LQD  N4   N  NR5   0  -0.525   3.1364   1.8703  -0.9030
 LQD  C5   C  CR56  0   0.012   3.4945   0.2128   0.5665
 LQD  N6   N  NR5   0  -0.400  -1.0255  -0.0320   0.7765
 LQD  C7   C  CR15  0  -0.022   0.2156  -1.4092  -0.6222
 LQD  C8   C  CR56  0   0.370   4.0783   1.3260  -0.0807
 LQD  C9   C  CH2   0  -0.261   0.1445  -0.3472   1.5646
 LQD  C10  C  CR6   0   0.000  -3.3031   0.8167   0.6652
 LQD  N13  N  NT    0  -0.418   0.4891  -2.7844  -0.9958
 LQD  H1   H  HCR5  0   0.249   1.6603  -1.7567   0.9632
 LQD  H2   H  HCR5  0   0.276   1.1127   1.4139  -1.3664
 LQD  H3   H  HCH2  0   0.189  -1.5223  -2.0776   0.4946
 LQD  H4   H  HCH2  0   0.242  -1.9352  -1.0007  -0.8540
 LQD  H10  H  HCR6  0   0.239   3.8426  -1.3794   1.9907
 LQD  H11  H  HCR6  0   0.261   5.8379   2.5644  -0.3513
 LQD  H12  H  HCR6  0   0.245  -2.2519   2.6099   0.1990
 LQD  H13  H  HCH3  0   0.192  -0.5498  -2.6940  -2.8635
 LQD  H14  H  HCH3  0   0.235  -0.2386  -4.3112  -2.2174
 LQD  H15  H  HCH3  0   0.239  -1.4862  -3.3104  -1.4921
 LQD  H16  H  HCH3  0   0.237   2.5800  -2.6228  -0.8292
 LQD  H17  H  HCH3  0   0.233   2.0070  -3.9581  -1.8191
 LQD  H18  H  HCH3  0   0.191   1.9725  -2.3049  -2.4572
 LQD  H19  H  HCR6  0   0.276  -6.3538   0.0068  -0.6266
 LQD  H20  H  HCH3  0   0.227  -6.6285  -1.3931   1.1653
 LQD  H21  H  HCH3  0   0.226  -5.8322  -2.1952  -0.2056
 LQD  H22  H  HCH3  0   0.258  -5.5914  -2.8038   1.4410
 LQD  H23  H  HCR6  0   0.244   6.1749  -0.7031   2.4122
 LQD  H24  H  HCR6  0   0.247   7.1595   1.2367   1.2571
 LQD  H25  H  HCR6  0   0.248  -3.9896   3.4986  -1.3162
 LQD  H26  H  HCR6  0   0.256  -6.0489   2.1669  -1.7157
 LQD  H28  H  HCR5  0   0.207   0.3395  -0.7501  -1.4988
 LQD  H29  H  HCH2  0   0.194  -0.0691  -1.1165   2.3270
 LQD  H30  H  HCH2  0   0.234   0.5249   0.5340   2.0850
 LQD  C12  C  CH2   0  -0.342  -2.1908   0.3249   1.5561
 LQD  C15  C  CH3   0  -0.528   3.3296   3.0267  -1.7410
 LQD  O17  O  O2    0  -0.468  -4.5646  -1.1184   1.0517
 LQD  H5   H  HCH2  0   0.217  -2.5267  -0.5061   2.1920
 LQD  H6   H  HCH2  0   0.245  -1.9039   1.1363   2.2308
 LQD  H7   H  HCH3  0   0.249   3.5334   3.9167  -1.1450
 LQD  H8   H  HCH3  0   0.250   4.1584   2.8744  -2.4325
 LQD  H9   H  HCH3  0   0.262   2.4279   3.2018  -2.3216

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
 LQD  C23  O17  single    1.412  0.020  1.412
 LQD  O17  C14  single    1.349  0.020  1.349
 LQD  C22  C14  aromatic  1.395  0.020  1.395
 LQD  C22  C27  aromatic  1.389  0.020  1.389
 LQD  C14  C10  aromatic  1.402  0.020  1.402
 LQD  C27  C26  aromatic  1.386  0.020  1.386
 LQD  C10  C12  single    1.508  0.020  1.508
 LQD  C10  C19  aromatic  1.389  0.020  1.389
 LQD  C12  N6   single    1.447  0.020  1.447
 LQD  C26  C19  aromatic  1.388  0.020  1.388
 LQD  C9   N6   single    1.445  0.020  1.445
 LQD  C9   C2   single    1.541  0.020  1.541
 LQD  C24  C25  aromatic  1.405  0.020  1.405
 LQD  C24  C16  aromatic  1.382  0.020  1.382
 LQD  C25  C18  aromatic  1.382  0.020  1.382
 LQD  N6   C11  single    1.446  0.020  1.446
 LQD  C16  C5   aromatic  1.400  0.020  1.400
 LQD  C18  C8   aromatic  1.395  0.020  1.395
 LQD  C5   C8   aromatic  1.414  0.020  1.414
 LQD  C5   C1   aromatic  1.432  0.020  1.432
 LQD  C8   N4   aromatic  1.364  0.020  1.364
 LQD  N4   C15  single    1.441  0.020  1.441
 LQD  N4   C3   aromatic  1.371  0.020  1.371
 LQD  C1   C2   single    1.494  0.020  1.494
 LQD  C1   C3   aromatic  1.367  0.020  1.367
 LQD  C2   C7   single    1.555  0.020  1.555
 LQD  C11  C7   single    1.529  0.020  1.529
 LQD  C7   N13  single    1.451  0.020  1.451
 LQD  N13  C20  single    1.450  0.020  1.450
 LQD  N13  C21  single    1.450  0.020  1.450
 LQD  C2   H1   single    0.970  0.020  1.090
 LQD  C3   H2   single    0.930  0.020  1.080
 LQD  C11  H3   single    0.970  0.020  1.090
 LQD  C11  H4   single    0.970  0.020  1.090
 LQD  C12  H5   single    0.970  0.020  1.090
 LQD  C12  H6   single    0.970  0.020  1.090
 LQD  C15  H7   single    0.970  0.020  1.090
 LQD  C15  H8   single    0.970  0.020  1.090
 LQD  C15  H9   single    0.970  0.020  1.090
 LQD  C16  H10  single    0.930  0.020  1.080
 LQD  C18  H11  single    0.930  0.020  1.080
 LQD  C19  H12  single    0.930  0.020  1.080
 LQD  C20  H13  single    0.970  0.020  1.090
 LQD  C20  H14  single    0.970  0.020  1.090
 LQD  C20  H15  single    0.970  0.020  1.090
 LQD  C21  H16  single    0.970  0.020  1.090
 LQD  C21  H17  single    0.970  0.020  1.090
 LQD  C21  H18  single    0.970  0.020  1.090
 LQD  C22  H19  single    0.930  0.020  1.080
 LQD  C23  H20  single    0.970  0.020  1.090
 LQD  C23  H21  single    0.970  0.020  1.090
 LQD  C23  H22  single    0.970  0.020  1.090
 LQD  C24  H23  single    0.930  0.020  1.080
 LQD  C25  H24  single    0.930  0.020  1.080
 LQD  C26  H25  single    0.930  0.020  1.080
 LQD  C27  H26  single    0.930  0.020  1.080
 LQD  C7   H28  single    0.970  0.020  1.090
 LQD  C9   H29  single    0.970  0.020  1.090
 LQD  C9   H30  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
 LQD  C5   C1   C3   105.74  3.000
 LQD  C3   C1   C2   127.97  3.000
 LQD  C5   C1   C2   126.25  3.000
 LQD  H1   C2   C9   108.67  3.000
 LQD  H1   C2   C7   109.03  3.000
 LQD  C9   C2   C7   103.55  3.000
 LQD  H1   C2   C1   108.56  3.000
 LQD  C7   C2   C1   113.93  3.000
 LQD  C9   C2   C1   112.90  3.000
 LQD  H2   C3   N4   119.84  3.000
 LQD  H2   C3   C1   129.39  3.000
 LQD  N4   C3   C1   110.76  3.000
 LQD  H4   C11  H3   107.77  3.000
 LQD  H4   C11  C7   113.24  3.000
 LQD  H3   C11  C7   109.98  3.000
 LQD  H4   C11  N6   111.24  3.000
 LQD  H3   C11  N6   112.04  3.000
 LQD  C7   C11  N6   102.61  3.000
 LQD  O17  C14  C10  116.74  3.000
 LQD  C10  C14  C22  120.06  3.000
 LQD  O17  C14  C22  123.21  3.000
 LQD  H10  C16  C5   120.75  3.000
 LQD  H10  C16  C24  120.23  3.000
 LQD  C5   C16  C24  119.02  3.000
 LQD  H11  C18  C8   121.66  3.000
 LQD  H11  C18  C25  120.88  3.000
 LQD  C8   C18  C25  117.46  3.000
 LQD  H12  C19  C10  118.45  3.000
 LQD  H12  C19  C26  119.61  3.000
 LQD  C10  C19  C26  121.95  3.000
 LQD  H15  C20  H14  107.31  3.000
 LQD  H15  C20  H13  107.86  3.000
 LQD  H14  C20  H13  107.58  3.000
 LQD  H15  C20  N13  111.05  3.000
 LQD  H14  C20  N13  109.59  3.000
 LQD  H13  C20  N13  113.22  3.000
 LQD  H18  C21  H17  107.88  3.000
 LQD  H18  C21  H16  107.40  3.000
 LQD  H17  C21  H16  107.46  3.000
 LQD  H18  C21  N13  113.06  3.000
 LQD  H17  C21  N13  109.75  3.000
 LQD  H16  C21  N13  111.07  3.000
 LQD  H19  C22  C27  118.86  3.000
 LQD  H19  C22  C14  121.02  3.000
 LQD  C27  C22  C14  120.12  3.000
 LQD  H22  C23  H21  108.71  3.000
 LQD  H22  C23  H20  108.74  3.000
 LQD  H21  C23  H20  108.71  3.000
 LQD  H22  C23  O17  106.47  3.000
 LQD  H21  C23  O17  112.04  3.000
 LQD  H20  C23  O17  112.05  3.000
 LQD  H23  C24  C25  119.19  3.000
 LQD  H23  C24  C16  119.76  3.000
 LQD  C25  C24  C16  121.05  3.000
 LQD  H24  C25  C24  119.34  3.000
 LQD  H24  C25  C18  119.37  3.000
 LQD  C24  C25  C18  121.29  3.000
 LQD  H25  C26  C27  120.66  3.000
 LQD  H25  C26  C19  120.37  3.000
 LQD  C27  C26  C19  118.97  3.000
 LQD  H26  C27  C26  120.37  3.000
 LQD  H26  C27  C22  119.17  3.000
 LQD  C26  C27  C22  120.47  3.000
 LQD  C8   N4   C15  125.33  3.000
 LQD  C15  N4   C3   126.11  3.000
 LQD  C8   N4   C3   108.56  3.000
 LQD  C8   C5   C16  119.00  3.000
 LQD  C8   C5   C1   107.17  3.000
 LQD  C16  C5   C1   133.83  3.000
 LQD  C9   N6   C12  114.33  3.000
 LQD  C9   N6   C11  103.96  3.000
 LQD  C12  N6   C11  114.84  3.000
 LQD  H28  C7   N13  109.89  3.000
 LQD  H28  C7   C11  107.58  3.000
 LQD  N13  C7   C11  113.76  3.000
 LQD  H28  C7   C2   108.99  3.000
 LQD  N13  C7   C2   112.73  3.000
 LQD  C11  C7   C2   103.58  3.000
 LQD  C5   C8   N4   107.76  3.000
 LQD  N4   C8   C18  130.05  3.000
 LQD  C5   C8   C18  122.18  3.000
 LQD  H30  C9   H29  107.50  3.000
 LQD  H30  C9   N6   111.46  3.000
 LQD  H29  C9   N6   111.83  3.000
 LQD  H30  C9   C2   112.89  3.000
 LQD  H29  C9   C2   109.81  3.000
 LQD  N6   C9   C2   103.40  3.000
 LQD  C19  C10  C14  118.43  3.000
 LQD  C19  C10  C12  118.86  3.000
 LQD  C14  C10  C12  122.68  3.000
 LQD  C7   N13  C21  111.02  3.000
 LQD  C21  N13  C20  109.86  3.000
 LQD  C7   N13  C20  111.64  3.000
 LQD  H6   C12  H5   106.51  3.000
 LQD  H6   C12  C10  108.42  3.000
 LQD  H5   C12  C10  111.29  3.000
 LQD  H6   C12  N6   107.71  3.000
 LQD  H5   C12  N6   111.81  3.000
 LQD  C10  C12  N6   110.87  3.000
 LQD  H9   C15  H8   108.33  3.000
 LQD  H9   C15  H7   108.40  3.000
 LQD  H8   C15  H7   108.58  3.000
 LQD  H9   C15  N4   109.19  3.000
 LQD  H8   C15  N4   111.03  3.000
 LQD  H7   C15  N4   111.23  3.000
 LQD  C23  O17  C14  118.84  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
 LQD  CONST_01  C24  C16  C5   C1   180.00   0.0  0
 LQD  CONST_02  C18  C8   C5   C1   180.00   0.0  0
 LQD  CONST_03  N4   C8   C5   C1     0.00   0.0  0
 LQD  CONST_04  C8   N4   C3   C1     0.00   0.0  0
 LQD  CONST_05  C18  C8   N4   C3   180.00   0.0  0
 LQD  CONST_06  C5   C8   N4   C3     0.00   0.0  0
 LQD  CONST_07  C16  C5   C1   C3   180.00   0.0  0
 LQD  CONST_08  C8   C5   C1   C3     0.00   0.0  0
 LQD  CONST_09  C26  C27  C22  C14    0.00   0.0  0
 LQD  CONST_10  C26  C19  C10  C14    0.00   0.0  0
 LQD  CONST_11  C18  C25  C24  C16    0.00   0.0  0
 LQD  CONST_12  C18  C8   C5   C16    0.00   0.0  0
 LQD  CONST_13  N4   C8   C5   C16  180.00   0.0  0
 LQD  CONST_14  C22  C14  C10  C19    0.00   0.0  0
 LQD  CONST_15  C22  C27  C26  C19    0.00   0.0  0
 LQD  CONST_16  C8   C18  C25  C24    0.00   0.0  0
 LQD  CONST_17  C8   C5   C16  C24    0.00   0.0  0
 LQD  CONST_18  C5   C16  C24  C25    0.00   0.0  0
 LQD  CONST_19  C5   C8   C18  C25    0.00   0.0  0
 LQD  CONST_20  N4   C8   C18  C25  180.00   0.0  0
 LQD  CONST_21  C10  C14  C22  C27    0.00   0.0  0
 LQD  CONST_22  C10  C19  C26  C27    0.00   0.0  0
 LQD  CONST_23  C5   C1   C3   N4     0.00   0.0  0
 LQD  CONST_24  C16  C5   C1   C2     0.00   0.0  0
 LQD  CONST_25  C8   C5   C1   C2   180.00   0.0  0
 LQD  CONST_26  N4   C3   C1   C2   180.00   0.0  0
 LQD  CONST_27  C15  N4   C3   C1   180.00   0.0  0
 LQD  CONST_28  C22  C14  C10  C12  180.00   0.0  0
 LQD  CONST_29  C26  C19  C10  C12  180.00   0.0  0
 LQD  CONST_30  C18  C8   N4   C15    0.00   0.0  0
 LQD  CONST_31  C5   C8   N4   C15  180.00   0.0  0
 LQD  CONST_32  O17  C14  C10  C19  180.00   0.0  0
 LQD  CONST_33  O17  C14  C22  C27  180.00   0.0  0
 LQD  CONST_34  H10  C16  C5   C1     0.00   0.0  0
 LQD  CONST_35  H2   C3   C1   C2     0.00   0.0  0
 LQD  CONST_36  H26  C27  C22  C14  180.00   0.0  0
 LQD  CONST_37  H12  C19  C10  C14  180.00   0.0  0
 LQD  CONST_38  H24  C25  C24  C16  180.00   0.0  0
 LQD  CONST_39  H23  C24  C25  C18  180.00   0.0  0
 LQD  CONST_40  H25  C26  C27  C22  180.00   0.0  0
 LQD  CONST_41  H11  C18  C25  C24  180.00   0.0  0
 LQD  CONST_42  H19  C22  C27  C26  180.00   0.0  0
 LQD  Var_01    C11  N6   C9   C2    45.07  30.0  1
 LQD  Var_02    C9   N6   C11  C7   -47.86  30.0  1
 LQD  Var_03    C10  C12  N6   C11  -67.61  30.0  1
 LQD  Var_04    N6   C12  C10  C14  108.73  30.0  2
 LQD  Var_05    C10  C14  O17  C23  179.97  30.0  2
 LQD  Var_06    H7   C15  N4   C3   116.62  30.0  2
 LQD  Var_07    H20  C23  O17  C14  -60.79  30.0  3
 LQD  Var_08    H13  C20  N13  C7    58.23  30.0  3
 LQD  Var_09    H16  C21  N13  C7    60.84  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
 LQD  chir_01  C2  C9   C1  C7   positiv
 LQD  chir_02  C7  N13  C2  C11  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
 LQD  plan-1  C14  0.020
 LQD  plan-1  C19  0.020
 LQD  plan-1  C22  0.020
 LQD  plan-1  C26  0.020
 LQD  plan-1  C27  0.020
 LQD  plan-1  C10  0.020
 LQD  plan-1  H12  0.020
 LQD  plan-1  H19  0.020
 LQD  plan-1  H25  0.020
 LQD  plan-1  H26  0.020
 LQD  plan-1  C12  0.020
 LQD  plan-1  O17  0.020
 LQD  plan-2  C1   0.020
 LQD  plan-2  C2   0.020
 LQD  plan-2  C3   0.020
 LQD  plan-2  C16  0.020
 LQD  plan-2  C18  0.020
 LQD  plan-2  C24  0.020
 LQD  plan-2  C25  0.020
 LQD  plan-2  N4   0.020
 LQD  plan-2  C5   0.020
 LQD  plan-2  C8   0.020
 LQD  plan-2  H2   0.020
 LQD  plan-2  H10  0.020
 LQD  plan-2  H11  0.020
 LQD  plan-2  H23  0.020
 LQD  plan-2  H24  0.020
 LQD  plan-2  C15  0.020

