# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:06:44 2021
#   Inital geometry file: a 136 line input string
#   Ligand name: 2-(3,4-dimethoxyphenyl)-5-(piperidin-4-yl)-3-(propan-2-yl)-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1OC)c2[nH]c3ccc(cc3c2C(C)C)C4CCNCC4
#
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
 QSM  QSM  2-(3,4-dimethoxyphenyl)-5-(piperidin-4-yl)-3-(propan-2-yl)-1H-indole  ligand  58  28  .  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_QSM
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
 QSM  N1   N  NH1   0  -0.575  277.0432  35.5255  174.0250
 QSM  C4   C  CR56  0   0.089  277.5929  29.9431  176.9270
 QSM  C5   C  CR16  0  -0.471  277.5239  31.1297  176.1844
 QSM  C6   C  CR5   0   0.271  278.0608  28.1509  178.2026
 QSM  C7   C  CR5   0   0.024  278.6314  29.2841  177.6696
 QSM  C8   C  CH1   0  -0.369  280.0681  29.7029  177.7905
 QSM  C10  C  CH3   0  -0.650  280.2304  30.9439  178.6698
 QSM  C13  C  CR16  0  -0.450  279.4461  27.4416  180.1376
 QSM  C15  C  CR6   0   0.306  279.7896  25.1057  180.6460
 QSM  C17  C  CR16  0  -0.324  278.4101  25.7601  178.7758
 QSM  C20  C  CH2   0  -0.317  277.1713  34.3958  173.1182
 QSM  C21  C  CH2   0  -0.318  275.9870  35.3130  175.0028
 QSM  C22  C  CH2   0  -0.417  276.1086  34.0006  175.7743
 QSM  C23  C  CH3   0  -0.438  280.2028  22.8488  181.2226
 QSM  O1   O  O2    0  -0.461  280.3888  24.2282  181.4688
 QSM  C14  C  CR6   0   0.333  280.0239  26.4680  180.9311
 QSM  O    O  O2    0  -0.464  280.8086  26.7117  181.9962
 QSM  C18  C  CH3   0  -0.442  281.0702  28.0573  182.3387
 QSM  C16  C  CR16  0  -0.373  278.9785  24.7708  179.5746
 QSM  C11  C  CR6   0   0.044  278.6444  27.1011  179.0390
 QSM  N    N  NR15  0  -0.743  276.7509  28.0607  177.7974
 QSM  C3   C  CR56  0   0.317  276.4333  29.1457  177.0364
 QSM  C2   C  CR16  0  -0.303  275.2281  29.5091  176.4424
 QSM  C1   C  CR16  0  -0.356  275.2008  30.6870  175.7214
 QSM  C9   C  CH3   0  -0.646  280.7321  29.9109  176.4279
 QSM  C    C  CR6   0   0.187  276.3376  31.5055  175.5764
 QSM  C12  C  CH1   0  -0.329  276.2220  32.8066  174.8191
 QSM  C19  C  CH2   0  -0.424  277.3568  33.0526  173.8218
 QSM  H22  H  HNH1  0   0.337  277.9208  35.6423  174.5196
 QSM  H2   H  HCR6  0   0.224  278.3946  31.7684  176.1035
 QSM  H4   H  HCH1  0   0.236  280.6080  28.8848  178.2751
 QSM  H8   H  HCH3  0   0.226  279.8341  30.7760  179.6727
 QSM  H10  H  HCH3  0   0.227  281.2834  31.2149  178.7671
 QSM  H9   H  HCH3  0   0.221  279.7066  31.8034  178.2478
 QSM  H12  H  HCR6  0   0.279  279.5820  28.4871  180.3787
 QSM  H14  H  HCR6  0   0.254  277.8034  25.4631  177.9298
 QSM  H20  H  HCH2  0   0.213  276.2700  34.3547  172.4963
 QSM  H21  H  HCH2  0   0.234  278.0070  34.5840  172.4404
 QSM  H23  H  HCH2  0   0.233  275.9765  36.1579  175.6948
 QSM  H24  H  HCH2  0   0.213  275.0259  35.3313  174.4761
 QSM  H25  H  HCH2  0   0.214  276.9956  34.0342  176.4178
 QSM  H26  H  HCH2  0   0.227  275.2457  33.8726  176.4342
 QSM  H27  H  HCH3  0   0.260  280.7544  22.3203  181.9961
 QSM  H28  H  HCH3  0   0.229  279.1500  22.5609  181.2828
 QSM  H29  H  HCH3  0   0.229  280.5934  22.5524  180.2455
 QSM  H15  H  HCH3  0   0.263  281.7310  28.0337  183.2014
 QSM  H17  H  HCH3  0   0.226  281.5693  28.5975  181.5292
 QSM  H16  H  HCH3  0   0.230  280.1577  28.5943  182.6116
 QSM  H13  H  HCR6  0   0.284  278.7818  23.7351  179.3335
 QSM  H3   H  HNR5  0   0.404  276.0912  27.3851  178.1464
 QSM  H1   H  HCR6  0   0.253  274.3418  28.8953  176.5444
 QSM  H    H  HCR6  0   0.239  274.2736  30.9960  175.2523
 QSM  H7   H  HCH3  0   0.228  281.7969  30.1143  176.5547
 QSM  H6   H  HCH3  0   0.228  280.6325  29.0263  175.7981
 QSM  H5   H  HCH3  0   0.216  280.3055  30.7550  175.8852
 QSM  H11  H  HCH1  0   0.227  275.2929  32.7664  174.2349
 QSM  H18  H  HCH2  0   0.229  277.3892  32.2457  173.0843
 QSM  H19  H  HCH2  0   0.214  278.3265  33.0532  174.3305

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
 QSM  C20  N1   single    1.454  0.020  1.454
 QSM  C20  C19  single    1.528  0.020  1.528
 QSM  N1   C21  single    1.455  0.020  1.455
 QSM  C19  C12  single    1.531  0.020  1.531
 QSM  C21  C22  single    1.527  0.020  1.527
 QSM  C12  C22  single    1.533  0.020  1.533
 QSM  C12  C    single    1.510  0.020  1.510
 QSM  C    C1   aromatic  1.408  0.020  1.408
 QSM  C    C5   aromatic  1.385  0.020  1.385
 QSM  C1   C2   aromatic  1.381  0.020  1.381
 QSM  C5   C4   aromatic  1.402  0.020  1.402
 QSM  C9   C8   single    1.530  0.020  1.530
 QSM  C2   C3   aromatic  1.392  0.020  1.392
 QSM  C4   C3   aromatic  1.412  0.020  1.412
 QSM  C4   C7   aromatic  1.437  0.020  1.437
 QSM  C3   N    aromatic  1.363  0.020  1.363
 QSM  C7   C8   single    1.501  0.020  1.501
 QSM  C7   C6   aromatic  1.376  0.020  1.376
 QSM  C8   C10  single    1.530  0.020  1.530
 QSM  N    C6   aromatic  1.374  0.020  1.374
 QSM  C6   C11  single    1.464  0.020  1.464
 QSM  C17  C11  aromatic  1.387  0.020  1.387
 QSM  C17  C16  aromatic  1.393  0.020  1.393
 QSM  C11  C13  aromatic  1.402  0.020  1.402
 QSM  C16  C15  aromatic  1.385  0.020  1.385
 QSM  C13  C14  aromatic  1.383  0.020  1.383
 QSM  C15  C14  aromatic  1.411  0.020  1.411
 QSM  C15  O1   single    1.344  0.020  1.344
 QSM  C23  O1   single    1.414  0.020  1.414
 QSM  C14  O    single    1.345  0.020  1.345
 QSM  O    C18  single    1.413  0.020  1.413
 QSM  N1   H22  single    0.890  0.020  1.040
 QSM  C5   H2   single    0.930  0.020  1.080
 QSM  C8   H4   single    0.970  0.020  1.090
 QSM  C10  H8   single    0.970  0.020  1.090
 QSM  C10  H10  single    0.970  0.020  1.090
 QSM  C10  H9   single    0.970  0.020  1.090
 QSM  C13  H12  single    0.930  0.020  1.080
 QSM  C17  H14  single    0.930  0.020  1.080
 QSM  C20  H20  single    0.970  0.020  1.090
 QSM  C20  H21  single    0.970  0.020  1.090
 QSM  C21  H23  single    0.970  0.020  1.090
 QSM  C21  H24  single    0.970  0.020  1.090
 QSM  C22  H25  single    0.970  0.020  1.090
 QSM  C22  H26  single    0.970  0.020  1.090
 QSM  C23  H27  single    0.970  0.020  1.090
 QSM  C23  H28  single    0.970  0.020  1.090
 QSM  C23  H29  single    0.970  0.020  1.090
 QSM  C18  H15  single    0.970  0.020  1.090
 QSM  C18  H17  single    0.970  0.020  1.090
 QSM  C18  H16  single    0.970  0.020  1.090
 QSM  C16  H13  single    0.930  0.020  1.080
 QSM  N    H3   single    0.860  0.020  1.020
 QSM  C2   H1   single    0.930  0.020  1.080
 QSM  C1   H    single    0.930  0.020  1.080
 QSM  C9   H7   single    0.970  0.020  1.090
 QSM  C9   H6   single    0.970  0.020  1.090
 QSM  C9   H5   single    0.970  0.020  1.090
 QSM  C12  H11  single    0.970  0.020  1.090
 QSM  C19  H18  single    0.970  0.020  1.090
 QSM  C19  H19  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
 QSM  H22  N1   C21  108.49  3.000
 QSM  H22  N1   C20  108.50  3.000
 QSM  C21  N1   C20  111.69  3.000
 QSM  C3   C4   C7   107.14  3.000
 QSM  C7   C4   C5   134.25  3.000
 QSM  C3   C4   C5   118.61  3.000
 QSM  H2   C5   C    119.73  3.000
 QSM  H2   C5   C4   119.96  3.000
 QSM  C    C5   C4   120.30  3.000
 QSM  N    C6   C11  120.10  3.000
 QSM  C11  C6   C7   130.29  3.000
 QSM  N    C6   C7   109.58  3.000
 QSM  C8   C7   C6   126.53  3.000
 QSM  C6   C7   C4   106.15  3.000
 QSM  C8   C7   C4   127.25  3.000
 QSM  H4   C8   C9   106.39  3.000
 QSM  H4   C8   C10  107.45  3.000
 QSM  C9   C8   C10  110.83  3.000
 QSM  H4   C8   C7   107.43  3.000
 QSM  C10  C8   C7   111.97  3.000
 QSM  C9   C8   C7   112.43  3.000
 QSM  H9   C10  H10  107.57  3.000
 QSM  H9   C10  H8   107.58  3.000
 QSM  H10  C10  H8   107.85  3.000
 QSM  H9   C10  C8   111.45  3.000
 QSM  H10  C10  C8   110.80  3.000
 QSM  H8   C10  C8   111.40  3.000
 QSM  H12  C13  C11  118.77  3.000
 QSM  H12  C13  C14  120.02  3.000
 QSM  C11  C13  C14  121.18  3.000
 QSM  C16  C15  C14  119.14  3.000
 QSM  C14  C15  O1   115.63  3.000
 QSM  C16  C15  O1   125.23  3.000
 QSM  H14  C17  C11  120.56  3.000
 QSM  H14  C17  C16  118.82  3.000
 QSM  C11  C17  C16  120.60  3.000
 QSM  H21  C20  H20  106.48  3.000
 QSM  H21  C20  C19  110.14  3.000
 QSM  H20  C20  C19  109.16  3.000
 QSM  H21  C20  N1   108.69  3.000
 QSM  H20  C20  N1   108.09  3.000
 QSM  C19  C20  N1   113.98  3.000
 QSM  H24  C21  H23  106.44  3.000
 QSM  H24  C21  C22  109.08  3.000
 QSM  H23  C21  C22  110.21  3.000
 QSM  H24  C21  N1   108.13  3.000
 QSM  H23  C21  N1   108.65  3.000
 QSM  C22  C21  N1   114.03  3.000
 QSM  H26  C22  H25  106.72  3.000
 QSM  H26  C22  C12  110.06  3.000
 QSM  H25  C22  C12  109.25  3.000
 QSM  H26  C22  C21  110.03  3.000
 QSM  H25  C22  C21  109.55  3.000
 QSM  C12  C22  C21  111.12  3.000
 QSM  H29  C23  H28  108.78  3.000
 QSM  H29  C23  H27  108.84  3.000
 QSM  H28  C23  H27  108.75  3.000
 QSM  H29  C23  O1   111.91  3.000
 QSM  H28  C23  O1   111.97  3.000
 QSM  H27  C23  O1   106.48  3.000
 QSM  C23  O1   C15  118.16  3.000
 QSM  O    C14  C15  115.57  3.000
 QSM  O    C14  C13  124.80  3.000
 QSM  C15  C14  C13  119.63  3.000
 QSM  C18  O    C14  118.19  3.000
 QSM  H16  C18  H17  108.85  3.000
 QSM  H16  C18  H15  108.66  3.000
 QSM  H17  C18  H15  108.71  3.000
 QSM  H16  C18  O    111.94  3.000
 QSM  H17  C18  O    112.05  3.000
 QSM  H15  C18  O    106.51  3.000
 QSM  H13  C16  C17  118.56  3.000
 QSM  H13  C16  C15  120.71  3.000
 QSM  C17  C16  C15  120.73  3.000
 QSM  C17  C11  C13  118.70  3.000
 QSM  C13  C11  C6   120.11  3.000
 QSM  C17  C11  C6   121.19  3.000
 QSM  H3   N    C3   125.12  3.000
 QSM  H3   N    C6   124.50  3.000
 QSM  C3   N    C6   109.55  3.000
 QSM  C2   C3   N    130.38  3.000
 QSM  N    C3   C4   107.55  3.000
 QSM  C2   C3   C4   122.06  3.000
 QSM  H1   C2   C1   121.08  3.000
 QSM  H1   C2   C3   121.37  3.000
 QSM  C1   C2   C3   117.55  3.000
 QSM  H    C1   C    118.70  3.000
 QSM  H    C1   C2   119.07  3.000
 QSM  C    C1   C2   122.23  3.000
 QSM  H5   C9   H6   107.74  3.000
 QSM  H5   C9   H7   107.17  3.000
 QSM  H6   C9   H7   107.90  3.000
 QSM  H5   C9   C8   112.25  3.000
 QSM  H6   C9   C8   111.38  3.000
 QSM  H7   C9   C8   110.20  3.000
 QSM  C12  C    C1   119.38  3.000
 QSM  C1   C    C5   119.24  3.000
 QSM  C12  C    C5   121.31  3.000
 QSM  H11  C12  C19  106.65  3.000
 QSM  H11  C12  C    107.46  3.000
 QSM  C19  C12  C    114.11  3.000
 QSM  H11  C12  C22  107.30  3.000
 QSM  C    C12  C22  111.36  3.000
 QSM  C19  C12  C22  109.60  3.000
 QSM  H19  C19  H18  106.70  3.000
 QSM  H19  C19  C12  110.73  3.000
 QSM  H18  C19  C12  110.04  3.000
 QSM  H19  C19  C20  108.72  3.000
 QSM  H18  C19  C20  109.98  3.000
 QSM  C12  C19  C20  110.58  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
 QSM  CONST_01  C1   C    C5   C4      0.00   0.0  0
 QSM  CONST_02  C1   C2   C3   C4      0.00   0.0  0
 QSM  CONST_03  C6   N    C3   C4      0.00   0.0  0
 QSM  CONST_04  N    C6   C7   C4      0.00   0.0  0
 QSM  CONST_05  C11  C6   C7   C4    180.00   0.0  0
 QSM  CONST_06  C2   C1   C    C5      0.00   0.0  0
 QSM  CONST_07  C2   C3   C4   C5      0.00   0.0  0
 QSM  CONST_08  N    C3   C4   C5    180.00   0.0  0
 QSM  CONST_09  C6   C7   C4   C5    180.00   0.0  0
 QSM  CONST_10  C3   C4   C7   C6      0.00   0.0  0
 QSM  CONST_11  C2   C3   N    C6    180.00   0.0  0
 QSM  CONST_12  C16  C17  C11  C6    180.00   0.0  0
 QSM  CONST_13  C14  C13  C11  C6    180.00   0.0  0
 QSM  CONST_14  C    C5   C4   C7    180.00   0.0  0
 QSM  CONST_15  C2   C3   C4   C7    180.00   0.0  0
 QSM  CONST_16  N    C3   C4   C7      0.00   0.0  0
 QSM  CONST_17  C3   N    C6   C7      0.00   0.0  0
 QSM  CONST_21  C16  C17  C11  C13     0.00   0.0  0
 QSM  CONST_22  C16  C15  C14  C13     0.00   0.0  0
 QSM  CONST_23  C11  C17  C16  C15     0.00   0.0  0
 QSM  CONST_24  C11  C13  C14  C15     0.00   0.0  0
 QSM  CONST_26  C14  C13  C11  C17     0.00   0.0  0
 QSM  CONST_27  C14  C15  C16  C17     0.00   0.0  0
 QSM  CONST_28  C3   N    C6   C11   180.00   0.0  0
 QSM  CONST_29  C1   C2   C3   N     180.00   0.0  0
 QSM  CONST_30  C    C1   C2   C3      0.00   0.0  0
 QSM  CONST_31  C    C5   C4   C3      0.00   0.0  0
 QSM  CONST_32  C12  C    C5   C4    180.00   0.0  0
 QSM  CONST_33  C12  C    C1   C2    180.00   0.0  0
 QSM  CONST_34  C8   C7   C4   C5      0.00   0.0  0
 QSM  CONST_35  C3   C4   C7   C8    180.00   0.0  0
 QSM  CONST_36  N    C6   C7   C8    180.00   0.0  0
 QSM  CONST_37  C11  C6   C7   C8      0.00   0.0  0
 QSM  CONST_38  O1   C15  C14  C13   180.00   0.0  0
 QSM  CONST_39  O1   C15  C16  C17   180.00   0.0  0
 QSM  CONST_40  C11  C13  C14  O     180.00   0.0  0
 QSM  CONST_41  C16  C15  C14  O     180.00   0.0  0
 QSM  CONST_42  H1   C2   C3   C4    180.00   0.0  0
 QSM  CONST_43  H3   N    C3   C4    180.00   0.0  0
 QSM  CONST_44  H    C1   C    C5    180.00   0.0  0
 QSM  CONST_45  H14  C17  C11  C6      0.00   0.0  0
 QSM  CONST_46  H12  C13  C11  C6      0.00   0.0  0
 QSM  CONST_47  H2   C5   C4   C7      0.00   0.0  0
 QSM  CONST_48  H13  C16  C15  C14   180.00   0.0  0
 QSM  Var_01    C12  C19  C20  N1     55.09  30.0  1
 QSM  Var_02    C12  C22  C21  N1    -53.62  30.0  1
 QSM  Var_03    C22  C21  N1   C20    53.06  30.0  1
 QSM  Var_04    C19  C20  N1   C21   -53.91  30.0  1
 QSM  Var_05    C9   C8   C7   C4    -53.28  30.0  2
 QSM  Var_06    C16  C15  O1   C23     1.02  30.0  1
 QSM  Var_07    H7   C9   C8   C7   -174.27  30.0  3
 QSM  Var_08    H8   C10  C8   C7     58.36  30.0  3
 QSM  Var_09    H27  C23  O1   C15  -179.43  30.0  3
 QSM  Var_10    H15  C18  O    C14  -178.81  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
 QSM  chir_01  C12  C19  C22  C  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
 QSM  plan-1  C6   0.020
 QSM  plan-1  C13  0.020
 QSM  plan-1  C15  0.020
 QSM  plan-1  C17  0.020
 QSM  plan-1  O1   0.020
 QSM  plan-1  C14  0.020
 QSM  plan-1  O    0.020
 QSM  plan-1  C16  0.020
 QSM  plan-1  C11  0.020
 QSM  plan-1  H12  0.020
 QSM  plan-1  H14  0.020
 QSM  plan-1  H13  0.020
 QSM  plan-2  C4   0.020
 QSM  plan-2  C5   0.020
 QSM  plan-2  C6   0.020
 QSM  plan-2  C7   0.020
 QSM  plan-2  C8   0.020
 QSM  plan-2  C11  0.020
 QSM  plan-2  N    0.020
 QSM  plan-2  C3   0.020
 QSM  plan-2  C2   0.020
 QSM  plan-2  C1   0.020
 QSM  plan-2  C    0.020
 QSM  plan-2  C12  0.020
 QSM  plan-2  H2   0.020
 QSM  plan-2  H3   0.020
 QSM  plan-2  H1   0.020
 QSM  plan-2  H    0.020

