# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 18:08:10 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: 1-(7-chloranyl-4-methoxy-1~{H}-indol-5-yl)-3-[1-(cyclohexylmethyl)piperidin-4-yl]propan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1c(cc(Cl)c2[nH]ccc12)C(=O)CCC3CCN(CC3)CC4CCCCC4
#
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
 C6H  C6H  1-(7-chloranyl-4-methoxy-1~{H}-indol-5-yl)-3-[1-(cyclohexylmethyl)piperidin-4-yl]propan-1-one  ligand  62  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C6H
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
 C6H  C01  C   CH3   0  -0.410   4.9980  -3.0184   1.7004
 C6H  O02  O   O2    0  -0.474   4.7011  -2.5077   0.4062
 C6H  C03  C   CR6   0   0.302   4.5696  -1.1646   0.3327
 C6H  C04  C   CR6   0  -0.163   3.3232  -0.5378   0.2675
 C6H  C05  C   C     0   0.399   2.0561  -1.3157   0.3526
 C6H  O06  O   O     0  -0.397   2.0131  -2.4054   0.8833
 C6H  C07  C   CH2   0  -0.601   0.8122  -0.7005  -0.2514
 C6H  C08  C   CH2   0  -0.401  -0.3619  -1.6644  -0.3366
 C6H  C09  C   CH1   0  -0.237  -1.6096  -1.0570  -0.9737
 C6H  C10  C   CH2   0  -0.418  -2.6951  -2.1182  -1.1356
 C6H  C11  C   CH2   0  -0.276  -3.9840  -1.5317  -1.6878
 C6H  N12  N   NT    0  -0.408  -4.4701  -0.4652  -0.8357
 C6H  C13  C   CH2   0  -0.238  -5.7851   0.0063  -1.2199
 C6H  C14  C   CH1   0  -0.256  -6.5352   0.7170  -0.0959
 C6H  C15  C   CH2   0  -0.412  -7.8983   1.1998  -0.5905
 C6H  C16  C   CH2   0  -0.431  -8.6926   1.8924   0.5135
 C6H  C17  C   CH2   0  -0.428  -8.8502   0.9901   1.7334
 C6H  C18  C   CH2   0  -0.432  -7.4925   0.5099   2.2351
 C6H  C19  C   CH2   0  -0.406  -6.7017  -0.1808   1.1285
 C6H  C20  C   CH2   0  -0.278  -3.4956   0.6039  -0.7526
 C6H  C21  C   CH2   0  -0.428  -2.1789   0.1113  -0.1716
 C6H  C22  C   CR16  0  -0.294   3.2599   0.8664   0.1029
 C6H  C23  C   CR6   0  -0.115   4.3910   1.6385   0.0449
 C6H  CL   CL  CL    0  -0.117   4.3111   3.3575  -0.1274
 C6H  C25  C   CR56  0   0.476   5.6334   1.0117   0.1167
 C6H  N26  N   NR15  0  -0.678   6.8898   1.5126   0.0573
 C6H  C27  C   CR15  0  -0.018   7.7892   0.4840   0.1389
 C6H  C28  C   CR15  0  -0.391   7.1256  -0.7011   0.2538
 C6H  C29  C   CR56  0  -0.038   5.7309  -0.3870   0.2494
 C6H  H1   H   HCH3  0   0.239   5.1281  -4.0931   1.5935
 C6H  H2   H   HCH3  0   0.222   5.9206  -2.5924   2.1016
 C6H  H3   H   HCH3  0   0.228   4.1827  -2.8271   2.3993
 C6H  H4   H   HCH2  0   0.274   0.5398   0.1727   0.3512
 C6H  H5   H   HCH2  0   0.264   1.0586  -0.3044  -1.2415
 C6H  H6   H   HCH2  0   0.229  -0.0627  -2.5441  -0.9139
 C6H  H7   H   HCH2  0   0.218  -0.6191  -2.0270   0.6628
 C6H  H8   H   HCH1  0   0.208  -1.3486  -0.6854  -1.9744
 C6H  H9   H   HCH2  0   0.225  -2.3471  -2.9200  -1.7930
 C6H  H10  H   HCH2  0   0.209  -2.9034  -2.5714  -0.1602
 C6H  H11  H   HCH2  0   0.176  -3.8128  -1.1834  -2.7237
 C6H  H12  H   HCH2  0   0.228  -4.7476  -2.3115  -1.7439
 C6H  H14  H   HCH2  0   0.190  -5.7403   0.6674  -2.1050
 C6H  H15  H   HCH2  0   0.213  -6.3798  -0.8631  -1.5210
 C6H  H16  H   HCH1  0   0.209  -5.9684   1.6058   0.2122
 C6H  H17  H   HCH2  0   0.222  -7.7704   1.8759  -1.4411
 C6H  H18  H   HCH2  0   0.203  -8.4700   0.3394  -0.9599
 C6H  H19  H   HCH2  0   0.207  -8.1750   2.8117   0.8087
 C6H  H20  H   HCH2  0   0.224  -9.6722   2.1970   0.1364
 C6H  H21  H   HCH2  0   0.223  -9.3876   1.5152   2.5271
 C6H  H22  H   HCH2  0   0.205  -9.4640   0.1234   1.4633
 C6H  H23  H   HCH2  0   0.205  -6.9201   1.3690   2.6030
 C6H  H24  H   HCH2  0   0.222  -7.6176  -0.1653   3.0855
 C6H  H25  H   HCH2  0   0.196  -7.2237  -1.0975   0.8254
 C6H  H26  H   HCH2  0   0.228  -5.7214  -0.4926   1.4938
 C6H  H27  H   HCH2  0   0.179  -3.3107   1.0496  -1.7486
 C6H  H28  H   HCH2  0   0.234  -3.8875   1.4047  -0.1222
 C6H  H29  H   HCH2  0   0.210  -2.3427  -0.2065   0.8639
 C6H  H30  H   HCH2  0   0.229  -1.4750   0.9463  -0.1423
 C6H  H31  H   HCR6  0   0.280   2.2998   1.3588   0.0395
 C6H  H32  H   HNR5  0   0.416   7.1293   2.4857  -0.0440
 C6H  H33  H   HCR5  0   0.291   8.8478   0.6828   0.1075
 C6H  H34  H   HCR5  0   0.260   7.5755  -1.6770   0.3350

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
 C6H  CL   C23  single    1.729  0.020  1.729
 C6H  C22  C23  aromatic  1.371  0.020  1.371
 C6H  C22  C04  aromatic  1.415  0.020  1.415
 C6H  O06  C05  double    1.213  0.020  1.213
 C6H  C23  C25  aromatic  1.393  0.020  1.393
 C6H  C05  C04  single    1.489  0.020  1.489
 C6H  C05  C07  single    1.513  0.020  1.513
 C6H  C08  C07  single    1.521  0.020  1.521
 C6H  C08  C09  single    1.527  0.020  1.527
 C6H  C04  C03  aromatic  1.397  0.020  1.397
 C6H  C25  N26  aromatic  1.354  0.020  1.354
 C6H  C25  C29  aromatic  1.408  0.020  1.408
 C6H  C21  C09  single    1.527  0.020  1.527
 C6H  C21  C20  single    1.521  0.020  1.521
 C6H  N26  C27  aromatic  1.369  0.020  1.369
 C6H  C09  C10  single    1.527  0.020  1.527
 C6H  C03  C29  aromatic  1.400  0.020  1.400
 C6H  C03  O02  single    1.351  0.020  1.351
 C6H  C29  C28  aromatic  1.430  0.020  1.430
 C6H  C20  N12  single    1.449  0.020  1.449
 C6H  C27  C28  aromatic  1.363  0.020  1.363
 C6H  O02  C01  single    1.423  0.020  1.423
 C6H  C10  C11  single    1.520  0.020  1.520
 C6H  C18  C19  single    1.525  0.020  1.525
 C6H  C18  C17  single    1.525  0.020  1.525
 C6H  N12  C11  single    1.449  0.020  1.449
 C6H  N12  C13  single    1.449  0.020  1.449
 C6H  C19  C14  single    1.527  0.020  1.527
 C6H  C14  C13  single    1.527  0.020  1.527
 C6H  C14  C15  single    1.528  0.020  1.528
 C6H  C17  C16  single    1.525  0.020  1.525
 C6H  C16  C15  single    1.526  0.020  1.526
 C6H  C01  H1   single    0.970  0.020  1.090
 C6H  C01  H2   single    0.970  0.020  1.090
 C6H  C01  H3   single    0.970  0.020  1.090
 C6H  C07  H4   single    0.970  0.020  1.090
 C6H  C07  H5   single    0.970  0.020  1.090
 C6H  C08  H6   single    0.970  0.020  1.090
 C6H  C08  H7   single    0.970  0.020  1.090
 C6H  C09  H8   single    0.970  0.020  1.090
 C6H  C10  H9   single    0.970  0.020  1.090
 C6H  C10  H10  single    0.970  0.020  1.090
 C6H  C11  H11  single    0.970  0.020  1.090
 C6H  C11  H12  single    0.970  0.020  1.090
 C6H  C13  H14  single    0.970  0.020  1.090
 C6H  C13  H15  single    0.970  0.020  1.090
 C6H  C14  H16  single    0.970  0.020  1.090
 C6H  C15  H17  single    0.970  0.020  1.090
 C6H  C15  H18  single    0.970  0.020  1.090
 C6H  C16  H19  single    0.970  0.020  1.090
 C6H  C16  H20  single    0.970  0.020  1.090
 C6H  C17  H21  single    0.970  0.020  1.090
 C6H  C17  H22  single    0.970  0.020  1.090
 C6H  C18  H23  single    0.970  0.020  1.090
 C6H  C18  H24  single    0.970  0.020  1.090
 C6H  C19  H25  single    0.970  0.020  1.090
 C6H  C19  H26  single    0.970  0.020  1.090
 C6H  C20  H27  single    0.970  0.020  1.090
 C6H  C20  H28  single    0.970  0.020  1.090
 C6H  C21  H29  single    0.970  0.020  1.090
 C6H  C21  H30  single    0.970  0.020  1.090
 C6H  C22  H31  single    0.930  0.020  1.080
 C6H  N26  H32  single    0.860  0.020  1.020
 C6H  C27  H33  single    0.930  0.020  1.080
 C6H  C28  H34  single    0.930  0.020  1.080

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
 C6H  H3   C01  H2   109.12  3.000
 C6H  H3   C01  H1   109.01  3.000
 C6H  H2   C01  H1   108.68  3.000
 C6H  H3   C01  O02  111.34  3.000
 C6H  H2   C01  O02  111.74  3.000
 C6H  H1   C01  O02  106.87  3.000
 C6H  C03  O02  C01  115.25  3.000
 C6H  C29  C03  C04  119.22  3.000
 C6H  C29  C03  O02  118.33  3.000
 C6H  C04  C03  O02  122.36  3.000
 C6H  C22  C04  C05  119.13  3.000
 C6H  C05  C04  C03  121.48  3.000
 C6H  C22  C04  C03  119.38  3.000
 C6H  C07  C05  O06  120.71  3.000
 C6H  C07  C05  C04  117.66  3.000
 C6H  O06  C05  C04  121.63  3.000
 C6H  H5   C07  H4   105.37  3.000
 C6H  H5   C07  C08  110.63  3.000
 C6H  H4   C07  C08  110.12  3.000
 C6H  H5   C07  C05  108.85  3.000
 C6H  H4   C07  C05  108.00  3.000
 C6H  C08  C07  C05  113.52  3.000
 C6H  H7   C08  H6   106.25  3.000
 C6H  H7   C08  C09  108.72  3.000
 C6H  H6   C08  C09  108.86  3.000
 C6H  H7   C08  C07  109.89  3.000
 C6H  H6   C08  C07  109.14  3.000
 C6H  C09  C08  C07  113.70  3.000
 C6H  H8   C09  C21  107.95  3.000
 C6H  H8   C09  C10  107.90  3.000
 C6H  C21  C09  C10  108.81  3.000
 C6H  H8   C09  C08  108.69  3.000
 C6H  C10  C09  C08  110.41  3.000
 C6H  C21  C09  C08  112.94  3.000
 C6H  H10  C10  H9   107.00  3.000
 C6H  H10  C10  C11  108.78  3.000
 C6H  H9   C10  C11  109.54  3.000
 C6H  H10  C10  C09  109.17  3.000
 C6H  H9   C10  C09  110.31  3.000
 C6H  C11  C10  C09  111.91  3.000
 C6H  H12  C11  H11  106.54  3.000
 C6H  H12  C11  N12  108.71  3.000
 C6H  H11  C11  N12  111.77  3.000
 C6H  H12  C11  C10  109.62  3.000
 C6H  H11  C11  C10  109.30  3.000
 C6H  N12  C11  C10  110.79  3.000
 C6H  C20  N12  C13  112.67  3.000
 C6H  C13  N12  C11  112.84  3.000
 C6H  C20  N12  C11  110.55  3.000
 C6H  H15  C13  H14  106.05  3.000
 C6H  H15  C13  C14  107.76  3.000
 C6H  H14  C13  C14  109.33  3.000
 C6H  H15  C13  N12  107.89  3.000
 C6H  H14  C13  N12  111.72  3.000
 C6H  C14  C13  N12  113.71  3.000
 C6H  H16  C14  C19  107.89  3.000
 C6H  H16  C14  C15  107.18  3.000
 C6H  C19  C14  C15  110.36  3.000
 C6H  H16  C14  C13  109.25  3.000
 C6H  C15  C14  C13  110.30  3.000
 C6H  C19  C14  C13  111.72  3.000
 C6H  H18  C15  H17  106.49  3.000
 C6H  H18  C15  C16  109.16  3.000
 C6H  H17  C15  C16  110.05  3.000
 C6H  H18  C15  C14  109.02  3.000
 C6H  H17  C15  C14  110.03  3.000
 C6H  C16  C15  C14  111.93  3.000
 C6H  H20  C16  H19  106.41  3.000
 C6H  H20  C16  C17  110.38  3.000
 C6H  H19  C16  C17  109.25  3.000
 C6H  H20  C16  C15  110.08  3.000
 C6H  H19  C16  C15  109.26  3.000
 C6H  C17  C16  C15  111.34  3.000
 C6H  H22  C17  H21  106.48  3.000
 C6H  H22  C17  C18  109.31  3.000
 C6H  H21  C17  C18  110.49  3.000
 C6H  H22  C17  C16  109.18  3.000
 C6H  H21  C17  C16  110.33  3.000
 C6H  C18  C17  C16  110.94  3.000
 C6H  H24  C18  H23  106.44  3.000
 C6H  H24  C18  C19  110.12  3.000
 C6H  H23  C18  C19  109.13  3.000
 C6H  H24  C18  C17  110.39  3.000
 C6H  H23  C18  C17  109.18  3.000
 C6H  C19  C18  C17  111.43  3.000
 C6H  H26  C19  H25  106.32  3.000
 C6H  H26  C19  C18  110.61  3.000
 C6H  H25  C19  C18  109.39  3.000
 C6H  H26  C19  C14  109.77  3.000
 C6H  H25  C19  C14  108.75  3.000
 C6H  C18  C19  C14  111.83  3.000
 C6H  H28  C20  H27  106.51  3.000
 C6H  H28  C20  C21  109.12  3.000
 C6H  H27  C20  C21  109.24  3.000
 C6H  H28  C20  N12  109.44  3.000
 C6H  H27  C20  N12  110.97  3.000
 C6H  C21  C20  N12  111.41  3.000
 C6H  H30  C21  H29  107.02  3.000
 C6H  H30  C21  C20  108.69  3.000
 C6H  H29  C21  C20  109.00  3.000
 C6H  H30  C21  C09  111.01  3.000
 C6H  H29  C21  C09  109.28  3.000
 C6H  C20  C21  C09  111.70  3.000
 C6H  H31  C22  C23  118.29  3.000
 C6H  H31  C22  C04  119.90  3.000
 C6H  C23  C22  C04  121.79  3.000
 C6H  C25  C23  CL   119.57  3.000
 C6H  C25  C23  C22  118.70  3.000
 C6H  CL   C23  C22  121.73  3.000
 C6H  C29  C25  N26  107.90  3.000
 C6H  C29  C25  C23  120.89  3.000
 C6H  N26  C25  C23  131.20  3.000
 C6H  H32  N26  C27  125.15  3.000
 C6H  H32  N26  C25  125.63  3.000
 C6H  C27  N26  C25  109.21  3.000
 C6H  H33  C27  C28  129.87  3.000
 C6H  H33  C27  N26  120.34  3.000
 C6H  C28  C27  N26  109.78  3.000
 C6H  H34  C28  C29  127.33  3.000
 C6H  H34  C28  C27  126.19  3.000
 C6H  C29  C28  C27  106.48  3.000
 C6H  C28  C29  C25  106.62  3.000
 C6H  C28  C29  C03  133.39  3.000
 C6H  C25  C29  C03  119.99  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
 C6H  CONST_01  C23  C22  C04  C03     0.00   0.0  0
 C6H  CONST_02  C23  C25  C29  C03     0.00   0.0  0
 C6H  CONST_03  N26  C25  C29  C03   180.00   0.0  0
 C6H  CONST_04  C27  C28  C29  C03   180.00   0.0  0
 C6H  CONST_05  C25  C23  C22  C04     0.00   0.0  0
 C6H  CONST_06  C25  C29  C03  C04     0.00   0.0  0
 C6H  CONST_07  C28  C29  C03  C04   180.00   0.0  0
 C6H  CONST_08  N26  C25  C23  C22   180.00   0.0  0
 C6H  CONST_09  C29  C25  C23  C22     0.00   0.0  0
 C6H  CONST_10  C29  C03  C04  C22     0.00   0.0  0
 C6H  CONST_11  C27  N26  C25  C23   180.00   0.0  0
 C6H  CONST_12  C28  C29  C25  C23   180.00   0.0  0
 C6H  CONST_13  C28  C27  N26  C25     0.00   0.0  0
 C6H  CONST_14  C27  C28  C29  C25     0.00   0.0  0
 C6H  CONST_15  C28  C29  C25  N26     0.00   0.0  0
 C6H  CONST_16  C29  C28  C27  N26     0.00   0.0  0
 C6H  CONST_17  C29  C25  N26  C27     0.00   0.0  0
 C6H  CONST_18  C22  C04  C03  O02   180.00   0.0  0
 C6H  CONST_19  C25  C29  C03  O02   180.00   0.0  0
 C6H  CONST_20  C28  C29  C03  O02     0.00   0.0  0
 C6H  CONST_21  CL   C23  C22  C04   180.00   0.0  0
 C6H  CONST_22  C23  C22  C04  C05   180.00   0.0  0
 C6H  CONST_23  C29  C03  C04  C05   180.00   0.0  0
 C6H  CONST_24  N26  C25  C23  CL      0.00   0.0  0
 C6H  CONST_25  C29  C25  C23  CL    180.00   0.0  0
 C6H  CONST_26  H31  C22  C04  C03   180.00   0.0  0
 C6H  CONST_27  H34  C28  C29  C03     0.00   0.0  0
 C6H  CONST_28  H32  N26  C25  C23     0.00   0.0  0
 C6H  CONST_29  H33  C27  N26  C25   180.00   0.0  0
 C6H  Var_01    N12  C20  C21  C09    56.39  30.0  1
 C6H  Var_02    N12  C11  C10  C09   -57.36  30.0  1
 C6H  Var_03    C20  N12  C11  C10    60.51  30.0  1
 C6H  Var_04    C21  C20  N12  C11   -60.27  30.0  1
 C6H  Var_05    C17  C18  C19  C14    55.64  30.0  1
 C6H  Var_06    C17  C16  C15  C14   -55.51  30.0  1
 C6H  Var_07    C18  C17  C16  C15    55.06  30.0  1
 C6H  Var_08    C19  C18  C17  C16   -55.18  30.0  1
 C6H  Var_09    C14  C13  N12  C11   158.34  30.0  3
 C6H  Var_10    C04  C03  O02  C01  -102.20  30.0  2
 C6H  Var_11    O06  C05  C04  C03    23.50  30.0  2
 C6H  Var_12    C08  C07  C05  C04   169.69  30.0  3
 C6H  Var_13    C09  C08  C07  C05  -178.72  30.0  1
 C6H  Var_14    H1   C01  O02  C03  -176.91  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
 C6H  chir_01  C09  C08  C21  C10  positiv
 C6H  chir_02  C14  C19  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
 C6H  plan-1  C04  0.020
 C6H  plan-1  C05  0.020
 C6H  plan-1  O06  0.020
 C6H  plan-1  C07  0.020
 C6H  plan-2  O02  0.020
 C6H  plan-2  C03  0.020
 C6H  plan-2  C04  0.020
 C6H  plan-2  C05  0.020
 C6H  plan-2  C22  0.020
 C6H  plan-2  C23  0.020
 C6H  plan-2  CL   0.020
 C6H  plan-2  C25  0.020
 C6H  plan-2  N26  0.020
 C6H  plan-2  C27  0.020
 C6H  plan-2  C28  0.020
 C6H  plan-2  C29  0.020
 C6H  plan-2  H31  0.020
 C6H  plan-2  H32  0.020
 C6H  plan-2  H33  0.020
 C6H  plan-2  H34  0.020

