# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 15:37:04 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: 1-(7-chloranyl-4-methoxy-1~{H}-indol-5-yl)-3-[1-(phenylmethyl)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
 C6K  C6K  1-(7-chloranyl-4-methoxy-1~{H}-indol-5-yl)-3-[1-(phenylmethyl)piperidin-4-yl]propan-1-one  ligand  56  29  .  2021-08-07  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_C6K
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
 C6K  C10  C   CH2   0  -0.433   3.2082   0.6879   1.8635
 C6K  N12  N   NT    0  -0.413   4.1600   0.6302  -0.3968
 C6K  C13  C   CH2   0  -0.312   4.9844  -0.0790  -1.3496
 C6K  C15  C   CR16  0  -0.316   7.1503  -1.3489  -1.1454
 C6K  C17  C   CR16  0  -0.272   9.1321  -0.3425  -0.2229
 C6K  C20  C   CH2   0  -0.282   2.8810   1.0076  -0.9723
 C6K  C21  C   CH2   0  -0.444   2.0734   1.8539  -0.0017
 C6K  C22  C   CR16  0  -0.297  -3.3629   0.9865   0.3828
 C6K  C28  C   CR15  0  -0.390  -6.2656  -1.7692  -0.7919
 C6K  C01  C   CH3   0  -0.409  -3.9403  -3.4165   1.2458
 C6K  C03  C   CR6   0   0.301  -3.8624  -1.3718   0.1075
 C6K  C04  C   CR6   0  -0.161  -2.9613  -0.3680   0.4744
 C6K  C05  C   C     0   0.399  -1.5806  -0.6849   0.9358
 C6K  O06  O   O     0  -0.395  -1.2768  -1.7923   1.3270
 C6K  C07  C   CH2   0  -0.601  -0.5527   0.4260   0.8914
 C6K  C08  C   CH2   0  -0.413   0.8537  -0.0204   1.2602
 C6K  C09  C   CH1   0  -0.255   1.8466   1.1435   1.3347
 C6K  C11  C   CH2   0  -0.283   3.9885  -0.1184   0.8363
 C6K  C14  C   CR6   0   0.084   6.4260  -0.1828  -0.9208
 C6K  C16  C   CR16  0  -0.241   8.4953  -1.4299  -0.8042
 C6K  C18  C   CR16  0  -0.242   8.4138   0.8242   0.0143
 C6K  C19  C   CR16  0  -0.284   7.0731   0.9029  -0.3333
 C6K  C23  C   CR6   0  -0.114  -4.6208   1.3452  -0.0262
 C6K  CL   CL  CL    0  -0.117  -5.1105   3.0013  -0.1132
 C6K  C25  C   CR56  0   0.476  -5.5177   0.3422  -0.3878
 C6K  N26  N   NR15  0  -0.678  -6.7904   0.4027  -0.8450
 C6K  C27  C   CR15  0  -0.018  -7.2419  -0.8665  -1.0902
 C6K  C29  C   CR56  0  -0.039  -5.1428  -1.0142  -0.3305
 C6K  H1   H   HCH2  0   0.225   3.7993   1.5675   2.1364
 C6K  H2   H   HCH2  0   0.227   3.0882   0.0935   2.7732
 C6K  H4   H   HCH2  0   0.207   4.5957  -1.0889  -1.5681
 C6K  H5   H   HCH2  0   0.248   4.9473   0.4683  -2.2974
 C6K  H6   H   HCR6  0   0.246   6.6576  -2.2063  -1.5896
 C6K  H7   H   HCR6  0   0.252  10.1782  -0.4043   0.0481
 C6K  H8   H   HCH2  0   0.234   3.0672   1.5812  -1.8840
 C6K  H9   H   HCH2  0   0.188   2.2965   0.1225  -1.2810
 C6K  H10  H   HCH2  0   0.226   2.6161   2.7856   0.1836
 C6K  H11  H   HCH2  0   0.234   1.1289   2.1369  -0.4713
 C6K  H12  H   HCR6  0   0.282  -2.6709   1.7705   0.6549
 C6K  H13  H   HCR5  0   0.259  -6.3397  -2.8400  -0.8865
 C6K  H14  H   HCH3  0   0.222  -5.0250  -3.3892   1.3753
 C6K  H15  H   HCH3  0   0.239  -3.6327  -4.4478   1.0873
 C6K  H16  H   HCH3  0   0.227  -3.4641  -3.0397   2.1519
 C6K  H17  H   HCH2  0   0.270  -0.5764   0.8730  -0.1072
 C6K  H18  H   HCH2  0   0.267  -0.8690   1.2255   1.5715
 C6K  H19  H   HCH2  0   0.230   0.8316  -0.5108   2.2367
 C6K  H20  H   HCH2  0   0.226   1.1943  -0.7803   0.5524
 C6K  H21  H   HCH1  0   0.226   1.4340   1.8731   2.0410
 C6K  H22  H   HCH2  0   0.239   4.9730  -0.3598   1.2434
 C6K  H23  H   HCH2  0   0.192   3.4892  -1.0854   0.6470
 C6K  H24  H   HCR6  0   0.252   9.0426  -2.3459  -0.9881
 C6K  H25  H   HCR6  0   0.251   8.9007   1.6762   0.4720
 C6K  H26  H   HCR6  0   0.242   6.5133   1.8090  -0.1367
 C6K  H27  H   HNR5  0   0.416  -7.3211   1.2446  -0.9998
 C6K  H28  H   HCR5  0   0.291  -8.2389  -1.0259  -1.4669
 C6K  O02  O   O2    0  -0.472  -3.5327  -2.6821   0.0974

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
 C6K  C15  C16  aromatic  1.390  0.020  1.390
 C6K  C15  C14  aromatic  1.391  0.020  1.391
 C6K  C16  C17  aromatic  1.388  0.020  1.388
 C6K  C13  C14  single    1.508  0.020  1.508
 C6K  C13  N12  single    1.446  0.020  1.446
 C6K  C14  C19  aromatic  1.394  0.020  1.394
 C6K  C01  O02  single    1.423  0.020  1.423
 C6K  C17  C18  aromatic  1.390  0.020  1.390
 C6K  C11  N12  single    1.453  0.020  1.453
 C6K  C11  C10  single    1.521  0.020  1.521
 C6K  N12  C20  single    1.452  0.020  1.452
 C6K  C28  C27  aromatic  1.363  0.020  1.363
 C6K  C28  C29  aromatic  1.430  0.020  1.430
 C6K  O02  C03  single    1.351  0.020  1.351
 C6K  C19  C18  aromatic  1.387  0.020  1.387
 C6K  C27  N26  aromatic  1.369  0.020  1.369
 C6K  C10  C09  single    1.530  0.020  1.530
 C6K  C20  C21  single    1.520  0.020  1.520
 C6K  C29  C03  aromatic  1.400  0.020  1.400
 C6K  C29  C25  aromatic  1.408  0.020  1.408
 C6K  C03  C04  aromatic  1.398  0.020  1.398
 C6K  C09  C21  single    1.530  0.020  1.530
 C6K  C09  C08  single    1.532  0.020  1.532
 C6K  N26  C25  aromatic  1.354  0.020  1.354
 C6K  C07  C08  single    1.521  0.020  1.521
 C6K  C07  C05  single    1.514  0.020  1.514
 C6K  C25  C23  aromatic  1.393  0.020  1.393
 C6K  C04  C05  single    1.490  0.020  1.490
 C6K  C04  C22  aromatic  1.416  0.020  1.416
 C6K  C05  O06  double    1.213  0.020  1.213
 C6K  C23  C22  aromatic  1.371  0.020  1.371
 C6K  C23  CL   single    1.729  0.020  1.729
 C6K  C10  H1   single    0.970  0.020  1.090
 C6K  C10  H2   single    0.970  0.020  1.090
 C6K  C13  H4   single    0.970  0.020  1.090
 C6K  C13  H5   single    0.970  0.020  1.090
 C6K  C15  H6   single    0.930  0.020  1.080
 C6K  C17  H7   single    0.930  0.020  1.080
 C6K  C20  H8   single    0.970  0.020  1.090
 C6K  C20  H9   single    0.970  0.020  1.090
 C6K  C21  H10  single    0.970  0.020  1.090
 C6K  C21  H11  single    0.970  0.020  1.090
 C6K  C22  H12  single    0.930  0.020  1.080
 C6K  C28  H13  single    0.930  0.020  1.080
 C6K  C01  H14  single    0.970  0.020  1.090
 C6K  C01  H15  single    0.970  0.020  1.090
 C6K  C01  H16  single    0.970  0.020  1.090
 C6K  C07  H17  single    0.970  0.020  1.090
 C6K  C07  H18  single    0.970  0.020  1.090
 C6K  C08  H19  single    0.970  0.020  1.090
 C6K  C08  H20  single    0.970  0.020  1.090
 C6K  C09  H21  single    0.970  0.020  1.090
 C6K  C11  H22  single    0.970  0.020  1.090
 C6K  C11  H23  single    0.970  0.020  1.090
 C6K  C16  H24  single    0.930  0.020  1.080
 C6K  C18  H25  single    0.930  0.020  1.080
 C6K  C19  H26  single    0.930  0.020  1.080
 C6K  N26  H27  single    0.860  0.020  1.020
 C6K  C27  H28  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
 C6K  H2   C10  H1   106.78  3.000
 C6K  H2   C10  C11  109.27  3.000
 C6K  H1   C10  C11  108.50  3.000
 C6K  H2   C10  C09  110.60  3.000
 C6K  H1   C10  C09  109.12  3.000
 C6K  C11  C10  C09  112.39  3.000
 C6K  C11  N12  C20  111.49  3.000
 C6K  C20  N12  C13  111.62  3.000
 C6K  C11  N12  C13  111.96  3.000
 C6K  H5   C13  H4   105.90  3.000
 C6K  H5   C13  C14  108.24  3.000
 C6K  H4   C13  C14  109.27  3.000
 C6K  H5   C13  N12  107.81  3.000
 C6K  H4   C13  N12  112.23  3.000
 C6K  C14  C13  N12  113.05  3.000
 C6K  H6   C15  C16  119.62  3.000
 C6K  H6   C15  C14  119.51  3.000
 C6K  C16  C15  C14  120.87  3.000
 C6K  H7   C17  C18  120.29  3.000
 C6K  H7   C17  C16  120.24  3.000
 C6K  C18  C17  C16  119.47  3.000
 C6K  H9   C20  H8   106.11  3.000
 C6K  H9   C20  C21  110.08  3.000
 C6K  H8   C20  C21  109.32  3.000
 C6K  H9   C20  N12  111.62  3.000
 C6K  H8   C20  N12  108.47  3.000
 C6K  C21  C20  N12  111.07  3.000
 C6K  H11  C21  H10  106.33  3.000
 C6K  H11  C21  C09  111.57  3.000
 C6K  H10  C21  C09  108.72  3.000
 C6K  H11  C21  C20  109.22  3.000
 C6K  H10  C21  C20  108.58  3.000
 C6K  C09  C21  C20  112.20  3.000
 C6K  H12  C22  C23  118.24  3.000
 C6K  H12  C22  C04  119.75  3.000
 C6K  C23  C22  C04  122.01  3.000
 C6K  H13  C28  C29  127.39  3.000
 C6K  H13  C28  C27  126.14  3.000
 C6K  C29  C28  C27  106.47  3.000
 C6K  H16  C01  H15  108.97  3.000
 C6K  H16  C01  H14  109.05  3.000
 C6K  H15  C01  H14  108.76  3.000
 C6K  H16  C01  O02  111.54  3.000
 C6K  H15  C01  O02  106.91  3.000
 C6K  H14  C01  O02  111.54  3.000
 C6K  C29  C03  C04  119.23  3.000
 C6K  C04  C03  O02  122.76  3.000
 C6K  C29  C03  O02  117.94  3.000
 C6K  C05  C04  C03  121.73  3.000
 C6K  C05  C04  C22  119.10  3.000
 C6K  C03  C04  C22  119.15  3.000
 C6K  C07  C05  O06  120.61  3.000
 C6K  O06  C05  C04  121.74  3.000
 C6K  C07  C05  C04  117.65  3.000
 C6K  H18  C07  H17  105.19  3.000
 C6K  H18  C07  C08  109.29  3.000
 C6K  H17  C07  C08  111.17  3.000
 C6K  H18  C07  C05  108.73  3.000
 C6K  H17  C07  C05  108.17  3.000
 C6K  C08  C07  C05  113.91  3.000
 C6K  H20  C08  H19  105.84  3.000
 C6K  H20  C08  C09  110.97  3.000
 C6K  H19  C08  C09  108.10  3.000
 C6K  H20  C08  C07  109.58  3.000
 C6K  H19  C08  C07  109.24  3.000
 C6K  C09  C08  C07  112.84  3.000
 C6K  H21  C09  C08  107.05  3.000
 C6K  H21  C09  C21  108.03  3.000
 C6K  C08  C09  C21  113.97  3.000
 C6K  H21  C09  C10  108.08  3.000
 C6K  C08  C09  C10  111.56  3.000
 C6K  C21  C09  C10  107.95  3.000
 C6K  H23  C11  H22  106.13  3.000
 C6K  H23  C11  N12  111.04  3.000
 C6K  H22  C11  N12  108.90  3.000
 C6K  H23  C11  C10  110.36  3.000
 C6K  H22  C11  C10  109.13  3.000
 C6K  N12  C11  C10  111.13  3.000
 C6K  C19  C14  C15  118.64  3.000
 C6K  C19  C14  C13  120.68  3.000
 C6K  C15  C14  C13  120.65  3.000
 C6K  H24  C16  C17  120.14  3.000
 C6K  H24  C16  C15  119.78  3.000
 C6K  C17  C16  C15  120.08  3.000
 C6K  H25  C18  C19  119.73  3.000
 C6K  H25  C18  C17  120.01  3.000
 C6K  C19  C18  C17  120.27  3.000
 C6K  H26  C19  C18  120.09  3.000
 C6K  H26  C19  C14  119.23  3.000
 C6K  C18  C19  C14  120.67  3.000
 C6K  C25  C23  CL   119.61  3.000
 C6K  CL   C23  C22  121.71  3.000
 C6K  C25  C23  C22  118.68  3.000
 C6K  C29  C25  N26  107.88  3.000
 C6K  N26  C25  C23  131.35  3.000
 C6K  C29  C25  C23  120.76  3.000
 C6K  H27  N26  C27  125.00  3.000
 C6K  H27  N26  C25  125.78  3.000
 C6K  C27  N26  C25  109.21  3.000
 C6K  H28  C27  N26  120.32  3.000
 C6K  H28  C27  C28  129.89  3.000
 C6K  N26  C27  C28  109.79  3.000
 C6K  C25  C29  C03  120.15  3.000
 C6K  C25  C29  C28  106.65  3.000
 C6K  C03  C29  C28  133.20  3.000
 C6K  C03  O02  C01  115.13  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
 C6K  CONST_01  C18  C17  C16  C15     0.00   0.0  0
 C6K  CONST_02  C18  C19  C14  C15     0.00   0.0  0
 C6K  CONST_03  C14  C15  C16  C17     0.00   0.0  0
 C6K  CONST_04  C14  C19  C18  C17     0.00   0.0  0
 C6K  CONST_05  C29  C03  C04  C22     0.00   0.0  0
 C6K  CONST_06  C29  C25  C23  C22     0.00   0.0  0
 C6K  CONST_07  N26  C25  C23  C22   180.00   0.0  0
 C6K  CONST_08  C25  N26  C27  C28     0.00   0.0  0
 C6K  CONST_09  C04  C03  C29  C28   180.00   0.0  0
 C6K  CONST_10  N26  C25  C29  C28     0.00   0.0  0
 C6K  CONST_11  C23  C25  C29  C28   180.00   0.0  0
 C6K  CONST_12  C27  C28  C29  C03   180.00   0.0  0
 C6K  CONST_13  N26  C25  C29  C03   180.00   0.0  0
 C6K  CONST_14  C23  C25  C29  C03     0.00   0.0  0
 C6K  CONST_15  C23  C22  C04  C03     0.00   0.0  0
 C6K  CONST_16  C25  C29  C03  C04     0.00   0.0  0
 C6K  CONST_17  C25  C23  C22  C04     0.00   0.0  0
 C6K  CONST_18  C19  C14  C15  C16     0.00   0.0  0
 C6K  CONST_19  C19  C18  C17  C16     0.00   0.0  0
 C6K  CONST_20  C27  N26  C25  C23   180.00   0.0  0
 C6K  CONST_21  C27  C28  C29  C25     0.00   0.0  0
 C6K  CONST_22  C29  C28  C27  N26     0.00   0.0  0
 C6K  CONST_23  C29  C25  N26  C27     0.00   0.0  0
 C6K  CONST_24  C16  C15  C14  C13   180.00   0.0  0
 C6K  CONST_25  C18  C19  C14  C13   180.00   0.0  0
 C6K  CONST_26  O02  C03  C04  C22   180.00   0.0  0
 C6K  CONST_27  O02  C03  C29  C28     0.00   0.0  0
 C6K  CONST_28  C25  C29  C03  O02   180.00   0.0  0
 C6K  CONST_29  CL   C23  C22  C04   180.00   0.0  0
 C6K  CONST_30  C29  C03  C04  C05   180.00   0.0  0
 C6K  CONST_31  C23  C22  C04  C05   180.00   0.0  0
 C6K  CONST_32  C29  C25  C23  CL    180.00   0.0  0
 C6K  CONST_33  N26  C25  C23  CL      0.00   0.0  0
 C6K  CONST_34  H7   C17  C16  C15   180.00   0.0  0
 C6K  CONST_35  H26  C19  C14  C15   180.00   0.0  0
 C6K  CONST_36  H6   C15  C16  C17   180.00   0.0  0
 C6K  CONST_37  H27  N26  C27  C28   180.00   0.0  0
 C6K  CONST_38  H13  C28  C29  C03     0.00   0.0  0
 C6K  CONST_39  H12  C22  C04  C03   180.00   0.0  0
 C6K  CONST_40  H24  C16  C15  C14   180.00   0.0  0
 C6K  CONST_41  H25  C18  C19  C14   180.00   0.0  0
 C6K  CONST_42  H28  C27  N26  C25   180.00   0.0  0
 C6K  Var_01    C20  N12  C11  C10   -58.46  30.0  1
 C6K  Var_02    C09  C10  C11  N12    56.25  30.0  1
 C6K  Var_03    C09  C21  C20  N12   -56.88  30.0  1
 C6K  Var_04    C11  N12  C20  C21    58.82  30.0  1
 C6K  Var_05    C15  C14  C13  N12   140.97  30.0  2
 C6K  Var_06    C14  C13  N12  C20   165.56  30.0  2
 C6K  Var_07    C07  C05  C04  C22   -17.80  30.0  2
 C6K  Var_08    C29  C03  O02  C01   -84.51  30.0  2
 C6K  Var_09    C08  C07  C05  C04  -174.75  30.0  1
 C6K  Var_10    C09  C08  C07  C05  -174.64  30.0  3
 C6K  Var_11    H14  C01  O02  C03    59.84  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
 C6K  chir_01  C09  C10  C21  C08  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
 C6K  plan-1  C13  0.020
 C6K  plan-1  C15  0.020
 C6K  plan-1  C17  0.020
 C6K  plan-1  C14  0.020
 C6K  plan-1  C16  0.020
 C6K  plan-1  C18  0.020
 C6K  plan-1  C19  0.020
 C6K  plan-1  H6   0.020
 C6K  plan-1  H7   0.020
 C6K  plan-1  H24  0.020
 C6K  plan-1  H25  0.020
 C6K  plan-1  H26  0.020
 C6K  plan-2  C22  0.020
 C6K  plan-2  C28  0.020
 C6K  plan-2  C03  0.020
 C6K  plan-2  C04  0.020
 C6K  plan-2  C05  0.020
 C6K  plan-2  C23  0.020
 C6K  plan-2  CL   0.020
 C6K  plan-2  C25  0.020
 C6K  plan-2  N26  0.020
 C6K  plan-2  C27  0.020
 C6K  plan-2  C29  0.020
 C6K  plan-2  H12  0.020
 C6K  plan-2  H13  0.020
 C6K  plan-2  H27  0.020
 C6K  plan-2  H28  0.020
 C6K  plan-2  O02  0.020
 C6K  plan-3  C04  0.020
 C6K  plan-3  C05  0.020
 C6K  plan-3  O06  0.020
 C6K  plan-3  C07  0.020

