# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 19:25:43 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: (3S)-3-[(3R)-1-acetylpiperidin-3-yl]-6-chloro-3-(3-chlorobenzyl)-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1CCC[C@@H](C1)[C@]2(Cc3cccc(Cl)c3)C(=O)Nc4cc(Cl)ccc24
#
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
 20Q  20Q  (3S)-3-[(3R)-1-acetylpiperidin-3-yl]-6-chloro-3-(3-chlorobenzyl)-1,3-dihydro-2H-indol-2-one  ligand  50  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_20Q
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
 20Q  C9   C   CR56  0   0.393   0.3956   1.1242   0.9992
 20Q  C2   C   CR5   0   0.571   0.1921  -1.1398   1.1793
 20Q  C3   C   CR5   0  -0.292  -0.3276  -0.7643  -0.2184
 20Q  C8   C   CR56  0   0.111  -0.1704   0.7324  -0.2094
 20Q  N1   N   NR15  0  -0.730   0.5899   0.0071   1.7951
 20Q  C7   C   CR16  0  -0.273   0.6841   2.4437   1.2872
 20Q  C4   C   CR16  0  -0.330  -0.4746   1.6773  -1.1628
 20Q  C5   C   CR16  0  -0.225  -0.1996   3.0201  -0.9093
 20Q  C6   C   CR6   0  -0.048   0.3739   3.3748   0.3013
 20Q  C13  C   CR6   0  -0.024   4.2369  -1.3095  -0.2685
 20Q  CL1  CL  CL    0  -0.135   5.3252  -2.2396   0.7143
 20Q  C12  C   CR16  0  -0.270   2.9200  -1.7240  -0.3902
 20Q  C11  C   CR6   0   0.130   2.0318  -0.9898  -1.1722
 20Q  C10  C   CH2   0  -0.506   0.5920  -1.4125  -1.2818
 20Q  C31  C   CH1   0  -0.207  -1.8069  -1.1670  -0.4357
 20Q  C16  C   CR16  0  -0.280   2.5005   0.1432  -1.8334
 20Q  C15  C   CR16  0  -0.247   3.8209   0.5445  -1.7039
 20Q  C14  C   CR16  0  -0.231   4.7049  -0.1774  -0.9144
 20Q  C32  C   CH2   0  -0.299  -2.7036  -0.5908   0.6658
 20Q  N33  N   NT    0  -0.440  -4.0966  -0.8844   0.3948
 20Q  C34  C   CH2   0  -0.321  -4.3778  -2.3077   0.3317
 20Q  C35  C   CH2   0  -0.428  -3.5474  -2.9543  -0.7680
 20Q  C36  C   CH2   0  -0.455  -2.0602  -2.6707  -0.5731
 20Q  O2   O   O     0  -0.441   0.2632  -2.2526   1.6556
 20Q  CL6  CL  CL    0  -0.127   0.7181   5.0467   0.6109
 20Q  C33  C   C     0   0.512  -4.9451   0.0939   0.0031
 20Q  O33  O   O     0  -0.504  -4.6019   1.2689  -0.0498
 20Q  C37  C   CH3   0  -0.805  -6.3563  -0.3136  -0.3563
 20Q  H1   H   HNR5  0   0.413   0.9945   0.0259   2.7197
 20Q  H2   H   HCR6  0   0.289   1.1264   2.7435   2.2274
 20Q  H3   H   HCR6  0   0.266  -0.9154   1.3905  -2.1095
 20Q  H4   H   HCR6  0   0.277  -0.4287   3.7746  -1.6487
 20Q  H6   H   HCH2  0   0.278   0.5230  -2.4972  -1.1954
 20Q  H7   H   HCH2  0   0.271   0.1997  -1.1457  -2.2666
 20Q  H8   H   HCH1  0   0.252  -2.1064  -0.6924  -1.3793
 20Q  H9   H   HCR6  0   0.254   1.8280   0.7142  -2.4600
 20Q  H10  H   HCR6  0   0.265   4.1713   1.4269  -2.2227
 20Q  H11  H   HCR6  0   0.278   5.7361   0.1320  -0.8123
 20Q  H12  H   HCH2  0   0.243  -2.4460  -1.0397   1.6316
 20Q  H13  H   HCH2  0   0.275  -2.5770   0.4848   0.7569
 20Q  H14  H   HCH2  0   0.243  -4.1189  -2.7504   1.2990
 20Q  H15  H   HCH2  0   0.275  -5.4376  -2.4861   0.1765
 20Q  H16  H   HCH2  0   0.243  -3.7249  -4.0316  -0.7722
 20Q  H17  H   HCH2  0   0.227  -3.8767  -2.5709  -1.7387
 20Q  H18  H   HCH2  0   0.249  -1.5036  -3.0780  -1.4185
 20Q  H19  H   HCH2  0   0.237  -1.7061  -3.1920   0.3198
 20Q  H20  H   HCH3  0   0.265  -6.8486  -0.8511   0.4544
 20Q  H21  H   HCH3  0   0.268  -6.9350   0.5791  -0.5789
 20Q  H22  H   HCH3  0   0.263  -6.3759  -0.9591  -1.2358
 20Q  H5   H   HCR6  0   0.272   2.5882  -2.6206   0.1177

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
 20Q  CL6  C6   single    1.735  0.020  1.735
 20Q  C6   C7   aromatic  1.391  0.020  1.391
 20Q  C6   C5   aromatic  1.386  0.020  1.386
 20Q  C7   C9   aromatic  1.381  0.020  1.381
 20Q  C5   C4   aromatic  1.394  0.020  1.394
 20Q  C9   N1   single    1.385  0.020  1.385
 20Q  C9   C8   aromatic  1.391  0.020  1.391
 20Q  CL1  C13  single    1.736  0.020  1.736
 20Q  N1   C2   single    1.361  0.020  1.361
 20Q  C13  C14  aromatic  1.385  0.020  1.385
 20Q  C13  C12  aromatic  1.386  0.020  1.386
 20Q  C14  C15  aromatic  1.388  0.020  1.388
 20Q  C4   C8   aromatic  1.376  0.020  1.376
 20Q  C8   C3   single    1.505  0.020  1.505
 20Q  C15  C16  aromatic  1.386  0.020  1.386
 20Q  C12  C11  aromatic  1.393  0.020  1.393
 20Q  C2   O2   double    1.213  0.020  1.213
 20Q  C2   C3   single    1.538  0.020  1.538
 20Q  C3   C10  single    1.548  0.020  1.548
 20Q  C3   C31  single    1.548  0.020  1.548
 20Q  C16  C11  aromatic  1.393  0.020  1.393
 20Q  C11  C10  single    1.505  0.020  1.505
 20Q  C31  C36  single    1.531  0.020  1.531
 20Q  C31  C32  single    1.533  0.020  1.533
 20Q  C37  C33  single    1.512  0.020  1.512
 20Q  C36  C35  single    1.526  0.020  1.526
 20Q  C32  N33  single    1.449  0.020  1.449
 20Q  C33  N33  single    1.353  0.020  1.353
 20Q  C33  O33  double    1.225  0.020  1.225
 20Q  C35  C34  single    1.522  0.020  1.522
 20Q  N33  C34  single    1.452  0.020  1.452
 20Q  N1   H1   single    0.860  0.020  1.020
 20Q  C7   H2   single    0.930  0.020  1.080
 20Q  C4   H3   single    0.930  0.020  1.080
 20Q  C5   H4   single    0.930  0.020  1.080
 20Q  C12  H5   single    0.930  0.020  1.080
 20Q  C10  H6   single    0.970  0.020  1.090
 20Q  C10  H7   single    0.970  0.020  1.090
 20Q  C31  H8   single    0.970  0.020  1.090
 20Q  C16  H9   single    0.930  0.020  1.080
 20Q  C15  H10  single    0.930  0.020  1.080
 20Q  C14  H11  single    0.930  0.020  1.080
 20Q  C32  H12  single    0.970  0.020  1.090
 20Q  C32  H13  single    0.970  0.020  1.090
 20Q  C34  H14  single    0.970  0.020  1.090
 20Q  C34  H15  single    0.970  0.020  1.090
 20Q  C35  H16  single    0.970  0.020  1.090
 20Q  C35  H17  single    0.970  0.020  1.090
 20Q  C36  H18  single    0.970  0.020  1.090
 20Q  C36  H19  single    0.970  0.020  1.090
 20Q  C37  H20  single    0.970  0.020  1.090
 20Q  C37  H21  single    0.970  0.020  1.090
 20Q  C37  H22  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
 20Q  C7   C9   N1   128.41  3.000
 20Q  N1   C9   C8   109.21  3.000
 20Q  C7   C9   C8   122.37  3.000
 20Q  O2   C2   N1   125.34  3.000
 20Q  O2   C2   C3   126.94  3.000
 20Q  N1   C2   C3   107.71  3.000
 20Q  C31  C3   C10  111.23  3.000
 20Q  C31  C3   C8   111.06  3.000
 20Q  C10  C3   C8   111.01  3.000
 20Q  C31  C3   C2   112.76  3.000
 20Q  C10  C3   C2   108.74  3.000
 20Q  C8   C3   C2   101.66  3.000
 20Q  C4   C8   C3   130.96  3.000
 20Q  C3   C8   C9   109.14  3.000
 20Q  C4   C8   C9   119.90  3.000
 20Q  H1   N1   C2   123.17  3.000
 20Q  H1   N1   C9   124.57  3.000
 20Q  C2   N1   C9   112.25  3.000
 20Q  H2   C7   C6   121.45  3.000
 20Q  H2   C7   C9   122.12  3.000
 20Q  C6   C7   C9   116.43  3.000
 20Q  H3   C4   C5   119.63  3.000
 20Q  H3   C4   C8   120.91  3.000
 20Q  C5   C4   C8   119.46  3.000
 20Q  H4   C5   C6   120.43  3.000
 20Q  H4   C5   C4   120.42  3.000
 20Q  C6   C5   C4   119.15  3.000
 20Q  CL6  C6   C5   119.00  3.000
 20Q  C5   C6   C7   122.69  3.000
 20Q  CL6  C6   C7   118.32  3.000
 20Q  C14  C13  C12  121.65  3.000
 20Q  C12  C13  CL1  119.01  3.000
 20Q  C14  C13  CL1  119.34  3.000
 20Q  H5   C12  C11  120.30  3.000
 20Q  H5   C12  C13  119.85  3.000
 20Q  C11  C12  C13  119.84  3.000
 20Q  C16  C11  C10  121.05  3.000
 20Q  C10  C11  C12  120.21  3.000
 20Q  C16  C11  C12  118.74  3.000
 20Q  H7   C10  H6   106.95  3.000
 20Q  H7   C10  C11  109.91  3.000
 20Q  H6   C10  C11  109.53  3.000
 20Q  H7   C10  C3   107.67  3.000
 20Q  H6   C10  C3   108.94  3.000
 20Q  C11  C10  C3   113.62  3.000
 20Q  H8   C31  C36  107.59  3.000
 20Q  H8   C31  C32  107.19  3.000
 20Q  C36  C31  C32  109.69  3.000
 20Q  H8   C31  C3   105.59  3.000
 20Q  C32  C31  C3   111.12  3.000
 20Q  C36  C31  C3   115.22  3.000
 20Q  H9   C16  C15  119.56  3.000
 20Q  H9   C16  C11  119.67  3.000
 20Q  C15  C16  C11  120.77  3.000
 20Q  H10  C15  C14  119.39  3.000
 20Q  H10  C15  C16  119.99  3.000
 20Q  C14  C15  C16  120.62  3.000
 20Q  H11  C14  C15  120.82  3.000
 20Q  H11  C14  C13  120.80  3.000
 20Q  C15  C14  C13  118.38  3.000
 20Q  H13  C32  H12  107.71  3.000
 20Q  H13  C32  N33  109.16  3.000
 20Q  H12  C32  N33  107.93  3.000
 20Q  H13  C32  C31  111.35  3.000
 20Q  H12  C32  C31  109.99  3.000
 20Q  N33  C32  C31  110.60  3.000
 20Q  C33  N33  C34  125.08  3.000
 20Q  C34  N33  C32  113.13  3.000
 20Q  C33  N33  C32  120.69  3.000
 20Q  H15  C34  H14  106.89  3.000
 20Q  H15  C34  C35  111.06  3.000
 20Q  H14  C34  C35  109.72  3.000
 20Q  H15  C34  N33  110.87  3.000
 20Q  H14  C34  N33  108.19  3.000
 20Q  C35  C34  N33  110.01  3.000
 20Q  H17  C35  H16  107.06  3.000
 20Q  H17  C35  C36  109.96  3.000
 20Q  H16  C35  C36  110.01  3.000
 20Q  H17  C35  C34  109.13  3.000
 20Q  H16  C35  C34  109.46  3.000
 20Q  C36  C35  C34  111.12  3.000
 20Q  H19  C36  H18  106.84  3.000
 20Q  H19  C36  C35  109.35  3.000
 20Q  H18  C36  C35  109.19  3.000
 20Q  H19  C36  C31  109.97  3.000
 20Q  H18  C36  C31  110.60  3.000
 20Q  C35  C36  C31  110.80  3.000
 20Q  C37  C33  O33  120.64  3.000
 20Q  O33  C33  N33  122.02  3.000
 20Q  C37  C33  N33  117.33  3.000
 20Q  H22  C37  H21  108.13  3.000
 20Q  H22  C37  H20  107.43  3.000
 20Q  H21  C37  H20  108.47  3.000
 20Q  H22  C37  C33  111.58  3.000
 20Q  H21  C37  C33  108.92  3.000
 20Q  H20  C37  C33  112.18  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
 20Q  CONST_01  C5   C6   C7   C9     0.00   0.0  0
 20Q  CONST_02  C5   C4   C8   C9     0.00   0.0  0
 20Q  CONST_03  C6   C7   C9   C8     0.00   0.0  0
 20Q  CONST_04  C6   C5   C4   C8     0.00   0.0  0
 20Q  CONST_05  C4   C5   C6   C7     0.00   0.0  0
 20Q  CONST_06  C4   C8   C9   C7     0.00   0.0  0
 20Q  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 20Q  CONST_08  C16  C11  C12  C13    0.00   0.0  0
 20Q  CONST_09  C15  C14  C13  C12    0.00   0.0  0
 20Q  CONST_10  C15  C16  C11  C12    0.00   0.0  0
 20Q  CONST_11  C14  C13  C12  C11    0.00   0.0  0
 20Q  CONST_12  C14  C15  C16  C11    0.00   0.0  0
 20Q  CONST_13  C3   C2   N1   C9     0.00   0.0  0
 20Q  CONST_14  CL6  C6   C7   C9   180.00   0.0  0
 20Q  CONST_15  CL6  C6   C5   C4   180.00   0.0  0
 20Q  CONST_16  C10  C11  C12  C13  180.00   0.0  0
 20Q  CONST_17  C15  C14  C13  CL1  180.00   0.0  0
 20Q  CONST_18  C11  C12  C13  CL1  180.00   0.0  0
 20Q  CONST_19  C15  C16  C11  C10  180.00   0.0  0
 20Q  CONST_20  O2   C2   N1   C9   180.00   0.0  0
 20Q  CONST_21  H3   C4   C8   C9   180.00   0.0  0
 20Q  CONST_22  H2   C7   C9   C8   180.00   0.0  0
 20Q  CONST_23  H4   C5   C4   C8   180.00   0.0  0
 20Q  CONST_24  H10  C15  C14  C13  180.00   0.0  0
 20Q  CONST_25  H11  C14  C13  C12  180.00   0.0  0
 20Q  CONST_26  H9   C16  C11  C12  180.00   0.0  0
 20Q  CONST_27  H5   C12  C11  C16  180.00   0.0  0
 20Q  CONST_28  H1   N1   C2   C3   180.00   0.0  0
 20Q  CONST_29  C37  C33  N33  C32  180.00   0.0  0
 20Q  CONST_30  O33  C33  N33  C32    0.00   0.0  0
 20Q  CONST_31  C37  C33  N33  C34    0.00   0.0  0
 20Q  CONST_32  O33  C33  N33  C34  180.00   0.0  0
 20Q  Var_01    C34  C35  C36  C31  -53.41  30.0  1
 20Q  Var_02    C34  N33  C32  C31   60.45  30.0  1
 20Q  Var_03    C35  C34  N33  C32  -59.57  30.0  1
 20Q  Var_04    C36  C35  C34  N33   55.25  30.0  1
 20Q  Var_05    C12  C11  C10  C3    90.89  30.0  2
 20Q  Var_06    H20  C37  C33  N33   55.83  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
 20Q  chir_01  C3   C2  C8   C31  positiv
 20Q  chir_02  C31  C3  C36  C32  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
 20Q  plan-1  C13  0.020
 20Q  plan-1  CL1  0.020
 20Q  plan-1  C12  0.020
 20Q  plan-1  C11  0.020
 20Q  plan-1  C10  0.020
 20Q  plan-1  C16  0.020
 20Q  plan-1  C15  0.020
 20Q  plan-1  C14  0.020
 20Q  plan-1  H9   0.020
 20Q  plan-1  H10  0.020
 20Q  plan-1  H11  0.020
 20Q  plan-1  H5   0.020
 20Q  plan-2  C32  0.020
 20Q  plan-2  N33  0.020
 20Q  plan-2  C34  0.020
 20Q  plan-2  C33  0.020
 20Q  plan-2  O33  0.020
 20Q  plan-2  C37  0.020
 20Q  plan-3  C9   0.020
 20Q  plan-3  C2   0.020
 20Q  plan-3  C3   0.020
 20Q  plan-3  C8   0.020
 20Q  plan-3  N1   0.020
 20Q  plan-3  C7   0.020
 20Q  plan-3  C4   0.020
 20Q  plan-3  C5   0.020
 20Q  plan-3  C6   0.020
 20Q  plan-3  O2   0.020
 20Q  plan-3  CL6  0.020
 20Q  plan-3  H1   0.020
 20Q  plan-3  H2   0.020
 20Q  plan-3  H3   0.020
 20Q  plan-3  H4   0.020

