# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 08:52:46 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-[(2-chlorophenyl)sulfonyl]-5-methyl-3-[(4R)-2-methyl-4,5-dihydro-1H-imidazol-4-yl]-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2n(cc([C@@H]3CNC(=N3)C)c2c1)[S](=O)(=O)c4ccccc4Cl
#
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
 9YO  9YO  1-[(2-chlorophenyl)sulfonyl]-5-methyl-3-[(4R)-2-methyl-4,5-dihydro-1H-imidazol-4-yl]-1H-indole  ligand  44  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YO
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
 9YO  C1   C   CR6   0  -0.134   2.7261  -0.6834   0.2743
 9YO  C2   C   CR16  0  -0.231   4.9380   0.1958  -0.0612
 9YO  C3   C   CR15  0  -0.258  -3.2454  -0.0594  -0.9497
 9YO  C4   C   CR5   0   0.436  -4.4115  -1.7154  -0.0915
 9YO  C5   C   CH3   0  -0.722  -1.0412   5.1800  -0.8433
 9YO  O18  O   OS    0  -0.611   1.0054  -2.3271   1.4420
 9YO  S19  S   S     0   1.391   1.3657  -0.9281   1.3846
 9YO  O8   O   OS    0  -0.613   1.6652  -0.2030   2.6016
 9YO  C12  C   CR16  0  -0.251   3.8357   0.0028   0.7547
 9YO  C26  C   CR6   0  -0.010   2.7270  -1.1853  -1.0266
 9YO  CL9  CL  CL    0  -0.078   1.3751  -2.0323  -1.6732
 9YO  C20  C   CR16  0  -0.196   3.8297  -0.9882  -1.8404
 9YO  C17  C   CR16  0  -0.241   4.9321  -0.3000  -1.3557
 9YO  N14  N   NR5   0  -0.765   0.0945  -0.1471   0.6369
 9YO  C24  C   CR15  0  -0.066  -1.0695  -0.7639   0.1757
 9YO  C15  C   CR56  0   0.385   0.0176   1.2182   0.3747
 9YO  C7   C   CR16  0  -0.265   0.9039   2.2571   0.6286
 9YO  C25  C   CR56  0   0.069  -1.2100   1.4361  -0.2671
 9YO  C23  C   CR16  0  -0.429  -1.5560   2.7254  -0.6737
 9YO  C16  C   CR6   0   0.098  -0.6856   3.7780  -0.4383
 9YO  C13  C   CR16  0  -0.311   0.5336   3.5233   0.2112
 9YO  C11  C   CR5   0   0.039  -1.8847   0.1666  -0.3672
 9YO  N6   N   N     0  -0.449  -3.5484  -1.4867  -1.0086
 9YO  C10  C   CH2   0  -0.298  -4.3633   0.5522  -0.0674
 9YO  N21  N   NR15  0  -0.625  -4.8063  -0.6314   0.6460
 9YO  C22  C   CH3   0  -0.742  -4.9594  -3.0622   0.2251
 9YO  H1   H   HCR6  0   0.283   5.7961   0.7324   0.3179
 9YO  H2   H   HCR5  0   0.254  -3.2694   0.3747  -1.9541
 9YO  H3   H   HCH3  0   0.247  -1.3975   5.7577   0.0122
 9YO  H4   H   HCH3  0   0.243  -0.1800   5.7098  -1.2507
 9YO  H5   H   HCH3  0   0.244  -1.8287   5.1914  -1.5956
 9YO  H6   H   HCR6  0   0.301   3.8414   0.3904   1.7635
 9YO  H7   H   HCR6  0   0.299   3.8256  -1.3728  -2.8510
 9YO  H8   H   HCR6  0   0.288   5.7869  -0.1517  -2.0013
 9YO  H9   H   HCR5  0   0.305  -1.2102  -1.8259   0.2787
 9YO  H11  H   HCR6  0   0.267   1.8488   2.1122   1.1328
 9YO  H12  H   HCR6  0   0.246  -2.4992   2.9052  -1.1772
 9YO  H13  H   HCR6  0   0.252   1.2124   4.3472   0.3957
 9YO  H15  H   HCH2  0   0.243  -4.0006   1.3271   0.6083
 9YO  H16  H   HCH3  0   0.258  -6.0392  -3.0845   0.0694
 9YO  H17  H   HCH3  0   0.257  -4.4999  -3.8197  -0.4040
 9YO  H18  H   HCH3  0   0.260  -4.7781  -3.3111   1.2711
 9YO  H10  H   HCH2  0   0.241  -5.1649   0.9796  -0.6776
 9YO  H14  H   HNR5  0   0.386  -5.7186  -0.6350   1.0749

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
 9YO  CL9  C26  single    1.721  0.020  1.721
 9YO  C20  C26  aromatic  1.385  0.020  1.385
 9YO  C20  C17  aromatic  1.387  0.020  1.387
 9YO  C26  C1   aromatic  1.394  0.020  1.394
 9YO  C17  C2   aromatic  1.386  0.020  1.386
 9YO  O8   S19  double    1.448  0.020  1.448
 9YO  C1   S19  single    1.773  0.020  1.773
 9YO  C1   C12  aromatic  1.390  0.020  1.390
 9YO  C24  C11  aromatic  1.351  0.020  1.351
 9YO  C24  N14  aromatic  1.396  0.020  1.396
 9YO  C2   C12  aromatic  1.385  0.020  1.385
 9YO  N6   C3   single    1.460  0.020  1.460
 9YO  N6   C4   double    1.280  0.020  1.280
 9YO  C3   C11  single    1.497  0.020  1.497
 9YO  C3   C10  single    1.550  0.020  1.550
 9YO  S19  N14  single    1.669  0.020  1.669
 9YO  S19  O18  double    1.446  0.020  1.446
 9YO  C4   C22  single    1.488  0.020  1.488
 9YO  C4   N21  single    1.369  0.020  1.369
 9YO  C11  C25  aromatic  1.441  0.020  1.441
 9YO  N14  C15  aromatic  1.392  0.020  1.392
 9YO  C10  N21  single    1.451  0.020  1.451
 9YO  C25  C15  aromatic  1.402  0.020  1.402
 9YO  C25  C23  aromatic  1.395  0.020  1.395
 9YO  C15  C7   aromatic  1.389  0.020  1.389
 9YO  C23  C16  aromatic  1.386  0.020  1.386
 9YO  C7   C13  aromatic  1.384  0.020  1.384
 9YO  C16  C13  aromatic  1.405  0.020  1.405
 9YO  C16  C5   single    1.502  0.020  1.502
 9YO  C2   H1   single    0.930  0.020  1.080
 9YO  C3   H2   single    0.970  0.020  1.090
 9YO  C5   H3   single    0.970  0.020  1.090
 9YO  C5   H4   single    0.970  0.020  1.090
 9YO  C5   H5   single    0.970  0.020  1.090
 9YO  C12  H6   single    0.930  0.020  1.080
 9YO  C20  H7   single    0.930  0.020  1.080
 9YO  C17  H8   single    0.930  0.020  1.080
 9YO  C24  H9   single    0.930  0.020  1.080
 9YO  C7   H11  single    0.930  0.020  1.080
 9YO  C23  H12  single    0.930  0.020  1.080
 9YO  C13  H13  single    0.930  0.020  1.080
 9YO  C10  H15  single    0.970  0.020  1.090
 9YO  C22  H16  single    0.970  0.020  1.090
 9YO  C22  H17  single    0.970  0.020  1.090
 9YO  C22  H18  single    0.970  0.020  1.090
 9YO  C10  H10  single    0.970  0.020  1.090
 9YO  N21  H14  single    0.890  0.020  1.040

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
 9YO  C26  C1   C12  119.97  3.000
 9YO  C12  C1   S19  117.65  3.000
 9YO  C26  C1   S19  122.35  3.000
 9YO  H1   C2   C17  120.57  3.000
 9YO  H1   C2   C12  119.64  3.000
 9YO  C17  C2   C12  119.80  3.000
 9YO  H2   C3   C10  110.50  3.000
 9YO  H2   C3   N6   110.25  3.000
 9YO  C10  C3   N6   105.01  3.000
 9YO  H2   C3   C11  108.48  3.000
 9YO  C10  C3   C11  111.99  3.000
 9YO  N6   C3   C11  110.59  3.000
 9YO  C22  C4   N21  119.72  3.000
 9YO  N21  C4   N6   116.04  3.000
 9YO  C22  C4   N6   124.22  3.000
 9YO  H5   C5   H4   107.94  3.000
 9YO  H5   C5   H3   107.44  3.000
 9YO  H4   C5   H3   107.06  3.000
 9YO  H5   C5   C16  111.54  3.000
 9YO  H4   C5   C16  111.55  3.000
 9YO  H3   C5   C16  111.09  3.000
 9YO  N14  S19  O8   107.45  3.000
 9YO  N14  S19  O18  106.31  3.000
 9YO  O8   S19  O18  120.18  3.000
 9YO  O18  S19  C1   110.46  3.000
 9YO  N14  S19  C1   103.85  3.000
 9YO  O8   S19  C1   107.37  3.000
 9YO  H6   C12  C2   119.72  3.000
 9YO  H6   C12  C1   120.25  3.000
 9YO  C2   C12  C1   120.03  3.000
 9YO  C20  C26  CL9  118.34  3.000
 9YO  C20  C26  C1   119.84  3.000
 9YO  CL9  C26  C1   121.81  3.000
 9YO  H7   C20  C17  120.41  3.000
 9YO  H7   C20  C26  119.71  3.000
 9YO  C17  C20  C26  119.88  3.000
 9YO  H8   C17  C20  119.18  3.000
 9YO  H8   C17  C2   120.34  3.000
 9YO  C20  C17  C2   120.48  3.000
 9YO  C15  N14  C24  108.97  3.000
 9YO  C15  N14  S19  125.83  3.000
 9YO  C24  N14  S19  125.21  3.000
 9YO  H9   C24  C11  129.74  3.000
 9YO  H9   C24  N14  120.90  3.000
 9YO  C11  C24  N14  109.37  3.000
 9YO  C25  C15  C7   121.74  3.000
 9YO  C7   C15  N14  131.59  3.000
 9YO  C25  C15  N14  106.67  3.000
 9YO  H11  C7   C13  119.83  3.000
 9YO  H11  C7   C15  122.88  3.000
 9YO  C13  C7   C15  117.29  3.000
 9YO  C11  C25  C23  132.66  3.000
 9YO  C23  C25  C15  119.60  3.000
 9YO  C11  C25  C15  107.74  3.000
 9YO  H12  C23  C16  119.95  3.000
 9YO  H12  C23  C25  120.28  3.000
 9YO  C16  C23  C25  119.77  3.000
 9YO  C13  C16  C23  119.07  3.000
 9YO  C13  C16  C5   119.96  3.000
 9YO  C23  C16  C5   120.96  3.000
 9YO  H13  C13  C16  118.99  3.000
 9YO  H13  C13  C7   118.48  3.000
 9YO  C16  C13  C7   122.53  3.000
 9YO  C25  C11  C24  107.24  3.000
 9YO  C25  C11  C3   125.83  3.000
 9YO  C24  C11  C3   126.93  3.000
 9YO  C4   N6   C3   106.60  3.000
 9YO  H10  C10  H15  108.16  3.000
 9YO  H10  C10  N21  111.65  3.000
 9YO  H15  C10  N21  112.12  3.000
 9YO  H10  C10  C3   111.41  3.000
 9YO  H15  C10  C3   113.17  3.000
 9YO  N21  C10  C3   100.26  3.000
 9YO  H14  N21  C10  119.22  3.000
 9YO  H14  N21  C4   119.16  3.000
 9YO  C10  N21  C4   107.03  3.000
 9YO  H18  C22  H17  109.03  3.000
 9YO  H18  C22  H16  107.26  3.000
 9YO  H17  C22  H16  108.76  3.000
 9YO  H18  C22  C4   110.45  3.000
 9YO  H17  C22  C4   110.62  3.000
 9YO  H16  C22  C4   110.64  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
 9YO  CONST_01  C17  C20  C26  C1      0.00   0.0  0
 9YO  CONST_02  C17  C2   C12  C1      0.00   0.0  0
 9YO  CONST_03  C26  C20  C17  C2      0.00   0.0  0
 9YO  CONST_04  C26  C1   C12  C2      0.00   0.0  0
 9YO  CONST_05  C20  C26  C1   C12     0.00   0.0  0
 9YO  CONST_06  C20  C17  C2   C12     0.00   0.0  0
 9YO  CONST_07  C25  C11  C24  N14     0.00   0.0  0
 9YO  CONST_08  C11  C25  C15  N14     0.00   0.0  0
 9YO  CONST_09  C23  C25  C15  N14   180.00   0.0  0
 9YO  CONST_10  C13  C7   C15  N14   180.00   0.0  0
 9YO  CONST_11  C15  C25  C11  C24     0.00   0.0  0
 9YO  CONST_12  C23  C25  C11  C24   180.00   0.0  0
 9YO  CONST_13  C25  C15  N14  C24     0.00   0.0  0
 9YO  CONST_14  C7   C15  N14  C24   180.00   0.0  0
 9YO  CONST_15  C11  C24  N14  C15     0.00   0.0  0
 9YO  CONST_16  C16  C23  C25  C15     0.00   0.0  0
 9YO  CONST_17  C16  C13  C7   C15     0.00   0.0  0
 9YO  CONST_18  C11  C25  C15  C7    180.00   0.0  0
 9YO  CONST_19  C23  C25  C15  C7      0.00   0.0  0
 9YO  CONST_20  C23  C16  C13  C7      0.00   0.0  0
 9YO  CONST_21  C13  C7   C15  C25     0.00   0.0  0
 9YO  CONST_22  C13  C16  C23  C25     0.00   0.0  0
 9YO  CONST_23  C11  C25  C23  C16   180.00   0.0  0
 9YO  CONST_24  N14  C24  C11  C3    180.00   0.0  0
 9YO  CONST_25  C15  C25  C11  C3    180.00   0.0  0
 9YO  CONST_26  C23  C25  C11  C3      0.00   0.0  0
 9YO  CONST_27  N21  C4   N6   C3      0.00   0.0  0
 9YO  CONST_29  C10  N21  C4   N6      0.00   0.0  0
 9YO  CONST_30  S19  C1   C12  C2    180.00   0.0  0
 9YO  CONST_31  C25  C23  C16  C5    180.00   0.0  0
 9YO  CONST_32  C7   C13  C16  C5    180.00   0.0  0
 9YO  CONST_33  C20  C26  C1   S19   180.00   0.0  0
 9YO  CONST_34  C11  C24  N14  S19   180.00   0.0  0
 9YO  CONST_35  C25  C15  N14  S19   180.00   0.0  0
 9YO  CONST_36  C7   C15  N14  S19     0.00   0.0  0
 9YO  CONST_37  CL9  C26  C1   C12   180.00   0.0  0
 9YO  CONST_38  C17  C20  C26  CL9   180.00   0.0  0
 9YO  CONST_39  C22  C4   N6   C3    180.00   0.0  0
 9YO  CONST_40  C22  C4   N21  C10   180.00   0.0  0
 9YO  CONST_41  H7   C20  C26  C1    180.00   0.0  0
 9YO  CONST_42  H1   C2   C12  C1    180.00   0.0  0
 9YO  CONST_43  H9   C24  C11  C3      0.00   0.0  0
 9YO  CONST_44  H8   C17  C2   C12   180.00   0.0  0
 9YO  CONST_45  H6   C12  C1   C26   180.00   0.0  0
 9YO  CONST_46  H11  C7   C15  N14     0.00   0.0  0
 9YO  CONST_47  H12  C23  C25  C15   180.00   0.0  0
 9YO  CONST_48  H13  C13  C7   C15   180.00   0.0  0
 9YO  Var_01    C24  N14  S19  C1    116.66  30.0  2
 9YO  Var_02    N14  S19  C1   C12   119.29  30.0  2
 9YO  Var_03    H15  C10  N21  C4   -141.20  30.0  1
 9YO  Var_04    H3   C5   C16  C23   100.43  30.0  2
 9YO  Var_05    H16  C22  C4   N6   -118.60  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
 9YO  chir_01  C3  N6  C11  C10  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
 9YO  plan-1  C1   0.020
 9YO  plan-1  C2   0.020
 9YO  plan-1  S19  0.020
 9YO  plan-1  C12  0.020
 9YO  plan-1  C26  0.020
 9YO  plan-1  CL9  0.020
 9YO  plan-1  C20  0.020
 9YO  plan-1  C17  0.020
 9YO  plan-1  H1   0.020
 9YO  plan-1  H6   0.020
 9YO  plan-1  H7   0.020
 9YO  plan-1  H8   0.020
 9YO  plan-2  C3   0.020
 9YO  plan-2  C5   0.020
 9YO  plan-2  S19  0.020
 9YO  plan-2  N14  0.020
 9YO  plan-2  C24  0.020
 9YO  plan-2  C15  0.020
 9YO  plan-2  C7   0.020
 9YO  plan-2  C25  0.020
 9YO  plan-2  C23  0.020
 9YO  plan-2  C16  0.020
 9YO  plan-2  C13  0.020
 9YO  plan-2  C11  0.020
 9YO  plan-2  H9   0.020
 9YO  plan-2  H11  0.020
 9YO  plan-2  H12  0.020
 9YO  plan-2  H13  0.020
 9YO  plan-3  C3   0.020
 9YO  plan-3  C4   0.020
 9YO  plan-3  N6   0.020
 9YO  plan-3  C10  0.020
 9YO  plan-3  N21  0.020
 9YO  plan-3  C22  0.020
 9YO  plan-3  H14  0.020

