# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 18:33:47 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 2-chloro-4-[({1-[(5-chloro-2-methoxyphenyl)sulfonyl]-4-methyl-2,3-dihydro-1H-indol-6-yl}carbonyl)amino]benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cl)cc1[S](=O)(=O)N2CCc3c(C)cc(cc23)C(=O)Nc4ccc(C(O)=O)c(Cl)c4
#
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
 0RK  0RK  '2-chloro-4-[({1-[(5-chloro-2-methoxyphenyl)sulfonyl]-4-methyl-2,3-dihydro-1H-indol-6-yl}carbonyl)amino]benzoic acid'  ligand  55  35  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0RK
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
 0RK  CL2  CL  CL    0  -0.117  -8.2314   1.5405  -0.4085
 0RK  C27  C   CR6   0  -0.055  -6.5195   1.3515  -0.5755
 0RK  C14  C   CR16  0  -0.189  -5.7780   0.8809   0.4937
 0RK  C31  C   CR16  0  -0.180  -5.9039   1.6682  -1.7757
 0RK  C26  C   CR16  0  -0.377  -4.5343   1.5172  -1.9193
 0RK  C21  C   CR6   0   0.476  -3.7653   1.0497  -0.8570
 0RK  O33  O   O2    0  -0.456  -2.4498   0.8602  -0.8962
 0RK  C35  C   CH3   0  -0.443  -1.7723   0.9042  -2.1412
 0RK  C3   C   CR6   0  -0.323  -4.4076   0.7311   0.3468
 0RK  S1   S   S     0   1.375  -3.4614   0.1233   1.7231
 0RK  O16  O   OS    0  -0.629  -2.3978   1.0554   2.0382
 0RK  O17  O   OS    0  -0.639  -4.4217  -0.2386   2.7507
 0RK  N2   N   NR5   0  -0.710  -2.7709  -1.2984   1.2370
 0RK  C12  C   CH2   0  -0.312  -3.6664  -2.3750   0.7557
 0RK  C19  C   CH2   0  -0.509  -3.0726  -2.7978  -0.5915
 0RK  C6   C   CR56  0  -0.009  -1.6628  -2.2976  -0.5035
 0RK  C4   C   CR56  0   0.446  -1.5402  -1.4018   0.5526
 0RK  C13  C   CR6   0   0.056  -0.5804  -2.5948  -1.3157
 0RK  C34  C   CH3   0  -0.735  -0.7236  -3.5280  -2.4792
 0RK  C18  C   CR16  0  -0.358   0.6368  -1.9862  -1.0142
 0RK  C9   C   CR6   0  -0.041   0.7619  -1.1093   0.0610
 0RK  C8   C   CR16  0  -0.315  -0.3373  -0.7988   0.8612
 0RK  C7   C   C     0   0.533   2.0546  -0.4401   0.3848
 0RK  O24  O   O     0  -0.447   2.0946   0.6611   0.8993
 0RK  N15  N   NH1   0  -0.764   3.1661  -1.1706   0.0789
 0RK  C23  C   CR6   0   0.401   4.5024  -0.8267   0.2142
 0RK  C20  C   CR16  0  -0.262   4.9559   0.4437   0.5659
 0RK  C10  C   CR6   0  -0.048   6.3170   0.6872   0.6662
 0RK  CL1  CL  CL    0  -0.098   6.7509   2.3093   1.0772
 0RK  C29  C   CR16  0  -0.335   5.4416  -1.8295  -0.0433
 0RK  C22  C   CR16  0  -0.256   6.7871  -1.5644   0.0525
 0RK  C5   C   CR6   0  -0.035   7.2707  -0.3024   0.4160
 0RK  C11  C   C     0   0.522   8.7307  -0.0793   0.5463
 0RK  O25  O   OH1   0  -0.595   9.4335  -1.0389  -0.0457
 0RK  O30  O   O     0  -0.429   9.2452   0.8439   1.1260
 0RK  H1   H   HCR6  0   0.307  -6.2619   0.6267   1.4261
 0RK  H2   H   HCR6  0   0.298  -6.4866   2.0339  -2.6100
 0RK  H3   H   HCR6  0   0.307  -4.0790   1.7740  -2.8657
 0RK  H4   H   HCH3  0   0.270  -0.7557   0.5765  -1.9411
 0RK  H5   H   HCH3  0   0.238  -2.2285   0.2291  -2.8684
 0RK  H6   H   HCH3  0   0.248  -1.7499   1.9158  -2.5505
 0RK  H7   H   HCH2  0   0.284  -3.6390  -3.1928   1.4752
 0RK  H8   H   HCH2  0   0.275  -4.6978  -2.0357   0.6740
 0RK  H9   H   HCH2  0   0.279  -3.1360  -3.8771  -0.7295
 0RK  H10  H   HCH2  0   0.270  -3.5956  -2.3351  -1.4339
 0RK  H11  H   HCH3  0   0.250  -1.4831  -3.1755  -3.1795
 0RK  H12  H   HCH3  0   0.254   0.2129  -3.6275  -3.0252
 0RK  H13  H   HCH3  0   0.252  -1.0286  -4.5236  -2.1516
 0RK  H14  H   HCR6  0   0.257   1.4842  -2.1937  -1.6574
 0RK  H15  H   HCR6  0   0.270  -0.2352  -0.1222   1.6954
 0RK  H16  H   HNH1  0   0.430   3.0090  -2.1221  -0.2174
 0RK  H17  H   HCR6  0   0.308   4.2648   1.2465   0.7591
 0RK  H18  H   HCR6  0   0.287   5.1124  -2.8222  -0.3228
 0RK  H19  H   HCR6  0   0.283   7.4800  -2.3679  -0.1502
 0RK  H20  H   HOH1  0   0.489  10.3791  -0.8851   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
 0RK  C35  O33  single    1.418  0.020  1.418
 0RK  O17  S1   double    1.452  0.020  1.452
 0RK  O33  C21  single    1.330  0.020  1.330
 0RK  C12  C19  single    1.532  0.020  1.532
 0RK  C12  N2   single    1.481  0.020  1.481
 0RK  C21  C26  aromatic  1.392  0.020  1.392
 0RK  C21  C3   aromatic  1.401  0.020  1.401
 0RK  S1   C3   single    1.777  0.020  1.777
 0RK  S1   N2   single    1.654  0.020  1.654
 0RK  S1   O16  double    1.449  0.020  1.449
 0RK  C26  C31  aromatic  1.385  0.020  1.385
 0RK  C19  C6   single    1.498  0.020  1.498
 0RK  C3   C14  aromatic  1.386  0.020  1.386
 0RK  N2   C4   single    1.412  0.020  1.412
 0RK  C31  C27  aromatic  1.385  0.020  1.385
 0RK  C14  C27  aromatic  1.384  0.020  1.384
 0RK  C6   C4   aromatic  1.390  0.020  1.390
 0RK  C6   C13  aromatic  1.386  0.020  1.386
 0RK  C4   C8   aromatic  1.380  0.020  1.380
 0RK  C27  CL2  single    1.730  0.020  1.730
 0RK  C34  C13  single    1.498  0.020  1.498
 0RK  C13  C18  aromatic  1.394  0.020  1.394
 0RK  C8   C9   aromatic  1.395  0.020  1.395
 0RK  C18  C9   aromatic  1.393  0.020  1.393
 0RK  C9   C7   single    1.491  0.020  1.491
 0RK  N15  C7   single    1.365  0.020  1.365
 0RK  N15  C23  single    1.386  0.020  1.386
 0RK  C29  C23  aromatic  1.398  0.020  1.398
 0RK  C29  C22  aromatic  1.375  0.020  1.375
 0RK  C7   O24  double    1.216  0.020  1.216
 0RK  C23  C20  aromatic  1.394  0.020  1.394
 0RK  C22  C5   aromatic  1.400  0.020  1.400
 0RK  C20  C10  aromatic  1.386  0.020  1.386
 0RK  C5   C10  aromatic  1.397  0.020  1.397
 0RK  C5   C11  single    1.483  0.020  1.483
 0RK  O30  C11  double    1.205  0.020  1.205
 0RK  C10  CL1  single    1.729  0.020  1.729
 0RK  C11  O25  single    1.329  0.020  1.329
 0RK  C14  H1   single    0.930  0.020  1.080
 0RK  C31  H2   single    0.930  0.020  1.080
 0RK  C26  H3   single    0.930  0.020  1.080
 0RK  C35  H4   single    0.970  0.020  1.090
 0RK  C35  H5   single    0.970  0.020  1.090
 0RK  C35  H6   single    0.970  0.020  1.090
 0RK  C12  H7   single    0.970  0.020  1.090
 0RK  C12  H8   single    0.970  0.020  1.090
 0RK  C19  H9   single    0.970  0.020  1.090
 0RK  C19  H10  single    0.970  0.020  1.090
 0RK  C34  H11  single    0.970  0.020  1.090
 0RK  C34  H12  single    0.970  0.020  1.090
 0RK  C34  H13  single    0.970  0.020  1.090
 0RK  C18  H14  single    0.930  0.020  1.080
 0RK  C8   H15  single    0.930  0.020  1.080
 0RK  N15  H16  single    0.860  0.020  1.020
 0RK  C20  H17  single    0.930  0.020  1.080
 0RK  C29  H18  single    0.930  0.020  1.080
 0RK  C22  H19  single    0.930  0.020  1.080
 0RK  O25  H20  single    0.850  0.020  0.980

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
 0RK  C31  C27  C14  120.60  3.000
 0RK  C14  C27  CL2  119.52  3.000
 0RK  C31  C27  CL2  119.88  3.000
 0RK  H1   C14  C3   120.57  3.000
 0RK  H1   C14  C27  120.44  3.000
 0RK  C3   C14  C27  118.99  3.000
 0RK  H2   C31  C26  119.31  3.000
 0RK  H2   C31  C27  120.41  3.000
 0RK  C26  C31  C27  120.27  3.000
 0RK  H3   C26  C21  121.00  3.000
 0RK  H3   C26  C31  118.77  3.000
 0RK  C21  C26  C31  120.23  3.000
 0RK  C3   C21  O33  116.51  3.000
 0RK  C3   C21  C26  118.60  3.000
 0RK  O33  C21  C26  124.88  3.000
 0RK  C35  O33  C21  119.61  3.000
 0RK  H6   C35  H5   109.37  3.000
 0RK  H6   C35  H4   109.23  3.000
 0RK  H5   C35  H4   109.08  3.000
 0RK  H6   C35  O33  111.58  3.000
 0RK  H5   C35  O33  111.46  3.000
 0RK  H4   C35  O33  106.02  3.000
 0RK  S1   C3   C21  119.94  3.000
 0RK  S1   C3   C14  118.76  3.000
 0RK  C21  C3   C14  121.30  3.000
 0RK  N2   S1   O17  105.66  3.000
 0RK  N2   S1   O16  108.09  3.000
 0RK  O17  S1   O16  119.46  3.000
 0RK  O16  S1   C3   109.83  3.000
 0RK  N2   S1   C3   106.78  3.000
 0RK  O17  S1   C3   106.33  3.000
 0RK  C4   N2   C12  108.44  3.000
 0RK  C4   N2   S1   124.71  3.000
 0RK  C12  N2   S1   117.91  3.000
 0RK  H8   C12  H7   107.89  3.000
 0RK  H8   C12  C19  112.79  3.000
 0RK  H7   C12  C19  111.34  3.000
 0RK  H8   C12  N2   111.76  3.000
 0RK  H7   C12  N2   108.41  3.000
 0RK  C19  C12  N2   104.60  3.000
 0RK  H10  C19  H9   107.07  3.000
 0RK  H10  C19  C6   110.72  3.000
 0RK  H9   C19  C6   113.13  3.000
 0RK  H10  C19  C12  112.03  3.000
 0RK  H9   C19  C12  111.23  3.000
 0RK  C6   C19  C12  102.76  3.000
 0RK  C13  C6   C4   120.98  3.000
 0RK  C13  C6   C19  128.97  3.000
 0RK  C4   C6   C19  110.04  3.000
 0RK  C8   C4   C6   121.87  3.000
 0RK  C8   C4   N2   128.26  3.000
 0RK  C6   C4   N2   109.79  3.000
 0RK  C18  C13  C34  121.56  3.000
 0RK  C18  C13  C6   117.50  3.000
 0RK  C34  C13  C6   120.94  3.000
 0RK  H13  C34  H12  107.91  3.000
 0RK  H13  C34  H11  107.01  3.000
 0RK  H12  C34  H11  107.84  3.000
 0RK  H13  C34  C13  111.20  3.000
 0RK  H12  C34  C13  111.36  3.000
 0RK  H11  C34  C13  111.32  3.000
 0RK  H14  C18  C9   120.55  3.000
 0RK  H14  C18  C13  118.08  3.000
 0RK  C9   C18  C13  121.35  3.000
 0RK  C7   C9   C8   117.31  3.000
 0RK  C7   C9   C18  121.86  3.000
 0RK  C8   C9   C18  120.81  3.000
 0RK  H15  C8   C9   120.57  3.000
 0RK  H15  C8   C4   121.95  3.000
 0RK  C9   C8   C4   117.47  3.000
 0RK  N15  C7   O24  123.55  3.000
 0RK  O24  C7   C9   121.78  3.000
 0RK  N15  C7   C9   114.66  3.000
 0RK  H16  N15  C23  114.37  3.000
 0RK  H16  N15  C7   116.35  3.000
 0RK  C23  N15  C7   129.08  3.000
 0RK  C29  C23  C20  118.80  3.000
 0RK  C20  C23  N15  124.34  3.000
 0RK  C29  C23  N15  116.85  3.000
 0RK  H17  C20  C10  119.09  3.000
 0RK  H17  C20  C23  121.06  3.000
 0RK  C10  C20  C23  119.85  3.000
 0RK  C5   C10  CL1  122.41  3.000
 0RK  CL1  C10  C20  115.37  3.000
 0RK  C5   C10  C20  122.20  3.000
 0RK  H18  C29  C22  119.51  3.000
 0RK  H18  C29  C23  120.07  3.000
 0RK  C22  C29  C23  120.43  3.000
 0RK  H19  C22  C5   119.86  3.000
 0RK  H19  C22  C29  118.12  3.000
 0RK  C5   C22  C29  122.02  3.000
 0RK  C11  C5   C22  119.92  3.000
 0RK  C11  C5   C10  123.36  3.000
 0RK  C22  C5   C10  116.71  3.000
 0RK  O30  C11  O25  122.80  3.000
 0RK  O25  C11  C5   111.90  3.000
 0RK  O30  C11  C5   125.29  3.000
 0RK  H20  O25  C11  109.62  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
 0RK  CONST_01  C21  C26  C31  C27     0.00   0.0  0
 0RK  CONST_02  C21  C3   C14  C27     0.00   0.0  0
 0RK  CONST_03  C26  C21  C3   C14     0.00   0.0  0
 0RK  CONST_04  C26  C31  C27  C14     0.00   0.0  0
 0RK  CONST_05  C3   C21  C26  C31     0.00   0.0  0
 0RK  CONST_06  C3   C14  C27  C31     0.00   0.0  0
 0RK  CONST_07  C9   C8   C4   C6      0.00   0.0  0
 0RK  CONST_08  C9   C18  C13  C6      0.00   0.0  0
 0RK  CONST_09  C18  C13  C6   C4      0.00   0.0  0
 0RK  CONST_10  C18  C9   C8   C4      0.00   0.0  0
 0RK  CONST_11  C8   C4   C6   C13     0.00   0.0  0
 0RK  CONST_12  C8   C9   C18  C13     0.00   0.0  0
 0RK  CONST_13  C5   C22  C29  C23     0.00   0.0  0
 0RK  CONST_14  C5   C10  C20  C23     0.00   0.0  0
 0RK  CONST_15  C22  C29  C23  C20     0.00   0.0  0
 0RK  CONST_16  C22  C5   C10  C20     0.00   0.0  0
 0RK  CONST_17  C29  C23  C20  C10     0.00   0.0  0
 0RK  CONST_18  C29  C22  C5   C10     0.00   0.0  0
 0RK  CONST_19  C26  C31  C27  CL2   180.00   0.0  0
 0RK  CONST_20  C3   C14  C27  CL2   180.00   0.0  0
 0RK  CONST_21  S1   C3   C14  C27   180.00   0.0  0
 0RK  CONST_22  O33  C21  C3   C14   180.00   0.0  0
 0RK  CONST_23  O33  C21  C26  C31   180.00   0.0  0
 0RK  CONST_24  S1   C3   C21  C26   180.00   0.0  0
 0RK  CONST_25  C34  C13  C6   C19     0.00   0.0  0
 0RK  CONST_26  C34  C13  C6   C4    180.00   0.0  0
 0RK  CONST_27  C7   C9   C8   C4    180.00   0.0  0
 0RK  CONST_28  C7   C9   C18  C13   180.00   0.0  0
 0RK  CONST_29  C9   C18  C13  C34   180.00   0.0  0
 0RK  CONST_30  C22  C29  C23  N15   180.00   0.0  0
 0RK  CONST_31  C10  C20  C23  N15   180.00   0.0  0
 0RK  CONST_32  CL1  C10  C20  C23   180.00   0.0  0
 0RK  CONST_33  C11  C5   C10  C20   180.00   0.0  0
 0RK  CONST_34  C22  C5   C10  CL1   180.00   0.0  0
 0RK  CONST_35  C11  C5   C22  C29   180.00   0.0  0
 0RK  CONST_36  H3   C26  C31  C27   180.00   0.0  0
 0RK  CONST_37  H2   C31  C27  C14   180.00   0.0  0
 0RK  CONST_38  H1   C14  C27  C31   180.00   0.0  0
 0RK  CONST_39  H15  C8   C4   N2      0.00   0.0  0
 0RK  CONST_40  H14  C18  C13  C6    180.00   0.0  0
 0RK  CONST_41  H19  C22  C29  C23   180.00   0.0  0
 0RK  CONST_42  H18  C29  C23  C20   180.00   0.0  0
 0RK  CONST_43  H17  C20  C23  C29   180.00   0.0  0
 0RK  CONST_44  C23  N15  C7   C9    180.00   0.0  0
 0RK  CONST_45  C29  C23  N15  C7    180.00   0.0  0
 0RK  CONST_46  C20  C23  N15  C7      0.00   0.0  0
 0RK  CONST_47  H16  N15  C23  C20   180.00   0.0  0
 0RK  CONST_48  C23  N15  C7   O24     0.00   0.0  0
 0RK  CONST_49  H20  O25  C11  C5    180.00   0.0  0
 0RK  Var_01    C6   C19  C12  N2     20.07  30.0  1
 0RK  Var_02    C4   C6   C19  C12   -14.39  30.0  1
 0RK  Var_03    C6   C4   N2   C12    11.15  30.0  1
 0RK  Var_04    C4   N2   C12  C19   -19.72  30.0  1
 0RK  Var_05    N2   S1   C3   C14   118.30  30.0  2
 0RK  Var_06    C12  N2   S1   C3    -57.05  30.0  3
 0RK  Var_07    C3   C21  O33  C35   167.59  30.0  2
 0RK  Var_08    N15  C7   C9   C18   -31.66  30.0  2
 0RK  Var_09    O30  C11  C5   C10    16.08  30.0  2
 0RK  Var_10    H11  C34  C13  C6     57.97  30.0  2
 0RK  Var_11    H4   C35  O33  C21  -171.63  30.0  3

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
 0RK  plan-1  CL2  0.020
 0RK  plan-1  C27  0.020
 0RK  plan-1  C14  0.020
 0RK  plan-1  C31  0.020
 0RK  plan-1  C26  0.020
 0RK  plan-1  C21  0.020
 0RK  plan-1  O33  0.020
 0RK  plan-1  C3   0.020
 0RK  plan-1  S1   0.020
 0RK  plan-1  H1   0.020
 0RK  plan-1  H2   0.020
 0RK  plan-1  H3   0.020
 0RK  plan-2  N15  0.020
 0RK  plan-2  C23  0.020
 0RK  plan-2  C20  0.020
 0RK  plan-2  C10  0.020
 0RK  plan-2  CL1  0.020
 0RK  plan-2  C29  0.020
 0RK  plan-2  C22  0.020
 0RK  plan-2  C5   0.020
 0RK  plan-2  C11  0.020
 0RK  plan-2  H17  0.020
 0RK  plan-2  H18  0.020
 0RK  plan-2  H19  0.020
 0RK  plan-3  N2   0.020
 0RK  plan-3  C19  0.020
 0RK  plan-3  C6   0.020
 0RK  plan-3  C4   0.020
 0RK  plan-3  C13  0.020
 0RK  plan-3  C34  0.020
 0RK  plan-3  C18  0.020
 0RK  plan-3  C9   0.020
 0RK  plan-3  C8   0.020
 0RK  plan-3  C7   0.020
 0RK  plan-3  H14  0.020
 0RK  plan-3  H15  0.020
 0RK  plan-4  C9   0.020
 0RK  plan-4  C7   0.020
 0RK  plan-4  O24  0.020
 0RK  plan-4  N15  0.020
 0RK  plan-4  C23  0.020
 0RK  plan-4  H16  0.020
 0RK  plan-5  C5   0.020
 0RK  plan-5  C11  0.020
 0RK  plan-5  O25  0.020
 0RK  plan-5  O30  0.020
 0RK  plan-5  H20  0.020

