# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 20:46:19 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  54  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  -0.118  -7.9707   2.0863  -0.4270
 0RK  C27  C   CR6    0  -0.056  -6.2629   1.8123  -0.4848
 0RK  C14  C   CR16   0  -0.189  -5.6670   1.0158   0.4767
 0RK  C31  C   CR16   0  -0.179  -5.5052   2.3871  -1.4921
 0RK  C26  C   CR16   0  -0.385  -4.1380   2.1722  -1.5463
 0RK  C21  C   CR6    0   0.486  -3.5125   1.3800  -0.5865
 0RK  O33  O   O2     0  -0.454  -2.2132   1.1087  -0.5553
 0RK  C35  C   CH3    0  -0.444  -1.3655   1.5878  -1.5868
 0RK  C3   C   CR6    0  -0.328  -4.2977   0.8038   0.4215
 0RK  S1   S   S      0   1.400  -3.5445  -0.2150   1.6673
 0RK  O16  O   OS     0  -0.629  -2.4396   0.4869   2.2879
 0RK  O17  O   OS     0  -0.638  -4.6287  -0.7015   2.5021
 0RK  N2   N   NR5    0  -0.747  -2.9525  -1.5387   0.8832
 0RK  C12  C   CH2    0  -0.290  -3.9318  -2.4235   0.2148
 0RK  C19  C   CH2    0  -0.507  -3.0715  -3.3864  -0.6128
 0RK  C6   C   CR56   0  -0.052  -1.7024  -2.7851  -0.5573
 0RK  C4   C   CR56   0   0.474  -1.6691  -1.7147   0.3305
 0RK  C13  C   CR6    0   0.069  -0.5647  -3.2004  -1.2311
 0RK  C34  C   CH3    0  -0.736  -0.6274  -4.3434  -2.1980
 0RK  C18  C   CR16   0  -0.370   0.6216  -2.5129  -0.9855
 0RK  C9   C   CR6    0  -0.033   0.6563  -1.4495  -0.0876
 0RK  C8   C   CR16   0  -0.321  -0.4913  -1.0350   0.5853
 0RK  C7   C   C      0   0.525   1.9019  -0.6580   0.1349
 0RK  O24  O   O      0  -0.459   1.8612   0.5401   0.3576
 0RK  N15  N   NH1    0  -0.757   3.0526  -1.3767   0.0708
 0RK  C23  C   CR6    0   0.367   4.3730  -0.9291   0.1451
 0RK  C20  C   CR16   0  -0.271   4.7476   0.4108   0.0961
 0RK  C10  C   CR6    0  -0.077   6.0966   0.7435   0.1200
 0RK  CL1  CL  CL     0  -0.134   6.4495   2.4460   0.0819
 0RK  C29  C   CR16   0  -0.335   5.3700  -1.9004   0.2569
 0RK  C22  C   CR16   0  -0.287   6.6981  -1.5307   0.3132
 0RK  C5   C   CR6    0  -0.020   7.1112  -0.2005   0.2248
 0RK  C11  C   C      0   0.376   8.6064   0.1031   0.2160
 0RK  O25  O   OC    -1  -0.594   9.3060  -0.6254   0.9436
 0RK  O30  O   O      0  -0.585   8.9881   1.0134  -0.5364
 0RK  H1   H   HCR6   0   0.307  -6.2614   0.5641   1.2582
 0RK  H2   H   HCR6   0   0.297  -5.9755   3.0041  -2.2455
 0RK  H3   H   HCR6   0   0.306  -3.5713   2.6294  -2.3452
 0RK  H4   H   HCH3   0   0.269  -0.3668   1.2434  -1.3342
 0RK  H5   H   HCH3   0   0.240  -1.6525   1.1827  -2.5590
 0RK  H6   H   HCH3   0   0.243  -1.3662   2.6784  -1.6321
 0RK  H7   H   HCH2   0   0.279  -4.5406  -2.9389   0.9529
 0RK  H8   H   HCH2   0   0.265  -4.5920  -1.8395  -0.4316
 0RK  H9   H   HCH2   0   0.277  -3.0697  -4.3902  -0.1821
 0RK  H10  H   HCH2   0   0.274  -3.4474  -3.4783  -1.6326
 0RK  H11  H   HCH3   0   0.249  -1.3442  -4.1464  -2.9973
 0RK  H12  H   HCH3   0   0.254   0.3420  -4.5306  -2.6566
 0RK  H13  H   HCH3   0   0.250  -0.9466  -5.2631  -1.7035
 0RK  H14  H   HCR6   0   0.257   1.5111  -2.8033  -1.5321
 0RK  H15  H   HCR6   0   0.280  -0.4419  -0.2062   1.2718
 0RK  H16  H   HNH1   0   0.424   2.9521  -2.3792   0.0201
 0RK  H17  H   HCR6   0   0.295   4.0110   1.1938   0.0344
 0RK  H18  H   HCR6   0   0.270   5.1019  -2.9493   0.3063
 0RK  H19  H   HCR6   0   0.260   7.4505  -2.3009   0.4170

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    1.328  0.020  1.328
 0RK  C12  C19  single    1.534  0.020  1.534
 0RK  C12  N2   single    1.479  0.020  1.479
 0RK  C21  C26  aromatic  1.393  0.020  1.393
 0RK  C21  C3   aromatic  1.402  0.020  1.402
 0RK  S1   C3   single    1.777  0.020  1.777
 0RK  S1   N2   single    1.648  0.020  1.648
 0RK  S1   O16  double    1.449  0.020  1.449
 0RK  C26  C31  aromatic  1.385  0.020  1.385
 0RK  C19  C6   single    1.496  0.020  1.496
 0RK  C3   C14  aromatic  1.387  0.020  1.387
 0RK  N2   C4   single    1.408  0.020  1.408
 0RK  C31  C27  aromatic  1.385  0.020  1.385
 0RK  C14  C27  aromatic  1.383  0.020  1.383
 0RK  C6   C4   aromatic  1.391  0.020  1.391
 0RK  C6   C13  aromatic  1.386  0.020  1.386
 0RK  C4   C8   aromatic  1.383  0.020  1.383
 0RK  C27  CL2  single    1.731  0.020  1.731
 0RK  C34  C13  single    1.498  0.020  1.498
 0RK  C13  C18  aromatic  1.393  0.020  1.393
 0RK  C8   C9   aromatic  1.393  0.020  1.393
 0RK  C18  C9   aromatic  1.392  0.020  1.392
 0RK  C9   C7   single    1.492  0.020  1.492
 0RK  N15  C7   single    1.358  0.020  1.358
 0RK  N15  C23  single    1.396  0.020  1.396
 0RK  C29  C23  aromatic  1.396  0.020  1.396
 0RK  C29  C22  aromatic  1.380  0.020  1.380
 0RK  C7   O24  double    1.219  0.020  1.219
 0RK  C23  C20  aromatic  1.392  0.020  1.392
 0RK  C22  C5   aromatic  1.396  0.020  1.396
 0RK  C20  C10  aromatic  1.390  0.020  1.390
 0RK  C5   C10  aromatic  1.390  0.020  1.390
 0RK  C5   C11  single    1.526  0.020  1.526
 0RK  O30  C11  deloc     1.241  0.020  1.241
 0RK  C10  CL1  single    1.739  0.020  1.739
 0RK  C11  O25  deloc     1.245  0.020  1.245
 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

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  120.57  3.000
 0RK  C14  C27  CL2  119.54  3.000
 0RK  C31  C27  CL2  119.89  3.000
 0RK  H1   C14  C3   120.52  3.000
 0RK  H1   C14  C27  120.42  3.000
 0RK  C3   C14  C27  119.06  3.000
 0RK  H2   C31  C26  119.37  3.000
 0RK  H2   C31  C27  120.36  3.000
 0RK  C26  C31  C27  120.27  3.000
 0RK  H3   C26  C21  120.96  3.000
 0RK  H3   C26  C31  118.74  3.000
 0RK  C21  C26  C31  120.30  3.000
 0RK  C3   C21  O33  116.57  3.000
 0RK  C3   C21  C26  118.54  3.000
 0RK  O33  C21  C26  124.88  3.000
 0RK  C35  O33  C21  119.91  3.000
 0RK  H6   C35  H5   109.49  3.000
 0RK  H6   C35  H4   109.08  3.000
 0RK  H5   C35  H4   109.35  3.000
 0RK  H6   C35  O33  111.55  3.000
 0RK  H5   C35  O33  111.42  3.000
 0RK  H4   C35  O33  105.86  3.000
 0RK  S1   C3   C21  120.16  3.000
 0RK  S1   C3   C14  118.58  3.000
 0RK  C21  C3   C14  121.26  3.000
 0RK  N2   S1   O17  105.82  3.000
 0RK  N2   S1   O16  108.60  3.000
 0RK  O17  S1   O16  119.04  3.000
 0RK  O16  S1   C3   110.23  3.000
 0RK  N2   S1   C3   106.21  3.000
 0RK  O17  S1   C3   106.18  3.000
 0RK  C4   N2   C12  110.56  3.000
 0RK  C4   N2   S1   127.90  3.000
 0RK  C12  N2   S1   117.22  3.000
 0RK  H8   C12  H7   108.47  3.000
 0RK  H8   C12  C19  110.80  3.000
 0RK  H7   C12  C19  112.52  3.000
 0RK  H8   C12  N2   110.33  3.000
 0RK  H7   C12  N2   110.34  3.000
 0RK  C19  C12  N2   104.36  3.000
 0RK  H10  C19  H9   106.96  3.000
 0RK  H10  C19  C6   112.57  3.000
 0RK  H9   C19  C6   110.68  3.000
 0RK  H10  C19  C12  111.35  3.000
 0RK  H9   C19  C12  111.41  3.000
 0RK  C6   C19  C12  103.94  3.000
 0RK  C13  C6   C4   121.41  3.000
 0RK  C13  C6   C19  127.78  3.000
 0RK  C4   C6   C19  110.78  3.000
 0RK  C8   C4   C6   121.06  3.000
 0RK  C8   C4   N2   129.95  3.000
 0RK  C6   C4   N2   108.95  3.000
 0RK  C18  C13  C34  121.73  3.000
 0RK  C18  C13  C6   117.74  3.000
 0RK  C34  C13  C6   120.53  3.000
 0RK  H13  C34  H12  107.84  3.000
 0RK  H13  C34  H11  106.96  3.000
 0RK  H12  C34  H11  107.90  3.000
 0RK  H13  C34  C13  111.26  3.000
 0RK  H12  C34  C13  111.45  3.000
 0RK  H11  C34  C13  111.24  3.000
 0RK  H14  C18  C9   120.63  3.000
 0RK  H14  C18  C13  118.55  3.000
 0RK  C9   C18  C13  120.80  3.000
 0RK  C7   C9   C8   117.23  3.000
 0RK  C7   C9   C18  121.47  3.000
 0RK  C8   C9   C18  121.20  3.000
 0RK  H15  C8   C9   119.92  3.000
 0RK  H15  C8   C4   122.30  3.000
 0RK  C9   C8   C4   117.78  3.000
 0RK  N15  C7   O24  123.84  3.000
 0RK  O24  C7   C9   121.36  3.000
 0RK  N15  C7   C9   114.80  3.000
 0RK  H16  N15  C23  114.55  3.000
 0RK  H16  N15  C7   116.35  3.000
 0RK  C23  N15  C7   128.98  3.000
 0RK  C29  C23  C20  118.70  3.000
 0RK  C20  C23  N15  124.14  3.000
 0RK  C29  C23  N15  117.16  3.000
 0RK  H17  C20  C10  119.41  3.000
 0RK  H17  C20  C23  121.18  3.000
 0RK  C10  C20  C23  119.41  3.000
 0RK  C5   C10  CL1  121.23  3.000
 0RK  CL1  C10  C20  115.53  3.000
 0RK  C5   C10  C20  123.19  3.000
 0RK  H18  C29  C22  119.71  3.000
 0RK  H18  C29  C23  120.02  3.000
 0RK  C22  C29  C23  120.27  3.000
 0RK  H19  C22  C5   118.61  3.000
 0RK  H19  C22  C29  118.86  3.000
 0RK  C5   C22  C29  122.53  3.000
 0RK  C11  C5   C22  118.69  3.000
 0RK  C11  C5   C10  125.44  3.000
 0RK  C22  C5   C10  115.85  3.000
 0RK  O30  C11  O25  127.64  3.000
 0RK  O25  C11  C5   115.53  3.000
 0RK  O30  C11  C5   116.79  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  Var_01    C6   C19  C12  N2   -11.14  30.0  1
 0RK  Var_02    C4   C6   C19  C12    7.55  30.0  1
 0RK  Var_03    C6   C4   N2   C12   -7.25  30.0  1
 0RK  Var_04    C4   N2   C12  C19   11.62  30.0  1
 0RK  Var_05    N2   S1   C3   C14  115.48  30.0  3
 0RK  Var_06    C12  N2   S1   C3   -63.42  30.0  3
 0RK  Var_07    C3   C21  O33  C35  176.18  30.0  2
 0RK  Var_08    N15  C7   C9   C18  -35.24  30.0  2
 0RK  Var_09    O30  C11  C5   C10  -37.01  30.0  2
 0RK  Var_10    H11  C34  C13  C6    58.36  30.0  2
 0RK  Var_11    H4   C35  O33  C21  179.68  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

