# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 13:06:54 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2S)-2-{[4-(4-chlorophenyl)-5-cyano-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](SC1=NC(=C(C#N)C(=O)N1)c2ccc(Cl)cc2)C(=O)Nc3ccc(cc3)[S](N)(=O)=O
#
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
 6KE  6KE  (2S)-2-{[4-(4-chlorophenyl)-5-cyano-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide  ligand  48  32  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6KE
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
 6KE  C1   C   CR6   0  -0.227  -6.2174  -0.6432  -0.2839
 6KE  C2   C   CR16  0  -0.221  -5.2650  -1.6472  -0.3832
 6KE  C3   C   CR16  0  -0.337  -3.9312  -1.3309  -0.2189
 6KE  C4   C   CR6   0   0.400  -3.5331  -0.0169   0.0393
 6KE  C5   C   CR16  0  -0.302  -4.5008   0.9876   0.1327
 6KE  C6   C   CR16  0  -0.206  -5.8365   0.6662  -0.0274
 6KE  O1   O   OS    0  -0.667  -8.5941   0.0912  -1.1619
 6KE  C7   C   C     0   0.609  -1.5013   1.3527   0.4375
 6KE  C10  C   CR6   0   0.381   2.3914   2.2852   0.0078
 6KE  C11  C   CR6   0   0.586   4.5932   3.1057  -0.5114
 6KE  C12  C   CR6   0  -0.247   4.9801   1.7125  -0.4830
 6KE  C13  C   CR6   0   0.354   4.0530   0.7385  -0.1732
 6KE  C8   C   CH1   0  -0.545  -0.0133   1.1488   0.6655
 6KE  C9   C   CH3   0  -0.633   0.2579   0.7438   2.1100
 6KE  O3   O   O     0  -0.441  -2.0086   2.4533   0.5169
 6KE  C14  C   CSP   0   0.018   6.3213   1.4407  -0.8442
 6KE  O2   O   OS    0  -0.653  -8.0205  -2.3421  -1.1007
 6KE  C16  C   CR16  0  -0.274   3.4753  -1.6310  -0.5659
 6KE  C17  C   CR16  0  -0.195   3.7501  -2.9844  -0.4903
 6KE  C18  C   CR6   0  -0.041   4.9310  -3.4009   0.1076
 6KE  C19  C   CR16  0  -0.194   5.8341  -2.4869   0.6275
 6KE  C20  C   CR16  0  -0.295   5.5578  -1.1332   0.5288
 6KE  C15  C   CR6   0   0.043   4.3828  -0.6913  -0.0761
 6KE  N4   N   N     0  -0.451   2.7578   1.0405   0.0434
 6KE  N5   N   NS    0  -0.241   7.4190   1.2557  -1.1460
 6KE  O4   O   O     0  -0.433   5.3258   4.0411  -0.7561
 6KE  N3   N   NR16  0  -0.689   3.2480   3.2974  -0.2265
 6KE  S2   S   S2    0   0.150   0.7376   2.7605   0.2579
 6KE  N2   N   NH1   0  -0.744  -2.1655   0.1983   0.1906
 6KE  S1   S   S     0   1.362  -7.9278  -1.0194  -0.4966
 6KE  N1   N   NC2   0  -0.887  -8.4600  -0.9879   1.0678
 6KE  H1   H   HCR6  0   0.288  -5.5474  -2.6707  -0.5865
 6KE  H2   H   HCR6  0   0.290  -3.1887  -2.1156  -0.2919
 6KE  H3   H   HCR6  0   0.298  -4.2300   2.0115   0.3266
 6KE  H4   H   HCR6  0   0.289  -6.5747   1.4531   0.0483
 6KE  H5   H   HCH1  0   0.339   0.3950   0.4049  -0.0205
 6KE  H6   H   HCH3  0   0.268   1.3274   0.6381   2.2773
 6KE  H7   H   HCH3  0   0.253  -0.1361   1.4820   2.8067
 6KE  H8   H   HCH3  0   0.259  -0.2074  -0.2185   2.3256
 6KE  H9   H   HCR6  0   0.276   2.5518  -1.3043  -1.0239
 6KE  H10  H   HCR6  0   0.289   3.0492  -3.7052  -0.8882
 6KE  H11  H   HCR6  0   0.291   6.7409  -2.8210   1.1117
 6KE  H12  H   HCR6  0   0.281   6.2558  -0.4325   0.9665
 6KE  H13  H   HNR6  0   0.447   2.9194   4.2576  -0.2206
 6KE  H14  H   HNH1  0   0.431  -1.5957  -0.6308   0.1036
 6KE  H15  H   HNC2  0   0.419  -9.4730  -0.9215   1.1133
 6KE  H16  H   HNC2  0   0.415  -8.1395  -1.7874   1.6049
 6KE  CL   CL  CL    0  -0.110   5.2768  -5.0901   0.2171

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
 6KE  CL   C18  single    1.728  0.020  1.728
 6KE  C19  C18  aromatic  1.386  0.020  1.386
 6KE  C19  C20  aromatic  1.385  0.020  1.385
 6KE  C18  C17  aromatic  1.388  0.020  1.388
 6KE  C20  C15  aromatic  1.393  0.020  1.393
 6KE  C17  C16  aromatic  1.383  0.020  1.383
 6KE  C15  C16  aromatic  1.395  0.020  1.395
 6KE  C15  C13  single    1.471  0.020  1.471
 6KE  N5   C14  triple    1.153  0.020  1.153
 6KE  C9   C8   single    1.525  0.020  1.525
 6KE  C14  C12  single    1.415  0.020  1.415
 6KE  C13  C12  double    1.380  0.020  1.380
 6KE  C13  N4   single    1.348  0.020  1.348
 6KE  C12  C11  single    1.446  0.020  1.446
 6KE  N4   C10  double    1.298  0.020  1.298
 6KE  C8   C7   single    1.519  0.020  1.519
 6KE  C8   S2   single    1.824  0.020  1.824
 6KE  C10  N3   single    1.347  0.020  1.347
 6KE  C10  S2   single    1.739  0.020  1.739
 6KE  C11  N3   single    1.388  0.020  1.388
 6KE  C11  O4   double    1.213  0.020  1.213
 6KE  C7   N2   single    1.354  0.020  1.354
 6KE  C7   O3   double    1.214  0.020  1.214
 6KE  N2   C4   single    1.393  0.020  1.393
 6KE  C4   C5   aromatic  1.398  0.020  1.398
 6KE  C4   C3   aromatic  1.397  0.020  1.397
 6KE  C5   C6   aromatic  1.383  0.020  1.383
 6KE  C3   C2   aromatic  1.381  0.020  1.381
 6KE  C6   C1   aromatic  1.388  0.020  1.388
 6KE  C2   C1   aromatic  1.387  0.020  1.387
 6KE  C1   S1   single    1.764  0.020  1.764
 6KE  N1   S1   single    1.653  0.020  1.653
 6KE  O1   S1   double    1.456  0.020  1.456
 6KE  S1   O2   double    1.457  0.020  1.457
 6KE  C2   H1   single    0.930  0.020  1.080
 6KE  C3   H2   single    0.930  0.020  1.080
 6KE  C5   H3   single    0.930  0.020  1.080
 6KE  C6   H4   single    0.930  0.020  1.080
 6KE  C8   H5   single    0.970  0.020  1.090
 6KE  C9   H6   single    0.970  0.020  1.090
 6KE  C9   H7   single    0.970  0.020  1.090
 6KE  C9   H8   single    0.970  0.020  1.090
 6KE  C16  H9   single    0.930  0.020  1.080
 6KE  C17  H10  single    0.930  0.020  1.080
 6KE  C19  H11  single    0.930  0.020  1.080
 6KE  C20  H12  single    0.930  0.020  1.080
 6KE  N3   H13  single    0.860  0.020  1.020
 6KE  N2   H14  single    0.860  0.020  1.020
 6KE  N1   H15  single    0.890  0.020  1.040
 6KE  N1   H16  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
 6KE  S1   C1   C6   119.32  3.000
 6KE  S1   C1   C2   120.17  3.000
 6KE  C6   C1   C2   120.51  3.000
 6KE  H1   C2   C3   119.45  3.000
 6KE  H1   C2   C1   121.29  3.000
 6KE  C3   C2   C1   119.27  3.000
 6KE  H2   C3   C4   119.91  3.000
 6KE  H2   C3   C2   119.24  3.000
 6KE  C4   C3   C2   120.85  3.000
 6KE  N2   C4   C5   124.16  3.000
 6KE  C5   C4   C3   119.40  3.000
 6KE  N2   C4   C3   116.44  3.000
 6KE  H3   C5   C6   119.00  3.000
 6KE  H3   C5   C4   121.41  3.000
 6KE  C6   C5   C4   119.59  3.000
 6KE  H4   C6   C5   118.81  3.000
 6KE  H4   C6   C1   120.80  3.000
 6KE  C5   C6   C1   120.39  3.000
 6KE  N2   C7   O3   125.41  3.000
 6KE  O3   C7   C8   121.40  3.000
 6KE  N2   C7   C8   113.16  3.000
 6KE  S2   C10  N3   115.12  3.000
 6KE  S2   C10  N4   121.78  3.000
 6KE  N3   C10  N4   123.10  3.000
 6KE  N3   C11  O4   121.34  3.000
 6KE  O4   C11  C12  125.82  3.000
 6KE  N3   C11  C12  112.84  3.000
 6KE  C14  C12  C13  123.95  3.000
 6KE  C13  C12  C11  120.31  3.000
 6KE  C14  C12  C11  115.69  3.000
 6KE  N4   C13  C15  115.02  3.000
 6KE  N4   C13  C12  121.58  3.000
 6KE  C15  C13  C12  123.40  3.000
 6KE  H5   C8   S2   107.93  3.000
 6KE  H5   C8   C9   110.36  3.000
 6KE  S2   C8   C9   111.91  3.000
 6KE  H5   C8   C7   111.33  3.000
 6KE  S2   C8   C7   104.54  3.000
 6KE  C9   C8   C7   110.62  3.000
 6KE  H8   C9   H7   108.50  3.000
 6KE  H8   C9   H6   107.66  3.000
 6KE  H7   C9   H6   108.86  3.000
 6KE  H8   C9   C8   110.24  3.000
 6KE  H7   C9   C8   111.21  3.000
 6KE  H6   C9   C8   110.28  3.000
 6KE  N5   C14  C12  180.00  3.000
 6KE  H9   C16  C15  120.05  3.000
 6KE  H9   C16  C17  119.24  3.000
 6KE  C15  C16  C17  120.71  3.000
 6KE  H10  C17  C18  120.67  3.000
 6KE  H10  C17  C16  120.23  3.000
 6KE  C18  C17  C16  119.10  3.000
 6KE  CL   C18  C19  119.38  3.000
 6KE  C19  C18  C17  121.21  3.000
 6KE  CL   C18  C17  119.41  3.000
 6KE  H11  C19  C20  120.09  3.000
 6KE  H11  C19  C18  120.71  3.000
 6KE  C20  C19  C18  119.19  3.000
 6KE  H12  C20  C15  120.96  3.000
 6KE  H12  C20  C19  118.40  3.000
 6KE  C15  C20  C19  120.60  3.000
 6KE  C20  C15  C16  119.16  3.000
 6KE  C16  C15  C13  119.06  3.000
 6KE  C20  C15  C13  121.74  3.000
 6KE  C13  N4   C10  118.81  3.000
 6KE  H13  N3   C11  116.45  3.000
 6KE  H13  N3   C10  120.29  3.000
 6KE  C11  N3   C10  123.25  3.000
 6KE  C8   S2   C10  100.49  3.000
 6KE  H14  N2   C7   116.03  3.000
 6KE  H14  N2   C4   114.70  3.000
 6KE  C7   N2   C4   129.28  3.000
 6KE  N1   S1   O2   112.91  3.000
 6KE  O2   S1   O1   118.29  3.000
 6KE  N1   S1   O1   105.70  3.000
 6KE  O2   S1   C1   107.77  3.000
 6KE  O1   S1   C1   109.64  3.000
 6KE  N1   S1   C1   101.19  3.000
 6KE  H16  N1   H15  110.03  3.000
 6KE  H16  N1   S1   112.60  3.000
 6KE  H15  N1   S1   111.38  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
 6KE  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 6KE  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 6KE  CONST_03  C5   C4   C3   C2     0.00   0.0  0
 6KE  CONST_04  C5   C6   C1   C2     0.00   0.0  0
 6KE  CONST_05  C6   C5   C4   C3     0.00   0.0  0
 6KE  CONST_06  C6   C1   C2   C3     0.00   0.0  0
 6KE  CONST_07  C19  C18  C17  C16    0.00   0.0  0
 6KE  CONST_08  C19  C20  C15  C16    0.00   0.0  0
 6KE  CONST_09  C20  C19  C18  C17    0.00   0.0  0
 6KE  CONST_10  C20  C15  C16  C17    0.00   0.0  0
 6KE  CONST_11  C15  C20  C19  C18    0.00   0.0  0
 6KE  CONST_12  C15  C16  C17  C18    0.00   0.0  0
 6KE  CONST_13  C19  C20  C15  C13  180.00   0.0  0
 6KE  CONST_14  C17  C16  C15  C13  180.00   0.0  0
 6KE  CONST_15  C12  C11  N3   C10    0.00   0.0  0
 6KE  CONST_16  N4   C10  N3   C11    0.00   0.0  0
 6KE  CONST_17  N3   C10  N4   C13    0.00   0.0  0
 6KE  CONST_18  N2   C4   C3   C2   180.00   0.0  0
 6KE  CONST_19  S1   C1   C2   C3   180.00   0.0  0
 6KE  CONST_20  S1   C1   C6   C5   180.00   0.0  0
 6KE  CONST_21  N2   C4   C5   C6   180.00   0.0  0
 6KE  CONST_22  CL   C18  C17  C16  180.00   0.0  0
 6KE  CONST_23  CL   C18  C19  C20  180.00   0.0  0
 6KE  CONST_24  O4   C11  N3   C10  180.00   0.0  0
 6KE  CONST_25  S2   C10  N3   C11  180.00   0.0  0
 6KE  CONST_26  S2   C10  N4   C13  180.00   0.0  0
 6KE  CONST_27  H3   C5   C6   C1   180.00   0.0  0
 6KE  CONST_28  H2   C3   C2   C1   180.00   0.0  0
 6KE  CONST_29  H4   C6   C1   C2   180.00   0.0  0
 6KE  CONST_30  H1   C2   C3   C4   180.00   0.0  0
 6KE  CONST_31  H12  C20  C15  C13    0.00   0.0  0
 6KE  CONST_32  H9   C16  C15  C13    0.00   0.0  0
 6KE  CONST_33  H11  C19  C18  C17  180.00   0.0  0
 6KE  CONST_34  H10  C17  C18  C19  180.00   0.0  0
 6KE  CONST_35  H13  N3   C11  C12  180.00   0.0  0
 6KE  CONST_36  C7   N2   C4   C3   180.00   0.0  0
 6KE  CONST_37  C7   N2   C4   C5     0.00   0.0  0
 6KE  CONST_38  H14  N2   C4   C3     0.00   0.0  0
 6KE  CONST_39  C8   C7   N2   C4   180.00   0.0  0
 6KE  CONST_40  O3   C7   N2   C4     0.00   0.0  0
 6KE  Var_01    C20  C15  C13  C12   41.13  30.0  3
 6KE  Var_02    N1   S1   C1   C2   103.99  30.0  2
 6KE  Var_03    N4   C10  S2   C8     4.65  30.0  3
 6KE  Var_04    H15  N1   S1   C1   163.62  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
 6KE  chir_01  C8  C9  C7  S2  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
 6KE  plan-1  C1   0.020
 6KE  plan-1  C2   0.020
 6KE  plan-1  C3   0.020
 6KE  plan-1  C4   0.020
 6KE  plan-1  C5   0.020
 6KE  plan-1  C6   0.020
 6KE  plan-1  N2   0.020
 6KE  plan-1  S1   0.020
 6KE  plan-1  H1   0.020
 6KE  plan-1  H2   0.020
 6KE  plan-1  H3   0.020
 6KE  plan-1  H4   0.020
 6KE  plan-2  C10  0.020
 6KE  plan-2  C11  0.020
 6KE  plan-2  C12  0.020
 6KE  plan-2  C13  0.020
 6KE  plan-2  C14  0.020
 6KE  plan-2  C15  0.020
 6KE  plan-2  N4   0.020
 6KE  plan-2  N5   0.020
 6KE  plan-2  O4   0.020
 6KE  plan-2  N3   0.020
 6KE  plan-2  S2   0.020
 6KE  plan-2  H13  0.020
 6KE  plan-3  C13  0.020
 6KE  plan-3  C16  0.020
 6KE  plan-3  C17  0.020
 6KE  plan-3  C18  0.020
 6KE  plan-3  C19  0.020
 6KE  plan-3  C20  0.020
 6KE  plan-3  C15  0.020
 6KE  plan-3  H9   0.020
 6KE  plan-3  H10  0.020
 6KE  plan-3  H11  0.020
 6KE  plan-3  H12  0.020
 6KE  plan-3  CL   0.020
 6KE  plan-4  C4   0.020
 6KE  plan-4  C7   0.020
 6KE  plan-4  C8   0.020
 6KE  plan-4  O3   0.020
 6KE  plan-4  N2   0.020
 6KE  plan-4  H14  0.020

