# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 06:09:05 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2R)-2-{[5-cyano-4-(3,4-dichlorophenyl)-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)c(Cl)c2)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
 ZHK  ZHK  (2R)-2-{[5-cyano-4-(3,4-dichlorophenyl)-6-oxo-1,6-dihydropyrimidin-2-yl]sulfanyl}-N-(4-sulfamoylphenyl)propanamide  ligand  48  33  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZHK
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
 ZHK  C1   C   CH3   0  -0.634  -0.0846  -1.0516   2.1178
 ZHK  C2   C   CH1   0  -0.549  -0.3620  -1.4002   0.6593
 ZHK  C3   C   C     0   0.612  -1.8557  -1.5133   0.3999
 ZHK  O4   O   O     0  -0.440  -2.4081  -2.5925   0.3313
 ZHK  N5   N   NH1   0  -0.746  -2.4696  -0.3102   0.3000
 ZHK  C6   C   CR6   0   0.398  -3.8263  -0.0216   0.1690
 ZHK  C7   C   CR16  0  -0.336  -4.1805   1.3312   0.2043
 ZHK  C8   C   CR16  0  -0.219  -5.4982   1.7202   0.0868
 ZHK  C9   C   CR6   0  -0.224  -6.4833   0.7530  -0.0747
 ZHK  C10  C   CR16  0  -0.222  -6.1457  -0.5909  -0.1130
 ZHK  C11  C   CR16  0  -0.298  -4.8231  -0.9852   0.0083
 ZHK  S12  S   S     0   1.361  -8.1717   1.2480  -0.2543
 ZHK  O13  O   OS    0  -0.657  -9.0076   0.0914   0.0187
 ZHK  O14  O   OS    0  -0.658  -8.3582   2.4791   0.4951
 ZHK  N15  N   NC2   0  -0.878  -8.4169   1.6319  -1.8343
 ZHK  S16  S   S2    0   0.154   0.3060  -3.0372   0.2109
 ZHK  C17  C   CR6   0   0.383   1.9898  -2.6490   0.0247
 ZHK  N18  N   NR16  0  -0.689   2.7995  -3.7022  -0.1948
 ZHK  C20  C   CR6   0   0.588   4.1604  -3.5802  -0.4393
 ZHK  O21  O   O     0  -0.431   4.8507  -4.5501  -0.6702
 ZHK  C22  C   CR6   0  -0.242   4.6198  -2.2091  -0.3860
 ZHK  C23  C   CR6   0   0.354   3.7358  -1.1932  -0.0897
 ZHK  N24  N   N     0  -0.452   2.4214  -1.4255   0.0855
 ZHK  C25  C   CR6   0   0.037   4.1410   0.2166   0.0353
 ZHK  C26  C   CR16  0  -0.288   5.3163   0.5885   0.6822
 ZHK  C27  C   CR16  0  -0.200   5.6548   1.9245   0.7984
 ZHK  C28  C   CR6   0  -0.002   4.8290   2.9009   0.2629
 ZHK  C29  C   CR6   0   0.020   3.6467   2.5349  -0.3754
 ZHK  C30  C   CR16  0  -0.232   3.2982   1.2004  -0.4751
 ZHK  CL1  CL  CL    0  -0.085   2.6048   3.7307  -1.0407
 ZHK  CL2  CL  CL    0  -0.078   5.2710   4.5535   0.4043
 ZHK  C33  C   CSP   0   0.017   5.9827  -2.0031  -0.7076
 ZHK  N34  N   NS    0  -0.238   7.0913  -1.8663  -0.9939
 ZHK  H1   H   HCH3  0   0.253  -0.5308  -1.7826   2.7902
 ZHK  H2   H   HCH3  0   0.268   0.9868  -1.0133   2.2995
 ZHK  H3   H   HCH3  0   0.257  -0.4934  -0.0693   2.3549
 ZHK  H4   H   HCH1  0   0.341   0.0906  -0.6582  -0.0014
 ZHK  H5   H   HNH1  0   0.431  -1.8691   0.5001   0.3471
 ZHK  H6   H   HCR6  0   0.290  -3.4158   2.0873   0.3325
 ZHK  H7   H   HCR6  0   0.289  -5.7435   2.7729   0.1286
 ZHK  H8   H   HCR6  0   0.288  -6.9055  -1.3511  -0.2308
 ZHK  H9   H   HCR6  0   0.296  -4.5901  -2.0361  -0.0217
 ZHK  H10  H   HNC2  0   0.416  -7.8793   2.4310  -2.1512
 ZHK  H11  H   HNC2  0   0.416  -8.3109   0.8469  -2.4670
 ZHK  H19  H   HNR6  0   0.448   2.4217  -4.6443  -0.2051
 ZHK  H12  H   HCR6  0   0.286   5.9620  -0.1506   1.1358
 ZHK  H13  H   HCR6  0   0.300   6.5611   2.2110   1.3129
 ZHK  H14  H   HCR6  0   0.295   2.3746   0.9246  -0.9648

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
 ZHK  CL1  C29  single    1.720  0.020  1.720
 ZHK  CL2  C28  single    1.717  0.020  1.717
 ZHK  C29  C28  aromatic  1.393  0.020  1.393
 ZHK  C29  C30  aromatic  1.383  0.020  1.383
 ZHK  C28  C27  aromatic  1.386  0.020  1.386
 ZHK  O13  S12  double    1.453  0.020  1.453
 ZHK  C30  C25  aromatic  1.392  0.020  1.392
 ZHK  C27  C26  aromatic  1.383  0.020  1.383
 ZHK  S12  N15  single    1.644  0.020  1.644
 ZHK  S12  O14  double    1.453  0.020  1.453
 ZHK  S12  C9   single    1.769  0.020  1.769
 ZHK  C8   C9   aromatic  1.390  0.020  1.390
 ZHK  C8   C7   aromatic  1.379  0.020  1.379
 ZHK  N34  C33  triple    1.153  0.020  1.153
 ZHK  C26  C25  aromatic  1.392  0.020  1.392
 ZHK  C9   C10  aromatic  1.386  0.020  1.386
 ZHK  C25  C23  single    1.472  0.020  1.472
 ZHK  C7   C6   aromatic  1.399  0.020  1.399
 ZHK  C33  C22  single    1.415  0.020  1.415
 ZHK  C10  C11  aromatic  1.385  0.020  1.385
 ZHK  C23  C22  double    1.379  0.020  1.379
 ZHK  C23  N24  single    1.346  0.020  1.346
 ZHK  C6   C11  aromatic  1.396  0.020  1.396
 ZHK  C6   N5   single    1.393  0.020  1.393
 ZHK  C22  C20  single    1.447  0.020  1.447
 ZHK  N5   C3   single    1.354  0.020  1.354
 ZHK  N24  C17  double    1.299  0.020  1.299
 ZHK  C20  O21  double    1.213  0.020  1.213
 ZHK  C20  N18  single    1.388  0.020  1.388
 ZHK  C3   O4   double    1.214  0.020  1.214
 ZHK  C3   C2   single    1.520  0.020  1.520
 ZHK  C17  N18  single    1.346  0.020  1.346
 ZHK  C17  S16  single    1.738  0.020  1.738
 ZHK  C2   S16  single    1.824  0.020  1.824
 ZHK  C2   C1   single    1.525  0.020  1.525
 ZHK  C1   H1   single    0.970  0.020  1.090
 ZHK  C1   H2   single    0.970  0.020  1.090
 ZHK  C1   H3   single    0.970  0.020  1.090
 ZHK  C2   H4   single    0.970  0.020  1.090
 ZHK  N5   H5   single    0.860  0.020  1.020
 ZHK  C7   H6   single    0.930  0.020  1.080
 ZHK  C8   H7   single    0.930  0.020  1.080
 ZHK  C10  H8   single    0.930  0.020  1.080
 ZHK  C11  H9   single    0.930  0.020  1.080
 ZHK  N15  H10  single    0.890  0.020  1.040
 ZHK  N15  H11  single    0.890  0.020  1.040
 ZHK  N18  H19  single    0.860  0.020  1.020
 ZHK  C26  H12  single    0.930  0.020  1.080
 ZHK  C27  H13  single    0.930  0.020  1.080
 ZHK  C30  H14  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
 ZHK  H3   C1   H2   107.54  3.000
 ZHK  H3   C1   H1   108.48  3.000
 ZHK  H2   C1   H1   108.92  3.000
 ZHK  H3   C1   C2   110.23  3.000
 ZHK  H2   C1   C2   110.31  3.000
 ZHK  H1   C1   C2   111.26  3.000
 ZHK  H4   C2   S16  108.02  3.000
 ZHK  H4   C2   C3   110.77  3.000
 ZHK  S16  C2   C3   104.54  3.000
 ZHK  H4   C2   C1   110.37  3.000
 ZHK  S16  C2   C1   111.94  3.000
 ZHK  C3   C2   C1   111.03  3.000
 ZHK  N5   C3   O4   125.39  3.000
 ZHK  O4   C3   C2   121.51  3.000
 ZHK  N5   C3   C2   113.07  3.000
 ZHK  H5   N5   C6   114.66  3.000
 ZHK  H5   N5   C3   116.10  3.000
 ZHK  C6   N5   C3   129.22  3.000
 ZHK  C11  C6   C7   119.33  3.000
 ZHK  C11  C6   N5   124.28  3.000
 ZHK  C7   C6   N5   116.39  3.000
 ZHK  H6   C7   C8   119.20  3.000
 ZHK  H6   C7   C6   119.96  3.000
 ZHK  C8   C7   C6   120.84  3.000
 ZHK  H7   C8   C9   121.40  3.000
 ZHK  H7   C8   C7   119.21  3.000
 ZHK  C9   C8   C7   119.39  3.000
 ZHK  S12  C9   C10  120.07  3.000
 ZHK  C10  C9   C8   120.35  3.000
 ZHK  S12  C9   C8   119.58  3.000
 ZHK  H8   C10  C11  118.70  3.000
 ZHK  H8   C10  C9   120.90  3.000
 ZHK  C11  C10  C9   120.40  3.000
 ZHK  H9   C11  C10  118.81  3.000
 ZHK  H9   C11  C6   121.50  3.000
 ZHK  C10  C11  C6   119.69  3.000
 ZHK  N15  S12  O14  106.17  3.000
 ZHK  O14  S12  O13  120.24  3.000
 ZHK  N15  S12  O13  106.29  3.000
 ZHK  O14  S12  C9   107.90  3.000
 ZHK  N15  S12  C9   107.77  3.000
 ZHK  O13  S12  C9   107.90  3.000
 ZHK  H11  N15  H10  111.08  3.000
 ZHK  H11  N15  S12  113.79  3.000
 ZHK  H10  N15  S12  113.91  3.000
 ZHK  C17  S16  C2   100.41  3.000
 ZHK  N24  C17  N18  123.00  3.000
 ZHK  N18  C17  S16  115.17  3.000
 ZHK  N24  C17  S16  121.83  3.000
 ZHK  H19  N18  C20  116.41  3.000
 ZHK  H19  N18  C17  120.25  3.000
 ZHK  C20  N18  C17  123.33  3.000
 ZHK  C22  C20  O21  125.75  3.000
 ZHK  O21  C20  N18  121.42  3.000
 ZHK  C22  C20  N18  112.83  3.000
 ZHK  C33  C22  C23  123.98  3.000
 ZHK  C23  C22  C20  120.17  3.000
 ZHK  C33  C22  C20  115.80  3.000
 ZHK  C25  C23  N24  115.02  3.000
 ZHK  N24  C23  C22  121.78  3.000
 ZHK  C25  C23  C22  123.19  3.000
 ZHK  C23  N24  C17  118.75  3.000
 ZHK  C30  C25  C26  119.51  3.000
 ZHK  C26  C25  C23  121.84  3.000
 ZHK  C30  C25  C23  118.61  3.000
 ZHK  H12  C26  C27  118.62  3.000
 ZHK  H12  C26  C25  121.10  3.000
 ZHK  C27  C26  C25  120.24  3.000
 ZHK  H13  C27  C28  119.78  3.000
 ZHK  H13  C27  C26  120.08  3.000
 ZHK  C28  C27  C26  120.13  3.000
 ZHK  CL2  C28  C29  120.62  3.000
 ZHK  C29  C28  C27  119.85  3.000
 ZHK  CL2  C28  C27  119.53  3.000
 ZHK  CL1  C29  C30  119.37  3.000
 ZHK  C30  C29  C28  120.04  3.000
 ZHK  CL1  C29  C28  120.59  3.000
 ZHK  H14  C30  C29  119.61  3.000
 ZHK  H14  C30  C25  120.19  3.000
 ZHK  C29  C30  C25  120.19  3.000
 ZHK  N34  C33  C22  180.00  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
 ZHK  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 ZHK  CONST_02  C9   C10  C11  C6      0.00   0.0  0
 ZHK  CONST_03  C10  C9   C8   C7      0.00   0.0  0
 ZHK  CONST_04  C10  C11  C6   C7      0.00   0.0  0
 ZHK  CONST_05  C11  C10  C9   C8      0.00   0.0  0
 ZHK  CONST_06  C11  C6   C7   C8      0.00   0.0  0
 ZHK  CONST_07  C28  C29  C30  C25     0.00   0.0  0
 ZHK  CONST_08  C28  C27  C26  C25     0.00   0.0  0
 ZHK  CONST_09  C29  C28  C27  C26     0.00   0.0  0
 ZHK  CONST_10  C29  C30  C25  C26     0.00   0.0  0
 ZHK  CONST_11  C30  C29  C28  C27     0.00   0.0  0
 ZHK  CONST_12  C30  C25  C26  C27     0.00   0.0  0
 ZHK  CONST_13  C29  C30  C25  C23   180.00   0.0  0
 ZHK  CONST_14  C27  C26  C25  C23   180.00   0.0  0
 ZHK  CONST_15  C22  C20  N18  C17     0.00   0.0  0
 ZHK  CONST_16  C23  N24  C17  N18     0.00   0.0  0
 ZHK  CONST_17  N24  C17  N18  C20     0.00   0.0  0
 ZHK  CONST_18  C8   C7   C6   N5    180.00   0.0  0
 ZHK  CONST_19  C10  C11  C6   N5    180.00   0.0  0
 ZHK  CONST_20  S12  C9   C8   C7    180.00   0.0  0
 ZHK  CONST_21  S12  C9   C10  C11   180.00   0.0  0
 ZHK  CONST_22  CL1  C29  C30  C25   180.00   0.0  0
 ZHK  CONST_23  CL2  C28  C27  C26   180.00   0.0  0
 ZHK  CONST_24  CL1  C29  C28  C27   180.00   0.0  0
 ZHK  CONST_25  CL2  C28  C29  C30   180.00   0.0  0
 ZHK  CONST_26  C23  N24  C17  S16   180.00   0.0  0
 ZHK  CONST_27  C20  N18  C17  S16   180.00   0.0  0
 ZHK  CONST_28  O21  C20  N18  C17   180.00   0.0  0
 ZHK  CONST_29  H7   C8   C7   C6    180.00   0.0  0
 ZHK  CONST_30  H8   C10  C11  C6    180.00   0.0  0
 ZHK  CONST_31  H9   C11  C6   C7    180.00   0.0  0
 ZHK  CONST_32  H6   C7   C8   C9    180.00   0.0  0
 ZHK  CONST_33  H14  C30  C25  C23     0.00   0.0  0
 ZHK  CONST_34  H12  C26  C25  C23     0.00   0.0  0
 ZHK  CONST_35  H13  C27  C26  C25   180.00   0.0  0
 ZHK  CONST_36  H19  N18  C20  C22   180.00   0.0  0
 ZHK  CONST_37  C7   C6   N5   C3    180.00   0.0  0
 ZHK  CONST_38  C11  C6   N5   C3      0.00   0.0  0
 ZHK  CONST_39  H5   N5   C6   C7      0.00   0.0  0
 ZHK  CONST_40  C6   N5   C3   C2    180.00   0.0  0
 ZHK  CONST_41  C6   N5   C3   O4      0.00   0.0  0
 ZHK  Var_01    C30  C25  C23  C22   140.60  30.0  2
 ZHK  Var_02    N24  C17  S16  C2     -6.36  30.0  2
 ZHK  Var_03    O13  S12  C9   C8   -162.24  30.0  2
 ZHK  Var_04    H10  N15  S12  C9    -64.30  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
 ZHK  chir_01  C2  C3  S16  C1  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
 ZHK  plan-1  N5   0.020
 ZHK  plan-1  C6   0.020
 ZHK  plan-1  C7   0.020
 ZHK  plan-1  C8   0.020
 ZHK  plan-1  C9   0.020
 ZHK  plan-1  C10  0.020
 ZHK  plan-1  C11  0.020
 ZHK  plan-1  S12  0.020
 ZHK  plan-1  H6   0.020
 ZHK  plan-1  H7   0.020
 ZHK  plan-1  H8   0.020
 ZHK  plan-1  H9   0.020
 ZHK  plan-2  S16  0.020
 ZHK  plan-2  C17  0.020
 ZHK  plan-2  N18  0.020
 ZHK  plan-2  C20  0.020
 ZHK  plan-2  O21  0.020
 ZHK  plan-2  C22  0.020
 ZHK  plan-2  C23  0.020
 ZHK  plan-2  N24  0.020
 ZHK  plan-2  C25  0.020
 ZHK  plan-2  C33  0.020
 ZHK  plan-2  N34  0.020
 ZHK  plan-2  H19  0.020
 ZHK  plan-3  C23  0.020
 ZHK  plan-3  C25  0.020
 ZHK  plan-3  C26  0.020
 ZHK  plan-3  C27  0.020
 ZHK  plan-3  C28  0.020
 ZHK  plan-3  C29  0.020
 ZHK  plan-3  C30  0.020
 ZHK  plan-3  CL1  0.020
 ZHK  plan-3  CL2  0.020
 ZHK  plan-3  H12  0.020
 ZHK  plan-3  H13  0.020
 ZHK  plan-3  H14  0.020
 ZHK  plan-4  C2   0.020
 ZHK  plan-4  C3   0.020
 ZHK  plan-4  O4   0.020
 ZHK  plan-4  N5   0.020
 ZHK  plan-4  C6   0.020
 ZHK  plan-4  H5   0.020

