# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 12:37:02 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2S)-3-cyclohexyl-2-[4-(cyclopentylsulfonyl)-2-oxopyridin-1(2H)-yl]-N-(1,3-thiazol-2-yl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1sccn1)[C@H](CC2CCCCC2)N3C=CC(=CC3=O)[S](=O)(=O)C4CCCC4
#
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
 8WJ  8WJ  (2S)-3-cyclohexyl-2-[4-(cyclopentylsulfonyl)-2-oxopyridin-1(2H)-yl]-N-(1,3-thiazol-2-yl)propanamide  ligand  60  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8WJ
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
 8WJ  N3   N  NH1   0  -0.709   3.2485  -1.2059  -0.4108
 8WJ  C4   C  CR5   0   0.293   3.9676  -2.3690  -0.2279
 8WJ  C6   C  CR15  0  -0.007   4.6022  -4.3287   0.4943
 8WJ  C7   C  CR15  0  -0.507   5.6307  -4.1171  -0.3594
 8WJ  C13  C  C     0  -0.432   2.1505   3.4561  -0.8136
 8WJ  C15  C  C     0  -0.431   2.5035   5.7827   0.0950
 8WJ  C17  C  C     0  -0.415   2.4574   3.8112   1.6553
 8WJ  C20  C  CR16  0  -0.409  -1.9280   0.5455   1.0282
 8WJ  C21  C  CR6   0  -0.018  -2.6204   0.4274  -0.1961
 8WJ  C22  C  CR16  0  -0.450  -1.9751   0.3654  -1.3832
 8WJ  C28  C  CH1   0  -0.421  -4.7099  -1.2941   0.5271
 8WJ  C2   C  C     0   0.586   2.0140  -0.9248   0.1008
 8WJ  N5   N  N     0  -0.392   3.6635  -3.3363   0.5678
 8WJ  S8   S  S2    0   0.216   5.4318  -2.5949  -1.1347
 8WJ  C9   C  CH1   0  -0.316   1.5595   0.5044  -0.2004
 8WJ  C11  C  CH2   0  -0.454   2.1948   1.4863   0.7896
 8WJ  C12  C  CR16  0  -0.229   1.7911   2.9460   0.5827
 8WJ  C14  C  C     0  -0.428   1.8285   4.9386  -0.9795
 8WJ  C16  C  C     0  -0.434   2.1264   5.2903   1.4871
 8WJ  N18  N  NR6   0  -0.520   0.1025   0.5331  -0.2055
 8WJ  C19  C  CR16  0   0.094  -0.5752   0.5795   0.9684
 8WJ  C23  C  CR6   0   0.607  -0.5336   0.3916  -1.4393
 8WJ  O24  O  O     0  -0.490   0.1110   0.2871  -2.4737
 8WJ  O27  O  OS    0  -0.663  -4.8751   1.3399   0.7915
 8WJ  O26  O  OS    0  -0.655  -4.8990   0.3807  -1.5322
 8WJ  C29  C  CH2   0  -0.458  -6.2336  -1.5677   0.5399
 8WJ  C30  C  CH2   0  -0.435  -6.4360  -2.6701  -0.4970
 8WJ  C31  C  CH2   0  -0.447  -5.1523  -3.4861  -0.3975
 8WJ  C32  C  CH2   0  -0.452  -4.0649  -2.4141  -0.3091
 8WJ  H1   H  HNH1  0   0.436   3.6687  -0.5075  -1.0066
 8WJ  H2   H  HCR5  0   0.277   4.4870  -5.2122   1.1052
 8WJ  H3   H  HCR5  0   0.312   6.4755  -4.7514  -0.5735
 8WJ  H4   H  H     0   0.214   3.2212   3.2930  -0.9866
 8WJ  H5   H  H     0   0.232   1.6239   2.8903  -1.5870
 8WJ  H6   H  H     0   0.209   3.5908   5.7243  -0.0275
 8WJ  H7   H  H     0   0.228   2.2337   6.8349  -0.0238
 8WJ  H8   H  H     0   0.230   2.1509   3.4678   2.6474
 8WJ  H9   H  H     0   0.211   3.5440   3.6745   1.6004
 8WJ  H10  H  HCR6  0   0.303  -2.4268   0.6078   1.9832
 8WJ  H11  H  HCR6  0   0.303  -2.5020   0.2681  -2.3223
 8WJ  H12  H  HCH1  0   0.326  -4.3070  -1.2547   1.5406
 8WJ  H13  H  HCH1  0   0.322   1.8751   0.7754  -1.2068
 8WJ  H14  H  HCH2  0   0.262   1.9936   1.1825   1.8210
 8WJ  H15  H  HCH2  0   0.269   3.2789   1.4008   0.6708
 8WJ  H16  H  HCR6  0   0.226   0.7051   3.0421   0.7132
 8WJ  H17  H  H     0   0.229   2.1332   5.2727  -1.9740
 8WJ  H18  H  H     0   0.211   0.7437   5.0799  -0.9239
 8WJ  H19  H  H     0   0.228   2.6415   5.8752   2.2529
 8WJ  H20  H  H     0   0.211   1.0539   5.4429   1.6489
 8WJ  H21  H  HCR6  0   0.324   0.0148   0.6657   1.8671
 8WJ  H22  H  HCH2  0   0.264  -6.4972  -1.9270   1.5346
 8WJ  H23  H  HCH2  0   0.264  -6.8479  -0.6857   0.3551
 8WJ  H24  H  HCH2  0   0.246  -7.3378  -3.2533  -0.3097
 8WJ  H25  H  HCH2  0   0.231  -6.5239  -2.2366  -1.4961
 8WJ  H26  H  HCH2  0   0.233  -5.1619  -4.0929   0.5113
 8WJ  H27  H  HCH2  0   0.247  -4.9996  -4.1594  -1.2410
 8WJ  H28  H  HCH2  0   0.254  -3.8256  -2.0670  -1.3163
 8WJ  H29  H  HCH2  0   0.266  -3.1380  -2.7659   0.1403
 8WJ  S25  S  S     0   1.215  -4.4041   0.3334  -0.1580
 8WJ  O1   O  O     0  -0.404   1.3459  -1.6909   0.7510

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
 8WJ  C16  C15  single    1.524  0.020  1.524
 8WJ  C16  C17  single    1.525  0.020  1.525
 8WJ  C15  C14  single    1.524  0.020  1.524
 8WJ  C17  C12  single    1.531  0.020  1.531
 8WJ  C14  C13  single    1.526  0.020  1.526
 8WJ  O26  S25  double    1.461  0.020  1.461
 8WJ  C12  C13  single    1.529  0.020  1.529
 8WJ  C12  C11  single    1.529  0.020  1.529
 8WJ  C31  C32  single    1.529  0.020  1.529
 8WJ  C31  C30  single    1.524  0.020  1.524
 8WJ  C32  C28  single    1.539  0.020  1.539
 8WJ  S25  C21  single    1.787  0.020  1.787
 8WJ  S25  O27  double    1.462  0.020  1.462
 8WJ  S25  C28  single    1.792  0.020  1.792
 8WJ  C20  C21  single    1.411  0.020  1.411
 8WJ  C20  C19  double    1.355  0.020  1.355
 8WJ  C30  C29  single    1.527  0.020  1.527
 8WJ  C21  C22  double    1.353  0.020  1.353
 8WJ  C19  N18  single    1.356  0.020  1.356
 8WJ  C11  C9   single    1.532  0.020  1.532
 8WJ  C28  C29  single    1.548  0.020  1.548
 8WJ  C22  C23  single    1.443  0.020  1.443
 8WJ  N18  C23  single    1.395  0.020  1.395
 8WJ  N18  C9   single    1.457  0.020  1.457
 8WJ  C23  O24  double    1.223  0.020  1.223
 8WJ  C9   C2   single    1.530  0.020  1.530
 8WJ  C2   O1   double    1.207  0.020  1.207
 8WJ  C2   N3   single    1.365  0.020  1.365
 8WJ  N3   C4   single    1.380  0.020  1.380
 8WJ  C4   S8   aromatic  1.737  0.020  1.737
 8WJ  C4   N5   aromatic  1.289  0.020  1.289
 8WJ  S8   C7   aromatic  1.720  0.020  1.720
 8WJ  N5   C6   aromatic  1.368  0.020  1.368
 8WJ  C6   C7   aromatic  1.353  0.020  1.353
 8WJ  N3   H1   single    0.860  0.020  1.020
 8WJ  C6   H2   single    0.930  0.020  1.080
 8WJ  C7   H3   single    0.930  0.020  1.080
 8WJ  C13  H4   single    0.970  0.020  1.090
 8WJ  C13  H5   single    0.970  0.020  1.090
 8WJ  C15  H6   single    0.970  0.020  1.090
 8WJ  C15  H7   single    0.970  0.020  1.090
 8WJ  C17  H8   single    0.970  0.020  1.090
 8WJ  C17  H9   single    0.970  0.020  1.090
 8WJ  C20  H10  single    0.930  0.020  1.080
 8WJ  C22  H11  single    0.930  0.020  1.080
 8WJ  C28  H12  single    0.970  0.020  1.090
 8WJ  C9   H13  single    0.970  0.020  1.090
 8WJ  C11  H14  single    0.970  0.020  1.090
 8WJ  C11  H15  single    0.970  0.020  1.090
 8WJ  C12  H16  single    0.970  0.020  1.090
 8WJ  C14  H17  single    0.970  0.020  1.090
 8WJ  C14  H18  single    0.970  0.020  1.090
 8WJ  C16  H19  single    0.970  0.020  1.090
 8WJ  C16  H20  single    0.970  0.020  1.090
 8WJ  C19  H21  single    0.930  0.020  1.080
 8WJ  C29  H22  single    0.970  0.020  1.090
 8WJ  C29  H23  single    0.970  0.020  1.090
 8WJ  C30  H24  single    0.970  0.020  1.090
 8WJ  C30  H25  single    0.970  0.020  1.090
 8WJ  C31  H26  single    0.970  0.020  1.090
 8WJ  C31  H27  single    0.970  0.020  1.090
 8WJ  C32  H28  single    0.970  0.020  1.090
 8WJ  C32  H29  single    0.970  0.020  1.090

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
 8WJ  H1   N3   C2   117.06  3.000
 8WJ  H1   N3   C4   116.39  3.000
 8WJ  C2   N3   C4   126.52  3.000
 8WJ  S8   C4   N5   115.06  3.000
 8WJ  N5   C4   N3   126.26  3.000
 8WJ  S8   C4   N3   118.67  3.000
 8WJ  H2   C6   N5   119.32  3.000
 8WJ  H2   C6   C7   124.45  3.000
 8WJ  N5   C6   C7   116.22  3.000
 8WJ  H3   C7   S8   121.46  3.000
 8WJ  H3   C7   C6   128.97  3.000
 8WJ  S8   C7   C6   109.57  3.000
 8WJ  H5   C13  H4   106.36  3.000
 8WJ  H5   C13  C14  108.91  3.000
 8WJ  H4   C13  C14  109.47  3.000
 8WJ  H5   C13  C12  111.10  3.000
 8WJ  H4   C13  C12  108.89  3.000
 8WJ  C14  C13  C12  111.94  3.000
 8WJ  H7   C15  H6   106.51  3.000
 8WJ  H7   C15  C16  110.45  3.000
 8WJ  H6   C15  C16  109.30  3.000
 8WJ  H7   C15  C14  110.32  3.000
 8WJ  H6   C15  C14  109.34  3.000
 8WJ  C16  C15  C14  110.82  3.000
 8WJ  H9   C17  H8   106.50  3.000
 8WJ  H9   C17  C16  109.29  3.000
 8WJ  H8   C17  C16  110.11  3.000
 8WJ  H9   C17  C12  109.02  3.000
 8WJ  H8   C17  C12  109.65  3.000
 8WJ  C16  C17  C12  112.11  3.000
 8WJ  H10  C20  C19  119.95  3.000
 8WJ  H10  C20  C21  123.07  3.000
 8WJ  C19  C20  C21  116.98  3.000
 8WJ  S25  C21  C22  119.51  3.000
 8WJ  C22  C21  C20  122.08  3.000
 8WJ  S25  C21  C20  118.40  3.000
 8WJ  H11  C22  C23  117.05  3.000
 8WJ  H11  C22  C21  122.27  3.000
 8WJ  C23  C22  C21  120.66  3.000
 8WJ  H12  C28  C32  112.09  3.000
 8WJ  H12  C28  C29  111.22  3.000
 8WJ  C32  C28  C29  106.75  3.000
 8WJ  H12  C28  S25  105.02  3.000
 8WJ  C29  C28  S25  109.37  3.000
 8WJ  C32  C28  S25  112.44  3.000
 8WJ  C9   C2   O1   122.33  3.000
 8WJ  O1   C2   N3   124.87  3.000
 8WJ  C9   C2   N3   112.78  3.000
 8WJ  C6   N5   C4   110.45  3.000
 8WJ  C7   S8   C4    88.70  3.000
 8WJ  H13  C9   N18  106.36  3.000
 8WJ  H13  C9   C11  108.51  3.000
 8WJ  N18  C9   C11  113.83  3.000
 8WJ  H13  C9   C2   109.17  3.000
 8WJ  N18  C9   C2   108.43  3.000
 8WJ  C11  C9   C2   110.39  3.000
 8WJ  H15  C11  H14  105.25  3.000
 8WJ  H15  C11  C12  108.76  3.000
 8WJ  H14  C11  C12  110.14  3.000
 8WJ  H15  C11  C9   106.89  3.000
 8WJ  H14  C11  C9   110.79  3.000
 8WJ  C12  C11  C9   114.52  3.000
 8WJ  H16  C12  C11  109.19  3.000
 8WJ  H16  C12  C17  107.33  3.000
 8WJ  C11  C12  C17  109.27  3.000
 8WJ  H16  C12  C13  108.16  3.000
 8WJ  C11  C12  C13  112.33  3.000
 8WJ  C17  C12  C13  110.43  3.000
 8WJ  H18  C14  H17  106.44  3.000
 8WJ  H18  C14  C15  109.36  3.000
 8WJ  H17  C14  C15  110.41  3.000
 8WJ  H18  C14  C13  109.19  3.000
 8WJ  H17  C14  C13  109.71  3.000
 8WJ  C15  C14  C13  111.59  3.000
 8WJ  H20  C16  H19  106.46  3.000
 8WJ  H20  C16  C17  109.35  3.000
 8WJ  H19  C16  C17  109.85  3.000
 8WJ  H20  C16  C15  109.41  3.000
 8WJ  H19  C16  C15  110.53  3.000
 8WJ  C17  C16  C15  111.13  3.000
 8WJ  C23  N18  C19  122.75  3.000
 8WJ  C23  N18  C9   117.18  3.000
 8WJ  C19  N18  C9   119.82  3.000
 8WJ  H21  C19  N18  116.78  3.000
 8WJ  H21  C19  C20  120.77  3.000
 8WJ  N18  C19  C20  122.44  3.000
 8WJ  O24  C23  N18  121.07  3.000
 8WJ  O24  C23  C22  123.90  3.000
 8WJ  N18  C23  C22  115.02  3.000
 8WJ  H23  C29  H22  106.56  3.000
 8WJ  H23  C29  C30  113.21  3.000
 8WJ  H22  C29  C30  110.47  3.000
 8WJ  H23  C29  C28  114.21  3.000
 8WJ  H22  C29  C28  107.69  3.000
 8WJ  C30  C29  C28  104.62  3.000
 8WJ  H25  C30  H24  107.63  3.000
 8WJ  H25  C30  C31  109.87  3.000
 8WJ  H24  C30  C31  113.52  3.000
 8WJ  H25  C30  C29  110.20  3.000
 8WJ  H24  C30  C29  112.29  3.000
 8WJ  C31  C30  C29  103.32  3.000
 8WJ  H27  C31  H26  107.56  3.000
 8WJ  H27  C31  C32  112.22  3.000
 8WJ  H26  C31  C32  110.33  3.000
 8WJ  H27  C31  C30  113.46  3.000
 8WJ  H26  C31  C30  110.13  3.000
 8WJ  C32  C31  C30  103.14  3.000
 8WJ  H29  C32  H28  107.27  3.000
 8WJ  H29  C32  C31  113.75  3.000
 8WJ  H28  C32  C31  108.99  3.000
 8WJ  H29  C32  C28  111.57  3.000
 8WJ  H28  C32  C28  111.20  3.000
 8WJ  C31  C32  C28  104.09  3.000
 8WJ  O26  S25  O27  118.65  3.000
 8WJ  O27  S25  C28  108.79  3.000
 8WJ  O26  S25  C28  109.33  3.000
 8WJ  C28  S25  C21  103.08  3.000
 8WJ  O27  S25  C21  107.42  3.000
 8WJ  O26  S25  C21  108.44  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
 8WJ  CONST_01  C6   C7   S8   C4     0.00   0.0  0
 8WJ  CONST_02  C7   C6   N5   C4     0.00   0.0  0
 8WJ  CONST_03  S8   C4   N5   C6     0.00   0.0  0
 8WJ  CONST_04  N5   C4   S8   C7     0.00   0.0  0
 8WJ  CONST_05  S8   C7   C6   N5     0.00   0.0  0
 8WJ  CONST_06  C19  N18  C23  C22    0.00   0.0  0
 8WJ  CONST_07  C7   S8   C4   N3   180.00   0.0  0
 8WJ  CONST_08  C6   N5   C4   N3   180.00   0.0  0
 8WJ  CONST_09  C9   N18  C23  C22  180.00   0.0  0
 8WJ  CONST_10  O24  C23  N18  C19  180.00   0.0  0
 8WJ  CONST_11  H3   C7   S8   C4   180.00   0.0  0
 8WJ  CONST_12  H2   C6   N5   C4   180.00   0.0  0
 8WJ  CONST_13  S8   C4   N3   C2   180.00   0.0  0
 8WJ  CONST_14  N5   C4   N3   C2     0.00   0.0  0
 8WJ  CONST_15  O24  C23  N18  C9     0.00   0.0  0
 8WJ  CONST_16  H1   N3   C4   N5   180.00   0.0  0
 8WJ  CONST_17  C9   C2   N3   C4   180.00   0.0  0
 8WJ  CONST_18  O1   C2   N3   C4     0.00   0.0  0
 8WJ  Var_01    C16  C15  C14  C13  -55.55  30.0  1
 8WJ  Var_02    C12  C17  C16  C15  -55.82  30.0  1
 8WJ  Var_03    C12  C13  C14  C15   55.19  30.0  1
 8WJ  Var_04    C14  C15  C16  C17   55.69  30.0  1
 8WJ  Var_05    C30  C31  C32  C28   36.20  30.0  1
 8WJ  Var_06    C31  C30  C29  C28   32.75  30.0  1
 8WJ  Var_07    C32  C31  C30  C29  -43.10  30.0  1
 8WJ  Var_08    C28  S25  C21  C20  -70.96  30.0  2

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
 8WJ  chir_01  C28  C32  S25  C29  negativ
 8WJ  chir_02  C9   N18  C11  C2   negativ
 8WJ  chir_03  C12  C11  C13  C17  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
 8WJ  plan-1  N3   0.020
 8WJ  plan-1  C4   0.020
 8WJ  plan-1  C6   0.020
 8WJ  plan-1  C7   0.020
 8WJ  plan-1  N5   0.020
 8WJ  plan-1  S8   0.020
 8WJ  plan-1  H2   0.020
 8WJ  plan-1  H3   0.020
 8WJ  plan-2  C20  0.020
 8WJ  plan-2  C21  0.020
 8WJ  plan-2  C22  0.020
 8WJ  plan-2  C9   0.020
 8WJ  plan-2  N18  0.020
 8WJ  plan-2  C19  0.020
 8WJ  plan-2  C23  0.020
 8WJ  plan-2  O24  0.020
 8WJ  plan-2  H10  0.020
 8WJ  plan-2  H11  0.020
 8WJ  plan-2  H21  0.020
 8WJ  plan-2  S25  0.020
 8WJ  plan-3  N3   0.020
 8WJ  plan-3  C4   0.020
 8WJ  plan-3  C2   0.020
 8WJ  plan-3  C9   0.020
 8WJ  plan-3  H1   0.020
 8WJ  plan-3  O1   0.020

