# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 12:46:03 2020
#   Inital geometry file: a 158 line input string
#   Ligand name: 2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=C(N=C(NC1=O)[C@@H]2CCCN2C(=O)CSc3ccccc3Cl)C(=O)NC4Cc5ccccc5C4
#
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
 KU9  KU9  2-[(2S)-1-{[(2-chlorophenyl)sulfanyl]acetyl}pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide  ligand  61  36  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KU9
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
 KU9  C1   C   CR6   0   0.482  -5.3146   0.9864  -1.0592
 KU9  C10  C   CR16  0  -0.252   5.0499   1.9971   1.6491
 KU9  C11  C   CR16  0  -0.303   3.8618   1.4556   2.1269
 KU9  C12  C   CR56  0   0.106   2.6936   1.6706   1.4164
 KU9  C13  C   CH2   0  -0.512   1.3025   1.1984   1.7215
 KU9  C14  C   CR6   0   0.515  -3.8743  -0.7486  -0.2430
 KU9  C15  C   CH1   0  -0.151  -3.7551  -2.2234   0.0467
 KU9  C17  C   CH2   0  -0.752   0.0021  -2.4802  -0.1712
 KU9  C18  C   CR6   0  -0.038   2.5694  -1.4905  -0.5239
 KU9  C19  C   CR16  0  -0.280   2.8892  -2.2145   0.6227
 KU9  C2   C   CR6   0   0.227  -4.2458   1.9098  -0.6889
 KU9  C20  C   CR16  0  -0.225   4.1636  -2.1497   1.1689
 KU9  C21  C   CR16  0  -0.265   5.1427  -1.3661   0.5817
 KU9  C22  C   CR16  0  -0.170   4.8460  -0.6445  -0.5639
 KU9  C23  C   CR6   0  -0.052   3.5764  -0.7151  -1.1038
 KU9  C24  C   CH2   0  -0.289  -2.1597  -3.1017   1.6362
 KU9  C25  C   CH2   0  -0.468  -3.5429  -3.6084   2.0129
 KU9  C26  C   CH2   0  -0.478  -4.4691  -2.5843   1.3669
 KU9  C3   C   CR6   0  -0.003  -3.1021   1.4085  -0.1457
 KU9  C4   C   C     0   0.550  -1.9239   2.2626   0.2092
 KU9  C5   C   CR15  0  -0.060   0.4365   2.1401   0.8708
 KU9  C6   C   CH2   0  -0.488   1.3219   2.4946  -0.3404
 KU9  C7   C   CR56  0   0.098   2.7049   2.4154   0.2387
 KU9  C8   C   CR16  0  -0.323   3.8891   2.9476  -0.2430
 KU9  C9   C   CR16  0  -0.259   5.0641   2.7357   0.4718
 KU9  N1   N   NH1   0  -0.666  -0.8368   1.5539   0.5440
 KU9  N2   N   N     0  -0.466  -2.9475   0.0697   0.0847
 KU9  N3   N   NT    0  -0.476  -2.3751  -2.5890   0.2889
 KU9  N4   N   NR16  0  -0.689  -5.0348  -0.3279  -0.8085
 KU9  O1   O   O     0  -0.470  -6.3603   1.3686  -1.5620
 KU9  O2   O   OH1   0  -0.590  -4.4777   3.1935  -0.9398
 KU9  O3   O   O     0  -0.479  -1.9645   3.4839   0.1827
 KU9  O4   O   O     0  -0.476  -1.7020  -1.9962  -1.7738
 KU9  S1   S   S2    0   0.102   0.9898  -1.4735  -1.3031
 KU9  CL1  CL  CL    0  -0.114   3.2322   0.1693  -2.5542
 KU9  H1   H   HCR6  0   0.244   5.9709   1.8410   2.1965
 KU9  H2   H   HCR6  0   0.236   3.8559   0.8750   3.0414
 KU9  H3   H   HCH2  0   0.239   1.1834   0.1595   1.3878
 KU9  H4   H   HCH2  0   0.263   1.0440   1.2287   2.7806
 KU9  H5   H   HCH1  0   0.304  -4.1697  -2.7922  -0.7914
 KU9  H6   H   HCH2  0   0.295   0.1196  -2.1255   0.8541
 KU9  H7   H   HCH2  0   0.334   0.3136  -3.5282  -0.1977
 KU9  H8   H   HCR6  0   0.272   2.1546  -2.8433   1.1051
 KU9  H9   H   HCR6  0   0.262   4.3831  -2.7203   2.0614
 KU9  H10  H   HCR6  0   0.261   6.1338  -1.3079   1.0101
 KU9  H11  H   HCR6  0   0.273   5.5949  -0.0229  -1.0338
 KU9  H12  H   HCH2  0   0.250  -1.8316  -2.3064   2.3129
 KU9  H13  H   HCH2  0   0.271  -1.4104  -3.8923   1.6425
 KU9  H14  H   HCH2  0   0.253  -3.7066  -4.6002   1.5883
 KU9  H15  H   HCH2  0   0.264  -3.6798  -3.6744   3.0908
 KU9  H16  H   HCH2  0   0.261  -4.5440  -1.7017   2.0051
 KU9  H17  H   HCH2  0   0.276  -5.4764  -2.9570   1.1909
 KU9  H18  H   HCR5  0   0.265   0.2537   3.0546   1.4398
 KU9  H19  H   HCH2  0   0.243   1.1959   1.7453  -1.1286
 KU9  H20  H   HCH2  0   0.254   1.0746   3.4673  -0.7673
 KU9  H21  H   HCR6  0   0.239   3.9035   3.5286  -1.1573
 KU9  H22  H   HCR6  0   0.245   5.9961   3.1515   0.1099
 KU9  H23  H   HNH1  0   0.393  -0.9099   0.5505   0.4706
 KU9  H24  H   HNR6  0   0.438  -5.7417  -1.0071  -1.0663
 KU9  H25  H   HOH1  0   0.475  -5.3506   3.2656  -1.3576
 KU9  C16  C   C     0   0.602  -1.4346  -2.3424  -0.6340

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
 KU9  C9   C10  aromatic  1.390  0.020  1.390
 KU9  C9   C8   aromatic  1.392  0.020  1.392
 KU9  C10  C11  aromatic  1.390  0.020  1.390
 KU9  C8   C7   aromatic  1.385  0.020  1.385
 KU9  C11  C12  aromatic  1.384  0.020  1.384
 KU9  C7   C12  aromatic  1.393  0.020  1.393
 KU9  C7   C6   single    1.501  0.020  1.501
 KU9  C12  C13  single    1.500  0.020  1.500
 KU9  S1   C17  single    1.808  0.020  1.808
 KU9  S1   C18  single    1.761  0.020  1.761
 KU9  C6   C5   single    1.542  0.020  1.542
 KU9  C13  C5   single    1.536  0.020  1.536
 KU9  O4   C16  double    1.221  0.020  1.221
 KU9  CL1  C23  single    1.733  0.020  1.733
 KU9  C17  C16  single    1.516  0.020  1.516
 KU9  C5   N1   single    1.439  0.020  1.439
 KU9  C18  C23  aromatic  1.397  0.020  1.397
 KU9  C18  C19  aromatic  1.393  0.020  1.393
 KU9  C16  N3   single    1.341  0.020  1.341
 KU9  C23  C22  aromatic  1.381  0.020  1.381
 KU9  C19  C20  aromatic  1.388  0.020  1.388
 KU9  N1   C4   single    1.340  0.020  1.340
 KU9  C22  C21  aromatic  1.386  0.020  1.386
 KU9  C20  C21  aromatic  1.385  0.020  1.385
 KU9  N3   C24  single    1.458  0.020  1.458
 KU9  N3   C15  single    1.448  0.020  1.448
 KU9  C4   O3   double    1.222  0.020  1.222
 KU9  C4   C3   single    1.498  0.020  1.498
 KU9  N2   C3   single    1.367  0.020  1.367
 KU9  N2   C14  double    1.279  0.020  1.279
 KU9  C24  C25  single    1.521  0.020  1.521
 KU9  C3   C2   double    1.362  0.020  1.362
 KU9  C15  C14  single    1.508  0.020  1.508
 KU9  C15  C26  single    1.544  0.020  1.544
 KU9  C14  N4   single    1.358  0.020  1.358
 KU9  C2   O2   single    1.328  0.020  1.328
 KU9  C2   C1   single    1.460  0.020  1.460
 KU9  C26  C25  single    1.524  0.020  1.524
 KU9  N4   C1   single    1.367  0.020  1.367
 KU9  C1   O1   double    1.222  0.020  1.222
 KU9  C10  H1   single    0.930  0.020  1.080
 KU9  C11  H2   single    0.930  0.020  1.080
 KU9  C13  H3   single    0.970  0.020  1.090
 KU9  C13  H4   single    0.970  0.020  1.090
 KU9  C15  H5   single    0.970  0.020  1.090
 KU9  C17  H6   single    0.970  0.020  1.090
 KU9  C17  H7   single    0.970  0.020  1.090
 KU9  C19  H8   single    0.930  0.020  1.080
 KU9  C20  H9   single    0.930  0.020  1.080
 KU9  C21  H10  single    0.930  0.020  1.080
 KU9  C22  H11  single    0.930  0.020  1.080
 KU9  C24  H12  single    0.970  0.020  1.090
 KU9  C24  H13  single    0.970  0.020  1.090
 KU9  C25  H14  single    0.970  0.020  1.090
 KU9  C25  H15  single    0.970  0.020  1.090
 KU9  C26  H16  single    0.970  0.020  1.090
 KU9  C26  H17  single    0.970  0.020  1.090
 KU9  C5   H18  single    0.970  0.020  1.090
 KU9  C6   H19  single    0.970  0.020  1.090
 KU9  C6   H20  single    0.970  0.020  1.090
 KU9  C8   H21  single    0.930  0.020  1.080
 KU9  C9   H22  single    0.930  0.020  1.080
 KU9  N1   H23  single    0.860  0.020  1.020
 KU9  N4   H24  single    0.860  0.020  1.020
 KU9  O2   H25  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
 KU9  O1   C1   N4   123.47  3.000
 KU9  O1   C1   C2   122.22  3.000
 KU9  N4   C1   C2   114.31  3.000
 KU9  H1   C10  C9   119.74  3.000
 KU9  H1   C10  C11  119.81  3.000
 KU9  C9   C10  C11  120.45  3.000
 KU9  H2   C11  C12  120.80  3.000
 KU9  H2   C11  C10  120.23  3.000
 KU9  C12  C11  C10  118.97  3.000
 KU9  C7   C12  C13  110.34  3.000
 KU9  C13  C12  C11  128.99  3.000
 KU9  C7   C12  C11  120.66  3.000
 KU9  H4   C13  H3   107.20  3.000
 KU9  H4   C13  C5   112.78  3.000
 KU9  H3   C13  C5   110.53  3.000
 KU9  H4   C13  C12  114.11  3.000
 KU9  H3   C13  C12  109.67  3.000
 KU9  C5   C13  C12  102.54  3.000
 KU9  N4   C14  N2   121.86  3.000
 KU9  N4   C14  C15  116.79  3.000
 KU9  N2   C14  C15  121.28  3.000
 KU9  H5   C15  N3   110.97  3.000
 KU9  H5   C15  C26  110.99  3.000
 KU9  N3   C15  C26  103.81  3.000
 KU9  H5   C15  C14  109.35  3.000
 KU9  C26  C15  C14  110.88  3.000
 KU9  N3   C15  C14  110.76  3.000
 KU9  H7   C17  H6   107.67  3.000
 KU9  H7   C17  S1   111.27  3.000
 KU9  H6   C17  S1   110.39  3.000
 KU9  H7   C17  C16  110.47  3.000
 KU9  H6   C17  C16  111.06  3.000
 KU9  S1   C17  C16  106.02  3.000
 KU9  S1   C18  C23  117.22  3.000
 KU9  C23  C18  C19  117.68  3.000
 KU9  S1   C18  C19  125.10  3.000
 KU9  H8   C19  C20  118.40  3.000
 KU9  H8   C19  C18  120.91  3.000
 KU9  C20  C19  C18  120.69  3.000
 KU9  O2   C2   C3   125.29  3.000
 KU9  O2   C2   C1   115.81  3.000
 KU9  C3   C2   C1   118.89  3.000
 KU9  H9   C20  C21  120.32  3.000
 KU9  H9   C20  C19  119.10  3.000
 KU9  C21  C20  C19  120.58  3.000
 KU9  H10  C21  C22  119.71  3.000
 KU9  H10  C21  C20  120.70  3.000
 KU9  C22  C21  C20  119.59  3.000
 KU9  H11  C22  C23  119.76  3.000
 KU9  H11  C22  C21  120.70  3.000
 KU9  C23  C22  C21  119.55  3.000
 KU9  CL1  C23  C22  118.91  3.000
 KU9  C22  C23  C18  121.91  3.000
 KU9  CL1  C23  C18  119.17  3.000
 KU9  H13  C24  H12  108.52  3.000
 KU9  H13  C24  N3   111.24  3.000
 KU9  H12  C24  N3   111.11  3.000
 KU9  H13  C24  C25  112.49  3.000
 KU9  H12  C24  C25  111.20  3.000
 KU9  N3   C24  C25  102.22  3.000
 KU9  H15  C25  H14  108.14  3.000
 KU9  H15  C25  C26  112.58  3.000
 KU9  H14  C25  C26  110.77  3.000
 KU9  H15  C25  C24  112.33  3.000
 KU9  H14  C25  C24  110.05  3.000
 KU9  C26  C25  C24  102.94  3.000
 KU9  H17  C26  H16  107.93  3.000
 KU9  H17  C26  C25  113.62  3.000
 KU9  H16  C26  C25  109.70  3.000
 KU9  H17  C26  C15  111.70  3.000
 KU9  H16  C26  C15  110.04  3.000
 KU9  C25  C26  C15  103.80  3.000
 KU9  N2   C3   C4   115.44  3.000
 KU9  N2   C3   C2   121.51  3.000
 KU9  C4   C3   C2   123.04  3.000
 KU9  O3   C4   N1   124.11  3.000
 KU9  O3   C4   C3   122.58  3.000
 KU9  N1   C4   C3   113.31  3.000
 KU9  H18  C5   N1   108.13  3.000
 KU9  H18  C5   C6   108.23  3.000
 KU9  N1   C5   C6   115.04  3.000
 KU9  H18  C5   C13  108.60  3.000
 KU9  N1   C5   C13  112.00  3.000
 KU9  C6   C5   C13  104.61  3.000
 KU9  H20  C6   H19  107.61  3.000
 KU9  H20  C6   C7   114.00  3.000
 KU9  H19  C6   C7   110.34  3.000
 KU9  H20  C6   C5   112.48  3.000
 KU9  H19  C6   C5   110.01  3.000
 KU9  C7   C6   C5   102.35  3.000
 KU9  C8   C7   C6   129.29  3.000
 KU9  C6   C7   C12  110.28  3.000
 KU9  C8   C7   C12  120.42  3.000
 KU9  H21  C8   C9   120.27  3.000
 KU9  H21  C8   C7   120.73  3.000
 KU9  C9   C8   C7   119.00  3.000
 KU9  H22  C9   C8   119.77  3.000
 KU9  H22  C9   C10  119.73  3.000
 KU9  C8   C9   C10  120.49  3.000
 KU9  H23  N1   C5   119.07  3.000
 KU9  H23  N1   C4   116.68  3.000
 KU9  C5   N1   C4   123.98  3.000
 KU9  C3   N2   C14  120.09  3.000
 KU9  C24  N3   C16  126.68  3.000
 KU9  C24  N3   C15  112.60  3.000
 KU9  C16  N3   C15  120.47  3.000
 KU9  H24  N4   C14  119.63  3.000
 KU9  H24  N4   C1   117.05  3.000
 KU9  C14  N4   C1   123.32  3.000
 KU9  H25  O2   C2   108.07  3.000
 KU9  C18  S1   C17  101.98  3.000
 KU9  O4   C16  N3   122.77  3.000
 KU9  N3   C16  C17  115.98  3.000
 KU9  O4   C16  C17  121.23  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
 KU9  CONST_01  C7   C8   C9   C10     0.00   0.0  0
 KU9  CONST_02  C7   C12  C11  C10     0.00   0.0  0
 KU9  CONST_03  C8   C9   C10  C11     0.00   0.0  0
 KU9  CONST_04  C8   C7   C12  C11     0.00   0.0  0
 KU9  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 KU9  CONST_06  C9   C8   C7   C12     0.00   0.0  0
 KU9  CONST_07  C21  C22  C23  C18     0.00   0.0  0
 KU9  CONST_08  C21  C20  C19  C18     0.00   0.0  0
 KU9  CONST_09  C22  C23  C18  C19     0.00   0.0  0
 KU9  CONST_10  C22  C21  C20  C19     0.00   0.0  0
 KU9  CONST_11  C23  C18  C19  C20     0.00   0.0  0
 KU9  CONST_12  C23  C22  C21  C20     0.00   0.0  0
 KU9  CONST_13  N2   C14  N4   C1      0.00   0.0  0
 KU9  CONST_14  C15  C14  N4   C1    180.00   0.0  0
 KU9  CONST_15  C2   C1   N4   C14     0.00   0.0  0
 KU9  CONST_16  C3   N2   C14  C15   180.00   0.0  0
 KU9  CONST_17  N4   C14  N2   C3      0.00   0.0  0
 KU9  CONST_18  CL1  C23  C18  C19   180.00   0.0  0
 KU9  CONST_19  S1   C18  C19  C20   180.00   0.0  0
 KU9  CONST_20  CL1  C23  C22  C21   180.00   0.0  0
 KU9  CONST_21  S1   C18  C23  C22   180.00   0.0  0
 KU9  CONST_22  O1   C1   N4   C14   180.00   0.0  0
 KU9  CONST_23  H21  C8   C9   C10   180.00   0.0  0
 KU9  CONST_24  H22  C9   C10  C11   180.00   0.0  0
 KU9  CONST_25  H1   C10  C11  C12   180.00   0.0  0
 KU9  CONST_26  H2   C11  C12  C13     0.00   0.0  0
 KU9  CONST_27  H11  C22  C23  C18   180.00   0.0  0
 KU9  CONST_28  H9   C20  C19  C18   180.00   0.0  0
 KU9  CONST_29  H10  C21  C20  C19   180.00   0.0  0
 KU9  CONST_30  H8   C19  C20  C21   180.00   0.0  0
 KU9  CONST_31  H24  N4   C14  C15     0.00   0.0  0
 KU9  CONST_32  O4   C16  N3   C15     0.00   0.0  0
 KU9  CONST_33  C17  C16  N3   C15   180.00   0.0  0
 KU9  CONST_34  C24  N3   C16  C17     0.00   0.0  0
 KU9  CONST_35  O4   C16  N3   C24   180.00   0.0  0
 KU9  CONST_36  C5   N1   C4   C3    180.00   0.0  0
 KU9  CONST_37  O3   C4   N1   C5      0.00   0.0  0
 KU9  CONST_38  H23  N1   C4   C3      0.00   0.0  0
 KU9  Var_01    C5   C13  C12  C11   161.29  30.0  1
 KU9  Var_02    C5   C6   C7   C12    19.13  30.0  1
 KU9  Var_03    C25  C24  N3   C15    24.23  30.0  1
 KU9  Var_04    C24  C25  C26  C15    36.19  30.0  1
 KU9  Var_05    N3   C24  C25  C26   -36.55  30.0  1
 KU9  Var_06    C23  C18  S1   C17  -175.84  30.0  2
 KU9  Var_07    N1   C4   C3   C2   -170.73  30.0  2
 KU9  Var_08    S1   C17  C16  N3   -157.04  30.0  1
 KU9  Var_09    H6   C17  S1   C18    50.65  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
 KU9  chir_01  C15  N3  C14  C26  positiv
 KU9  chir_02  C5   N1  C13  C6   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
 KU9  plan-1  C18  0.020
 KU9  plan-1  C19  0.020
 KU9  plan-1  C20  0.020
 KU9  plan-1  C21  0.020
 KU9  plan-1  C22  0.020
 KU9  plan-1  C23  0.020
 KU9  plan-1  S1   0.020
 KU9  plan-1  CL1  0.020
 KU9  plan-1  H8   0.020
 KU9  plan-1  H9   0.020
 KU9  plan-1  H10  0.020
 KU9  plan-1  H11  0.020
 KU9  plan-2  C10  0.020
 KU9  plan-2  C11  0.020
 KU9  plan-2  C12  0.020
 KU9  plan-2  C13  0.020
 KU9  plan-2  C6   0.020
 KU9  plan-2  C7   0.020
 KU9  plan-2  C8   0.020
 KU9  plan-2  C9   0.020
 KU9  plan-2  H1   0.020
 KU9  plan-2  H2   0.020
 KU9  plan-2  H21  0.020
 KU9  plan-2  H22  0.020
 KU9  plan-3  C1   0.020
 KU9  plan-3  C14  0.020
 KU9  plan-3  C15  0.020
 KU9  plan-3  C2   0.020
 KU9  plan-3  C3   0.020
 KU9  plan-3  C4   0.020
 KU9  plan-3  N2   0.020
 KU9  plan-3  N4   0.020
 KU9  plan-3  O1   0.020
 KU9  plan-3  O2   0.020
 KU9  plan-3  H24  0.020
 KU9  plan-4  C3   0.020
 KU9  plan-4  C4   0.020
 KU9  plan-4  C5   0.020
 KU9  plan-4  N1   0.020
 KU9  plan-4  O3   0.020
 KU9  plan-4  H23  0.020
 KU9  plan-5  C15  0.020
 KU9  plan-5  C17  0.020
 KU9  plan-5  C24  0.020
 KU9  plan-5  N3   0.020
 KU9  plan-5  O4   0.020
 KU9  plan-5  C16  0.020

