# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:14:38 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: 2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)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)c3c(Cl)cncc3Cl)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
 GY8  GY8  2-[(2S)-1-(3,5-dichloropyridine-4-carbonyl)pyrrolidin-2-yl]-N-(2,3-dihydro-1H-inden-2-yl)-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxamide  ligand  56  35  .  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_GY8
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
 GY8  C1   C   CR6   0  -0.159  -5.1942  -0.0904  -0.8002
 GY8  C10  C   CR56  0   0.087   6.5620   0.6826   0.5777
 GY8  C11  C   CR56  0   0.088   6.0984   1.7299  -0.2172
 GY8  C12  C   CR16  0  -0.322   6.8816   2.8535  -0.4279
 GY8  C13  C   CR16  0  -0.260   8.1391   2.9212   0.1645
 GY8  C14  C   CR16  0  -0.260   8.6021   1.8764   0.9567
 GY8  C15  C   CR16  0  -0.325   7.8140   0.7490   1.1683
 GY8  C16  C   CH2   0  -0.499   4.7187   1.4299  -0.7273
 GY8  C17  C   CR6   0   0.236   0.6619  -3.0410  -0.9622
 GY8  C18  C   CR6   0   0.483  -0.7385  -3.1992  -0.5758
 GY8  C19  C   CH2   0  -0.478  -1.2529  -0.5019   2.8828
 GY8  C2   C   CR6   0   0.191  -4.2954   0.8976  -0.4344
 GY8  C20  C   CH2   0  -0.479  -2.4800   0.2493   3.3839
 GY8  C21  C   CH2   0  -0.277  -3.4393   0.1856   2.2039
 GY8  C22  C   CR6   0  -0.164  -4.7785   2.1950  -0.3752
 GY8  C23  C   CR16  0  -0.008  -6.1068   2.4530  -0.6797
 GY8  C24  C   CR16  0  -0.009  -6.5088   0.2433  -1.0924
 GY8  C3   C   C     0   0.510  -2.8445   0.5946  -0.1906
 GY8  C4   C   CH1   0  -0.146  -1.1465  -0.0598   1.4166
 GY8  C5   C   CR6   0   0.510  -0.4967  -1.0893   0.5387
 GY8  C6   C   CR6   0  -0.011   1.3367  -1.9292  -0.5555
 GY8  C7   C   C     0   0.551   2.7729  -1.6796  -0.8997
 GY8  C8   C   CR15  0  -0.074   4.6151  -0.0933  -0.5381
 GY8  C9   C   CH2   0  -0.487   5.5277  -0.4017   0.6671
 GY8  N1   N   NT    0  -0.484  -2.5333   0.2069   1.0509
 GY8  N2   N   N     0  -0.473   0.7300  -0.9598   0.1979
 GY8  N3   N   NH1   0  -0.666   3.2564  -0.5393  -0.3860
 GY8  N4   N   NR16  0  -0.679  -1.2301  -2.1761   0.1830
 GY8  N5   N   N     0  -0.393  -6.9438   1.4909  -1.0325
 GY8  O1   O   O     0  -0.433  -2.0394   0.6878  -1.0987
 GY8  O2   O   O     0  -0.479   3.4203  -2.4537  -1.5899
 GY8  O4   O   O     0  -0.466  -1.4018  -4.1688  -0.9073
 GY8  CL1  CL  CL    0  -0.081  -4.6886  -1.7356  -0.8877
 GY8  CL2  CL  CL    0  -0.073  -3.7358   3.4752   0.1085
 GY8  H1   H   HCR6  0   0.247   6.5271   3.6686  -1.0476
 GY8  H2   H   HCR6  0   0.252   8.7646   3.7900   0.0032
 GY8  H3   H   HCR6  0   0.252   9.5839   1.9391   1.4083
 GY8  H4   H   HCR6  0   0.247   8.1804  -0.0647   1.7827
 GY8  H5   H   HCH2  0   0.253   3.9679   1.9452  -0.1167
 GY8  H6   H   HCH2  0   0.262   4.5545   1.7342  -1.7617
 GY8  H7   H   HCH2  0   0.281  -0.3432  -0.2642   3.4303
 GY8  H8   H   HCH2  0   0.262  -1.4132  -1.5804   2.9524
 GY8  H9   H   HCH2  0   0.271  -2.9067  -0.1908   4.2830
 GY8  H10  H   HCH2  0   0.256  -2.2253   1.2879   3.6013
 GY8  H11  H   HCH2  0   0.262  -4.0277  -0.7350   2.2102
 GY8  H12  H   HCH2  0   0.273  -4.1274   1.0288   2.1837
 GY8  H13  H   HCR6  0   0.303  -6.4925   3.4643  -0.6338
 GY8  H14  H   HCR6  0   0.303  -7.2182  -0.5235  -1.3798
 GY8  H15  H   HCH1  0   0.309  -0.5459   0.8497   1.3353
 GY8  H16  H   HCR5  0   0.270   5.0332  -0.5818  -1.4194
 GY8  H17  H   HCH2  0   0.258   5.9400  -1.4110   0.6304
 GY8  H18  H   HCH2  0   0.252   4.9614  -0.3175   1.6011
 GY8  H19  H   HNH1  0   0.404   2.6352  -0.0011   0.2013
 GY8  H20  H   HNR6  0   0.418  -2.1993  -2.2455   0.4724
 GY8  H21  H   HOH1  0   0.476   0.4729  -4.6818  -1.8450
 GY8  O3   O   OH1   0  -0.586   1.1695  -4.0224  -1.6962

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
 GY8  C14  C13  aromatic  1.391  0.020  1.391
 GY8  C14  C15  aromatic  1.392  0.020  1.392
 GY8  C13  C12  aromatic  1.392  0.020  1.392
 GY8  C15  C10  aromatic  1.386  0.020  1.386
 GY8  C12  C11  aromatic  1.386  0.020  1.386
 GY8  C10  C11  aromatic  1.394  0.020  1.394
 GY8  C10  C9   single    1.501  0.020  1.501
 GY8  C11  C16  single    1.501  0.020  1.501
 GY8  O1   C3   double    1.217  0.020  1.217
 GY8  C9   C8   single    1.543  0.020  1.543
 GY8  C16  C8   single    1.538  0.020  1.538
 GY8  CL2  C22  single    1.721  0.020  1.721
 GY8  C3   C2   single    1.502  0.020  1.502
 GY8  C3   N1   single    1.337  0.020  1.337
 GY8  C8   N3   single    1.438  0.020  1.438
 GY8  C22  C2   aromatic  1.386  0.020  1.386
 GY8  C22  C23  aromatic  1.387  0.020  1.387
 GY8  C2   C1   aromatic  1.385  0.020  1.385
 GY8  C23  N5   aromatic  1.323  0.020  1.323
 GY8  C21  N1   single    1.466  0.020  1.466
 GY8  C21  C20  single    1.522  0.020  1.522
 GY8  N3   C7   single    1.341  0.020  1.341
 GY8  C1   CL1  single    1.723  0.020  1.723
 GY8  C1   C24  aromatic  1.387  0.020  1.387
 GY8  N1   C4   single    1.459  0.020  1.459
 GY8  N5   C24  aromatic  1.323  0.020  1.323
 GY8  C7   O2   double    1.223  0.020  1.223
 GY8  C7   C6   single    1.498  0.020  1.498
 GY8  C20  C19  single    1.524  0.020  1.524
 GY8  N2   C6   single    1.369  0.020  1.369
 GY8  N2   C5   double    1.280  0.020  1.280
 GY8  C4   C5   single    1.501  0.020  1.501
 GY8  C4   C19  single    1.535  0.020  1.535
 GY8  C6   C17  double    1.363  0.020  1.363
 GY8  C5   N4   single    1.359  0.020  1.359
 GY8  C17  O3   single    1.326  0.020  1.326
 GY8  C17  C18  single    1.461  0.020  1.461
 GY8  N4   C18  single    1.365  0.020  1.365
 GY8  C18  O4   double    1.221  0.020  1.221
 GY8  C12  H1   single    0.930  0.020  1.080
 GY8  C13  H2   single    0.930  0.020  1.080
 GY8  C14  H3   single    0.930  0.020  1.080
 GY8  C15  H4   single    0.930  0.020  1.080
 GY8  C16  H5   single    0.970  0.020  1.090
 GY8  C16  H6   single    0.970  0.020  1.090
 GY8  C19  H7   single    0.970  0.020  1.090
 GY8  C19  H8   single    0.970  0.020  1.090
 GY8  C20  H9   single    0.970  0.020  1.090
 GY8  C20  H10  single    0.970  0.020  1.090
 GY8  C21  H11  single    0.970  0.020  1.090
 GY8  C21  H12  single    0.970  0.020  1.090
 GY8  C23  H13  single    0.930  0.020  1.080
 GY8  C24  H14  single    0.930  0.020  1.080
 GY8  C4   H15  single    0.970  0.020  1.090
 GY8  C8   H16  single    0.970  0.020  1.090
 GY8  C9   H17  single    0.970  0.020  1.090
 GY8  C9   H18  single    0.970  0.020  1.090
 GY8  N3   H19  single    0.860  0.020  1.020
 GY8  N4   H20  single    0.860  0.020  1.020
 GY8  O3   H21  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
 GY8  CL1  C1   C24  119.80  3.000
 GY8  C24  C1   C2   119.93  3.000
 GY8  CL1  C1   C2   120.27  3.000
 GY8  C9   C10  C15  129.18  3.000
 GY8  C9   C10  C11  110.33  3.000
 GY8  C15  C10  C11  120.49  3.000
 GY8  C16  C11  C12  129.03  3.000
 GY8  C16  C11  C10  110.44  3.000
 GY8  C12  C11  C10  120.52  3.000
 GY8  H1   C12  C13  120.17  3.000
 GY8  H1   C12  C11  120.79  3.000
 GY8  C13  C12  C11  119.04  3.000
 GY8  H2   C13  C14  119.71  3.000
 GY8  H2   C13  C12  119.84  3.000
 GY8  C14  C13  C12  120.45  3.000
 GY8  H3   C14  C15  119.81  3.000
 GY8  H3   C14  C13  119.74  3.000
 GY8  C15  C14  C13  120.45  3.000
 GY8  H4   C15  C14  120.21  3.000
 GY8  H4   C15  C10  120.74  3.000
 GY8  C14  C15  C10  119.05  3.000
 GY8  H6   C16  H5   107.10  3.000
 GY8  H6   C16  C8   112.50  3.000
 GY8  H5   C16  C8   110.53  3.000
 GY8  H6   C16  C11  113.89  3.000
 GY8  H5   C16  C11  110.25  3.000
 GY8  C8   C16  C11  102.59  3.000
 GY8  O3   C17  C6   125.40  3.000
 GY8  O3   C17  C18  115.66  3.000
 GY8  C6   C17  C18  118.94  3.000
 GY8  O4   C18  N4   123.40  3.000
 GY8  O4   C18  C17  122.33  3.000
 GY8  N4   C18  C17  114.26  3.000
 GY8  H8   C19  H7   107.84  3.000
 GY8  H8   C19  C4   110.81  3.000
 GY8  H7   C19  C4   111.09  3.000
 GY8  H8   C19  C20  110.34  3.000
 GY8  H7   C19  C20  113.59  3.000
 GY8  C4   C19  C20  103.17  3.000
 GY8  C3   C2   C22  121.25  3.000
 GY8  C22  C2   C1   116.94  3.000
 GY8  C3   C2   C1   121.72  3.000
 GY8  H10  C20  H9   108.17  3.000
 GY8  H10  C20  C21  109.96  3.000
 GY8  H9   C20  C21  112.12  3.000
 GY8  H10  C20  C19  110.30  3.000
 GY8  H9   C20  C19  112.84  3.000
 GY8  C21  C20  C19  103.41  3.000
 GY8  H12  C21  H11  108.20  3.000
 GY8  H12  C21  N1   111.39  3.000
 GY8  H11  C21  N1   110.46  3.000
 GY8  H12  C21  C20  112.36  3.000
 GY8  H11  C21  C20  111.73  3.000
 GY8  N1   C21  C20  102.68  3.000
 GY8  CL2  C22  C23  120.25  3.000
 GY8  C23  C22  C2   119.91  3.000
 GY8  CL2  C22  C2   119.83  3.000
 GY8  H13  C23  N5   117.70  3.000
 GY8  H13  C23  C22  120.35  3.000
 GY8  N5   C23  C22  121.95  3.000
 GY8  H14  C24  N5   117.67  3.000
 GY8  H14  C24  C1   120.40  3.000
 GY8  N5   C24  C1   121.94  3.000
 GY8  O1   C3   N1   124.12  3.000
 GY8  N1   C3   C2   115.71  3.000
 GY8  O1   C3   C2   120.16  3.000
 GY8  H15  C4   N1   110.58  3.000
 GY8  H15  C4   C5   106.82  3.000
 GY8  N1   C4   C5   112.98  3.000
 GY8  H15  C4   C19  110.41  3.000
 GY8  C5   C4   C19  113.02  3.000
 GY8  N1   C4   C19  103.08  3.000
 GY8  N4   C5   N2   121.92  3.000
 GY8  N4   C5   C4   117.92  3.000
 GY8  N2   C5   C4   120.09  3.000
 GY8  N2   C6   C7   115.67  3.000
 GY8  N2   C6   C17  121.49  3.000
 GY8  C7   C6   C17  122.83  3.000
 GY8  O2   C7   N3   124.32  3.000
 GY8  O2   C7   C6   122.14  3.000
 GY8  N3   C7   C6   113.55  3.000
 GY8  H16  C8   N3   107.98  3.000
 GY8  H16  C8   C9   108.35  3.000
 GY8  N3   C8   C9   114.47  3.000
 GY8  H16  C8   C16  108.55  3.000
 GY8  N3   C8   C16  112.56  3.000
 GY8  C9   C8   C16  104.72  3.000
 GY8  H18  C9   H17  107.17  3.000
 GY8  H18  C9   C8   110.17  3.000
 GY8  H17  C9   C8   112.46  3.000
 GY8  H18  C9   C10  110.58  3.000
 GY8  H17  C9   C10  113.95  3.000
 GY8  C8   C9   C10  102.52  3.000
 GY8  C4   N1   C3   120.46  3.000
 GY8  C4   N1   C21  112.80  3.000
 GY8  C3   N1   C21  126.18  3.000
 GY8  C6   N2   C5   119.97  3.000
 GY8  H19  N3   C8   118.50  3.000
 GY8  H19  N3   C7   117.01  3.000
 GY8  C8   N3   C7   124.33  3.000
 GY8  H20  N4   C5   119.74  3.000
 GY8  H20  N4   C18  116.85  3.000
 GY8  C5   N4   C18  123.41  3.000
 GY8  C24  N5   C23  119.34  3.000
 GY8  H21  O3   C17  108.22  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
 GY8  CONST_01  C23  C22  C2   C1      0.00   0.0  0
 GY8  CONST_02  C23  N5   C24  C1      0.00   0.0  0
 GY8  CONST_03  C13  C14  C15  C10     0.00   0.0  0
 GY8  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 GY8  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 GY8  CONST_06  C14  C15  C10  C11     0.00   0.0  0
 GY8  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 GY8  CONST_08  C15  C10  C11  C12     0.00   0.0  0
 GY8  CONST_09  N5   C23  C22  C2      0.00   0.0  0
 GY8  CONST_10  N5   C24  C1   C2      0.00   0.0  0
 GY8  CONST_11  C24  C1   C2   C22     0.00   0.0  0
 GY8  CONST_12  C24  N5   C23  C22     0.00   0.0  0
 GY8  CONST_13  C5   N4   C18  C17     0.00   0.0  0
 GY8  CONST_14  N2   C5   N4   C18     0.00   0.0  0
 GY8  CONST_15  C4   C5   N4   C18   180.00   0.0  0
 GY8  CONST_16  C6   N2   C5   C4    180.00   0.0  0
 GY8  CONST_17  N4   C5   N2   C6      0.00   0.0  0
 GY8  CONST_18  CL2  C22  C2   C1    180.00   0.0  0
 GY8  CONST_19  CL1  C1   C2   C22   180.00   0.0  0
 GY8  CONST_20  C3   C2   C22  C23   180.00   0.0  0
 GY8  CONST_21  C3   C2   C1   C24   180.00   0.0  0
 GY8  CONST_22  CL2  C22  C23  N5    180.00   0.0  0
 GY8  CONST_23  CL1  C1   C24  N5    180.00   0.0  0
 GY8  CONST_24  C21  N1   C3   C2      0.00   0.0  0
 GY8  CONST_25  C4   N1   C3   C2    180.00   0.0  0
 GY8  CONST_26  O4   C18  N4   C5    180.00   0.0  0
 GY8  CONST_27  H3   C14  C15  C10   180.00   0.0  0
 GY8  CONST_28  H1   C12  C11  C10   180.00   0.0  0
 GY8  CONST_29  H2   C13  C12  C11   180.00   0.0  0
 GY8  CONST_30  H4   C15  C10  C11   180.00   0.0  0
 GY8  CONST_31  H13  C23  C22  C2    180.00   0.0  0
 GY8  CONST_32  H14  C24  C1   C2    180.00   0.0  0
 GY8  CONST_33  H20  N4   C18  C17   180.00   0.0  0
 GY8  CONST_34  O1   C3   N1   C21   180.00   0.0  0
 GY8  CONST_35  O1   C3   N1   C4      0.00   0.0  0
 GY8  CONST_36  C8   N3   C7   C6    180.00   0.0  0
 GY8  CONST_37  O2   C7   N3   C8      0.00   0.0  0
 GY8  CONST_38  H19  N3   C7   C6      0.00   0.0  0
 GY8  Var_01    C8   C16  C11  C10   -18.42  30.0  1
 GY8  Var_02    C8   C9   C10  C11    18.62  30.0  1
 GY8  Var_03    N1   C21  C20  C19   -32.55  30.0  1
 GY8  Var_04    C4   N1   C21  C20    14.44  30.0  1
 GY8  Var_05    C4   C19  C20  C21    38.85  30.0  1
 GY8  Var_06    N1   C3   C2   C1    -87.11  30.0  2
 GY8  Var_07    N3   C7   C6   C17  -179.00  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
 GY8  chir_01  C4  N1  C5   C19  positiv
 GY8  chir_02  C8  N3  C16  C9   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
 GY8  plan-1  C1   0.020
 GY8  plan-1  C2   0.020
 GY8  plan-1  C22  0.020
 GY8  plan-1  C23  0.020
 GY8  plan-1  C24  0.020
 GY8  plan-1  C3   0.020
 GY8  plan-1  N5   0.020
 GY8  plan-1  CL1  0.020
 GY8  plan-1  CL2  0.020
 GY8  plan-1  H13  0.020
 GY8  plan-1  H14  0.020
 GY8  plan-2  C10  0.020
 GY8  plan-2  C11  0.020
 GY8  plan-2  C12  0.020
 GY8  plan-2  C13  0.020
 GY8  plan-2  C14  0.020
 GY8  plan-2  C15  0.020
 GY8  plan-2  C16  0.020
 GY8  plan-2  C9   0.020
 GY8  plan-2  H1   0.020
 GY8  plan-2  H2   0.020
 GY8  plan-2  H3   0.020
 GY8  plan-2  H4   0.020
 GY8  plan-3  C17  0.020
 GY8  plan-3  C18  0.020
 GY8  plan-3  C4   0.020
 GY8  plan-3  C5   0.020
 GY8  plan-3  C6   0.020
 GY8  plan-3  C7   0.020
 GY8  plan-3  N2   0.020
 GY8  plan-3  N4   0.020
 GY8  plan-3  O4   0.020
 GY8  plan-3  H20  0.020
 GY8  plan-3  O3   0.020
 GY8  plan-4  C2   0.020
 GY8  plan-4  C21  0.020
 GY8  plan-4  C3   0.020
 GY8  plan-4  C4   0.020
 GY8  plan-4  N1   0.020
 GY8  plan-4  O1   0.020
 GY8  plan-5  C6   0.020
 GY8  plan-5  C7   0.020
 GY8  plan-5  C8   0.020
 GY8  plan-5  N3   0.020
 GY8  plan-5  O2   0.020
 GY8  plan-5  H19  0.020

