# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 04:47:14 2022
#   Inital geometry file: a 156 line input string
#   Ligand name: 2-{(2S)-1-[(2-chlorophenoxy)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-N-(2-phenylethyl)-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)COc3ccccc3Cl)C(=O)NCCc4ccccc4
#
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
 G2K  G2K  2-{(2S)-1-[(2-chlorophenoxy)acetyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide  ligand  60  35  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G2K
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
 G2K  C1   C   CR6   0   0.479  -4.8612   1.1450  -1.5502
 G2K  C10  C   CR16  0  -0.272   5.7028   2.2184   0.9321
 G2K  C11  C   CR16  0  -0.232   5.0139   1.5593   1.9409
 G2K  C12  C   CR16  0  -0.289   3.6662   1.2661   1.7874
 G2K  C13  C   CR6   0   0.517  -3.6642  -0.4029  -0.1654
 G2K  C14  C   CH1   0  -0.144  -3.6425  -1.7922   0.4183
 G2K  C15  C   CH2   0  -0.478  -4.4052  -1.8607   1.7554
 G2K  C16  C   CH2   0  -0.468  -3.5737  -2.8237   2.5953
 G2K  C17  C   CH2   0  -0.290  -2.1487  -2.4777   2.1914
 G2K  C19  C   CH2   0  -0.323   0.0802  -2.4315   0.3850
 G2K  C2   C   CR6   0   0.229  -3.8030   2.0978  -1.2281
 G2K  C20  C   CR6   0   0.450   2.2879  -1.9639  -0.2831
 G2K  C21  C   CR16  0  -0.381   2.8418  -2.4258   0.9074
 G2K  C22  C   CR16  0  -0.232   4.1929  -2.2385   1.1696
 G2K  C23  C   CR16  0  -0.261   5.0090  -1.5939   0.2565
 G2K  C24  C   CR16  0  -0.185   4.4678  -1.1318  -0.9343
 G2K  C25  C   CR6   0  -0.150   3.1242  -1.3195  -1.1976
 G2K  C3   C   CR6   0  -0.002  -2.7889   1.7019  -0.4094
 G2K  C4   C   C     0   0.539  -1.5865   2.5499  -0.1212
 G2K  C5   C   CH2   0  -0.270   0.6045   2.3964   1.0015
 G2K  C6   C   CH2   0  -0.531   1.5306   1.3041   0.4594
 G2K  C7   C   CR6   0   0.148   2.9866   1.6236   0.6271
 G2K  C8   C   CR16  0  -0.300   3.6863   2.2862  -0.3783
 G2K  C9   C   CR16  0  -0.241   5.0340   2.5820  -0.2300
 G2K  N1   N   NH1   0  -0.642  -0.7739   2.0146   0.8029
 G2K  N2   N   N     0  -0.460  -2.7643   0.4521   0.1421
 G2K  N3   N   NT    0  -0.483  -2.2929  -2.1839   0.7708
 G2K  N4   N   NR16  0  -0.693  -4.6932  -0.0922  -0.9937
 G2K  O1   O   O     0  -0.472  -5.7988   1.4339  -2.2790
 G2K  O2   O   OH1   0  -0.591  -3.9133   3.2976  -1.7883
 G2K  O3   O   O     0  -0.475  -1.3803   3.6039  -0.7042
 G2K  O4   O   O2    0  -0.448   0.9908  -2.0782  -0.6217
 G2K  O5   O   O     0  -0.469  -1.5353  -1.9829  -1.3359
 G2K  CL1  CL  CL    0  -0.111   2.4447  -0.7097  -2.6666
 G2K  H1   H   HCR6  0   0.248   6.7550   2.4447   1.0490
 G2K  H2   H   HCR6  0   0.246   5.5290   1.2637   2.8462
 G2K  H3   H   HCR6  0   0.237   3.1405   0.7342   2.5719
 G2K  H4   H   HCH1  0   0.299  -4.0710  -2.4913  -0.3074
 G2K  H5   H   HCH2  0   0.261  -4.4229  -0.8770   2.2288
 G2K  H6   H   HCH2  0   0.274  -5.4354  -2.1817   1.6143
 G2K  H7   H   HCH2  0   0.263  -3.7424  -2.7039   3.6641
 G2K  H8   H   HCH2  0   0.251  -3.7947  -3.8586   2.3287
 G2K  H9   H   HCH2  0   0.251  -1.7837  -1.6039   2.7406
 G2K  H10  H   HCH2  0   0.268  -1.4574  -3.3029   2.3585
 G2K  H11  H   HCH2  0   0.255   0.2447  -1.8322   1.2888
 G2K  H12  H   HCH2  0   0.278   0.1821  -3.4857   0.6747
 G2K  H13  H   HCR6  0   0.287   2.2306  -2.9321   1.6426
 G2K  H14  H   HCR6  0   0.261   4.6000  -2.6007   2.1042
 G2K  H15  H   HCR6  0   0.254   6.0564  -1.4325   0.4689
 G2K  H16  H   HCR6  0   0.268   5.0830  -0.6065  -1.6518
 G2K  H17  H   HCH2  0   0.248   0.7929   2.5512   2.0664
 G2K  H18  H   HCH2  0   0.251   0.7873   3.3458   0.5001
 G2K  H19  H   HCH2  0   0.241   1.3024   0.3708   0.9816
 G2K  H20  H   HCH2  0   0.246   1.3040   1.1408  -0.5964
 G2K  H21  H   HCR6  0   0.241   3.1734   2.5622  -1.2926
 G2K  H22  H   HCR6  0   0.248   5.5639   3.0923  -1.0244
 G2K  H23  H   HNH1  0   0.400  -1.0560   1.1103   1.1550
 G2K  H24  H   HNR6  0   0.438  -5.3780  -0.8020  -1.2286
 G2K  H25  H   HOH1  0   0.475  -4.7290   3.3109  -2.3140
 G2K  C18  C   C     0   0.545  -1.3183  -2.1807  -0.1546

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
 G2K  CL1  C25  single    1.730  0.020  1.730
 G2K  C24  C25  aromatic  1.382  0.020  1.382
 G2K  C24  C23  aromatic  1.387  0.020  1.387
 G2K  C25  C20  aromatic  1.397  0.020  1.397
 G2K  C23  C22  aromatic  1.384  0.020  1.384
 G2K  C20  O4   single    1.345  0.020  1.345
 G2K  C20  C21  aromatic  1.392  0.020  1.392
 G2K  O4   C19  single    1.403  0.020  1.403
 G2K  C22  C21  aromatic  1.389  0.020  1.389
 G2K  C19  C18  single    1.520  0.020  1.520
 G2K  C12  C11  aromatic  1.388  0.020  1.388
 G2K  C12  C7   aromatic  1.391  0.020  1.391
 G2K  C6   C7   single    1.500  0.020  1.500
 G2K  C6   C5   single    1.531  0.020  1.531
 G2K  C11  C10  aromatic  1.388  0.020  1.388
 G2K  O5   C18  double    1.217  0.020  1.217
 G2K  C7   C8   aromatic  1.393  0.020  1.393
 G2K  C18  N3   single    1.344  0.020  1.344
 G2K  C5   N1   single    1.444  0.020  1.444
 G2K  N1   C4   single    1.342  0.020  1.342
 G2K  C10  C9   aromatic  1.389  0.020  1.389
 G2K  C8   C9   aromatic  1.388  0.020  1.388
 G2K  N3   C17  single    1.458  0.020  1.458
 G2K  N3   C14  single    1.449  0.020  1.449
 G2K  C17  C16  single    1.521  0.020  1.521
 G2K  C4   O3   double    1.222  0.020  1.222
 G2K  C4   C3   single    1.499  0.020  1.499
 G2K  N2   C3   single    1.366  0.020  1.366
 G2K  N2   C13  double    1.279  0.020  1.279
 G2K  C14  C13  single    1.507  0.020  1.507
 G2K  C14  C15  single    1.541  0.020  1.541
 G2K  C3   C2   double    1.362  0.020  1.362
 G2K  C13  N4   single    1.357  0.020  1.357
 G2K  C16  C15  single    1.525  0.020  1.525
 G2K  C2   O2   single    1.329  0.020  1.329
 G2K  C2   C1   single    1.460  0.020  1.460
 G2K  N4   C1   single    1.367  0.020  1.367
 G2K  C1   O1   double    1.222  0.020  1.222
 G2K  C10  H1   single    0.930  0.020  1.080
 G2K  C11  H2   single    0.930  0.020  1.080
 G2K  C12  H3   single    0.930  0.020  1.080
 G2K  C14  H4   single    0.970  0.020  1.090
 G2K  C15  H5   single    0.970  0.020  1.090
 G2K  C15  H6   single    0.970  0.020  1.090
 G2K  C16  H7   single    0.970  0.020  1.090
 G2K  C16  H8   single    0.970  0.020  1.090
 G2K  C17  H9   single    0.970  0.020  1.090
 G2K  C17  H10  single    0.970  0.020  1.090
 G2K  C19  H11  single    0.970  0.020  1.090
 G2K  C19  H12  single    0.970  0.020  1.090
 G2K  C21  H13  single    0.930  0.020  1.080
 G2K  C22  H14  single    0.930  0.020  1.080
 G2K  C23  H15  single    0.930  0.020  1.080
 G2K  C24  H16  single    0.930  0.020  1.080
 G2K  C5   H17  single    0.970  0.020  1.090
 G2K  C5   H18  single    0.970  0.020  1.090
 G2K  C6   H19  single    0.970  0.020  1.090
 G2K  C6   H20  single    0.970  0.020  1.090
 G2K  C8   H21  single    0.930  0.020  1.080
 G2K  C9   H22  single    0.930  0.020  1.080
 G2K  N1   H23  single    0.890  0.020  1.040
 G2K  N4   H24  single    0.860  0.020  1.020
 G2K  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
 G2K  O1   C1   N4   123.43  3.000
 G2K  O1   C1   C2   122.24  3.000
 G2K  N4   C1   C2   114.32  3.000
 G2K  H1   C10  C9   120.23  3.000
 G2K  H1   C10  C11  120.21  3.000
 G2K  C9   C10  C11  119.56  3.000
 G2K  H2   C11  C12  119.79  3.000
 G2K  H2   C11  C10  120.08  3.000
 G2K  C12  C11  C10  120.13  3.000
 G2K  H3   C12  C7   119.52  3.000
 G2K  H3   C12  C11  119.65  3.000
 G2K  C7   C12  C11  120.82  3.000
 G2K  N4   C13  N2   121.82  3.000
 G2K  N4   C13  C14  117.29  3.000
 G2K  N2   C13  C14  120.86  3.000
 G2K  H4   C14  N3   110.68  3.000
 G2K  H4   C14  C15  110.67  3.000
 G2K  N3   C14  C15  103.76  3.000
 G2K  H4   C14  C13  109.04  3.000
 G2K  C15  C14  C13  111.71  3.000
 G2K  N3   C14  C13  110.91  3.000
 G2K  H6   C15  H5   107.85  3.000
 G2K  H6   C15  C16  113.67  3.000
 G2K  H5   C15  C16  109.82  3.000
 G2K  H6   C15  C14  111.66  3.000
 G2K  H5   C15  C14  110.13  3.000
 G2K  C16  C15  C14  103.66  3.000
 G2K  H8   C16  H7   108.23  3.000
 G2K  H8   C16  C17  109.91  3.000
 G2K  H7   C16  C17  112.39  3.000
 G2K  H8   C16  C15  110.73  3.000
 G2K  H7   C16  C15  112.76  3.000
 G2K  C17  C16  C15  102.76  3.000
 G2K  H10  C17  H9   108.43  3.000
 G2K  H10  C17  N3   111.40  3.000
 G2K  H9   C17  N3   111.16  3.000
 G2K  H10  C17  C16  112.42  3.000
 G2K  H9   C17  C16  111.14  3.000
 G2K  N3   C17  C16  102.24  3.000
 G2K  H12  C19  H11  107.05  3.000
 G2K  H12  C19  O4   111.78  3.000
 G2K  H11  C19  O4   110.87  3.000
 G2K  H12  C19  C18  109.73  3.000
 G2K  H11  C19  C18  109.90  3.000
 G2K  O4   C19  C18  107.52  3.000
 G2K  O2   C2   C3   125.29  3.000
 G2K  O2   C2   C1   115.85  3.000
 G2K  C3   C2   C1   118.86  3.000
 G2K  O4   C20  C25  116.85  3.000
 G2K  O4   C20  C21  124.80  3.000
 G2K  C25  C20  C21  118.34  3.000
 G2K  H13  C21  C22  118.97  3.000
 G2K  H13  C21  C20  120.78  3.000
 G2K  C22  C21  C20  120.25  3.000
 G2K  H14  C22  C23  120.26  3.000
 G2K  H14  C22  C21  118.95  3.000
 G2K  C23  C22  C21  120.78  3.000
 G2K  H15  C23  C24  119.80  3.000
 G2K  H15  C23  C22  120.75  3.000
 G2K  C24  C23  C22  119.44  3.000
 G2K  H16  C24  C25  119.52  3.000
 G2K  H16  C24  C23  120.63  3.000
 G2K  C25  C24  C23  119.84  3.000
 G2K  CL1  C25  C24  119.73  3.000
 G2K  C24  C25  C20  121.34  3.000
 G2K  CL1  C25  C20  118.91  3.000
 G2K  N2   C3   C4   115.17  3.000
 G2K  N2   C3   C2   121.46  3.000
 G2K  C4   C3   C2   123.25  3.000
 G2K  O3   C4   N1   124.78  3.000
 G2K  O3   C4   C3   122.10  3.000
 G2K  N1   C4   C3   113.10  3.000
 G2K  H18  C5   H17  107.23  3.000
 G2K  H18  C5   N1   109.11  3.000
 G2K  H17  C5   N1   109.64  3.000
 G2K  H18  C5   C6   110.94  3.000
 G2K  H17  C5   C6   109.99  3.000
 G2K  N1   C5   C6   109.88  3.000
 G2K  H20  C6   H19  106.90  3.000
 G2K  H20  C6   C7   109.95  3.000
 G2K  H19  C6   C7   109.32  3.000
 G2K  H20  C6   C5   108.87  3.000
 G2K  H19  C6   C5   108.27  3.000
 G2K  C7   C6   C5   113.30  3.000
 G2K  C8   C7   C6   120.55  3.000
 G2K  C8   C7   C12  118.61  3.000
 G2K  C6   C7   C12  120.84  3.000
 G2K  H21  C8   C9   119.69  3.000
 G2K  H21  C8   C7   119.49  3.000
 G2K  C9   C8   C7   120.81  3.000
 G2K  H22  C9   C8   119.82  3.000
 G2K  H22  C9   C10  120.10  3.000
 G2K  C8   C9   C10  120.08  3.000
 G2K  H23  N1   C5   117.07  3.000
 G2K  H23  N1   C4   115.33  3.000
 G2K  C5   N1   C4   124.56  3.000
 G2K  C3   N2   C13  120.12  3.000
 G2K  C18  N3   C17  126.86  3.000
 G2K  C17  N3   C14  112.56  3.000
 G2K  C18  N3   C14  120.48  3.000
 G2K  H24  N4   C13  119.56  3.000
 G2K  H24  N4   C1   117.15  3.000
 G2K  C13  N4   C1   123.29  3.000
 G2K  H25  O2   C2   108.09  3.000
 G2K  C20  O4   C19  117.82  3.000
 G2K  O5   C18  N3   122.64  3.000
 G2K  N3   C18  C19  114.98  3.000
 G2K  O5   C18  C19  122.37  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
 G2K  CONST_01  C7   C12  C11  C10     0.00   0.0  0
 G2K  CONST_02  C7   C8   C9   C10     0.00   0.0  0
 G2K  CONST_03  C8   C7   C12  C11     0.00   0.0  0
 G2K  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 G2K  CONST_05  C9   C10  C11  C12     0.00   0.0  0
 G2K  CONST_06  C9   C8   C7   C12     0.00   0.0  0
 G2K  CONST_07  C23  C24  C25  C20     0.00   0.0  0
 G2K  CONST_08  C23  C22  C21  C20     0.00   0.0  0
 G2K  CONST_09  C24  C25  C20  C21     0.00   0.0  0
 G2K  CONST_10  C24  C23  C22  C21     0.00   0.0  0
 G2K  CONST_11  C25  C24  C23  C22     0.00   0.0  0
 G2K  CONST_12  C25  C20  C21  C22     0.00   0.0  0
 G2K  CONST_13  N2   C13  N4   C1      0.00   0.0  0
 G2K  CONST_14  C14  C13  N4   C1    180.00   0.0  0
 G2K  CONST_15  C2   C1   N4   C13     0.00   0.0  0
 G2K  CONST_16  C3   N2   C13  C14   180.00   0.0  0
 G2K  CONST_17  N4   C13  N2   C3      0.00   0.0  0
 G2K  CONST_18  C6   C7   C12  C11   180.00   0.0  0
 G2K  CONST_19  CL1  C25  C20  C21   180.00   0.0  0
 G2K  CONST_20  O4   C20  C21  C22   180.00   0.0  0
 G2K  CONST_21  CL1  C25  C24  C23   180.00   0.0  0
 G2K  CONST_22  O4   C20  C25  C24   180.00   0.0  0
 G2K  CONST_23  C9   C8   C7   C6    180.00   0.0  0
 G2K  CONST_24  O1   C1   N4   C13   180.00   0.0  0
 G2K  CONST_25  H3   C12  C11  C10   180.00   0.0  0
 G2K  CONST_26  H21  C8   C9   C10   180.00   0.0  0
 G2K  CONST_27  H22  C9   C10  C11   180.00   0.0  0
 G2K  CONST_28  H1   C10  C11  C12   180.00   0.0  0
 G2K  CONST_29  H16  C24  C25  C20   180.00   0.0  0
 G2K  CONST_30  H14  C22  C21  C20   180.00   0.0  0
 G2K  CONST_31  H15  C23  C22  C21   180.00   0.0  0
 G2K  CONST_32  H13  C21  C22  C23   180.00   0.0  0
 G2K  CONST_33  H2   C11  C12  C7    180.00   0.0  0
 G2K  CONST_34  H24  N4   C13  C14     0.00   0.0  0
 G2K  CONST_35  C19  C18  N3   C14   180.00   0.0  0
 G2K  CONST_36  O5   C18  N3   C14     0.00   0.0  0
 G2K  CONST_37  C19  C18  N3   C17     0.00   0.0  0
 G2K  CONST_38  O5   C18  N3   C17   180.00   0.0  0
 G2K  CONST_40  H23  N1   C4   C3      0.00   0.0  0
 G2K  Var_01    C16  C17  N3   C14    23.46  30.0  1
 G2K  Var_02    C17  C16  C15  C14    37.04  30.0  1
 G2K  Var_03    N3   C17  C16  C15   -36.62  30.0  1
 G2K  Var_04    C5   C6   C7   C12    88.60  30.0  3
 G2K  Var_05    C25  C20  O4   C19  -165.52  30.0  2
 G2K  Var_06    N1   C4   C3   C2    174.36  30.0  2
 G2K  Var_07    N1   C5   C6   C7    180.00  30.0  3
 G2K  Var_08    O4   C19  C18  N3   -165.93  30.0  1
 G2K  Var_09    H11  C19  O4   C20    46.89  30.0  3
 G2K  Var_10    C6   C5   N1   C4   -106.05  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
 G2K  chir_01  C14  N3  C13  C15  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
 G2K  plan-1  C10  0.020
 G2K  plan-1  C11  0.020
 G2K  plan-1  C12  0.020
 G2K  plan-1  C6   0.020
 G2K  plan-1  C7   0.020
 G2K  plan-1  C8   0.020
 G2K  plan-1  C9   0.020
 G2K  plan-1  H1   0.020
 G2K  plan-1  H2   0.020
 G2K  plan-1  H3   0.020
 G2K  plan-1  H21  0.020
 G2K  plan-1  H22  0.020
 G2K  plan-2  C20  0.020
 G2K  plan-2  C21  0.020
 G2K  plan-2  C22  0.020
 G2K  plan-2  C23  0.020
 G2K  plan-2  C24  0.020
 G2K  plan-2  C25  0.020
 G2K  plan-2  O4   0.020
 G2K  plan-2  CL1  0.020
 G2K  plan-2  H13  0.020
 G2K  plan-2  H14  0.020
 G2K  plan-2  H15  0.020
 G2K  plan-2  H16  0.020
 G2K  plan-3  C1   0.020
 G2K  plan-3  C13  0.020
 G2K  plan-3  C14  0.020
 G2K  plan-3  C2   0.020
 G2K  plan-3  C3   0.020
 G2K  plan-3  C4   0.020
 G2K  plan-3  N2   0.020
 G2K  plan-3  N4   0.020
 G2K  plan-3  O1   0.020
 G2K  plan-3  O2   0.020
 G2K  plan-3  H24  0.020
 G2K  plan-4  C14  0.020
 G2K  plan-4  C17  0.020
 G2K  plan-4  C19  0.020
 G2K  plan-4  N3   0.020
 G2K  plan-4  O5   0.020
 G2K  plan-4  C18  0.020
 G2K  plan-5  C3   0.020
 G2K  plan-5  C4   0.020
 G2K  plan-5  C5   0.020
 G2K  plan-5  N1   0.020
 G2K  plan-5  O3   0.020
 G2K  plan-5  H23  0.020

