# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 04:47:29 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 5-hydroxy-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=C(O)C(=O)NC(=N1)[C@@H]2CCCN2C(=O)COc3ccccc3
#
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
 G1K  G1K  '5-hydroxy-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxylic acid'  ligand  43  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_G1K
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
 G1K  C1   C  CR6   0   0.479  -3.7751   0.5370  -1.4202
 G1K  C10  C  C     0   0.543   0.7451  -1.1647  -0.5912
 G1K  C11  C  CH2   0  -0.314   2.1675  -1.0438  -0.0751
 G1K  C12  C  CR6   0   0.383   4.1148   0.1907  -0.5863
 G1K  C13  C  CR16  0  -0.377   4.8524  -0.4196   0.4246
 G1K  C14  C  CR16  0  -0.241   6.1830  -0.0588   0.6141
 G1K  C15  C  CR16  0  -0.280   6.7847   0.8977  -0.1867
 G1K  C16  C  CR16  0  -0.240   6.0396   1.5023  -1.1949
 G1K  C17  C  CR16  0  -0.345   4.7158   1.1552  -1.3972
 G1K  C2   C  CR6   0   0.249  -3.5418   1.5147  -0.3598
 G1K  C3   C  CR6   0  -0.036  -2.6438   1.2171   0.6245
 G1K  C4   C  C     0   0.532  -2.3607   2.1746   1.7244
 G1K  C5   C  CR6   0   0.504  -2.1540  -0.8171  -0.2862
 G1K  C6   C  CH1   0  -0.145  -1.4416  -2.1449  -0.2665
 G1K  C7   C  CH2   0  -0.477  -2.0053  -3.0868   0.8112
 G1K  C8   C  CH2   0  -0.473  -0.7757  -3.8241   1.3296
 G1K  C9   C  CH2   0  -0.282   0.3033  -2.7520   1.2982
 G1K  N1   N  N     0  -0.398  -1.9634   0.0338   0.6500
 G1K  N2   N  NT    0  -0.479  -0.0498  -1.9861   0.1101
 G1K  N3   N  NR16  0  -0.693  -3.0317  -0.5991  -1.3011
 G1K  O1   O  O     0  -0.470  -4.5655   0.7421  -2.3293
 G1K  O2   O  OH1   0  -0.583  -4.2383   2.6379  -0.4499
 G1K  O3   O  OH1   0  -0.580  -1.4612   1.7096   2.5755
 G1K  O4   O  O     0  -0.429  -2.8869   3.2553   1.8324
 G1K  O5   O  O2    0  -0.465   2.8196  -0.0835  -0.8570
 G1K  O6   O  O     0  -0.478   0.3527  -0.5600  -1.5751
 G1K  H1   H  HCH2  0   0.262   2.1544  -0.7591   0.9852
 G1K  H2   H  HCH2  0   0.266   2.6654  -2.0201  -0.1416
 G1K  H3   H  HCR6  0   0.281   4.4167  -1.1703   1.0701
 G1K  H4   H  HCR6  0   0.260   6.7479  -0.5396   1.4024
 G1K  H5   H  HCR6  0   0.254   7.8195   1.1715  -0.0310
 G1K  H6   H  HCR6  0   0.259   6.4938   2.2516  -1.8306
 G1K  H7   H  HCR6  0   0.263   4.1364   1.6248  -2.1822
 G1K  H8   H  HCH1  0   0.293  -1.5117  -2.6069  -1.2565
 G1K  H9   H  HCH2  0   0.259  -2.4562  -2.5028   1.6149
 G1K  H10  H  HCH2  0   0.272  -2.7699  -3.7458   0.4045
 G1K  H11  H  HCH2  0   0.262  -0.9214  -4.2347   2.3274
 G1K  H12  H  HCH2  0   0.250  -0.5052  -4.6442   0.6622
 G1K  H13  H  HCH2  0   0.252   0.2657  -2.1225   2.1922
 G1K  H14  H  HCH2  0   0.265   1.3040  -3.1758   1.2193
 G1K  H15  H  HNR6  0   0.437  -3.1447  -1.3019  -2.0231
 G1K  H16  H  HOH1  0   0.478  -4.7943   2.5864  -1.2444
 G1K  H17  H  HOH1  0   0.485  -1.3087   2.3704   3.2674

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
 G1K  O4   C4   double    1.207  0.020  1.207
 G1K  O2   C2   single    1.325  0.020  1.325
 G1K  C4   O3   single    1.323  0.020  1.323
 G1K  C4   C3   single    1.486  0.020  1.486
 G1K  C2   C3   double    1.365  0.020  1.365
 G1K  C2   C1   single    1.461  0.020  1.461
 G1K  C3   N1   single    1.365  0.020  1.365
 G1K  O1   C1   double    1.222  0.020  1.222
 G1K  C1   N3   single    1.363  0.020  1.363
 G1K  N1   C5   double    1.279  0.020  1.279
 G1K  N3   C5   single    1.359  0.020  1.359
 G1K  C5   C6   single    1.507  0.020  1.507
 G1K  O6   C10  double    1.220  0.020  1.220
 G1K  C13  C14  aromatic  1.392  0.020  1.392
 G1K  C13  C12  aromatic  1.392  0.020  1.392
 G1K  C14  C15  aromatic  1.385  0.020  1.385
 G1K  O5   C12  single    1.351  0.020  1.351
 G1K  O5   C11  single    1.400  0.020  1.400
 G1K  C10  C11  single    1.518  0.020  1.518
 G1K  C10  N2   single    1.341  0.020  1.341
 G1K  C6   N2   single    1.451  0.020  1.451
 G1K  C6   C7   single    1.538  0.020  1.538
 G1K  C12  C17  aromatic  1.396  0.020  1.396
 G1K  C15  C16  aromatic  1.392  0.020  1.392
 G1K  N2   C9   single    1.457  0.020  1.457
 G1K  C17  C16  aromatic  1.383  0.020  1.383
 G1K  C7   C8   single    1.525  0.020  1.525
 G1K  C9   C8   single    1.521  0.020  1.521
 G1K  C11  H1   single    0.970  0.020  1.090
 G1K  C11  H2   single    0.970  0.020  1.090
 G1K  C13  H3   single    0.930  0.020  1.080
 G1K  C14  H4   single    0.930  0.020  1.080
 G1K  C15  H5   single    0.930  0.020  1.080
 G1K  C16  H6   single    0.930  0.020  1.080
 G1K  C17  H7   single    0.930  0.020  1.080
 G1K  C6   H8   single    0.970  0.020  1.090
 G1K  C7   H9   single    0.970  0.020  1.090
 G1K  C7   H10  single    0.970  0.020  1.090
 G1K  C8   H11  single    0.970  0.020  1.090
 G1K  C8   H12  single    0.970  0.020  1.090
 G1K  C9   H13  single    0.970  0.020  1.090
 G1K  C9   H14  single    0.970  0.020  1.090
 G1K  N3   H15  single    0.860  0.020  1.020
 G1K  O2   H16  single    0.850  0.020  0.980
 G1K  O3   H17  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
 G1K  O1   C1   N3   123.89  3.000
 G1K  N3   C1   C2   114.04  3.000
 G1K  O1   C1   C2   122.07  3.000
 G1K  O6   C10  N2   122.33  3.000
 G1K  N2   C10  C11  115.24  3.000
 G1K  O6   C10  C11  122.43  3.000
 G1K  H2   C11  H1   107.13  3.000
 G1K  H2   C11  O5   111.41  3.000
 G1K  H1   C11  O5   111.54  3.000
 G1K  H2   C11  C10  109.48  3.000
 G1K  H1   C11  C10  109.74  3.000
 G1K  O5   C11  C10  107.54  3.000
 G1K  O5   C12  C17  115.88  3.000
 G1K  C17  C12  C13  119.77  3.000
 G1K  O5   C12  C13  124.35  3.000
 G1K  H3   C13  C14  118.93  3.000
 G1K  H3   C13  C12  121.61  3.000
 G1K  C14  C13  C12  119.46  3.000
 G1K  H4   C14  C15  120.08  3.000
 G1K  H4   C14  C13  118.88  3.000
 G1K  C15  C14  C13  121.04  3.000
 G1K  H5   C15  C16  120.43  3.000
 G1K  H5   C15  C14  120.48  3.000
 G1K  C16  C15  C14  119.10  3.000
 G1K  H6   C16  C17  119.30  3.000
 G1K  H6   C16  C15  120.09  3.000
 G1K  C17  C16  C15  120.61  3.000
 G1K  H7   C17  C16  120.61  3.000
 G1K  H7   C17  C12  119.36  3.000
 G1K  C16  C17  C12  120.03  3.000
 G1K  O2   C2   C3   125.43  3.000
 G1K  C3   C2   C1   118.84  3.000
 G1K  O2   C2   C1   115.73  3.000
 G1K  N1   C3   C4   116.74  3.000
 G1K  N1   C3   C2   122.02  3.000
 G1K  C4   C3   C2   121.24  3.000
 G1K  O4   C4   O3   123.62  3.000
 G1K  O3   C4   C3   112.30  3.000
 G1K  O4   C4   C3   124.08  3.000
 G1K  N3   C5   N1   122.41  3.000
 G1K  N3   C5   C6   117.15  3.000
 G1K  N1   C5   C6   120.39  3.000
 G1K  H8   C6   N2   110.02  3.000
 G1K  H8   C6   C7   110.59  3.000
 G1K  N2   C6   C7   103.70  3.000
 G1K  H8   C6   C5   109.25  3.000
 G1K  C7   C6   C5   112.05  3.000
 G1K  N2   C6   C5   111.13  3.000
 G1K  H10  C7   H9   108.00  3.000
 G1K  H10  C7   C8   113.64  3.000
 G1K  H9   C7   C8   109.98  3.000
 G1K  H10  C7   C6   111.50  3.000
 G1K  H9   C7   C6   109.86  3.000
 G1K  C8   C7   C6   103.81  3.000
 G1K  H12  C8   H11  108.07  3.000
 G1K  H12  C8   C9   109.94  3.000
 G1K  H11  C8   C9   112.31  3.000
 G1K  H12  C8   C7   110.82  3.000
 G1K  H11  C8   C7   112.71  3.000
 G1K  C9   C8   C7   102.96  3.000
 G1K  H14  C9   H13  108.33  3.000
 G1K  H14  C9   N2   111.59  3.000
 G1K  H13  C9   N2   110.83  3.000
 G1K  H14  C9   C8   112.26  3.000
 G1K  H13  C9   C8   111.36  3.000
 G1K  N2   C9   C8   102.44  3.000
 G1K  C5   N1   C3   119.24  3.000
 G1K  C9   N2   C6   112.74  3.000
 G1K  C9   N2   C10  127.21  3.000
 G1K  C6   N2   C10  120.00  3.000
 G1K  H15  N3   C5   119.50  3.000
 G1K  H15  N3   C1   117.06  3.000
 G1K  C5   N3   C1   123.44  3.000
 G1K  H16  O2   C2   108.16  3.000
 G1K  H17  O3   C4   109.08  3.000
 G1K  C12  O5   C11  118.29  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
 G1K  CONST_01  C15  C14  C13  C12     0.00   0.0  0
 G1K  CONST_02  C15  C16  C17  C12     0.00   0.0  0
 G1K  CONST_03  C16  C15  C14  C13     0.00   0.0  0
 G1K  CONST_04  C16  C17  C12  C13     0.00   0.0  0
 G1K  CONST_05  C17  C12  C13  C14     0.00   0.0  0
 G1K  CONST_06  C17  C16  C15  C14     0.00   0.0  0
 G1K  CONST_07  N1   C5   N3   C1      0.00   0.0  0
 G1K  CONST_08  C6   C5   N3   C1    180.00   0.0  0
 G1K  CONST_09  C5   N3   C1   C2      0.00   0.0  0
 G1K  CONST_10  N3   C5   N1   C3      0.00   0.0  0
 G1K  CONST_11  C6   C5   N1   C3    180.00   0.0  0
 G1K  CONST_12  O5   C12  C13  C14   180.00   0.0  0
 G1K  CONST_13  O5   C12  C17  C16   180.00   0.0  0
 G1K  CONST_14  O1   C1   N3   C5    180.00   0.0  0
 G1K  CONST_15  H4   C14  C13  C12   180.00   0.0  0
 G1K  CONST_16  H6   C16  C17  C12   180.00   0.0  0
 G1K  CONST_17  H5   C15  C14  C13   180.00   0.0  0
 G1K  CONST_18  H7   C17  C12  C13   180.00   0.0  0
 G1K  CONST_19  H3   C13  C14  C15   180.00   0.0  0
 G1K  CONST_20  H15  N3   C1   C2    180.00   0.0  0
 G1K  CONST_21  C6   N2   C10  C11   180.00   0.0  0
 G1K  CONST_22  C9   N2   C10  C11     0.00   0.0  0
 G1K  CONST_23  O6   C10  N2   C6      0.00   0.0  0
 G1K  CONST_24  O6   C10  N2   C9    180.00   0.0  0
 G1K  CONST_25  H17  O3   C4   C3    180.00   0.0  0
 G1K  Var_01    C8   C9   N2   C6     21.90  30.0  1
 G1K  Var_02    C9   C8   C7   C6     36.64  30.0  1
 G1K  Var_03    N2   C9   C8   C7    -35.45  30.0  1
 G1K  Var_04    C13  C12  O5   C11    -0.02  30.0  2
 G1K  Var_05    O4   C4   C3   C2      0.13  30.0  2
 G1K  Var_06    O5   C11  C10  N2   -175.76  30.0  3
 G1K  Var_07    H1   C11  O5   C12    60.07  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
 G1K  chir_01  C6  C5  N2  C7  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
 G1K  plan-1  C12  0.020
 G1K  plan-1  C13  0.020
 G1K  plan-1  C14  0.020
 G1K  plan-1  C15  0.020
 G1K  plan-1  C16  0.020
 G1K  plan-1  C17  0.020
 G1K  plan-1  O5   0.020
 G1K  plan-1  H3   0.020
 G1K  plan-1  H4   0.020
 G1K  plan-1  H5   0.020
 G1K  plan-1  H6   0.020
 G1K  plan-1  H7   0.020
 G1K  plan-2  C1   0.020
 G1K  plan-2  C2   0.020
 G1K  plan-2  C3   0.020
 G1K  plan-2  C4   0.020
 G1K  plan-2  C5   0.020
 G1K  plan-2  C6   0.020
 G1K  plan-2  N1   0.020
 G1K  plan-2  N3   0.020
 G1K  plan-2  O1   0.020
 G1K  plan-2  O2   0.020
 G1K  plan-2  H15  0.020
 G1K  plan-3  C10  0.020
 G1K  plan-3  C11  0.020
 G1K  plan-3  C6   0.020
 G1K  plan-3  C9   0.020
 G1K  plan-3  N2   0.020
 G1K  plan-3  O6   0.020
 G1K  plan-4  C3   0.020
 G1K  plan-4  C4   0.020
 G1K  plan-4  O3   0.020
 G1K  plan-4  O4   0.020
 G1K  plan-4  H17  0.020

