# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 05:10:05 2022
#   Inital geometry file: a 128 line input string
#   Ligand name: 2-{(2R)-1-[2-(4-chlorophenoxy)-2-methylpropanoyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(Cl)cc1)C(=O)N2CCC[C@@H]2C3=NC(=C(O)C(=O)N3)C(O)=O
#
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
 G3K  G3K  '2-{(2R)-1-[2-(4-chlorophenoxy)-2-methylpropanoyl]pyrrolidin-2-yl}-5-hydroxy-6-oxo-1,6-dihydropyrimidine-4-carboxylic acid'  ligand  48  29  .  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_G3K
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
 G3K  C1   C   CR6    0   0.449   3.6344   1.4285  -1.4178
 G3K  C10  C   C      0   0.554  -0.2893  -1.0465   0.0445
 G3K  C11  C   CT     0   0.093  -1.1563  -1.2566   1.3070
 G3K  C12  C   CH3    0  -0.714  -1.9703  -2.5439   1.4617
 G3K  C13  C   CH3    0  -0.667  -0.1817  -1.1273   2.4807
 G3K  C14  C   CR6    0   0.406  -3.0440   0.0897   0.5836
 G3K  C15  C   CR16   0  -0.360  -3.9414   1.0812   0.9851
 G3K  C16  C   CR16   0  -0.198  -5.0377   1.4076   0.2073
 G3K  C17  C   CR6    0  -0.066  -5.2514   0.7356  -0.9867
 G3K  C18  C   CR16   0  -0.206  -4.3733  -0.2496  -1.4004
 G3K  C19  C   CR16   0  -0.359  -3.2702  -0.5721  -0.6215
 G3K  C2   C   CR6    0   0.185   3.9954   1.4764  -0.0254
 G3K  C3   C   CR6    0  -0.001   3.5144   0.5406   0.8386
 G3K  C4   C   C      0   0.378   3.8155   0.5888   2.3280
 G3K  C5   C   CR6    0   0.504   2.3928  -0.5418  -0.8249
 G3K  C6   C   CH1    0  -0.133   1.5617  -1.6859  -1.3451
 G3K  C7   C   CH2    0  -0.473   2.3759  -2.9782  -1.4619
 G3K  C8   C   CH2    0  -0.477   1.3329  -4.0604  -1.2319
 G3K  C9   C   CH2    0  -0.281   0.4629  -3.4703  -0.1303
 G3K  N1   N   N      0  -0.418   2.7207  -0.4854   0.4168
 G3K  N2   N   NT     0  -0.490   0.4963  -2.0370  -0.4149
 G3K  N3   N   NR16   0  -0.691   2.8178   0.3700  -1.7307
 G3K  O1   O   O      0  -0.503   4.0066   2.2477  -2.2548
 G3K  O2   O   OH1    0  -0.626   4.7807   2.4932   0.3802
 G3K  O3   O   OC    -1  -0.577   2.8252   0.7259   3.0649
 G3K  O4   O   O      0  -0.593   5.0094   0.4798   2.6518
 G3K  O5   O   O2     0  -0.482  -2.0141  -0.1268   1.4244
 G3K  O6   O   O      0  -0.474  -0.2238   0.0714  -0.4441
 G3K  CL1  CL  CL     0  -0.142  -6.6293   1.1319  -1.9655
 G3K  H1   H   HCH3   0   0.260  -1.3443  -3.3646   1.8037
 G3K  H2   H   HCH3   0   0.269  -2.7183  -2.3782   2.2377
 G3K  H3   H   HCH3   0   0.253  -2.4885  -2.8671   0.5610
 G3K  H4   H   HCH3   0   0.267   0.4190  -0.2209   2.4233
 G3K  H5   H   HCH3   0   0.246  -0.7358  -1.1335   3.4205
 G3K  H6   H   HCH3   0   0.235   0.5075  -1.9705   2.4922
 G3K  H7   H   HCR6   0   0.272  -3.7761   1.6001   1.9207
 G3K  H8   H   HCR6   0   0.279  -5.7217   2.1769   0.5392
 G3K  H9   H   HCR6   0   0.281  -4.5339  -0.7744  -2.3323
 G3K  H10  H   HCR6   0   0.281  -2.6137  -1.3467  -0.9892
 G3K  H11  H   HCH1   0   0.284   1.1448  -1.4158  -2.3215
 G3K  H12  H   HCH2   0   0.268   2.8805  -3.0496  -2.4239
 G3K  H13  H   HCH2   0   0.255   3.1343  -3.0141  -0.6767
 G3K  H14  H   HCH2   0   0.248   0.7392  -4.2187  -2.1342
 G3K  H15  H   HCH2   0   0.262   1.7658  -5.0163  -0.9412
 G3K  H16  H   HCH2   0   0.268  -0.5500  -3.8595  -0.1730
 G3K  H17  H   HCH2   0   0.245   0.8786  -3.6914   0.8567
 G3K  H18  H   HNR6   0   0.426   2.5089   0.2981  -2.6926
 G3K  H19  H   HOH1   0   0.465   4.9706   3.0550  -0.3838

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
 G3K  C13  C11  single    1.531  0.020  1.531
 G3K  O1   C1   double    1.229  0.020  1.229
 G3K  C12  C11  single    1.531  0.020  1.531
 G3K  C19  C18  aromatic  1.388  0.020  1.388
 G3K  C19  C14  aromatic  1.393  0.020  1.393
 G3K  O5   C11  single    1.423  0.020  1.423
 G3K  O5   C14  single    1.347  0.020  1.347
 G3K  C11  C10  single    1.546  0.020  1.546
 G3K  C18  C17  aromatic  1.383  0.020  1.383
 G3K  C14  C15  aromatic  1.396  0.020  1.396
 G3K  C1   N3   single    1.373  0.020  1.373
 G3K  C1   C2   single    1.439  0.020  1.439
 G3K  O2   C2   single    1.347  0.020  1.347
 G3K  N3   C5   single    1.354  0.020  1.354
 G3K  C2   C3   double    1.361  0.020  1.361
 G3K  C10  O6   double    1.222  0.020  1.222
 G3K  C10  N2   single    1.345  0.020  1.345
 G3K  C17  CL1  single    1.736  0.020  1.736
 G3K  C17  C16  aromatic  1.387  0.020  1.387
 G3K  C9   N2   single    1.462  0.020  1.462
 G3K  C9   C8   single    1.523  0.020  1.523
 G3K  C15  C16  aromatic  1.383  0.020  1.383
 G3K  N2   C6   single    1.457  0.020  1.457
 G3K  C5   N1   double    1.285  0.020  1.285
 G3K  C5   C6   single    1.507  0.020  1.507
 G3K  C3   N1   single    1.364  0.020  1.364
 G3K  C3   C4   single    1.520  0.020  1.520
 G3K  C8   C7   single    1.520  0.020  1.520
 G3K  O4   C4   deloc     1.242  0.020  1.242
 G3K  C6   C7   single    1.532  0.020  1.532
 G3K  C4   O3   deloc     1.242  0.020  1.242
 G3K  C12  H1   single    0.970  0.020  1.090
 G3K  C12  H2   single    0.970  0.020  1.090
 G3K  C12  H3   single    0.970  0.020  1.090
 G3K  C13  H4   single    0.970  0.020  1.090
 G3K  C13  H5   single    0.970  0.020  1.090
 G3K  C13  H6   single    0.970  0.020  1.090
 G3K  C15  H7   single    0.930  0.020  1.080
 G3K  C16  H8   single    0.930  0.020  1.080
 G3K  C18  H9   single    0.930  0.020  1.080
 G3K  C19  H10  single    0.930  0.020  1.080
 G3K  C6   H11  single    0.970  0.020  1.090
 G3K  C7   H12  single    0.970  0.020  1.090
 G3K  C7   H13  single    0.970  0.020  1.090
 G3K  C8   H14  single    0.970  0.020  1.090
 G3K  C8   H15  single    0.970  0.020  1.090
 G3K  C9   H16  single    0.970  0.020  1.090
 G3K  C9   H17  single    0.970  0.020  1.090
 G3K  N3   H18  single    0.860  0.020  1.020
 G3K  O2   H19  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
 G3K  O1   C1   N3   122.60  3.000
 G3K  N3   C1   C2   113.28  3.000
 G3K  O1   C1   C2   124.11  3.000
 G3K  O6   C10  N2   120.39  3.000
 G3K  N2   C10  C11  120.42  3.000
 G3K  O6   C10  C11  118.75  3.000
 G3K  O5   C11  C13  104.68  3.000
 G3K  O5   C11  C12  109.80  3.000
 G3K  C13  C11  C12  109.39  3.000
 G3K  O5   C11  C10  107.31  3.000
 G3K  C12  C11  C10  119.67  3.000
 G3K  C13  C11  C10  104.92  3.000
 G3K  H3   C12  H2   107.90  3.000
 G3K  H3   C12  H1   108.07  3.000
 G3K  H2   C12  H1   106.60  3.000
 G3K  H3   C12  C11  114.79  3.000
 G3K  H2   C12  C11  107.99  3.000
 G3K  H1   C12  C11  111.13  3.000
 G3K  H6   C13  H5   107.93  3.000
 G3K  H6   C13  H4   107.21  3.000
 G3K  H5   C13  H4   109.29  3.000
 G3K  H6   C13  C11  110.21  3.000
 G3K  H5   C13  C11  109.67  3.000
 G3K  H4   C13  C11  112.40  3.000
 G3K  O5   C14  C19  125.99  3.000
 G3K  O5   C14  C15  115.22  3.000
 G3K  C19  C14  C15  118.80  3.000
 G3K  H7   C15  C16  119.59  3.000
 G3K  H7   C15  C14  119.39  3.000
 G3K  C16  C15  C14  121.01  3.000
 G3K  H8   C16  C17  120.76  3.000
 G3K  H8   C16  C15  119.77  3.000
 G3K  C17  C16  C15  119.47  3.000
 G3K  CL1  C17  C18  119.86  3.000
 G3K  CL1  C17  C16  119.82  3.000
 G3K  C18  C17  C16  120.32  3.000
 G3K  H9   C18  C19  119.25  3.000
 G3K  H9   C18  C17  120.60  3.000
 G3K  C19  C18  C17  120.14  3.000
 G3K  H10  C19  C18  117.30  3.000
 G3K  H10  C19  C14  122.45  3.000
 G3K  C18  C19  C14  120.25  3.000
 G3K  O2   C2   C3   122.26  3.000
 G3K  C3   C2   C1   120.16  3.000
 G3K  O2   C2   C1   117.55  3.000
 G3K  N1   C3   C4   116.23  3.000
 G3K  C4   C3   C2   122.00  3.000
 G3K  N1   C3   C2   121.76  3.000
 G3K  O4   C4   O3   128.44  3.000
 G3K  O3   C4   C3   115.26  3.000
 G3K  O4   C4   C3   116.30  3.000
 G3K  N3   C5   N1   122.46  3.000
 G3K  N1   C5   C6   120.50  3.000
 G3K  N3   C5   C6   116.97  3.000
 G3K  H11  C6   N2   110.49  3.000
 G3K  H11  C6   C7   110.02  3.000
 G3K  N2   C6   C7   103.53  3.000
 G3K  H11  C6   C5   109.29  3.000
 G3K  C7   C6   C5   111.94  3.000
 G3K  N2   C6   C5   111.46  3.000
 G3K  H13  C7   H12  108.14  3.000
 G3K  H13  C7   C8   110.13  3.000
 G3K  H12  C7   C8   113.88  3.000
 G3K  H13  C7   C6   110.00  3.000
 G3K  H12  C7   C6   111.66  3.000
 G3K  C8   C7   C6   102.96  3.000
 G3K  H15  C8   H14  108.03  3.000
 G3K  H15  C8   C9   111.98  3.000
 G3K  H14  C8   C9   110.09  3.000
 G3K  H15  C8   C7   113.11  3.000
 G3K  H14  C8   C7   110.57  3.000
 G3K  C9   C8   C7   103.03  3.000
 G3K  H17  C9   H16  108.51  3.000
 G3K  H17  C9   N2   111.43  3.000
 G3K  H16  C9   N2   111.41  3.000
 G3K  H17  C9   C8   110.94  3.000
 G3K  H16  C9   C8   111.44  3.000
 G3K  N2   C9   C8   103.07  3.000
 G3K  C5   N1   C3   118.69  3.000
 G3K  C9   N2   C6   112.16  3.000
 G3K  C6   N2   C10  117.88  3.000
 G3K  C9   N2   C10  129.96  3.000
 G3K  H18  N3   C5   119.47  3.000
 G3K  H18  N3   C1   116.91  3.000
 G3K  C5   N3   C1   123.61  3.000
 G3K  H19  O2   C2   108.37  3.000
 G3K  C14  O5   C11  122.47  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
 G3K  CONST_01  C17  C18  C19  C14    0.00   0.0  0
 G3K  CONST_02  C17  C16  C15  C14    0.00   0.0  0
 G3K  CONST_03  C18  C19  C14  C15    0.00   0.0  0
 G3K  CONST_04  C18  C17  C16  C15    0.00   0.0  0
 G3K  CONST_05  C19  C18  C17  C16    0.00   0.0  0
 G3K  CONST_06  C19  C14  C15  C16    0.00   0.0  0
 G3K  CONST_07  N1   C5   N3   C1     0.00   0.0  0
 G3K  CONST_08  C6   C5   N3   C1   180.00   0.0  0
 G3K  CONST_09  C5   N3   C1   C2     0.00   0.0  0
 G3K  CONST_10  N3   C5   N1   C3     0.00   0.0  0
 G3K  CONST_11  C6   C5   N1   C3   180.00   0.0  0
 G3K  CONST_12  CL1  C17  C16  C15  180.00   0.0  0
 G3K  CONST_13  O5   C14  C15  C16  180.00   0.0  0
 G3K  CONST_14  O5   C14  C19  C18  180.00   0.0  0
 G3K  CONST_15  CL1  C17  C18  C19  180.00   0.0  0
 G3K  CONST_16  O1   C1   N3   C5   180.00   0.0  0
 G3K  CONST_17  H9   C18  C19  C14  180.00   0.0  0
 G3K  CONST_18  H8   C16  C15  C14  180.00   0.0  0
 G3K  CONST_19  H10  C19  C14  C15  180.00   0.0  0
 G3K  CONST_20  H7   C15  C16  C17  180.00   0.0  0
 G3K  CONST_21  H18  N3   C1   C2   180.00   0.0  0
 G3K  CONST_24  O6   C10  N2   C6     0.00   0.0  0
 G3K  CONST_25  O6   C10  N2   C9   180.00   0.0  0
 G3K  Var_01    C8   C9   N2   C6   -14.99  30.0  1
 G3K  Var_02    C9   C8   C7   C6   -39.14  30.0  1
 G3K  Var_03    N2   C9   C8   C7    33.21  30.0  1
 G3K  Var_04    C19  C14  O5   C11  -12.68  30.0  2
 G3K  Var_05    O4   C4   C3   C2   -62.70  30.0  2
 G3K  Var_06    N2   C10  C11  C12  -45.53  30.0  3
 G3K  Var_07    H4   C13  C11  C10   50.87  30.0  3
 G3K  Var_08    H1   C12  C11  C10   79.92  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
 G3K  chir_01  C6  N2  C5  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
 G3K  plan-1  C1   0.020
 G3K  plan-1  C2   0.020
 G3K  plan-1  C3   0.020
 G3K  plan-1  C4   0.020
 G3K  plan-1  C5   0.020
 G3K  plan-1  C6   0.020
 G3K  plan-1  N1   0.020
 G3K  plan-1  N3   0.020
 G3K  plan-1  O1   0.020
 G3K  plan-1  O2   0.020
 G3K  plan-1  H18  0.020
 G3K  plan-2  C14  0.020
 G3K  plan-2  C15  0.020
 G3K  plan-2  C16  0.020
 G3K  plan-2  C17  0.020
 G3K  plan-2  C18  0.020
 G3K  plan-2  C19  0.020
 G3K  plan-2  O5   0.020
 G3K  plan-2  CL1  0.020
 G3K  plan-2  H7   0.020
 G3K  plan-2  H8   0.020
 G3K  plan-2  H9   0.020
 G3K  plan-2  H10  0.020
 G3K  plan-3  C10  0.020
 G3K  plan-3  C11  0.020
 G3K  plan-3  C6   0.020
 G3K  plan-3  C9   0.020
 G3K  plan-3  N2   0.020
 G3K  plan-3  O6   0.020
 G3K  plan-4  C3   0.020
 G3K  plan-4  C4   0.020
 G3K  plan-4  O3   0.020
 G3K  plan-4  O4   0.020

