# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 20:22:36 2022
#   Inital geometry file: a 148 line input string
#   Ligand name: 2-[(2S)-1-(2,6-difluorobenzene-1-carbonyl)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)c3c(F)cccc3F)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
 GY7  GY7  2-[(2S)-1-(2,6-difluorobenzene-1-carbonyl)pyrrolidin-2-yl]-5-hydroxy-6-oxo-N-(2-phenylethyl)-1,6-dihydropyrimidine-4-carboxamide  ligand  56  34  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GY7
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
 GY7  C1   C  CR6   0   0.593    5.4536  -0.2536  -0.7340
 GY7  C10  C  CR6   0   0.124   -6.2635  -1.2379   0.6641
 GY7  C11  C  CR16  0  -0.304   -6.8501  -2.0315  -0.3195
 GY7  C12  C  CR16  0  -0.240   -8.2149  -2.2853  -0.3080
 GY7  C13  C  CR16  0  -0.271   -9.0157  -1.7468   0.6912
 GY7  C14  C  CR16  0  -0.240   -8.4419  -0.9541   1.6766
 GY7  C15  C  CR16  0  -0.307   -7.0762  -0.7025   1.6603
 GY7  C16  C  CR6   0   0.235   -0.3781   2.6934  -1.4627
 GY7  C17  C  CR6   0   0.484    1.0545   2.8011  -1.2001
 GY7  C18  C  CH2   0  -0.476    1.5004   0.5982   2.6426
 GY7  C19  C  CH2   0  -0.477    2.7268  -0.0839   3.2355
 GY7  C2   C  CR6   0  -0.463    4.5312  -1.2537  -0.4752
 GY7  C20  C  CH2   0  -0.276    3.6910  -0.1396   2.0594
 GY7  C21  C  CR6   0   0.570    4.9913  -2.5592  -0.5358
 GY7  C22  C  CR16  0  -0.418    6.3040  -2.8741  -0.8207
 GY7  C23  C  CR16  0  -0.224    7.1902  -1.8355  -1.0703
 GY7  C24  C  CR16  0  -0.415    6.7752  -0.5118  -1.0316
 GY7  C3   C  C     0   0.539    3.0844  -0.9520  -0.2366
 GY7  C4   C  CH1   0  -0.139    1.4066  -0.0163   1.2386
 GY7  C5   C  CR6   0   0.510    0.7638   0.9091   0.2461
 GY7  C6   C  CR6   0  -0.004   -1.0912   1.7160  -0.8366
 GY7  C7   C  C     0   0.550   -2.5676   1.5480  -1.0167
 GY7  C8   C  CH2   0  -0.229   -4.5084   0.2577  -0.2888
 GY7  C9   C  CH2   0  -0.563   -4.7930  -0.9302   0.6246
 GY7  F1   F  F     0  -0.302    5.0243   1.0162  -0.6983
 GY7  F2   F  F     0  -0.293    4.1195  -3.5399  -0.2817
 GY7  N1   N  NT    0  -0.496    2.7938  -0.3219   0.9139
 GY7  N2   N  N     0  -0.474   -0.4923   0.8234   0.0123
 GY7  N3   N  NH1   0  -0.661   -3.0942   0.5551  -0.2914
 GY7  N4   N  NR16  0  -0.681    1.5358   1.8703  -0.3245
 GY7  O1   O  O     0  -0.450    2.2363  -1.2426  -1.0625
 GY7  O2   O  O     0  -0.483   -3.2255   2.2661  -1.7571
 GY7  O4   O  O     0  -0.468    1.7517   3.6567  -1.7223
 GY7  H1   H  HCR6  0   0.249   -6.2317  -2.4600  -1.0999
 GY7  H2   H  HCR6  0   0.254   -8.6537  -2.9060  -1.0789
 GY7  H3   H  HCR6  0   0.255  -10.0793  -1.9471   0.7039
 GY7  H4   H  HCR6  0   0.254   -9.0572  -0.5321   2.4610
 GY7  H5   H  HCR6  0   0.248   -6.6343  -0.0875   2.4360
 GY7  H6   H  HCH2  0   0.279    0.5874   0.4292   3.2098
 GY7  H7   H  HCH2  0   0.259    1.6622   1.6768   2.5798
 GY7  H8   H  HCH2  0   0.268    3.1439   0.4597   4.0812
 GY7  H9   H  HCH2  0   0.254    2.4794  -1.0935   3.5683
 GY7  H10  H  HCH2  0   0.257    4.2519   0.7931   1.9690
 GY7  H11  H  HCH2  0   0.275    4.4028  -0.9594   2.1359
 GY7  H12  H  HCR6  0   0.293    6.6249  -3.9065  -0.8485
 GY7  H13  H  HCR6  0   0.289    8.2223  -2.0619  -1.2987
 GY7  H14  H  HCR6  0   0.294    7.4608   0.3003  -1.2308
 GY7  H15  H  HCH1  0   0.304    0.8044  -0.9281   1.2589
 GY7  H16  H  HCH2  0   0.241   -4.8473   0.0336  -1.3040
 GY7  H17  H  HCH2  0   0.241   -5.0771   1.1284   0.0513
 GY7  H18  H  HCH2  0   0.258   -4.4338  -0.7056   1.6322
 GY7  H19  H  HCH2  0   0.259   -4.2353  -1.8011   0.2698
 GY7  H20  H  HNH1  0   0.410   -2.4721   0.0304   0.3053
 GY7  H21  H  HNR6  0   0.420    2.5266   1.9076  -0.1138
 GY7  H22  H  HOH1  0   0.475   -0.1508   4.1654  -2.5959
 GY7  O3   O  OH1   0  -0.588   -0.8749   3.5852  -2.3114

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
 GY7  F2   C21  single    1.337  0.020  1.337
 GY7  C22  C21  aromatic  1.380  0.020  1.380
 GY7  C22  C23  aromatic  1.388  0.020  1.388
 GY7  C21  C2   aromatic  1.386  0.020  1.386
 GY7  C23  C24  aromatic  1.388  0.020  1.388
 GY7  O1   C3   double    1.219  0.020  1.219
 GY7  C2   C3   single    1.497  0.020  1.497
 GY7  C2   C1   aromatic  1.385  0.020  1.385
 GY7  C3   N1   single    1.344  0.020  1.344
 GY7  C24  C1   aromatic  1.379  0.020  1.379
 GY7  C1   F1   single    1.341  0.020  1.341
 GY7  N1   C4   single    1.457  0.020  1.457
 GY7  N1   C20  single    1.466  0.020  1.466
 GY7  C4   C18  single    1.535  0.020  1.535
 GY7  C4   C5   single    1.502  0.020  1.502
 GY7  C20  C19  single    1.522  0.020  1.522
 GY7  N4   C5   single    1.358  0.020  1.358
 GY7  N4   C17  single    1.365  0.020  1.365
 GY7  C18  C19  single    1.523  0.020  1.523
 GY7  C5   N2   double    1.281  0.020  1.281
 GY7  O4   C17  double    1.221  0.020  1.221
 GY7  C17  C16  single    1.460  0.020  1.460
 GY7  N2   C6   single    1.370  0.020  1.370
 GY7  C16  C6   double    1.362  0.020  1.362
 GY7  C16  O3   single    1.328  0.020  1.328
 GY7  C6   C7   single    1.497  0.020  1.497
 GY7  C14  C13  aromatic  1.389  0.020  1.389
 GY7  C14  C15  aromatic  1.389  0.020  1.389
 GY7  C13  C12  aromatic  1.389  0.020  1.389
 GY7  C15  C10  aromatic  1.393  0.020  1.393
 GY7  N3   C7   single    1.338  0.020  1.338
 GY7  N3   C8   single    1.445  0.020  1.445
 GY7  C7   O2   double    1.223  0.020  1.223
 GY7  C12  C11  aromatic  1.388  0.020  1.388
 GY7  C8   C9   single    1.525  0.020  1.525
 GY7  C10  C11  aromatic  1.393  0.020  1.393
 GY7  C10  C9   single    1.503  0.020  1.503
 GY7  C11  H1   single    0.930  0.020  1.080
 GY7  C12  H2   single    0.930  0.020  1.080
 GY7  C13  H3   single    0.930  0.020  1.080
 GY7  C14  H4   single    0.930  0.020  1.080
 GY7  C15  H5   single    0.930  0.020  1.080
 GY7  C18  H6   single    0.970  0.020  1.090
 GY7  C18  H7   single    0.970  0.020  1.090
 GY7  C19  H8   single    0.970  0.020  1.090
 GY7  C19  H9   single    0.970  0.020  1.090
 GY7  C20  H10  single    0.970  0.020  1.090
 GY7  C20  H11  single    0.970  0.020  1.090
 GY7  C22  H12  single    0.930  0.020  1.080
 GY7  C23  H13  single    0.930  0.020  1.080
 GY7  C24  H14  single    0.930  0.020  1.080
 GY7  C4   H15  single    0.970  0.020  1.090
 GY7  C8   H16  single    0.970  0.020  1.090
 GY7  C8   H17  single    0.970  0.020  1.090
 GY7  C9   H18  single    0.970  0.020  1.090
 GY7  C9   H19  single    0.970  0.020  1.090
 GY7  N3   H20  single    0.860  0.020  1.020
 GY7  N4   H21  single    0.860  0.020  1.020
 GY7  O3   H22  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
 GY7  F1   C1   C24  119.33  3.000
 GY7  F1   C1   C2   117.75  3.000
 GY7  C24  C1   C2   122.92  3.000
 GY7  C9   C10  C15  120.74  3.000
 GY7  C9   C10  C11  120.66  3.000
 GY7  C15  C10  C11  118.57  3.000
 GY7  H1   C11  C12  119.63  3.000
 GY7  H1   C11  C10  119.55  3.000
 GY7  C12  C11  C10  120.81  3.000
 GY7  H2   C12  C13  120.05  3.000
 GY7  H2   C12  C11  119.83  3.000
 GY7  C13  C12  C11  120.12  3.000
 GY7  H3   C13  C14  120.22  3.000
 GY7  H3   C13  C12  120.21  3.000
 GY7  C14  C13  C12  119.57  3.000
 GY7  H4   C14  C15  119.78  3.000
 GY7  H4   C14  C13  120.12  3.000
 GY7  C15  C14  C13  120.10  3.000
 GY7  H5   C15  C14  119.69  3.000
 GY7  H5   C15  C10  119.48  3.000
 GY7  C14  C15  C10  120.83  3.000
 GY7  O3   C16  C6   125.44  3.000
 GY7  O3   C16  C17  115.63  3.000
 GY7  C6   C16  C17  118.93  3.000
 GY7  O4   C17  N4   123.41  3.000
 GY7  O4   C17  C16  122.33  3.000
 GY7  N4   C17  C16  114.26  3.000
 GY7  H7   C18  H6   107.92  3.000
 GY7  H7   C18  C4   110.58  3.000
 GY7  H6   C18  C4   111.30  3.000
 GY7  H7   C18  C19  110.19  3.000
 GY7  H6   C18  C19  113.77  3.000
 GY7  C4   C18  C19  103.05  3.000
 GY7  H9   C19  H8   108.18  3.000
 GY7  H9   C19  C20  110.21  3.000
 GY7  H8   C19  C20  112.09  3.000
 GY7  H9   C19  C18  110.51  3.000
 GY7  H8   C19  C18  112.78  3.000
 GY7  C20  C19  C18  103.04  3.000
 GY7  C3   C2   C21  121.19  3.000
 GY7  C3   C2   C1   121.87  3.000
 GY7  C21  C2   C1   116.81  3.000
 GY7  H11  C20  H10  108.25  3.000
 GY7  H11  C20  N1   111.19  3.000
 GY7  H10  C20  N1   110.84  3.000
 GY7  H11  C20  C19  112.80  3.000
 GY7  H10  C20  C19  110.98  3.000
 GY7  N1   C20  C19  102.74  3.000
 GY7  F2   C21  C22  119.50  3.000
 GY7  C22  C21  C2   122.69  3.000
 GY7  F2   C21  C2   117.80  3.000
 GY7  H12  C22  C23  121.35  3.000
 GY7  H12  C22  C21  120.37  3.000
 GY7  C23  C22  C21  118.28  3.000
 GY7  H13  C23  C24  119.41  3.000
 GY7  H13  C23  C22  119.40  3.000
 GY7  C24  C23  C22  121.19  3.000
 GY7  H14  C24  C23  121.44  3.000
 GY7  H14  C24  C1   120.45  3.000
 GY7  C23  C24  C1   118.11  3.000
 GY7  O1   C3   N1   122.79  3.000
 GY7  N1   C3   C2   116.11  3.000
 GY7  O1   C3   C2   121.09  3.000
 GY7  H15  C4   N1   110.72  3.000
 GY7  H15  C4   C5   106.89  3.000
 GY7  N1   C4   C5   112.92  3.000
 GY7  H15  C4   C18  110.52  3.000
 GY7  C5   C4   C18  112.58  3.000
 GY7  N1   C4   C18  103.27  3.000
 GY7  N4   C5   N2   121.88  3.000
 GY7  N2   C5   C4   119.95  3.000
 GY7  N4   C5   C4   118.06  3.000
 GY7  N2   C6   C7   115.64  3.000
 GY7  C7   C6   C16  122.79  3.000
 GY7  N2   C6   C16  121.57  3.000
 GY7  O2   C7   N3   123.51  3.000
 GY7  O2   C7   C6   122.51  3.000
 GY7  N3   C7   C6   113.98  3.000
 GY7  H17  C8   H16  106.89  3.000
 GY7  H17  C8   N3   110.21  3.000
 GY7  H16  C8   N3   110.11  3.000
 GY7  H17  C8   C9   109.67  3.000
 GY7  H16  C8   C9   109.79  3.000
 GY7  N3   C8   C9   110.12  3.000
 GY7  H19  C9   H18  107.17  3.000
 GY7  H19  C9   C8   109.32  3.000
 GY7  H18  C9   C8   109.31  3.000
 GY7  H19  C9   C10  110.16  3.000
 GY7  H18  C9   C10  109.84  3.000
 GY7  C8   C9   C10  110.96  3.000
 GY7  C4   N1   C3   119.68  3.000
 GY7  C4   N1   C20  112.48  3.000
 GY7  C3   N1   C20  126.50  3.000
 GY7  C6   N2   C5   119.89  3.000
 GY7  H20  N3   C8   119.68  3.000
 GY7  H20  N3   C7   117.64  3.000
 GY7  C8   N3   C7   122.62  3.000
 GY7  H21  N4   C5   119.62  3.000
 GY7  H21  N4   C17  116.92  3.000
 GY7  C5   N4   C17  123.46  3.000
 GY7  H22  O3   C16  108.04  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
 GY7  CONST_01  C22  C21  C2   C1      0.00   0.0  0
 GY7  CONST_02  C22  C23  C24  C1      0.00   0.0  0
 GY7  CONST_03  C13  C14  C15  C10     0.00   0.0  0
 GY7  CONST_04  C13  C12  C11  C10     0.00   0.0  0
 GY7  CONST_05  C14  C13  C12  C11     0.00   0.0  0
 GY7  CONST_06  C14  C15  C10  C11     0.00   0.0  0
 GY7  CONST_07  C15  C14  C13  C12     0.00   0.0  0
 GY7  CONST_08  C15  C10  C11  C12     0.00   0.0  0
 GY7  CONST_09  C23  C22  C21  C2      0.00   0.0  0
 GY7  CONST_10  C23  C24  C1   C2      0.00   0.0  0
 GY7  CONST_11  C24  C23  C22  C21     0.00   0.0  0
 GY7  CONST_12  C24  C1   C2   C21     0.00   0.0  0
 GY7  CONST_13  C5   N4   C17  C16     0.00   0.0  0
 GY7  CONST_14  C4   C5   N4   C17   180.00   0.0  0
 GY7  CONST_15  N2   C5   N4   C17     0.00   0.0  0
 GY7  CONST_16  C6   N2   C5   C4    180.00   0.0  0
 GY7  CONST_17  N4   C5   N2   C6      0.00   0.0  0
 GY7  CONST_18  F2   C21  C2   C1    180.00   0.0  0
 GY7  CONST_19  C9   C10  C11  C12   180.00   0.0  0
 GY7  CONST_20  C9   C10  C15  C14   180.00   0.0  0
 GY7  CONST_21  F1   C1   C2   C21   180.00   0.0  0
 GY7  CONST_22  C3   C2   C21  C22   180.00   0.0  0
 GY7  CONST_23  F2   C21  C22  C23   180.00   0.0  0
 GY7  CONST_24  F1   C1   C24  C23   180.00   0.0  0
 GY7  CONST_25  C3   C2   C1   C24   180.00   0.0  0
 GY7  CONST_26  C4   N1   C3   C2    180.00   0.0  0
 GY7  CONST_27  C20  N1   C3   C2      0.00   0.0  0
 GY7  CONST_28  O4   C17  N4   C5    180.00   0.0  0
 GY7  CONST_29  H13  C23  C24  C1    180.00   0.0  0
 GY7  CONST_30  H4   C14  C15  C10   180.00   0.0  0
 GY7  CONST_31  H2   C12  C11  C10   180.00   0.0  0
 GY7  CONST_32  H3   C13  C12  C11   180.00   0.0  0
 GY7  CONST_33  H5   C15  C10  C11   180.00   0.0  0
 GY7  CONST_34  H1   C11  C12  C13   180.00   0.0  0
 GY7  CONST_35  H12  C22  C21  C2    180.00   0.0  0
 GY7  CONST_36  H14  C24  C1   C2    180.00   0.0  0
 GY7  CONST_37  H21  N4   C17  C16   180.00   0.0  0
 GY7  CONST_38  O1   C3   N1   C20   180.00   0.0  0
 GY7  CONST_39  O1   C3   N1   C4      0.00   0.0  0
 GY7  CONST_40  C8   N3   C7   C6    180.00   0.0  0
 GY7  CONST_41  H20  N3   C7   C6      0.00   0.0  0
 GY7  CONST_42  O2   C7   N3   C8      0.00   0.0  0
 GY7  Var_01    N1   C20  C19  C18   -33.68  30.0  1
 GY7  Var_02    C4   N1   C20  C19    15.75  30.0  1
 GY7  Var_03    C4   C18  C19  C20    39.38  30.0  1
 GY7  Var_04    N1   C3   C2   C1    -69.52  30.0  2
 GY7  Var_05    C8   C9   C10  C11    84.07  30.0  2
 GY7  Var_06    N3   C7   C6   C16  -178.29  30.0  2
 GY7  Var_07    N3   C8   C9   C10   178.80  30.0  1
 GY7  Var_08    C9   C8   N3   C7    179.59  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
 GY7  chir_01  C4  N1  C18  C5  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
 GY7  plan-1  C10  0.020
 GY7  plan-1  C11  0.020
 GY7  plan-1  C12  0.020
 GY7  plan-1  C13  0.020
 GY7  plan-1  C14  0.020
 GY7  plan-1  C15  0.020
 GY7  plan-1  C9   0.020
 GY7  plan-1  H1   0.020
 GY7  plan-1  H2   0.020
 GY7  plan-1  H3   0.020
 GY7  plan-1  H4   0.020
 GY7  plan-1  H5   0.020
 GY7  plan-2  C1   0.020
 GY7  plan-2  C2   0.020
 GY7  plan-2  C21  0.020
 GY7  plan-2  C22  0.020
 GY7  plan-2  C23  0.020
 GY7  plan-2  C24  0.020
 GY7  plan-2  C3   0.020
 GY7  plan-2  F1   0.020
 GY7  plan-2  F2   0.020
 GY7  plan-2  H12  0.020
 GY7  plan-2  H13  0.020
 GY7  plan-2  H14  0.020
 GY7  plan-3  C16  0.020
 GY7  plan-3  C17  0.020
 GY7  plan-3  C4   0.020
 GY7  plan-3  C5   0.020
 GY7  plan-3  C6   0.020
 GY7  plan-3  C7   0.020
 GY7  plan-3  N2   0.020
 GY7  plan-3  N4   0.020
 GY7  plan-3  O4   0.020
 GY7  plan-3  H21  0.020
 GY7  plan-3  O3   0.020
 GY7  plan-4  C6   0.020
 GY7  plan-4  C7   0.020
 GY7  plan-4  C8   0.020
 GY7  plan-4  N3   0.020
 GY7  plan-4  O2   0.020
 GY7  plan-4  H20  0.020
 GY7  plan-5  C2   0.020
 GY7  plan-5  C20  0.020
 GY7  plan-5  C3   0.020
 GY7  plan-5  C4   0.020
 GY7  plan-5  N1   0.020
 GY7  plan-5  O1   0.020

