# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 20:19:35 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: 5-hydroxy-N-(2-methoxyethyl)-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCNC(=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
 GY5  GY5  5-hydroxy-N-(2-methoxyethyl)-6-oxo-2-[(2S)-1-(phenoxyacetyl)pyrrolidin-2-yl]-1,6-dihydropyrimidine-4-carboxamide  ligand  54  30  .  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_GY5
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
 GY5  N     N  NR5   0  -0.511  -1.1403  -0.8821   1.4103
 GY5  C     C  CR16  0  -0.241  -7.4181   0.5513   0.2069
 GY5  O     O  O     0  -0.465  -1.1804   0.8187  -0.0574
 GY5  C01   C  CR6   0   0.512   0.9825  -1.0119   0.1569
 GY5  C02   C  CR6   0  -0.006   2.7119  -0.5654  -1.2815
 GY5  C03   C  CR6   0   0.233   2.2190  -1.4065  -2.2332
 GY5  C04   C  CR6   0   0.484   0.9798  -2.1299  -1.9649
 GY5  C05   C  C     0   0.550   3.9739   0.2168  -1.4716
 GY5  C06   C  CH2   0  -0.293   5.5194   1.7601  -0.3814
 GY5  C07   C  CH2   0  -0.480  -0.6079  -2.0891   3.3394
 GY5  C08   C  CH2   0  -0.475   0.6101  -2.0600   2.4254
 GY5  C09   C  CR15  0  -0.139   0.3140  -0.8762   1.4943
 GY5  C1    C  CH2   0  -0.173   5.4522   2.7887   0.7233
 GY5  C10   C  CH2   0  -0.283  -1.7584  -1.7761   2.3921
 GY5  C11   C  C     0   0.534  -1.7786   0.0276   0.6491
 GY5  C12   C  CH2   0  -0.311  -3.2935  -0.0124   0.7293
 GY5  C13   C  CR16  0  -0.279  -7.8575   1.3281  -0.8522
 GY5  C14   C  CR16  0  -0.240  -6.9186   1.9150  -1.6953
 GY5  C15   C  CR16  0  -0.344  -5.5645   1.7275  -1.4819
 GY5  C16   C  CR6   0   0.384  -5.1280   0.9432  -0.4129
 GY5  C17   C  CR16  0  -0.375  -6.0598   0.3514   0.4350
 GY5  N01   N  N     0  -0.474   2.0728  -0.3839  -0.0838
 GY5  N02   N  NR16  0  -0.678   0.4349  -1.8715  -0.7411
 GY5  N03   N  NH1   0  -0.650   4.3118   0.9688  -0.4179
 GY5  O01   O  OH1   0  -0.588   2.7739  -1.6376  -3.4171
 GY5  O02   O  O     0  -0.471   0.4851  -2.8973  -2.7768
 GY5  O03   O  O     0  -0.485   4.6258   0.1661  -2.5057
 GY5  O1    O  O2    0  -0.466  -3.7884   0.8187  -0.2815
 GY5  O11   O  O2    0  -0.488   5.3079   2.1278   1.9556
 GY5  C18   C  CH3   0  -0.395   5.1898   3.0170   3.0375
 GY5  H10   H  HCH2  0   0.250   5.6460   2.2823  -1.3307
 GY5  H03   H  HCH2  0   0.243   6.3994   1.1225  -0.2471
 GY5  H05   H  HCH2  0   0.268  -0.7377  -3.0464   3.8410
 GY5  H11   H  HCH2  0   0.253  -0.5282  -1.3133   4.1030
 GY5  H07   H  HCH2  0   0.278   1.5523  -1.9254   2.9527
 GY5  H06   H  HCH2  0   0.256   0.6743  -2.9905   1.8560
 GY5  H08   H  HCR5  0   0.298   0.6749   0.0569   1.9350
 GY5  H13   H  HCH2  0   0.222   6.3702   3.3912   0.6997
 GY5  H12   H  HCH2  0   0.210   4.6111   3.4744   0.5475
 GY5  H1    H  HCH2  0   0.269  -2.5908  -1.2931   2.9038
 GY5  H09   H  HCH2  0   0.260  -2.1325  -2.6808   1.9068
 GY5  H2    H  HCH2  0   0.266  -3.6501  -1.0437   0.6152
 GY5  H3    H  HCH2  0   0.268  -3.6035   0.3293   1.7259
 GY5  H120  H  HCR6  0   0.254  -8.9153   1.4760  -1.0233
 GY5  H130  H  HCR6  0   0.259  -7.2431   2.5230  -2.5300
 GY5  H14   H  HCR6  0   0.264  -4.8356   2.1840  -2.1401
 GY5  H15   H  HCR6  0   0.279  -5.7568  -0.2600   1.2744
 GY5  H01   H  HNR6  0   0.430  -0.4356  -2.3400  -0.5158
 GY5  H04   H  HNH1  0   0.404   3.7510   0.8880   0.4177
 GY5  H02   H  HOH1  0   0.475   2.2173  -2.2763  -3.8906
 GY5  H112  H  HCH3  0   0.206   6.0762   3.6536   3.1425
 GY5  H111  H  HCH3  0   0.207   4.3154   3.6703   2.9374
 GY5  H113  H  HCH3  0   0.235   5.0789   2.4284   3.9473
 GY5  H     H  HCR6  0   0.261  -8.1331   0.0873   0.8741

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
 GY5  O02  C04   double    1.222  0.020  1.222
 GY5  C    C17   aromatic  1.392  0.020  1.392
 GY5  C    C13   aromatic  1.385  0.020  1.385
 GY5  C17  C16   aromatic  1.392  0.020  1.392
 GY5  O01  C03   single    1.328  0.020  1.328
 GY5  C04  C03   single    1.460  0.020  1.460
 GY5  C04  N02   single    1.364  0.020  1.364
 GY5  C13  C14   aromatic  1.392  0.020  1.392
 GY5  C03  C02   double    1.362  0.020  1.362
 GY5  C16  O1    single    1.352  0.020  1.352
 GY5  C16  C15   aromatic  1.396  0.020  1.396
 GY5  O1   C12   single    1.399  0.020  1.399
 GY5  N02  C01   single    1.358  0.020  1.358
 GY5  C14  C15   aromatic  1.384  0.020  1.384
 GY5  C12  C11   single    1.518  0.020  1.518
 GY5  C02  N01   single    1.370  0.020  1.370
 GY5  C02  C05   single    1.497  0.020  1.497
 GY5  C01  N01   double    1.281  0.020  1.281
 GY5  C01  C09   single    1.501  0.020  1.501
 GY5  O03  C05   double    1.223  0.020  1.223
 GY5  C05  N03   single    1.338  0.020  1.338
 GY5  C09  N     single    1.457  0.020  1.457
 GY5  C09  C08   single    1.535  0.020  1.535
 GY5  C11  N     single    1.347  0.020  1.347
 GY5  C11  O     double    1.218  0.020  1.218
 GY5  N    C10   single    1.465  0.020  1.465
 GY5  C08  C07   single    1.523  0.020  1.523
 GY5  N03  C06   single    1.444  0.020  1.444
 GY5  C06  C1    single    1.511  0.020  1.511
 GY5  C18  O11   single    1.405  0.020  1.405
 GY5  C10  C07   single    1.523  0.020  1.523
 GY5  C1   O11   single    1.406  0.020  1.406
 GY5  C    H     single    0.930  0.020  1.080
 GY5  C06  H10   single    0.970  0.020  1.090
 GY5  C06  H03   single    0.970  0.020  1.090
 GY5  C07  H05   single    0.970  0.020  1.090
 GY5  C07  H11   single    0.970  0.020  1.090
 GY5  C08  H07   single    0.970  0.020  1.090
 GY5  C08  H06   single    0.970  0.020  1.090
 GY5  C09  H08   single    0.970  0.020  1.090
 GY5  C1   H13   single    0.970  0.020  1.090
 GY5  C1   H12   single    0.970  0.020  1.090
 GY5  C10  H1    single    0.970  0.020  1.090
 GY5  C10  H09   single    0.970  0.020  1.090
 GY5  C12  H2    single    0.970  0.020  1.090
 GY5  C12  H3    single    0.970  0.020  1.090
 GY5  C13  H120  single    0.930  0.020  1.080
 GY5  C14  H130  single    0.930  0.020  1.080
 GY5  C15  H14   single    0.930  0.020  1.080
 GY5  C17  H15   single    0.930  0.020  1.080
 GY5  N02  H01   single    0.860  0.020  1.020
 GY5  N03  H04   single    0.860  0.020  1.020
 GY5  O01  H02   single    0.850  0.020  0.980
 GY5  C18  H112  single    0.970  0.020  1.090
 GY5  C18  H111  single    0.970  0.020  1.090
 GY5  C18  H113  single    0.970  0.020  1.090

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
 GY5  C11   N    C10   126.23  3.000
 GY5  C10   N    C09   112.65  3.000
 GY5  C11   N    C09   120.20  3.000
 GY5  H     C    C17   118.82  3.000
 GY5  H     C    C13   120.15  3.000
 GY5  C17   C    C13   121.03  3.000
 GY5  N02   C01  N01   121.94  3.000
 GY5  N01   C01  C09   120.14  3.000
 GY5  N02   C01  C09   117.81  3.000
 GY5  N01   C02  C05   115.80  3.000
 GY5  C05   C02  C03   122.61  3.000
 GY5  N01   C02  C03   121.59  3.000
 GY5  O01   C03  C04   115.62  3.000
 GY5  C04   C03  C02   118.99  3.000
 GY5  O01   C03  C02   125.38  3.000
 GY5  O02   C04  N02   123.59  3.000
 GY5  N02   C04  C03   114.21  3.000
 GY5  O02   C04  C03   122.20  3.000
 GY5  O03   C05  N03   123.67  3.000
 GY5  N03   C05  C02   113.99  3.000
 GY5  O03   C05  C02   122.34  3.000
 GY5  H03   C06  H10   106.99  3.000
 GY5  H03   C06  N03   110.86  3.000
 GY5  H10   C06  N03   109.72  3.000
 GY5  H03   C06  C1    110.03  3.000
 GY5  H10   C06  C1    108.39  3.000
 GY5  N03   C06  C1    110.75  3.000
 GY5  H11   C07  H05   108.15  3.000
 GY5  H11   C07  C10   110.14  3.000
 GY5  H05   C07  C10   112.17  3.000
 GY5  H11   C07  C08   110.36  3.000
 GY5  H05   C07  C08   112.87  3.000
 GY5  C10   C07  C08   103.12  3.000
 GY5  H06   C08  H07   107.88  3.000
 GY5  H06   C08  C09   110.60  3.000
 GY5  H07   C08  C09   111.44  3.000
 GY5  H06   C08  C07   110.09  3.000
 GY5  H07   C08  C07   113.83  3.000
 GY5  C09   C08  C07   102.97  3.000
 GY5  H08   C09  C08   110.49  3.000
 GY5  H08   C09  C01   106.81  3.000
 GY5  C08   C09  C01   112.63  3.000
 GY5  H08   C09  N     110.87  3.000
 GY5  C08   C09  N     102.97  3.000
 GY5  C01   C09  N     113.13  3.000
 GY5  H12   C1   H13   107.09  3.000
 GY5  H12   C1   O11   110.78  3.000
 GY5  H13   C1   O11   111.26  3.000
 GY5  H12   C1   C06   109.98  3.000
 GY5  H13   C1   C06   108.70  3.000
 GY5  O11   C1   C06   108.99  3.000
 GY5  H09   C10  H1    108.29  3.000
 GY5  H09   C10  C07   111.40  3.000
 GY5  H1    C10  C07   112.08  3.000
 GY5  H09   C10  N     110.62  3.000
 GY5  H1    C10  N     111.50  3.000
 GY5  C07   C10  N     102.92  3.000
 GY5  C12   C11  O     122.56  3.000
 GY5  O     C11  N     122.26  3.000
 GY5  C12   C11  N     115.17  3.000
 GY5  H3    C12  H2    107.16  3.000
 GY5  H3    C12  O1    111.77  3.000
 GY5  H2    C12  O1    111.61  3.000
 GY5  H3    C12  C11   108.76  3.000
 GY5  H2    C12  C11   110.11  3.000
 GY5  O1    C12  C11   107.41  3.000
 GY5  H120  C13  C14   120.42  3.000
 GY5  H120  C13  C     120.52  3.000
 GY5  C14   C13  C     119.06  3.000
 GY5  H130  C14  C15   119.24  3.000
 GY5  H130  C14  C13   120.11  3.000
 GY5  C15   C14  C13   120.65  3.000
 GY5  H14   C15  C16   119.46  3.000
 GY5  H14   C15  C14   120.52  3.000
 GY5  C16   C15  C14   120.02  3.000
 GY5  O1    C16  C17   124.41  3.000
 GY5  O1    C16  C15   115.86  3.000
 GY5  C17   C16  C15   119.74  3.000
 GY5  H15   C17  C16   121.70  3.000
 GY5  H15   C17  C     118.80  3.000
 GY5  C16   C17  C     119.50  3.000
 GY5  C02   N01  C01   119.77  3.000
 GY5  H01   N02  C04   117.05  3.000
 GY5  H01   N02  C01   119.45  3.000
 GY5  C04   N02  C01   123.49  3.000
 GY5  H04   N03  C06   119.17  3.000
 GY5  H04   N03  C05   117.81  3.000
 GY5  C06   N03  C05   122.62  3.000
 GY5  H02   O01  C03   108.05  3.000
 GY5  C16   O1   C12   118.39  3.000
 GY5  C18   O11  C1    112.71  3.000
 GY5  H113  C18  H111  108.49  3.000
 GY5  H113  C18  H112  108.43  3.000
 GY5  H111  C18  H112  107.92  3.000
 GY5  H113  C18  O11   108.04  3.000
 GY5  H111  C18  O11   111.95  3.000
 GY5  H112  C18  O11   111.91  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
 GY5  CONST_01  C15   C16  C17  C       0.00   0.0  0
 GY5  CONST_02  C15   C14  C13  C       0.00   0.0  0
 GY5  CONST_03  C16   C17  C    C13     0.00   0.0  0
 GY5  CONST_04  C16   C15  C14  C13     0.00   0.0  0
 GY5  CONST_05  C17   C    C13  C14     0.00   0.0  0
 GY5  CONST_06  C17   C16  C15  C14     0.00   0.0  0
 GY5  CONST_07  C03   C04  N02  C01     0.00   0.0  0
 GY5  CONST_08  N02   C01  N01  C02     0.00   0.0  0
 GY5  CONST_09  C09   C01  N01  C02   180.00   0.0  0
 GY5  CONST_10  N01   C01  N02  C04     0.00   0.0  0
 GY5  CONST_11  C09   C01  N02  C04   180.00   0.0  0
 GY5  CONST_12  O1    C16  C17  C     180.00   0.0  0
 GY5  CONST_13  O1    C16  C15  C14   180.00   0.0  0
 GY5  CONST_14  O02   C04  N02  C01   180.00   0.0  0
 GY5  CONST_15  H130  C14  C13  C     180.00   0.0  0
 GY5  CONST_16  H15   C17  C    C13   180.00   0.0  0
 GY5  CONST_17  H14   C15  C14  C13   180.00   0.0  0
 GY5  CONST_18  H     C    C13  C14   180.00   0.0  0
 GY5  CONST_19  H120  C13  C14  C15   180.00   0.0  0
 GY5  CONST_20  H01   N02  C04  C03   180.00   0.0  0
 GY5  CONST_21  C09   N    C11  O       0.00   0.0  0
 GY5  CONST_22  C10   N    C11  O     180.00   0.0  0
 GY5  CONST_23  C12   C11  N    C09   180.00   0.0  0
 GY5  CONST_24  C12   C11  N    C10     0.00   0.0  0
 GY5  CONST_25  C06   N03  C05  C02   180.00   0.0  0
 GY5  CONST_26  H04   N03  C05  C02     0.00   0.0  0
 GY5  CONST_27  O03   C05  N03  C06     0.00   0.0  0
 GY5  Var_01    C08   C07  C10  N     -32.33  30.0  1
 GY5  Var_02    C09   N    C10  C07    13.29  30.0  1
 GY5  Var_03    C10   C07  C08  C09    39.48  30.0  1
 GY5  Var_04    O03   C05  C02  C03     1.41  30.0  2
 GY5  Var_05    C17   C16  O1   C12     3.40  30.0  2
 GY5  Var_06    O1    C12  C11  N    -169.76  30.0  3
 GY5  Var_07    C1    C06  N03  C05   163.77  30.0  3
 GY5  Var_08    O11   C1   C06  N03    60.41  30.0  3
 GY5  Var_09    H112  C18  O11  C1    -60.91  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
 GY5  chir_01  C09  C01  N  C08  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
 GY5  plan-1  C     0.020
 GY5  plan-1  C13   0.020
 GY5  plan-1  C14   0.020
 GY5  plan-1  C15   0.020
 GY5  plan-1  C16   0.020
 GY5  plan-1  C17   0.020
 GY5  plan-1  O1    0.020
 GY5  plan-1  H120  0.020
 GY5  plan-1  H130  0.020
 GY5  plan-1  H14   0.020
 GY5  plan-1  H15   0.020
 GY5  plan-1  H     0.020
 GY5  plan-2  C01   0.020
 GY5  plan-2  C02   0.020
 GY5  plan-2  C03   0.020
 GY5  plan-2  C04   0.020
 GY5  plan-2  C05   0.020
 GY5  plan-2  C09   0.020
 GY5  plan-2  N01   0.020
 GY5  plan-2  N02   0.020
 GY5  plan-2  O01   0.020
 GY5  plan-2  O02   0.020
 GY5  plan-2  H01   0.020
 GY5  plan-3  N     0.020
 GY5  plan-3  O     0.020
 GY5  plan-3  C09   0.020
 GY5  plan-3  C10   0.020
 GY5  plan-3  C11   0.020
 GY5  plan-3  C12   0.020
 GY5  plan-4  C02   0.020
 GY5  plan-4  C05   0.020
 GY5  plan-4  C06   0.020
 GY5  plan-4  N03   0.020
 GY5  plan-4  O03   0.020
 GY5  plan-4  H04   0.020

