# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:56:54 2022
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-[4-[3-[bis(fluoranyl)methoxy]pyridin-2-yl]oxy-2-methyl-phenyl]-1,5-dimethyl-pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)NC(=O)C(=C1c2ccc(Oc3ncccc3OC(F)F)cc2C)C
#
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
 G3U  G3U  6-[4-[3-[bis(fluoranyl)methoxy]pyridin-2-yl]oxy-2-methyl-phenyl]-1,5-dimethyl-pyrimidine-2,4-dione  ligand  45  28  .  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_G3U
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
 G3U  C10  C  CR6   0   0.483  107.7501  116.8805  135.9405
 G3U  C13  C  CR16  0  -0.312  105.5897  116.5377  138.1549
 G3U  C15  C  CR6   0  -0.069  104.2978  118.2962  139.1848
 G3U  C17  C  CR16  0  -0.362  106.4522  118.7875  138.2607
 G3U  C21  C  CR6   0   0.695  101.8515  118.8827  141.9330
 G3U  C24  C  CR6   0   0.567  100.8198  119.6571  139.8290
 G3U  C26  C  CR6   0  -0.196  102.0226  119.2517  139.1304
 G3U  C02  C  CH1   0   0.645  110.8768  117.1189  136.4140
 G3U  C05  C  CR6   0   0.179  108.9330  116.4008  135.3641
 G3U  C06  C  CR16  0  -0.199  108.9600  116.2022  134.0015
 G3U  C07  C  CR16  0  -0.339  107.8178  116.4798  133.2565
 G3U  C08  C  CR16  0  -0.058  106.7072  116.9553  133.9234
 G3U  C12  C  CR6   0   0.380  106.5831  117.4626  137.8849
 G3U  C14  C  CR16  0  -0.241  104.4459  116.9667  138.8074
 G3U  C16  C  CR6   0   0.113  105.3078  119.2255  138.9199
 G3U  C18  C  CH3   0  -0.747  105.1634  120.6651  139.3161
 G3U  C19  C  CR6   0   0.377  103.0418  118.7258  139.8474
 G3U  F01  F  F     0  -0.329  111.5888  117.4245  135.3032
 G3U  F03  F  F     0  -0.308  111.7454  116.6495  137.3195
 G3U  N09  N  N     0  -0.433  106.6783  117.1505  135.2406
 G3U  N20  N  NR6   0  -0.558  102.9800  118.5556  141.2173
 G3U  N23  N  NR16  0  -0.721  100.8395  119.4277  141.1889
 G3U  O04  O  O2    0  -0.485  110.0141  116.0940  136.1528
 G3U  O11  O  O2    0  -0.513  107.7525  117.0638  137.2750
 G3U  O22  O  O     0  -0.476  101.7407  118.7151  143.1311
 G3U  O25  O  O     0  -0.451   99.8452  120.1619  139.3006
 G3U  H1   H  HCR6  0   0.276  105.6995  115.5026  137.8591
 G3U  H2   H  HCR6  0   0.270  107.2470  119.4891  138.0376
 G3U  H3   H  HCH3  0   0.279  103.9425  118.0984  143.0052
 G3U  H4   H  HCH3  0   0.264  104.2121  116.9167  141.7207
 G3U  H5   H  HCH3  0   0.265  105.0294  118.4875  141.6751
 G3U  H6   H  HCH1  0   0.204  110.3992  118.0302  136.7814
 G3U  H7   H  HCR6  0   0.297  109.8536  115.8165  133.5282
 G3U  H8   H  HCR6  0   0.278  107.7993  116.3312  132.1865
 G3U  H9   H  HCR6  0   0.274  105.7963  117.1891  133.3857
 G3U  H10  H  HCR6  0   0.268  103.6546  116.2577  139.0167
 G3U  H11  H  HCH3  0   0.258  104.3224  121.1347  138.8030
 G3U  H12  H  HCH3  0   0.253  104.9842  120.7720  140.3875
 G3U  H13  H  HCH3  0   0.260  106.0602  121.2310  139.0712
 G3U  H14  H  HCH3  0   0.252  102.9798  119.1129  137.2063
 G3U  H15  H  HCH3  0   0.249  101.2337  118.9043  137.1685
 G3U  H16  H  HCH3  0   0.246  101.9182  120.5042  137.3914
 G3U  H17  H  HNR6  0   0.421  100.0089  119.6844  141.7084
 G3U  C27  C  CH3   0  -0.721  102.0466  119.4515  137.6486
 G3U  C28  C  CH3   0  -0.535  104.1076  117.9774  141.9415

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
 G3U  C07  C06  aromatic  1.392  0.020  1.392
 G3U  C07  C08  aromatic  1.380  0.020  1.380
 G3U  C06  C05  aromatic  1.377  0.020  1.377
 G3U  C08  N09  aromatic  1.332  0.020  1.332
 G3U  C05  O04  single    1.373  0.020  1.373
 G3U  C05  C10  aromatic  1.401  0.020  1.401
 G3U  F01  C02  single    1.354  0.020  1.354
 G3U  N09  C10  aromatic  1.308  0.020  1.308
 G3U  C02  O04  single    1.365  0.020  1.365
 G3U  C02  F03  single    1.340  0.020  1.340
 G3U  C10  O11  single    1.347  0.020  1.347
 G3U  O11  C12  single    1.378  0.020  1.378
 G3U  C27  C26  single    1.495  0.020  1.495
 G3U  C12  C13  aromatic  1.384  0.020  1.384
 G3U  C12  C17  aromatic  1.383  0.020  1.383
 G3U  C13  C14  aromatic  1.385  0.020  1.385
 G3U  C17  C16  aromatic  1.391  0.020  1.391
 G3U  C14  C15  aromatic  1.390  0.020  1.390
 G3U  C16  C15  aromatic  1.398  0.020  1.398
 G3U  C16  C18  single    1.500  0.020  1.500
 G3U  O25  C24  double    1.218  0.020  1.218
 G3U  C26  C24  single    1.449  0.020  1.449
 G3U  C26  C19  double    1.353  0.020  1.353
 G3U  C15  C19  single    1.484  0.020  1.484
 G3U  C24  N23  single    1.379  0.020  1.379
 G3U  C19  N20  single    1.382  0.020  1.382
 G3U  N23  C21  single    1.369  0.020  1.369
 G3U  N20  C21  single    1.376  0.020  1.376
 G3U  N20  C28  single    1.460  0.020  1.460
 G3U  C21  O22  double    1.215  0.020  1.215
 G3U  C13  H1   single    0.930  0.020  1.080
 G3U  C17  H2   single    0.930  0.020  1.080
 G3U  C28  H3   single    0.970  0.020  1.090
 G3U  C28  H4   single    0.970  0.020  1.090
 G3U  C28  H5   single    0.970  0.020  1.090
 G3U  C02  H6   single    0.970  0.020  1.090
 G3U  C06  H7   single    0.930  0.020  1.080
 G3U  C07  H8   single    0.930  0.020  1.080
 G3U  C08  H9   single    0.930  0.020  1.080
 G3U  C14  H10  single    0.930  0.020  1.080
 G3U  C18  H11  single    0.970  0.020  1.090
 G3U  C18  H12  single    0.970  0.020  1.090
 G3U  C18  H13  single    0.970  0.020  1.090
 G3U  C27  H14  single    0.970  0.020  1.090
 G3U  C27  H15  single    0.970  0.020  1.090
 G3U  C27  H16  single    0.970  0.020  1.090
 G3U  N23  H17  single    0.860  0.020  1.020

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
 G3U  O11  C10  N09  120.22  3.000
 G3U  O11  C10  C05  116.92  3.000
 G3U  N09  C10  C05  122.85  3.000
 G3U  H1   C13  C14  120.59  3.000
 G3U  H1   C13  C12  120.87  3.000
 G3U  C14  C13  C12  118.54  3.000
 G3U  C19  C15  C16  120.26  3.000
 G3U  C19  C15  C14  119.24  3.000
 G3U  C16  C15  C14  120.50  3.000
 G3U  H2   C17  C16  119.81  3.000
 G3U  H2   C17  C12  119.66  3.000
 G3U  C16  C17  C12  120.53  3.000
 G3U  O22  C21  N23  121.56  3.000
 G3U  O22  C21  N20  123.72  3.000
 G3U  N23  C21  N20  114.72  3.000
 G3U  O25  C24  N23  120.53  3.000
 G3U  N23  C24  C26  114.65  3.000
 G3U  O25  C24  C26  124.82  3.000
 G3U  C27  C26  C19  124.41  3.000
 G3U  C19  C26  C24  118.60  3.000
 G3U  C27  C26  C24  116.98  3.000
 G3U  H6   C02  O04  114.49  3.000
 G3U  H6   C02  F03  110.39  3.000
 G3U  O04  C02  F03  106.03  3.000
 G3U  H6   C02  F01  108.50  3.000
 G3U  F03  C02  F01  107.01  3.000
 G3U  O04  C02  F01  110.17  3.000
 G3U  O04  C05  C06  121.38  3.000
 G3U  O04  C05  C10  120.35  3.000
 G3U  C06  C05  C10  118.23  3.000
 G3U  H7   C06  C07  120.97  3.000
 G3U  H7   C06  C05  120.02  3.000
 G3U  C07  C06  C05  119.00  3.000
 G3U  H8   C07  C08  120.81  3.000
 G3U  H8   C07  C06  121.12  3.000
 G3U  C08  C07  C06  118.07  3.000
 G3U  H9   C08  N09  116.17  3.000
 G3U  H9   C08  C07  120.75  3.000
 G3U  N09  C08  C07  123.09  3.000
 G3U  O11  C12  C17  118.54  3.000
 G3U  C17  C12  C13  121.27  3.000
 G3U  O11  C12  C13  120.14  3.000
 G3U  H10  C14  C15  119.73  3.000
 G3U  H10  C14  C13  119.46  3.000
 G3U  C15  C14  C13  120.81  3.000
 G3U  C18  C16  C17  120.42  3.000
 G3U  C18  C16  C15  121.23  3.000
 G3U  C17  C16  C15  118.35  3.000
 G3U  H13  C18  H12  107.77  3.000
 G3U  H13  C18  H11  107.78  3.000
 G3U  H12  C18  H11  107.03  3.000
 G3U  H13  C18  C16  111.12  3.000
 G3U  H12  C18  C16  111.66  3.000
 G3U  H11  C18  C16  111.28  3.000
 G3U  N20  C19  C26  122.66  3.000
 G3U  N20  C19  C15  116.42  3.000
 G3U  C26  C19  C15  120.92  3.000
 G3U  C08  N09  C10  118.75  3.000
 G3U  C19  N20  C28  120.40  3.000
 G3U  C28  N20  C21  118.02  3.000
 G3U  C19  N20  C21  121.54  3.000
 G3U  H17  N23  C24  116.87  3.000
 G3U  H17  N23  C21  115.36  3.000
 G3U  C24  N23  C21  127.77  3.000
 G3U  C05  O04  C02  116.09  3.000
 G3U  C12  O11  C10  118.45  3.000
 G3U  H16  C27  H15  107.00  3.000
 G3U  H16  C27  H14  107.81  3.000
 G3U  H15  C27  H14  107.72  3.000
 G3U  H16  C27  C26  111.13  3.000
 G3U  H15  C27  C26  110.91  3.000
 G3U  H14  C27  C26  112.05  3.000
 G3U  H5   C28  H4   109.05  3.000
 G3U  H5   C28  H3   108.52  3.000
 G3U  H4   C28  H3   108.82  3.000
 G3U  H5   C28  N20  110.36  3.000
 G3U  H4   C28  N20  111.07  3.000
 G3U  H3   C28  N20  108.98  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
 G3U  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 G3U  CONST_02  C07  C08  N09  C10     0.00   0.0  0
 G3U  CONST_03  C16  C17  C12  C13     0.00   0.0  0
 G3U  CONST_04  C16  C15  C14  C13     0.00   0.0  0
 G3U  CONST_05  C12  C13  C14  C15     0.00   0.0  0
 G3U  CONST_06  C12  C17  C16  C15     0.00   0.0  0
 G3U  CONST_07  C14  C13  C12  C17     0.00   0.0  0
 G3U  CONST_08  C14  C15  C16  C17     0.00   0.0  0
 G3U  CONST_09  C08  C07  C06  C05     0.00   0.0  0
 G3U  CONST_10  C08  N09  C10  C05     0.00   0.0  0
 G3U  CONST_11  N09  C08  C07  C06     0.00   0.0  0
 G3U  CONST_12  N09  C10  C05  C06     0.00   0.0  0
 G3U  CONST_13  C19  C15  C14  C13   180.00   0.0  0
 G3U  CONST_14  C19  C15  C16  C17   180.00   0.0  0
 G3U  CONST_15  C26  C24  N23  C21     0.00   0.0  0
 G3U  CONST_16  N20  C21  N23  C24     0.00   0.0  0
 G3U  CONST_17  N23  C21  N20  C19     0.00   0.0  0
 G3U  CONST_18  O11  C10  C05  C06   180.00   0.0  0
 G3U  CONST_19  O04  C05  C06  C07   180.00   0.0  0
 G3U  CONST_20  O11  C10  N09  C08   180.00   0.0  0
 G3U  CONST_21  C18  C16  C17  C12   180.00   0.0  0
 G3U  CONST_22  O11  C12  C13  C14   180.00   0.0  0
 G3U  CONST_23  C18  C16  C15  C14   180.00   0.0  0
 G3U  CONST_24  O11  C12  C17  C16   180.00   0.0  0
 G3U  CONST_25  C19  C15  C16  C18     0.00   0.0  0
 G3U  CONST_26  O04  C05  C10  N09   180.00   0.0  0
 G3U  CONST_27  O25  C24  N23  C21   180.00   0.0  0
 G3U  CONST_28  O22  C21  N23  C24   180.00   0.0  0
 G3U  CONST_29  N23  C21  N20  C28   180.00   0.0  0
 G3U  CONST_30  O22  C21  N20  C19   180.00   0.0  0
 G3U  CONST_31  H7   C06  C05  C10   180.00   0.0  0
 G3U  CONST_32  H9   C08  N09  C10   180.00   0.0  0
 G3U  CONST_33  H2   C17  C12  C13   180.00   0.0  0
 G3U  CONST_34  H1   C13  C14  C15   180.00   0.0  0
 G3U  CONST_35  H8   C07  C06  C05   180.00   0.0  0
 G3U  CONST_36  H10  C14  C13  C12   180.00   0.0  0
 G3U  CONST_37  H17  N23  C24  C26   180.00   0.0  0
 G3U  CONST_38  O22  C21  N20  C28     0.00   0.0  0
 G3U  Var_01    C14  C15  C19  C26   -94.39  30.0  2
 G3U  Var_02    C13  C12  O11  C10    79.54  30.0  2
 G3U  Var_03    N09  C10  O11  C12     3.78  30.0  1
 G3U  Var_04    C06  C05  O04  C02    94.21  30.0  2
 G3U  Var_05    H11  C18  C16  C15   -62.35  30.0  2
 G3U  Var_06    H3   C28  N20  C21   -12.42  30.0  3
 G3U  Var_07    H14  C27  C26  C24  -179.48  30.0  3
 G3U  Var_08    F01  C02  O04  C05   -72.09  30.0  2

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
 G3U  plan-1  C15  0.020
 G3U  plan-1  C21  0.020
 G3U  plan-1  C24  0.020
 G3U  plan-1  C26  0.020
 G3U  plan-1  C19  0.020
 G3U  plan-1  N20  0.020
 G3U  plan-1  N23  0.020
 G3U  plan-1  O22  0.020
 G3U  plan-1  O25  0.020
 G3U  plan-1  H17  0.020
 G3U  plan-1  C27  0.020
 G3U  plan-1  C28  0.020
 G3U  plan-2  C10  0.020
 G3U  plan-2  C05  0.020
 G3U  plan-2  C06  0.020
 G3U  plan-2  C07  0.020
 G3U  plan-2  C08  0.020
 G3U  plan-2  N09  0.020
 G3U  plan-2  O04  0.020
 G3U  plan-2  O11  0.020
 G3U  plan-2  H7   0.020
 G3U  plan-2  H8   0.020
 G3U  plan-2  H9   0.020
 G3U  plan-3  C13  0.020
 G3U  plan-3  C15  0.020
 G3U  plan-3  C17  0.020
 G3U  plan-3  C12  0.020
 G3U  plan-3  C14  0.020
 G3U  plan-3  C16  0.020
 G3U  plan-3  C18  0.020
 G3U  plan-3  C19  0.020
 G3U  plan-3  O11  0.020
 G3U  plan-3  H1   0.020
 G3U  plan-3  H2   0.020
 G3U  plan-3  H10  0.020

