# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 18:19:14 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-{3-[(E)-2-cyanoethenyl]-5-fluorophenoxy}-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cc(Oc2ccc(O[S](F)(=O)=O)cc2OCCN3C=CC(=O)NC3=O)cc(\C=C\C#N)c1
#
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
 X2G  X2G  '4-{3-[(E)-2-cyanoethenyl]-5-fluorophenoxy}-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate'  ligand  49  34  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_X2G
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
 X2G  C13  C  C1    0  -0.204  47.8789  -29.9530  27.3315
 X2G  C15  C  C1    0  -0.350  48.8758  -30.8413  27.4447
 X2G  C17  C  CSP   0   0.090  49.2550  -31.3585  28.7109
 X2G  C00  C  CR16  0  -0.422  45.6966  -29.5450  19.6766
 X2G  C01  C  CR6   0   0.332  46.4392  -28.7524  18.8174
 X2G  C02  C  CR16  0  -0.319  47.6420  -28.1814  19.1663
 X2G  C03  C  CR16  0  -0.315  48.1296  -28.4332  20.4430
 X2G  C04  C  CR6   0   0.244  47.4202  -29.2246  21.3224
 X2G  C05  C  CR6   0   0.384  46.1863  -29.7844  20.9540
 X2G  C0C  C  CR6   0   0.438  47.4126  -29.1364  23.6906
 X2G  C0D  C  CH2   0  -0.198  44.2785  -31.0442  21.6079
 X2G  C0E  C  CH2   0  -0.355  43.6990  -31.5387  22.9141
 X2G  C0K  C  CR6   0   0.736  44.5871  -33.7951  23.1760
 X2G  C0N  C  CR6   0   0.568  46.2948  -34.2637  24.9101
 X2G  C0O  C  CR16  0  -0.505  46.2120  -32.8733  25.2803
 X2G  C0P  C  CR16  0   0.127  45.3705  -32.0624  24.6177
 X2G  C0V  C  CR16  0  -0.498  46.3967  -28.1888  23.7523
 X2G  C0W  C  CR6   0   0.567  45.8983  -27.8640  24.9982
 X2G  C0X  C  CR16  0  -0.486  46.3642  -28.4297  26.1665
 X2G  C0Y  C  CR6   0   0.151  47.3998  -29.3631  26.0858
 X2G  C0Z  C  CR16  0  -0.414  47.9215  -29.7154  24.8428
 X2G  N0H  N  NR6   0  -0.520  44.5658  -32.4844  23.6023
 X2G  N0M  N  NR16  0  -0.731  45.4496  -34.6066  23.8638
 X2G  N19  N  NS    0  -0.261  49.5802  -31.7902  29.7298
 X2G  O0A  O  O2    0  -0.494  47.9821  -29.5381  22.5270
 X2G  O0B  O  O2    0  -0.459  45.5648  -30.5141  21.8852
 X2G  O0S  O  O     0  -0.464  47.0112  -35.1018  25.4251
 X2G  O1C  O  OS    0  -0.578  43.9457  -27.3201  18.2544
 X2G  O1D  O  OS    0  -0.572  44.5670  -27.5728  15.8288
 X2G  H16  H  H     0   0.299  47.3671  -29.6311  28.2311
 X2G  H18  H  H     0   0.327  49.4443  -31.2090  26.5995
 X2G  H06  H  HCR6  0   0.319  44.7705  -29.9855  19.3344
 X2G  H08  H  HCR6  0   0.295  48.2019  -27.5728  18.4706
 X2G  H09  H  HCR6  0   0.293  49.0796  -28.0179  20.7519
 X2G  H0G  H  HCH2  0   0.260  43.6084  -30.2741  21.2146
 X2G  H0F  H  HCH2  0   0.257  44.3495  -31.8470  20.8695
 X2G  H0J  H  HCH2  0   0.282  43.5255  -30.7021  23.5895
 X2G  H0I  H  HCH2  0   0.298  42.7321  -31.9987  22.7190
 X2G  H0T  H  HCR6  0   0.282  46.8164  -32.4962  26.0903
 X2G  H0U  H  HCR6  0   0.302  45.2765  -31.0169  24.8749
 X2G  H10  H  HCR6  0   0.309  45.9996  -27.7045  22.8692
 X2G  H12  H  HCR6  0   0.291  45.9380  -28.1478  27.1203
 X2G  H14  H  HCR6  0   0.279  48.7116  -30.4489  24.7487
 X2G  H0R  H  HNR6  0   0.427  45.4691  -35.5724  23.5598
 X2G  F    F  F     0  -0.391  45.8593  -26.1815  17.3322
 X2G  F11  F  F     0  -0.306  44.9174  -26.9569  25.0681
 X2G  O07  O  OC2   0  -0.585  45.9674  -28.5788  17.5099
 X2G  O0Q  O  O     0  -0.477  43.8940  -34.1977  22.2652
 X2G  S1A  S  S     0   1.745  44.9082  -27.4416  17.2062

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
 X2G  O1D  S1A  double    1.425  0.020  1.425
 X2G  S1A  O07  single    1.583  0.020  1.583
 X2G  S1A  O1C  double    1.428  0.020  1.428
 X2G  O07  C01  single    1.401  0.020  1.401
 X2G  C01  C02  aromatic  1.376  0.020  1.376
 X2G  C01  C00  aromatic  1.385  0.020  1.385
 X2G  C02  C03  aromatic  1.390  0.020  1.390
 X2G  C00  C05  aromatic  1.389  0.020  1.389
 X2G  C03  C04  aromatic  1.379  0.020  1.379
 X2G  O0Q  C0K  double    1.213  0.020  1.213
 X2G  C05  C04  aromatic  1.404  0.020  1.404
 X2G  C05  O0B  single    1.336  0.020  1.336
 X2G  C0D  O0B  single    1.419  0.020  1.419
 X2G  C0D  C0E  single    1.512  0.020  1.512
 X2G  C04  O0A  single    1.366  0.020  1.366
 X2G  C0K  N0M  single    1.369  0.020  1.369
 X2G  C0K  N0H  single    1.379  0.020  1.379
 X2G  C0E  N0H  single    1.456  0.020  1.456
 X2G  N0M  C0N  single    1.388  0.020  1.388
 X2G  N0H  C0P  single    1.363  0.020  1.363
 X2G  O0A  C0C  single    1.356  0.020  1.356
 X2G  C0V  C0C  aromatic  1.391  0.020  1.391
 X2G  C0V  C0W  aromatic  1.381  0.020  1.381
 X2G  C0N  O0S  double    1.217  0.020  1.217
 X2G  C0N  C0O  single    1.441  0.020  1.441
 X2G  C0C  C0Z  aromatic  1.386  0.020  1.386
 X2G  C0P  C0O  double    1.343  0.020  1.343
 X2G  F11  C0W  single    1.338  0.020  1.338
 X2G  C0W  C0X  aromatic  1.379  0.020  1.379
 X2G  C0Z  C0Y  aromatic  1.393  0.020  1.393
 X2G  C0X  C0Y  aromatic  1.396  0.020  1.396
 X2G  C0Y  C13  single    1.459  0.020  1.459
 X2G  C13  C15  double    1.340  0.020  1.340
 X2G  C15  C17  single    1.419  0.020  1.419
 X2G  C17  N19  triple    1.153  0.020  1.153
 X2G  C13  H16  single    0.930  0.020  1.080
 X2G  C15  H18  single    0.930  0.020  1.080
 X2G  C00  H06  single    0.930  0.020  1.080
 X2G  C02  H08  single    0.930  0.020  1.080
 X2G  C03  H09  single    0.930  0.020  1.080
 X2G  C0D  H0G  single    0.970  0.020  1.090
 X2G  C0D  H0F  single    0.970  0.020  1.090
 X2G  C0E  H0J  single    0.970  0.020  1.090
 X2G  C0E  H0I  single    0.970  0.020  1.090
 X2G  C0O  H0T  single    0.930  0.020  1.080
 X2G  C0P  H0U  single    0.930  0.020  1.080
 X2G  C0V  H10  single    0.930  0.020  1.080
 X2G  C0X  H12  single    0.930  0.020  1.080
 X2G  C0Z  H14  single    0.930  0.020  1.080
 X2G  N0M  H0R  single    0.860  0.020  1.020
 X2G  S1A  F    single    1.584  0.020  1.584

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
 X2G  H16  C13  C0Y  115.69  3.000
 X2G  H16  C13  C15  118.55  3.000
 X2G  C0Y  C13  C15  125.76  3.000
 X2G  H18  C15  C17  115.61  3.000
 X2G  H18  C15  C13  123.35  3.000
 X2G  C17  C15  C13  121.05  3.000
 X2G  N19  C17  C15  180.00  3.000
 X2G  H06  C00  C05  121.53  3.000
 X2G  H06  C00  C01  119.74  3.000
 X2G  C05  C00  C01  118.70  3.000
 X2G  O07  C01  C02  118.65  3.000
 X2G  C02  C01  C00  123.28  3.000
 X2G  O07  C01  C00  118.00  3.000
 X2G  H08  C02  C03  120.78  3.000
 X2G  H08  C02  C01  121.55  3.000
 X2G  C03  C02  C01  117.67  3.000
 X2G  H09  C03  C04  119.32  3.000
 X2G  H09  C03  C02  120.06  3.000
 X2G  C04  C03  C02  120.61  3.000
 X2G  O0A  C04  C05  120.09  3.000
 X2G  O0A  C04  C03  118.85  3.000
 X2G  C05  C04  C03  120.89  3.000
 X2G  O0B  C05  C04  116.33  3.000
 X2G  O0B  C05  C00  124.82  3.000
 X2G  C04  C05  C00  118.85  3.000
 X2G  O0A  C0C  C0Z  115.80  3.000
 X2G  C0Z  C0C  C0V  121.06  3.000
 X2G  O0A  C0C  C0V  123.14  3.000
 X2G  H0F  C0D  H0G  108.30  3.000
 X2G  H0F  C0D  O0B  110.34  3.000
 X2G  H0G  C0D  O0B  111.26  3.000
 X2G  H0F  C0D  C0E  111.61  3.000
 X2G  H0G  C0D  C0E  107.82  3.000
 X2G  O0B  C0D  C0E  107.51  3.000
 X2G  H0I  C0E  H0J  107.12  3.000
 X2G  H0I  C0E  N0H  109.83  3.000
 X2G  H0J  C0E  N0H  107.50  3.000
 X2G  H0I  C0E  C0D  108.89  3.000
 X2G  H0J  C0E  C0D  110.21  3.000
 X2G  N0H  C0E  C0D  113.11  3.000
 X2G  O0Q  C0K  N0M  122.70  3.000
 X2G  N0M  C0K  N0H  114.70  3.000
 X2G  O0Q  C0K  N0H  122.60  3.000
 X2G  O0S  C0N  N0M  120.49  3.000
 X2G  O0S  C0N  C0O  126.13  3.000
 X2G  N0M  C0N  C0O  113.38  3.000
 X2G  H0T  C0O  C0P  120.68  3.000
 X2G  H0T  C0O  C0N  119.86  3.000
 X2G  C0P  C0O  C0N  119.45  3.000
 X2G  H0U  C0P  N0H  115.19  3.000
 X2G  H0U  C0P  C0O  121.40  3.000
 X2G  N0H  C0P  C0O  123.41  3.000
 X2G  H10  C0V  C0W  119.90  3.000
 X2G  H10  C0V  C0C  122.45  3.000
 X2G  C0W  C0V  C0C  117.65  3.000
 X2G  F11  C0W  C0X  118.78  3.000
 X2G  C0X  C0W  C0V  123.09  3.000
 X2G  F11  C0W  C0V  118.12  3.000
 X2G  H12  C0X  C0Y  121.14  3.000
 X2G  H12  C0X  C0W  120.45  3.000
 X2G  C0Y  C0X  C0W  118.41  3.000
 X2G  C0Z  C0Y  C0X  119.88  3.000
 X2G  C0X  C0Y  C13  117.67  3.000
 X2G  C0Z  C0Y  C13  122.44  3.000
 X2G  H14  C0Z  C0Y  121.49  3.000
 X2G  H14  C0Z  C0C  118.61  3.000
 X2G  C0Y  C0Z  C0C  119.89  3.000
 X2G  C0P  N0H  C0K  121.05  3.000
 X2G  C0P  N0H  C0E  120.18  3.000
 X2G  C0K  N0H  C0E  118.73  3.000
 X2G  H0R  N0M  C0N  116.75  3.000
 X2G  H0R  N0M  C0K  115.24  3.000
 X2G  C0N  N0M  C0K  128.01  3.000
 X2G  C0C  O0A  C04  121.06  3.000
 X2G  C0D  O0B  C05  119.31  3.000
 X2G  S1A  O07  C01  119.56  3.000
 X2G  F    S1A  O1D  107.09  3.000
 X2G  F    S1A  O1C  106.18  3.000
 X2G  O1D  S1A  O1C  123.77  3.000
 X2G  F    S1A  O07   98.88  3.000
 X2G  O1C  S1A  O07  111.79  3.000
 X2G  O1D  S1A  O07  106.22  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
 X2G  CONST_01  C03  C02  C01  C00     0.00   0.0  0
 X2G  CONST_02  C03  C04  C05  C00     0.00   0.0  0
 X2G  CONST_03  C04  C03  C02  C01     0.00   0.0  0
 X2G  CONST_04  C04  C05  C00  C01     0.00   0.0  0
 X2G  CONST_05  C05  C00  C01  C02     0.00   0.0  0
 X2G  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 X2G  CONST_07  C0X  C0W  C0V  C0C     0.00   0.0  0
 X2G  CONST_08  C0X  C0Y  C0Z  C0C     0.00   0.0  0
 X2G  CONST_09  C0Y  C0Z  C0C  C0V     0.00   0.0  0
 X2G  CONST_10  C0Y  C0X  C0W  C0V     0.00   0.0  0
 X2G  CONST_11  C0Z  C0C  C0V  C0W     0.00   0.0  0
 X2G  CONST_12  C0Z  C0Y  C0X  C0W     0.00   0.0  0
 X2G  CONST_13  C0O  C0N  N0M  C0K     0.00   0.0  0
 X2G  CONST_14  N0H  C0K  N0M  C0N     0.00   0.0  0
 X2G  CONST_15  N0M  C0K  N0H  C0P     0.00   0.0  0
 X2G  CONST_16  C0C  C0Z  C0Y  C13   180.00   0.0  0
 X2G  CONST_17  C0W  C0X  C0Y  C13   180.00   0.0  0
 X2G  CONST_18  O0A  C04  C05  C00   180.00   0.0  0
 X2G  CONST_19  O0B  C05  C00  C01   180.00   0.0  0
 X2G  CONST_20  O0A  C04  C03  C02   180.00   0.0  0
 X2G  CONST_21  O07  C01  C02  C03   180.00   0.0  0
 X2G  CONST_22  O0B  C05  C04  C03   180.00   0.0  0
 X2G  CONST_23  O07  C01  C00  C05   180.00   0.0  0
 X2G  CONST_24  F11  C0W  C0V  C0C   180.00   0.0  0
 X2G  CONST_25  O0A  C0C  C0V  C0W   180.00   0.0  0
 X2G  CONST_26  O0A  C0C  C0Z  C0Y   180.00   0.0  0
 X2G  CONST_27  F11  C0W  C0X  C0Y   180.00   0.0  0
 X2G  CONST_28  N0M  C0K  N0H  C0E   180.00   0.0  0
 X2G  CONST_29  O0S  C0N  N0M  C0K   180.00   0.0  0
 X2G  CONST_30  O0Q  C0K  N0M  C0N   180.00   0.0  0
 X2G  CONST_31  O0Q  C0K  N0H  C0P   180.00   0.0  0
 X2G  CONST_32  H08  C02  C01  C00   180.00   0.0  0
 X2G  CONST_33  H09  C03  C02  C01   180.00   0.0  0
 X2G  CONST_34  H06  C00  C01  C02   180.00   0.0  0
 X2G  CONST_35  H14  C0Z  C0C  C0V   180.00   0.0  0
 X2G  CONST_36  H12  C0X  C0W  C0V   180.00   0.0  0
 X2G  CONST_37  H10  C0V  C0W  C0X   180.00   0.0  0
 X2G  CONST_38  H0R  N0M  C0N  C0O   180.00   0.0  0
 X2G  CONST_39  O0Q  C0K  N0H  C0E     0.00   0.0  0
 X2G  Var_01    C0V  C0C  O0A  C04   -12.64  30.0  2
 X2G  Var_02    C0Z  C0Y  C13  C15     2.39  30.0  3
 X2G  Var_03    C0K  N0H  C0E  C0D   -79.22  30.0  3
 X2G  Var_04    C0Y  C13  C15  C17  -179.58   0.0  2
 X2G  Var_05    O1D  S1A  O07  C01  -176.38  30.0  2
 X2G  Var_06    C0E  C0D  O0B  C05  -167.36  30.0  1
 X2G  Var_07    O0B  C0D  C0E  N0H   -54.63  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
 X2G  plan-1  C00  0.020
 X2G  plan-1  C01  0.020
 X2G  plan-1  C02  0.020
 X2G  plan-1  C03  0.020
 X2G  plan-1  C04  0.020
 X2G  plan-1  C05  0.020
 X2G  plan-1  O0A  0.020
 X2G  plan-1  O0B  0.020
 X2G  plan-1  H06  0.020
 X2G  plan-1  H08  0.020
 X2G  plan-1  H09  0.020
 X2G  plan-1  O07  0.020
 X2G  plan-2  C13  0.020
 X2G  plan-2  C15  0.020
 X2G  plan-2  C17  0.020
 X2G  plan-2  C0Y  0.020
 X2G  plan-2  H16  0.020
 X2G  plan-2  H18  0.020
 X2G  plan-3  C0E  0.020
 X2G  plan-3  C0K  0.020
 X2G  plan-3  C0N  0.020
 X2G  plan-3  C0O  0.020
 X2G  plan-3  C0P  0.020
 X2G  plan-3  N0H  0.020
 X2G  plan-3  N0M  0.020
 X2G  plan-3  O0S  0.020
 X2G  plan-3  H0T  0.020
 X2G  plan-3  H0U  0.020
 X2G  plan-3  H0R  0.020
 X2G  plan-3  O0Q  0.020
 X2G  plan-4  C13  0.020
 X2G  plan-4  C0C  0.020
 X2G  plan-4  C0V  0.020
 X2G  plan-4  C0W  0.020
 X2G  plan-4  C0X  0.020
 X2G  plan-4  C0Y  0.020
 X2G  plan-4  C0Z  0.020
 X2G  plan-4  O0A  0.020
 X2G  plan-4  H10  0.020
 X2G  plan-4  H12  0.020
 X2G  plan-4  H14  0.020
 X2G  plan-4  F11  0.020

