# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 23:38:55 2021
#   Inital geometry file: a 140 line input string
#   Ligand name: 4-{3-chloro-5-[(E)-2-cyanoethenyl]phenoxy}-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: F[S](=O)(=O)Oc1ccc(Oc2cc(Cl)cc(\C=C\C#N)c2)c(OCCN3C=CC(=O)NC3=O)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
 X2J  X2J  '4-{3-chloro-5-[(E)-2-cyanoethenyl]phenoxy}-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_X2J
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
 X2J  C15   C   C1    0  -0.348  48.7469  -31.0436  27.4345
 X2J  C00   C   CR16  0  -0.422  45.4935  -29.6224  19.7002
 X2J  C01   C   CR6   0   0.330  46.2447  -28.8290  18.8491
 X2J  C02   C   CR16  0  -0.319  47.4618  -28.2889  19.1984
 X2J  C03   C   CR16  0  -0.315  47.9529  -28.5700  20.4672
 X2J  C04   C   CR6   0   0.245  47.2334  -29.3601  21.3397
 X2J  C05   C   CR6   0   0.383  45.9879  -29.8925  20.9696
 X2J  C0C   C   CR6   0   0.421  47.2365  -29.3108  23.7109
 X2J  C0D   C   CH2   0  -0.199  44.0633  -31.1322  21.6176
 X2J  C0E   C   CH2   0  -0.354  43.4847  -31.6317  22.9226
 X2J  C0K   C   CR6   0   0.737  44.3510  -33.9005  23.1557
 X2J  C0N   C   CR6   0   0.568  46.0739  -34.4008  24.8659
 X2J  C0O   C   CR16  0  -0.505  46.0084  -33.0134  25.2492
 X2J  C0P   C   CR16  0   0.127  45.1649  -32.1893  24.6058
 X2J  C0V   C   CR16  0  -0.298  46.2135  -28.3724  23.7945
 X2J  C0W   C   CR6   0  -0.024  45.7120  -28.0603  25.0471
 X2J  C0X   C   CR16  0  -0.280  46.2049  -28.6419  26.2013
 X2J  C0Y   C   CR6   0   0.132  47.2493  -29.5631  26.1027
 X2J  C0Z   C   CR16  0  -0.398  47.7617  -29.8972  24.8511
 X2J  C13   C   C1    0  -0.205  47.7454  -30.1588  27.3388
 X2J  C17   C   CSP   0   0.091  49.1439  -31.5676  28.6924
 X2J  N0H   N   NR6   0  -0.520  44.3443  -32.5943  23.5967
 X2J  N0M   N   NR16  0  -0.731  45.2137  -34.7261  23.8261
 X2J  N19   N   NS    0  -0.261  49.4817  -32.0084  29.7032
 X2J  O0B   O   O2    0  -0.459  45.3589  -30.6249  21.8939
 X2J  O0S   O   O     0  -0.464  46.7886  -35.2502  25.3649
 X2J  O1C   O   OS    0  -0.579  43.7840  -27.3204  18.3416
 X2J  O1D   O   OS    0  -0.572  44.3853  -27.5201  15.9066
 X2J  CL11  CL  CL    0  -0.105  44.4288  -26.9076  25.1647
 X2J  H18   H   H     0   0.327  49.3064  -31.4036  26.5800
 X2J  H06   H   HCR6  0   0.320  44.5564  -30.0392  19.3580
 X2J  H08   H   HCR6  0   0.296  48.0289  -27.6797  18.5089
 X2J  H09   H   HCR6  0   0.293  48.9120  -28.1768  20.7769
 X2J  H0G   H   HCH2  0   0.262  43.4027  -30.3480  21.2362
 X2J  H0F   H   HCH2  0   0.258  44.1184  -31.9279  20.8704
 X2J  H0J   H   HCH2  0   0.281  43.3273  -30.7992  23.6070
 X2J  H0I   H   HCH2  0   0.299  42.5105  -32.0771  22.7305
 X2J  H0T   H   HCR6  0   0.281  46.6265  -32.6486  26.0544
 X2J  H0U   H   HCR6  0   0.303  45.0820  -31.1458  24.8752
 X2J  H10   H   HCR6  0   0.310  45.8130  -27.8875  22.9140
 X2J  H12   H   HCR6  0   0.291  45.7912  -28.3841  27.1668
 X2J  H14   H   HCR6  0   0.281  48.5585  -30.6217  24.7420
 X2J  H16   H   H     0   0.300  47.2423  -29.8444  28.2461
 X2J  H0R   H   HNR6  0   0.427  45.2215  -35.6889  23.5123
 X2J  F1    F   F     0  -0.391  45.7275  -26.2141  17.4440
 X2J  O0A   O   O2    0  -0.494  47.7966  -29.6974  22.5374
 X2J  O07   O   OC2   0  -0.585  45.7637  -28.6171  17.5506
 X2J  O0Q   O   O     0  -0.477  43.6452  -34.2876  22.2480
 X2J  S1A   S   S     0   1.746  44.7376  -27.4403  17.2851

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
 X2J  O1D   S1A  double    1.425  0.020  1.425
 X2J  S1A   O07  single    1.584  0.020  1.584
 X2J  S1A   O1C  double    1.428  0.020  1.428
 X2J  O07   C01  single    1.401  0.020  1.401
 X2J  C01   C02  aromatic  1.377  0.020  1.377
 X2J  C01   C00  aromatic  1.385  0.020  1.385
 X2J  C02   C03  aromatic  1.389  0.020  1.389
 X2J  C00   C05  aromatic  1.389  0.020  1.389
 X2J  C03   C04  aromatic  1.379  0.020  1.379
 X2J  O0Q   C0K  double    1.213  0.020  1.213
 X2J  C05   C04  aromatic  1.404  0.020  1.404
 X2J  C05   O0B  single    1.337  0.020  1.337
 X2J  C0D   O0B  single    1.419  0.020  1.419
 X2J  C0D   C0E  single    1.512  0.020  1.512
 X2J  C04   O0A  single    1.366  0.020  1.366
 X2J  C0K   N0M  single    1.369  0.020  1.369
 X2J  C0K   N0H  single    1.379  0.020  1.379
 X2J  C0E   N0H  single    1.456  0.020  1.456
 X2J  N0M   C0N  single    1.388  0.020  1.388
 X2J  O0A   C0C  single    1.357  0.020  1.357
 X2J  N0H   C0P  single    1.362  0.020  1.362
 X2J  C0N   O0S  double    1.217  0.020  1.217
 X2J  C0N   C0O  single    1.441  0.020  1.441
 X2J  C0V   C0C  aromatic  1.391  0.020  1.391
 X2J  C0V   C0W  aromatic  1.385  0.020  1.385
 X2J  C0C   C0Z  aromatic  1.386  0.020  1.386
 X2J  C0P   C0O  double    1.343  0.020  1.343
 X2J  CL11  C0W  single    1.729  0.020  1.729
 X2J  C0W   C0X  aromatic  1.383  0.020  1.383
 X2J  C0Z   C0Y  aromatic  1.393  0.020  1.393
 X2J  C0X   C0Y  aromatic  1.396  0.020  1.396
 X2J  C0Y   C13  single    1.459  0.020  1.459
 X2J  C13   C15  double    1.340  0.020  1.340
 X2J  C15   C17  single    1.419  0.020  1.419
 X2J  C17   N19  triple    1.153  0.020  1.153
 X2J  C15   H18  single    0.930  0.020  1.080
 X2J  C00   H06  single    0.930  0.020  1.080
 X2J  C02   H08  single    0.930  0.020  1.080
 X2J  C03   H09  single    0.930  0.020  1.080
 X2J  C0D   H0G  single    0.970  0.020  1.090
 X2J  C0D   H0F  single    0.970  0.020  1.090
 X2J  C0E   H0J  single    0.970  0.020  1.090
 X2J  C0E   H0I  single    0.970  0.020  1.090
 X2J  C0O   H0T  single    0.930  0.020  1.080
 X2J  C0P   H0U  single    0.930  0.020  1.080
 X2J  C0V   H10  single    0.930  0.020  1.080
 X2J  C0X   H12  single    0.930  0.020  1.080
 X2J  C0Z   H14  single    0.930  0.020  1.080
 X2J  C13   H16  single    0.930  0.020  1.080
 X2J  N0M   H0R  single    0.860  0.020  1.020
 X2J  S1A   F1   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
 X2J  H18   C15  C17  115.59  3.000
 X2J  H18   C15  C13  123.33  3.000
 X2J  C17   C15  C13  121.08  3.000
 X2J  H06   C00  C05  121.52  3.000
 X2J  H06   C00  C01  119.77  3.000
 X2J  C05   C00  C01  118.69  3.000
 X2J  O07   C01  C02  118.65  3.000
 X2J  C02   C01  C00  123.26  3.000
 X2J  O07   C01  C00  118.03  3.000
 X2J  H08   C02  C03  120.75  3.000
 X2J  H08   C02  C01  121.55  3.000
 X2J  C03   C02  C01  117.70  3.000
 X2J  H09   C03  C04  119.31  3.000
 X2J  H09   C03  C02  120.08  3.000
 X2J  C04   C03  C02  120.61  3.000
 X2J  O0A   C04  C05  120.21  3.000
 X2J  O0A   C04  C03  118.75  3.000
 X2J  C05   C04  C03  120.87  3.000
 X2J  O0B   C05  C04  116.29  3.000
 X2J  O0B   C05  C00  124.83  3.000
 X2J  C04   C05  C00  118.87  3.000
 X2J  O0A   C0C  C0Z  115.77  3.000
 X2J  C0Z   C0C  C0V  120.99  3.000
 X2J  O0A   C0C  C0V  123.23  3.000
 X2J  H0F   C0D  H0G  108.30  3.000
 X2J  H0F   C0D  O0B  110.33  3.000
 X2J  H0G   C0D  O0B  111.29  3.000
 X2J  H0F   C0D  C0E  111.64  3.000
 X2J  H0G   C0D  C0E  107.85  3.000
 X2J  O0B   C0D  C0E  107.43  3.000
 X2J  H0I   C0E  H0J  107.12  3.000
 X2J  H0I   C0E  N0H  109.86  3.000
 X2J  H0J   C0E  N0H  107.44  3.000
 X2J  H0I   C0E  C0D  108.98  3.000
 X2J  H0J   C0E  C0D  110.19  3.000
 X2J  N0H   C0E  C0D  113.07  3.000
 X2J  O0Q   C0K  N0M  122.71  3.000
 X2J  N0M   C0K  N0H  114.69  3.000
 X2J  O0Q   C0K  N0H  122.60  3.000
 X2J  O0S   C0N  N0M  120.49  3.000
 X2J  O0S   C0N  C0O  126.13  3.000
 X2J  N0M   C0N  C0O  113.37  3.000
 X2J  H0T   C0O  C0P  120.66  3.000
 X2J  H0T   C0O  C0N  119.88  3.000
 X2J  C0P   C0O  C0N  119.46  3.000
 X2J  H0U   C0P  N0H  115.18  3.000
 X2J  H0U   C0P  C0O  121.40  3.000
 X2J  N0H   C0P  C0O  123.41  3.000
 X2J  H10   C0V  C0W  120.06  3.000
 X2J  H10   C0V  C0C  121.72  3.000
 X2J  C0W   C0V  C0C  118.22  3.000
 X2J  CL11  C0W  C0X  119.21  3.000
 X2J  C0X   C0W  C0V  122.07  3.000
 X2J  CL11  C0W  C0V  118.72  3.000
 X2J  H12   C0X  C0Y  120.43  3.000
 X2J  H12   C0X  C0W  120.55  3.000
 X2J  C0Y   C0X  C0W  119.02  3.000
 X2J  C13   C0Y  C0Z  122.56  3.000
 X2J  C13   C0Y  C0X  117.64  3.000
 X2J  C0Z   C0Y  C0X  119.79  3.000
 X2J  H14   C0Z  C0Y  121.45  3.000
 X2J  H14   C0Z  C0C  118.64  3.000
 X2J  C0Y   C0Z  C0C  119.90  3.000
 X2J  H16   C13  C0Y  115.65  3.000
 X2J  H16   C13  C15  118.60  3.000
 X2J  C0Y   C13  C15  125.75  3.000
 X2J  N19   C17  C15  180.00  3.000
 X2J  C0P   N0H  C0K  121.05  3.000
 X2J  C0P   N0H  C0E  120.13  3.000
 X2J  C0K   N0H  C0E  118.76  3.000
 X2J  H0R   N0M  C0N  116.75  3.000
 X2J  H0R   N0M  C0K  115.24  3.000
 X2J  C0N   N0M  C0K  128.01  3.000
 X2J  C0D   O0B  C05  119.41  3.000
 X2J  C0C   O0A  C04  121.20  3.000
 X2J  S1A   O07  C01  119.36  3.000
 X2J  F1    S1A  O1D  107.15  3.000
 X2J  F1    S1A  O1C  106.15  3.000
 X2J  O1D   S1A  O1C  123.72  3.000
 X2J  F1    S1A  O07   98.83  3.000
 X2J  O1C   S1A  O07  111.78  3.000
 X2J  O1D   S1A  O07  106.30  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
 X2J  CONST_01  C03   C02  C01  C00     0.00   0.0  0
 X2J  CONST_02  C03   C04  C05  C00     0.00   0.0  0
 X2J  CONST_03  C04   C03  C02  C01     0.00   0.0  0
 X2J  CONST_04  C04   C05  C00  C01     0.00   0.0  0
 X2J  CONST_05  C05   C00  C01  C02     0.00   0.0  0
 X2J  CONST_06  C05   C04  C03  C02     0.00   0.0  0
 X2J  CONST_07  C0X   C0W  C0V  C0C     0.00   0.0  0
 X2J  CONST_08  C0X   C0Y  C0Z  C0C     0.00   0.0  0
 X2J  CONST_09  C0Y   C0Z  C0C  C0V     0.00   0.0  0
 X2J  CONST_10  C0Y   C0X  C0W  C0V     0.00   0.0  0
 X2J  CONST_11  C0Z   C0C  C0V  C0W     0.00   0.0  0
 X2J  CONST_12  C0Z   C0Y  C0X  C0W     0.00   0.0  0
 X2J  CONST_13  C0O   C0N  N0M  C0K     0.00   0.0  0
 X2J  CONST_14  N0H   C0K  N0M  C0N     0.00   0.0  0
 X2J  CONST_15  N0M   C0K  N0H  C0P     0.00   0.0  0
 X2J  CONST_16  O0A   C04  C05  C00   180.00   0.0  0
 X2J  CONST_17  O0B   C05  C00  C01   180.00   0.0  0
 X2J  CONST_18  O0A   C04  C03  C02   180.00   0.0  0
 X2J  CONST_19  O07   C01  C02  C03   180.00   0.0  0
 X2J  CONST_20  O0B   C05  C04  C03   180.00   0.0  0
 X2J  CONST_21  O07   C01  C00  C05   180.00   0.0  0
 X2J  CONST_22  CL11  C0W  C0V  C0C   180.00   0.0  0
 X2J  CONST_23  C13   C0Y  C0Z  C0C   180.00   0.0  0
 X2J  CONST_24  O0A   C0C  C0V  C0W   180.00   0.0  0
 X2J  CONST_25  C13   C0Y  C0X  C0W   180.00   0.0  0
 X2J  CONST_26  O0A   C0C  C0Z  C0Y   180.00   0.0  0
 X2J  CONST_27  CL11  C0W  C0X  C0Y   180.00   0.0  0
 X2J  CONST_28  N0M   C0K  N0H  C0E   180.00   0.0  0
 X2J  CONST_29  O0S   C0N  N0M  C0K   180.00   0.0  0
 X2J  CONST_30  O0Q   C0K  N0M  C0N   180.00   0.0  0
 X2J  CONST_31  O0Q   C0K  N0H  C0P   180.00   0.0  0
 X2J  CONST_32  H08   C02  C01  C00   180.00   0.0  0
 X2J  CONST_33  H09   C03  C02  C01   180.00   0.0  0
 X2J  CONST_34  H06   C00  C01  C02   180.00   0.0  0
 X2J  CONST_35  H14   C0Z  C0C  C0V   180.00   0.0  0
 X2J  CONST_36  H12   C0X  C0W  C0V   180.00   0.0  0
 X2J  CONST_37  H10   C0V  C0W  C0X   180.00   0.0  0
 X2J  CONST_38  H0R   N0M  C0N  C0O   180.00   0.0  0
 X2J  CONST_39  O0Q   C0K  N0H  C0E     0.00   0.0  0
 X2J  Var_01    C0V   C0C  O0A  C04   -11.53  30.0  2
 X2J  Var_02    C0Z   C0Y  C13  C15     1.96  30.0  2
 X2J  Var_03    C0K   N0H  C0E  C0D   -79.03  30.0  3
 X2J  Var_04    C17   C15  C13  C0Y  -179.59   0.0  2
 X2J  Var_05    O1D   S1A  O07  C01  -177.10  30.0  1
 X2J  Var_06    C0E   C0D  O0B  C05  -167.26  30.0  1
 X2J  Var_07    O0B   C0D  C0E  N0H   -54.45  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
 X2J  plan-1  C00   0.020
 X2J  plan-1  C01   0.020
 X2J  plan-1  C02   0.020
 X2J  plan-1  C03   0.020
 X2J  plan-1  C04   0.020
 X2J  plan-1  C05   0.020
 X2J  plan-1  O0B   0.020
 X2J  plan-1  H06   0.020
 X2J  plan-1  H08   0.020
 X2J  plan-1  H09   0.020
 X2J  plan-1  O0A   0.020
 X2J  plan-1  O07   0.020
 X2J  plan-2  C15   0.020
 X2J  plan-2  C0Y   0.020
 X2J  plan-2  C13   0.020
 X2J  plan-2  C17   0.020
 X2J  plan-2  H18   0.020
 X2J  plan-2  H16   0.020
 X2J  plan-3  C0E   0.020
 X2J  plan-3  C0K   0.020
 X2J  plan-3  C0N   0.020
 X2J  plan-3  C0O   0.020
 X2J  plan-3  C0P   0.020
 X2J  plan-3  N0H   0.020
 X2J  plan-3  N0M   0.020
 X2J  plan-3  O0S   0.020
 X2J  plan-3  H0T   0.020
 X2J  plan-3  H0U   0.020
 X2J  plan-3  H0R   0.020
 X2J  plan-3  O0Q   0.020
 X2J  plan-4  C0C   0.020
 X2J  plan-4  C0V   0.020
 X2J  plan-4  C0W   0.020
 X2J  plan-4  C0X   0.020
 X2J  plan-4  C0Y   0.020
 X2J  plan-4  C0Z   0.020
 X2J  plan-4  C13   0.020
 X2J  plan-4  CL11  0.020
 X2J  plan-4  H10   0.020
 X2J  plan-4  H12   0.020
 X2J  plan-4  H14   0.020
 X2J  plan-4  O0A   0.020

