# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 09:56:15 2021
#   Inital geometry file: a 142 line input string
#   Ligand name: 4-[(6-cyanonaphthalen-1-yl)oxy]-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(Oc2cccc3cc(ccc23)C#N)c(OCCN4C=CC(=O)NC4=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
 X2V  X2V  '4-[(6-cyanonaphthalen-1-yl)oxy]-3-[2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)ethoxy]phenyl sulfurofluoridate'  ligand  51  35  .  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_X2V
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
 X2V  C1   C  CR6   0   0.014  472.5288  -16.9240  128.1116
 X2V  C2   C  CR16  0  -0.244  472.7336  -17.8252  127.0398
 X2V  C4   C  CR66  0   0.034  472.1989  -16.0572  125.4815
 X2V  C7   C  CR16  0  -0.324  472.2678  -16.1009  120.8214
 X2V  C8   C  CR16  0  -0.320  471.5987  -16.0684  119.6028
 X2V  C10  C  CR16  0  -0.406  469.5194  -16.5521  120.7671
 X2V  C11  C  CR6   0   0.400  470.1948  -16.5817  121.9776
 X2V  C12  C  CH2   0  -0.227  468.3169  -17.2859  123.2867
 X2V  C14  C  CR16  0   0.097  468.9277  -19.7229  125.1791
 X2V  C16  C  CR6   0   0.572  471.0816  -20.7170  125.5635
 X2V  C17  C  CR6   0   0.738  470.4349  -19.8475  123.3311
 X2V  C20  C  CR16  0  -0.327  471.5976  -13.8224  126.2979
 X2V  C21  C  CR66  0   0.131  471.9891  -15.1561  126.5579
 X2V  C22  C  CR16  0  -0.311  472.1660  -15.6198  127.8776
 X2V  C    C  CSP   0   0.054  472.6988  -17.3795  129.4533
 X2V  C13  C  CH2   0  -0.379  468.2515  -18.7833  123.0351
 X2V  C15  C  CR16  0  -0.499  469.7854  -20.3012  126.0361
 X2V  C18  C  CR16  0  -0.336  471.6318  -14.2829  123.9276
 X2V  C19  C  CR16  0  -0.252  471.4232  -13.4048  125.0090
 X2V  C3   C  CR16  0  -0.281  472.5721  -17.3938  125.7553
 X2V  C5   C  CR6   0   0.354  472.0108  -15.5767  124.1612
 X2V  C6   C  CR6   0   0.261  471.5797  -16.3567  121.9878
 X2V  C9   C  CR6   0   0.322  470.2412  -16.2958  119.6125
 X2V  F    F  F     0  -0.391  470.1104  -14.1824  117.4468
 X2V  N1   N  NR6   0  -0.513  469.2103  -19.5018  123.8635
 X2V  N2   N  NR16  0  -0.736  471.2908  -20.4493  124.2188
 X2V  O1   O  OC2   0  -0.586  469.5555  -16.3262  118.3893
 X2V  O2   O  OS    0  -0.581  468.2289  -14.2898  118.9498
 X2V  O3   O  OS    0  -0.573  468.1471  -15.3726  116.6801
 X2V  S    S  S     0   1.745  468.8329  -15.0143  117.8771
 X2V  H1   H  HCR6  0   0.278  473.0125  -18.8493  127.2446
 X2V  H2   H  HCR6  0   0.290  473.3369  -15.9395  120.8589
 X2V  H3   H  HCR6  0   0.292  472.1350  -15.8843  118.6826
 X2V  H4   H  HCR6  0   0.308  468.4566  -16.7418  120.7008
 X2V  H5   H  HCH2  0   0.266  467.6174  -16.7645  122.6283
 X2V  H6   H  HCH2  0   0.280  468.0163  -17.0626  124.3103
 X2V  H7   H  HCR6  0   0.325  467.9458  -19.4031  125.5003
 X2V  H8   H  HCR6  0   0.264  471.4407  -13.1441  127.1265
 X2V  H9   H  HCR6  0   0.283  472.0118  -14.9372  128.7034
 X2V  H10  H  HCH2  0   0.299  467.2479  -19.1346  123.2753
 X2V  H11  H  HCH2  0   0.295  468.4355  -19.0334  121.9934
 X2V  H12  H  HCR6  0   0.293  469.5127  -20.4614  127.0673
 X2V  H13  H  HCR6  0   0.286  471.4913  -13.9213  122.9167
 X2V  H14  H  HCR6  0   0.271  471.1253  -12.3860  124.8015
 X2V  H15  H  HCR6  0   0.263  472.7366  -18.0847  124.9412
 X2V  H16  H  HNR6  0   0.426  472.1831  -20.7323  123.8314
 X2V  O    O  O2    0  -0.504  472.2622  -16.4700  123.1644
 X2V  N    N  NS    0  -0.249  472.8313  -17.7558  130.5343
 X2V  O4   O  O2    0  -0.465  469.6369  -16.7899  123.1759
 X2V  O6   O  O     0  -0.471  470.7364  -19.6518  122.1735
 X2V  O5   O  O     0  -0.467  471.9492  -21.2540  126.2284

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
 X2V  F    S    single    1.584  0.020  1.584
 X2V  O3   S    double    1.425  0.020  1.425
 X2V  S    O1   single    1.583  0.020  1.583
 X2V  S    O2   double    1.428  0.020  1.428
 X2V  O1   C9   single    1.403  0.020  1.403
 X2V  C9   C8   aromatic  1.376  0.020  1.376
 X2V  C9   C10  aromatic  1.386  0.020  1.386
 X2V  C8   C7   aromatic  1.391  0.020  1.391
 X2V  C10  C11  aromatic  1.386  0.020  1.386
 X2V  C7   C6   aromatic  1.378  0.020  1.378
 X2V  O6   C17  double    1.212  0.020  1.212
 X2V  C11  C6   aromatic  1.403  0.020  1.403
 X2V  C11  O4   single    1.338  0.020  1.338
 X2V  C6   O    single    1.365  0.020  1.365
 X2V  C13  C12  single    1.520  0.020  1.520
 X2V  C13  N1   single    1.457  0.020  1.457
 X2V  C12  O4   single    1.414  0.020  1.414
 X2V  C17  N1   single    1.379  0.020  1.379
 X2V  C17  N2   single    1.372  0.020  1.372
 X2V  N1   C14  single    1.364  0.020  1.364
 X2V  N2   C16  single    1.387  0.020  1.387
 X2V  O    C5   single    1.362  0.020  1.362
 X2V  C18  C5   aromatic  1.368  0.020  1.368
 X2V  C18  C19  aromatic  1.409  0.020  1.409
 X2V  C14  C15  double    1.343  0.020  1.343
 X2V  C5   C4   aromatic  1.418  0.020  1.418
 X2V  C16  C15  single    1.441  0.020  1.441
 X2V  C16  O5   double    1.218  0.020  1.218
 X2V  C19  C20  aromatic  1.366  0.020  1.366
 X2V  C4   C3   aromatic  1.414  0.020  1.414
 X2V  C4   C21  aromatic  1.419  0.020  1.419
 X2V  C3   C2   aromatic  1.365  0.020  1.365
 X2V  C20  C21  aromatic  1.414  0.020  1.414
 X2V  C21  C22  aromatic  1.410  0.020  1.410
 X2V  C2   C1   aromatic  1.415  0.020  1.415
 X2V  C22  C1   aromatic  1.374  0.020  1.374
 X2V  C1   C    single    1.427  0.020  1.427
 X2V  C    N    triple    1.152  0.020  1.152
 X2V  C2   H1   single    0.930  0.020  1.080
 X2V  C7   H2   single    0.930  0.020  1.080
 X2V  C8   H3   single    0.930  0.020  1.080
 X2V  C10  H4   single    0.930  0.020  1.080
 X2V  C12  H5   single    0.970  0.020  1.090
 X2V  C12  H6   single    0.970  0.020  1.090
 X2V  C14  H7   single    0.930  0.020  1.080
 X2V  C20  H8   single    0.930  0.020  1.080
 X2V  C22  H9   single    0.930  0.020  1.080
 X2V  C13  H10  single    0.970  0.020  1.090
 X2V  C13  H11  single    0.970  0.020  1.090
 X2V  C15  H12  single    0.930  0.020  1.080
 X2V  C18  H13  single    0.930  0.020  1.080
 X2V  C19  H14  single    0.930  0.020  1.080
 X2V  C3   H15  single    0.930  0.020  1.080
 X2V  N2   H16  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
 X2V  C    C1   C22  119.64  3.000
 X2V  C    C1   C2   119.44  3.000
 X2V  C22  C1   C2   120.92  3.000
 X2V  H1   C2   C3   120.55  3.000
 X2V  H1   C2   C1   119.81  3.000
 X2V  C3   C2   C1   119.63  3.000
 X2V  C5   C4   C3   122.38  3.000
 X2V  C3   C4   C21  119.48  3.000
 X2V  C5   C4   C21  118.14  3.000
 X2V  H2   C7   C6   119.46  3.000
 X2V  H2   C7   C8   120.16  3.000
 X2V  C6   C7   C8   120.38  3.000
 X2V  H3   C8   C9   121.57  3.000
 X2V  H3   C8   C7   120.75  3.000
 X2V  C9   C8   C7   117.68  3.000
 X2V  H4   C10  C9   119.55  3.000
 X2V  H4   C10  C11  121.90  3.000
 X2V  C9   C10  C11  118.54  3.000
 X2V  O4   C11  C6   115.46  3.000
 X2V  O4   C11  C10  125.60  3.000
 X2V  C6   C11  C10  118.93  3.000
 X2V  H6   C12  H5   106.95  3.000
 X2V  H6   C12  O4   105.02  3.000
 X2V  H5   C12  O4   112.51  3.000
 X2V  H6   C12  C13  110.21  3.000
 X2V  H5   C12  C13  110.04  3.000
 X2V  O4   C12  C13  111.88  3.000
 X2V  H7   C14  N1   115.26  3.000
 X2V  H7   C14  C15  121.17  3.000
 X2V  N1   C14  C15  123.57  3.000
 X2V  N2   C16  C15  113.45  3.000
 X2V  C15  C16  O5   126.09  3.000
 X2V  N2   C16  O5   120.46  3.000
 X2V  O6   C17  N2   122.24  3.000
 X2V  N2   C17  N1   114.46  3.000
 X2V  O6   C17  N1   123.30  3.000
 X2V  H8   C20  C19  120.81  3.000
 X2V  H8   C20  C21  119.38  3.000
 X2V  C19  C20  C21  119.81  3.000
 X2V  C22  C21  C20  121.13  3.000
 X2V  C22  C21  C4   118.85  3.000
 X2V  C20  C21  C4   120.01  3.000
 X2V  H9   C22  C21  119.26  3.000
 X2V  H9   C22  C1   120.42  3.000
 X2V  C21  C22  C1   120.31  3.000
 X2V  N    C    C1   180.00  3.000
 X2V  H11  C13  H10  107.04  3.000
 X2V  H11  C13  N1   108.67  3.000
 X2V  H10  C13  N1   108.77  3.000
 X2V  H11  C13  C12  112.21  3.000
 X2V  H10  C13  C12  108.70  3.000
 X2V  N1   C13  C12  111.31  3.000
 X2V  H12  C15  C16  119.88  3.000
 X2V  H12  C15  C14  120.82  3.000
 X2V  C16  C15  C14  119.30  3.000
 X2V  H13  C18  C5   120.74  3.000
 X2V  H13  C18  C19  119.30  3.000
 X2V  C5   C18  C19  119.96  3.000
 X2V  H14  C19  C18  118.73  3.000
 X2V  H14  C19  C20  120.28  3.000
 X2V  C18  C19  C20  120.99  3.000
 X2V  H15  C3   C4   119.91  3.000
 X2V  H15  C3   C2   119.28  3.000
 X2V  C4   C3   C2   120.81  3.000
 X2V  C18  C5   O    123.12  3.000
 X2V  C18  C5   C4   121.08  3.000
 X2V  O    C5   C4   115.78  3.000
 X2V  O    C6   C11  119.11  3.000
 X2V  O    C6   C7   119.69  3.000
 X2V  C11  C6   C7   121.09  3.000
 X2V  O1   C9   C10  117.90  3.000
 X2V  C10  C9   C8   123.38  3.000
 X2V  O1   C9   C8   118.66  3.000
 X2V  C13  N1   C17  119.25  3.000
 X2V  C17  N1   C14  121.05  3.000
 X2V  C13  N1   C14  119.49  3.000
 X2V  H16  N2   C17  115.12  3.000
 X2V  H16  N2   C16  116.72  3.000
 X2V  C17  N2   C16  128.16  3.000
 X2V  S    O1   C9   119.17  3.000
 X2V  O3   S    O2   123.69  3.000
 X2V  O2   S    O1   111.74  3.000
 X2V  O3   S    O1   106.44  3.000
 X2V  O2   S    F    106.18  3.000
 X2V  O1   S    F     98.92  3.000
 X2V  O3   S    F    106.97  3.000
 X2V  C6   O    C5   118.96  3.000
 X2V  C12  O4   C11  120.92  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
 X2V  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 X2V  CONST_02  C4   C21  C22  C1      0.00   0.0  0
 X2V  CONST_03  C20  C21  C22  C1    180.00   0.0  0
 X2V  CONST_04  C5   C4   C3   C2    180.00   0.0  0
 X2V  CONST_05  C21  C4   C3   C2      0.00   0.0  0
 X2V  CONST_06  C21  C22  C1   C2      0.00   0.0  0
 X2V  CONST_07  C19  C18  C5   C4      0.00   0.0  0
 X2V  CONST_08  C19  C20  C21  C4      0.00   0.0  0
 X2V  CONST_09  C10  C9   C8   C7      0.00   0.0  0
 X2V  CONST_10  C10  C11  C6   C7      0.00   0.0  0
 X2V  CONST_11  C11  C10  C9   C8      0.00   0.0  0
 X2V  CONST_12  C11  C6   C7   C8      0.00   0.0  0
 X2V  CONST_13  C5   C18  C19  C20     0.00   0.0  0
 X2V  CONST_14  C5   C4   C21  C20     0.00   0.0  0
 X2V  CONST_15  C3   C4   C21  C20   180.00   0.0  0
 X2V  CONST_16  C18  C5   C4   C21     0.00   0.0  0
 X2V  CONST_17  C18  C19  C20  C21     0.00   0.0  0
 X2V  CONST_18  C5   C4   C21  C22   180.00   0.0  0
 X2V  CONST_19  C3   C4   C21  C22     0.00   0.0  0
 X2V  CONST_20  C19  C20  C21  C22   180.00   0.0  0
 X2V  CONST_21  C3   C2   C1   C22     0.00   0.0  0
 X2V  CONST_22  C3   C4   C5   C18   180.00   0.0  0
 X2V  CONST_23  C9   C8   C7   C6      0.00   0.0  0
 X2V  CONST_24  C9   C10  C11  C6      0.00   0.0  0
 X2V  CONST_25  N2   C17  N1   C14     0.00   0.0  0
 X2V  CONST_26  N1   C17  N2   C16     0.00   0.0  0
 X2V  CONST_27  C15  C16  N2   C17     0.00   0.0  0
 X2V  CONST_28  O1   C9   C8   C7    180.00   0.0  0
 X2V  CONST_29  O4   C11  C6   C7    180.00   0.0  0
 X2V  CONST_30  O    C6   C7   C8    180.00   0.0  0
 X2V  CONST_31  O    C6   C11  C10   180.00   0.0  0
 X2V  CONST_32  O1   C9   C10  C11   180.00   0.0  0
 X2V  CONST_33  O    C5   C4   C21   180.00   0.0  0
 X2V  CONST_34  C    C1   C22  C21   180.00   0.0  0
 X2V  CONST_35  C3   C2   C1   C     180.00   0.0  0
 X2V  CONST_36  C19  C18  C5   O     180.00   0.0  0
 X2V  CONST_37  C3   C4   C5   O       0.00   0.0  0
 X2V  CONST_38  O4   C11  C10  C9    180.00   0.0  0
 X2V  CONST_39  C17  N2   C16  O5    180.00   0.0  0
 X2V  CONST_40  O6   C17  N1   C14   180.00   0.0  0
 X2V  CONST_41  O6   C17  N2   C16   180.00   0.0  0
 X2V  CONST_42  N2   C17  N1   C13   180.00   0.0  0
 X2V  CONST_43  H15  C3   C2   C1    180.00   0.0  0
 X2V  CONST_44  H9   C22  C1   C2    180.00   0.0  0
 X2V  CONST_45  H13  C18  C5   C4    180.00   0.0  0
 X2V  CONST_46  H1   C2   C3   C4    180.00   0.0  0
 X2V  CONST_47  H8   C20  C21  C4    180.00   0.0  0
 X2V  CONST_48  H4   C10  C9   C8    180.00   0.0  0
 X2V  CONST_49  H3   C8   C9   C10   180.00   0.0  0
 X2V  CONST_50  H2   C7   C6   C11   180.00   0.0  0
 X2V  CONST_51  H14  C19  C20  C21   180.00   0.0  0
 X2V  CONST_52  H16  N2   C16  C15   180.00   0.0  0
 X2V  CONST_53  O6   C17  N1   C13     0.00   0.0  0
 X2V  Var_01    C17  N1   C13  C12   -96.71  30.0  3
 X2V  Var_02    C6   C11  O4   C12  -167.39  30.0  1
 X2V  Var_03    C13  C12  O4   C11    77.78  30.0  1
 X2V  Var_04    F    S    O1   C9     73.55  30.0  2
 X2V  Var_05    O4   C12  C13  N1     52.00  30.0  3

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
 X2V  plan-1  C14  0.020
 X2V  plan-1  C16  0.020
 X2V  plan-1  C17  0.020
 X2V  plan-1  C13  0.020
 X2V  plan-1  C15  0.020
 X2V  plan-1  N1   0.020
 X2V  plan-1  N2   0.020
 X2V  plan-1  H7   0.020
 X2V  plan-1  H12  0.020
 X2V  plan-1  H16  0.020
 X2V  plan-1  O6   0.020
 X2V  plan-1  O5   0.020
 X2V  plan-2  C7   0.020
 X2V  plan-2  C8   0.020
 X2V  plan-2  C10  0.020
 X2V  plan-2  C11  0.020
 X2V  plan-2  C6   0.020
 X2V  plan-2  C9   0.020
 X2V  plan-2  O1   0.020
 X2V  plan-2  H2   0.020
 X2V  plan-2  H3   0.020
 X2V  plan-2  H4   0.020
 X2V  plan-2  O    0.020
 X2V  plan-2  O4   0.020
 X2V  plan-3  C1   0.020
 X2V  plan-3  C2   0.020
 X2V  plan-3  C4   0.020
 X2V  plan-3  C20  0.020
 X2V  plan-3  C21  0.020
 X2V  plan-3  C22  0.020
 X2V  plan-3  C    0.020
 X2V  plan-3  C18  0.020
 X2V  plan-3  C19  0.020
 X2V  plan-3  C3   0.020
 X2V  plan-3  C5   0.020
 X2V  plan-3  H1   0.020
 X2V  plan-3  H8   0.020
 X2V  plan-3  H9   0.020
 X2V  plan-3  H13  0.020
 X2V  plan-3  H14  0.020
 X2V  plan-3  H15  0.020
 X2V  plan-3  O    0.020
 X2V  plan-3  N    0.020

