# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 20:02:31 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: 6-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]-4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3,5-bis(fluoranyl)phenyl]methoxy]-1-methyl-pyrimidin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N=C(OCc2cc(F)c(Oc3ccc(Cl)c(c3)C(F)(F)F)c(F)c2)C=C1N4CC[S](=O)(=O)CC4
#
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
 VQ7  VQ7  6-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]-4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3,5-bis(fluoranyl)phenyl]methoxy]-1-methyl-pyrimidin-2-one  ligand  57  38  .  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_VQ7
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
 VQ7  O4   O   O     0  -0.499  -6.0192  -3.9507  -0.8711
 VQ7  C22  C   CR6   0   0.600  -5.3817  -2.9820  -0.4924
 VQ7  N    N   NR6   0  -0.561  -6.0726  -1.8137  -0.1266
 VQ7  C    C   CH3   0  -0.561  -7.5158  -1.9492   0.0372
 VQ7  N2   N   N     0  -0.544  -4.0330  -3.0000  -0.3767
 VQ7  C7   C   CR6   0   0.588  -3.4102  -1.9283   0.0177
 VQ7  C6   C   CR16  0  -0.538  -4.0370  -0.7024   0.2999
 VQ7  C1   C   CR6   0   0.689  -5.4031  -0.6670   0.1987
 VQ7  N1   N   NT    0  -0.494  -6.1461   0.4597   0.4484
 VQ7  C5   C   CH2   0  -0.370  -5.6376   1.4663   1.3608
 VQ7  C4   C   CH2   0  -0.620  -4.8341   2.5884   0.7005
 VQ7  S    S   S     0   1.211  -5.8183   3.4020  -0.5488
 VQ7  O    O   OS    0  -0.671  -4.9690   4.2504  -1.3808
 VQ7  O1   O   OS    0  -0.681  -6.9808   4.0044   0.1060
 VQ7  C3   C   CH2   0  -0.611  -6.3767   1.9888  -1.4878
 VQ7  C2   C   CH2   0  -0.364  -7.0531   0.9708  -0.5713
 VQ7  O2   O   O2    0  -0.456  -2.0909  -1.9381   0.1321
 VQ7  C8   C   CH2   0  -0.247  -1.3886  -3.1453  -0.1785
 VQ7  C9   C   CR6   0   0.102   0.0708  -2.8103  -0.1120
 VQ7  C21  C   CR16  0  -0.463   0.7012  -2.2634  -1.2252
 VQ7  C20  C   CR6   0   0.548   2.0362  -1.9351  -1.1446
 VQ7  F4   F   F     0  -0.292   2.6650  -1.4087  -2.1960
 VQ7  C12  C   CR6   0  -0.012   2.7700  -2.1235   0.0188
 VQ7  C11  C   CR6   0   0.531   2.1152  -2.6616   1.1150
 VQ7  F    F   F     0  -0.291   2.8113  -2.8396   2.2370
 VQ7  C10  C   CR16  0  -0.468   0.7808  -3.0111   1.0649
 VQ7  O3   O   O2    0  -0.487   4.1002  -1.8502   0.0703
 VQ7  C13  C   CR6   0   0.409   4.5037  -0.5517   0.1685
 VQ7  C19  C   CR16  0  -0.391   5.8672  -0.3337   0.0231
 VQ7  C17  C   CR6   0  -0.115   6.3823   0.9493   0.1109
 VQ7  C18  C   CT    0   1.075   7.8582   1.1707  -0.0611
 VQ7  F3   F   F     0  -0.297   8.5158   0.0279  -0.2672
 VQ7  F2   F   F     0  -0.308   8.1183   1.9628  -1.1070
 VQ7  F1   F   F     0  -0.308   8.4047   1.7438   1.0159
 VQ7  C16  C   CR6   0  -0.082   5.5166   2.0178   0.3442
 VQ7  CL   CL  CL    0  -0.104   6.0938   3.6438   0.4490
 VQ7  C15  C   CR16  0  -0.186   4.1608   1.7917   0.4937
 VQ7  C14  C   CR16  0  -0.339   3.6451   0.5081   0.4078
 VQ7  H1   H   HCH3  0   0.262  -8.0405  -1.8956  -0.9155
 VQ7  H2   H   HCH3  0   0.279  -7.7310  -2.9117   0.4916
 VQ7  H3   H   HCH3  0   0.274  -7.8836  -1.1693   0.6958
 VQ7  H4   H   HCR6  0   0.288  -3.4533   0.1754   0.5243
 VQ7  H5   H   HCH2  0   0.300  -6.4927   1.8998   1.8846
 VQ7  H6   H   HCH2  0   0.307  -5.0191   0.9886   2.1187
 VQ7  H7   H   HCH2  0   0.335  -4.5629   3.3500   1.4339
 VQ7  H8   H   HCH2  0   0.307  -3.9250   2.2359   0.2132
 VQ7  H9   H   HCH2  0   0.335  -7.0733   2.3651  -2.2396
 VQ7  H10  H   HCH2  0   0.310  -5.5084   1.5651  -1.9953
 VQ7  H11  H   HCH2  0   0.311  -7.4231   0.1661  -1.2005
 VQ7  H12  H   HCH2  0   0.288  -7.9210   1.4183  -0.0843
 VQ7  H13  H   HCH2  0   0.262  -1.6458  -3.9245   0.5413
 VQ7  H14  H   HCH2  0   0.262  -1.6618  -3.4994  -1.1736
 VQ7  H15  H   HCR6  0   0.294   0.1623  -2.1015  -2.1502
 VQ7  H16  H   HCR6  0   0.295   0.3036  -3.4339   1.9395
 VQ7  H17  H   HCR6  0   0.297   6.5125  -1.1823  -0.1582
 VQ7  H18  H   HCR6  0   0.300   3.4926   2.6212   0.6779
 VQ7  H19  H   HCR6  0   0.302   2.5802   0.3662   0.5355

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
 VQ7  C3   C2   single    1.528  0.020  1.528
 VQ7  C3   S    single    1.786  0.020  1.786
 VQ7  O1   S    double    1.464  0.020  1.464
 VQ7  C2   N1   single    1.457  0.020  1.457
 VQ7  S    O    double    1.461  0.020  1.461
 VQ7  S    C4   single    1.786  0.020  1.786
 VQ7  C    N    single    1.459  0.020  1.459
 VQ7  N1   C1   single    1.373  0.020  1.373
 VQ7  N1   C5   single    1.451  0.020  1.451
 VQ7  N    C1   single    1.367  0.020  1.367
 VQ7  N    C22  single    1.406  0.020  1.406
 VQ7  C1   C6   double    1.370  0.020  1.370
 VQ7  O4   C22  double    1.220  0.020  1.220
 VQ7  C22  N2   single    1.354  0.020  1.354
 VQ7  C5   C4   single    1.530  0.020  1.530
 VQ7  C6   C7   single    1.405  0.020  1.405
 VQ7  N2   C7   double    1.301  0.020  1.301
 VQ7  C7   O2   single    1.324  0.020  1.324
 VQ7  O2   C8   single    1.431  0.020  1.431
 VQ7  C8   C9   single    1.499  0.020  1.499
 VQ7  C21  C9   aromatic  1.391  0.020  1.391
 VQ7  C21  C20  aromatic  1.377  0.020  1.377
 VQ7  C9   C10  aromatic  1.389  0.020  1.389
 VQ7  F4   C20  single    1.333  0.020  1.333
 VQ7  C20  C12  aromatic  1.388  0.020  1.388
 VQ7  C10  C11  aromatic  1.380  0.020  1.380
 VQ7  C12  C11  aromatic  1.386  0.020  1.386
 VQ7  C12  O3   single    1.359  0.020  1.359
 VQ7  C14  C15  aromatic  1.386  0.020  1.386
 VQ7  C14  C13  aromatic  1.385  0.020  1.385
 VQ7  C15  C16  aromatic  1.383  0.020  1.383
 VQ7  C11  F    single    1.332  0.020  1.332
 VQ7  O3   C13  single    1.363  0.020  1.363
 VQ7  C13  C19  aromatic  1.388  0.020  1.388
 VQ7  C16  CL   single    1.729  0.020  1.729
 VQ7  C16  C17  aromatic  1.395  0.020  1.395
 VQ7  C19  C17  aromatic  1.385  0.020  1.385
 VQ7  C17  C18  single    1.502  0.020  1.502
 VQ7  F2   C18  single    1.338  0.020  1.338
 VQ7  C18  F3   single    1.334  0.020  1.334
 VQ7  C18  F1   single    1.337  0.020  1.337
 VQ7  C    H1   single    0.970  0.020  1.090
 VQ7  C    H2   single    0.970  0.020  1.090
 VQ7  C    H3   single    0.970  0.020  1.090
 VQ7  C6   H4   single    0.930  0.020  1.080
 VQ7  C5   H5   single    0.970  0.020  1.090
 VQ7  C5   H6   single    0.970  0.020  1.090
 VQ7  C4   H7   single    0.970  0.020  1.090
 VQ7  C4   H8   single    0.970  0.020  1.090
 VQ7  C3   H9   single    0.970  0.020  1.090
 VQ7  C3   H10  single    0.970  0.020  1.090
 VQ7  C2   H11  single    0.970  0.020  1.090
 VQ7  C2   H12  single    0.970  0.020  1.090
 VQ7  C8   H13  single    0.970  0.020  1.090
 VQ7  C8   H14  single    0.970  0.020  1.090
 VQ7  C21  H15  single    0.930  0.020  1.080
 VQ7  C10  H16  single    0.930  0.020  1.080
 VQ7  C19  H17  single    0.930  0.020  1.080
 VQ7  C15  H18  single    0.930  0.020  1.080
 VQ7  C14  H19  single    0.930  0.020  1.080

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
 VQ7  N2   C22  N    118.58  3.000
 VQ7  N2   C22  O4   122.45  3.000
 VQ7  N    C22  O4   118.94  3.000
 VQ7  C1   N    C    122.39  3.000
 VQ7  C1   N    C22  121.22  3.000
 VQ7  C    N    C22  115.99  3.000
 VQ7  H3   C    H2   108.42  3.000
 VQ7  H3   C    H1   109.41  3.000
 VQ7  H2   C    H1   108.32  3.000
 VQ7  H3   C    N    109.68  3.000
 VQ7  H2   C    N    108.99  3.000
 VQ7  H1   C    N    111.95  3.000
 VQ7  C7   N2   C22  119.47  3.000
 VQ7  O2   C7   C6   115.68  3.000
 VQ7  O2   C7   N2   119.81  3.000
 VQ7  C6   C7   N2   124.47  3.000
 VQ7  H4   C6   C1   122.29  3.000
 VQ7  H4   C6   C7   120.71  3.000
 VQ7  C1   C6   C7   116.89  3.000
 VQ7  N1   C1   C6   123.19  3.000
 VQ7  C6   C1   N    118.96  3.000
 VQ7  N1   C1   N    117.82  3.000
 VQ7  C2   N1   C5   114.52  3.000
 VQ7  C5   N1   C1   119.62  3.000
 VQ7  C2   N1   C1   119.84  3.000
 VQ7  H6   C5   H5   106.56  3.000
 VQ7  H6   C5   C4   108.90  3.000
 VQ7  H5   C5   C4   109.08  3.000
 VQ7  H6   C5   N1   109.42  3.000
 VQ7  H5   C5   N1   107.61  3.000
 VQ7  C4   C5   N1   114.93  3.000
 VQ7  H8   C4   H7   108.59  3.000
 VQ7  H8   C4   S    107.11  3.000
 VQ7  H7   C4   S    106.80  3.000
 VQ7  H8   C4   C5   113.19  3.000
 VQ7  H7   C4   C5   110.62  3.000
 VQ7  S    C4   C5   110.28  3.000
 VQ7  C3   S    O1   108.21  3.000
 VQ7  O1   S    O    118.52  3.000
 VQ7  C3   S    O    109.99  3.000
 VQ7  O    S    C4   110.04  3.000
 VQ7  O1   S    C4   108.19  3.000
 VQ7  C3   S    C4   100.34  3.000
 VQ7  H10  C3   H9   108.74  3.000
 VQ7  H10  C3   C2   111.87  3.000
 VQ7  H9   C3   C2   111.12  3.000
 VQ7  H10  C3   S    107.63  3.000
 VQ7  H9   C3   S    106.78  3.000
 VQ7  C2   C3   S    110.50  3.000
 VQ7  H12  C2   H11  106.94  3.000
 VQ7  H12  C2   C3   110.28  3.000
 VQ7  H11  C2   C3   107.27  3.000
 VQ7  H12  C2   N1   109.06  3.000
 VQ7  H11  C2   N1   110.95  3.000
 VQ7  C3   C2   N1   112.20  3.000
 VQ7  C8   O2   C7   118.46  3.000
 VQ7  H14  C8   H13  108.11  3.000
 VQ7  H14  C8   C9   110.91  3.000
 VQ7  H13  C8   C9   111.09  3.000
 VQ7  H14  C8   O2   110.42  3.000
 VQ7  H13  C8   O2   110.09  3.000
 VQ7  C9   C8   O2   106.24  3.000
 VQ7  C10  C9   C21  120.21  3.000
 VQ7  C10  C9   C8   120.20  3.000
 VQ7  C21  C9   C8   119.58  3.000
 VQ7  H15  C21  C20  119.79  3.000
 VQ7  H15  C21  C9   121.12  3.000
 VQ7  C20  C21  C9   119.09  3.000
 VQ7  C12  C20  F4   117.72  3.000
 VQ7  C12  C20  C21  121.94  3.000
 VQ7  F4   C20  C21  120.34  3.000
 VQ7  O3   C12  C11  120.71  3.000
 VQ7  O3   C12  C20  121.45  3.000
 VQ7  C11  C12  C20  117.77  3.000
 VQ7  C10  C11  F    120.13  3.000
 VQ7  F    C11  C12  118.11  3.000
 VQ7  C10  C11  C12  121.76  3.000
 VQ7  H16  C10  C11  119.72  3.000
 VQ7  H16  C10  C9   121.05  3.000
 VQ7  C11  C10  C9   119.23  3.000
 VQ7  C13  O3   C12  118.95  3.000
 VQ7  C14  C13  C19  120.45  3.000
 VQ7  C19  C13  O3   115.64  3.000
 VQ7  C14  C13  O3   123.91  3.000
 VQ7  H17  C19  C17  121.03  3.000
 VQ7  H17  C19  C13  118.71  3.000
 VQ7  C17  C19  C13  120.26  3.000
 VQ7  C16  C17  C18  121.06  3.000
 VQ7  C18  C17  C19  119.64  3.000
 VQ7  C16  C17  C19  119.29  3.000
 VQ7  F1   C18  F2   107.26  3.000
 VQ7  F1   C18  F3   106.87  3.000
 VQ7  F2   C18  F3   106.89  3.000
 VQ7  F1   C18  C17  111.88  3.000
 VQ7  F3   C18  C17  112.06  3.000
 VQ7  F2   C18  C17  111.58  3.000
 VQ7  C15  C16  CL   118.34  3.000
 VQ7  CL   C16  C17  121.57  3.000
 VQ7  C15  C16  C17  120.09  3.000
 VQ7  H18  C15  C14  119.42  3.000
 VQ7  H18  C15  C16  119.93  3.000
 VQ7  C14  C15  C16  120.64  3.000
 VQ7  H19  C14  C15  118.72  3.000
 VQ7  H19  C14  C13  122.02  3.000
 VQ7  C15  C14  C13  119.26  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
 VQ7  CONST_01  C12  C20  C21  C9     0.00   0.0  0
 VQ7  CONST_02  C12  C11  C10  C9     0.00   0.0  0
 VQ7  CONST_03  C11  C10  C9   C21    0.00   0.0  0
 VQ7  CONST_04  C11  C12  C20  C21    0.00   0.0  0
 VQ7  CONST_05  C10  C9   C21  C20    0.00   0.0  0
 VQ7  CONST_06  C10  C11  C12  C20    0.00   0.0  0
 VQ7  CONST_07  C16  C15  C14  C13    0.00   0.0  0
 VQ7  CONST_08  C16  C17  C19  C13    0.00   0.0  0
 VQ7  CONST_09  C15  C14  C13  C19    0.00   0.0  0
 VQ7  CONST_10  C15  C16  C17  C19    0.00   0.0  0
 VQ7  CONST_11  C14  C15  C16  C17    0.00   0.0  0
 VQ7  CONST_12  C14  C13  C19  C17    0.00   0.0  0
 VQ7  CONST_13  N1   C1   N    C22  180.00   0.0  0
 VQ7  CONST_14  C6   C1   N    C22    0.00   0.0  0
 VQ7  CONST_17  C7   N2   C22  N      0.00   0.0  0
 VQ7  CONST_18  C1   N    C22  N2     0.00   0.0  0
 VQ7  CONST_21  C20  C21  C9   C8   180.00   0.0  0
 VQ7  CONST_22  C11  C10  C9   C8   180.00   0.0  0
 VQ7  CONST_23  F4   C20  C21  C9   180.00   0.0  0
 VQ7  CONST_24  F    C11  C10  C9   180.00   0.0  0
 VQ7  CONST_25  O3   C12  C20  C21  180.00   0.0  0
 VQ7  CONST_26  F    C11  C12  C20  180.00   0.0  0
 VQ7  CONST_27  C11  C12  C20  F4   180.00   0.0  0
 VQ7  CONST_28  O3   C12  C11  C10  180.00   0.0  0
 VQ7  CONST_29  C15  C14  C13  O3   180.00   0.0  0
 VQ7  CONST_30  C17  C19  C13  O3   180.00   0.0  0
 VQ7  CONST_31  C18  C17  C19  C13  180.00   0.0  0
 VQ7  CONST_32  CL   C16  C17  C19  180.00   0.0  0
 VQ7  CONST_33  C15  C16  C17  C18  180.00   0.0  0
 VQ7  CONST_34  C14  C15  C16  CL   180.00   0.0  0
 VQ7  CONST_35  C1   N    C22  O4   180.00   0.0  0
 VQ7  CONST_36  C7   N2   C22  O4   180.00   0.0  0
 VQ7  CONST_37  N1   C1   N    C      0.00   0.0  0
 VQ7  CONST_38  C6   C1   N    C    180.00   0.0  0
 VQ7  CONST_39  N2   C22  N    C    180.00   0.0  0
 VQ7  CONST_40  H16  C10  C9   C21  180.00   0.0  0
 VQ7  CONST_41  H15  C21  C20  C12  180.00   0.0  0
 VQ7  CONST_42  H18  C15  C14  C13  180.00   0.0  0
 VQ7  CONST_43  H19  C14  C13  C19  180.00   0.0  0
 VQ7  CONST_44  H17  C19  C17  C16  180.00   0.0  0
 VQ7  CONST_45  C    N    C22  O4     0.00   0.0  0
 VQ7  Var_01    C3   C2   N1   C1   -90.72  30.0  1
 VQ7  Var_02    C4   C5   N1   C1    92.25  30.0  1
 VQ7  Var_03    S    C3   C2   N1   -61.24  30.0  1
 VQ7  Var_04    S    C4   C5   N1    57.02  30.0  1
 VQ7  Var_05    C3   S    C4   C5   -51.08  30.0  1
 VQ7  Var_06    C2   C3   S    C4    53.97  30.0  1
 VQ7  Var_07    C14  C13  O3   C12    9.41  30.0  2
 VQ7  Var_08    C9   C8   O2   C7   173.66  30.0  3
 VQ7  Var_09    C21  C9   C8   O2   -84.95  30.0  2
 VQ7  Var_10    F2   C18  C17  C19  118.79  30.0  2
 VQ7  Var_11    H1   C    N    C22  -82.16  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
 VQ7  plan-1  O4   0.020
 VQ7  plan-1  C22  0.020
 VQ7  plan-1  N    0.020
 VQ7  plan-1  C    0.020
 VQ7  plan-1  N2   0.020
 VQ7  plan-1  C7   0.020
 VQ7  plan-1  C6   0.020
 VQ7  plan-1  C1   0.020
 VQ7  plan-1  N1   0.020
 VQ7  plan-1  C5   0.020
 VQ7  plan-1  C2   0.020
 VQ7  plan-1  O2   0.020
 VQ7  plan-1  H4   0.020
 VQ7  plan-2  C8   0.020
 VQ7  plan-2  C9   0.020
 VQ7  plan-2  C21  0.020
 VQ7  plan-2  C20  0.020
 VQ7  plan-2  F4   0.020
 VQ7  plan-2  C12  0.020
 VQ7  plan-2  C11  0.020
 VQ7  plan-2  F    0.020
 VQ7  plan-2  C10  0.020
 VQ7  plan-2  O3   0.020
 VQ7  plan-2  H15  0.020
 VQ7  plan-2  H16  0.020
 VQ7  plan-3  O3   0.020
 VQ7  plan-3  C13  0.020
 VQ7  plan-3  C19  0.020
 VQ7  plan-3  C17  0.020
 VQ7  plan-3  C18  0.020
 VQ7  plan-3  C16  0.020
 VQ7  plan-3  CL   0.020
 VQ7  plan-3  C15  0.020
 VQ7  plan-3  C14  0.020
 VQ7  plan-3  H17  0.020
 VQ7  plan-3  H18  0.020
 VQ7  plan-3  H19  0.020

