# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:47:50 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 2-(5,6-dimethoxypyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(cnc1OC)N2C(=O)N(Cc3c(F)cc(F)cc3F)c4ncccc4[S]2(=O)=O
#
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
 NU8  NU8  2-(5,6-dimethoxypyridin-3-yl)-1,1-bis(oxidanylidene)-4-[[2,4,6-tris(fluoranyl)phenyl]methyl]pyrido[2,3-e][1,2,4]thiadiazin-3-one  ligand  48  33  .  2021-08-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NU8
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
 NU8  N1   N  N     0  -0.442  -2.8189  -1.6535   2.0107
 NU8  N3   N  NR6   0  -0.612  -1.5674  -0.0342   0.9136
 NU8  C4   C  CR66  0   0.623  -1.8096  -1.3728   1.2105
 NU8  C5   C  CR6   0   0.772  -0.3298   0.4713   0.5815
 NU8  C6   C  CR66  0  -0.321  -0.9976  -2.3816   0.6943
 NU8  C7   C  CR6   0   0.477   4.5130   0.7669  -0.4781
 NU8  C8   C  CR6   0   0.252   4.2264   0.2060   0.7946
 NU8  C10  C  CR6   0   0.224   1.9832  -0.0294   0.0145
 NU8  C13  C  CR6   0   0.557  -3.5728   2.7820  -2.6717
 NU8  C15  C  CR6   0   0.576  -2.8108   2.9777  -0.4484
 NU8  C17  C  CR6   0   0.584  -3.4395   0.8800  -1.2957
 NU8  C20  C  CH3   0  -0.444   4.9951  -0.4542   2.9229
 NU8  C1   C  CR16  0  -0.123  -1.2000  -3.6993   1.0621
 NU8  C11  C  CR16  0  -0.081   2.3567   0.5271  -1.1828
 NU8  C12  C  CH2   0  -0.383  -2.6371   0.9540   1.0856
 NU8  C14  C  CR16  0  -0.576  -3.1071   3.5878  -1.6528
 NU8  C16  C  CR6   0  -0.301  -2.9614   1.6180  -0.2213
 NU8  C18  C  CR16  0  -0.568  -3.7513   1.4197  -2.5263
 NU8  C19  C  CH3   0  -0.416   6.1044   1.6834  -1.9527
 NU8  C2   C  CR16  0  -0.341  -2.2533  -3.9774   1.9144
 NU8  C3   C  CR16  0  -0.023  -3.0421  -2.9186   2.3397
 NU8  C9   C  CR16  0  -0.281   2.9323  -0.1977   1.0277
 NU8  F2   F  F     0  -0.295  -2.3696   3.7501   0.5454
 NU8  F3   F  F     0  -0.296  -3.6090  -0.4342  -1.1200
 NU8  N2   N  N     0  -0.449   3.6120   0.9149  -1.4126
 NU8  N4   N  NR6   0  -0.807   0.6464  -0.4630   0.2378
 NU8  O1   O  O     0  -0.427  -0.0888   1.6521   0.6064
 NU8  O4   O  O2    0  -0.458   5.7697   1.1424  -0.6807
 NU8  O5   O  O2    0  -0.455   5.2487   0.1159   1.6511
 NU8  S1   S  S     0   1.378   0.1975  -1.9224  -0.4823
 NU8  H1   H  HCH3  0   0.236   4.2706   0.1343   3.4913
 NU8  H2   H  HCH3  0   0.235   4.6318  -1.4814   2.8393
 NU8  H3   H  HCH3  0   0.267   5.9430  -0.4566   3.4539
 NU8  H4   H  HCR6  0   0.307  -0.5616  -4.4867   0.6840
 NU8  H5   H  HCR6  0   0.275   1.6421   0.6708  -1.9850
 NU8  H6   H  HCH2  0   0.316  -3.5026   0.4237   1.4723
 NU8  H7   H  HCH2  0   0.300  -2.3551   1.6809   1.8428
 NU8  H8   H  HCR6  0   0.310  -2.9765   4.6530  -1.7876
 NU8  H9   H  HCR6  0   0.311  -4.1223   0.8041  -3.3346
 NU8  H10  H  HCH3  0   0.234   5.9336   0.9618  -2.7522
 NU8  H11  H  HCH3  0   0.234   5.5362   2.5884  -2.1695
 NU8  H12  H  HCH3  0   0.250   7.1628   1.9238  -1.9022
 NU8  H13  H  HCR6  0   0.294  -2.4660  -4.9868   2.2327
 NU8  H14  H  HCR6  0   0.292  -3.8914  -3.0969   2.9876
 NU8  H15  H  HCR6  0   0.306   2.6274  -0.6365   1.9680
 NU8  F1   F  F     0  -0.301  -3.8664   3.3425  -3.8470
 NU8  O2   O  OS    0  -0.601  -0.4467  -1.6424  -1.7482
 NU8  O3   O  OS    0  -0.610   1.3444  -2.8007  -0.4407

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
 NU8  F3   C17  single    1.337  0.020  1.337
 NU8  C18  C17  aromatic  1.379  0.020  1.379
 NU8  C18  C13  aromatic  1.382  0.020  1.382
 NU8  C17  C16  aromatic  1.388  0.020  1.388
 NU8  F1   C13  single    1.335  0.020  1.335
 NU8  C13  C14  aromatic  1.380  0.020  1.380
 NU8  C16  C12  single    1.501  0.020  1.501
 NU8  C16  C15  aromatic  1.387  0.020  1.387
 NU8  C12  N3   single    1.466  0.020  1.466
 NU8  C14  C15  aromatic  1.382  0.020  1.382
 NU8  C15  F2   single    1.334  0.020  1.334
 NU8  O1   C5   double    1.205  0.020  1.205
 NU8  N1   C3   aromatic  1.326  0.020  1.326
 NU8  N1   C4   aromatic  1.318  0.020  1.318
 NU8  N3   C5   single    1.377  0.020  1.377
 NU8  N3   C4   single    1.392  0.020  1.392
 NU8  C5   N4   single    1.394  0.020  1.394
 NU8  C3   C2   aromatic  1.387  0.020  1.387
 NU8  C4   C6   aromatic  1.394  0.020  1.394
 NU8  N4   C10  single    1.423  0.020  1.423
 NU8  N4   S1   single    1.688  0.020  1.688
 NU8  C2   C1   aromatic  1.383  0.020  1.383
 NU8  C6   C1   aromatic  1.383  0.020  1.383
 NU8  C6   S1   single    1.739  0.020  1.739
 NU8  C10  C9   aromatic  1.398  0.020  1.398
 NU8  C10  C11  aromatic  1.372  0.020  1.372
 NU8  C9   C8   aromatic  1.376  0.020  1.376
 NU8  C20  O5   single    1.417  0.020  1.417
 NU8  O3   S1   double    1.445  0.020  1.445
 NU8  C11  N2   aromatic  1.334  0.020  1.334
 NU8  S1   O2   double    1.448  0.020  1.448
 NU8  C8   O5   single    1.337  0.020  1.337
 NU8  C8   C7   aromatic  1.420  0.020  1.420
 NU8  N2   C7   aromatic  1.307  0.020  1.307
 NU8  C7   O4   single    1.327  0.020  1.327
 NU8  O4   C19  single    1.422  0.020  1.422
 NU8  C20  H1   single    0.970  0.020  1.090
 NU8  C20  H2   single    0.970  0.020  1.090
 NU8  C20  H3   single    0.970  0.020  1.090
 NU8  C1   H4   single    0.930  0.020  1.080
 NU8  C11  H5   single    0.930  0.020  1.080
 NU8  C12  H6   single    0.970  0.020  1.090
 NU8  C12  H7   single    0.970  0.020  1.090
 NU8  C14  H8   single    0.930  0.020  1.080
 NU8  C18  H9   single    0.930  0.020  1.080
 NU8  C19  H10  single    0.970  0.020  1.090
 NU8  C19  H11  single    0.970  0.020  1.090
 NU8  C19  H12  single    0.970  0.020  1.090
 NU8  C2   H13  single    0.930  0.020  1.080
 NU8  C3   H14  single    0.930  0.020  1.080
 NU8  C9   H15  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
 NU8  C3   N1   C4   118.86  3.000
 NU8  C12  N3   C5   115.87  3.000
 NU8  C5   N3   C4   124.09  3.000
 NU8  C12  N3   C4   119.74  3.000
 NU8  C6   C4   N3   121.02  3.000
 NU8  C6   C4   N1   121.11  3.000
 NU8  N3   C4   N1   117.86  3.000
 NU8  O1   C5   N4   121.43  3.000
 NU8  N4   C5   N3   116.27  3.000
 NU8  O1   C5   N3   122.28  3.000
 NU8  S1   C6   C1   122.15  3.000
 NU8  S1   C6   C4   117.38  3.000
 NU8  C1   C6   C4   120.38  3.000
 NU8  O4   C7   N2   120.78  3.000
 NU8  O4   C7   C8   116.08  3.000
 NU8  N2   C7   C8   123.14  3.000
 NU8  O5   C8   C9   126.24  3.000
 NU8  O5   C8   C7   116.52  3.000
 NU8  C9   C8   C7   117.24  3.000
 NU8  N4   C10  C9   119.16  3.000
 NU8  C9   C10  C11  119.76  3.000
 NU8  N4   C10  C11  121.07  3.000
 NU8  F1   C13  C18  118.58  3.000
 NU8  F1   C13  C14  118.63  3.000
 NU8  C18  C13  C14  122.79  3.000
 NU8  F2   C15  C16  118.80  3.000
 NU8  F2   C15  C14  117.68  3.000
 NU8  C16  C15  C14  123.51  3.000
 NU8  F3   C17  C18  118.25  3.000
 NU8  C18  C17  C16  124.07  3.000
 NU8  F3   C17  C16  117.68  3.000
 NU8  H3   C20  H2   108.99  3.000
 NU8  H3   C20  H1   108.99  3.000
 NU8  H2   C20  H1   109.01  3.000
 NU8  H3   C20  O5   106.47  3.000
 NU8  H2   C20  O5   111.66  3.000
 NU8  H1   C20  O5   111.65  3.000
 NU8  H4   C1   C2   121.22  3.000
 NU8  H4   C1   C6   120.95  3.000
 NU8  C2   C1   C6   117.83  3.000
 NU8  H5   C11  N2   117.03  3.000
 NU8  H5   C11  C10  121.34  3.000
 NU8  N2   C11  C10  121.63  3.000
 NU8  H7   C12  H6   106.57  3.000
 NU8  H7   C12  C16  111.51  3.000
 NU8  H6   C12  C16  110.71  3.000
 NU8  H7   C12  N3   110.07  3.000
 NU8  H6   C12  N3   107.10  3.000
 NU8  C16  C12  N3   110.70  3.000
 NU8  H8   C14  C15  121.16  3.000
 NU8  H8   C14  C13  121.58  3.000
 NU8  C15  C14  C13  117.26  3.000
 NU8  C12  C16  C17  120.86  3.000
 NU8  C12  C16  C15  123.56  3.000
 NU8  C17  C16  C15  115.59  3.000
 NU8  H9   C18  C17  121.44  3.000
 NU8  H9   C18  C13  121.78  3.000
 NU8  C17  C18  C13  116.77  3.000
 NU8  H12  C19  H11  109.46  3.000
 NU8  H12  C19  H10  109.46  3.000
 NU8  H11  C19  H10  108.77  3.000
 NU8  H12  C19  O4   105.77  3.000
 NU8  H11  C19  O4   111.77  3.000
 NU8  H10  C19  O4   111.54  3.000
 NU8  H13  C2   C3   120.75  3.000
 NU8  H13  C2   C1   121.31  3.000
 NU8  C3   C2   C1   117.94  3.000
 NU8  H14  C3   C2   120.25  3.000
 NU8  H14  C3   N1   115.94  3.000
 NU8  C2   C3   N1   123.81  3.000
 NU8  H15  C9   C10  119.17  3.000
 NU8  H15  C9   C8   122.12  3.000
 NU8  C10  C9   C8   118.71  3.000
 NU8  C11  N2   C7   119.53  3.000
 NU8  S1   N4   C10  116.51  3.000
 NU8  S1   N4   C5   119.89  3.000
 NU8  C10  N4   C5   119.49  3.000
 NU8  C19  O4   C7   117.84  3.000
 NU8  C20  O5   C8   117.74  3.000
 NU8  O3   S1   O2   119.73  3.000
 NU8  O2   S1   N4   108.91  3.000
 NU8  O3   S1   N4   107.58  3.000
 NU8  O2   S1   C6   109.69  3.000
 NU8  O3   S1   C6   111.44  3.000
 NU8  N4   S1   C6    97.03  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
 NU8  CONST_01  C1   C2   C3   N1      0.00   0.0  0
 NU8  CONST_02  C1   C6   C4   N1      0.00   0.0  0
 NU8  CONST_03  C2   C3   N1   C4      0.00   0.0  0
 NU8  CONST_04  C2   C1   C6   C4      0.00   0.0  0
 NU8  CONST_05  C3   N1   C4   C6      0.00   0.0  0
 NU8  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 NU8  CONST_07  C10  C9   C8   C7      0.00   0.0  0
 NU8  CONST_08  C10  C11  N2   C7      0.00   0.0  0
 NU8  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 NU8  CONST_10  C11  N2   C7   C8      0.00   0.0  0
 NU8  CONST_11  C16  C17  C18  C13     0.00   0.0  0
 NU8  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 NU8  CONST_13  C18  C17  C16  C15     0.00   0.0  0
 NU8  CONST_14  C18  C13  C14  C15     0.00   0.0  0
 NU8  CONST_15  C14  C13  C18  C17     0.00   0.0  0
 NU8  CONST_16  C14  C15  C16  C17     0.00   0.0  0
 NU8  CONST_17  N2   C11  C10  C9      0.00   0.0  0
 NU8  CONST_18  N2   C7   C8   C9      0.00   0.0  0
 NU8  CONST_19  N4   C10  C9   C8    180.00   0.0  0
 NU8  CONST_20  N4   C10  C11  N2    180.00   0.0  0
 NU8  CONST_21  C10  N4   C5   N3    180.00   0.0  0
 NU8  CONST_23  N4   C5   N3   C4      0.00   0.0  0
 NU8  CONST_24  O5   C8   C9   C10   180.00   0.0  0
 NU8  CONST_25  F3   C17  C18  C13   180.00   0.0  0
 NU8  CONST_26  F2   C15  C14  C13   180.00   0.0  0
 NU8  CONST_27  F3   C17  C16  C15   180.00   0.0  0
 NU8  CONST_28  F1   C13  C14  C15   180.00   0.0  0
 NU8  CONST_29  F1   C13  C18  C17   180.00   0.0  0
 NU8  CONST_30  F2   C15  C16  C17   180.00   0.0  0
 NU8  CONST_31  O4   C7   N2   C11   180.00   0.0  0
 NU8  CONST_32  C18  C17  C16  C12   180.00   0.0  0
 NU8  CONST_33  C14  C15  C16  C12   180.00   0.0  0
 NU8  CONST_34  O4   C7   C8   C9    180.00   0.0  0
 NU8  CONST_35  O5   C8   C7   N2    180.00   0.0  0
 NU8  CONST_37  O1   C5   N4   C10     0.00   0.0  0
 NU8  CONST_38  N4   C5   N3   C12   180.00   0.0  0
 NU8  CONST_40  H13  C2   C3   N1    180.00   0.0  0
 NU8  CONST_41  H14  C3   N1   C4    180.00   0.0  0
 NU8  CONST_42  H4   C1   C6   C4    180.00   0.0  0
 NU8  CONST_43  H15  C9   C8   C7    180.00   0.0  0
 NU8  CONST_44  H5   C11  N2   C7    180.00   0.0  0
 NU8  CONST_45  H9   C18  C13  C14   180.00   0.0  0
 NU8  CONST_46  H8   C14  C15  C16   180.00   0.0  0
 NU8  CONST_47  O1   C5   N3   C12     0.00   0.0  0
 NU8  Var_01    C9   C10  N4   C5    100.41  30.0  2
 NU8  Var_02    C17  C16  C12  N3     61.83  30.0  2
 NU8  Var_03    C16  C12  N3   C4   -119.33  30.0  3
 NU8  Var_04    O3   S1   C6   C4    151.05  30.0  1
 NU8  Var_05    C9   C8   O5   C20     0.38  30.0  2
 NU8  Var_06    N2   C7   O4   C19    -1.24  30.0  2
 NU8  Var_07    H10  C19  O4   C7    -61.29  30.0  3
 NU8  Var_08    H1   C20  O5   C8    -62.36  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
 NU8  plan-1  C7   0.020
 NU8  plan-1  C8   0.020
 NU8  plan-1  C10  0.020
 NU8  plan-1  C11  0.020
 NU8  plan-1  C9   0.020
 NU8  plan-1  N2   0.020
 NU8  plan-1  N4   0.020
 NU8  plan-1  O4   0.020
 NU8  plan-1  O5   0.020
 NU8  plan-1  H5   0.020
 NU8  plan-1  H15  0.020
 NU8  plan-2  C13  0.020
 NU8  plan-2  C15  0.020
 NU8  plan-2  C17  0.020
 NU8  plan-2  C12  0.020
 NU8  plan-2  C14  0.020
 NU8  plan-2  C16  0.020
 NU8  plan-2  C18  0.020
 NU8  plan-2  F2   0.020
 NU8  plan-2  F3   0.020
 NU8  plan-2  H8   0.020
 NU8  plan-2  H9   0.020
 NU8  plan-2  F1   0.020
 NU8  plan-3  N1   0.020
 NU8  plan-3  N3   0.020
 NU8  plan-3  C4   0.020
 NU8  plan-3  C5   0.020
 NU8  plan-3  C6   0.020
 NU8  plan-3  C10  0.020
 NU8  plan-3  C1   0.020
 NU8  plan-3  C12  0.020
 NU8  plan-3  C2   0.020
 NU8  plan-3  C3   0.020
 NU8  plan-3  N4   0.020
 NU8  plan-3  O1   0.020
 NU8  plan-3  S1   0.020
 NU8  plan-3  H4   0.020
 NU8  plan-3  H13  0.020
 NU8  plan-3  H14  0.020

