# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 05:56:15 2020
#   Inital geometry file: a 88 line input string
#   Ligand name: 4-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]-1,2,5-thiadiazole-3-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1nsnc1C(=O)Nc2c(F)c(F)c(c(F)c2F)c3ccccc3
#
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
 Y9B  Y9B  4-oxidanyl-~{N}-[2,3,5,6-tetrakis(fluoranyl)-4-phenyl-phenyl]-1,2,5-thiadiazole-3-carboxamide  ligand  32  25  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Y9B
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
 Y9B  C01  C  CR5   0  -0.030   3.8598   0.0066  -0.0605
 Y9B  C02  C  C     0   0.607   2.4272  -0.1501  -0.3766
 Y9B  N03  N  NH1   0  -0.725   1.5666   0.3205   0.5441
 Y9B  O05  O  O     0  -0.466   2.0900  -0.6787  -1.4261
 Y9B  C06  C  CR5   0   0.479   4.9094  -0.4371  -0.9384
 Y9B  O07  O  OH1   0  -0.586   4.7420  -1.0224  -2.1071
 Y9B  N08  N  N     0  -0.544   6.0991  -0.2035  -0.4630
 Y9B  S09  S  S2    0   0.598   5.9269   0.5251   0.9906
 Y9B  N10  N  N     0  -0.501   4.3031   0.5544   1.0376
 Y9B  C11  C  CR6   0  -0.403  -2.6164   0.1186   0.0558
 Y9B  C12  C  CR6   0   0.421  -1.8458  -1.0305   0.1483
 Y9B  F13  F  F     0  -0.285  -2.4338  -2.2241   0.1085
 Y9B  C14  C  CR6   0   0.426  -0.4759  -0.9746   0.3137
 Y9B  F15  F  F     0  -0.283   0.2176  -2.0994   0.4381
 Y9B  C16  C  CR6   0  -0.039   0.1798   0.2461   0.3741
 Y9B  C17  C  CR6   0   0.419  -0.5808   1.4009   0.2734
 Y9B  F18  F  F     0  -0.281   0.0212   2.5845   0.3145
 Y9B  C19  C  CR6   0   0.419  -1.9523   1.3337   0.1260
 Y9B  F20  F  F     0  -0.285  -2.6399   2.4686   0.0212
 Y9B  C21  C  CR16  0  -0.255  -6.8499  -0.0801  -0.3986
 Y9B  C23  C  CR16  0  -0.242  -6.2976   0.5014   0.7350
 Y9B  C25  C  CR16  0  -0.275  -4.9197   0.5687   0.8825
 Y9B  C27  C  CR6   0   0.108  -4.0846   0.0503  -0.1039
 Y9B  C28  C  CR16  0  -0.275  -4.6413  -0.5344  -1.2387
 Y9B  C30  C  CR16  0  -0.243  -6.0196  -0.5968  -1.3844
 Y9B  H1   H  HNH1  0   0.437   1.9341   0.7901   1.3612
 Y9B  H2   H  HOH1  0   0.489   3.7855  -1.0938  -2.2842
 Y9B  H5   H  HCR6  0   0.263  -7.9248  -0.1312  -0.5135
 Y9B  H6   H  HCR6  0   0.263  -6.9389   0.9026   1.5087
 Y9B  H7   H  HCR6  0   0.262  -4.4957   1.0102   1.7753
 Y9B  H8   H  HCR6  0   0.262  -4.0009  -0.9291  -2.0172
 Y9B  H9   H  HCR6  0   0.264  -6.4443  -1.0493  -2.2705

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
 Y9B  C01  C02  single    1.475  0.020  1.475
 Y9B  C01  C06  aromatic  1.439  0.020  1.439
 Y9B  C01  N10  aromatic  1.305  0.020  1.305
 Y9B  C02  N03  single    1.345  0.020  1.345
 Y9B  C02  O05  double    1.223  0.020  1.223
 Y9B  N03  C16  single    1.399  0.020  1.399
 Y9B  C06  O07  single    1.318  0.020  1.318
 Y9B  C06  N08  aromatic  1.302  0.020  1.302
 Y9B  N08  S09  aromatic  1.635  0.020  1.635
 Y9B  S09  N10  aromatic  1.625  0.020  1.625
 Y9B  C11  C12  aromatic  1.387  0.020  1.387
 Y9B  C11  C19  aromatic  1.387  0.020  1.387
 Y9B  C11  C27  single    1.478  0.020  1.478
 Y9B  C12  F13  single    1.331  0.020  1.331
 Y9B  C12  C14  aromatic  1.381  0.020  1.381
 Y9B  C14  F15  single    1.327  0.020  1.327
 Y9B  C14  C16  aromatic  1.387  0.020  1.387
 Y9B  C16  C17  aromatic  1.386  0.020  1.386
 Y9B  C17  F18  single    1.329  0.020  1.329
 Y9B  C17  C19  aromatic  1.381  0.020  1.381
 Y9B  C19  F20  single    1.331  0.020  1.331
 Y9B  C21  C23  aromatic  1.389  0.020  1.389
 Y9B  C21  C30  aromatic  1.389  0.020  1.389
 Y9B  C23  C25  aromatic  1.387  0.020  1.387
 Y9B  C25  C27  aromatic  1.393  0.020  1.393
 Y9B  C27  C28  aromatic  1.393  0.020  1.393
 Y9B  C28  C30  aromatic  1.387  0.020  1.387
 Y9B  N03  H1   single    0.860  0.020  1.020
 Y9B  O07  H2   single    0.850  0.020  0.980
 Y9B  C21  H5   single    0.930  0.020  1.080
 Y9B  C23  H6   single    0.930  0.020  1.080
 Y9B  C25  H7   single    0.930  0.020  1.080
 Y9B  C28  H8   single    0.930  0.020  1.080
 Y9B  C30  H9   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
 Y9B  N10  C01  C06  113.28  3.000
 Y9B  N10  C01  C02  123.70  3.000
 Y9B  C06  C01  C02  123.02  3.000
 Y9B  O05  C02  N03  124.21  3.000
 Y9B  O05  C02  C01  119.85  3.000
 Y9B  N03  C02  C01  115.94  3.000
 Y9B  H1   N03  C16  118.88  3.000
 Y9B  H1   N03  C02  118.87  3.000
 Y9B  C16  N03  C02  122.16  3.000
 Y9B  N08  C06  O07  121.30  3.000
 Y9B  N08  C06  C01  112.86  3.000
 Y9B  O07  C06  C01  125.84  3.000
 Y9B  H2   O07  C06  108.55  3.000
 Y9B  S09  N08  C06  107.95  3.000
 Y9B  N10  S09  N08   97.99  3.000
 Y9B  S09  N10  C01  107.92  3.000
 Y9B  C27  C11  C19  121.44  3.000
 Y9B  C27  C11  C12  121.38  3.000
 Y9B  C19  C11  C12  117.17  3.000
 Y9B  C14  C12  F13  118.56  3.000
 Y9B  C14  C12  C11  121.72  3.000
 Y9B  F13  C12  C11  119.71  3.000
 Y9B  C16  C14  F15  119.65  3.000
 Y9B  C16  C14  C12  120.65  3.000
 Y9B  F15  C14  C12  119.69  3.000
 Y9B  C17  C16  C14  118.07  3.000
 Y9B  C17  C16  N03  120.55  3.000
 Y9B  C14  C16  N03  121.38  3.000
 Y9B  C19  C17  F18  119.78  3.000
 Y9B  C19  C17  C16  120.80  3.000
 Y9B  F18  C17  C16  119.42  3.000
 Y9B  F20  C19  C17  118.68  3.000
 Y9B  F20  C19  C11  119.72  3.000
 Y9B  C17  C19  C11  121.58  3.000
 Y9B  H5   C21  C30  120.06  3.000
 Y9B  H5   C21  C23  120.10  3.000
 Y9B  C30  C21  C23  119.84  3.000
 Y9B  H6   C23  C25  119.64  3.000
 Y9B  H6   C23  C21  120.22  3.000
 Y9B  C25  C23  C21  120.14  3.000
 Y9B  H7   C25  C27  120.07  3.000
 Y9B  H7   C25  C23  119.78  3.000
 Y9B  C27  C25  C23  120.14  3.000
 Y9B  C28  C27  C25  119.59  3.000
 Y9B  C28  C27  C11  120.30  3.000
 Y9B  C25  C27  C11  120.12  3.000
 Y9B  H8   C28  C30  119.72  3.000
 Y9B  H8   C28  C27  120.17  3.000
 Y9B  C30  C28  C27  120.11  3.000
 Y9B  H9   C30  C28  119.66  3.000
 Y9B  H9   C30  C21  120.16  3.000
 Y9B  C28  C30  C21  120.18  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
 Y9B  CONST_01  S09  N08  C06  C01     0.00   0.0  0
 Y9B  CONST_02  N08  S09  N10  C01     0.00   0.0  0
 Y9B  CONST_03  S09  N10  C01  C06     0.00   0.0  0
 Y9B  CONST_04  N10  S09  N08  C06     0.00   0.0  0
 Y9B  CONST_05  N10  C01  C06  N08     0.00   0.0  0
 Y9B  CONST_06  C16  C14  C12  C11     0.00   0.0  0
 Y9B  CONST_07  C16  C17  C19  C11     0.00   0.0  0
 Y9B  CONST_08  C23  C25  C27  C11   180.00   0.0  0
 Y9B  CONST_09  C30  C28  C27  C11   180.00   0.0  0
 Y9B  CONST_10  C17  C19  C11  C12     0.00   0.0  0
 Y9B  CONST_13  C17  C16  C14  C12     0.00   0.0  0
 Y9B  CONST_14  C19  C11  C12  C14     0.00   0.0  0
 Y9B  CONST_15  C27  C11  C12  C14   180.00   0.0  0
 Y9B  CONST_16  C19  C17  C16  C14     0.00   0.0  0
 Y9B  CONST_17  C27  C11  C19  C17   180.00   0.0  0
 Y9B  CONST_20  C27  C25  C23  C21     0.00   0.0  0
 Y9B  CONST_21  C27  C28  C30  C21     0.00   0.0  0
 Y9B  CONST_22  C28  C30  C21  C23     0.00   0.0  0
 Y9B  CONST_23  C28  C27  C25  C23     0.00   0.0  0
 Y9B  CONST_24  C30  C21  C23  C25     0.00   0.0  0
 Y9B  CONST_25  C30  C28  C27  C25     0.00   0.0  0
 Y9B  CONST_26  N08  C06  C01  C02   180.00   0.0  0
 Y9B  CONST_27  S09  N10  C01  C02   180.00   0.0  0
 Y9B  CONST_28  C12  C14  C16  N03   180.00   0.0  0
 Y9B  CONST_29  C19  C17  C16  N03   180.00   0.0  0
 Y9B  CONST_30  N10  C01  C06  O07   180.00   0.0  0
 Y9B  CONST_31  S09  N08  C06  O07   180.00   0.0  0
 Y9B  CONST_32  F15  C14  C12  C11   180.00   0.0  0
 Y9B  CONST_33  F18  C17  C19  C11   180.00   0.0  0
 Y9B  CONST_34  F20  C19  C11  C12   180.00   0.0  0
 Y9B  CONST_35  C19  C11  C12  F13   180.00   0.0  0
 Y9B  CONST_36  C27  C11  C12  F13     0.00   0.0  0
 Y9B  CONST_37  C16  C14  C12  F13   180.00   0.0  0
 Y9B  CONST_38  F18  C17  C16  C14   180.00   0.0  0
 Y9B  CONST_39  C17  C16  C14  F15   180.00   0.0  0
 Y9B  CONST_40  F20  C19  C17  C16   180.00   0.0  0
 Y9B  CONST_41  C27  C11  C19  F20     0.00   0.0  0
 Y9B  CONST_42  H7   C25  C27  C11     0.00   0.0  0
 Y9B  CONST_43  H8   C28  C27  C11     0.00   0.0  0
 Y9B  CONST_44  H9   C30  C21  C23   180.00   0.0  0
 Y9B  CONST_45  H5   C21  C23  C25   180.00   0.0  0
 Y9B  CONST_46  H6   C23  C25  C27   180.00   0.0  0
 Y9B  CONST_47  C16  N03  C02  C01   180.00   0.0  0
 Y9B  CONST_51  C16  N03  C02  O05     0.00   0.0  0
 Y9B  Var_01    C06  C01  C02  N03  -179.76  30.0  1

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
 Y9B  plan-1  C01  0.020
 Y9B  plan-1  C02  0.020
 Y9B  plan-1  C06  0.020
 Y9B  plan-1  O07  0.020
 Y9B  plan-1  N08  0.020
 Y9B  plan-1  S09  0.020
 Y9B  plan-1  N10  0.020
 Y9B  plan-2  N03  0.020
 Y9B  plan-2  C11  0.020
 Y9B  plan-2  C12  0.020
 Y9B  plan-2  F13  0.020
 Y9B  plan-2  C14  0.020
 Y9B  plan-2  F15  0.020
 Y9B  plan-2  C16  0.020
 Y9B  plan-2  C17  0.020
 Y9B  plan-2  F18  0.020
 Y9B  plan-2  C19  0.020
 Y9B  plan-2  F20  0.020
 Y9B  plan-2  C27  0.020
 Y9B  plan-3  C11  0.020
 Y9B  plan-3  C21  0.020
 Y9B  plan-3  C23  0.020
 Y9B  plan-3  C25  0.020
 Y9B  plan-3  C27  0.020
 Y9B  plan-3  C28  0.020
 Y9B  plan-3  C30  0.020
 Y9B  plan-3  H5   0.020
 Y9B  plan-3  H6   0.020
 Y9B  plan-3  H7   0.020
 Y9B  plan-3  H8   0.020
 Y9B  plan-3  H9   0.020
 Y9B  plan-4  C01  0.020
 Y9B  plan-4  C02  0.020
 Y9B  plan-4  N03  0.020
 Y9B  plan-4  O05  0.020
 Y9B  plan-4  C16  0.020
 Y9B  plan-4  H1   0.020

