# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 10:59:12 2022
#   Inital geometry file: a 73 line input string
#   Ligand name: (5Z)-5-(quinoxalin-6-ylmethylidene)-1,3-thiazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1NC(=O)/C(S1)=C/c2ccc3nccnc3c2
#
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
 QYT  QYT  (5Z)-5-(quinoxalin-6-ylmethylidene)-1,3-thiazolidine-2,4-dione  ligand  25  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QYT
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
 QYT  C1   C  CR16  0  -0.292  -2.7546  -1.8478  -0.3693
 QYT  C2   C  CR16  0  -0.289  -1.4128  -2.0639  -0.2542
 QYT  C3   C  CR6   0   0.154  -0.5137  -1.0103   0.0682
 QYT  C7   C  CR5   0   0.641   3.3446  -1.1127   0.1557
 QYT  C11  C  CR5   0   0.430   3.8100   1.1676  -0.2173
 QYT  C13  C  CR66  0   0.267  -2.4018   0.4947   0.1991
 QYT  C14  C  CR66  0   0.229  -3.2809  -0.5578  -0.1468
 QYT  C16  C  CR16  0  -0.108  -5.0352   0.8650  -0.0234
 QYT  N18  N  N     0  -0.377  -2.8706   1.7426   0.4409
 QYT  C4   C  CR16  0  -0.383  -1.0195   0.2508   0.3002
 QYT  C5   C  C1    0  -0.244   0.8981  -1.3500   0.1460
 QYT  C6   C  CR5   0  -0.299   1.9711  -0.5524   0.0712
 QYT  S8   S  S2    0   0.102   2.0313   1.1778  -0.1930
 QYT  N9   N  NR15  0  -0.683   4.2634  -0.1058  -0.0144
 QYT  O12  O  O     0  -0.387   4.4775   2.1484  -0.3843
 QYT  N15  N  N     0  -0.376  -4.6126  -0.3448  -0.2549
 QYT  C17  C  CR16  0  -0.109  -4.1550   1.9193   0.3304
 QYT  H1   H  HCR6  0   0.278  -3.4312  -2.6532  -0.6231
 QYT  H2   H  HCR6  0   0.276  -1.0145  -3.0568  -0.4205
 QYT  H16  H  HCR6  0   0.284  -6.0986   1.0573  -0.1057
 QYT  H4   H  HCR6  0   0.269  -0.3985   1.0841   0.6023
 QYT  H5   H  H     0   0.295   1.1142  -2.4079   0.2556
 QYT  HN9  H  HNR5  0   0.445   5.2590  -0.2936   0.0026
 QYT  H17  H  HCR6  0   0.283  -4.5510   2.9106   0.5176
 QYT  O10  O  O     0  -0.402   3.6278  -2.2702   0.3406

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
 QYT  C1   C2   aromatic  1.364  0.020  1.364
 QYT  C1   C14  aromatic  1.411  0.020  1.411
 QYT  C1   H1   single    0.930  0.020  1.080
 QYT  C2   C3   aromatic  1.422  0.020  1.422
 QYT  C2   H2   single    0.930  0.020  1.080
 QYT  C3   C4   aromatic  1.378  0.020  1.378
 QYT  C3   C5   single    1.454  0.020  1.454
 QYT  C7   C6   single    1.486  0.020  1.486
 QYT  C7   N9   single    1.374  0.020  1.374
 QYT  C7   O10  double    1.206  0.020  1.206
 QYT  C11  S8   single    1.779  0.020  1.779
 QYT  C11  N9   single    1.367  0.020  1.367
 QYT  C11  O12  double    1.198  0.020  1.198
 QYT  C13  C14  aromatic  1.414  0.020  1.414
 QYT  C13  N18  aromatic  1.355  0.020  1.355
 QYT  C13  C4   aromatic  1.407  0.020  1.407
 QYT  C14  N15  aromatic  1.353  0.020  1.353
 QYT  C16  N15  aromatic  1.302  0.020  1.302
 QYT  C16  C17  aromatic  1.418  0.020  1.418
 QYT  C16  H16  single    0.930  0.020  1.080
 QYT  N18  C17  aromatic  1.301  0.020  1.301
 QYT  C4   H4   single    0.930  0.020  1.080
 QYT  C5   C6   double    1.339  0.020  1.339
 QYT  C5   H5   single    0.930  0.020  1.080
 QYT  C6   S8   single    1.751  0.020  1.751
 QYT  N9   HN9  single    0.860  0.020  1.020
 QYT  C17  H17  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
 QYT  H1   C1   C14  118.97  3.000
 QYT  H1   C1   C2   121.13  3.000
 QYT  C14  C1   C2   119.90  3.000
 QYT  H2   C2   C3   118.80  3.000
 QYT  H2   C2   C1   119.62  3.000
 QYT  C3   C2   C1   121.58  3.000
 QYT  C5   C3   C4   124.12  3.000
 QYT  C5   C3   C2   116.93  3.000
 QYT  C4   C3   C2   118.95  3.000
 QYT  O10  C7   N9   124.43  3.000
 QYT  O10  C7   C6   126.00  3.000
 QYT  N9   C7   C6   109.56  3.000
 QYT  O12  C11  N9   126.77  3.000
 QYT  O12  C11  S8   123.66  3.000
 QYT  N9   C11  S8   109.57  3.000
 QYT  C4   C13  N18  119.13  3.000
 QYT  C4   C13  C14  119.94  3.000
 QYT  N18  C13  C14  120.93  3.000
 QYT  N15  C14  C13  120.94  3.000
 QYT  N15  C14  C1   119.90  3.000
 QYT  C13  C14  C1   119.15  3.000
 QYT  H16  C16  C17  119.73  3.000
 QYT  H16  C16  N15  118.02  3.000
 QYT  C17  C16  N15  122.25  3.000
 QYT  C17  N18  C13  116.84  3.000
 QYT  H4   C4   C13  116.76  3.000
 QYT  H4   C4   C3   122.74  3.000
 QYT  C13  C4   C3   120.46  3.000
 QYT  H5   C5   C6   115.26  3.000
 QYT  H5   C5   C3   115.24  3.000
 QYT  C6   C5   C3   129.48  3.000
 QYT  S8   C6   C5   128.64  3.000
 QYT  S8   C6   C7   110.45  3.000
 QYT  C5   C6   C7   120.86  3.000
 QYT  C6   S8   C11   91.76  3.000
 QYT  HN9  N9   C11  120.07  3.000
 QYT  HN9  N9   C7   121.28  3.000
 QYT  C11  N9   C7   118.65  3.000
 QYT  C16  N15  C14  116.84  3.000
 QYT  H17  C17  N18  118.05  3.000
 QYT  H17  C17  C16  119.76  3.000
 QYT  N18  C17  C16  122.19  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
 QYT  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 QYT  CONST_02  N18  C13  C14  C1    180.00   0.0  0
 QYT  CONST_03  C4   C13  C14  C1      0.00   0.0  0
 QYT  CONST_04  C16  N15  C14  C1    180.00   0.0  0
 QYT  CONST_05  C13  C14  C1   C2      0.00   0.0  0
 QYT  CONST_06  N15  C14  C1   C2    180.00   0.0  0
 QYT  CONST_07  C13  C4   C3   C2      0.00   0.0  0
 QYT  CONST_08  C14  C1   C2   C3      0.00   0.0  0
 QYT  CONST_09  C14  C13  C4   C3      0.00   0.0  0
 QYT  CONST_10  N18  C13  C4   C3    180.00   0.0  0
 QYT  CONST_11  C16  N15  C14  C13     0.00   0.0  0
 QYT  CONST_12  C16  C17  N18  C13     0.00   0.0  0
 QYT  CONST_13  C17  N18  C13  C14     0.00   0.0  0
 QYT  CONST_14  C17  C16  N15  C14     0.00   0.0  0
 QYT  CONST_15  N15  C14  C13  N18     0.00   0.0  0
 QYT  CONST_16  N15  C16  C17  N18     0.00   0.0  0
 QYT  CONST_17  N15  C14  C13  C4    180.00   0.0  0
 QYT  CONST_18  C17  N18  C13  C4    180.00   0.0  0
 QYT  CONST_19  C6   C7   N9   C11     0.00   0.0  0
 QYT  CONST_20  C5   C3   C2   C1    180.00   0.0  0
 QYT  CONST_21  C5   C3   C4   C13   180.00   0.0  0
 QYT  CONST_22  O10  C7   N9   C11   180.00   0.0  0
 QYT  CONST_23  H4   C4   C3   C2    180.00   0.0  0
 QYT  CONST_24  H1   C1   C2   C3    180.00   0.0  0
 QYT  CONST_25  H17  C17  N18  C13   180.00   0.0  0
 QYT  CONST_26  H2   C2   C1   C14   180.00   0.0  0
 QYT  CONST_27  H16  C16  N15  C14   180.00   0.0  0
 QYT  CONST_28  HN9  N9   C7   C6    180.00   0.0  0
 QYT  Var_01    C7   C6   C5   C3   -179.09   0.0  2
 QYT  Var_02    C6   C5   C3   C2    160.16  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
 QYT  plan-1  C3   0.020
 QYT  plan-1  C7   0.020
 QYT  plan-1  C11  0.020
 QYT  plan-1  C5   0.020
 QYT  plan-1  C6   0.020
 QYT  plan-1  S8   0.020
 QYT  plan-1  N9   0.020
 QYT  plan-1  O12  0.020
 QYT  plan-1  H5   0.020
 QYT  plan-1  HN9  0.020
 QYT  plan-1  O10  0.020
 QYT  plan-2  C1   0.020
 QYT  plan-2  C2   0.020
 QYT  plan-2  C3   0.020
 QYT  plan-2  C13  0.020
 QYT  plan-2  C14  0.020
 QYT  plan-2  C16  0.020
 QYT  plan-2  N18  0.020
 QYT  plan-2  C4   0.020
 QYT  plan-2  C5   0.020
 QYT  plan-2  N15  0.020
 QYT  plan-2  C17  0.020
 QYT  plan-2  H1   0.020
 QYT  plan-2  H2   0.020
 QYT  plan-2  H16  0.020
 QYT  plan-2  H4   0.020
 QYT  plan-2  H17  0.020

