# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 22:26:04 2020
#   Inital geometry file: a 72 line input string
#   Ligand name: 5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)c2csc3N=CNC(=O)c23
#
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
 FQD  FQD  5-(4-fluorophenyl)thieno[2,3-d]pyrimidin-4(3H)-one  ligand  24  17  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FQD
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
 FQD  C1   C  CR5   0   0.203   0.2392   0.7148  -0.0372
 FQD  C2   C  CR15  0  -0.553   0.7209   1.9834  -0.1430
 FQD  C6   C  CR16  0   0.159   3.6842  -1.5462   0.1554
 FQD  C10  C  CR16  0  -0.401  -3.4101   0.9048   0.8636
 FQD  C9   C  CR6   0   0.518  -3.9374  -0.0013  -0.0336
 FQD  C7   C  CR16  0  -0.282  -2.0380   1.1134   0.8629
 FQD  C11  C  CR16  0  -0.404  -3.1438  -0.6994  -0.9256
 FQD  C8   C  CR16  0  -0.259  -1.7760  -0.4812  -0.9101
 FQD  C5   C  CR6   0   0.053  -1.2054   0.4267  -0.0182
 FQD  C    C  CR56  0  -0.094   1.3099  -0.2369   0.0323
 FQD  C4   C  CR6   0   0.526   1.2550  -1.6675   0.2267
 FQD  O    O  O     0  -0.446   0.2646  -2.3598   0.3689
 FQD  N1   N  NR16  0  -0.652   2.5271  -2.2314   0.2535
 FQD  N    N  N     0  -0.430   3.7574  -0.2655   0.0173
 FQD  C3   C  CR56  0  -0.019   2.5589   0.3582  -0.0346
 FQD  S    S  S2    0   0.257   2.4395   2.0678  -0.1718
 FQD  H1   H  HCR5  0   0.305   0.1408   2.8897  -0.2329
 FQD  H2   H  HCR6  0   0.309   4.5880  -2.1395   0.2037
 FQD  H3   H  HCR6  0   0.281  -4.0520   1.4360   1.5537
 FQD  H4   H  HCR6  0   0.265  -1.6100   1.8151   1.5673
 FQD  H5   H  HCR6  0   0.281  -3.5869  -1.3970  -1.6244
 FQD  H6   H  HCR6  0   0.260  -1.1518  -1.0113  -1.6161
 FQD  H7   H  HNR6  0   0.438   2.5799  -3.2351   0.3735
 FQD  F    F  F     0  -0.315  -5.2635  -0.2107  -0.0442

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
 FQD  S    C3   aromatic  1.719  0.020  1.719
 FQD  S    C2   aromatic  1.721  0.020  1.721
 FQD  N    C3   single    1.352  0.020  1.352
 FQD  N    C6   double    1.290  0.020  1.290
 FQD  C3   C    aromatic  1.385  0.020  1.385
 FQD  C2   C1   aromatic  1.361  0.020  1.361
 FQD  C6   N1   single    1.348  0.020  1.348
 FQD  C    C1   aromatic  1.434  0.020  1.434
 FQD  C    C4   single    1.445  0.020  1.445
 FQD  C1   C5   single    1.473  0.020  1.473
 FQD  N1   C4   single    1.392  0.020  1.392
 FQD  C4   O    double    1.217  0.020  1.217
 FQD  C7   C5   aromatic  1.393  0.020  1.393
 FQD  C7   C10  aromatic  1.388  0.020  1.388
 FQD  C5   C8   aromatic  1.395  0.020  1.395
 FQD  C10  C9   aromatic  1.380  0.020  1.380
 FQD  C8   C11  aromatic  1.385  0.020  1.385
 FQD  C9   C11  aromatic  1.383  0.020  1.383
 FQD  C9   F    single    1.343  0.020  1.343
 FQD  C2   H1   single    0.930  0.020  1.080
 FQD  C6   H2   single    0.930  0.020  1.080
 FQD  C10  H3   single    0.930  0.020  1.080
 FQD  C7   H4   single    0.930  0.020  1.080
 FQD  C11  H5   single    0.930  0.020  1.080
 FQD  C8   H6   single    0.930  0.020  1.080
 FQD  N1   H7   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
 FQD  C    C1   C5   126.99  3.000
 FQD  C5   C1   C2   122.03  3.000
 FQD  C    C1   C2   110.98  3.000
 FQD  H1   C2   S    119.60  3.000
 FQD  H1   C2   C1   126.77  3.000
 FQD  S    C2   C1   113.61  3.000
 FQD  H2   C6   N    120.11  3.000
 FQD  H2   C6   N1   115.78  3.000
 FQD  N    C6   N1   124.12  3.000
 FQD  H3   C10  C7   120.87  3.000
 FQD  H3   C10  C9   120.70  3.000
 FQD  C7   C10  C9   118.43  3.000
 FQD  C11  C9   F    118.88  3.000
 FQD  F    C9   C10  119.01  3.000
 FQD  C11  C9   C10  122.11  3.000
 FQD  H4   C7   C5   119.65  3.000
 FQD  H4   C7   C10  119.21  3.000
 FQD  C5   C7   C10  121.14  3.000
 FQD  H5   C11  C8   120.87  3.000
 FQD  H5   C11  C9   120.46  3.000
 FQD  C8   C11  C9   118.68  3.000
 FQD  H6   C8   C5   120.03  3.000
 FQD  H6   C8   C11  119.04  3.000
 FQD  C5   C8   C11  120.91  3.000
 FQD  C8   C5   C7   118.73  3.000
 FQD  C8   C5   C1   121.35  3.000
 FQD  C7   C5   C1   119.85  3.000
 FQD  C3   C    C4   117.78  3.000
 FQD  C4   C    C1   129.44  3.000
 FQD  C3   C    C1   112.69  3.000
 FQD  N1   C4   O    120.75  3.000
 FQD  O    C4   C    127.59  3.000
 FQD  N1   C4   C    111.66  3.000
 FQD  H7   N1   C4   116.86  3.000
 FQD  H7   N1   C6   117.89  3.000
 FQD  C4   N1   C6   125.25  3.000
 FQD  C3   N    C6   114.31  3.000
 FQD  S    C3   N    121.56  3.000
 FQD  N    C3   C    126.82  3.000
 FQD  S    C3   C    111.62  3.000
 FQD  C3   S    C2    91.10  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
 FQD  CONST_01  C3   S    C2   C1     0.00  0.0  0
 FQD  CONST_02  S    C3   C    C1     0.00  0.0  0
 FQD  CONST_03  C10  C7   C5   C1   180.00  0.0  0
 FQD  CONST_04  C11  C8   C5   C1   180.00  0.0  0
 FQD  CONST_05  C    C3   S    C2     0.00  0.0  0
 FQD  CONST_06  C3   C    C1   C2     0.00  0.0  0
 FQD  CONST_09  C8   C5   C7   C10    0.00  0.0  0
 FQD  CONST_10  C8   C11  C9   C10    0.00  0.0  0
 FQD  CONST_11  C5   C7   C10  C9     0.00  0.0  0
 FQD  CONST_12  C5   C8   C11  C9     0.00  0.0  0
 FQD  CONST_14  C11  C8   C5   C7     0.00  0.0  0
 FQD  CONST_15  C11  C9   C10  C7     0.00  0.0  0
 FQD  CONST_17  S    C2   C1   C5   180.00  0.0  0
 FQD  CONST_18  C3   C    C1   C5   180.00  0.0  0
 FQD  CONST_19  S    C2   C1   C      0.00  0.0  0
 FQD  CONST_20  C4   C    C1   C5     0.00  0.0  0
 FQD  CONST_21  C    C4   N1   C6     0.00  0.0  0
 FQD  CONST_22  N    C6   N1   C4     0.00  0.0  0
 FQD  CONST_23  C3   N    C6   N1     0.00  0.0  0
 FQD  CONST_24  C7   C10  C9   F    180.00  0.0  0
 FQD  CONST_25  C8   C11  C9   F    180.00  0.0  0
 FQD  CONST_26  O    C4   N1   C6   180.00  0.0  0
 FQD  CONST_27  H4   C7   C5   C1     0.00  0.0  0
 FQD  CONST_28  H6   C8   C5   C1     0.00  0.0  0
 FQD  CONST_29  H5   C11  C9   C10  180.00  0.0  0
 FQD  CONST_30  H3   C10  C9   C11  180.00  0.0  0
 FQD  CONST_31  H1   C2   C1   C5     0.00  0.0  0
 FQD  CONST_32  H7   N1   C4   C    180.00  0.0  0
 FQD  CONST_33  H2   C6   N1   C4   180.00  0.0  0

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
 FQD  plan-1  C1   0.020
 FQD  plan-1  C10  0.020
 FQD  plan-1  C9   0.020
 FQD  plan-1  C7   0.020
 FQD  plan-1  C11  0.020
 FQD  plan-1  C8   0.020
 FQD  plan-1  C5   0.020
 FQD  plan-1  H3   0.020
 FQD  plan-1  H4   0.020
 FQD  plan-1  H5   0.020
 FQD  plan-1  H6   0.020
 FQD  plan-1  F    0.020
 FQD  plan-2  C1   0.020
 FQD  plan-2  C2   0.020
 FQD  plan-2  C6   0.020
 FQD  plan-2  C5   0.020
 FQD  plan-2  C    0.020
 FQD  plan-2  C4   0.020
 FQD  plan-2  O    0.020
 FQD  plan-2  N1   0.020
 FQD  plan-2  N    0.020
 FQD  plan-2  C3   0.020
 FQD  plan-2  S    0.020
 FQD  plan-2  H1   0.020
 FQD  plan-2  H2   0.020
 FQD  plan-2  H7   0.020

