# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 20:53:53 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-[3,5-bis(fluoranyl)phenoxy]-2-methyl-~{N}-(2-sulfanylethyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1cc(F)cc(F)c1)C(=O)NCCS
#
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
 T5Q  T5Q  2-[3,5-bis(fluoranyl)phenoxy]-2-methyl-~{N}-(2-sulfanylethyl)propanamide  ligand  33  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_T5Q
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
 T5Q  C1   C  CT    0   0.053  15.2635  20.4780   0.0542
 T5Q  C2   C  CR6   0   0.422  17.2370  21.1143   1.3532
 T5Q  C3   C  CR16  0  -0.521  17.8681  22.1824   1.9982
 T5Q  C4   C  CR6   0   0.558  19.0738  21.9610   2.6250
 T5Q  C5   C  CR16  0  -0.589  19.7016  20.7280   2.6514
 T5Q  C6   C  CR6   0   0.566  19.0448  19.7039   2.0044
 T5Q  C7   C  CR16  0  -0.540  17.8326  19.8537   1.3542
 T5Q  C9   C  C     0   0.538  16.0643  19.8032  -1.0791
 T5Q  C8   C  CH3   0  -0.658  14.1530  21.3117  -0.5828
 T5Q  N    N  NH1   0  -0.618  16.8601  20.6248  -1.7815
 T5Q  C    C  CH3   0  -0.662  14.6473  19.4643   1.0077
 T5Q  O    O  O2    0  -0.487  16.0783  21.4313   0.7492
 T5Q  C10  C  CH2   0  -0.288  17.7442  20.1636  -2.8265
 T5Q  C11  C  CH2   0  -0.565  19.1152  19.7551  -2.3071
 T5Q  F    F  F     0  -0.306  19.6739  22.9872   3.2388
 T5Q  F1   F  F     0  -0.306  19.6056  18.4891   1.9995
 T5Q  O1   O  O     0  -0.466  15.9320  18.6159  -1.3259
 T5Q  S    S  S2    0  -0.242  20.0908  21.1370  -1.6357
 T5Q  H1   H  HCR6  0   0.294  17.4164  23.1658   1.9980
 T5Q  H2   H  HCR6  0   0.301  20.6497  20.5785   3.1496
 T5Q  H3   H  HCR6  0   0.303  17.4012  18.9862   0.8781
 T5Q  H4   H  HCH3  0   0.254  13.5362  21.7711   0.1900
 T5Q  H5   H  HCH3  0   0.250  14.5490  22.0997  -1.2228
 T5Q  H6   H  HCH3  0   0.249  13.5120  20.6715  -1.1878
 T5Q  H7   H  HNH1  0   0.407  16.9228  21.5957  -1.5178
 T5Q  H8   H  HCH3  0   0.248  14.1111  19.9956   1.7941
 T5Q  H9   H  HCH3  0   0.251  13.9265  18.8444   0.4781
 T5Q  H10  H  HCH3  0   0.252  15.3674  18.7991   1.4793
 T5Q  H11  H  HCH2  0   0.263  17.8482  20.9596  -3.5632
 T5Q  H12  H  HCH2  0   0.261  17.2866  19.3125  -3.3313
 T5Q  H13  H  HCH2  0   0.279  19.0316  18.9693  -1.5564
 T5Q  H14  H  HCH2  0   0.288  19.7104  19.3594  -3.1308
 T5Q  H15  H  HSH1  0   0.211  19.3542  21.3724  -0.5432

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
 T5Q  C10  C11  single    1.522  0.020  1.522
 T5Q  C10  N    single    1.444  0.020  1.444
 T5Q  C11  S    single    1.820  0.020  1.820
 T5Q  N    C9   single    1.342  0.020  1.342
 T5Q  O1   C9   double    1.220  0.020  1.220
 T5Q  C9   C1   single    1.543  0.020  1.543
 T5Q  C8   C1   single    1.528  0.020  1.528
 T5Q  C1   O    single    1.434  0.020  1.434
 T5Q  C1   C    single    1.522  0.020  1.522
 T5Q  O    C2   single    1.345  0.020  1.345
 T5Q  C7   C2   aromatic  1.394  0.020  1.394
 T5Q  C7   C6   aromatic  1.384  0.020  1.384
 T5Q  C2   C3   aromatic  1.398  0.020  1.398
 T5Q  F1   C6   single    1.338  0.020  1.338
 T5Q  C6   C5   aromatic  1.378  0.020  1.378
 T5Q  C3   C4   aromatic  1.377  0.020  1.377
 T5Q  C5   C4   aromatic  1.384  0.020  1.384
 T5Q  C4   F    single    1.338  0.020  1.338
 T5Q  C3   H1   single    0.930  0.020  1.080
 T5Q  C5   H2   single    0.930  0.020  1.080
 T5Q  C7   H3   single    0.930  0.020  1.080
 T5Q  C8   H4   single    0.970  0.020  1.090
 T5Q  C8   H5   single    0.970  0.020  1.090
 T5Q  C8   H6   single    0.970  0.020  1.090
 T5Q  N    H7   single    0.860  0.020  1.020
 T5Q  C    H8   single    0.970  0.020  1.090
 T5Q  C    H9   single    0.970  0.020  1.090
 T5Q  C    H10  single    0.970  0.020  1.090
 T5Q  C10  H11  single    0.970  0.020  1.090
 T5Q  C10  H12  single    0.970  0.020  1.090
 T5Q  C11  H13  single    0.970  0.020  1.090
 T5Q  C11  H14  single    0.970  0.020  1.090
 T5Q  S    H15  single    1.200  0.020  1.300

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
 T5Q  O    C1   C    111.67  3.000
 T5Q  C    C1   C8   109.30  3.000
 T5Q  O    C1   C8   104.62  3.000
 T5Q  C    C1   C9   112.27  3.000
 T5Q  O    C1   C9   110.60  3.000
 T5Q  C8   C1   C9   108.04  3.000
 T5Q  O    C2   C7   125.57  3.000
 T5Q  C7   C2   C3   119.84  3.000
 T5Q  O    C2   C3   114.58  3.000
 T5Q  H1   C3   C4   120.78  3.000
 T5Q  H1   C3   C2   120.37  3.000
 T5Q  C4   C3   C2   118.84  3.000
 T5Q  F    C4   C5   118.11  3.000
 T5Q  F    C4   C3   118.57  3.000
 T5Q  C5   C4   C3   123.32  3.000
 T5Q  H2   C5   C6   122.11  3.000
 T5Q  H2   C5   C4   121.98  3.000
 T5Q  C6   C5   C4   115.91  3.000
 T5Q  F1   C6   C7   117.63  3.000
 T5Q  F1   C6   C5   118.47  3.000
 T5Q  C7   C6   C5   123.90  3.000
 T5Q  H3   C7   C6   118.05  3.000
 T5Q  H3   C7   C2   123.75  3.000
 T5Q  C6   C7   C2   118.20  3.000
 T5Q  O1   C9   N    123.66  3.000
 T5Q  O1   C9   C1   121.19  3.000
 T5Q  N    C9   C1   115.11  3.000
 T5Q  H6   C8   H5   108.22  3.000
 T5Q  H6   C8   H4   107.97  3.000
 T5Q  H5   C8   H4   108.49  3.000
 T5Q  H6   C8   C1   109.79  3.000
 T5Q  H5   C8   C1   112.05  3.000
 T5Q  H4   C8   C1   110.22  3.000
 T5Q  H7   N    C10  117.31  3.000
 T5Q  H7   N    C9   119.31  3.000
 T5Q  C10  N    C9   123.09  3.000
 T5Q  H10  C    H9   107.52  3.000
 T5Q  H10  C    H8   108.11  3.000
 T5Q  H9   C    H8   107.63  3.000
 T5Q  H10  C    C1   114.27  3.000
 T5Q  H9   C    C1   110.04  3.000
 T5Q  H8   C    C1   109.05  3.000
 T5Q  C2   O    C1   123.41  3.000
 T5Q  H12  C10  H11  107.29  3.000
 T5Q  H12  C10  C11  109.06  3.000
 T5Q  H11  C10  C11  109.93  3.000
 T5Q  H12  C10  N    109.11  3.000
 T5Q  H11  C10  N    108.32  3.000
 T5Q  C11  C10  N    112.97  3.000
 T5Q  H14  C11  H13  107.49  3.000
 T5Q  H14  C11  S    105.16  3.000
 T5Q  H13  C11  S    109.54  3.000
 T5Q  H14  C11  C10  109.35  3.000
 T5Q  H13  C11  C10  111.07  3.000
 T5Q  S    C11  C10  113.89  3.000
 T5Q  H15  S    C11   98.02  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
 T5Q  CONST_01  C5   C6   C7   C2     0.00   0.0  0
 T5Q  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 T5Q  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 T5Q  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 T5Q  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 T5Q  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 T5Q  CONST_07  F1   C6   C7   C2   180.00   0.0  0
 T5Q  CONST_08  F    C4   C3   C2   180.00   0.0  0
 T5Q  CONST_09  O    C2   C3   C4   180.00   0.0  0
 T5Q  CONST_10  F1   C6   C5   C4   180.00   0.0  0
 T5Q  CONST_11  O    C2   C7   C6   180.00   0.0  0
 T5Q  CONST_12  F    C4   C5   C6   180.00   0.0  0
 T5Q  CONST_13  H3   C7   C2   C3   180.00   0.0  0
 T5Q  CONST_14  H2   C5   C4   C3   180.00   0.0  0
 T5Q  CONST_15  H1   C3   C4   C5   180.00   0.0  0
 T5Q  CONST_16  C10  N    C9   C1   180.00   0.0  0
 T5Q  CONST_17  O1   C9   N    C10    0.00   0.0  0
 T5Q  CONST_18  H7   N    C9   C1     0.00   0.0  0
 T5Q  Var_01    C7   C2   O    C1     2.44  30.0  2
 T5Q  Var_02    C9   C1   O    C2   -57.98  30.0  3
 T5Q  Var_03    C11  C10  N    C9   -88.37  30.0  2
 T5Q  Var_04    N    C9   C1   C8    72.93  30.0  2
 T5Q  Var_05    S    C11  C10  N    -66.24  30.0  3
 T5Q  Var_06    H4   C8   C1   C9   177.54  30.0  3
 T5Q  Var_07    H8   C    C1   C9   179.00  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
 T5Q  plan-1  C2   0.020
 T5Q  plan-1  C3   0.020
 T5Q  plan-1  C4   0.020
 T5Q  plan-1  C5   0.020
 T5Q  plan-1  C6   0.020
 T5Q  plan-1  C7   0.020
 T5Q  plan-1  O    0.020
 T5Q  plan-1  F    0.020
 T5Q  plan-1  F1   0.020
 T5Q  plan-1  H1   0.020
 T5Q  plan-1  H2   0.020
 T5Q  plan-1  H3   0.020
 T5Q  plan-2  C1   0.020
 T5Q  plan-2  C9   0.020
 T5Q  plan-2  N    0.020
 T5Q  plan-2  C10  0.020
 T5Q  plan-2  O1   0.020
 T5Q  plan-2  H7   0.020

