# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 01:36:31 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(4-fluoranylphenoxy)-2-methyl-~{N}-(2-sulfanylethyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(F)cc1)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
 T5T  T5T  2-(4-fluoranylphenoxy)-2-methyl-~{N}-(2-sulfanylethyl)propanamide  ligand  33  17  .  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_T5T
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
 T5T  O1   O  O     0  -0.470  16.1797  17.7188  -0.9913
 T5T  C7   C  CR16  0  -0.347  17.7662  19.6710   1.5550
 T5T  C2   C  CR6   0   0.369  16.9990  20.8035   1.2915
 T5T  C3   C  CR16  0  -0.328  17.4357  22.0416   1.7673
 T5T  C4   C  CR16  0  -0.396  18.6071  22.1524   2.4951
 T5T  C5   C  CR6   0   0.506  19.3473  21.0123   2.7492
 T5T  C6   C  CR16  0  -0.405  18.9434  19.7796   2.2881
 T5T  C1   C  CT    0   0.058  15.2211  19.6756   0.0480
 T5T  C8   C  CH3   0  -0.658  14.0426  20.2065  -0.7673
 T5T  C9   C  C     0   0.534  16.1683  18.9371  -0.9199
 T5T  C10  C  CH2   0  -0.286  17.9095  19.2338  -2.6206
 T5T  C11  C  CH2   0  -0.565  19.2859  19.0727  -1.9922
 T5T  N    N  NH1   0  -0.618  16.9196  19.7341  -1.6961
 T5T  C    C  CH3   0  -0.662  14.6972  18.7630   1.1493
 T5T  O    O  O2    0  -0.495  15.8503  20.8432   0.5754
 T5T  F    F  F     0  -0.318  20.4854  21.1108   3.4583
 T5T  S    S  S2    0  -0.246  20.0481  20.6419  -1.4747
 T5T  H2   H  HCR6  0   0.275  16.8489  22.9269   1.5579
 T5T  H3   H  HCR6  0   0.282  18.9366  23.1173   2.8580
 T5T  H4   H  HCR6  0   0.283  19.5355  18.8964   2.4887
 T5T  H5   H  HCH3  0   0.252  13.3269  20.7039  -0.1119
 T5T  H6   H  HCH3  0   0.248  14.3608  20.9148  -1.5323
 T5T  H7   H  HCH3  0   0.246  13.5296  19.3813  -1.2599
 T5T  H8   H  HCH2  0   0.262  17.9654  19.9200  -3.4653
 T5T  H9   H  HCH2  0   0.260  17.5804  18.2695  -3.0084
 T5T  H10  H  HCH2  0   0.278  19.2543  18.3869  -1.1455
 T5T  H11  H  HCH2  0   0.287  19.9706  18.6505  -2.7286
 T5T  H12  H  HNH1  0   0.406  16.8626  20.7331  -1.5747
 T5T  H13  H  HCH3  0   0.246  14.0537  19.3395   1.8143
 T5T  H14  H  HCH3  0   0.248  14.0959  17.9650   0.7183
 T5T  H15  H  HCH3  0   0.249  15.4757  18.2997   1.7512
 T5T  H16  H  HSH1  0   0.216  19.2729  20.8832  -0.4100
 T5T  H1   H  HCR6  0   0.289  17.4873  18.6867   1.2096

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
 T5T  C10  C11  single    1.522  0.020  1.522
 T5T  C10  N    single    1.444  0.020  1.444
 T5T  C11  S    single    1.820  0.020  1.820
 T5T  N    C9   single    1.342  0.020  1.342
 T5T  O1   C9   double    1.220  0.020  1.220
 T5T  C9   C1   single    1.543  0.020  1.543
 T5T  C8   C1   single    1.528  0.020  1.528
 T5T  C1   O    single    1.427  0.020  1.427
 T5T  C1   C    single    1.523  0.020  1.523
 T5T  O    C2   single    1.354  0.020  1.354
 T5T  C7   C2   aromatic  1.393  0.020  1.393
 T5T  C7   C6   aromatic  1.391  0.020  1.391
 T5T  C2   C3   aromatic  1.396  0.020  1.396
 T5T  C6   C5   aromatic  1.377  0.020  1.377
 T5T  C3   C4   aromatic  1.383  0.020  1.383
 T5T  C5   C4   aromatic  1.383  0.020  1.383
 T5T  C5   F    single    1.345  0.020  1.345
 T5T  C7   H1   single    0.930  0.020  1.080
 T5T  C3   H2   single    0.930  0.020  1.080
 T5T  C4   H3   single    0.930  0.020  1.080
 T5T  C6   H4   single    0.930  0.020  1.080
 T5T  C8   H5   single    0.970  0.020  1.090
 T5T  C8   H6   single    0.970  0.020  1.090
 T5T  C8   H7   single    0.970  0.020  1.090
 T5T  C10  H8   single    0.970  0.020  1.090
 T5T  C10  H9   single    0.970  0.020  1.090
 T5T  C11  H10  single    0.970  0.020  1.090
 T5T  C11  H11  single    0.970  0.020  1.090
 T5T  N    H12  single    0.860  0.020  1.020
 T5T  C    H13  single    0.970  0.020  1.090
 T5T  C    H14  single    0.970  0.020  1.090
 T5T  C    H15  single    0.970  0.020  1.090
 T5T  S    H16  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
 T5T  H1   C7   C6   117.28  3.000
 T5T  H1   C7   C2   122.57  3.000
 T5T  C6   C7   C2   120.15  3.000
 T5T  O    C2   C3   114.80  3.000
 T5T  C3   C2   C7   118.96  3.000
 T5T  O    C2   C7   126.23  3.000
 T5T  H2   C3   C4   119.68  3.000
 T5T  H2   C3   C2   119.32  3.000
 T5T  C4   C3   C2   121.00  3.000
 T5T  H3   C4   C5   120.69  3.000
 T5T  H3   C4   C3   120.37  3.000
 T5T  C5   C4   C3   118.94  3.000
 T5T  F    C5   C6   119.37  3.000
 T5T  F    C5   C4   119.32  3.000
 T5T  C6   C5   C4   121.31  3.000
 T5T  H4   C6   C5   120.55  3.000
 T5T  H4   C6   C7   119.81  3.000
 T5T  C5   C6   C7   119.65  3.000
 T5T  O    C1   C    112.00  3.000
 T5T  C    C1   C9   112.21  3.000
 T5T  O    C1   C9   110.66  3.000
 T5T  C    C1   C8   109.18  3.000
 T5T  O    C1   C8   104.65  3.000
 T5T  C9   C1   C8   107.76  3.000
 T5T  H7   C8   H6   108.20  3.000
 T5T  H7   C8   H5   107.95  3.000
 T5T  H6   C8   H5   108.48  3.000
 T5T  H7   C8   C1   109.95  3.000
 T5T  H6   C8   C1   112.03  3.000
 T5T  H5   C8   C1   110.12  3.000
 T5T  N    C9   C1   114.97  3.000
 T5T  C1   C9   O1   121.36  3.000
 T5T  N    C9   O1   123.62  3.000
 T5T  H9   C10  H8   107.25  3.000
 T5T  H9   C10  N    109.10  3.000
 T5T  H8   C10  N    108.26  3.000
 T5T  H9   C10  C11  109.05  3.000
 T5T  H8   C10  C11  109.90  3.000
 T5T  N    C10  C11  113.11  3.000
 T5T  H11  C11  H10  107.40  3.000
 T5T  H11  C11  S    105.24  3.000
 T5T  H10  C11  S    109.50  3.000
 T5T  H11  C11  C10  109.27  3.000
 T5T  H10  C11  C10  111.18  3.000
 T5T  S    C11  C10  113.89  3.000
 T5T  H12  N    C10  117.34  3.000
 T5T  H12  N    C9   119.15  3.000
 T5T  C10  N    C9   123.24  3.000
 T5T  H15  C    H14  107.59  3.000
 T5T  H15  C    H13  108.07  3.000
 T5T  H14  C    H13  107.65  3.000
 T5T  H15  C    C1   114.15  3.000
 T5T  H14  C    C1   110.06  3.000
 T5T  H13  C    C1   109.10  3.000
 T5T  C1   O    C2   123.05  3.000
 T5T  H16  S    C11   97.99  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
 T5T  CONST_01  C4   C3   C2   C7    0.00   0.0  0
 T5T  CONST_02  C4   C5   C6   C7    0.00   0.0  0
 T5T  CONST_03  C5   C6   C7   C2    0.00   0.0  0
 T5T  CONST_04  C5   C4   C3   C2    0.00   0.0  0
 T5T  CONST_05  C6   C7   C2   C3    0.00   0.0  0
 T5T  CONST_06  C6   C5   C4   C3    0.00   0.0  0
 T5T  CONST_07  F    C5   C6   C7  180.00   0.0  0
 T5T  CONST_08  F    C5   C4   C3  180.00   0.0  0
 T5T  CONST_09  O    C2   C3   C4  180.00   0.0  0
 T5T  CONST_10  O    C2   C7   C6  180.00   0.0  0
 T5T  CONST_11  H2   C3   C2   C7  180.00   0.0  0
 T5T  CONST_12  H4   C6   C7   C2  180.00   0.0  0
 T5T  CONST_13  H3   C4   C3   C2  180.00   0.0  0
 T5T  CONST_14  H1   C7   C2   C3  180.00   0.0  0
 T5T  CONST_15  C10  N    C9   O1    0.00   0.0  0
 T5T  CONST_16  C10  N    C9   C1  180.00   0.0  0
 T5T  CONST_17  H12  N    C9   O1  180.00   0.0  0
 T5T  Var_01    C9   C1   O    C2  -59.72  30.0  2
 T5T  Var_02    C11  C10  N    C9  -89.22  30.0  1
 T5T  Var_03    S    C11  C10  N   -65.21  30.0  3
 T5T  Var_04    H13  C    C1   C8  -61.85  30.0  3
 T5T  Var_05    H5   C8   C1   C9  177.80  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
 T5T  plan-1  C7   0.020
 T5T  plan-1  C2   0.020
 T5T  plan-1  C3   0.020
 T5T  plan-1  C4   0.020
 T5T  plan-1  C5   0.020
 T5T  plan-1  C6   0.020
 T5T  plan-1  O    0.020
 T5T  plan-1  F    0.020
 T5T  plan-1  H2   0.020
 T5T  plan-1  H3   0.020
 T5T  plan-1  H4   0.020
 T5T  plan-1  H1   0.020
 T5T  plan-2  O1   0.020
 T5T  plan-2  C1   0.020
 T5T  plan-2  C9   0.020
 T5T  plan-2  C10  0.020
 T5T  plan-2  N    0.020
 T5T  plan-2  H12  0.020

