# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 17:59:48 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(4-bromanyl-3-methoxy-phenoxy)-2-methyl-~{N}-(2-sulfanylethyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC(C)(C)C(=O)NCCS)ccc1Br
#
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
 T5Z  T5Z  2-(4-bromanyl-3-methoxy-phenoxy)-2-methyl-~{N}-(2-sulfanylethyl)propanamide  ligand  37  19  .  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_T5Z
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
 T5Z  C1   C   CT    0   0.064  15.4024  18.9864  -0.4976
 T5Z  C2   C   CR6   0   0.418  16.4613  20.8470   0.6850
 T5Z  C3   C   CR16  0  -0.495  17.6220  20.1881   1.0799
 T5Z  C4   C   CR6   0   0.480  18.4797  20.7694   2.0125
 T5Z  C5   C   CH3   0  -0.446  19.9686  18.9221   1.9337
 T5Z  C6   C   CR6   0  -0.256  18.1593  22.0237   2.5393
 T5Z  C10  C   C     0   0.532  16.5842  18.3875  -1.2845
 T5Z  C11  C   CH2   0  -0.305  18.2686  18.7987  -3.0074
 T5Z  N    N   NH1   0  -0.618  17.2012  19.2252  -2.1316
 T5Z  C    C   CH3   0  -0.656  14.1823  18.9364  -1.4167
 T5Z  O    O   O2    0  -0.503  15.5967  20.3807  -0.2455
 T5Z  C12  C   CH2   0  -0.548  19.6359  18.7502  -2.3429
 T5Z  C7   C   CR16  0  -0.208  17.0063  22.6759   2.1395
 T5Z  C8   C   CR16  0  -0.374  16.1517  22.0938   1.2195
 T5Z  C9   C   CH3   0  -0.673  15.1190  18.2093   0.7804
 T5Z  O1   O   O2    0  -0.454  19.6104  20.1962   2.4380
 T5Z  O2   O   O     0  -0.472  16.8744  17.2063  -1.1789
 T5Z  S    S   S2    0  -0.253  20.1357  20.4268  -1.8244
 T5Z  BR   BR  BR    0  -0.045  19.3057  22.8246   3.8021
 T5Z  H1   H   HCR6  0   0.310  17.8863  19.2308   0.6570
 T5Z  H2   H   HCH3  0   0.265  20.9018  18.6531   2.4211
 T5Z  H3   H   HCH3  0   0.234  19.2161  18.1653   2.1686
 T5Z  H4   H   HCH3  0   0.234  20.1270  18.9480   0.8530
 T5Z  H5   H   HCH2  0   0.268  18.2913  19.4780  -3.8596
 T5Z  H6   H   HCH2  0   0.268  18.0424  17.8057  -3.3973
 T5Z  H7   H   HNH1  0   0.409  16.9107  20.1890  -2.1705
 T5Z  H8   H   HCH3  0   0.252  13.3020  19.3068  -0.8907
 T5Z  H9   H   HCH3  0   0.248  14.3303  19.5389  -2.3133
 T5Z  H10  H   HCH3  0   0.245  13.9858  17.9103  -1.7248
 T5Z  H11  H   HCH2  0   0.274  19.6192  18.0855  -1.4797
 T5Z  H12  H   HCH2  0   0.279  20.3610  18.3657  -3.0596
 T5Z  H13  H   HCR6  0   0.279  16.7606  23.6455   2.5521
 T5Z  H14  H   HCR6  0   0.268  15.2491  22.6058   0.9142
 T5Z  H15  H   HCH3  0   0.252  15.9736  18.1469   1.4511
 T5Z  H16  H   HCH3  0   0.248  14.2963  18.6836   1.3164
 T5Z  H17  H   HCH3  0   0.253  14.8147  17.1933   0.5386
 T5Z  H18  H   HSH1  0   0.226  21.3798  20.1228  -1.4394

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
 T5Z  C11  C12  single    1.521  0.020  1.521
 T5Z  C11  N    single    1.445  0.020  1.445
 T5Z  C12  S    single    1.825  0.020  1.825
 T5Z  N    C10  single    1.342  0.020  1.342
 T5Z  O2   C10  double    1.221  0.020  1.221
 T5Z  C    C1   single    1.528  0.020  1.528
 T5Z  C10  C1   single    1.541  0.020  1.541
 T5Z  C1   O    single    1.430  0.020  1.430
 T5Z  C1   C9   single    1.522  0.020  1.522
 T5Z  O    C2   single    1.353  0.020  1.353
 T5Z  C2   C3   aromatic  1.392  0.020  1.392
 T5Z  C2   C8   aromatic  1.391  0.020  1.391
 T5Z  C3   C4   aromatic  1.394  0.020  1.394
 T5Z  C8   C7   aromatic  1.384  0.020  1.384
 T5Z  C5   O1   single    1.416  0.020  1.416
 T5Z  C4   O1   single    1.337  0.020  1.337
 T5Z  C4   C6   aromatic  1.398  0.020  1.398
 T5Z  C7   C6   aromatic  1.384  0.020  1.384
 T5Z  C6   BR   single    1.884  0.020  1.884
 T5Z  C3   H1   single    0.930  0.020  1.080
 T5Z  C5   H2   single    0.970  0.020  1.090
 T5Z  C5   H3   single    0.970  0.020  1.090
 T5Z  C5   H4   single    0.970  0.020  1.090
 T5Z  C11  H5   single    0.970  0.020  1.090
 T5Z  C11  H6   single    0.970  0.020  1.090
 T5Z  N    H7   single    0.860  0.020  1.020
 T5Z  C    H8   single    0.970  0.020  1.090
 T5Z  C    H9   single    0.970  0.020  1.090
 T5Z  C    H10  single    0.970  0.020  1.090
 T5Z  C12  H11  single    0.970  0.020  1.090
 T5Z  C12  H12  single    0.970  0.020  1.090
 T5Z  C7   H13  single    0.930  0.020  1.080
 T5Z  C8   H14  single    0.930  0.020  1.080
 T5Z  C9   H15  single    0.970  0.020  1.090
 T5Z  C9   H16  single    0.970  0.020  1.090
 T5Z  C9   H17  single    0.970  0.020  1.090
 T5Z  S    H18  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
 T5Z  C9   C1   O    112.02  3.000
 T5Z  C9   C1   C    109.85  3.000
 T5Z  O    C1   C    104.26  3.000
 T5Z  C9   C1   C10  111.91  3.000
 T5Z  O    C1   C10  111.39  3.000
 T5Z  C    C1   C10  107.00  3.000
 T5Z  C8   C2   O    115.52  3.000
 T5Z  C8   C2   C3   120.05  3.000
 T5Z  O    C2   C3   124.39  3.000
 T5Z  H1   C3   C4   118.77  3.000
 T5Z  H1   C3   C2   120.85  3.000
 T5Z  C4   C3   C2   120.36  3.000
 T5Z  O1   C4   C6   117.30  3.000
 T5Z  C6   C4   C3   119.04  3.000
 T5Z  O1   C4   C3   123.67  3.000
 T5Z  H4   C5   H3   109.20  3.000
 T5Z  H4   C5   H2   108.97  3.000
 T5Z  H3   C5   H2   108.88  3.000
 T5Z  H4   C5   O1   111.56  3.000
 T5Z  H3   C5   O1   111.86  3.000
 T5Z  H2   C5   O1   106.27  3.000
 T5Z  BR   C6   C7   120.02  3.000
 T5Z  BR   C6   C4   119.65  3.000
 T5Z  C7   C6   C4   120.34  3.000
 T5Z  O2   C10  N    123.33  3.000
 T5Z  O2   C10  C1   120.94  3.000
 T5Z  N    C10  C1   115.62  3.000
 T5Z  H6   C11  H5   106.99  3.000
 T5Z  H6   C11  C12  108.28  3.000
 T5Z  H5   C11  C12  110.04  3.000
 T5Z  H6   C11  N    109.41  3.000
 T5Z  H5   C11  N    107.78  3.000
 T5Z  C12  C11  N    114.12  3.000
 T5Z  H7   N    C11  118.16  3.000
 T5Z  H7   N    C10  119.28  3.000
 T5Z  C11  N    C10  122.55  3.000
 T5Z  H10  C    H9   108.21  3.000
 T5Z  H10  C    H8   108.11  3.000
 T5Z  H9   C    H8   108.57  3.000
 T5Z  H10  C    C1   110.18  3.000
 T5Z  H9   C    C1   111.60  3.000
 T5Z  H8   C    C1   110.07  3.000
 T5Z  C2   O    C1   122.96  3.000
 T5Z  H12  C12  H11  108.43  3.000
 T5Z  H12  C12  S    109.20  3.000
 T5Z  H11  C12  S    109.85  3.000
 T5Z  H12  C12  C11  108.79  3.000
 T5Z  H11  C12  C11  110.60  3.000
 T5Z  S    C12  C11  109.94  3.000
 T5Z  H13  C7   C8   119.36  3.000
 T5Z  H13  C7   C6   120.09  3.000
 T5Z  C8   C7   C6   120.55  3.000
 T5Z  H14  C8   C7   120.25  3.000
 T5Z  H14  C8   C2   120.09  3.000
 T5Z  C7   C8   C2   119.66  3.000
 T5Z  H17  C9   H16  107.73  3.000
 T5Z  H17  C9   H15  107.65  3.000
 T5Z  H16  C9   H15  108.33  3.000
 T5Z  H17  C9   C1   110.01  3.000
 T5Z  H16  C9   C1   109.33  3.000
 T5Z  H15  C9   C1   113.61  3.000
 T5Z  C5   O1   C4   119.09  3.000
 T5Z  H18  S    C12   97.34  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
 T5Z  CONST_01  C6   C4   C3   C2      0.00   0.0  0
 T5Z  CONST_02  C6   C7   C8   C2      0.00   0.0  0
 T5Z  CONST_03  C7   C8   C2   C3      0.00   0.0  0
 T5Z  CONST_04  C7   C6   C4   C3      0.00   0.0  0
 T5Z  CONST_05  C8   C2   C3   C4      0.00   0.0  0
 T5Z  CONST_06  C8   C7   C6   C4      0.00   0.0  0
 T5Z  CONST_07  O1   C4   C3   C2    180.00   0.0  0
 T5Z  CONST_08  BR   C6   C4   C3    180.00   0.0  0
 T5Z  CONST_09  O    C2   C3   C4    180.00   0.0  0
 T5Z  CONST_10  C7   C8   C2   O     180.00   0.0  0
 T5Z  CONST_11  O1   C4   C6   C7    180.00   0.0  0
 T5Z  CONST_12  BR   C6   C7   C8    180.00   0.0  0
 T5Z  CONST_13  H13  C7   C8   C2    180.00   0.0  0
 T5Z  CONST_14  H14  C8   C2   C3    180.00   0.0  0
 T5Z  CONST_15  H1   C3   C4   C6    180.00   0.0  0
 T5Z  CONST_16  C11  N    C10  C1    180.00   0.0  0
 T5Z  CONST_17  O2   C10  N    C11     0.00   0.0  0
 T5Z  CONST_18  H7   N    C10  C1      0.00   0.0  0
 T5Z  Var_01    C3   C2   O    C1     29.02  30.0  2
 T5Z  Var_02    C6   C4   O1   C5    179.70  30.0  1
 T5Z  Var_03    C    C1   O    C2    170.03  30.0  3
 T5Z  Var_04    H2   C5   O1   C4   -179.31  30.0  3
 T5Z  Var_05    C12  C11  N    C10   -82.37  30.0  2
 T5Z  Var_06    S    C12  C11  N     -63.68  30.0  3
 T5Z  Var_07    H8   C    C1   C10   177.33  30.0  3
 T5Z  Var_08    H15  C9   C1   C10    57.30  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
 T5Z  plan-1  C2   0.020
 T5Z  plan-1  C3   0.020
 T5Z  plan-1  C4   0.020
 T5Z  plan-1  C6   0.020
 T5Z  plan-1  O    0.020
 T5Z  plan-1  C7   0.020
 T5Z  plan-1  C8   0.020
 T5Z  plan-1  O1   0.020
 T5Z  plan-1  BR   0.020
 T5Z  plan-1  H1   0.020
 T5Z  plan-1  H13  0.020
 T5Z  plan-1  H14  0.020
 T5Z  plan-2  C1   0.020
 T5Z  plan-2  C10  0.020
 T5Z  plan-2  C11  0.020
 T5Z  plan-2  N    0.020
 T5Z  plan-2  O2   0.020
 T5Z  plan-2  H7   0.020

