# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 02:44:08 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-(4-bromanylphenoxy)-2-methyl-~{N}-(2-sulfanylethyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(Oc1ccc(Br)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
 T5N  T5N  2-(4-bromanylphenoxy)-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_T5N
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
 T5N  N    N   NH1   0  -0.619  17.1646  18.9524  -1.9742
 T5N  C    C   CH3   0  -0.665  14.9683  17.9590   0.8853
 T5N  O    O   O2    0  -0.491  15.6341  20.1328  -0.0212
 T5N  C1   C   CT    0   0.055  15.3667  18.7654  -0.3430
 T5N  C10  C   CH2   0  -0.284  18.3137  18.5606  -2.7568
 T5N  C11  C   CH2   0  -0.564  19.6355  18.8028  -2.0428
 T5N  C2   C   CR6   0   0.385  16.6464  20.5181   0.7836
 T5N  C3   C   CR16  0  -0.362  17.6461  19.6956   1.2983
 T5N  C4   C   CR16  0  -0.218  18.6529  20.2336   2.0922
 T5N  C5   C   CR6   0  -0.132  18.6671  21.5872   2.3745
 T5N  C6   C   CR16  0  -0.213  17.6782  22.4189   1.8656
 T5N  C7   C   CR16  0  -0.338  16.6763  21.8827   1.0787
 T5N  C8   C   CH3   0  -0.658  14.1876  18.8249  -1.3132
 T5N  C9   C   C     0   0.536  16.5601  18.1393  -1.0939
 T5N  O1   O   O     0  -0.469  16.8769  16.9733  -0.9221
 T5N  S    S   S2    0  -0.247  19.9805  20.5583  -1.7103
 T5N  BR   BR  BR    0  -0.053  20.0385  22.3104   3.4534
 T5N  H1   H   HNH1  0   0.407  16.8507  19.9064  -2.0583
 T5N  H2   H   HCH3  0   0.247  14.1431  18.4615   1.3903
 T5N  H3   H   HCH3  0   0.250  14.6199  16.9729   0.5846
 T5N  H4   H   HCH3  0   0.250  15.7698  17.8167   1.6073
 T5N  H5   H   HCH2  0   0.262  18.2908  19.1176  -3.6928
 T5N  H6   H   HCH2  0   0.259  18.2336  17.5021  -3.0061
 T5N  H7   H   HCH2  0   0.278  19.6888  18.2372  -1.1128
 T5N  H8   H   HCH2  0   0.286  20.4544  18.4631  -2.6780
 T5N  H9   H   HCR6  0   0.290  17.6851  18.6341   1.1040
 T5N  H10  H   HCR6  0   0.284  19.4199  19.5749   2.4769
 T5N  H11  H   HCR6  0   0.281  17.6771  23.4804   2.0750
 T5N  H12  H   HCR6  0   0.276  15.9057  22.5299   0.6793
 T5N  H13  H   HCH3  0   0.253  13.3067  19.2222  -0.8081
 T5N  H14  H   HCH3  0   0.249  14.4053  19.4517  -2.1774
 T5N  H15  H   HCH3  0   0.246  13.9484  17.8238  -1.6699
 T5N  H16  H   HSH1  0   0.217  19.0755  20.7403  -0.7412

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
 T5N  C10  C11  single    1.522  0.020  1.522
 T5N  C10  N    single    1.444  0.020  1.444
 T5N  C11  S    single    1.820  0.020  1.820
 T5N  N    C9   single    1.342  0.020  1.342
 T5N  O1   C9   double    1.220  0.020  1.220
 T5N  C9   C1   single    1.543  0.020  1.543
 T5N  C8   C1   single    1.528  0.020  1.528
 T5N  C1   O    single    1.430  0.020  1.430
 T5N  C1   C    single    1.522  0.020  1.522
 T5N  O    C2   single    1.349  0.020  1.349
 T5N  C2   C3   aromatic  1.393  0.020  1.393
 T5N  C2   C7   aromatic  1.396  0.020  1.396
 T5N  C3   C4   aromatic  1.390  0.020  1.390
 T5N  C7   C6   aromatic  1.382  0.020  1.382
 T5N  C4   C5   aromatic  1.383  0.020  1.383
 T5N  C6   C5   aromatic  1.389  0.020  1.389
 T5N  C5   BR   single    1.889  0.020  1.889
 T5N  N    H1   single    0.860  0.020  1.020
 T5N  C    H2   single    0.970  0.020  1.090
 T5N  C    H3   single    0.970  0.020  1.090
 T5N  C    H4   single    0.970  0.020  1.090
 T5N  C10  H5   single    0.970  0.020  1.090
 T5N  C10  H6   single    0.970  0.020  1.090
 T5N  C11  H7   single    0.970  0.020  1.090
 T5N  C11  H8   single    0.970  0.020  1.090
 T5N  C3   H9   single    0.930  0.020  1.080
 T5N  C4   H10  single    0.930  0.020  1.080
 T5N  C6   H11  single    0.930  0.020  1.080
 T5N  C7   H12  single    0.930  0.020  1.080
 T5N  C8   H13  single    0.970  0.020  1.090
 T5N  C8   H14  single    0.970  0.020  1.090
 T5N  C8   H15  single    0.970  0.020  1.090
 T5N  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
 T5N  H1   N    C9   119.21  3.000
 T5N  H1   N    C10  117.34  3.000
 T5N  C9   N    C10  123.32  3.000
 T5N  H4   C    H3   107.50  3.000
 T5N  H4   C    H2   108.08  3.000
 T5N  H3   C    H2   107.66  3.000
 T5N  H4   C    C1   114.32  3.000
 T5N  H3   C    C1   109.93  3.000
 T5N  H2   C    C1   109.13  3.000
 T5N  C2   O    C1   123.20  3.000
 T5N  C9   C1   C8   107.68  3.000
 T5N  C8   C1   O    104.47  3.000
 T5N  C9   C1   O    110.67  3.000
 T5N  O    C1   C    111.95  3.000
 T5N  C8   C1   C    109.33  3.000
 T5N  C9   C1   C    112.34  3.000
 T5N  H6   C10  H5   107.36  3.000
 T5N  H6   C10  C11  109.00  3.000
 T5N  H5   C10  C11  109.87  3.000
 T5N  H6   C10  N    109.19  3.000
 T5N  H5   C10  N    108.07  3.000
 T5N  C11  C10  N    113.18  3.000
 T5N  H8   C11  H7   107.38  3.000
 T5N  H8   C11  S    105.34  3.000
 T5N  H7   C11  S    109.60  3.000
 T5N  H8   C11  C10  109.23  3.000
 T5N  H7   C11  C10  111.12  3.000
 T5N  S    C11  C10  113.83  3.000
 T5N  C7   C2   C3   118.91  3.000
 T5N  C7   C2   O    114.91  3.000
 T5N  C3   C2   O    126.16  3.000
 T5N  H9   C3   C4   117.19  3.000
 T5N  H9   C3   C2   122.67  3.000
 T5N  C4   C3   C2   120.14  3.000
 T5N  H10  C4   C5   121.08  3.000
 T5N  H10  C4   C3   118.74  3.000
 T5N  C5   C4   C3   120.18  3.000
 T5N  BR   C5   C6   119.80  3.000
 T5N  BR   C5   C4   119.92  3.000
 T5N  C6   C5   C4   120.27  3.000
 T5N  H11  C6   C7   119.34  3.000
 T5N  H11  C6   C5   121.16  3.000
 T5N  C7   C6   C5   119.50  3.000
 T5N  H12  C7   C6   119.61  3.000
 T5N  H12  C7   C2   119.40  3.000
 T5N  C6   C7   C2   120.99  3.000
 T5N  H15  C8   H14  108.23  3.000
 T5N  H15  C8   H13  108.01  3.000
 T5N  H14  C8   H13  108.62  3.000
 T5N  H15  C8   C1   109.97  3.000
 T5N  H14  C8   C1   111.83  3.000
 T5N  H13  C8   C1   110.09  3.000
 T5N  O1   C9   C1   121.34  3.000
 T5N  C1   C9   N    114.94  3.000
 T5N  O1   C9   N    123.65  3.000
 T5N  H16  S    C11   97.78  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
 T5N  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 T5N  CONST_02  C5   C6   C7   C2     0.00   0.0  0
 T5N  CONST_03  C6   C7   C2   C3     0.00   0.0  0
 T5N  CONST_04  C6   C5   C4   C3     0.00   0.0  0
 T5N  CONST_05  C7   C2   C3   C4     0.00   0.0  0
 T5N  CONST_06  C7   C6   C5   C4     0.00   0.0  0
 T5N  CONST_07  C4   C3   C2   O    180.00   0.0  0
 T5N  CONST_08  C6   C7   C2   O    180.00   0.0  0
 T5N  CONST_09  BR   C5   C4   C3   180.00   0.0  0
 T5N  CONST_10  BR   C5   C6   C7   180.00   0.0  0
 T5N  CONST_11  H10  C4   C3   C2   180.00   0.0  0
 T5N  CONST_12  H11  C6   C7   C2   180.00   0.0  0
 T5N  CONST_13  H12  C7   C2   C3   180.00   0.0  0
 T5N  CONST_14  H9   C3   C4   C5   180.00   0.0  0
 T5N  CONST_15  C10  N    C9   C1   180.00   0.0  0
 T5N  CONST_16  O1   C9   N    C10    0.00   0.0  0
 T5N  CONST_17  H1   N    C9   C1     0.00   0.0  0
 T5N  Var_01    C3   C2   O    C1     7.14  30.0  2
 T5N  Var_02    C9   C1   O    C2   -62.01  30.0  2
 T5N  Var_03    S    C11  C10  N    -63.98  30.0  3
 T5N  Var_04    C9   N    C10  C11  -87.29  30.0  3
 T5N  Var_05    H13  C8   C1   C     55.20  30.0  3
 T5N  Var_06    H2   C    C1   O     53.11  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
 T5N  plan-1  O    0.020
 T5N  plan-1  C2   0.020
 T5N  plan-1  C3   0.020
 T5N  plan-1  C4   0.020
 T5N  plan-1  C5   0.020
 T5N  plan-1  C6   0.020
 T5N  plan-1  C7   0.020
 T5N  plan-1  BR   0.020
 T5N  plan-1  H9   0.020
 T5N  plan-1  H10  0.020
 T5N  plan-1  H11  0.020
 T5N  plan-1  H12  0.020
 T5N  plan-2  N    0.020
 T5N  plan-2  C1   0.020
 T5N  plan-2  C10  0.020
 T5N  plan-2  C9   0.020
 T5N  plan-2  O1   0.020
 T5N  plan-2  H1   0.020

