# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 18:18:05 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: 2-methyl-2-(4-methylphenoxy)-~{N}-(2-sulfanylethyl)propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(OC(C)(C)C(=O)NCCS)cc1
#
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
 T6N  T6N  2-methyl-2-(4-methylphenoxy)-~{N}-(2-sulfanylethyl)propanamide  ligand  36  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_T6N
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
 T6N  C2   C  CR6   0   0.348  16.7093  20.7078   0.9862
 T6N  C3   C  CR16  0  -0.318  17.9198  20.0798   1.2554
 T6N  C6   C  CH3   0  -0.719  19.4546  22.4040   3.8525
 T6N  C8   C  CR16  0  -0.324  16.3904  21.8809   1.6647
 T6N  C9   C  CH3   0  -0.655  14.2134  18.8846  -0.9273
 T6N  C10  C  C     0   0.535  16.5857  18.2283  -1.0334
 T6N  C11  C  CH2   0  -0.307  18.1801  18.5505  -2.8570
 T6N  C12  C  CH2   0  -0.544  19.5799  18.3423  -2.2958
 T6N  N    N  NH1   0  -0.619  17.2241  19.0384  -1.8912
 T6N  C    C  CH3   0  -0.678  15.3497  18.1494   1.1730
 T6N  O    O  O2    0  -0.511  15.8080  20.2849   0.0569
 T6N  C1   C  CT    0   0.071  15.5247  18.8988  -0.1414
 T6N  C4   C  CR16  0  -0.296  18.7887  20.6271   2.1907
 T6N  C5   C  CR6   0   0.083  18.4914  21.8032   2.8705
 T6N  C7   C  CR16  0  -0.287  17.2740  22.4192   2.5862
 T6N  O1   O  O     0  -0.477  16.7611  17.0200  -0.9960
 T6N  S    S  S2    0  -0.258  20.2931  19.9462  -1.7986
 T6N  H1   H  HCR6  0   0.273  18.2174  19.1739   0.7464
 T6N  H2   H  HCH3  0   0.244  20.0687  23.1752   3.3824
 T6N  H3   H  HCH3  0   0.241  18.9334  22.8738   4.6867
 T6N  H4   H  HCH3  0   0.241  20.1327  21.6546   4.2597
 T6N  H5   H  HCR6  0   0.257  15.4452  22.3702   1.4649
 T6N  H6   H  HCH3  0   0.249  13.4086  19.2999  -0.3197
 T6N  H7   H  HCH3  0   0.246  14.2907  19.4685  -1.8452
 T6N  H8   H  HCH3  0   0.242  13.9439  17.8642  -1.1960
 T6N  H9   H  HCH2  0   0.267  18.2085  19.2578  -3.6864
 T6N  H10  H  HCH2  0   0.268  17.8326  17.6004  -3.2645
 T6N  H11  H  HCH2  0   0.276  19.5488  17.6738  -1.4368
 T6N  H12  H  HCH2  0   0.275  20.2046  17.8871  -3.0639
 T6N  H13  H  HNH1  0   0.407  17.0350  20.0271  -1.8623
 T6N  H14  H  HCH3  0   0.246  14.6165  18.6666   1.7931
 T6N  H15  H  HCH3  0   0.253  14.9738  17.1465   0.9827
 T6N  H16  H  HCH3  0   0.251  16.2730  18.0539   1.7414
 T6N  H17  H  HCR6  0   0.249  19.7250  20.1184   2.3879
 T6N  H18  H  HCR6  0   0.246  17.0024  23.3337   3.1008
 T6N  H19  H  HSH1  0   0.225  21.3930  19.4710  -1.2051

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
 T6N  C11  C12  single    1.522  0.020  1.522
 T6N  C11  N    single    1.444  0.020  1.444
 T6N  C12  S    single    1.824  0.020  1.824
 T6N  N    C10  single    1.342  0.020  1.342
 T6N  O1   C10  double    1.221  0.020  1.221
 T6N  C10  C1   single    1.540  0.020  1.540
 T6N  C9   C1   single    1.529  0.020  1.529
 T6N  C1   O    single    1.429  0.020  1.429
 T6N  C1   C    single    1.523  0.020  1.523
 T6N  O    C2   single    1.362  0.020  1.362
 T6N  C2   C3   aromatic  1.390  0.020  1.390
 T6N  C2   C8   aromatic  1.392  0.020  1.392
 T6N  C3   C4   aromatic  1.389  0.020  1.389
 T6N  C8   C7   aromatic  1.386  0.020  1.386
 T6N  C4   C5   aromatic  1.391  0.020  1.391
 T6N  C7   C5   aromatic  1.394  0.020  1.394
 T6N  C5   C6   single    1.501  0.020  1.501
 T6N  C3   H1   single    0.930  0.020  1.080
 T6N  C6   H2   single    0.970  0.020  1.090
 T6N  C6   H3   single    0.970  0.020  1.090
 T6N  C6   H4   single    0.970  0.020  1.090
 T6N  C8   H5   single    0.930  0.020  1.080
 T6N  C9   H6   single    0.970  0.020  1.090
 T6N  C9   H7   single    0.970  0.020  1.090
 T6N  C9   H8   single    0.970  0.020  1.090
 T6N  C11  H9   single    0.970  0.020  1.090
 T6N  C11  H10  single    0.970  0.020  1.090
 T6N  C12  H11  single    0.970  0.020  1.090
 T6N  C12  H12  single    0.970  0.020  1.090
 T6N  N    H13  single    0.860  0.020  1.020
 T6N  C    H14  single    0.970  0.020  1.090
 T6N  C    H15  single    0.970  0.020  1.090
 T6N  C    H16  single    0.970  0.020  1.090
 T6N  C4   H17  single    0.930  0.020  1.080
 T6N  C7   H18  single    0.930  0.020  1.080
 T6N  S    H19  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
 T6N  O    C2   C8   116.27  3.000
 T6N  C8   C2   C3   119.06  3.000
 T6N  O    C2   C3   124.62  3.000
 T6N  H1   C3   C4   118.36  3.000
 T6N  H1   C3   C2   121.82  3.000
 T6N  C4   C3   C2   119.82  3.000
 T6N  H4   C6   H3   107.94  3.000
 T6N  H4   C6   H2   107.25  3.000
 T6N  H3   C6   H2   107.09  3.000
 T6N  H4   C6   C5   111.63  3.000
 T6N  H3   C6   C5   111.49  3.000
 T6N  H2   C6   C5   111.21  3.000
 T6N  H5   C8   C7   120.25  3.000
 T6N  H5   C8   C2   119.39  3.000
 T6N  C7   C8   C2   120.36  3.000
 T6N  H8   C9   H7   108.15  3.000
 T6N  H8   C9   H6   108.16  3.000
 T6N  H7   C9   H6   108.50  3.000
 T6N  H8   C9   C1   110.35  3.000
 T6N  H7   C9   C1   111.52  3.000
 T6N  H6   C9   C1   110.06  3.000
 T6N  O1   C10  C1   120.79  3.000
 T6N  C1   C10  N    115.81  3.000
 T6N  O1   C10  N    123.27  3.000
 T6N  H10  C11  H9   106.81  3.000
 T6N  H10  C11  N    109.47  3.000
 T6N  H9   C11  N    107.87  3.000
 T6N  H10  C11  C12  108.15  3.000
 T6N  H9   C11  C12  110.19  3.000
 T6N  N    C11  C12  114.11  3.000
 T6N  H12  C12  H11  108.42  3.000
 T6N  H12  C12  S    109.58  3.000
 T6N  H11  C12  S    109.63  3.000
 T6N  H12  C12  C11  108.93  3.000
 T6N  H11  C12  C11  110.40  3.000
 T6N  S    C12  C11  109.86  3.000
 T6N  H13  N    C11  118.38  3.000
 T6N  H13  N    C10  119.03  3.000
 T6N  C11  N    C10  122.60  3.000
 T6N  H16  C    H15  107.67  3.000
 T6N  H16  C    H14  108.36  3.000
 T6N  H15  C    H14  107.72  3.000
 T6N  H16  C    C1   113.35  3.000
 T6N  H15  C    C1   110.02  3.000
 T6N  H14  C    C1   109.55  3.000
 T6N  C1   O    C2   121.82  3.000
 T6N  O    C1   C    112.36  3.000
 T6N  C    C1   C10  111.40  3.000
 T6N  O    C1   C10  111.49  3.000
 T6N  C    C1   C9   109.91  3.000
 T6N  O    C1   C9   104.50  3.000
 T6N  C10  C1   C9   106.81  3.000
 T6N  H17  C4   C5   119.53  3.000
 T6N  H17  C4   C3   118.56  3.000
 T6N  C5   C4   C3   121.91  3.000
 T6N  C7   C5   C4   117.45  3.000
 T6N  C7   C5   C6   121.14  3.000
 T6N  C4   C5   C6   121.40  3.000
 T6N  H18  C7   C5   119.67  3.000
 T6N  H18  C7   C8   118.93  3.000
 T6N  C5   C7   C8   121.40  3.000
 T6N  H19  S    C12   97.48  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
 T6N  CONST_01  C5   C4   C3   C2     0.00   0.0  0
 T6N  CONST_02  C5   C7   C8   C2     0.00   0.0  0
 T6N  CONST_03  C7   C8   C2   C3     0.00   0.0  0
 T6N  CONST_04  C7   C5   C4   C3     0.00   0.0  0
 T6N  CONST_05  C4   C3   C2   C8     0.00   0.0  0
 T6N  CONST_06  C4   C5   C7   C8     0.00   0.0  0
 T6N  CONST_07  C6   C5   C4   C3   180.00   0.0  0
 T6N  CONST_08  C8   C7   C5   C6   180.00   0.0  0
 T6N  CONST_09  C4   C3   C2   O    180.00   0.0  0
 T6N  CONST_10  C7   C8   C2   O    180.00   0.0  0
 T6N  CONST_11  H17  C4   C3   C2   180.00   0.0  0
 T6N  CONST_12  H18  C7   C8   C2   180.00   0.0  0
 T6N  CONST_13  H5   C8   C2   C3   180.00   0.0  0
 T6N  CONST_14  H1   C3   C2   C8   180.00   0.0  0
 T6N  CONST_15  O1   C10  N    C11    0.00   0.0  0
 T6N  CONST_16  C1   C10  N    C11  180.00   0.0  0
 T6N  CONST_17  H13  N    C10  C1     0.00   0.0  0
 T6N  Var_01    H2   C6   C5   C4    95.63  30.0  2
 T6N  Var_02    C10  C1   O    C2   -81.37  30.0  2
 T6N  Var_03    N    C10  C1   C9    87.29  30.0  1
 T6N  Var_04    C12  C11  N    C10  -82.47  30.0  1
 T6N  Var_05    S    C12  C11  N    -65.27  30.0  3
 T6N  Var_06    H14  C    C1   C9   -63.60  30.0  3
 T6N  Var_07    H6   C9   C1   C10  176.89  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
 T6N  plan-1  C2   0.020
 T6N  plan-1  C3   0.020
 T6N  plan-1  C6   0.020
 T6N  plan-1  C8   0.020
 T6N  plan-1  O    0.020
 T6N  plan-1  C4   0.020
 T6N  plan-1  C5   0.020
 T6N  plan-1  C7   0.020
 T6N  plan-1  H1   0.020
 T6N  plan-1  H5   0.020
 T6N  plan-1  H17  0.020
 T6N  plan-1  H18  0.020
 T6N  plan-2  C10  0.020
 T6N  plan-2  C11  0.020
 T6N  plan-2  N    0.020
 T6N  plan-2  C1   0.020
 T6N  plan-2  O1   0.020
 T6N  plan-2  H13  0.020

