# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 04:20:15 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: ~{N}-(4-methoxyphenyl)-2-[(2~{S})-3-oxidanylidenethiomorpholin-2-yl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(NC(=O)C[C@@H]2SCCNC2=O)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
 T4N  T4N  ~{N}-(4-methoxyphenyl)-2-[(2~{S})-3-oxidanylidenethiomorpholin-2-yl]ethanamide  ligand  35  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_T4N
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
 T4N  C1   C  CH3   0  -0.435  -32.1121  -15.1277  19.0606
 T4N  C3   C  CR6   0   0.377  -30.6815  -14.2341  17.3944
 T4N  C8   C  C     0   0.528  -29.1903  -12.1538  12.9343
 T4N  C10  C  CH2   0  -0.572  -29.1429  -11.0795  11.8649
 T4N  C11  C  CH1   0  -0.539  -27.7045  -10.7586  11.5005
 T4N  C14  C  CH2   0  -0.544  -25.2787   -9.5602  12.2751
 T4N  C15  C  CH2   0  -0.306  -25.1897   -9.9415  10.8031
 T4N  C19  C  CR16  0  -0.265  -29.1339  -13.3418  15.7689
 T4N  C20  C  CR16  0  -0.340  -29.3871  -14.1177  16.8835
 T4N  O2   O  O2    0  -0.467  -30.8256  -15.0023  18.4909
 T4N  C4   C  CR16  0  -0.377  -31.7210  -13.5597  16.7604
 T4N  C5   C  CR16  0  -0.294  -31.4607  -12.7947  15.6301
 T4N  C6   C  CR6   0   0.315  -30.1747  -12.6733  15.1247
 T4N  N7   N  NH1   0  -0.733  -29.9485  -11.8416  14.0094
 T4N  O9   O  O     0  -0.464  -28.5849  -13.2041  12.8132
 T4N  S13  S  S2    0   0.008  -26.8899  -10.0443  12.9832
 T4N  N16  N  NH1   0  -0.620  -26.3219   -9.4510  10.0515
 T4N  C17  C  C     0   0.598  -27.5923   -9.7683  10.3573
 T4N  O18  O  O     0  -0.474  -28.5620   -9.3046   9.7805
 T4N  H1   H  HCH3  0   0.258  -32.0042  -15.7707  19.9307
 T4N  H2   H  HCH3  0   0.227  -32.5126  -14.1632  19.3843
 T4N  H3   H  HCH3  0   0.227  -32.8233  -15.5892  18.3700
 T4N  H4   H  HCH2  0   0.273  -29.6725  -10.1759  12.1694
 T4N  H5   H  HCH2  0   0.299  -29.6531  -11.4686  10.9803
 T4N  H6   H  HCH1  0   0.321  -27.1900  -11.6858  11.2340
 T4N  H7   H  HCH2  0   0.281  -24.4833  -10.0555  12.8307
 T4N  H8   H  HCH2  0   0.276  -25.1651   -8.4835  12.3953
 T4N  H9   H  HCH2  0   0.261  -25.0980  -11.0257  10.7047
 T4N  H10  H  HCH2  0   0.292  -24.2873   -9.5100  10.3742
 T4N  H11  H  HCR6  0   0.264  -28.1174  -13.2452  15.4151
 T4N  H12  H  HCR6  0   0.263  -28.5720  -14.6309  17.3785
 T4N  H13  H  HCR6  0   0.279  -32.7388  -13.6195  17.1208
 T4N  H14  H  HCR6  0   0.268  -32.2806  -12.2826  15.1411
 T4N  H15  H  HNH1  0   0.412  -30.4792  -10.9848  13.9723
 T4N  H16  H  HNH1  0   0.401  -26.1699   -8.7522   9.3400

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
 T4N  O18  C17  double    1.220  0.020  1.220
 T4N  C17  C11  single    1.517  0.020  1.517
 T4N  C17  N16  single    1.345  0.020  1.345
 T4N  C11  C10  single    1.518  0.020  1.518
 T4N  C11  S13  single    1.836  0.020  1.836
 T4N  C10  C8   single    1.517  0.020  1.517
 T4N  C15  N16  single    1.445  0.020  1.445
 T4N  C15  C14  single    1.523  0.020  1.523
 T4N  C14  S13  single    1.825  0.020  1.825
 T4N  O9   C8   double    1.218  0.020  1.218
 T4N  C8   N7   single    1.352  0.020  1.352
 T4N  N7   C6   single    1.410  0.020  1.410
 T4N  C6   C19  aromatic  1.395  0.020  1.395
 T4N  C6   C5   aromatic  1.387  0.020  1.387
 T4N  C19  C20  aromatic  1.381  0.020  1.381
 T4N  C5   C4   aromatic  1.389  0.020  1.389
 T4N  C20  C3   aromatic  1.396  0.020  1.396
 T4N  C4   C3   aromatic  1.392  0.020  1.392
 T4N  C3   O2   single    1.347  0.020  1.347
 T4N  C1   O2   single    1.413  0.020  1.413
 T4N  C1   H1   single    0.970  0.020  1.090
 T4N  C1   H2   single    0.970  0.020  1.090
 T4N  C1   H3   single    0.970  0.020  1.090
 T4N  C10  H4   single    0.970  0.020  1.090
 T4N  C10  H5   single    0.970  0.020  1.090
 T4N  C11  H6   single    0.970  0.020  1.090
 T4N  C14  H7   single    0.970  0.020  1.090
 T4N  C14  H8   single    0.970  0.020  1.090
 T4N  C15  H9   single    0.970  0.020  1.090
 T4N  C15  H10  single    0.970  0.020  1.090
 T4N  C19  H11  single    0.930  0.020  1.080
 T4N  C20  H12  single    0.930  0.020  1.080
 T4N  C4   H13  single    0.930  0.020  1.080
 T4N  C5   H14  single    0.930  0.020  1.080
 T4N  N7   H15  single    0.860  0.020  1.020
 T4N  N16  H16  single    0.860  0.020  1.020

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
 T4N  H3   C1   H2   108.73  3.000
 T4N  H3   C1   H1   108.68  3.000
 T4N  H2   C1   H1   108.73  3.000
 T4N  H3   C1   O2   112.03  3.000
 T4N  H2   C1   O2   112.00  3.000
 T4N  H1   C1   O2   106.55  3.000
 T4N  C4   C3   O2   124.57  3.000
 T4N  O2   C3   C20  116.40  3.000
 T4N  C4   C3   C20  119.02  3.000
 T4N  O9   C8   N7   123.82  3.000
 T4N  N7   C8   C10  114.50  3.000
 T4N  O9   C8   C10  121.68  3.000
 T4N  H5   C10  H4   107.12  3.000
 T4N  H5   C10  C11  108.86  3.000
 T4N  H4   C10  C11  110.61  3.000
 T4N  H5   C10  C8   107.70  3.000
 T4N  H4   C10  C8   112.01  3.000
 T4N  C11  C10  C8   110.40  3.000
 T4N  H6   C11  C17  109.59  3.000
 T4N  H6   C11  S13  108.54  3.000
 T4N  C17  C11  S13  108.77  3.000
 T4N  H6   C11  C10  108.97  3.000
 T4N  S13  C11  C10  107.98  3.000
 T4N  C17  C11  C10  112.90  3.000
 T4N  H8   C14  H7   108.48  3.000
 T4N  H8   C14  S13  108.14  3.000
 T4N  H7   C14  S13  109.04  3.000
 T4N  H8   C14  C15  110.36  3.000
 T4N  H7   C14  C15  109.66  3.000
 T4N  S13  C14  C15  111.10  3.000
 T4N  H10  C15  H9   106.76  3.000
 T4N  H10  C15  N16  108.07  3.000
 T4N  H9   C15  N16  110.84  3.000
 T4N  H10  C15  C14  109.27  3.000
 T4N  H9   C15  C14  109.90  3.000
 T4N  N16  C15  C14  111.84  3.000
 T4N  H11  C19  C6   120.53  3.000
 T4N  H11  C19  C20  119.12  3.000
 T4N  C6   C19  C20  120.34  3.000
 T4N  H12  C20  C19  119.80  3.000
 T4N  H12  C20  C3   119.40  3.000
 T4N  C19  C20  C3   120.79  3.000
 T4N  C3   O2   C1   118.46  3.000
 T4N  H13  C4   C5   118.54  3.000
 T4N  H13  C4   C3   121.63  3.000
 T4N  C5   C4   C3   119.83  3.000
 T4N  H14  C5   C6   119.72  3.000
 T4N  H14  C5   C4   119.06  3.000
 T4N  C6   C5   C4   121.22  3.000
 T4N  N7   C6   C5   119.26  3.000
 T4N  C5   C6   C19  118.79  3.000
 T4N  N7   C6   C19  121.90  3.000
 T4N  H15  N7   C6   116.48  3.000
 T4N  H15  N7   C8   117.51  3.000
 T4N  C6   N7   C8   125.66  3.000
 T4N  C14  S13  C11  100.46  3.000
 T4N  H16  N16  C17  117.79  3.000
 T4N  H16  N16  C15  118.95  3.000
 T4N  C17  N16  C15  122.81  3.000
 T4N  O18  C17  N16  123.63  3.000
 T4N  N16  C17  C11  113.29  3.000
 T4N  O18  C17  C11  123.08  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
 T4N  CONST_01  C6   C19  C20  C3      0.00   0.0  0
 T4N  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 T4N  CONST_03  C4   C5   C6   C19     0.00   0.0  0
 T4N  CONST_04  C4   C3   C20  C19     0.00   0.0  0
 T4N  CONST_05  C5   C6   C19  C20     0.00   0.0  0
 T4N  CONST_06  C5   C4   C3   C20     0.00   0.0  0
 T4N  CONST_07  C15  N16  C17  C11     0.00   0.0  0
 T4N  CONST_08  O2   C3   C20  C19   180.00   0.0  0
 T4N  CONST_09  N7   C6   C19  C20   180.00   0.0  0
 T4N  CONST_10  C5   C4   C3   O2    180.00   0.0  0
 T4N  CONST_11  N7   C6   C5   C4    180.00   0.0  0
 T4N  CONST_12  O18  C17  N16  C15   180.00   0.0  0
 T4N  CONST_13  H11  C19  C20  C3    180.00   0.0  0
 T4N  CONST_14  H14  C5   C4   C3    180.00   0.0  0
 T4N  CONST_15  H13  C4   C3   C20   180.00   0.0  0
 T4N  CONST_16  H12  C20  C3   C4    180.00   0.0  0
 T4N  CONST_17  H16  N16  C17  C11   180.00   0.0  0
 T4N  CONST_21  C6   N7   C8   C10   180.00   0.0  0
 T4N  CONST_22  O9   C8   N7   C6      0.00   0.0  0
 T4N  Var_01    C15  C14  S13  C11    -1.54  30.0  1
 T4N  Var_02    C17  N16  C15  C14   -57.64  30.0  1
 T4N  Var_03    N16  C15  C14  S13    51.94  30.0  1
 T4N  Var_04    C20  C3   O2   C1    178.70  30.0  1
 T4N  Var_05    O9   C8   C10  C11   -51.60  30.0  3
 T4N  Var_06    H1   C1   O2   C3   -179.27  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 T4N  chir_01  C11  C17  C10  S13  positiv

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
 T4N  plan-1  C3   0.020
 T4N  plan-1  C19  0.020
 T4N  plan-1  C20  0.020
 T4N  plan-1  O2   0.020
 T4N  plan-1  C4   0.020
 T4N  plan-1  C5   0.020
 T4N  plan-1  C6   0.020
 T4N  plan-1  N7   0.020
 T4N  plan-1  H11  0.020
 T4N  plan-1  H12  0.020
 T4N  plan-1  H13  0.020
 T4N  plan-1  H14  0.020
 T4N  plan-2  C8   0.020
 T4N  plan-2  C10  0.020
 T4N  plan-2  C6   0.020
 T4N  plan-2  N7   0.020
 T4N  plan-2  O9   0.020
 T4N  plan-2  H15  0.020
 T4N  plan-3  C11  0.020
 T4N  plan-3  C15  0.020
 T4N  plan-3  N16  0.020
 T4N  plan-3  C17  0.020
 T4N  plan-3  O18  0.020
 T4N  plan-3  H16  0.020

