# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 13:04:38 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: (4-chlorophenyl)(thiomorpholin-4-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc(cc1)C(=O)N2CCSCC2
#
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
 I8D  I8D  "(4-chlorophenyl)(thiomorpholin-4-yl)methanone"
  ligand  27  15  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_I8D
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
 I8D  N1   N   NT    0  -0.452  12.8487  20.8733  24.2644
 I8D  C4   C   CR6   0  -0.061  13.8917  22.3563  22.6208
 I8D  C5   C   CR16  0  -0.264  13.8795  23.6024  23.2386
 I8D  C6   C   CR16  0  -0.197  14.7285  24.6120  22.8122
 I8D  C7   C   C     0   0.521  12.9109  21.2849  22.9822
 I8D  C8   C   CH2   0  -0.332  13.8502  21.1469  25.2780
 I8D  C10  C   CH2   0  -0.625  11.6754  19.7518  26.1174
 I8D  C1   C   CR6   0  -0.041  15.5993  24.3617  21.7637
 I8D  C2   C   CR16  0  -0.201  15.6249  23.1282  21.1301
 I8D  C3   C   CR16  0  -0.274  14.7565  22.1351  21.5535
 I8D  O1   O   O     0  -0.478  12.1850  20.8217  22.1131
 I8D  C9   C   CH2   0  -0.539  13.2943  21.9400  26.4562
 I8D  S1   S   S2    0  -0.018  11.6214  21.3732  26.9203
 I8D  C11  C   CH2   0  -0.242  11.8234  19.8926  24.6105
 I8D  H3   H   HCR6  0   0.278  13.1911  23.8055  24.0491
 I8D  H4   H   HCR6  0   0.283  14.7062  25.5808  23.2922
 I8D  H6   H   HCH2  0   0.276  14.2607  20.1975  25.6297
 I8D  H5   H   HCH2  0   0.295  14.6881  21.6881  24.8448
 I8D  H9   H   HCH2  0   0.281  12.4644  19.1418  26.5577
 I8D  H10  H   HCH2  0   0.303  10.7308  19.2552  26.3376
 I8D  H1   H   HCR6  0   0.283  16.3071  22.9436  20.3116
 I8D  H2   H   HCR6  0   0.272  14.7670  21.1773  21.0494
 I8D  H7   H   HCH2  0   0.274  13.9736  21.8452  27.3033
 I8D  H8   H   HCH2  0   0.273  13.2117  22.9985  26.2107
 I8D  H12  H   HCH2  0   0.250  12.0618  18.9160  24.1758
 I8D  H11  H   HCH2  0   0.253  10.8732  20.2164  24.1873
 I8D  CL1  CL  CL    0  -0.120  16.6710  25.6130  21.2330

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
 I8D  CL1  C1   single    1.731  0.020  1.731
 I8D  C1   C2   aromatic  1.387  0.020  1.387
 I8D  C2   C3   aromatic  1.385  0.020  1.385
 I8D  C3   C4   aromatic  1.391  0.020  1.391
 I8D  C4   C5   aromatic  1.391  0.020  1.391
 I8D  C5   C6   aromatic  1.386  0.020  1.386
 I8D  C4   C7   single    1.497  0.020  1.497
 I8D  C7   O1   double    1.223  0.020  1.223
 I8D  C7   N1   single    1.348  0.020  1.348
 I8D  N1   C8   single    1.451  0.020  1.451
 I8D  C8   C9   single    1.525  0.020  1.525
 I8D  C9   S1   single    1.826  0.020  1.826
 I8D  S1   C10  single    1.810  0.020  1.810
 I8D  C10  C11  single    1.521  0.020  1.521
 I8D  C1   C6   aromatic  1.386  0.020  1.386
 I8D  N1   C11  single    1.460  0.020  1.460
 I8D  C5   H3   single    0.930  0.020  1.080
 I8D  C6   H4   single    0.930  0.020  1.080
 I8D  C8   H6   single    0.970  0.020  1.090
 I8D  C8   H5   single    0.970  0.020  1.090
 I8D  C10  H9   single    0.970  0.020  1.090
 I8D  C10  H10  single    0.970  0.020  1.090
 I8D  C2   H1   single    0.930  0.020  1.080
 I8D  C3   H2   single    0.930  0.020  1.080
 I8D  C9   H7   single    0.970  0.020  1.090
 I8D  C9   H8   single    0.970  0.020  1.090
 I8D  C11  H12  single    0.970  0.020  1.090
 I8D  C11  H11  single    0.970  0.020  1.090

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
 I8D  C11  N1   C8   116.47  3.000
 I8D  C11  N1   C7   117.57  3.000
 I8D  C8   N1   C7   125.10  3.000
 I8D  C3   C4   C7   118.60  3.000
 I8D  C7   C4   C5   121.89  3.000
 I8D  C3   C4   C5   119.25  3.000
 I8D  H3   C5   C6   118.89  3.000
 I8D  H3   C5   C4   120.41  3.000
 I8D  C6   C5   C4   120.69  3.000
 I8D  H4   C6   C1   120.71  3.000
 I8D  H4   C6   C5   120.21  3.000
 I8D  C1   C6   C5   119.08  3.000
 I8D  O1   C7   C4   119.22  3.000
 I8D  O1   C7   N1   122.19  3.000
 I8D  C4   C7   N1   118.58  3.000
 I8D  H5   C8   H6   105.74  3.000
 I8D  H5   C8   C9   109.25  3.000
 I8D  H6   C8   C9   109.88  3.000
 I8D  H5   C8   N1   110.33  3.000
 I8D  H6   C8   N1   108.69  3.000
 I8D  C9   C8   N1   112.71  3.000
 I8D  H10  C10  H9   106.90  3.000
 I8D  H10  C10  C11  109.08  3.000
 I8D  H9   C10  C11  112.43  3.000
 I8D  H10  C10  S1   107.02  3.000
 I8D  H9   C10  S1   110.10  3.000
 I8D  C11  C10  S1   111.07  3.000
 I8D  C2   C1   CL1  119.44  3.000
 I8D  C2   C1   C6   121.19  3.000
 I8D  CL1  C1   C6   119.37  3.000
 I8D  H1   C2   C3   120.28  3.000
 I8D  H1   C2   C1   120.61  3.000
 I8D  C3   C2   C1   119.10  3.000
 I8D  H2   C3   C2   119.07  3.000
 I8D  H2   C3   C4   120.26  3.000
 I8D  C2   C3   C4   120.66  3.000
 I8D  H8   C9   H7   107.87  3.000
 I8D  H8   C9   S1   106.81  3.000
 I8D  H7   C9   S1   110.27  3.000
 I8D  H8   C9   C8   111.02  3.000
 I8D  H7   C9   C8   109.15  3.000
 I8D  S1   C9   C8   111.64  3.000
 I8D  C9   S1   C10   97.93  3.000
 I8D  H11  C11  H12  107.50  3.000
 I8D  H11  C11  C10  109.12  3.000
 I8D  H12  C11  C10  109.39  3.000
 I8D  H11  C11  N1   108.70  3.000
 I8D  H12  C11  N1   110.60  3.000
 I8D  C10  C11  N1   111.43  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
 I8D  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 I8D  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 I8D  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 I8D  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 I8D  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 I8D  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 I8D  CONST_07  CL1  C1   C6   C5    180.00   0.0  0
 I8D  CONST_08  C7   C4   C5   C6    180.00   0.0  0
 I8D  CONST_09  C2   C3   C4   C7    180.00   0.0  0
 I8D  CONST_10  C3   C2   C1   CL1   180.00   0.0  0
 I8D  CONST_12  C11  N1   C7   C4    180.00   0.0  0
 I8D  CONST_13  H1   C2   C3   C4    180.00   0.0  0
 I8D  CONST_14  H4   C6   C5   C4    180.00   0.0  0
 I8D  CONST_15  H2   C3   C4   C5    180.00   0.0  0
 I8D  CONST_16  H1   C2   C1   C6    180.00   0.0  0
 I8D  CONST_17  H2   C3   C2   C1    180.00   0.0  0
 I8D  CONST_18  H3   C5   C6   C1    180.00   0.0  0
 I8D  CONST_19  H4   C6   C1   C2    180.00   0.0  0
 I8D  CONST_20  H3   C5   C4   C3    180.00   0.0  0
 I8D  CONST_21  O1   C7   N1   C8    180.00   0.0  0
 I8D  CONST_22  C11  N1   C7   O1      0.00   0.0  0
 I8D  Var_01    S1   C9   C8   N1     40.12  30.0  1
 I8D  Var_02    S1   C10  C11  N1     45.68  30.0  1
 I8D  Var_03    C10  C11  N1   C8     22.41  30.0  1
 I8D  Var_04    C10  S1   C9   C8     19.05  30.0  1
 I8D  Var_05    C11  N1   C8   C9    -71.51  30.0  1
 I8D  Var_06    C11  C10  S1   C9    -63.02  30.0  1
 I8D  Var_07    C3   C4   C7   N1    128.57  30.0  2
 I8D  Var_08    C5   C4   C7   N1    -57.36  30.0  2
 I8D  Var_09    C9   C8   N1   C7    119.43  30.0  1
 I8D  Var_10    C10  C11  N1   C7   -167.68  30.0  1
 I8D  Var_11    H7   C9   C8   N1    162.28  30.0  1
 I8D  Var_12    H8   C9   C8   N1    -78.95  30.0  1
 I8D  Var_13    H9   C10  C11  N1    -78.19  30.0  1
 I8D  Var_14    H10  C10  C11  N1    163.41  30.0  1
 I8D  Var_15    H12  C11  N1   C8    -99.50  30.0  1
 I8D  Var_16    H11  C11  N1   C8    142.70  30.0  1
 I8D  Var_17    H7   C9   S1   C10  -102.46  30.0  1
 I8D  Var_18    H8   C9   S1   C10   140.59  30.0  1
 I8D  Var_19    H9   C10  S1   C9     62.18  30.0  1
 I8D  Var_20    H10  C10  S1   C9    178.02  30.0  1
 I8D  Var_21    H6   C8   C9   S1    -81.27  30.0  1
 I8D  Var_22    H5   C8   C9   S1    163.15  30.0  1
 I8D  Var_23    H12  C11  C10  S1    168.29  30.0  1
 I8D  Var_24    H11  C11  C10  S1    -74.36  30.0  1
 I8D  Var_25    H6   C8   N1   C11    50.55  30.0  1
 I8D  Var_26    H5   C8   N1   C11   166.06  30.0  1
 I8D  Var_27    O1   C7   C4   C5    121.90  30.0  2
 I8D  Var_28    O1   C7   C4   C3    -52.16  30.0  2
 I8D  Var_29    H6   C8   N1   C7   -118.51  30.0  1
 I8D  Var_30    H5   C8   N1   C7     -3.00  30.0  1
 I8D  Var_31    H12  C11  N1   C7     70.41  30.0  1
 I8D  Var_32    H11  C11  N1   C7    -47.39  30.0  1

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
 I8D  plan-1  C4   0.020
 I8D  plan-1  C5   0.020
 I8D  plan-1  C6   0.020
 I8D  plan-1  C7   0.020
 I8D  plan-1  C1   0.020
 I8D  plan-1  C2   0.020
 I8D  plan-1  C3   0.020
 I8D  plan-1  H3   0.020
 I8D  plan-1  H4   0.020
 I8D  plan-1  H1   0.020
 I8D  plan-1  H2   0.020
 I8D  plan-1  CL1  0.020
 I8D  plan-2  N1   0.020
 I8D  plan-2  C4   0.020
 I8D  plan-2  C7   0.020
 I8D  plan-2  C8   0.020
 I8D  plan-2  O1   0.020
 I8D  plan-2  C11  0.020

