# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:49:11 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(2,4-dichlorophenoxy)-N-(2-sulfanylethyl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: SCCNC(=O)COc1ccc(Cl)cc1Cl
#
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
 NXN  NXN  2-(2,4-dichlorophenoxy)-N-(2-sulfanylethyl)acetamide  ligand  27  16  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NXN
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
 NXN  O17   O   O     0  -0.473  -1.5131   0.0141   2.1565
 NXN  C12   C   C     0   0.517  -0.2968  -0.0083   2.1274
 NXN  N1    N   NH1   0  -0.644   0.4723  -0.0277   3.2244
 NXN  C14   C   CH2   0  -0.232  -0.0908  -0.0375   4.5586
 NXN  C15   C   CH2   0  -0.598   1.0288  -0.0154   5.5843
 NXN  S19   S   S2    0  -0.242   0.2822  -0.0196   7.2459
 NXN  C9    C   CH2   0  -0.307   0.4976  -0.0145   0.8294
 NXN  O18   O   O2    0  -0.441  -0.4229  -0.0008  -0.2302
 NXN  C10   C   CR6   0   0.474   0.0460   0.0001  -1.4841
 NXN  C6    C   CR16  0  -0.391   1.3912  -0.0125  -1.8382
 NXN  C5    C   CR16  0  -0.193   1.7754  -0.0103  -3.1723
 NXN  C8    C   CR6   0  -0.164  -0.9068   0.0151  -2.5088
 NXN  CL4   CL  CL    0  -0.094  -2.5803   0.0310  -2.0913
 NXN  C11   C   CR16  0  -0.162  -0.5368   0.0172  -3.8396
 NXN  C16   C   CR6   0  -0.072   0.8121   0.0044  -4.1630
 NXN  CL3   CL  CL    0  -0.123   1.2828   0.0070  -5.8293
 NXN  H1    H   HNH1  0   0.411   1.4749  -0.0659   3.1252
 NXN  H141  H   HCH2  0   0.249  -0.7088  -0.9281   4.6999
 NXN  H142  H   HCH2  0   0.250  -0.7387   0.8317   4.6945
 NXN  H151  H   HCH2  0   0.281   1.6406   0.8789   5.4627
 NXN  H152  H   HCH2  0   0.281   1.6674  -0.8920   5.4719
 NXN  H19   H   HSH1  0   0.232   1.4252  -0.0034   7.9388
 NXN  H91   H   HCH2  0   0.272   1.1556   0.8621   0.8026
 NXN  H92   H   HCH2  0   0.271   1.1339  -0.9070   0.7985
 NXN  H6    H   HCR6  0   0.304   2.1659  -0.0237  -1.0847
 NXN  H5    H   HCR6  0   0.289   2.8271  -0.0198  -3.4228
 NXN  H11   H   HCR6  0   0.302  -1.2937   0.0285  -4.6113

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
 NXN  O17  C12   double    1.217  0.020  1.217
 NXN  C12  N1    single    1.340  0.020  1.340
 NXN  C12  C9    single    1.522  0.020  1.522
 NXN  N1   C14   single    1.448  0.020  1.448
 NXN  N1   H1    single    0.860  0.020  1.020
 NXN  C14  C15   single    1.519  0.020  1.519
 NXN  C14  H141  single    0.970  0.020  1.090
 NXN  C14  H142  single    0.970  0.020  1.090
 NXN  C15  S19   single    1.822  0.020  1.822
 NXN  C15  H151  single    0.970  0.020  1.090
 NXN  C15  H152  single    0.970  0.020  1.090
 NXN  S19  H19   single    1.200  0.020  1.300
 NXN  C9   O18   single    1.404  0.020  1.404
 NXN  C9   H91   single    0.970  0.020  1.090
 NXN  C9   H92   single    0.970  0.020  1.090
 NXN  O18  C10   single    1.339  0.020  1.339
 NXN  C10  C6    aromatic  1.391  0.020  1.391
 NXN  C10  C8    aromatic  1.399  0.020  1.399
 NXN  C6   C5    aromatic  1.388  0.020  1.388
 NXN  C6   H6    single    0.930  0.020  1.080
 NXN  C5   C16   aromatic  1.382  0.020  1.382
 NXN  C5   H5    single    0.930  0.020  1.080
 NXN  C8   CL4   single    1.725  0.020  1.725
 NXN  C8   C11   aromatic  1.381  0.020  1.381
 NXN  C11  C16   aromatic  1.387  0.020  1.387
 NXN  C11  H11   single    0.930  0.020  1.080
 NXN  C16  CL3   single    1.732  0.020  1.732

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
 NXN  C9    C12  N1    113.49  3.000
 NXN  C9    C12  O17   122.84  3.000
 NXN  N1    C12  O17   123.67  3.000
 NXN  H1    N1   C14   118.50  3.000
 NXN  H1    N1   C12   119.39  3.000
 NXN  C14   N1   C12   122.09  3.000
 NXN  H142  C14  H141  107.26  3.000
 NXN  H142  C14  C15   109.98  3.000
 NXN  H141  C14  C15   109.96  3.000
 NXN  H142  C14  N1    109.86  3.000
 NXN  H141  C14  N1    110.14  3.000
 NXN  C15   C14  N1    109.60  3.000
 NXN  H152  C15  H151  108.62  3.000
 NXN  H152  C15  S19   109.41  3.000
 NXN  H151  C15  S19   109.49  3.000
 NXN  H152  C15  C14   110.51  3.000
 NXN  H151  C15  C14   110.50  3.000
 NXN  S19   C15  C14   108.29  3.000
 NXN  H19   S19  C15    97.02  3.000
 NXN  H92   C9   H91   107.57  3.000
 NXN  H92   C9   O18   111.54  3.000
 NXN  H91   C9   O18   111.55  3.000
 NXN  H92   C9   C12   109.29  3.000
 NXN  H91   C9   C12   109.33  3.000
 NXN  O18   C9   C12   107.55  3.000
 NXN  C10   O18  C9    118.51  3.000
 NXN  C8    C10  C6    118.17  3.000
 NXN  C8    C10  O18   116.57  3.000
 NXN  C6    C10  O18   125.25  3.000
 NXN  H6    C6   C5    118.14  3.000
 NXN  H6    C6   C10   121.05  3.000
 NXN  C5    C6   C10   120.81  3.000
 NXN  H5    C5   C16   120.80  3.000
 NXN  H5    C5   C6    119.46  3.000
 NXN  C16   C5   C6    119.74  3.000
 NXN  C11   C8   CL4   119.54  3.000
 NXN  C11   C8   C10   121.55  3.000
 NXN  CL4   C8   C10   118.91  3.000
 NXN  H11   C11  C16   120.97  3.000
 NXN  H11   C11  C8    120.02  3.000
 NXN  C16   C11  C8    119.01  3.000
 NXN  CL3   C16  C11   119.25  3.000
 NXN  CL3   C16  C5    120.03  3.000
 NXN  C11   C16  C5    120.72  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
 NXN  CONST_01  C16  C5   C6   C10     0.00   0.0  0
 NXN  CONST_02  C16  C11  C8   C10     0.00   0.0  0
 NXN  CONST_03  C11  C8   C10  C6      0.00   0.0  0
 NXN  CONST_04  C11  C16  C5   C6      0.00   0.0  0
 NXN  CONST_05  C8   C10  C6   C5      0.00   0.0  0
 NXN  CONST_06  C8   C11  C16  C5      0.00   0.0  0
 NXN  CONST_07  C5   C6   C10  O18   180.00   0.0  0
 NXN  CONST_08  C11  C8   C10  O18   180.00   0.0  0
 NXN  CONST_09  CL4  C8   C10  C6    180.00   0.0  0
 NXN  CONST_10  CL3  C16  C5   C6    180.00   0.0  0
 NXN  CONST_11  CL3  C16  C11  C8    180.00   0.0  0
 NXN  CONST_12  C16  C11  C8   CL4   180.00   0.0  0
 NXN  CONST_13  H5   C5   C6   C10   180.00   0.0  0
 NXN  CONST_14  H11  C11  C8   C10   180.00   0.0  0
 NXN  CONST_15  H6   C6   C10  C8    180.00   0.0  0
 NXN  CONST_16  C14  N1   C12  O17     0.00   0.0  0
 NXN  CONST_17  C9   C12  N1   C14   180.00   0.0  0
 NXN  CONST_18  H1   N1   C12  O17   180.00   0.0  0
 NXN  Var_01    C6   C10  O18  C9      0.05  30.0  2
 NXN  Var_02    H91  C9   O18  C10    59.97  30.0  2
 NXN  Var_03    O18  C9   C12  O17    -0.44  30.0  3
 NXN  Var_04    C15  C14  N1   C12  -178.24  30.0  3
 NXN  Var_05    S19  C15  C14  N1    179.70  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
 NXN  plan-1  O18  0.020
 NXN  plan-1  C10  0.020
 NXN  plan-1  C6   0.020
 NXN  plan-1  C5   0.020
 NXN  plan-1  C8   0.020
 NXN  plan-1  CL4  0.020
 NXN  plan-1  C11  0.020
 NXN  plan-1  C16  0.020
 NXN  plan-1  CL3  0.020
 NXN  plan-1  H6   0.020
 NXN  plan-1  H5   0.020
 NXN  plan-1  H11  0.020
 NXN  plan-2  O17  0.020
 NXN  plan-2  C12  0.020
 NXN  plan-2  N1   0.020
 NXN  plan-2  C14  0.020
 NXN  plan-2  C9   0.020
 NXN  plan-2  H1   0.020

