# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 00:01:41 2020
#   Inital geometry file: a 52 line input string
#   Ligand name: 1-(methylsulfanyl)-4-nitrobenzene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccc(cc1)[N+]([O-])=O
#
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
 259  259  1-(methylsulfanyl)-4-nitrobenzene  ligand  18  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_259
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
 259  CAA   C  CH3    0  -0.802   3.6926   1.1666  -0.0208
 259  SAH   S  S2     0   0.087   3.0094  -0.4994  -0.0314
 259  CAI   C  CR6    0  -0.098   1.2825  -0.2425  -0.0178
 259  CAD   C  CR16   0  -0.258   0.4760  -1.3874  -0.0290
 259  CAF   C  CR16   0  -0.253  -0.8974  -1.2796  -0.0217
 259  CAJ   C  CR6    0   0.233  -1.4799  -0.0162  -0.0016
 259  NAK   N  N      1   0.327  -2.9209   0.1038   0.0055
 259  OAC   O  O     -1  -0.386  -3.5789  -0.9119  -0.0098
 259  OAB   O  O      0  -0.387  -3.4025   1.2143   0.0263
 259  CAG   C  CR16   0  -0.247  -0.6991   1.1302   0.0115
 259  CAE   C  CR16   0  -0.252   0.6787   1.0158   0.0035
 259  HAA1  H  HCH3   0   0.283   3.3974   1.7254  -0.9064
 259  HAA2  H  HCH3   0   0.283   3.4107   1.7089   0.8794
 259  HAA3  H  HCH3   0   0.303   4.7734   1.0429  -0.0303
 259  HAD   H  HCR6   0   0.283   0.9264  -2.3717  -0.0452
 259  HAF   H  HCR6   0   0.300  -1.5016  -2.1751  -0.0316
 259  HAG   H  HCR6   0   0.300  -1.1469   2.1133   0.0274
 259  HAE   H  HCR6   0   0.284   1.2714   1.9192   0.0129

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
 259  CAA  SAH   single    1.801  0.020  1.801
 259  SAH  CAI   single    1.746  0.020  1.746
 259  CAI  CAD   aromatic  1.400  0.020  1.400
 259  CAI  CAE   aromatic  1.396  0.020  1.396
 259  CAD  CAF   aromatic  1.378  0.020  1.378
 259  CAF  CAJ   aromatic  1.391  0.020  1.391
 259  CAJ  NAK   single    1.446  0.020  1.446
 259  CAJ  CAG   aromatic  1.387  0.020  1.387
 259  NAK  OAC   single    1.210  0.020  1.210
 259  NAK  OAB   double    1.211  0.020  1.211
 259  CAG  CAE   aromatic  1.383  0.020  1.383
 259  CAA  HAA1  single    0.970  0.020  1.090
 259  CAA  HAA2  single    0.970  0.020  1.090
 259  CAA  HAA3  single    0.970  0.020  1.090
 259  CAD  HAD   single    0.930  0.020  1.080
 259  CAF  HAF   single    0.930  0.020  1.080
 259  CAG  HAG   single    0.930  0.020  1.080
 259  CAE  HAE   single    0.930  0.020  1.080

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
 259  HAA3  CAA  HAA2  108.74  3.000
 259  HAA3  CAA  HAA1  108.71  3.000
 259  HAA2  CAA  HAA1  110.31  3.000
 259  HAA3  CAA  SAH   105.76  3.000
 259  HAA2  CAA  SAH   111.58  3.000
 259  HAA1  CAA  SAH   111.56  3.000
 259  CAI   SAH  CAA   103.83  3.000
 259  CAE   CAI  CAD   119.21  3.000
 259  CAE   CAI  SAH   124.10  3.000
 259  CAD   CAI  SAH   116.69  3.000
 259  HAD   CAD  CAF   119.07  3.000
 259  HAD   CAD  CAI   120.26  3.000
 259  CAF   CAD  CAI   120.67  3.000
 259  HAF   CAF  CAJ   121.25  3.000
 259  HAF   CAF  CAD   119.51  3.000
 259  CAJ   CAF  CAD   119.24  3.000
 259  CAG   CAJ  NAK   119.49  3.000
 259  CAG   CAJ  CAF   121.00  3.000
 259  NAK   CAJ  CAF   119.51  3.000
 259  OAB   NAK  OAC   123.63  3.000
 259  OAB   NAK  CAJ   118.21  3.000
 259  OAC   NAK  CAJ   118.17  3.000
 259  HAG   CAG  CAE   119.23  3.000
 259  HAG   CAG  CAJ   121.26  3.000
 259  CAE   CAG  CAJ   119.50  3.000
 259  HAE   CAE  CAG   118.52  3.000
 259  HAE   CAE  CAI   121.10  3.000
 259  CAG   CAE  CAI   120.38  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
 259  CONST_01  CAJ   CAF  CAD  CAI    0.00   0.0  0
 259  CONST_02  CAJ   CAG  CAE  CAI    0.00   0.0  0
 259  CONST_03  CAG   CAE  CAI  CAD    0.00   0.0  0
 259  CONST_04  CAG   CAJ  CAF  CAD    0.00   0.0  0
 259  CONST_05  CAE   CAI  CAD  CAF    0.00   0.0  0
 259  CONST_06  CAE   CAG  CAJ  CAF    0.00   0.0  0
 259  CONST_07  CAF   CAD  CAI  SAH  180.00   0.0  0
 259  CONST_08  CAG   CAE  CAI  SAH  180.00   0.0  0
 259  CONST_09  NAK   CAJ  CAF  CAD  180.00   0.0  0
 259  CONST_10  CAE   CAG  CAJ  NAK  180.00   0.0  0
 259  CONST_11  HAF   CAF  CAD  CAI  180.00   0.0  0
 259  CONST_12  HAG   CAG  CAE  CAI  180.00   0.0  0
 259  CONST_13  HAE   CAE  CAI  CAD  180.00   0.0  0
 259  CONST_14  HAD   CAD  CAF  CAJ  180.00   0.0  0
 259  CONST_15  OAC   NAK  CAJ  CAF    0.00   0.0  0
 259  CONST_16  OAB   NAK  CAJ  CAF  180.00   0.0  0
 259  CONST_17  CAG   CAJ  NAK  OAC  180.00   0.0  0
 259  CONST_18  CAG   CAJ  NAK  OAB    0.00   0.0  0
 259  Var_01    CAD   CAI  SAH  CAA  179.72  30.0  2
 259  Var_02    HAA1  CAA  SAH  CAI  -61.89  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
 259  plan-1  SAH  0.020
 259  plan-1  CAI  0.020
 259  plan-1  CAD  0.020
 259  plan-1  CAF  0.020
 259  plan-1  CAJ  0.020
 259  plan-1  NAK  0.020
 259  plan-1  CAG  0.020
 259  plan-1  CAE  0.020
 259  plan-1  HAD  0.020
 259  plan-1  HAF  0.020
 259  plan-1  HAG  0.020
 259  plan-1  HAE  0.020
 259  plan-2  CAJ  0.020
 259  plan-2  NAK  0.020
 259  plan-2  OAC  0.020
 259  plan-2  OAB  0.020

