# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 03:16:13 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: N-benzylthioformamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: S=CNCc1ccccc1
#
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
 9BE  9BE  'N-benzylthioformamide    '  ligand  19  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9BE
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
 9BE  S01  S  S1    0  -0.369  -3.7098   0.0416   0.3355
 9BE  C02  C  C1    0  -0.104  -2.6026   0.0140  -0.8933
 9BE  N03  N  NH1   0  -0.492  -1.2950  -0.0080  -0.7550
 9BE  C04  C  CH2   0  -0.326  -0.6098  -0.0114   0.5269
 9BE  C05  C  CR6   0   0.054   0.8773  -0.0135   0.3151
 9BE  C06  C  CR16  0  -0.282   1.5709  -1.2146   0.1956
 9BE  C07  C  CR16  0  -0.241   2.9391  -1.2177  -0.0395
 9BE  C08  C  CR16  0  -0.261   3.6268  -0.0167  -0.1570
 9BE  C09  C  CR16  0  -0.241   2.9424   1.1858  -0.0372
 9BE  C10  C  CR16  0  -0.282   1.5741   1.1859   0.1977
 9BE  H2   H  H     0   0.293  -2.9170   0.0125  -1.9346
 9BE  H3   H  HCH2  0   0.268  -0.9250   0.8654   1.0971
 9BE  H4   H  HCH2  0   0.268  -0.9278  -0.8883   1.0958
 9BE  H5   H  HCR6  0   0.257   1.0385  -2.1535   0.2925
 9BE  H6   H  HCR6  0   0.259   3.4685  -2.1573  -0.1302
 9BE  H7   H  HCR6  0   0.260   4.6940  -0.0182  -0.3368
 9BE  H8   H  HCR6  0   0.259   3.4740   2.1244  -0.1259
 9BE  H9   H  HCR6  0   0.256   1.0440   2.1260   0.2960
 9BE  H1   H  HNH1  0   0.423  -0.7302  -0.0258  -1.5915

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
 9BE  S01  C02  double    1.654  0.020  1.654
 9BE  C07  C06  aromatic  1.388  0.020  1.388
 9BE  C07  C08  aromatic  1.389  0.020  1.389
 9BE  C02  N03  single    1.315  0.020  1.315
 9BE  C06  C05  aromatic  1.392  0.020  1.392
 9BE  C08  C09  aromatic  1.389  0.020  1.389
 9BE  C05  C04  single    1.502  0.020  1.502
 9BE  C05  C10  aromatic  1.392  0.020  1.392
 9BE  N03  C04  single    1.453  0.020  1.453
 9BE  C09  C10  aromatic  1.388  0.020  1.388
 9BE  C02  H2   single    0.930  0.020  1.080
 9BE  C04  H3   single    0.970  0.020  1.090
 9BE  C04  H4   single    0.970  0.020  1.090
 9BE  C06  H5   single    0.930  0.020  1.080
 9BE  C07  H6   single    0.930  0.020  1.080
 9BE  C08  H7   single    0.930  0.020  1.080
 9BE  C09  H8   single    0.930  0.020  1.080
 9BE  C10  H9   single    0.930  0.020  1.080
 9BE  N03  H1   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
 9BE  H2   C02  N03  112.84  3.000
 9BE  H2   C02  S01  121.17  3.000
 9BE  N03  C02  S01  125.99  3.000
 9BE  H1   N03  C04  117.84  3.000
 9BE  H1   N03  C02  118.00  3.000
 9BE  C04  N03  C02  124.17  3.000
 9BE  H4   C04  H3   106.76  3.000
 9BE  H4   C04  C05  111.13  3.000
 9BE  H3   C04  C05  111.12  3.000
 9BE  H4   C04  N03  108.90  3.000
 9BE  H3   C04  N03  108.81  3.000
 9BE  C05  C04  N03  110.02  3.000
 9BE  C10  C05  C06  119.13  3.000
 9BE  C10  C05  C04  120.41  3.000
 9BE  C06  C05  C04  120.43  3.000
 9BE  H5   C06  C07  119.83  3.000
 9BE  H5   C06  C05  119.67  3.000
 9BE  C07  C06  C05  120.49  3.000
 9BE  H6   C07  C08  120.10  3.000
 9BE  H6   C07  C06  119.88  3.000
 9BE  C08  C07  C06  120.03  3.000
 9BE  H7   C08  C09  120.10  3.000
 9BE  H7   C08  C07  120.08  3.000
 9BE  C09  C08  C07  119.83  3.000
 9BE  H8   C09  C10  119.86  3.000
 9BE  H8   C09  C08  120.12  3.000
 9BE  C10  C09  C08  120.02  3.000
 9BE  H9   C10  C09  119.83  3.000
 9BE  H9   C10  C05  119.67  3.000
 9BE  C09  C10  C05  120.50  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
 9BE  CONST_01  C08  C07  C06  C05     0.00   0.0  0
 9BE  CONST_02  C08  C09  C10  C05     0.00   0.0  0
 9BE  CONST_03  C09  C08  C07  C06     0.00   0.0  0
 9BE  CONST_04  C09  C10  C05  C06     0.00   0.0  0
 9BE  CONST_05  C10  C05  C06  C07     0.00   0.0  0
 9BE  CONST_06  C10  C09  C08  C07     0.00   0.0  0
 9BE  CONST_07  C07  C06  C05  C04   180.00   0.0  0
 9BE  CONST_08  C09  C10  C05  C04   180.00   0.0  0
 9BE  CONST_09  H6   C07  C06  C05   180.00   0.0  0
 9BE  CONST_10  H8   C09  C10  C05   180.00   0.0  0
 9BE  CONST_11  H7   C08  C07  C06   180.00   0.0  0
 9BE  CONST_12  H9   C10  C05  C06   180.00   0.0  0
 9BE  CONST_13  H5   C06  C07  C08   180.00   0.0  0
 9BE  Var_01    C06  C05  C04  N03   -89.13  30.0  2
 9BE  Var_02    C05  C04  N03  C02  -178.97  30.0  3
 9BE  Var_03    C04  N03  C02  S01     0.00  30.0  2

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
 9BE  plan-1  C04  0.020
 9BE  plan-1  C05  0.020
 9BE  plan-1  C06  0.020
 9BE  plan-1  C07  0.020
 9BE  plan-1  C08  0.020
 9BE  plan-1  C09  0.020
 9BE  plan-1  C10  0.020
 9BE  plan-1  H5   0.020
 9BE  plan-1  H6   0.020
 9BE  plan-1  H7   0.020
 9BE  plan-1  H8   0.020
 9BE  plan-1  H9   0.020
 9BE  plan-2  S01  0.020
 9BE  plan-2  C02  0.020
 9BE  plan-2  N03  0.020
 9BE  plan-2  H2   0.020

