# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 20:28:05 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: 2-[(methylsulfonyl)methyl]-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)Cc1[nH]c2ccccc2n1
#
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
 T6J  T6J  2-[(methylsulfonyl)methyl]-1H-benzimidazole  ligand  24  14  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T6J
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
 T6J  N1  N  NR15  0  -0.679  -0.5634   1.0188  -0.4817
 T6J  C4  C  CR16  0  -0.330  -3.0511  -1.4445  -0.1019
 T6J  C5  C  CR16  0  -0.270  -4.1544  -0.7326   0.3290
 T6J  C6  C  CR16  0  -0.276  -4.1015   0.6586   0.5170
 T6J  C7  C  CR16  0  -0.305  -2.9454   1.3792   0.2795
 T6J  C8  C  CR56  0   0.342  -1.8397   0.6550  -0.1535
 T6J  N   N  N     0  -0.450  -0.6457  -1.1815  -0.7730
 T6J  C   C  CH3   0  -0.791   4.2076   0.0671  -0.4290
 T6J  O   O  OS    0  -0.677   2.2930   1.4723   0.7329
 T6J  C2  C  CR5   0   0.451   0.0959  -0.1119  -0.8421
 T6J  C3  C  CR56  0   0.135  -1.8733  -0.7367  -0.3456
 T6J  O1  O  OS    0  -0.671   2.3363  -1.0072   1.0982
 T6J  S   S  S     0   1.193   2.5531   0.1312   0.2116
 T6J  H9  H  HNR5  0   0.423  -0.1795   1.9511  -0.4615
 T6J  H5  H  HCR6  0   0.257  -3.0946  -2.5164  -0.2457
 T6J  H6  H  HCR6  0   0.255  -5.0815  -1.2539   0.5286
 T6J  H7  H  HCR6  0   0.258  -4.9880   1.1778   0.8564
 T6J  H8  H  HCR6  0   0.269  -2.9061   2.4507   0.4237
 T6J  H1  H  HCH3  0   0.318   4.8811   0.2288   0.4117
 T6J  H   H  HCH3  0   0.300   4.3878  -0.9115  -0.8673
 T6J  H2  H  HCH3  0   0.300   4.3426   0.8516  -1.1700
 T6J  H4  H  HCH2  0   0.339   1.7898  -1.0502  -1.7067
 T6J  H3  H  HCH2  0   0.339   1.7450   0.7153  -1.9458
 T6J  C1  C  CH2   0  -0.730   1.5198  -0.0976  -1.2538

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
 T6J  C   S   single    1.775  0.020  1.775
 T6J  O   S   double    1.462  0.020  1.462
 T6J  S   O1  double    1.459  0.020  1.459
 T6J  C1  S   single    1.808  0.020  1.808
 T6J  C2  C1  single    1.482  0.020  1.482
 T6J  C2  N   aromatic  1.303  0.020  1.303
 T6J  N   C3  aromatic  1.374  0.020  1.374
 T6J  C3  C4  aromatic  1.396  0.020  1.396
 T6J  C4  C5  aromatic  1.382  0.020  1.382
 T6J  C5  C6  aromatic  1.405  0.020  1.405
 T6J  C6  C7  aromatic  1.383  0.020  1.383
 T6J  C7  C8  aromatic  1.391  0.020  1.391
 T6J  C3  C8  aromatic  1.405  0.020  1.405
 T6J  C8  N1  aromatic  1.367  0.020  1.367
 T6J  N1  C2  aromatic  1.358  0.020  1.358
 T6J  N1  H9  single    0.860  0.020  1.020
 T6J  C4  H5  single    0.930  0.020  1.080
 T6J  C5  H6  single    0.930  0.020  1.080
 T6J  C6  H7  single    0.930  0.020  1.080
 T6J  C7  H8  single    0.930  0.020  1.080
 T6J  C   H1  single    0.970  0.020  1.090
 T6J  C   H   single    0.970  0.020  1.090
 T6J  C   H2  single    0.970  0.020  1.090
 T6J  C1  H4  single    0.970  0.020  1.090
 T6J  C1  H3  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
 T6J  H9  N1  C2  126.19  3.000
 T6J  H9  N1  C8  126.62  3.000
 T6J  C2  N1  C8  107.19  3.000
 T6J  H5  C4  C3  120.86  3.000
 T6J  H5  C4  C5  121.30  3.000
 T6J  C3  C4  C5  117.83  3.000
 T6J  H6  C5  C6  118.99  3.000
 T6J  H6  C5  C4  119.55  3.000
 T6J  C6  C5  C4  121.46  3.000
 T6J  H7  C6  C7  119.26  3.000
 T6J  H7  C6  C5  119.10  3.000
 T6J  C7  C6  C5  121.64  3.000
 T6J  H8  C7  C8  121.89  3.000
 T6J  H8  C7  C6  121.57  3.000
 T6J  C8  C7  C6  116.54  3.000
 T6J  C3  C8  C7  122.63  3.000
 T6J  C3  C8  N1  104.66  3.000
 T6J  C7  C8  N1  132.72  3.000
 T6J  C3  N   C2  105.02  3.000
 T6J  H2  C   H   110.73  3.000
 T6J  H2  C   H1  110.00  3.000
 T6J  H   C   H1  110.01  3.000
 T6J  H2  C   S   109.60  3.000
 T6J  H   C   S   109.42  3.000
 T6J  H1  C   S   107.00  3.000
 T6J  C1  C2  N   124.69  3.000
 T6J  N   C2  N1  113.15  3.000
 T6J  C1  C2  N1  122.15  3.000
 T6J  N   C3  C8  109.99  3.000
 T6J  C8  C3  C4  119.91  3.000
 T6J  N   C3  C4  130.10  3.000
 T6J  O1  S   C1  107.99  3.000
 T6J  C1  S   O   107.67  3.000
 T6J  O1  S   O   118.19  3.000
 T6J  C1  S   C   103.63  3.000
 T6J  O1  S   C   109.24  3.000
 T6J  O   S   C   109.12  3.000
 T6J  H3  C1  H4  109.69  3.000
 T6J  H3  C1  S   107.57  3.000
 T6J  H4  C1  S   107.83  3.000
 T6J  H3  C1  C2  112.43  3.000
 T6J  H4  C1  C2  110.20  3.000
 T6J  S   C1  C2  108.98  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
 T6J  CONST_01  C6  C7  C8  N1  180.00   0.0  0
 T6J  CONST_02  N   C3  C8  N1    0.00   0.0  0
 T6J  CONST_03  C4  C3  C8  N1  180.00   0.0  0
 T6J  CONST_04  C3  N   C2  N1    0.00   0.0  0
 T6J  CONST_05  C2  N   C3  C4  180.00   0.0  0
 T6J  CONST_06  C7  C8  C3  C4    0.00   0.0  0
 T6J  CONST_07  C7  C6  C5  C4    0.00   0.0  0
 T6J  CONST_08  N   C3  C4  C5  180.00   0.0  0
 T6J  CONST_09  C8  C3  C4  C5    0.00   0.0  0
 T6J  CONST_10  C8  C7  C6  C5    0.00   0.0  0
 T6J  CONST_11  C3  C4  C5  C6    0.00   0.0  0
 T6J  CONST_12  C3  C8  C7  C6    0.00   0.0  0
 T6J  CONST_13  N   C3  C8  C7  180.00   0.0  0
 T6J  CONST_14  C2  N1  C8  C7  180.00   0.0  0
 T6J  CONST_15  C2  N   C3  C8    0.00   0.0  0
 T6J  CONST_16  N   C2  N1  C8    0.00   0.0  0
 T6J  CONST_17  C3  C8  N1  C2    0.00   0.0  0
 T6J  CONST_18  C1  C2  N1  C8  180.00   0.0  0
 T6J  CONST_19  C3  N   C2  C1  180.00   0.0  0
 T6J  CONST_20  H8  C7  C8  N1    0.00   0.0  0
 T6J  CONST_21  H7  C6  C5  C4  180.00   0.0  0
 T6J  CONST_22  H5  C4  C5  C6  180.00   0.0  0
 T6J  CONST_23  H6  C5  C6  C7  180.00   0.0  0
 T6J  CONST_24  H9  N1  C8  C7    0.00   0.0  0
 T6J  Var_01    S   C1  C2  N1   74.34  30.0  2
 T6J  Var_02    C2  C1  S   C   178.00  30.0  1
 T6J  Var_03    H1  C   S   O    63.93  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
 T6J  plan-1  N1  0.020
 T6J  plan-1  C4  0.020
 T6J  plan-1  C5  0.020
 T6J  plan-1  C6  0.020
 T6J  plan-1  C7  0.020
 T6J  plan-1  C8  0.020
 T6J  plan-1  N   0.020
 T6J  plan-1  C2  0.020
 T6J  plan-1  C3  0.020
 T6J  plan-1  H9  0.020
 T6J  plan-1  H5  0.020
 T6J  plan-1  H6  0.020
 T6J  plan-1  H7  0.020
 T6J  plan-1  H8  0.020
 T6J  plan-1  C1  0.020

