# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 22:25:52 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 1-(1-methylethyl)-1H-benzimidazole-2-sulfonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)n1c2ccccc2nc1[S](O)(=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
 QQQ  QQQ  '1-(1-methylethyl)-1H-benzimidazole-2-sulfonic acid'  ligand  28  16  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QQQ
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
 QQQ  O11   O  OS    0  -0.705  -2.5846  -0.0136  -1.3411
 QQQ  S10   S  S     0   1.460  -2.2959  -0.6386   0.0978
 QQQ  O13   O  OS    0  -0.622  -2.7924   0.2552   1.1229
 QQQ  O12   O  OS    0  -0.606  -2.6830  -2.0254   0.1121
 QQQ  C8    C  CR5   0   0.196  -0.5301  -0.5768   0.0416
 QQQ  N7    N  N     0  -0.420   0.1478  -1.6813   0.0656
 QQQ  C3    C  CR56  0   0.124   1.4533  -1.2734   0.0481
 QQQ  C4    C  CR16  0  -0.310   2.6181  -2.0454   0.0588
 QQQ  C5    C  CR16  0  -0.270   3.8247  -1.3821   0.0325
 QQQ  C6    C  CR16  0  -0.261   3.8811   0.0230  -0.0035
 QQQ  C1    C  CR16  0  -0.301   2.7424   0.8022  -0.0134
 QQQ  C2    C  CR56  0   0.370   1.5181   0.1300   0.0137
 QQQ  N9    N  NR5   0  -0.525   0.2124   0.5615   0.0121
 QQQ  C14   C  CH1   0  -0.150  -0.2510   1.9553  -0.0291
 QQQ  C15   C  CH3   0  -0.653   0.1820   2.7073   1.2207
 QQQ  C16   C  CH3   0  -0.651   0.1703   2.6275  -1.3271
 QQQ  HO11  H  H     0   0.514  -3.4363   0.4583  -1.3729
 QQQ  H4    H  HCR6  0   0.267   2.5638  -3.1256   0.0855
 QQQ  H5    H  HCR6  0   0.263   4.7477  -1.9464   0.0399
 QQQ  H6    H  HCR6  0   0.266   4.8471   0.5098  -0.0239
 QQQ  H1    H  HCR6  0   0.272   2.8227   1.8787  -0.0411
 QQQ  H14   H  HCH1  0   0.271  -1.3369   1.9241  -0.0193
 QQQ  H15   H  HCH3  0   0.236   1.2631   2.8157   1.2950
 QQQ  H15A  H  HCH3  0   0.251  -0.2484   3.7078   1.1996
 QQQ  H15B  H  HCH3  0   0.249  -0.1764   2.2057   2.1192
 QQQ  H16   H  HCH3  0   0.251  -0.2589   3.6281  -1.3652
 QQQ  H16A  H  HCH3  0   0.236   1.2507   2.7292  -1.4181
 QQQ  H16B  H  HCH3  0   0.248  -0.1971   2.0719  -2.1895

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
 QQQ  S10  O11   single    1.595  0.020  1.595
 QQQ  O11  HO11  single    0.850  0.020  0.980
 QQQ  O13  S10   double    1.448  0.020  1.448
 QQQ  C8   S10   single    1.768  0.020  1.768
 QQQ  S10  O12   double    1.440  0.020  1.440
 QQQ  N7   C8    aromatic  1.296  0.020  1.296
 QQQ  C8   N9    aromatic  1.359  0.020  1.359
 QQQ  C3   N7    aromatic  1.368  0.020  1.368
 QQQ  C4   C3    aromatic  1.397  0.020  1.397
 QQQ  C3   C2    aromatic  1.405  0.020  1.405
 QQQ  C4   C5    aromatic  1.377  0.020  1.377
 QQQ  C4   H4    single    0.930  0.020  1.080
 QQQ  C5   C6    aromatic  1.407  0.020  1.407
 QQQ  C5   H5    single    0.930  0.020  1.080
 QQQ  C6   C1    aromatic  1.380  0.020  1.380
 QQQ  C6   H6    single    0.930  0.020  1.080
 QQQ  C2   C1    aromatic  1.397  0.020  1.397
 QQQ  C1   H1    single    0.930  0.020  1.080
 QQQ  C2   N9    aromatic  1.375  0.020  1.375
 QQQ  N9   C14   single    1.469  0.020  1.469
 QQQ  C14  C16   single    1.521  0.020  1.521
 QQQ  C14  C15   single    1.522  0.020  1.522
 QQQ  C14  H14   single    0.970  0.020  1.090
 QQQ  C15  H15   single    0.970  0.020  1.090
 QQQ  C15  H15A  single    0.970  0.020  1.090
 QQQ  C15  H15B  single    0.970  0.020  1.090
 QQQ  C16  H16   single    0.970  0.020  1.090
 QQQ  C16  H16A  single    0.970  0.020  1.090
 QQQ  C16  H16B  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
 QQQ  HO11  O11  S10   112.18  3.000
 QQQ  C8    S10  O12   107.61  3.000
 QQQ  O12   S10  O13   119.69  3.000
 QQQ  C8    S10  O13   110.09  3.000
 QQQ  O12   S10  O11   109.74  3.000
 QQQ  C8    S10  O11    97.96  3.000
 QQQ  O13   S10  O11   109.55  3.000
 QQQ  N9    C8   N7    115.36  3.000
 QQQ  N9    C8   S10   125.14  3.000
 QQQ  N7    C8   S10   119.47  3.000
 QQQ  C3    N7   C8    104.17  3.000
 QQQ  C2    C3   C4    120.90  3.000
 QQQ  C2    C3   N7    110.01  3.000
 QQQ  C4    C3   N7    129.10  3.000
 QQQ  H4    C4   C5    121.69  3.000
 QQQ  H4    C4   C3    120.66  3.000
 QQQ  C5    C4   C3    117.65  3.000
 QQQ  H5    C5   C6    119.15  3.000
 QQQ  H5    C5   C4    119.74  3.000
 QQQ  C6    C5   C4    121.11  3.000
 QQQ  H6    C6   C1    118.85  3.000
 QQQ  H6    C6   C5    119.06  3.000
 QQQ  C1    C6   C5    122.09  3.000
 QQQ  H1    C1   C2    123.05  3.000
 QQQ  H1    C1   C6    120.12  3.000
 QQQ  C2    C1   C6    116.83  3.000
 QQQ  N9    C2   C1    132.94  3.000
 QQQ  N9    C2   C3    105.64  3.000
 QQQ  C1    C2   C3    121.42  3.000
 QQQ  C14   N9   C2    126.66  3.000
 QQQ  C14   N9   C8    128.51  3.000
 QQQ  C2    N9   C8    104.82  3.000
 QQQ  H14   C14  C16   107.29  3.000
 QQQ  H14   C14  C15   106.93  3.000
 QQQ  C16   C14  C15   113.81  3.000
 QQQ  H14   C14  N9    106.72  3.000
 QQQ  C15   C14  N9    110.85  3.000
 QQQ  C16   C14  N9    110.84  3.000
 QQQ  H15B  C15  H15A  107.99  3.000
 QQQ  H15B  C15  H15   108.43  3.000
 QQQ  H15A  C15  H15   107.59  3.000
 QQQ  H15B  C15  C14   110.87  3.000
 QQQ  H15A  C15  C14   109.00  3.000
 QQQ  H15   C15  C14   112.81  3.000
 QQQ  H16B  C16  H16A  108.42  3.000
 QQQ  H16B  C16  H16   107.93  3.000
 QQQ  H16A  C16  H16   107.59  3.000
 QQQ  H16B  C16  C14   110.89  3.000
 QQQ  H16A  C16  C14   112.79  3.000
 QQQ  H16   C16  C14   109.06  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
 QQQ  CONST_01  C4   C3   N7   C8    180.00   0.0  0
 QQQ  CONST_02  C2   C3   N7   C8      0.00   0.0  0
 QQQ  CONST_03  C3   C2   N9   C8      0.00   0.0  0
 QQQ  CONST_04  C1   C2   N9   C8    180.00   0.0  0
 QQQ  CONST_05  C2   N9   C8   N7      0.00   0.0  0
 QQQ  CONST_06  C5   C4   C3   N7    180.00   0.0  0
 QQQ  CONST_07  C1   C2   C3   N7    180.00   0.0  0
 QQQ  CONST_08  N9   C2   C3   N7      0.00   0.0  0
 QQQ  CONST_09  N9   C8   N7   C3      0.00   0.0  0
 QQQ  CONST_10  C6   C5   C4   C3      0.00   0.0  0
 QQQ  CONST_11  C6   C1   C2   C3      0.00   0.0  0
 QQQ  CONST_12  C1   C2   C3   C4      0.00   0.0  0
 QQQ  CONST_13  N9   C2   C3   C4    180.00   0.0  0
 QQQ  CONST_14  C1   C6   C5   C4      0.00   0.0  0
 QQQ  CONST_15  C2   C3   C4   C5      0.00   0.0  0
 QQQ  CONST_16  C2   C1   C6   C5      0.00   0.0  0
 QQQ  CONST_17  N9   C2   C1   C6    180.00   0.0  0
 QQQ  CONST_18  C3   N7   C8   S10   180.00   0.0  0
 QQQ  CONST_19  C2   N9   C8   S10   180.00   0.0  0
 QQQ  CONST_20  C14  N9   C8   N7    180.00   0.0  0
 QQQ  CONST_21  C14  N9   C2   C3    180.00   0.0  0
 QQQ  CONST_22  C14  N9   C2   C1      0.00   0.0  0
 QQQ  CONST_23  H4   C4   C3   N7      0.00   0.0  0
 QQQ  CONST_24  H5   C5   C4   C3    180.00   0.0  0
 QQQ  CONST_25  H1   C1   C2   C3    180.00   0.0  0
 QQQ  CONST_26  H6   C6   C5   C4    180.00   0.0  0
 QQQ  Var_01    N7   C8   S10  O11  -115.94  30.0  2
 QQQ  Var_02    C16  C14  N9   C8   -115.80  30.0  2
 QQQ  Var_03    H16  C16  C14  N9    175.21  30.0  3
 QQQ  Var_04    H15  C15  C14  N9     65.40  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
 QQQ  plan-1  S10  0.020
 QQQ  plan-1  C8   0.020
 QQQ  plan-1  N7   0.020
 QQQ  plan-1  C3   0.020
 QQQ  plan-1  C4   0.020
 QQQ  plan-1  C5   0.020
 QQQ  plan-1  C6   0.020
 QQQ  plan-1  C1   0.020
 QQQ  plan-1  C2   0.020
 QQQ  plan-1  N9   0.020
 QQQ  plan-1  C14  0.020
 QQQ  plan-1  H4   0.020
 QQQ  plan-1  H5   0.020
 QQQ  plan-1  H6   0.020
 QQQ  plan-1  H1   0.020

