# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 21:42:55 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: 4-[2-(benzimidazol-1-yl)ethanoyl]benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1ccc(cc1)C(=O)Cn2cnc3ccccc23
#
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
 6YH  6YH  4-[2-(benzimidazol-1-yl)ethanoyl]benzenesulfonamide  ligand  35  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6YH
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
 6YH  O12  O  O     0  -0.357  -1.3641  -0.4003   1.5452
 6YH  C11  C  C     0   0.368  -0.8131  -0.5263   0.4794
 6YH  C4   C  CR6   0   0.001   0.6548  -0.3280   0.3312
 6YH  C3   C  CR16  0  -0.242   1.3865   0.0907   1.4397
 6YH  C2   C  CR16  0  -0.224   2.7522   0.2975   1.3428
 6YH  C5   C  CR16  0  -0.281   1.3076  -0.5451  -0.8825
 6YH  C6   C  CR16  0  -0.191   2.6720  -0.3450  -0.9895
 6YH  C1   C  CR6   0  -0.202   3.3804   0.0753   0.1274
 6YH  S7   S  S     0   1.366   5.1236   0.3765  -0.0345
 6YH  O9   O  OS    0  -0.645   5.5829   0.9799   1.2078
 6YH  N10  N  NC2   0  -0.886   5.6894  -1.1550  -0.2550
 6YH  O8   O  OS    0  -0.660   5.3660   1.0819  -1.2833
 6YH  C13  C  CH2   0  -0.463  -1.6083  -0.8888  -0.7659
 6YH  N14  N  NR5   0  -0.503  -3.0118  -0.9506  -0.4957
 6YH  C18  C  CR56  0   0.348  -3.8650   0.1162  -0.3668
 6YH  C20  C  CR16  0  -0.307  -3.6873   1.4832  -0.5434
 6YH  C21  C  CR16  0  -0.275  -4.7973   2.2835  -0.3363
 6YH  C22  C  CR16  0  -0.272  -6.0367   1.7384   0.0333
 6YH  C23  C  CR16  0  -0.322  -6.2023   0.3764   0.2082
 6YH  C19  C  CR56  0   0.126  -5.0952  -0.4472   0.0068
 6YH  N17  N  N     0  -0.465  -4.9722  -1.8144   0.1147
 6YH  C16  C  CR15  0   0.111  -3.7301  -2.0601  -0.1795
 6YH  H1   H  HCR6  0   0.282   0.8907   0.2649   2.3848
 6YH  H2   H  HCR6  0   0.292   3.3087   0.6296   2.2077
 6YH  H3   H  HCR6  0   0.286   0.7681  -0.8722  -1.7603
 6YH  H4   H  HCR6  0   0.296   3.1678  -0.5192  -1.9349
 6YH  H5   H  HNC2  0   0.424   6.5845  -1.1579  -0.7353
 6YH  H6   H  HNC2  0   0.420   5.7476  -1.6843   0.6090
 6YH  H7   H  HCH2  0   0.315  -1.4165  -0.1641  -1.5610
 6YH  H8   H  HCH2  0   0.330  -1.2721  -1.8565  -1.1459
 6YH  H9   H  HCR6  0   0.269  -2.7345   1.9115  -0.8277
 6YH  H10  H  HCR6  0   0.258  -4.7072   3.3546  -0.4600
 6YH  H11  H  HCR6  0   0.254  -6.8772   2.4025   0.1860
 6YH  H12  H  HCR6  0   0.257  -7.1586  -0.0407   0.4959
 6YH  H13  H  HCR5  0   0.292  -3.2746  -3.0402  -0.1971

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
 6YH  N17  C16  aromatic  1.300  0.020  1.300
 6YH  N17  C19  aromatic  1.377  0.020  1.377
 6YH  C16  N14  aromatic  1.359  0.020  1.359
 6YH  C19  C23  aromatic  1.394  0.020  1.394
 6YH  C19  C18  aromatic  1.404  0.020  1.404
 6YH  N14  C18  aromatic  1.372  0.020  1.372
 6YH  N14  C13  single    1.431  0.020  1.431
 6YH  C23  C22  aromatic  1.383  0.020  1.383
 6YH  O12  C11  double    1.206  0.020  1.206
 6YH  C18  C20  aromatic  1.390  0.020  1.390
 6YH  C13  C11  single    1.521  0.020  1.521
 6YH  C11  C4   single    1.489  0.020  1.489
 6YH  C22  C21  aromatic  1.404  0.020  1.404
 6YH  C4   C3   aromatic  1.393  0.020  1.393
 6YH  C4   C5   aromatic  1.395  0.020  1.395
 6YH  C20  C21  aromatic  1.384  0.020  1.384
 6YH  C3   C2   aromatic  1.385  0.020  1.385
 6YH  C5   C6   aromatic  1.383  0.020  1.383
 6YH  C2   C1   aromatic  1.386  0.020  1.386
 6YH  C6   C1   aromatic  1.388  0.020  1.388
 6YH  C1   S7   single    1.776  0.020  1.776
 6YH  N10  S7   single    1.648  0.020  1.648
 6YH  O8   S7   double    1.455  0.020  1.455
 6YH  S7   O9   double    1.455  0.020  1.455
 6YH  C3   H1   single    0.930  0.020  1.080
 6YH  C2   H2   single    0.930  0.020  1.080
 6YH  C5   H3   single    0.930  0.020  1.080
 6YH  C6   H4   single    0.930  0.020  1.080
 6YH  N10  H5   single    0.890  0.020  1.040
 6YH  N10  H6   single    0.890  0.020  1.040
 6YH  C13  H7   single    0.970  0.020  1.090
 6YH  C13  H8   single    0.970  0.020  1.090
 6YH  C20  H9   single    0.930  0.020  1.080
 6YH  C21  H10  single    0.930  0.020  1.080
 6YH  C22  H11  single    0.930  0.020  1.080
 6YH  C23  H12  single    0.930  0.020  1.080
 6YH  C16  H13  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
 6YH  C13  C11  C4   117.75  3.000
 6YH  C4   C11  O12  121.63  3.000
 6YH  C13  C11  O12  120.62  3.000
 6YH  C5   C4   C3   119.57  3.000
 6YH  C5   C4   C11  121.82  3.000
 6YH  C3   C4   C11  118.61  3.000
 6YH  H1   C3   C2   119.30  3.000
 6YH  H1   C3   C4   120.21  3.000
 6YH  C2   C3   C4   120.49  3.000
 6YH  H2   C2   C1   121.18  3.000
 6YH  H2   C2   C3   119.85  3.000
 6YH  C1   C2   C3   118.97  3.000
 6YH  H3   C5   C6   118.25  3.000
 6YH  H3   C5   C4   121.33  3.000
 6YH  C6   C5   C4   120.42  3.000
 6YH  H4   C6   C1   121.21  3.000
 6YH  H4   C6   C5   119.77  3.000
 6YH  C1   C6   C5   119.02  3.000
 6YH  S7   C1   C6   118.62  3.000
 6YH  S7   C1   C2   119.83  3.000
 6YH  C6   C1   C2   121.53  3.000
 6YH  O8   S7   N10  106.18  3.000
 6YH  O8   S7   O9   118.63  3.000
 6YH  N10  S7   O9   113.03  3.000
 6YH  O9   S7   C1   107.59  3.000
 6YH  O8   S7   C1   108.90  3.000
 6YH  N10  S7   C1   101.04  3.000
 6YH  H6   N10  H5   110.52  3.000
 6YH  H6   N10  S7   112.99  3.000
 6YH  H5   N10  S7   111.63  3.000
 6YH  H8   C13  H7   106.28  3.000
 6YH  H8   C13  N14  109.23  3.000
 6YH  H7   C13  N14  109.77  3.000
 6YH  H8   C13  C11  109.56  3.000
 6YH  H7   C13  C11  110.23  3.000
 6YH  N14  C13  C11  111.62  3.000
 6YH  C16  N14  C18  106.51  3.000
 6YH  C18  N14  C13  126.45  3.000
 6YH  C16  N14  C13  126.71  3.000
 6YH  C19  C18  C20  122.73  3.000
 6YH  C20  C18  N14  132.32  3.000
 6YH  C19  C18  N14  104.94  3.000
 6YH  H9   C20  C21  121.09  3.000
 6YH  H9   C20  C18  122.34  3.000
 6YH  C21  C20  C18  116.56  3.000
 6YH  H10  C21  C22  119.21  3.000
 6YH  H10  C21  C20  119.24  3.000
 6YH  C22  C21  C20  121.54  3.000
 6YH  H11  C22  C23  119.57  3.000
 6YH  H11  C22  C21  119.00  3.000
 6YH  C23  C22  C21  121.43  3.000
 6YH  H12  C23  C19  120.82  3.000
 6YH  H12  C23  C22  121.26  3.000
 6YH  C19  C23  C22  117.92  3.000
 6YH  N17  C19  C23  130.24  3.000
 6YH  C23  C19  C18  119.81  3.000
 6YH  N17  C19  C18  109.94  3.000
 6YH  C16  N17  C19  104.79  3.000
 6YH  H13  C16  N17  125.29  3.000
 6YH  H13  C16  N14  120.91  3.000
 6YH  N17  C16  N14  113.79  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
 6YH  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 6YH  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 6YH  CONST_03  C6   C5   C4   C3      0.00   0.0  0
 6YH  CONST_04  C6   C1   C2   C3      0.00   0.0  0
 6YH  CONST_05  C5   C4   C3   C2      0.00   0.0  0
 6YH  CONST_06  C5   C6   C1   C2      0.00   0.0  0
 6YH  CONST_07  C19  N17  C16  N14     0.00   0.0  0
 6YH  CONST_08  N17  C19  C18  N14     0.00   0.0  0
 6YH  CONST_09  C23  C19  C18  N14   180.00   0.0  0
 6YH  CONST_10  C21  C20  C18  N14   180.00   0.0  0
 6YH  CONST_11  C16  N17  C19  C18     0.00   0.0  0
 6YH  CONST_12  C22  C23  C19  C18     0.00   0.0  0
 6YH  CONST_13  N17  C16  N14  C18     0.00   0.0  0
 6YH  CONST_14  C22  C21  C20  C18     0.00   0.0  0
 6YH  CONST_15  N17  C19  C18  C20   180.00   0.0  0
 6YH  CONST_16  C23  C19  C18  C20     0.00   0.0  0
 6YH  CONST_17  C16  N14  C18  C20   180.00   0.0  0
 6YH  CONST_18  C23  C22  C21  C20     0.00   0.0  0
 6YH  CONST_19  C19  C23  C22  C21     0.00   0.0  0
 6YH  CONST_20  C19  C18  C20  C21     0.00   0.0  0
 6YH  CONST_21  N17  C19  C23  C22   180.00   0.0  0
 6YH  CONST_22  C16  N17  C19  C23   180.00   0.0  0
 6YH  CONST_23  C16  N14  C18  C19     0.00   0.0  0
 6YH  CONST_24  C2   C3   C4   C11   180.00   0.0  0
 6YH  CONST_25  C6   C5   C4   C11   180.00   0.0  0
 6YH  CONST_26  S7   C1   C2   C3    180.00   0.0  0
 6YH  CONST_27  S7   C1   C6   C5    180.00   0.0  0
 6YH  CONST_28  N17  C16  N14  C13   180.00   0.0  0
 6YH  CONST_29  C19  C18  N14  C13   180.00   0.0  0
 6YH  CONST_30  C20  C18  N14  C13     0.00   0.0  0
 6YH  CONST_31  H2   C2   C3   C4    180.00   0.0  0
 6YH  CONST_32  H4   C6   C5   C4    180.00   0.0  0
 6YH  CONST_33  H3   C5   C4   C3    180.00   0.0  0
 6YH  CONST_34  H1   C3   C4   C5    180.00   0.0  0
 6YH  CONST_35  H9   C20  C18  N14     0.00   0.0  0
 6YH  CONST_36  H12  C23  C19  C18   180.00   0.0  0
 6YH  CONST_37  H13  C16  N14  C18   180.00   0.0  0
 6YH  CONST_38  H10  C21  C20  C18   180.00   0.0  0
 6YH  CONST_39  H11  C22  C21  C20   180.00   0.0  0
 6YH  Var_01    C3   C4   C11  O12    -3.88  30.0  2
 6YH  Var_02    C16  N14  C13  C11   -94.62  30.0  3
 6YH  Var_03    N14  C13  C11  C4   -175.69  30.0  1
 6YH  Var_04    N10  S7   C1   C2    112.56  30.0  2
 6YH  Var_05    H5   N10  S7   C1    156.49  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
 6YH  plan-1  C11  0.020
 6YH  plan-1  C4   0.020
 6YH  plan-1  C3   0.020
 6YH  plan-1  C2   0.020
 6YH  plan-1  C5   0.020
 6YH  plan-1  C6   0.020
 6YH  plan-1  C1   0.020
 6YH  plan-1  S7   0.020
 6YH  plan-1  H1   0.020
 6YH  plan-1  H2   0.020
 6YH  plan-1  H3   0.020
 6YH  plan-1  H4   0.020
 6YH  plan-2  C13  0.020
 6YH  plan-2  N14  0.020
 6YH  plan-2  C18  0.020
 6YH  plan-2  C20  0.020
 6YH  plan-2  C21  0.020
 6YH  plan-2  C22  0.020
 6YH  plan-2  C23  0.020
 6YH  plan-2  C19  0.020
 6YH  plan-2  N17  0.020
 6YH  plan-2  C16  0.020
 6YH  plan-2  H9   0.020
 6YH  plan-2  H10  0.020
 6YH  plan-2  H11  0.020
 6YH  plan-2  H12  0.020
 6YH  plan-2  H13  0.020
 6YH  plan-3  O12  0.020
 6YH  plan-3  C11  0.020
 6YH  plan-3  C4   0.020
 6YH  plan-3  C13  0.020

