# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 21:33:07 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 2-phenyl-N,N-dipropyl-1H-benzimidazole-5-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCN(CCC)[S](=O)(=O)c1ccc2[nH]c(nc2c1)c3ccccc3
#
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
 OE1  OE1  2-phenyl-N,N-dipropyl-1H-benzimidazole-5-sulfonamide  ligand  48  25  .  2021-08-17  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_OE1
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
 OE1  C1    C  CH3   0  -0.665  -2.1274   3.8961   0.9378
 OE1  C2    C  CH2   0  -0.436  -2.2293   2.3801   0.8529
 OE1  C3    C  CH2   0  -0.302  -3.3412   1.9568  -0.0993
 OE1  N4    N  N     0  -0.578  -3.5763   0.5177  -0.1707
 OE1  C5    C  CH2   0  -0.290  -4.2595  -0.1152   0.9577
 OE1  C6    C  CH2   0  -0.414  -5.7437  -0.3306   0.7030
 OE1  C7    C  CH3   0  -0.672  -6.4393  -0.9071   1.9279
 OE1  S8    S  S     0   1.376  -2.7766  -0.4082  -1.2550
 OE1  O9    O  OS    0  -0.655  -3.4820  -1.6800  -1.3280
 OE1  O10   O  OS    0  -0.656  -2.6018   0.3830  -2.4644
 OE1  C11   C  CR6   0  -0.201  -1.1579  -0.7503  -0.6149
 OE1  C12   C  CR16  0  -0.266  -1.0104  -1.7827   0.3265
 OE1  C13   C  CR16  0  -0.295   0.2236  -2.0642   0.8785
 OE1  C14   C  CR56  0   0.357   1.2956  -1.2904   0.4508
 OE1  C15   C  CR56  0   0.171   1.1558  -0.2611  -0.4974
 OE1  C16   C  CR16  0  -0.332  -0.0906   0.0176  -1.0477
 OE1  N17   N  N     0  -0.475   2.3696   0.3220  -0.7400
 OE1  C18   C  CR5   0   0.486   3.2202  -0.3148   0.0224
 OE1  N19   N  NR15  0  -0.729   2.6224  -1.2953   0.7587
 OE1  C21   C  CR6   0   0.018   4.6508  -0.0264   0.0888
 OE1  C22   C  CR16  0  -0.285   5.1375   1.1338  -0.5164
 OE1  C23   C  CR16  0  -0.239   6.4894   1.4295  -0.4738
 OE1  C24   C  CR16  0  -0.254   7.3738   0.5725   0.1708
 OE1  C25   C  CR16  0  -0.237   6.8968  -0.5845   0.7713
 OE1  C26   C  CR16  0  -0.303   5.5436  -0.8843   0.7310
 OE1  H11C  H  HCH3  0   0.236  -1.3443   4.1982   1.6328
 OE1  H12C  H  HCH3  0   0.223  -1.8945   4.3344  -0.0342
 OE1  H13C  H  HCH3  0   0.223  -3.0642   4.3377   1.2825
 OE1  H21C  H  HCH2  0   0.232  -1.2768   1.9629   0.5212
 OE1  H22C  H  HCH2  0   0.227  -2.4170   1.9699   1.8490
 OE1  H31C  H  HCH2  0   0.253  -4.2859   2.4094   0.2142
 OE1  H32C  H  HCH2  0   0.263  -3.1471   2.3388  -1.1011
 OE1  H51C  H  HCH2  0   0.251  -3.7832  -1.0608   1.2229
 OE1  H52C  H  HCH2  0   0.252  -4.1227   0.5327   1.8262
 OE1  H61C  H  HCH2  0   0.224  -6.2042   0.6217   0.4261
 OE1  H62C  H  HCH2  0   0.228  -5.8674  -1.0007  -0.1494
 OE1  H71C  H  HCH3  0   0.235  -7.4942  -1.0954   1.7295
 OE1  H72C  H  HCH3  0   0.222  -5.9864  -1.8528   2.2308
 OE1  H73C  H  HCH3  0   0.222  -6.3807  -0.2251   2.7779
 OE1  H12   H  HCR6  0   0.279  -1.8606  -2.3840   0.6173
 OE1  H16   H  HCR6  0   0.286  -0.2050   0.8017  -1.7839
 OE1  H13   H  HCR6  0   0.281   0.3410  -2.8615   1.5994
 OE1  H19   H  HNR5  0   0.429   3.0655  -1.8963   1.4357
 OE1  H22   H  HCR6  0   0.261   4.4514   1.8033  -1.0174
 OE1  H26   H  HCR6  0   0.251   5.2034  -1.8021   1.1938
 OE1  H23   H  HCR6  0   0.265   6.8546   2.3333  -0.9430
 OE1  H24   H  HCR6  0   0.265   8.4299   0.8055   0.2031
 OE1  H25   H  HCR6  0   0.267   7.5784  -1.2606   1.2698

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
 OE1  C1   C2    single    1.522  0.020  1.522
 OE1  C2   C3    single    1.524  0.020  1.524
 OE1  C3   N4    single    1.460  0.020  1.460
 OE1  N4   C5    single    1.463  0.020  1.463
 OE1  N4   S8    single    1.635  0.020  1.635
 OE1  C5   C6    single    1.521  0.020  1.521
 OE1  C6   C7    single    1.522  0.020  1.522
 OE1  S8   O9    double    1.456  0.020  1.456
 OE1  S8   O10   double    1.456  0.020  1.456
 OE1  S8   C11   single    1.774  0.020  1.774
 OE1  C11  C12   aromatic  1.405  0.020  1.405
 OE1  C11  C16   aromatic  1.384  0.020  1.384
 OE1  C12  C13   aromatic  1.381  0.020  1.381
 OE1  C13  C14   aromatic  1.390  0.020  1.390
 OE1  C14  C15   aromatic  1.406  0.020  1.406
 OE1  C14  N19   aromatic  1.362  0.020  1.362
 OE1  C15  C16   aromatic  1.391  0.020  1.391
 OE1  C15  N17   aromatic  1.368  0.020  1.368
 OE1  N17  C18   aromatic  1.308  0.020  1.308
 OE1  C18  N19   aromatic  1.364  0.020  1.364
 OE1  C18  C21   single    1.461  0.020  1.461
 OE1  C21  C22   aromatic  1.396  0.020  1.396
 OE1  C21  C26   aromatic  1.395  0.020  1.395
 OE1  C22  C23   aromatic  1.385  0.020  1.385
 OE1  C23  C24   aromatic  1.390  0.020  1.390
 OE1  C24  C25   aromatic  1.388  0.020  1.388
 OE1  C25  C26   aromatic  1.387  0.020  1.387
 OE1  C1   H11C  single    0.970  0.020  1.090
 OE1  C1   H12C  single    0.970  0.020  1.090
 OE1  C1   H13C  single    0.970  0.020  1.090
 OE1  C2   H21C  single    0.970  0.020  1.090
 OE1  C2   H22C  single    0.970  0.020  1.090
 OE1  C3   H31C  single    0.970  0.020  1.090
 OE1  C3   H32C  single    0.970  0.020  1.090
 OE1  C5   H51C  single    0.970  0.020  1.090
 OE1  C5   H52C  single    0.970  0.020  1.090
 OE1  C6   H61C  single    0.970  0.020  1.090
 OE1  C6   H62C  single    0.970  0.020  1.090
 OE1  C7   H71C  single    0.970  0.020  1.090
 OE1  C7   H72C  single    0.970  0.020  1.090
 OE1  C7   H73C  single    0.970  0.020  1.090
 OE1  C12  H12   single    0.930  0.020  1.080
 OE1  C16  H16   single    0.930  0.020  1.080
 OE1  C13  H13   single    0.930  0.020  1.080
 OE1  N19  H19   single    0.860  0.020  1.020
 OE1  C22  H22   single    0.930  0.020  1.080
 OE1  C26  H26   single    0.930  0.020  1.080
 OE1  C23  H23   single    0.930  0.020  1.080
 OE1  C24  H24   single    0.930  0.020  1.080
 OE1  C25  H25   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
 OE1  H13C  C1   H12C  107.57  3.000
 OE1  H13C  C1   H11C  107.65  3.000
 OE1  H12C  C1   H11C  107.66  3.000
 OE1  H13C  C1   C2    111.29  3.000
 OE1  H12C  C1   C2    111.38  3.000
 OE1  H11C  C1   C2    111.09  3.000
 OE1  H22C  C2   H21C  106.46  3.000
 OE1  H22C  C2   C3    109.86  3.000
 OE1  H21C  C2   C3    109.92  3.000
 OE1  H22C  C2   C1    109.53  3.000
 OE1  H21C  C2   C1    109.83  3.000
 OE1  C3    C2   C1    111.12  3.000
 OE1  H32C  C3   H31C  105.81  3.000
 OE1  H32C  C3   N4    109.23  3.000
 OE1  H31C  C3   N4    106.43  3.000
 OE1  H32C  C3   C2    110.31  3.000
 OE1  H31C  C3   C2    109.65  3.000
 OE1  N4    C3   C2    114.95  3.000
 OE1  S8    N4   C5    119.67  3.000
 OE1  S8    N4   C3    120.80  3.000
 OE1  C5    N4   C3    117.64  3.000
 OE1  H52C  C5   H51C  105.43  3.000
 OE1  H52C  C5   C6    109.84  3.000
 OE1  H51C  C5   C6    110.11  3.000
 OE1  H52C  C5   N4    107.35  3.000
 OE1  H51C  C5   N4    111.00  3.000
 OE1  C6    C5   N4    112.81  3.000
 OE1  H62C  C6   H61C  106.81  3.000
 OE1  H62C  C6   C7    110.14  3.000
 OE1  H61C  C6   C7    109.95  3.000
 OE1  H62C  C6   C5    109.17  3.000
 OE1  H61C  C6   C5    109.27  3.000
 OE1  C7    C6   C5    111.39  3.000
 OE1  H73C  C7   H72C  107.64  3.000
 OE1  H73C  C7   H71C  107.56  3.000
 OE1  H72C  C7   H71C  107.61  3.000
 OE1  H73C  C7   C6    111.44  3.000
 OE1  H72C  C7   C6    111.21  3.000
 OE1  H71C  C7   C6    111.18  3.000
 OE1  C11   S8   O10   107.15  3.000
 OE1  C11   S8   O9    106.96  3.000
 OE1  O10   S8   O9    119.42  3.000
 OE1  C11   S8   N4    108.44  3.000
 OE1  O10   S8   N4    107.58  3.000
 OE1  O9    S8   N4    106.92  3.000
 OE1  C16   C11  C12   122.42  3.000
 OE1  C16   C11  S8    118.93  3.000
 OE1  C12   C11  S8    118.64  3.000
 OE1  H12   C12  C13   118.80  3.000
 OE1  H12   C12  C11   120.42  3.000
 OE1  C13   C12  C11   120.77  3.000
 OE1  H13   C13  C14   122.15  3.000
 OE1  H13   C13  C12   120.92  3.000
 OE1  C14   C13  C12   116.93  3.000
 OE1  N19   C14  C15   104.59  3.000
 OE1  N19   C14  C13   132.84  3.000
 OE1  C15   C14  C13   122.57  3.000
 OE1  N17   C15  C16   129.75  3.000
 OE1  N17   C15  C14   110.08  3.000
 OE1  C16   C15  C14   120.17  3.000
 OE1  H16   C16  C15   120.62  3.000
 OE1  H16   C16  C11   122.23  3.000
 OE1  C15   C16  C11   117.14  3.000
 OE1  C18   N17  C15   105.43  3.000
 OE1  C21   C18  N19   123.13  3.000
 OE1  C21   C18  N17   124.56  3.000
 OE1  N19   C18  N17   112.31  3.000
 OE1  H19   N19  C18   126.76  3.000
 OE1  H19   N19  C14   125.61  3.000
 OE1  C18   N19  C14   107.60  3.000
 OE1  C26   C21  C22   119.18  3.000
 OE1  C26   C21  C18   121.75  3.000
 OE1  C22   C21  C18   119.07  3.000
 OE1  H22   C22  C23   120.09  3.000
 OE1  H22   C22  C21   119.60  3.000
 OE1  C23   C22  C21   120.31  3.000
 OE1  H23   C23  C24   120.10  3.000
 OE1  H23   C23  C22   119.65  3.000
 OE1  C24   C23  C22   120.25  3.000
 OE1  H24   C24  C25   120.12  3.000
 OE1  H24   C24  C23   120.14  3.000
 OE1  C25   C24  C23   119.73  3.000
 OE1  H25   C25  C26   119.55  3.000
 OE1  H25   C25  C24   120.25  3.000
 OE1  C26   C25  C24   120.20  3.000
 OE1  H26   C26  C25   118.52  3.000
 OE1  H26   C26  C21   121.14  3.000
 OE1  C25   C26  C21   120.34  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
 OE1  CONST_01  C14   C13  C12  C11     0.00   0.0  0
 OE1  CONST_02  C14   C15  C16  C11     0.00   0.0  0
 OE1  CONST_03  N17   C15  C16  C11   180.00   0.0  0
 OE1  CONST_04  C15   C16  C11  C12     0.00   0.0  0
 OE1  CONST_05  C15   C14  C13  C12     0.00   0.0  0
 OE1  CONST_06  N19   C14  C13  C12   180.00   0.0  0
 OE1  CONST_07  C16   C11  C12  C13     0.00   0.0  0
 OE1  CONST_08  C16   C15  C14  C13     0.00   0.0  0
 OE1  CONST_09  N17   C15  C14  C13   180.00   0.0  0
 OE1  CONST_10  C18   N19  C14  C13   180.00   0.0  0
 OE1  CONST_11  C18   N17  C15  C14     0.00   0.0  0
 OE1  CONST_12  N17   C18  N19  C14     0.00   0.0  0
 OE1  CONST_13  C21   C18  N19  C14   180.00   0.0  0
 OE1  CONST_14  C18   N19  C14  C15     0.00   0.0  0
 OE1  CONST_15  N19   C18  N17  C15     0.00   0.0  0
 OE1  CONST_16  C21   C18  N17  C15   180.00   0.0  0
 OE1  CONST_17  N19   C14  C15  C16   180.00   0.0  0
 OE1  CONST_18  C18   N17  C15  C16   180.00   0.0  0
 OE1  CONST_19  N19   C14  C15  N17     0.00   0.0  0
 OE1  CONST_20  C22   C21  C18  N17     0.00   0.0  0
 OE1  CONST_21  C26   C21  C18  N17   180.00   0.0  0
 OE1  CONST_22  C23   C22  C21  C18   180.00   0.0  0
 OE1  CONST_23  C25   C26  C21  C18   180.00   0.0  0
 OE1  CONST_24  C22   C21  C18  N19   180.00   0.0  0
 OE1  CONST_25  C26   C21  C18  N19     0.00   0.0  0
 OE1  CONST_26  C24   C23  C22  C21     0.00   0.0  0
 OE1  CONST_27  C24   C25  C26  C21     0.00   0.0  0
 OE1  CONST_28  C25   C26  C21  C22     0.00   0.0  0
 OE1  CONST_29  C25   C24  C23  C22     0.00   0.0  0
 OE1  CONST_30  C26   C21  C22  C23     0.00   0.0  0
 OE1  CONST_31  C26   C25  C24  C23     0.00   0.0  0
 OE1  CONST_32  C13   C12  C11  S8    180.00   0.0  0
 OE1  CONST_33  C15   C16  C11  S8    180.00   0.0  0
 OE1  CONST_34  H13   C13  C12  C11   180.00   0.0  0
 OE1  CONST_35  H16   C16  C11  C12   180.00   0.0  0
 OE1  CONST_36  H19   N19  C14  C13     0.00   0.0  0
 OE1  CONST_37  H12   C12  C13  C14   180.00   0.0  0
 OE1  CONST_38  H22   C22  C21  C18     0.00   0.0  0
 OE1  CONST_39  H26   C26  C21  C18     0.00   0.0  0
 OE1  CONST_40  H23   C23  C22  C21   180.00   0.0  0
 OE1  CONST_41  H25   C25  C26  C21   180.00   0.0  0
 OE1  CONST_42  H24   C24  C23  C22   180.00   0.0  0
 OE1  Var_01    C12   C11  S8   N4     81.12  30.0  2
 OE1  Var_02    C11   S8   N4   C3     80.37  30.0  3
 OE1  Var_03    N4    C3   C2   C1   -175.80  30.0  3
 OE1  Var_04    C5    N4   C3   C2     74.35  30.0  3
 OE1  Var_05    C6    C5   N4   C3     98.80  30.0  3
 OE1  Var_06    C7    C6   C5   N4   -176.34  30.0  3
 OE1  Var_07    H11C  C1   C2   C3    178.96  30.0  3
 OE1  Var_08    H71C  C7   C6   C5   -177.85  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
 OE1  plan-1  C18  0.020
 OE1  plan-1  C21  0.020
 OE1  plan-1  C22  0.020
 OE1  plan-1  C23  0.020
 OE1  plan-1  C24  0.020
 OE1  plan-1  C25  0.020
 OE1  plan-1  C26  0.020
 OE1  plan-1  H22  0.020
 OE1  plan-1  H26  0.020
 OE1  plan-1  H23  0.020
 OE1  plan-1  H24  0.020
 OE1  plan-1  H25  0.020
 OE1  plan-2  S8   0.020
 OE1  plan-2  C11  0.020
 OE1  plan-2  C12  0.020
 OE1  plan-2  C13  0.020
 OE1  plan-2  C14  0.020
 OE1  plan-2  C15  0.020
 OE1  plan-2  C16  0.020
 OE1  plan-2  N17  0.020
 OE1  plan-2  C18  0.020
 OE1  plan-2  N19  0.020
 OE1  plan-2  C21  0.020
 OE1  plan-2  H12  0.020
 OE1  plan-2  H16  0.020
 OE1  plan-2  H13  0.020
 OE1  plan-2  H19  0.020

