# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 22:36:07 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: 2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[S](=O)(=O)c1cc(ccc1Cl)C(=O)CSc2[nH]c3cc4OCCOc4cc3n2
#
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
 E36  E36  2-chloro-5-[(6,7-dihydro-1H-[1,4]dioxino[2,3-f]benzimidazol-2-ylsulfanyl)acetyl]benzenesulfonamide  ligand  42  28  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E36
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
 E36  O1    O   O2    0  -0.487   -7.0265  -2.3725  -0.0020
 E36  C2    C   CH2   0  -0.225   -8.3887  -2.2160   0.3573
 E36  C3    C   CH2   0  -0.223   -8.9811  -1.0350  -0.3697
 E36  O4    O   O2    0  -0.485   -8.2900   0.1511  -0.0125
 E36  C5    C   CR6   0   0.309   -6.9380   0.0403   0.0005
 E36  C6    C   CR6   0   0.313   -6.3032  -1.2218   0.0046
 E36  C7    C   CR16  0  -0.457   -4.9226  -1.3256   0.0121
 E36  C8    C   CR56  0   0.148   -4.1724  -0.1548   0.0169
 E36  N9    N   N     0  -0.469   -2.8051   0.0203   0.0251
 E36  C10   C   CR5   0   0.304   -2.6363   1.3113   0.0407
 E36  N11   N   NR15  0  -0.711   -3.8013   2.0113   0.0433
 E36  C12   C   CR56  0   0.335   -4.8187   1.0884   0.0285
 E36  C13   C   CR16  0  -0.424   -6.1982   1.2131   0.0137
 E36  S14   S   S2    0   0.089   -1.1167   2.1644   0.0598
 E36  C15   C   CH2   0  -0.706   -0.0117   0.7360   0.0111
 E36  C16   C   C     0   0.399    1.4048   1.2459   0.0197
 E36  O17   O   O     0  -0.372    1.6365   2.4330   0.0476
 E36  C18   C   CR6   0   0.029    2.4994   0.2418  -0.0078
 E36  C19   C   CR16  0  -0.272    3.8157   0.6960  -0.0017
 E36  C20   C   CR6   0  -0.118    4.8689  -0.1987  -0.0243
 E36  C21   C   CR6   0  -0.016    4.6108  -1.5705  -0.0555
 E36  C22   C   CR16  0  -0.177    3.3041  -2.0300  -0.0599
 E36  C23   C   CR16  0  -0.286    2.2551  -1.1275  -0.0376
 E36  S24   S   S     0   1.385    6.5281   0.4552  -0.0484
 E36  O25   O   OS    0  -0.650    7.2518  -0.1617  -1.1447
 E36  CL26  CL  CL    0  -0.070    5.8770  -2.7291  -0.0771
 E36  O27   O   OS    0  -0.641    6.3972   1.9020  -0.0069
 E36  N28   N   NC2   0  -0.885    7.1506  -0.1251   1.3497
 E36  H2    H   HCH2  0   0.259   -8.9030  -3.1344   0.0772
 E36  H2A   H   HCH2  0   0.239   -8.4835  -2.0831   1.4409
 E36  H3    H   HCH2  0   0.240   -8.9317  -1.1899  -1.4531
 E36  H3A   H   HCH2  0   0.259  -10.0245  -0.8957  -0.0897
 E36  H7    H   HCR6  0   0.265   -4.4506  -2.3001   0.0143
 E36  HN11  H   HNR5  0   0.423   -3.9017   3.0142   0.0526
 E36  H13   H   HCR6  0   0.278   -6.6963   2.1741   0.0114
 E36  H15   H   HCH2  0   0.328   -0.1902   0.0877   0.8712
 E36  H15A  H   HCH2  0   0.328   -0.1977   0.1432  -0.8870
 E36  H19   H   HCR6  0   0.297    4.0113   1.7591   0.0226
 E36  H22   H   HCR6  0   0.304    3.1067  -3.0925  -0.0812
 E36  H23   H   HCR6  0   0.291    1.2462  -1.5177  -0.0427
 E36  HN28  H   HNC2  0   0.426    7.0469   0.4993   2.1407
 E36  HN2A  H   HNC2  0   0.426    8.0916  -0.4879   1.2568

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
 E36  O1   C2    single    1.417  0.020  1.417
 E36  O1   C6    single    1.359  0.020  1.359
 E36  C2   C3    single    1.508  0.020  1.508
 E36  C3   O4    single    1.418  0.020  1.418
 E36  O4   C5    single    1.357  0.020  1.357
 E36  C5   C6    aromatic  1.413  0.020  1.413
 E36  C5   C13   aromatic  1.387  0.020  1.387
 E36  C6   C7    aromatic  1.385  0.020  1.385
 E36  C7   C8    aromatic  1.391  0.020  1.391
 E36  C8   N9    aromatic  1.378  0.020  1.378
 E36  C8   C12   aromatic  1.401  0.020  1.401
 E36  N9   C10   aromatic  1.302  0.020  1.302
 E36  C10  N11   aromatic  1.359  0.020  1.359
 E36  C10  S14   single    1.743  0.020  1.743
 E36  N11  C12   aromatic  1.374  0.020  1.374
 E36  C12  C13   aromatic  1.385  0.020  1.385
 E36  S14  C15   single    1.807  0.020  1.807
 E36  C15  C16   single    1.505  0.020  1.505
 E36  C16  O17   double    1.210  0.020  1.210
 E36  C16  C18   single    1.486  0.020  1.486
 E36  C18  C19   aromatic  1.393  0.020  1.393
 E36  C18  C23   aromatic  1.391  0.020  1.391
 E36  C19  C20   aromatic  1.382  0.020  1.382
 E36  C20  C21   aromatic  1.396  0.020  1.396
 E36  C20  S24   single    1.783  0.020  1.783
 E36  C21  C22   aromatic  1.385  0.020  1.385
 E36  C21  CL26  single    1.716  0.020  1.716
 E36  C22  C23   aromatic  1.384  0.020  1.384
 E36  S24  O25   double    1.451  0.020  1.451
 E36  S24  O27   double    1.453  0.020  1.453
 E36  S24  N28   single    1.637  0.020  1.637
 E36  C2   H2    single    0.970  0.020  1.090
 E36  C2   H2A   single    0.970  0.020  1.090
 E36  C3   H3    single    0.970  0.020  1.090
 E36  C3   H3A   single    0.970  0.020  1.090
 E36  C7   H7    single    0.930  0.020  1.080
 E36  N11  HN11  single    0.860  0.020  1.020
 E36  C13  H13   single    0.930  0.020  1.080
 E36  C15  H15   single    0.970  0.020  1.090
 E36  C15  H15A  single    0.970  0.020  1.090
 E36  C19  H19   single    0.930  0.020  1.080
 E36  C22  H22   single    0.930  0.020  1.080
 E36  C23  H23   single    0.930  0.020  1.080
 E36  N28  HN28  single    0.890  0.020  1.040
 E36  N28  HN2A  single    0.890  0.020  1.040

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
 E36  C6    O1   C2    114.62  3.000
 E36  H2A   C2   H2    108.40  3.000
 E36  H2A   C2   C3    110.35  3.000
 E36  H2    C2   C3    110.54  3.000
 E36  H2A   C2   O1    110.32  3.000
 E36  H2    C2   O1    107.18  3.000
 E36  C3    C2   O1    109.99  3.000
 E36  H3A   C3   H3    108.39  3.000
 E36  H3A   C3   O4    107.16  3.000
 E36  H3    C3   O4    110.20  3.000
 E36  H3A   C3   C2    110.64  3.000
 E36  H3    C3   C2    110.38  3.000
 E36  O4    C3   C2    110.00  3.000
 E36  C5    O4   C3    114.81  3.000
 E36  C13   C5   C6    121.05  3.000
 E36  C13   C5   O4    117.56  3.000
 E36  C6    C5   O4    121.38  3.000
 E36  C7    C6   C5    121.00  3.000
 E36  C7    C6   O1    117.85  3.000
 E36  C5    C6   O1    121.15  3.000
 E36  H7    C7   C8    121.50  3.000
 E36  H7    C7   C6    120.15  3.000
 E36  C8    C7   C6    118.35  3.000
 E36  C12   C8   N9    110.17  3.000
 E36  C12   C8   C7    119.88  3.000
 E36  N9    C8   C7    129.95  3.000
 E36  C10   N9   C8    104.75  3.000
 E36  S14   C10  N11   119.68  3.000
 E36  S14   C10  N9    126.76  3.000
 E36  N11   C10  N9    113.55  3.000
 E36  HN11  N11  C12   126.50  3.000
 E36  HN11  N11  C10   126.71  3.000
 E36  C12   N11  C10   106.78  3.000
 E36  C13   C12  N11   132.63  3.000
 E36  C13   C12  C8    122.63  3.000
 E36  N11   C12  C8    104.75  3.000
 E36  H13   C13  C12   122.56  3.000
 E36  H13   C13  C5    120.35  3.000
 E36  C12   C13  C5    117.08  3.000
 E36  C15   S14  C10    98.39  3.000
 E36  H15A  C15  H15   107.32  3.000
 E36  H15A  C15  C16   110.42  3.000
 E36  H15   C15  C16   110.51  3.000
 E36  H15A  C15  S14   110.31  3.000
 E36  H15   C15  S14   110.38  3.000
 E36  C16   C15  S14   107.91  3.000
 E36  C18   C16  O17   121.50  3.000
 E36  C18   C16  C15   117.66  3.000
 E36  O17   C16  C15   120.84  3.000
 E36  C23   C18  C19   119.15  3.000
 E36  C23   C18  C16   122.43  3.000
 E36  C19   C18  C16   118.42  3.000
 E36  H19   C19  C20   119.93  3.000
 E36  H19   C19  C18   119.46  3.000
 E36  C20   C19  C18   120.60  3.000
 E36  S24   C20  C21   122.14  3.000
 E36  S24   C20  C19   118.15  3.000
 E36  C21   C20  C19   119.70  3.000
 E36  CL26  C21  C22   118.16  3.000
 E36  CL26  C21  C20   121.81  3.000
 E36  C22   C21  C20   120.03  3.000
 E36  H22   C22  C23   120.19  3.000
 E36  H22   C22  C21   119.90  3.000
 E36  C23   C22  C21   119.91  3.000
 E36  H23   C23  C22   118.14  3.000
 E36  H23   C23  C18   121.26  3.000
 E36  C22   C23  C18   120.61  3.000
 E36  N28   S24  O27   111.27  3.000
 E36  N28   S24  O25   107.75  3.000
 E36  O27   S24  O25   119.32  3.000
 E36  N28   S24  C20   102.26  3.000
 E36  O27   S24  C20   106.31  3.000
 E36  O25   S24  C20   108.56  3.000
 E36  HN2A  N28  HN28  112.80  3.000
 E36  HN2A  N28  S24   113.71  3.000
 E36  HN28  N28  S24   114.17  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
 E36  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 E36  CONST_02  C8    C12  C13  C5      0.00   0.0  0
 E36  CONST_03  N11   C12  C13  C5    180.00   0.0  0
 E36  CONST_04  C12   C13  C5   C6      0.00   0.0  0
 E36  CONST_05  N9    C8   C7   C6    180.00   0.0  0
 E36  CONST_06  C12   C8   C7   C6      0.00   0.0  0
 E36  CONST_07  C13   C5   C6   C7      0.00   0.0  0
 E36  CONST_08  C10   N9   C8   C7    180.00   0.0  0
 E36  CONST_09  N11   C12  C8   C7    180.00   0.0  0
 E36  CONST_10  C13   C12  C8   C7      0.00   0.0  0
 E36  CONST_11  N11   C10  N9   C8      0.00   0.0  0
 E36  CONST_12  C10   N11  C12  C8      0.00   0.0  0
 E36  CONST_13  N11   C12  C8   N9      0.00   0.0  0
 E36  CONST_14  C13   C12  C8   N9    180.00   0.0  0
 E36  CONST_15  C12   N11  C10  N9      0.00   0.0  0
 E36  CONST_16  C12   C8   N9   C10     0.00   0.0  0
 E36  CONST_17  C13   C12  N11  C10   180.00   0.0  0
 E36  CONST_18  C21   C20  C19  C18     0.00   0.0  0
 E36  CONST_19  C21   C22  C23  C18     0.00   0.0  0
 E36  CONST_20  C22   C23  C18  C19     0.00   0.0  0
 E36  CONST_21  C22   C21  C20  C19     0.00   0.0  0
 E36  CONST_22  C23   C18  C19  C20     0.00   0.0  0
 E36  CONST_23  C23   C22  C21  C20     0.00   0.0  0
 E36  CONST_24  S14   C10  N9   C8    180.00   0.0  0
 E36  CONST_25  S14   C10  N11  C12   180.00   0.0  0
 E36  CONST_26  C20   C19  C18  C16   180.00   0.0  0
 E36  CONST_27  C22   C23  C18  C16   180.00   0.0  0
 E36  CONST_28  S24   C20  C19  C18   180.00   0.0  0
 E36  CONST_29  CL26  C21  C20  C19   180.00   0.0  0
 E36  CONST_30  S24   C20  C21  C22   180.00   0.0  0
 E36  CONST_31  CL26  C21  C22  C23   180.00   0.0  0
 E36  CONST_32  H7    C7   C6   O1      0.00   0.0  0
 E36  CONST_33  H13   C13  C5   O4      0.00   0.0  0
 E36  CONST_34  HN11  N11  C12  C8    180.00   0.0  0
 E36  CONST_35  H22   C22  C23  C18   180.00   0.0  0
 E36  CONST_36  H23   C23  C18  C19   180.00   0.0  0
 E36  CONST_37  H19   C19  C20  C21   180.00   0.0  0
 E36  Var_01    O4    C3   C2   O1    -60.94  30.0  1
 E36  Var_02    C5    C6   O1   C2    -16.70  30.0  1
 E36  Var_03    C6    C5   O4   C3    -15.71  30.0  1
 E36  Var_04    C19   C18  C16  C15   179.93  30.0  2
 E36  Var_05    O25   S24  C20  C19  -128.24  30.0  2
 E36  Var_06    C16   C15  S14  C10   179.98  30.0  3
 E36  Var_07    C18   C16  C15  S14   179.64  30.0  3
 E36  Var_08    HN28  N28  S24  C20   -92.14  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
 E36  plan-1  C16   0.020
 E36  plan-1  C18   0.020
 E36  plan-1  C19   0.020
 E36  plan-1  C20   0.020
 E36  plan-1  C21   0.020
 E36  plan-1  C22   0.020
 E36  plan-1  C23   0.020
 E36  plan-1  S24   0.020
 E36  plan-1  CL26  0.020
 E36  plan-1  H19   0.020
 E36  plan-1  H22   0.020
 E36  plan-1  H23   0.020
 E36  plan-2  O1    0.020
 E36  plan-2  O4    0.020
 E36  plan-2  C5    0.020
 E36  plan-2  C6    0.020
 E36  plan-2  C7    0.020
 E36  plan-2  C8    0.020
 E36  plan-2  N9    0.020
 E36  plan-2  C10   0.020
 E36  plan-2  N11   0.020
 E36  plan-2  C12   0.020
 E36  plan-2  C13   0.020
 E36  plan-2  S14   0.020
 E36  plan-2  H7    0.020
 E36  plan-2  HN11  0.020
 E36  plan-2  H13   0.020
 E36  plan-3  C15   0.020
 E36  plan-3  C16   0.020
 E36  plan-3  O17   0.020
 E36  plan-3  C18   0.020

