# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 14:26:47 2021
#   Inital geometry file: a 139 line input string
#   Ligand name: 5-chloranyl-2-[[(1~{S},2~{R})-2-(2,3-dihydro-1~{H}-inden-4-yl)-1-(2-oxidanylidene-3~{H}-1,3,4-oxadiazol-5-yl)propyl]sulfamoyl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@H](N[S](=O)(=O)c1ccc(Cl)cc1C(N)=O)C2=NNC(=O)O2)c3cccc4CCCc34
#
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
 E6O  E6O  5-chloranyl-2-[[(1~{S},2~{R})-2-(2,3-dihydro-1~{H}-inden-4-yl)-1-(2-oxidanylidene-3~{H}-1,3,4-oxadiazol-5-yl)propyl]sulfamoyl]benzamide  ligand  53  32  .  2022-07-24  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_E6O
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
 E6O  C1   C   CH2   0  -0.510  46.9251  29.1418  11.5620
 E6O  C2   C   CR56  0   0.034  46.2026  27.9345  11.0182
 E6O  C3   C   CR56  0   0.106  45.4194  28.3037   9.9224
 E6O  C4   C   CH2   0  -0.489  45.5640  29.7736   9.6400
 E6O  C5   C   CH2   0  -0.460  46.8446  30.1452  10.4013
 E6O  C6   C   CR6   0   0.083  46.2088  26.6222  11.4777
 E6O  C7   C   CR16  0  -0.322  45.4188  25.6881  10.8035
 E6O  C8   C   CR16  0  -0.242  44.6451  26.0537   9.7130
 E6O  C9   C   CR16  0  -0.343  44.6382  27.3713   9.2630
 E6O  C11  C   CH3   0  -0.639  46.2443  25.5815  13.7784
 E6O  C26  C   CR6   0  -0.025  52.8469  24.3313   9.7437
 E6O  C25  C   CR16  0  -0.195  51.9376  23.2943   9.6251
 E6O  C24  C   CR6   0  -0.016  51.0656  23.0076  10.6693
 E6O  C29  C   C     0   0.445  50.1635  21.8121  10.4628
 E6O  N31  N   NH2   0  -0.798  49.0434  22.0848   9.7933
 E6O  O30  O   O     0  -0.457  50.5329  20.7040  10.8066
 E6O  C27  C   CR16  0  -0.204  52.9211  25.0962  10.8985
 E6O  C28  C   CR16  0  -0.240  52.0603  24.8101  11.9403
 E6O  C23  C   CR6   0  -0.236  51.1359  23.7762  11.8263
 E6O  S20  S   S     0   1.394  50.0199  23.5613  13.1943
 E6O  O21  O   OS    0  -0.631  49.1601  22.4324  12.9016
 E6O  O22  O   OS    0  -0.637  50.7968  23.6121  14.4171
 E6O  C12  C   CH1   0  -0.175  48.1367  25.1991  12.1467
 E6O  C13  C   CR5   0   0.568  48.8348  25.7206  10.9346
 E6O  N17  N   N     0  -0.253  48.8657  25.1974   9.7734
 E6O  N16  N   NR15  0  -0.501  49.6585  26.0293   9.0507
 E6O  C15  C   CR5   0   0.658  50.1125  27.0671   9.7821
 E6O  O18  O   O     0  -0.436  50.8202  27.9961   9.5138
 E6O  O14  O   O     0  -0.451  49.5620  26.8498  11.0233
 E6O  C10  C   CH1   0  -0.345  47.0654  26.1908  12.6461
 E6O  H1   H   HCH2  0   0.244  47.9537  28.9481  11.8663
 E6O  H2   H   HCH2  0   0.250  46.4015  29.5193  12.4467
 E6O  H3   H   HCH2  0   0.248  45.6217  29.9997   8.5742
 E6O  H4   H   HCH2  0   0.246  44.6996  30.3181  10.0340
 E6O  H5   H   HCH2  0   0.236  47.7074  30.0062   9.7459
 E6O  H6   H   HCH2  0   0.239  46.8542  31.1811  10.7389
 E6O  H7   H   HCR6  0   0.247  45.4028  24.6543  11.1295
 E6O  H8   H   HCR6  0   0.252  44.0442  25.3078   9.2087
 E6O  H9   H   HCR6  0   0.246  44.0363  27.6549   8.4080
 E6O  H10  H   HCH3  0   0.246  46.8661  25.3560  14.6434
 E6O  H11  H   HCH3  0   0.249  45.4716  26.2808  14.0963
 E6O  H12  H   HCH3  0   0.228  45.7532  24.6586  13.4667
 E6O  H13  H   HCR6  0   0.305  51.9015  22.7087   8.7159
 E6O  H14  H   HNH2  0   0.409  48.3836  21.3518   9.5842
 E6O  H15  H   HNH2  0   0.430  48.7893  23.0333   9.5555
 E6O  H16  H   HCR6  0   0.305  53.6358  25.9019  10.9867
 E6O  H17  H   HCR6  0   0.305  52.1173  25.4070  12.8416
 E6O  H19  H   HCH1  0   0.307  47.6444  24.2701  11.8492
 E6O  H20  H   HNR5  0   0.450  49.8425  25.8534   8.0750
 E6O  H21  H   HCH1  0   0.274  47.5851  27.0685  13.0389
 E6O  N19  N   NC1   0  -0.737  49.0683  24.9040  13.2205
 E6O  CL   CL  CL    0  -0.091  53.9012  24.6814   8.4275
 E6O  H18  H   HNC1  0   0.429  49.4939  25.7024  13.6801

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
 E6O  CL   C26  single    1.722  0.020  1.722
 E6O  N16  N17  single    1.358  0.020  1.358
 E6O  N16  C15  single    1.348  0.020  1.348
 E6O  N17  C13  double    1.274  0.020  1.274
 E6O  O18  C15  double    1.198  0.020  1.198
 E6O  C9   C8   aromatic  1.392  0.020  1.392
 E6O  C9   C3   aromatic  1.384  0.020  1.384
 E6O  C15  O14  single    1.375  0.020  1.375
 E6O  C8   C7   aromatic  1.386  0.020  1.386
 E6O  C26  C25  aromatic  1.384  0.020  1.384
 E6O  C26  C27  aromatic  1.387  0.020  1.387
 E6O  C25  C24  aromatic  1.390  0.020  1.390
 E6O  C4   C3   single    1.504  0.020  1.504
 E6O  C4   C5   single    1.535  0.020  1.535
 E6O  C3   C2   aromatic  1.397  0.020  1.397
 E6O  N31  C29  single    1.333  0.020  1.333
 E6O  C27  C28  aromatic  1.381  0.020  1.381
 E6O  C7   C6   aromatic  1.397  0.020  1.397
 E6O  C13  O14  single    1.346  0.020  1.346
 E6O  C13  C12  single    1.493  0.020  1.493
 E6O  C24  C29  single    1.512  0.020  1.512
 E6O  C24  C23  aromatic  1.391  0.020  1.391
 E6O  C5   C1   single    1.536  0.020  1.536
 E6O  C2   C6   aromatic  1.390  0.020  1.390
 E6O  C2   C1   single    1.508  0.020  1.508
 E6O  C29  O30  double    1.218  0.020  1.218
 E6O  C28  C23  aromatic  1.392  0.020  1.392
 E6O  C6   C10  single    1.512  0.020  1.512
 E6O  C23  S20  single    1.779  0.020  1.779
 E6O  C12  C10  single    1.543  0.020  1.543
 E6O  C12  N19  single    1.452  0.020  1.452
 E6O  O21  S20  double    1.449  0.020  1.449
 E6O  C10  C11  single    1.526  0.020  1.526
 E6O  N19  S20  single    1.646  0.020  1.646
 E6O  S20  O22  double    1.450  0.020  1.450
 E6O  C1   H1   single    0.970  0.020  1.090
 E6O  C1   H2   single    0.970  0.020  1.090
 E6O  C4   H3   single    0.970  0.020  1.090
 E6O  C4   H4   single    0.970  0.020  1.090
 E6O  C5   H5   single    0.970  0.020  1.090
 E6O  C5   H6   single    0.970  0.020  1.090
 E6O  C7   H7   single    0.930  0.020  1.080
 E6O  C8   H8   single    0.930  0.020  1.080
 E6O  C9   H9   single    0.930  0.020  1.080
 E6O  C11  H10  single    0.970  0.020  1.090
 E6O  C11  H11  single    0.970  0.020  1.090
 E6O  C11  H12  single    0.970  0.020  1.090
 E6O  C25  H13  single    0.930  0.020  1.080
 E6O  N31  H14  single    0.860  0.020  1.020
 E6O  N31  H15  single    0.860  0.020  1.020
 E6O  C27  H16  single    0.930  0.020  1.080
 E6O  C28  H17  single    0.930  0.020  1.080
 E6O  N19  H18  single    0.890  0.020  1.040
 E6O  C12  H19  single    0.970  0.020  1.090
 E6O  N16  H20  single    0.860  0.020  1.020
 E6O  C10  H21  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
 E6O  H2   C1   H1   106.67  3.000
 E6O  H2   C1   C5   111.10  3.000
 E6O  H1   C1   C5   112.11  3.000
 E6O  H2   C1   C2   109.76  3.000
 E6O  H1   C1   C2   114.23  3.000
 E6O  C5   C1   C2   103.02  3.000
 E6O  C6   C2   C3   120.75  3.000
 E6O  C6   C2   C1   129.35  3.000
 E6O  C3   C2   C1   109.87  3.000
 E6O  C9   C3   C4   128.57  3.000
 E6O  C4   C3   C2   110.60  3.000
 E6O  C9   C3   C2   120.82  3.000
 E6O  H4   C4   H3   106.87  3.000
 E6O  H4   C4   C5   111.08  3.000
 E6O  H3   C4   C5   112.96  3.000
 E6O  H4   C4   C3   110.03  3.000
 E6O  H3   C4   C3   113.03  3.000
 E6O  C5   C4   C3   102.92  3.000
 E6O  H6   C5   H5   107.44  3.000
 E6O  H6   C5   C4   113.02  3.000
 E6O  H5   C5   C4   109.29  3.000
 E6O  H6   C5   C1   112.73  3.000
 E6O  H5   C5   C1   109.20  3.000
 E6O  C4   C5   C1   105.09  3.000
 E6O  C10  C6   C7   120.17  3.000
 E6O  C10  C6   C2   121.83  3.000
 E6O  C7   C6   C2   117.98  3.000
 E6O  H7   C7   C8   118.67  3.000
 E6O  H7   C7   C6   120.06  3.000
 E6O  C8   C7   C6   121.26  3.000
 E6O  H8   C8   C9   119.92  3.000
 E6O  H8   C8   C7   119.64  3.000
 E6O  C9   C8   C7   120.44  3.000
 E6O  H9   C9   C8   120.37  3.000
 E6O  H9   C9   C3   120.89  3.000
 E6O  C8   C9   C3   118.74  3.000
 E6O  H12  C11  H11  107.89  3.000
 E6O  H12  C11  H10  108.00  3.000
 E6O  H11  C11  H10  107.82  3.000
 E6O  H12  C11  C10  111.59  3.000
 E6O  H11  C11  C10  109.99  3.000
 E6O  H10  C11  C10  111.40  3.000
 E6O  C27  C26  C25  121.30  3.000
 E6O  C27  C26  CL   119.43  3.000
 E6O  C25  C26  CL   119.27  3.000
 E6O  H13  C25  C24  119.91  3.000
 E6O  H13  C25  C26  119.95  3.000
 E6O  C24  C25  C26  120.14  3.000
 E6O  C23  C24  C29  125.51  3.000
 E6O  C23  C24  C25  118.63  3.000
 E6O  C29  C24  C25  115.77  3.000
 E6O  O30  C29  N31  125.65  3.000
 E6O  O30  C29  C24  120.00  3.000
 E6O  N31  C29  C24  114.09  3.000
 E6O  H15  N31  H14  117.98  3.000
 E6O  H15  N31  C29  121.44  3.000
 E6O  H14  N31  C29  120.35  3.000
 E6O  H16  C27  C28  120.33  3.000
 E6O  H16  C27  C26  120.97  3.000
 E6O  C28  C27  C26  118.71  3.000
 E6O  H17  C28  C23  120.85  3.000
 E6O  H17  C28  C27  118.75  3.000
 E6O  C23  C28  C27  120.40  3.000
 E6O  S20  C23  C28  116.34  3.000
 E6O  S20  C23  C24  122.78  3.000
 E6O  C28  C23  C24  120.82  3.000
 E6O  N19  S20  O22  105.54  3.000
 E6O  O22  S20  O21  121.05  3.000
 E6O  N19  S20  O21  107.20  3.000
 E6O  O22  S20  C23  107.96  3.000
 E6O  N19  S20  C23  106.05  3.000
 E6O  O21  S20  C23  108.13  3.000
 E6O  H19  C12  C10  108.77  3.000
 E6O  H19  C12  C13  106.66  3.000
 E6O  C10  C12  C13  111.28  3.000
 E6O  H19  C12  N19  108.52  3.000
 E6O  C10  C12  N19  109.68  3.000
 E6O  C13  C12  N19  111.80  3.000
 E6O  O14  C13  N17  113.04  3.000
 E6O  O14  C13  C12  119.49  3.000
 E6O  N17  C13  C12  127.44  3.000
 E6O  N16  N17  C13  104.35  3.000
 E6O  H20  N16  C15  126.70  3.000
 E6O  H20  N16  N17  120.99  3.000
 E6O  C15  N16  N17  112.30  3.000
 E6O  O14  C15  O18  124.13  3.000
 E6O  O14  C15  N16  103.48  3.000
 E6O  O18  C15  N16  132.38  3.000
 E6O  C15  O14  C13  106.82  3.000
 E6O  H21  C10  C12  107.60  3.000
 E6O  H21  C10  C11  108.05  3.000
 E6O  C12  C10  C11  110.93  3.000
 E6O  H21  C10  C6   108.54  3.000
 E6O  C11  C10  C6   112.50  3.000
 E6O  C12  C10  C6   109.07  3.000
 E6O  H18  N19  C12  116.36  3.000
 E6O  H18  N19  S20  114.00  3.000
 E6O  C12  N19  S20  121.67  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
 E6O  CONST_01  C8   C9   C3   C2     0.00   0.0  0
 E6O  CONST_02  C8   C7   C6   C2     0.00   0.0  0
 E6O  CONST_03  C7   C8   C9   C3     0.00   0.0  0
 E6O  CONST_04  C7   C6   C2   C3     0.00   0.0  0
 E6O  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 E6O  CONST_06  C9   C3   C2   C6     0.00   0.0  0
 E6O  CONST_07  C23  C24  C25  C26    0.00   0.0  0
 E6O  CONST_08  C23  C28  C27  C26    0.00   0.0  0
 E6O  CONST_09  C28  C27  C26  C25    0.00   0.0  0
 E6O  CONST_10  C28  C23  C24  C25    0.00   0.0  0
 E6O  CONST_11  C27  C26  C25  C24    0.00   0.0  0
 E6O  CONST_12  C27  C28  C23  C24    0.00   0.0  0
 E6O  CONST_13  C10  C6   C2   C1     0.00   0.0  0
 E6O  CONST_14  C10  C6   C2   C3   180.00   0.0  0
 E6O  CONST_15  C10  C6   C7   C8   180.00   0.0  0
 E6O  CONST_16  C24  C25  C26  CL   180.00   0.0  0
 E6O  CONST_17  C28  C27  C26  CL   180.00   0.0  0
 E6O  CONST_18  C29  C24  C25  C26  180.00   0.0  0
 E6O  CONST_19  S20  C23  C24  C25  180.00   0.0  0
 E6O  CONST_20  C28  C23  C24  C29  180.00   0.0  0
 E6O  CONST_21  S20  C23  C28  C27  180.00   0.0  0
 E6O  CONST_22  H9   C9   C3   C2   180.00   0.0  0
 E6O  CONST_23  H7   C7   C6   C2   180.00   0.0  0
 E6O  CONST_24  H8   C8   C9   C3   180.00   0.0  0
 E6O  CONST_25  H17  C28  C27  C26  180.00   0.0  0
 E6O  CONST_26  H16  C27  C26  C25  180.00   0.0  0
 E6O  CONST_27  H13  C25  C26  C27  180.00   0.0  0
 E6O  CONST_28  H14  N31  C29  C24  180.00   0.0  0
 E6O  CONST_29  H15  N31  C29  C24    0.00   0.0  0
 E6O  Var_01    C3   C4   C5   C1   -27.67  30.0  1
 E6O  Var_02    C5   C4   C3   C2    17.22  30.0  1
 E6O  Var_03    C4   C5   C1   C2    28.01  30.0  1
 E6O  Var_04    C5   C1   C2   C3   -18.02  30.0  1
 E6O  Var_05    N31  C29  C24  C25  -85.12  30.0  2
 E6O  Var_06    O21  S20  C23  C24    4.04  30.0  2
 E6O  Var_07    C12  N19  S20  C23   65.75  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 E6O  chir_01  C12  C13  C10  N19  positiv
 E6O  chir_02  C10  C11  C12  C6   negativ

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
 E6O  plan-1  C12  0.020
 E6O  plan-1  C13  0.020
 E6O  plan-1  N17  0.020
 E6O  plan-1  N16  0.020
 E6O  plan-1  C15  0.020
 E6O  plan-1  O18  0.020
 E6O  plan-1  O14  0.020
 E6O  plan-1  H20  0.020
 E6O  plan-2  C26  0.020
 E6O  plan-2  C25  0.020
 E6O  plan-2  C24  0.020
 E6O  plan-2  C29  0.020
 E6O  plan-2  C27  0.020
 E6O  plan-2  C28  0.020
 E6O  plan-2  C23  0.020
 E6O  plan-2  S20  0.020
 E6O  plan-2  H13  0.020
 E6O  plan-2  H16  0.020
 E6O  plan-2  H17  0.020
 E6O  plan-2  CL   0.020
 E6O  plan-3  C1   0.020
 E6O  plan-3  C2   0.020
 E6O  plan-3  C3   0.020
 E6O  plan-3  C4   0.020
 E6O  plan-3  C6   0.020
 E6O  plan-3  C7   0.020
 E6O  plan-3  C8   0.020
 E6O  plan-3  C9   0.020
 E6O  plan-3  C10  0.020
 E6O  plan-3  H7   0.020
 E6O  plan-3  H8   0.020
 E6O  plan-3  H9   0.020
 E6O  plan-4  C24  0.020
 E6O  plan-4  C29  0.020
 E6O  plan-4  N31  0.020
 E6O  plan-4  O30  0.020
 E6O  plan-4  H14  0.020
 E6O  plan-4  H15  0.020

