# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:21:43 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-cyclopentyl-2-[4-(trifluoromethyl)phenyl]-3H-benzimidazole-4-sulfonamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1ccc(cc1)c2[nH]c3c(cccc3[S](=O)(=O)NC4CCCC4)n2
#
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
 SZC  SZC  N-cyclopentyl-2-[4-(trifluoromethyl)phenyl]-3H-benzimidazole-4-sulfonamide  ligand  46  28  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SZC
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
 SZC  C1    C  CR16  0  -0.260   3.1738  -2.6411   1.4089
 SZC  C2    C  CR16  0  -0.270  -3.2460  -1.3133   0.8938
 SZC  C3    C  CR16  0  -0.291  -2.6382   0.2397  -0.8355
 SZC  C4    C  CR16  0  -0.259  -4.5764  -0.9691   0.7388
 SZC  C5    C  CR16  0  -0.250  -3.9688   0.5849  -0.9937
 SZC  C6    C  CR16  0  -0.319   1.8496  -2.7204   1.7988
 SZC  C7    C  CR16  0  -0.272   3.5705  -1.8435   0.3302
 SZC  C8    C  CR6   0   0.025  -2.2621  -0.7138   0.1088
 SZC  C9    C  CR6   0  -0.202  -4.9425  -0.0197  -0.2084
 SZC  C10   C  CR56  0   0.164   0.9047  -1.9948   1.0762
 SZC  C11   C  CR56  0   0.405   1.3031  -1.1993  -0.0126
 SZC  C12   C  CR6   0  -0.265   2.6417  -1.1092  -0.3882
 SZC  C13   C  CR5   0   0.494  -0.8673  -1.0987   0.3057
 SZC  C14   C  CH2   0  -0.454   5.0134   3.4134   1.6459
 SZC  C15   C  CH2   0  -0.451   4.1898   2.4218   2.5075
 SZC  C16   C  CH2   0  -0.432   4.5572   3.1955   0.1993
 SZC  C17   C  CH2   0  -0.441   3.2670   1.6851   1.5321
 SZC  C18   C  CR15  0  -0.104   4.0103   1.7700   0.1985
 SZC  C19   C  CT    0   1.055  -6.3718   0.3998  -0.3536
 SZC  N20   N  N     0  -0.467  -0.4496  -1.9053   1.2436
 SZC  N21   N  NR15  0  -0.738   0.1516  -0.6414  -0.4787
 SZC  N22   N  NC1   0  -0.726   3.1966   1.5026  -0.9829
 SZC  O23   O  OS    0  -0.645   4.5040  -0.3461  -2.0350
 SZC  O24   O  OS    0  -0.663   2.0928   0.0571  -2.6543
 SZC  F25   F  F     0  -0.313  -6.6268   1.5172   0.3443
 SZC  F26   F  F     0  -0.307  -6.6905   0.6622  -1.6262
 SZC  F27   F  F     0  -0.303  -7.2241  -0.5320   0.0827
 SZC  S28   S  S     0   1.368   3.1500   0.0102  -1.6526
 SZC  H1    H  HCR6  0   0.272   3.9257  -3.2020   1.9462
 SZC  H2    H  HCR6  0   0.271  -2.9696  -2.0551   1.6300
 SZC  H3    H  HCR6  0   0.261  -1.9084   0.7372  -1.4603
 SZC  H4    H  HCR6  0   0.280  -5.3158  -1.4527   1.3621
 SZC  H5    H  HCR6  0   0.283  -4.2282   1.3283  -1.7355
 SZC  H6    H  HCR6  0   0.274   1.5502  -3.3309   2.6404
 SZC  H7    H  HCR6  0   0.286   4.6168  -1.8021   0.0606
 SZC  H14A  H  HCH2  0   0.234   6.0795   3.2045   1.7440
 SZC  H15   H  HCH2  0   0.234   4.8526   1.7137   3.0066
 SZC  H15A  H  HCH2  0   0.238   3.6245   2.9260   3.2907
 SZC  H16   H  HCH2  0   0.230   3.7471   3.8845  -0.0578
 SZC  H16A  H  HCH2  0   0.247   5.3518   3.3372  -0.5332
 SZC  H17   H  HCH2  0   0.246   3.0446   0.6629   1.8406
 SZC  H17A  H  HCH2  0   0.229   2.3120   2.2112   1.4336
 SZC  H18   H  HCR5  0   0.265   4.8506   1.0692   0.1980
 SZC  HN21  H  HNR5  0   0.426   0.0682  -0.0697  -1.3049
 SZC  HN22  H  HNC1  0   0.409   2.2934   1.9647  -0.9851
 SZC  H14   H  HCH2  0   0.237   4.8676   4.4475   1.9574

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
 SZC  C1   C6    aromatic  1.383  0.020  1.383
 SZC  C1   C7    aromatic  1.399  0.020  1.399
 SZC  C2   C4    aromatic  1.383  0.020  1.383
 SZC  C2   C8    aromatic  1.394  0.020  1.394
 SZC  C3   C5    aromatic  1.384  0.020  1.384
 SZC  C3   C8    aromatic  1.394  0.020  1.394
 SZC  C4   C9    aromatic  1.390  0.020  1.390
 SZC  C5   C9    aromatic  1.389  0.020  1.389
 SZC  C6   C10   aromatic  1.393  0.020  1.393
 SZC  C7   C12   aromatic  1.385  0.020  1.385
 SZC  C8   C13   single    1.460  0.020  1.460
 SZC  C9   C19   single    1.497  0.020  1.497
 SZC  C10  C11   aromatic  1.406  0.020  1.406
 SZC  C10  N20   aromatic  1.368  0.020  1.368
 SZC  C11  C12   aromatic  1.393  0.020  1.393
 SZC  C11  N21   aromatic  1.362  0.020  1.362
 SZC  C12  S28   single    1.764  0.020  1.764
 SZC  C13  N20   aromatic  1.306  0.020  1.306
 SZC  C13  N21   aromatic  1.365  0.020  1.365
 SZC  C14  C15   single    1.550  0.020  1.550
 SZC  C14  C16   single    1.532  0.020  1.532
 SZC  C15  C17   single    1.532  0.020  1.532
 SZC  C16  C18   single    1.527  0.020  1.527
 SZC  C17  C18   single    1.529  0.020  1.529
 SZC  C18  N22   single    1.459  0.020  1.459
 SZC  C19  F25   single    1.342  0.020  1.342
 SZC  C19  F26   single    1.338  0.020  1.338
 SZC  C19  F27   single    1.336  0.020  1.336
 SZC  N22  S28   single    1.636  0.020  1.636
 SZC  O23  S28   double    1.451  0.020  1.451
 SZC  O24  S28   double    1.457  0.020  1.457
 SZC  C1   H1    single    0.930  0.020  1.080
 SZC  C2   H2    single    0.930  0.020  1.080
 SZC  C3   H3    single    0.930  0.020  1.080
 SZC  C4   H4    single    0.930  0.020  1.080
 SZC  C5   H5    single    0.930  0.020  1.080
 SZC  C6   H6    single    0.930  0.020  1.080
 SZC  C7   H7    single    0.930  0.020  1.080
 SZC  C14  H14   single    0.970  0.020  1.090
 SZC  C14  H14A  single    0.970  0.020  1.090
 SZC  C15  H15   single    0.970  0.020  1.090
 SZC  C15  H15A  single    0.970  0.020  1.090
 SZC  C16  H16   single    0.970  0.020  1.090
 SZC  C16  H16A  single    0.970  0.020  1.090
 SZC  C17  H17   single    0.970  0.020  1.090
 SZC  C17  H17A  single    0.970  0.020  1.090
 SZC  C18  H18   single    0.970  0.020  1.090
 SZC  N21  HN21  single    0.860  0.020  1.020
 SZC  N22  HN22  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
 SZC  H1    C1   C7   118.80  3.000
 SZC  H1    C1   C6   119.75  3.000
 SZC  C7    C1   C6   121.45  3.000
 SZC  H2    C2   C8   119.87  3.000
 SZC  H2    C2   C4   119.55  3.000
 SZC  C8    C2   C4   120.58  3.000
 SZC  H3    C3   C8   121.59  3.000
 SZC  H3    C3   C5   117.90  3.000
 SZC  C8    C3   C5   120.51  3.000
 SZC  H4    C4   C9   121.21  3.000
 SZC  H4    C4   C2   118.81  3.000
 SZC  C9    C4   C2   119.99  3.000
 SZC  H5    C5   C9   121.24  3.000
 SZC  H5    C5   C3   118.72  3.000
 SZC  C9    C5   C3   120.04  3.000
 SZC  H6    C6   C10  120.63  3.000
 SZC  H6    C6   C1   121.12  3.000
 SZC  C10   C6   C1   118.25  3.000
 SZC  H7    C7   C12  119.95  3.000
 SZC  H7    C7   C1   119.24  3.000
 SZC  C12   C7   C1   120.81  3.000
 SZC  C13   C8   C3   121.97  3.000
 SZC  C13   C8   C2   119.00  3.000
 SZC  C3    C8   C2   119.03  3.000
 SZC  C19   C9   C5   119.50  3.000
 SZC  C19   C9   C4   120.60  3.000
 SZC  C5    C9   C4   119.85  3.000
 SZC  N20   C10  C11  109.78  3.000
 SZC  N20   C10  C6   129.95  3.000
 SZC  C11   C10  C6   120.27  3.000
 SZC  N21   C11  C12  133.92  3.000
 SZC  N21   C11  C10  104.91  3.000
 SZC  C12   C11  C10  121.17  3.000
 SZC  S28   C12  C11  120.75  3.000
 SZC  S28   C12  C7   121.01  3.000
 SZC  C11   C12  C7   118.05  3.000
 SZC  N21   C13  N20  112.40  3.000
 SZC  N21   C13  C8   123.18  3.000
 SZC  N20   C13  C8   124.42  3.000
 SZC  H14A  C14  H14  106.66  3.000
 SZC  H14A  C14  C16  110.41  3.000
 SZC  H14   C14  C16  111.40  3.000
 SZC  H14A  C14  C15  110.29  3.000
 SZC  H14   C14  C15  112.15  3.000
 SZC  C16   C14  C15  105.99  3.000
 SZC  H15A  C15  H15  106.66  3.000
 SZC  H15A  C15  C17  111.58  3.000
 SZC  H15   C15  C17  110.20  3.000
 SZC  H15A  C15  C14  112.28  3.000
 SZC  H15   C15  C14  110.28  3.000
 SZC  C17   C15  C14  105.89  3.000
 SZC  H16A  C16  H16  107.46  3.000
 SZC  H16A  C16  C18  112.46  3.000
 SZC  H16   C16  C18  108.82  3.000
 SZC  H16A  C16  C14  113.51  3.000
 SZC  H16   C16  C14  110.66  3.000
 SZC  C18   C16  C14  103.88  3.000
 SZC  H17A  C17  H17  107.33  3.000
 SZC  H17A  C17  C18  108.59  3.000
 SZC  H17   C17  C18  113.45  3.000
 SZC  H17A  C17  C15  110.59  3.000
 SZC  H17   C17  C15  113.18  3.000
 SZC  C18   C17  C15  103.64  3.000
 SZC  H18   C18  N22  108.09  3.000
 SZC  H18   C18  C17  109.76  3.000
 SZC  N22   C18  C17  115.14  3.000
 SZC  H18   C18  C16  108.84  3.000
 SZC  N22   C18  C16  111.79  3.000
 SZC  C17   C18  C16  103.03  3.000
 SZC  F27   C19  F26  107.18  3.000
 SZC  F27   C19  F25  106.84  3.000
 SZC  F26   C19  F25  106.62  3.000
 SZC  F27   C19  C9   112.46  3.000
 SZC  F26   C19  C9   112.01  3.000
 SZC  F25   C19  C9   111.37  3.000
 SZC  C13   N20  C10  105.62  3.000
 SZC  HN21  N21  C13  126.81  3.000
 SZC  HN21  N21  C11  125.65  3.000
 SZC  C13   N21  C11  107.29  3.000
 SZC  HN22  N22  S28  112.90  3.000
 SZC  HN22  N22  C18  114.50  3.000
 SZC  S28   N22  C18  120.95  3.000
 SZC  O24   S28  O23  120.24  3.000
 SZC  O24   S28  N22  105.82  3.000
 SZC  O23   S28  N22  107.77  3.000
 SZC  O24   S28  C12  107.71  3.000
 SZC  O23   S28  C12  107.57  3.000
 SZC  N22   S28  C12  107.08  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
 SZC  CONST_01  C11   C10  C6   C1     0.00   0.0  0
 SZC  CONST_02  N20   C10  C6   C1   180.00   0.0  0
 SZC  CONST_03  C11   C12  C7   C1     0.00   0.0  0
 SZC  CONST_04  C5    C9   C4   C2     0.00   0.0  0
 SZC  CONST_05  C5    C3   C8   C2     0.00   0.0  0
 SZC  CONST_06  N20   C13  C8   C2     0.00   0.0  0
 SZC  CONST_07  N21   C13  C8   C2   180.00   0.0  0
 SZC  CONST_08  C4    C9   C5   C3     0.00   0.0  0
 SZC  CONST_09  C4    C2   C8   C3     0.00   0.0  0
 SZC  CONST_10  N20   C13  C8   C3   180.00   0.0  0
 SZC  CONST_11  N21   C13  C8   C3     0.00   0.0  0
 SZC  CONST_12  C13   C8   C2   C4   180.00   0.0  0
 SZC  CONST_13  C13   C8   C3   C5   180.00   0.0  0
 SZC  CONST_14  C12   C7   C1   C6     0.00   0.0  0
 SZC  CONST_15  C12   C11  C10  C6     0.00   0.0  0
 SZC  CONST_16  N21   C11  C10  C6   180.00   0.0  0
 SZC  CONST_17  C13   N20  C10  C6   180.00   0.0  0
 SZC  CONST_18  C10   C6   C1   C7     0.00   0.0  0
 SZC  CONST_19  C10   C11  C12  C7     0.00   0.0  0
 SZC  CONST_20  N21   C11  C12  C7   180.00   0.0  0
 SZC  CONST_21  C9    C4   C2   C8     0.00   0.0  0
 SZC  CONST_22  C9    C5   C3   C8     0.00   0.0  0
 SZC  CONST_23  C10   N20  C13  C8   180.00   0.0  0
 SZC  CONST_24  C11   N21  C13  C8   180.00   0.0  0
 SZC  CONST_25  C13   N21  C11  C10    0.00   0.0  0
 SZC  CONST_26  N21   C13  N20  C10    0.00   0.0  0
 SZC  CONST_27  C13   N20  C10  C11    0.00   0.0  0
 SZC  CONST_28  N20   C13  N21  C11    0.00   0.0  0
 SZC  CONST_29  N20   C10  C11  C12  180.00   0.0  0
 SZC  CONST_30  C13   N21  C11  C12  180.00   0.0  0
 SZC  CONST_31  N21   C11  C10  N20    0.00   0.0  0
 SZC  CONST_32  S28   C12  C7   C1   180.00   0.0  0
 SZC  CONST_33  C19   C9   C4   C2   180.00   0.0  0
 SZC  CONST_34  C19   C9   C5   C3   180.00   0.0  0
 SZC  CONST_35  S28   C12  C11  C10  180.00   0.0  0
 SZC  CONST_36  S28   C12  C11  N21    0.00   0.0  0
 SZC  CONST_37  H3    C3   C8   C2   180.00   0.0  0
 SZC  CONST_38  H2    C2   C8   C3   180.00   0.0  0
 SZC  CONST_39  H5    C5   C9   C4   180.00   0.0  0
 SZC  CONST_40  H4    C4   C9   C5   180.00   0.0  0
 SZC  CONST_41  H7    C7   C1   C6   180.00   0.0  0
 SZC  CONST_42  H6    C6   C1   C7   180.00   0.0  0
 SZC  CONST_43  HN21  N21  C13  C8     0.00   0.0  0
 SZC  CONST_44  H1    C1   C6   C10  180.00   0.0  0
 SZC  Var_01    C18   C17  C15  C14   25.59  30.0  1
 SZC  Var_02    C18   C16  C14  C15  -23.91  30.0  1
 SZC  Var_03    C17   C15  C14  C16   -1.08  30.0  1
 SZC  Var_04    F25   C19  C9   C4    95.65  30.0  2
 SZC  Var_05    N22   S28  C12  C7   -97.07  30.0  2
 SZC  Var_06    C18   N22  S28  C12   56.33  30.0  2

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
 SZC  chir_01  C18  C16  C17  N22  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
 SZC  plan-1  C2    0.020
 SZC  plan-1  C3    0.020
 SZC  plan-1  C4    0.020
 SZC  plan-1  C5    0.020
 SZC  plan-1  C8    0.020
 SZC  plan-1  C9    0.020
 SZC  plan-1  C13   0.020
 SZC  plan-1  C19   0.020
 SZC  plan-1  H2    0.020
 SZC  plan-1  H3    0.020
 SZC  plan-1  H4    0.020
 SZC  plan-1  H5    0.020
 SZC  plan-2  C1    0.020
 SZC  plan-2  C6    0.020
 SZC  plan-2  C7    0.020
 SZC  plan-2  C8    0.020
 SZC  plan-2  C10   0.020
 SZC  plan-2  C11   0.020
 SZC  plan-2  C12   0.020
 SZC  plan-2  C13   0.020
 SZC  plan-2  N20   0.020
 SZC  plan-2  N21   0.020
 SZC  plan-2  S28   0.020
 SZC  plan-2  H1    0.020
 SZC  plan-2  H6    0.020
 SZC  plan-2  H7    0.020
 SZC  plan-2  HN21  0.020

