# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 20:24:12 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 1-({5-[4-(methylsulfonyl)phenoxy]-2-pyridin-2-yl-1H-benzimidazol-6-yl}methyl)pyrrolidine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1ccc(Oc2cc3nc([nH]c3cc2CN4C(=O)CCC4=O)c5ccccn5)cc1
#
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
 TK1  TK1  1-({5-[4-(methylsulfonyl)phenoxy]-2-pyridin-2-yl-1H-benzimidazol-6-yl}methyl)pyrrolidine-2,5-dione  ligand  54  34  .  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_TK1
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
 TK1  C1    C  CH3   0  -0.795  -6.3180   0.4500   1.6012
 TK1  C2    C  CR16  0  -0.151   6.9592  -4.0213   0.0904
 TK1  C3    C  CR16  0  -0.315   8.0119  -3.2600   0.5759
 TK1  C4    C  CR16  0  -0.304   5.7596  -3.3958  -0.2058
 TK1  C5    C  CR16  0  -0.341  -1.7184  -0.2375   0.2795
 TK1  C6    C  CR16  0  -0.304  -3.0739   0.0387  -1.7045
 TK1  C7    C  CR16  0  -0.225  -2.8487  -0.6085   0.9909
 TK1  C8    C  CR16  0  -0.218  -4.1938  -0.3444  -0.9964
 TK1  C9    C  CR16  0  -0.070   7.8166  -1.8957   0.7449
 TK1  C10   C  CR16  0  -0.367   2.3947   1.6175  -0.4378
 TK1  C11   C  CR16  0  -0.390   1.1375  -0.7694  -1.3308
 TK1  C12   C  CH2   0  -0.590  -2.2161   2.9515   1.7649
 TK1  C13   C  CH2   0  -0.590  -3.0889   3.0937   0.5263
 TK1  C15   C  CR6   0   0.377  -1.8337   0.0936  -1.0673
 TK1  C16   C  CR6   0  -0.237  -4.0798  -0.6551   0.3559
 TK1  C17   C  CR6   0   0.164   5.6676  -2.0237   0.0001
 TK1  C18   C  CR6   0   0.047   1.0862   1.6412  -0.8904
 TK1  C19   C  CR56  0   0.370   3.0611   0.4009  -0.4401
 TK1  C20   C  CR56  0   0.149   2.4538  -0.7904  -0.8740
 TK1  C21   C  CR6   0   0.277   0.4863   0.4455  -1.3286
 TK1  C22   C  CR5   0   0.459   4.4290  -1.3027  -0.2906
 TK1  C23   C  CR5   0   0.555  -0.8068   2.8649   1.2384
 TK1  C24   C  CR5   0   0.556  -2.1244   3.1768  -0.6281
 TK1  N25   N  NR15  0  -0.707   4.3232   0.0316  -0.0745
 TK1  N26   N  N     0  -0.440   6.6738  -1.2876   0.4654
 TK1  N27   N  N     0  -0.478   3.3329  -1.8333  -0.7690
 TK1  N28   N  NR5   0  -0.519  -0.8491   2.9794  -0.1356
 TK1  O30   O  O     0  -0.426  -2.3860   3.3754  -1.7881
 TK1  O31   O  OS    0  -0.668  -5.1045  -1.6896   2.5401
 TK1  O32   O  OS    0  -0.669  -6.3976  -1.8861   0.3919
 TK1  S34   S  S     0   1.218  -5.5249  -1.1068   1.2675
 TK1  H1    H  HCH3  0   0.295  -6.5882   0.9287   0.6628
 TK1  H1A   H  HCH3  0   0.316  -7.2155   0.2407   2.1827
 TK1  H1B   H  HCH3  0   0.290  -5.6445   1.0845   2.1731
 TK1  H2    H  HCR6  0   0.281   7.0704  -5.0872  -0.0562
 TK1  H3    H  HCR6  0   0.279   8.9648  -3.7076   0.8211
 TK1  H4    H  HCR6  0   0.275   4.9126  -3.9499  -0.5856
 TK1  H5    H  HCR6  0   0.303  -0.7628  -0.2194   0.7862
 TK1  H6    H  HCR6  0   0.288  -3.1522   0.2915  -2.7534
 TK1  H7    H  HCR6  0   0.296  -2.7520  -0.8551   2.0395
 TK1  H8    H  HCR6  0   0.291  -5.1486  -0.3931  -1.5032
 TK1  H9    H  HCR6  0   0.271   8.6180  -1.2701   1.1206
 TK1  H10   H  HCR6  0   0.274   2.8734   2.5255  -0.0950
 TK1  H11   H  HCR6  0   0.279   0.6483  -1.6687  -1.6831
 TK1  H12   H  HCH2  0   0.309  -2.2892   3.8120   2.4312
 TK1  H12A  H  HCH2  0   0.295  -2.4407   2.0668   2.3606
 TK1  H13   H  HCH2  0   0.287  -3.7466   2.2369   0.3683
 TK1  H13A  H  HCH2  0   0.310  -3.7209   3.9810   0.5413
 TK1  H14   H  HCH2  0   0.293   1.0080   3.7591  -0.6474
 TK1  H14A  H  HCH2  0   0.292   0.0350   3.1693  -1.9792
 TK1  HN25  H  HNR5  0   0.422   5.0598   0.6197   0.2851
 TK1  O33   O  O2    0  -0.502  -0.7981   0.5107  -1.8273
 TK1  C14   C  CH2   0  -0.393   0.3453   2.9510  -0.9577
 TK1  O29   O  O     0  -0.420   0.2115   2.7337   1.8709

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
 TK1  C1   S34   single    1.779  0.020  1.779
 TK1  C2   C3    aromatic  1.387  0.020  1.387
 TK1  C2   C4    aromatic  1.385  0.020  1.385
 TK1  C3   C9    aromatic  1.389  0.020  1.389
 TK1  C4   C17   aromatic  1.390  0.020  1.390
 TK1  C5   C7    aromatic  1.386  0.020  1.386
 TK1  C5   C15   aromatic  1.392  0.020  1.392
 TK1  C6   C8    aromatic  1.379  0.020  1.379
 TK1  C6   C15   aromatic  1.395  0.020  1.395
 TK1  C7   C16   aromatic  1.386  0.020  1.386
 TK1  C8   C16   aromatic  1.392  0.020  1.392
 TK1  C9   N26   aromatic  1.324  0.020  1.324
 TK1  C10  C18   aromatic  1.385  0.020  1.385
 TK1  C10  C19   aromatic  1.387  0.020  1.387
 TK1  C11  C20   aromatic  1.393  0.020  1.393
 TK1  C11  C21   aromatic  1.378  0.020  1.378
 TK1  C12  C13   single    1.522  0.020  1.522
 TK1  C12  C23   single    1.507  0.020  1.507
 TK1  C13  C24   single    1.507  0.020  1.507
 TK1  C14  C18   single    1.506  0.020  1.506
 TK1  C14  N28   single    1.450  0.020  1.450
 TK1  C15  O33   single    1.351  0.020  1.351
 TK1  C16  S34   single    1.767  0.020  1.767
 TK1  C17  C22   single    1.462  0.020  1.462
 TK1  C17  N26   aromatic  1.331  0.020  1.331
 TK1  C18  C21   aromatic  1.408  0.020  1.408
 TK1  C19  C20   aromatic  1.406  0.020  1.406
 TK1  C19  N25   aromatic  1.365  0.020  1.365
 TK1  C20  N27   aromatic  1.368  0.020  1.368
 TK1  C21  O33   single    1.379  0.020  1.379
 TK1  C22  N25   aromatic  1.356  0.020  1.356
 TK1  C22  N27   aromatic  1.308  0.020  1.308
 TK1  C23  N28   single    1.379  0.020  1.379
 TK1  C23  O29   double    1.206  0.020  1.206
 TK1  C24  N28   single    1.381  0.020  1.381
 TK1  C24  O30   double    1.206  0.020  1.206
 TK1  O31  S34   double    1.461  0.020  1.461
 TK1  O32  S34   double    1.461  0.020  1.461
 TK1  C1   H1    single    0.970  0.020  1.090
 TK1  C1   H1A   single    0.970  0.020  1.090
 TK1  C1   H1B   single    0.970  0.020  1.090
 TK1  C2   H2    single    0.930  0.020  1.080
 TK1  C3   H3    single    0.930  0.020  1.080
 TK1  C4   H4    single    0.930  0.020  1.080
 TK1  C5   H5    single    0.930  0.020  1.080
 TK1  C6   H6    single    0.930  0.020  1.080
 TK1  C7   H7    single    0.930  0.020  1.080
 TK1  C8   H8    single    0.930  0.020  1.080
 TK1  C9   H9    single    0.930  0.020  1.080
 TK1  C10  H10   single    0.930  0.020  1.080
 TK1  C11  H11   single    0.930  0.020  1.080
 TK1  C12  H12   single    0.970  0.020  1.090
 TK1  C12  H12A  single    0.970  0.020  1.090
 TK1  C13  H13   single    0.970  0.020  1.090
 TK1  C13  H13A  single    0.970  0.020  1.090
 TK1  C14  H14   single    0.970  0.020  1.090
 TK1  C14  H14A  single    0.970  0.020  1.090
 TK1  N25  HN25  single    0.860  0.020  1.020

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
 TK1  H1B   C1   H1A  109.96  3.000
 TK1  H1B   C1   H1   110.53  3.000
 TK1  H1A   C1   H1   109.89  3.000
 TK1  H1B   C1   S34  109.46  3.000
 TK1  H1A   C1   S34  107.41  3.000
 TK1  H1    C1   S34  109.52  3.000
 TK1  H2    C2   C4   120.35  3.000
 TK1  H2    C2   C3   120.68  3.000
 TK1  C4    C2   C3   118.97  3.000
 TK1  H3    C3   C9   120.21  3.000
 TK1  H3    C3   C2   121.41  3.000
 TK1  C9    C3   C2   118.37  3.000
 TK1  H4    C4   C17  120.40  3.000
 TK1  H4    C4   C2   121.48  3.000
 TK1  C17   C4   C2   118.12  3.000
 TK1  H5    C5   C15  121.50  3.000
 TK1  H5    C5   C7   118.98  3.000
 TK1  C15   C5   C7   119.52  3.000
 TK1  H6    C6   C15  119.86  3.000
 TK1  H6    C6   C8   120.26  3.000
 TK1  C15   C6   C8   119.88  3.000
 TK1  H7    C7   C16  121.06  3.000
 TK1  H7    C7   C5   119.06  3.000
 TK1  C16   C7   C5   119.88  3.000
 TK1  H8    C8   C16  121.14  3.000
 TK1  H8    C8   C6   119.25  3.000
 TK1  C16   C8   C6   119.61  3.000
 TK1  H9    C9   N26  116.50  3.000
 TK1  H9    C9   C3   120.35  3.000
 TK1  N26   C9   C3   123.15  3.000
 TK1  H10   C10  C19  121.60  3.000
 TK1  H10   C10  C18  120.47  3.000
 TK1  C19   C10  C18  117.93  3.000
 TK1  H11   C11  C21  121.27  3.000
 TK1  H11   C11  C20  121.40  3.000
 TK1  C21   C11  C20  117.33  3.000
 TK1  H12A  C12  H12  107.02  3.000
 TK1  H12A  C12  C23  109.69  3.000
 TK1  H12   C12  C23  108.75  3.000
 TK1  H12A  C12  C13  113.73  3.000
 TK1  H12   C12  C13  112.65  3.000
 TK1  C23   C12  C13  104.91  3.000
 TK1  H13A  C13  H13  106.96  3.000
 TK1  H13A  C13  C24  109.69  3.000
 TK1  H13   C13  C24  108.55  3.000
 TK1  H13A  C13  C12  113.42  3.000
 TK1  H13   C13  C12  112.96  3.000
 TK1  C24   C13  C12  105.17  3.000
 TK1  O33   C15  C6   115.89  3.000
 TK1  O33   C15  C5   123.68  3.000
 TK1  C6    C15  C5   120.41  3.000
 TK1  S34   C16  C8   119.41  3.000
 TK1  S34   C16  C7   119.90  3.000
 TK1  C8    C16  C7   120.68  3.000
 TK1  N26   C17  C22  115.93  3.000
 TK1  N26   C17  C4   123.20  3.000
 TK1  C22   C17  C4   120.87  3.000
 TK1  C21   C18  C14  121.00  3.000
 TK1  C21   C18  C10  119.33  3.000
 TK1  C14   C18  C10  119.62  3.000
 TK1  N25   C19  C20  104.65  3.000
 TK1  N25   C19  C10  132.93  3.000
 TK1  C20   C19  C10  122.43  3.000
 TK1  N27   C20  C19  110.17  3.000
 TK1  N27   C20  C11  130.07  3.000
 TK1  C19   C20  C11  119.77  3.000
 TK1  O33   C21  C18  117.98  3.000
 TK1  O33   C21  C11  118.75  3.000
 TK1  C18   C21  C11  123.21  3.000
 TK1  N27   C22  N25  113.07  3.000
 TK1  N27   C22  C17  125.62  3.000
 TK1  N25   C22  C17  121.31  3.000
 TK1  O29   C23  N28  123.88  3.000
 TK1  O29   C23  C12  127.79  3.000
 TK1  N28   C23  C12  108.33  3.000
 TK1  O30   C24  N28  124.53  3.000
 TK1  O30   C24  C13  127.41  3.000
 TK1  N28   C24  C13  108.06  3.000
 TK1  HN25  N25  C22  124.99  3.000
 TK1  HN25  N25  C19  127.80  3.000
 TK1  C22   N25  C19  107.20  3.000
 TK1  C17   N26  C9   118.18  3.000
 TK1  C22   N27  C20  104.91  3.000
 TK1  C24   N28  C23  113.29  3.000
 TK1  C24   N28  C14  124.13  3.000
 TK1  C23   N28  C14  122.53  3.000
 TK1  O32   S34  O31  118.74  3.000
 TK1  O32   S34  C16  108.39  3.000
 TK1  O31   S34  C16  108.41  3.000
 TK1  O32   S34  C1   108.24  3.000
 TK1  O31   S34  C1   108.30  3.000
 TK1  C16   S34  C1   103.75  3.000
 TK1  C21   O33  C15  119.74  3.000
 TK1  H14A  C14  H14  106.94  3.000
 TK1  H14A  C14  N28  107.04  3.000
 TK1  H14   C14  N28  108.95  3.000
 TK1  H14A  C14  C18  110.86  3.000
 TK1  H14   C14  C18  109.44  3.000
 TK1  N28   C14  C18  113.38  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
 TK1  CONST_01  N26   C9   C3   C2      0.00   0.0  0
 TK1  CONST_02  C22   C17  C4   C2    180.00   0.0  0
 TK1  CONST_03  N26   C17  C4   C2      0.00   0.0  0
 TK1  CONST_04  C17   C4   C2   C3      0.00   0.0  0
 TK1  CONST_05  C17   N26  C9   C3      0.00   0.0  0
 TK1  CONST_06  C9    C3   C2   C4      0.00   0.0  0
 TK1  CONST_07  N25   C22  C17  C4    180.00   0.0  0
 TK1  CONST_08  N27   C22  C17  C4      0.00   0.0  0
 TK1  CONST_09  C9    N26  C17  C4      0.00   0.0  0
 TK1  CONST_10  C8    C16  C7   C5      0.00   0.0  0
 TK1  CONST_11  C8    C6   C15  C5      0.00   0.0  0
 TK1  CONST_12  C7    C16  C8   C6      0.00   0.0  0
 TK1  CONST_13  C7    C5   C15  C6      0.00   0.0  0
 TK1  CONST_14  C22   C17  N26  C9    180.00   0.0  0
 TK1  CONST_15  C11   C21  C18  C10     0.00   0.0  0
 TK1  CONST_16  C11   C20  C19  C10     0.00   0.0  0
 TK1  CONST_17  N27   C20  C19  C10   180.00   0.0  0
 TK1  CONST_18  C22   N25  C19  C10   180.00   0.0  0
 TK1  CONST_19  N25   C19  C20  C11   180.00   0.0  0
 TK1  CONST_20  C22   N27  C20  C11   180.00   0.0  0
 TK1  CONST_21  C16   C7   C5   C15     0.00   0.0  0
 TK1  CONST_22  C16   C8   C6   C15     0.00   0.0  0
 TK1  CONST_23  C19   N25  C22  C17   180.00   0.0  0
 TK1  CONST_24  C20   N27  C22  C17   180.00   0.0  0
 TK1  CONST_25  C20   C19  C10  C18     0.00   0.0  0
 TK1  CONST_26  N25   C19  C10  C18   180.00   0.0  0
 TK1  CONST_27  C20   C11  C21  C18     0.00   0.0  0
 TK1  CONST_28  C21   C18  C10  C19     0.00   0.0  0
 TK1  CONST_29  C21   C11  C20  C19     0.00   0.0  0
 TK1  CONST_30  C22   N27  C20  C19     0.00   0.0  0
 TK1  CONST_31  N27   C22  N25  C19     0.00   0.0  0
 TK1  CONST_32  C22   N25  C19  C20     0.00   0.0  0
 TK1  CONST_33  N25   C22  N27  C20     0.00   0.0  0
 TK1  CONST_34  N27   C20  C11  C21   180.00   0.0  0
 TK1  CONST_35  N27   C20  C19  N25     0.00   0.0  0
 TK1  CONST_36  N26   C17  C22  N25     0.00   0.0  0
 TK1  CONST_37  N27   C22  C17  N26   180.00   0.0  0
 TK1  CONST_38  C24   N28  C23  C12     0.00   0.0  0
 TK1  CONST_39  S34   C16  C7   C5    180.00   0.0  0
 TK1  CONST_40  S34   C16  C8   C6    180.00   0.0  0
 TK1  CONST_41  O33   C15  C5   C7    180.00   0.0  0
 TK1  CONST_42  O33   C15  C6   C8    180.00   0.0  0
 TK1  CONST_43  O33   C21  C18  C10   180.00   0.0  0
 TK1  CONST_44  C14   C18  C21  C11   180.00   0.0  0
 TK1  CONST_45  C19   C10  C18  C14   180.00   0.0  0
 TK1  CONST_46  O33   C21  C11  C20   180.00   0.0  0
 TK1  CONST_47  C14   N28  C23  C12   180.00   0.0  0
 TK1  CONST_48  O29   C23  N28  C24   180.00   0.0  0
 TK1  CONST_49  H9    C9   C3   C2    180.00   0.0  0
 TK1  CONST_50  H4    C4   C2   C3    180.00   0.0  0
 TK1  CONST_51  H3    C3   C2   C4    180.00   0.0  0
 TK1  CONST_52  H6    C6   C15  C5    180.00   0.0  0
 TK1  CONST_53  H5    C5   C15  C6    180.00   0.0  0
 TK1  CONST_54  H8    C8   C16  C7    180.00   0.0  0
 TK1  CONST_55  H7    C7   C16  C8    180.00   0.0  0
 TK1  CONST_56  H2    C2   C3   C9    180.00   0.0  0
 TK1  CONST_57  HN25  N25  C19  C10     0.00   0.0  0
 TK1  CONST_58  H11   C11  C21  C18   180.00   0.0  0
 TK1  CONST_59  H10   C10  C19  C20   180.00   0.0  0
 TK1  CONST_60  O29   C23  N28  C14     0.00   0.0  0
 TK1  Var_01    N28   C24  C13  C12     5.00  30.0  1
 TK1  Var_02    N28   C23  C12  C13     1.45  30.0  1
 TK1  Var_03    C23   N28  C24  C13    -4.40  30.0  1
 TK1  Var_04    C24   C13  C12  C23    -3.83  30.0  1
 TK1  Var_05    N28   C14  C18  C10  -119.85  30.0  3
 TK1  Var_06    C18   C21  O33  C15  -103.67  30.0  1
 TK1  Var_07    C7    C16  S34  C1    101.10  30.0  2
 TK1  Var_08    H1    C1   S34  C16    61.71  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
 TK1  plan-1  C2    0.020
 TK1  plan-1  C3    0.020
 TK1  plan-1  C4    0.020
 TK1  plan-1  C9    0.020
 TK1  plan-1  C17   0.020
 TK1  plan-1  C22   0.020
 TK1  plan-1  N26   0.020
 TK1  plan-1  H2    0.020
 TK1  plan-1  H3    0.020
 TK1  plan-1  H4    0.020
 TK1  plan-1  H9    0.020
 TK1  plan-2  C5    0.020
 TK1  plan-2  C6    0.020
 TK1  plan-2  C7    0.020
 TK1  plan-2  C8    0.020
 TK1  plan-2  C15   0.020
 TK1  plan-2  C16   0.020
 TK1  plan-2  S34   0.020
 TK1  plan-2  H5    0.020
 TK1  plan-2  H6    0.020
 TK1  plan-2  H7    0.020
 TK1  plan-2  H8    0.020
 TK1  plan-2  O33   0.020
 TK1  plan-3  C10   0.020
 TK1  plan-3  C11   0.020
 TK1  plan-3  C17   0.020
 TK1  plan-3  C18   0.020
 TK1  plan-3  C19   0.020
 TK1  plan-3  C20   0.020
 TK1  plan-3  C21   0.020
 TK1  plan-3  C22   0.020
 TK1  plan-3  N25   0.020
 TK1  plan-3  N27   0.020
 TK1  plan-3  H10   0.020
 TK1  plan-3  H11   0.020
 TK1  plan-3  HN25  0.020
 TK1  plan-3  O33   0.020
 TK1  plan-3  C14   0.020
 TK1  plan-4  C12   0.020
 TK1  plan-4  C23   0.020
 TK1  plan-4  C24   0.020
 TK1  plan-4  N28   0.020
 TK1  plan-4  C14   0.020
 TK1  plan-4  O29   0.020
 TK1  plan-5  C13   0.020
 TK1  plan-5  C24   0.020
 TK1  plan-5  N28   0.020
 TK1  plan-5  O30   0.020

