# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 23:43:04 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: (2Z)-2-[(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)methylidene]-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cccc2C(=O)/C(Oc12)=C/c3ccc(cc3)C(=O)NCCc4[nH]c5ccccc5n4
#
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
 KYJ  KYJ  (2Z)-2-[(4-{[2-(1H-benzimidazol-2-yl)ethyl]carbamoyl}phenyl)methylidene]-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide  ligand  54  34  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_KYJ
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
 KYJ  N    N  NH2   0  -0.805  -6.3511  -3.7547  -1.0830
 KYJ  C    C  C     0   0.495  -5.8842  -2.7848  -0.2854
 KYJ  O    O  O     0  -0.466  -4.8508  -2.8792   0.3588
 KYJ  C1   C  CR6   0  -0.154  -6.7300  -1.5548  -0.2141
 KYJ  C10  C  CR16  0  -0.313  -1.8619  -0.0319   0.3598
 KYJ  C11  C  CR16  0  -0.242  -0.5515  -0.4699   0.3733
 KYJ  C12  C  CR6   0  -0.037   0.5086   0.4302   0.4674
 KYJ  C13  C  C     0   0.535   1.9017  -0.1159   0.4563
 KYJ  C2   C  CR16  0  -0.268  -8.1217  -1.5855  -0.3028
 KYJ  C3   C  CR16  0  -0.258  -8.9090  -0.4388  -0.1980
 KYJ  C4   C  CR16  0  -0.283  -8.3203   0.7988  -0.0073
 KYJ  C5   C  CR56  0  -0.126  -6.9365   0.8509   0.0851
 KYJ  C6   C  CR5   0   0.340  -6.0057   1.9617   0.2639
 KYJ  C7   C  CR5   0   0.298  -4.6761   1.2980   0.2642
 KYJ  C8   C  C1    0  -0.439  -3.4912   1.9012   0.4011
 KYJ  C9   C  CR6   0   0.173  -2.1524   1.3386   0.4203
 KYJ  N1   N  NH1   0  -0.653   2.8443   0.6428   1.0349
 KYJ  O1   O  O     0  -0.385  -6.2285   3.1469   0.3851
 KYJ  O2   O  O     0  -0.486   2.1433  -1.2041  -0.0496
 KYJ  C14  C  CH2   0  -0.278   4.2417   0.2737   1.0581
 KYJ  C15  C  CH2   0  -0.551   4.9460   0.6304  -0.2470
 KYJ  C16  C  CR5   0   0.473   6.3935   0.2858  -0.2191
 KYJ  N3   N  NR15  0  -0.702   7.2302   0.6238  -1.2361
 KYJ  C22  C  CR56  0   0.326   8.4802   0.1672  -0.9131
 KYJ  C21  C  CR16  0  -0.308   9.7066   0.2277  -1.5633
 KYJ  C20  C  CR16  0  -0.281  10.7834  -0.3552  -0.9156
 KYJ  C19  C  CR16  0  -0.272  10.6395  -0.9760   0.3339
 KYJ  C18  C  CR16  0  -0.336   9.4132  -1.0310   0.9740
 KYJ  C17  C  CR56  0   0.135   8.3174  -0.4487   0.3391
 KYJ  N2   N  N     0  -0.486   7.0043  -0.3548   0.7402
 KYJ  C23  C  CR16  0  -0.285   0.2273   1.7928   0.5268
 KYJ  C24  C  CR16  0  -0.281  -1.0823   2.2362   0.5026
 KYJ  O3   O  O     0  -0.481  -4.8441  -0.0488   0.1018
 KYJ  C25  C  CR56  0   0.450  -6.1692  -0.3022  -0.0019
 KYJ  H1   H  HNH2  0   0.410  -5.8414  -4.6192  -1.1711
 KYJ  H2   H  HNH2  0   0.416  -7.1308  -3.6180  -1.7028
 KYJ  H3   H  HCR6  0   0.276  -2.6485  -0.7692   0.3054
 KYJ  H4   H  HCR6  0   0.266  -0.3511  -1.5312   0.3177
 KYJ  H5   H  HCR6  0   0.283  -8.6216  -2.5358  -0.4423
 KYJ  H6   H  HCR6  0   0.278  -9.9840  -0.5275  -0.2654
 KYJ  H7   H  HCR6  0   0.282  -8.9169   1.6983   0.0681
 KYJ  H8   H  H     0   0.288  -3.5552   2.9791   0.5068
 KYJ  H9   H  HNH1  0   0.413   2.5852   1.5014   1.4906
 KYJ  H10  H  HCH2  0   0.263   4.7050   0.7986   1.8912
 KYJ  H11  H  HCH2  0   0.253   4.3356  -0.7925   1.2597
 KYJ  H12  H  HCH2  0   0.277   4.4690   0.1075  -1.0806
 KYJ  H13  H  HCH2  0   0.272   4.8323   1.6989  -0.4493
 KYJ  H14  H  HNR5  0   0.418   6.9715   1.1189  -2.0750
 KYJ  H15  H  HCR6  0   0.265   9.8207   0.7073  -2.5266
 KYJ  H16  H  HCR6  0   0.254  11.7588  -0.3288  -1.3835
 KYJ  H17  H  HCR6  0   0.251  11.5073  -1.4201   0.8039
 KYJ  H18  H  HCR6  0   0.252   9.3043  -1.5119   1.9378
 KYJ  H20  H  HCR6  0   0.265   1.0190   2.5297   0.5666
 KYJ  H21  H  HCR6  0   0.270  -1.2792   3.3001   0.5401

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
 KYJ  C14  C15  single    1.525  0.020  1.525
 KYJ  C14  N1   single    1.445  0.020  1.445
 KYJ  C15  C16  single    1.488  0.020  1.488
 KYJ  N1   C13  single    1.341  0.020  1.341
 KYJ  C23  C24  aromatic  1.383  0.020  1.383
 KYJ  C23  C12  aromatic  1.393  0.020  1.393
 KYJ  C24  C9   aromatic  1.399  0.020  1.399
 KYJ  C13  C12  single    1.496  0.020  1.496
 KYJ  C13  O2   double    1.224  0.020  1.224
 KYJ  C12  C11  aromatic  1.394  0.020  1.394
 KYJ  C16  N3   aromatic  1.360  0.020  1.360
 KYJ  C16  N2   aromatic  1.305  0.020  1.305
 KYJ  C9   C8   single    1.452  0.020  1.452
 KYJ  C9   C10  aromatic  1.402  0.020  1.402
 KYJ  N3   C22  aromatic  1.369  0.020  1.369
 KYJ  C8   C7   double    1.337  0.020  1.337
 KYJ  O1   C6   double    1.212  0.020  1.212
 KYJ  N2   C17  aromatic  1.376  0.020  1.376
 KYJ  C11  C10  aromatic  1.382  0.020  1.382
 KYJ  C7   C6   single    1.486  0.020  1.486
 KYJ  C7   O3   single    1.367  0.020  1.367
 KYJ  C6   C5   single    1.460  0.020  1.460
 KYJ  C22  C17  aromatic  1.405  0.020  1.405
 KYJ  C22  C21  aromatic  1.389  0.020  1.389
 KYJ  C17  C18  aromatic  1.394  0.020  1.394
 KYJ  O3   C25  single    1.353  0.020  1.353
 KYJ  C21  C20  aromatic  1.385  0.020  1.385
 KYJ  C5   C25  aromatic  1.388  0.020  1.388
 KYJ  C5   C4   aromatic  1.388  0.020  1.388
 KYJ  C18  C19  aromatic  1.384  0.020  1.384
 KYJ  C25  C1   aromatic  1.389  0.020  1.389
 KYJ  C4   C3   aromatic  1.384  0.020  1.384
 KYJ  C20  C19  aromatic  1.403  0.020  1.403
 KYJ  C1   C2   aromatic  1.395  0.020  1.395
 KYJ  C1   C    single    1.494  0.020  1.494
 KYJ  C3   C2   aromatic  1.395  0.020  1.395
 KYJ  N    C    single    1.340  0.020  1.340
 KYJ  C    O    double    1.221  0.020  1.221
 KYJ  N    H1   single    0.860  0.020  1.020
 KYJ  N    H2   single    0.860  0.020  1.020
 KYJ  C10  H3   single    0.930  0.020  1.080
 KYJ  C11  H4   single    0.930  0.020  1.080
 KYJ  C2   H5   single    0.930  0.020  1.080
 KYJ  C3   H6   single    0.930  0.020  1.080
 KYJ  C4   H7   single    0.930  0.020  1.080
 KYJ  C8   H8   single    0.930  0.020  1.080
 KYJ  N1   H9   single    0.860  0.020  1.020
 KYJ  C14  H10  single    0.970  0.020  1.090
 KYJ  C14  H11  single    0.970  0.020  1.090
 KYJ  C15  H12  single    0.970  0.020  1.090
 KYJ  C15  H13  single    0.970  0.020  1.090
 KYJ  N3   H14  single    0.860  0.020  1.020
 KYJ  C21  H15  single    0.930  0.020  1.080
 KYJ  C20  H16  single    0.930  0.020  1.080
 KYJ  C19  H17  single    0.930  0.020  1.080
 KYJ  C18  H18  single    0.930  0.020  1.080
 KYJ  C23  H20  single    0.930  0.020  1.080
 KYJ  C24  H21  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
 KYJ  H2   N    H1   117.08  3.000
 KYJ  H2   N    C    122.61  3.000
 KYJ  H1   N    C    119.80  3.000
 KYJ  C1   C    O    121.15  3.000
 KYJ  O    C    N    123.57  3.000
 KYJ  C1   C    N    115.28  3.000
 KYJ  C25  C1   C2   115.63  3.000
 KYJ  C2   C1   C    122.92  3.000
 KYJ  C25  C1   C    121.41  3.000
 KYJ  H3   C10  C9   121.25  3.000
 KYJ  H3   C10  C11  118.36  3.000
 KYJ  C9   C10  C11  120.39  3.000
 KYJ  H4   C11  C12  119.75  3.000
 KYJ  H4   C11  C10  119.10  3.000
 KYJ  C12  C11  C10  121.15  3.000
 KYJ  C23  C12  C13  123.05  3.000
 KYJ  C13  C12  C11  118.16  3.000
 KYJ  C23  C12  C11  118.75  3.000
 KYJ  O2   C13  N1   122.85  3.000
 KYJ  O2   C13  C12  120.74  3.000
 KYJ  N1   C13  C12  116.40  3.000
 KYJ  H5   C2   C3   118.07  3.000
 KYJ  H5   C2   C1   119.22  3.000
 KYJ  C3   C2   C1   122.70  3.000
 KYJ  H6   C3   C4   120.34  3.000
 KYJ  H6   C3   C2   119.29  3.000
 KYJ  C4   C3   C2   120.37  3.000
 KYJ  H7   C4   C5   120.92  3.000
 KYJ  H7   C4   C3   121.24  3.000
 KYJ  C5   C4   C3   117.83  3.000
 KYJ  C25  C5   C6   106.69  3.000
 KYJ  C25  C5   C4   121.06  3.000
 KYJ  C6   C5   C4   132.24  3.000
 KYJ  O1   C6   C7   126.95  3.000
 KYJ  C7   C6   C5   103.34  3.000
 KYJ  O1   C6   C5   129.71  3.000
 KYJ  O3   C7   C8   124.45  3.000
 KYJ  O3   C7   C6   109.27  3.000
 KYJ  C8   C7   C6   126.27  3.000
 KYJ  H8   C8   C9   115.98  3.000
 KYJ  H8   C8   C7   113.95  3.000
 KYJ  C9   C8   C7   130.07  3.000
 KYJ  C24  C9   C8   117.21  3.000
 KYJ  C8   C9   C10  124.69  3.000
 KYJ  C24  C9   C10  118.10  3.000
 KYJ  H9   N1   C14  117.36  3.000
 KYJ  H9   N1   C13  119.82  3.000
 KYJ  C14  N1   C13  122.81  3.000
 KYJ  H11  C14  H10  107.09  3.000
 KYJ  H11  C14  C15  110.33  3.000
 KYJ  H10  C14  C15  110.22  3.000
 KYJ  H11  C14  N1   109.65  3.000
 KYJ  H10  C14  N1   107.50  3.000
 KYJ  C15  C14  N1   111.90  3.000
 KYJ  H13  C15  H12  106.31  3.000
 KYJ  H13  C15  C16  109.32  3.000
 KYJ  H12  C15  C16  109.14  3.000
 KYJ  H13  C15  C14  109.80  3.000
 KYJ  H12  C15  C14  109.82  3.000
 KYJ  C16  C15  C14  112.27  3.000
 KYJ  N2   C16  N3   112.57  3.000
 KYJ  N2   C16  C15  125.63  3.000
 KYJ  N3   C16  C15  121.80  3.000
 KYJ  H14  N3   C22  126.47  3.000
 KYJ  H14  N3   C16  125.93  3.000
 KYJ  C22  N3   C16  107.60  3.000
 KYJ  C17  C22  C21  122.58  3.000
 KYJ  C21  C22  N3   132.91  3.000
 KYJ  C17  C22  N3   104.51  3.000
 KYJ  H15  C21  C20  121.39  3.000
 KYJ  H15  C21  C22  121.93  3.000
 KYJ  C20  C21  C22  116.68  3.000
 KYJ  H16  C20  C19  119.24  3.000
 KYJ  H16  C20  C21  119.22  3.000
 KYJ  C19  C20  C21  121.54  3.000
 KYJ  H17  C19  C18  119.55  3.000
 KYJ  H17  C19  C20  119.09  3.000
 KYJ  C18  C19  C20  121.35  3.000
 KYJ  H18  C18  C17  120.79  3.000
 KYJ  H18  C18  C19  121.22  3.000
 KYJ  C17  C18  C19  117.98  3.000
 KYJ  N2   C17  C18  130.23  3.000
 KYJ  C18  C17  C22  119.86  3.000
 KYJ  N2   C17  C22  109.90  3.000
 KYJ  C17  N2   C16  105.41  3.000
 KYJ  H20  C23  C24  118.36  3.000
 KYJ  H20  C23  C12  121.33  3.000
 KYJ  C24  C23  C12  120.29  3.000
 KYJ  H21  C24  C23  119.12  3.000
 KYJ  H21  C24  C9   119.57  3.000
 KYJ  C23  C24  C9   121.31  3.000
 KYJ  C25  O3   C7   108.30  3.000
 KYJ  O3   C25  C5   112.40  3.000
 KYJ  C5   C25  C1   122.39  3.000
 KYJ  O3   C25  C1   125.18  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
 KYJ  CONST_01  C4   C5   C25  C1      0.00   0.0  0
 KYJ  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 KYJ  CONST_03  C23  C24  C9   C10     0.00   0.0  0
 KYJ  CONST_04  C23  C12  C11  C10     0.00   0.0  0
 KYJ  CONST_05  C24  C23  C12  C11     0.00   0.0  0
 KYJ  CONST_06  C24  C9   C10  C11     0.00   0.0  0
 KYJ  CONST_07  C9   C24  C23  C12     0.00   0.0  0
 KYJ  CONST_08  C9   C10  C11  C12     0.00   0.0  0
 KYJ  CONST_09  C5   C25  C1   C2      0.00   0.0  0
 KYJ  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 KYJ  CONST_11  C25  C5   C4   C3      0.00   0.0  0
 KYJ  CONST_12  C25  C1   C2   C3      0.00   0.0  0
 KYJ  CONST_13  C17  C22  N3   C16     0.00   0.0  0
 KYJ  CONST_14  C21  C22  N3   C16   180.00   0.0  0
 KYJ  CONST_15  C22  C17  N2   C16     0.00   0.0  0
 KYJ  CONST_16  C18  C17  N2   C16   180.00   0.0  0
 KYJ  CONST_17  C17  N2   C16  N3      0.00   0.0  0
 KYJ  CONST_18  N2   C17  C22  N3      0.00   0.0  0
 KYJ  CONST_19  C18  C17  C22  N3    180.00   0.0  0
 KYJ  CONST_20  C20  C21  C22  N3    180.00   0.0  0
 KYJ  CONST_21  N2   C16  N3   C22     0.00   0.0  0
 KYJ  CONST_22  C19  C18  C17  C22     0.00   0.0  0
 KYJ  CONST_23  C19  C20  C21  C22     0.00   0.0  0
 KYJ  CONST_24  N2   C17  C22  C21   180.00   0.0  0
 KYJ  CONST_25  C18  C17  C22  C21     0.00   0.0  0
 KYJ  CONST_26  C18  C19  C20  C21     0.00   0.0  0
 KYJ  CONST_27  C17  C22  C21  C20     0.00   0.0  0
 KYJ  CONST_28  C17  C18  C19  C20     0.00   0.0  0
 KYJ  CONST_29  N2   C17  C18  C19   180.00   0.0  0
 KYJ  CONST_30  O3   C25  C1   C       0.00   0.0  0
 KYJ  CONST_31  C5   C25  C1   C     180.00   0.0  0
 KYJ  CONST_32  C3   C2   C1   C     180.00   0.0  0
 KYJ  CONST_33  C13  C12  C11  C10   180.00   0.0  0
 KYJ  CONST_34  C8   C9   C10  C11   180.00   0.0  0
 KYJ  CONST_35  C24  C23  C12  C13   180.00   0.0  0
 KYJ  CONST_36  C23  C24  C9   C8    180.00   0.0  0
 KYJ  CONST_37  C22  N3   C16  C15   180.00   0.0  0
 KYJ  CONST_38  C17  N2   C16  C15   180.00   0.0  0
 KYJ  CONST_39  H6   C3   C2   C1    180.00   0.0  0
 KYJ  CONST_40  H21  C24  C9   C10   180.00   0.0  0
 KYJ  CONST_41  H20  C23  C12  C11   180.00   0.0  0
 KYJ  CONST_42  H3   C10  C11  C12   180.00   0.0  0
 KYJ  CONST_43  H7   C4   C3   C2    180.00   0.0  0
 KYJ  CONST_44  H5   C2   C3   C4    180.00   0.0  0
 KYJ  CONST_45  H4   C11  C10  C9    180.00   0.0  0
 KYJ  CONST_46  H15  C21  C22  N3      0.00   0.0  0
 KYJ  CONST_47  H18  C18  C17  C22   180.00   0.0  0
 KYJ  CONST_48  H16  C20  C21  C22   180.00   0.0  0
 KYJ  CONST_49  H14  N3   C22  C21     0.00   0.0  0
 KYJ  CONST_50  H17  C19  C20  C21   180.00   0.0  0
 KYJ  CONST_51  C14  N1   C13  C12   180.00   0.0  0
 KYJ  CONST_52  H1   N    C    C1    180.00   0.0  0
 KYJ  CONST_53  H2   N    C    C1      0.00   0.0  0
 KYJ  CONST_54  H9   N1   C13  C12     0.00   0.0  0
 KYJ  CONST_55  C14  N1   C13  O2      0.00   0.0  0
 KYJ  Var_01    C7   C8   C9   C10    -3.52  30.0  2
 KYJ  Var_02    C9   C8   C7   C6    179.65  30.0  2
 KYJ  Var_03    C25  C1   C    N    -149.09  30.0  2
 KYJ  Var_04    N1   C13  C12  C11  -155.58  30.0  2
 KYJ  Var_05    N3   C16  C15  C14  -174.30  30.0  2
 KYJ  Var_06    C16  C15  C14  N1    178.53  30.0  3
 KYJ  Var_07    C15  C14  N1   C13    81.56  30.0  1

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
 KYJ  plan-1  C10  0.020
 KYJ  plan-1  C11  0.020
 KYJ  plan-1  C12  0.020
 KYJ  plan-1  C13  0.020
 KYJ  plan-1  C8   0.020
 KYJ  plan-1  C9   0.020
 KYJ  plan-1  C23  0.020
 KYJ  plan-1  C24  0.020
 KYJ  plan-1  H3   0.020
 KYJ  plan-1  H4   0.020
 KYJ  plan-1  H20  0.020
 KYJ  plan-1  H21  0.020
 KYJ  plan-2  C    0.020
 KYJ  plan-2  C1   0.020
 KYJ  plan-2  C2   0.020
 KYJ  plan-2  C3   0.020
 KYJ  plan-2  C4   0.020
 KYJ  plan-2  C5   0.020
 KYJ  plan-2  C6   0.020
 KYJ  plan-2  C7   0.020
 KYJ  plan-2  C8   0.020
 KYJ  plan-2  O1   0.020
 KYJ  plan-2  O3   0.020
 KYJ  plan-2  C25  0.020
 KYJ  plan-2  H5   0.020
 KYJ  plan-2  H6   0.020
 KYJ  plan-2  H7   0.020
 KYJ  plan-3  C15  0.020
 KYJ  plan-3  C16  0.020
 KYJ  plan-3  N3   0.020
 KYJ  plan-3  C22  0.020
 KYJ  plan-3  C21  0.020
 KYJ  plan-3  C20  0.020
 KYJ  plan-3  C19  0.020
 KYJ  plan-3  C18  0.020
 KYJ  plan-3  C17  0.020
 KYJ  plan-3  N2   0.020
 KYJ  plan-3  H14  0.020
 KYJ  plan-3  H15  0.020
 KYJ  plan-3  H16  0.020
 KYJ  plan-3  H17  0.020
 KYJ  plan-3  H18  0.020
 KYJ  plan-4  N    0.020
 KYJ  plan-4  C    0.020
 KYJ  plan-4  O    0.020
 KYJ  plan-4  C1   0.020
 KYJ  plan-4  H1   0.020
 KYJ  plan-4  H2   0.020
 KYJ  plan-5  C12  0.020
 KYJ  plan-5  C13  0.020
 KYJ  plan-5  N1   0.020
 KYJ  plan-5  O2   0.020
 KYJ  plan-5  C14  0.020
 KYJ  plan-5  H9   0.020

