# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 13:05:20 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 2-({[1-phenyl-2-(propan-2-yl)-1H-benzimidazol-6-yl]oxy}methyl)quinoline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)c1nc2ccc(OCc3ccc4ccccc4n3)cc2n1c5ccccc5
#
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
 P98  P98  2-({[1-phenyl-2-(propan-2-yl)-1H-benzimidazol-6-yl]oxy}methyl)quinoline  ligand  53  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_P98
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
 P98  C25  C  CR16  0  -0.244   4.3731  -3.8892   0.2518
 P98  C15  C  CR16  0  -0.256  -8.3944  -1.0908   0.2670
 P98  C14  C  CR16  0  -0.256  -8.3700   0.3200   0.3120
 P98  C24  C  CR16  0  -0.260   4.5252  -3.2654  -0.9797
 P98  C26  C  CR16  0  -0.258   3.9393  -3.1593   1.3508
 P98  C16  C  CR16  0  -0.312  -7.2263  -1.7967   0.1732
 P98  C9   C  CR16  0  -0.179  -4.7479  -1.7842   0.0186
 P98  C13  C  CR16  0  -0.300  -7.1838   1.0006   0.2623
 P98  C4   C  CR16  0  -0.324   1.3594   2.9536  -0.3979
 P98  C23  C  CR16  0  -0.257   4.2399  -1.9146  -1.1162
 P98  C27  C  CR16  0  -0.263   3.6652  -1.8048   1.2245
 P98  C1   C  CR16  0  -0.392   0.0917   2.4096  -0.2562
 P98  C10  C  CR16  0  -0.326  -3.5905  -1.0607  -0.0331
 P98  C3   C  CR16  0  -0.417   1.0039   0.1641  -0.0080
 P98  C11  C  CR66  0   0.078  -5.9876  -1.1192   0.1186
 P98  C12  C  CR66  0   0.200  -5.9617   0.2962   0.1634
 P98  C17  C  CR56  0   0.126   2.4598   2.1090  -0.3431
 P98  C18  C  CR56  0   0.340   2.2573   0.7359  -0.1442
 P98  C22  C  CR6   0   0.260   3.8187  -1.1873  -0.0101
 P98  C2   C  CR6   0   0.399  -0.0844   1.0288  -0.0649
 P98  C7   C  CR6   0   0.173  -3.6728   0.3497   0.0200
 P98  C20  C  CR5   0   0.486   4.4050   1.2276  -0.3363
 P98  C29  C  CH3   0  -0.645   6.6045   2.0724  -1.1445
 P98  C30  C  CH3   0  -0.646   6.3701   1.0541   1.1526
 P98  C6   C  CH2   0  -0.214  -2.4551   1.2308  -0.0644
 P98  C28  C  CH1   0  -0.366   5.8862   1.0264  -0.3016
 P98  N8   N  N     0  -0.457  -4.8056   0.9952   0.1164
 P98  N21  N  N     0  -0.473   3.8055   2.3748  -0.4570
 P98  N19  N  NR5   0  -0.652   3.5192   0.1907  -0.1463
 P98  H1   H  HCR6  0   0.265   4.5901  -4.9442   0.3551
 P98  H3   H  HCR6  0   0.264  -9.3014   0.8660   0.3876
 P98  H4   H  HCR6  0   0.267   4.8577  -3.8310  -1.8400
 P98  H5   H  HCR6  0   0.267   3.8186  -3.6420   2.3115
 P98  H6   H  HCR6  0   0.263  -7.2370  -2.8793   0.1391
 P98  H7   H  HCR6  0   0.272  -4.7221  -2.8665  -0.0181
 P98  H8   H  HCR6  0   0.260  -7.1574   2.0822   0.2963
 P98  H9   H  HCR6  0   0.259   1.4811   4.0188  -0.5459
 P98  H10  H  HCR6  0   0.275   4.3419  -1.4252  -2.0767
 P98  H11  H  HCR6  0   0.275   3.3355  -1.2299   2.0805
 P98  H12  H  HCR6  0   0.280  -0.7592   3.0752  -0.2935
 P98  H13  H  HCR6  0   0.270  -2.6359  -1.5586  -0.1146
 P98  H14  H  HCR6  0   0.273   0.8611  -0.8992   0.1388
 P98  H15  H  HCH3  0   0.227   6.3996   3.0798  -0.7836
 P98  H16  H  HCH3  0   0.234   7.6813   1.9093  -1.0979
 P98  H17  H  HCH3  0   0.234   6.3024   2.0207  -2.1906
 P98  H18  H  HCH3  0   0.236   5.8848   0.2880   1.7590
 P98  H19  H  HCH3  0   0.240   7.4452   0.8771   1.1955
 P98  H20  H  HCH3  0   0.230   6.1655   2.0245   1.6067
 P98  H21  H  HCH2  0   0.254  -2.4627   1.7482  -1.0319
 P98  H22  H  HCH2  0   0.251  -2.5197   1.9986   0.7146
 P98  H23  H  HCH1  0   0.261   6.1137   0.0389  -0.7120
 P98  O5   O  O2    0  -0.487  -1.2980   0.4465   0.0798
 P98  H2   H  HCR6  0   0.263  -9.3424  -1.6106   0.3076

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
 P98  C16  C15  aromatic  1.368  0.020  1.368
 P98  C16  C11  aromatic  1.413  0.020  1.413
 P98  C15  C14  aromatic  1.412  0.020  1.412
 P98  C9   C11  aromatic  1.410  0.020  1.410
 P98  C9   C10  aromatic  1.366  0.020  1.366
 P98  C11  C12  aromatic  1.416  0.020  1.416
 P98  C14  C13  aromatic  1.369  0.020  1.369
 P98  C10  C7   aromatic  1.414  0.020  1.414
 P98  C12  C13  aromatic  1.414  0.020  1.414
 P98  C12  N8   aromatic  1.352  0.020  1.352
 P98  C1   C4   aromatic  1.387  0.020  1.387
 P98  C1   C2   aromatic  1.405  0.020  1.405
 P98  C7   N8   aromatic  1.307  0.020  1.307
 P98  C7   C6   single    1.505  0.020  1.505
 P98  O5   C2   single    1.354  0.020  1.354
 P98  O5   C6   single    1.405  0.020  1.405
 P98  C4   C17  aromatic  1.388  0.020  1.388
 P98  C2   C3   aromatic  1.391  0.020  1.391
 P98  C17  N21  aromatic  1.376  0.020  1.376
 P98  C17  C18  aromatic  1.402  0.020  1.402
 P98  C3   C18  aromatic  1.384  0.020  1.384
 P98  N21  C20  aromatic  1.300  0.020  1.300
 P98  C18  N19  aromatic  1.375  0.020  1.375
 P98  C20  N19  aromatic  1.377  0.020  1.377
 P98  C20  C28  single    1.495  0.020  1.495
 P98  N19  C22  single    1.417  0.020  1.417
 P98  C29  C28  single    1.523  0.020  1.523
 P98  C28  C30  single    1.533  0.020  1.533
 P98  C22  C23  aromatic  1.389  0.020  1.389
 P98  C22  C27  aromatic  1.389  0.020  1.389
 P98  C23  C24  aromatic  1.387  0.020  1.387
 P98  C27  C26  aromatic  1.388  0.020  1.388
 P98  C24  C25  aromatic  1.389  0.020  1.389
 P98  C26  C25  aromatic  1.389  0.020  1.389
 P98  C25  H1   single    0.930  0.020  1.080
 P98  C15  H2   single    0.930  0.020  1.080
 P98  C14  H3   single    0.930  0.020  1.080
 P98  C24  H4   single    0.930  0.020  1.080
 P98  C26  H5   single    0.930  0.020  1.080
 P98  C16  H6   single    0.930  0.020  1.080
 P98  C9   H7   single    0.930  0.020  1.080
 P98  C13  H8   single    0.930  0.020  1.080
 P98  C4   H9   single    0.930  0.020  1.080
 P98  C23  H10  single    0.930  0.020  1.080
 P98  C27  H11  single    0.930  0.020  1.080
 P98  C1   H12  single    0.930  0.020  1.080
 P98  C10  H13  single    0.930  0.020  1.080
 P98  C3   H14  single    0.930  0.020  1.080
 P98  C29  H15  single    0.970  0.020  1.090
 P98  C29  H16  single    0.970  0.020  1.090
 P98  C29  H17  single    0.970  0.020  1.090
 P98  C30  H18  single    0.970  0.020  1.090
 P98  C30  H19  single    0.970  0.020  1.090
 P98  C30  H20  single    0.970  0.020  1.090
 P98  C6   H21  single    0.970  0.020  1.090
 P98  C6   H22  single    0.970  0.020  1.090
 P98  C28  H23  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
 P98  H1   C25  C26  119.97  3.000
 P98  H1   C25  C24  120.04  3.000
 P98  C26  C25  C24  119.99  3.000
 P98  H2   C15  C16  120.18  3.000
 P98  H2   C15  C14  119.61  3.000
 P98  C16  C15  C14  120.21  3.000
 P98  H3   C14  C13  119.84  3.000
 P98  H3   C14  C15  119.44  3.000
 P98  C13  C14  C15  120.72  3.000
 P98  H4   C24  C23  119.60  3.000
 P98  H4   C24  C25  120.26  3.000
 P98  C23  C24  C25  120.13  3.000
 P98  H5   C26  C27  119.62  3.000
 P98  H5   C26  C25  120.20  3.000
 P98  C27  C26  C25  120.18  3.000
 P98  H6   C16  C11  119.12  3.000
 P98  H6   C16  C15  120.63  3.000
 P98  C11  C16  C15  120.25  3.000
 P98  H7   C9   C11  119.63  3.000
 P98  H7   C9   C10  120.51  3.000
 P98  C11  C9   C10  119.85  3.000
 P98  H8   C13  C12  118.61  3.000
 P98  H8   C13  C14  121.13  3.000
 P98  C12  C13  C14  120.26  3.000
 P98  H9   C4   C17  121.00  3.000
 P98  H9   C4   C1   120.19  3.000
 P98  C17  C4   C1   118.81  3.000
 P98  H10  C23  C22  119.88  3.000
 P98  H10  C23  C24  120.53  3.000
 P98  C22  C23  C24  119.59  3.000
 P98  H11  C27  C22  120.02  3.000
 P98  H11  C27  C26  120.44  3.000
 P98  C22  C27  C26  119.54  3.000
 P98  H12  C1   C2   120.74  3.000
 P98  H12  C1   C4   118.33  3.000
 P98  C2   C1   C4   120.93  3.000
 P98  H13  C10  C7   120.95  3.000
 P98  H13  C10  C9   120.51  3.000
 P98  C7   C10  C9   118.53  3.000
 P98  H14  C3   C2   120.84  3.000
 P98  H14  C3   C18  122.57  3.000
 P98  C2   C3   C18  116.59  3.000
 P98  C12  C11  C9   117.22  3.000
 P98  C12  C11  C16  119.60  3.000
 P98  C9   C11  C16  123.18  3.000
 P98  N8   C12  C11  122.09  3.000
 P98  N8   C12  C13  118.94  3.000
 P98  C11  C12  C13  118.97  3.000
 P98  N21  C17  C18  110.00  3.000
 P98  C18  C17  C4   119.14  3.000
 P98  N21  C17  C4   130.86  3.000
 P98  N19  C18  C17  104.81  3.000
 P98  N19  C18  C3   131.87  3.000
 P98  C17  C18  C3   123.31  3.000
 P98  N19  C22  C27  119.64  3.000
 P98  C27  C22  C23  120.56  3.000
 P98  N19  C22  C23  119.79  3.000
 P98  O5   C2   C3   115.44  3.000
 P98  C3   C2   C1   121.22  3.000
 P98  O5   C2   C1   123.34  3.000
 P98  N8   C7   C6   114.58  3.000
 P98  C6   C7   C10  122.33  3.000
 P98  N8   C7   C10  123.08  3.000
 P98  N19  C20  N21  112.37  3.000
 P98  N19  C20  C28  122.19  3.000
 P98  N21  C20  C28  125.29  3.000
 P98  H17  C29  H16  107.92  3.000
 P98  H17  C29  H15  108.04  3.000
 P98  H16  C29  H15  108.06  3.000
 P98  H17  C29  C28  111.58  3.000
 P98  H16  C29  C28  109.84  3.000
 P98  H15  C29  C28  111.27  3.000
 P98  H20  C30  H19  108.24  3.000
 P98  H20  C30  H18  108.05  3.000
 P98  H19  C30  H18  107.63  3.000
 P98  H20  C30  C28  110.60  3.000
 P98  H19  C30  C28  110.22  3.000
 P98  H18  C30  C28  111.97  3.000
 P98  H22  C6   H21  107.22  3.000
 P98  H22  C6   O5   111.51  3.000
 P98  H21  C6   O5   111.06  3.000
 P98  H22  C6   C7   108.82  3.000
 P98  H21  C6   C7   108.66  3.000
 P98  O5   C6   C7   109.49  3.000
 P98  H23  C28  C30  107.86  3.000
 P98  H23  C28  C29  108.32  3.000
 P98  C30  C28  C29  111.33  3.000
 P98  H23  C28  C20  108.60  3.000
 P98  C30  C28  C20  109.41  3.000
 P98  C29  C28  C20  111.22  3.000
 P98  C7   N8   C12  119.23  3.000
 P98  C20  N21  C17  105.83  3.000
 P98  C20  N19  C22  127.57  3.000
 P98  C22  N19  C18  125.43  3.000
 P98  C20  N19  C18  106.98  3.000
 P98  C6   O5   C2   119.15  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
 P98  CONST_01  C22  C23  C24  C25    0.00   0.0  0
 P98  CONST_02  C22  C27  C26  C25    0.00   0.0  0
 P98  CONST_03  C9   C11  C16  C15  180.00   0.0  0
 P98  CONST_04  C12  C11  C16  C15    0.00   0.0  0
 P98  CONST_05  C12  C13  C14  C15    0.00   0.0  0
 P98  CONST_06  C11  C16  C15  C14    0.00   0.0  0
 P98  CONST_07  C11  C12  C13  C14    0.00   0.0  0
 P98  CONST_08  N8   C12  C13  C14  180.00   0.0  0
 P98  CONST_09  N19  C22  C23  C24  180.00   0.0  0
 P98  CONST_10  C27  C22  C23  C24    0.00   0.0  0
 P98  CONST_11  C27  C26  C25  C24    0.00   0.0  0
 P98  CONST_12  N19  C22  C27  C26  180.00   0.0  0
 P98  CONST_13  C23  C22  C27  C26    0.00   0.0  0
 P98  CONST_14  C23  C24  C25  C26    0.00   0.0  0
 P98  CONST_15  C13  C14  C15  C16    0.00   0.0  0
 P98  CONST_16  C10  C9   C11  C16  180.00   0.0  0
 P98  CONST_17  C13  C12  C11  C16    0.00   0.0  0
 P98  CONST_18  N8   C12  C11  C16  180.00   0.0  0
 P98  CONST_19  C13  C12  C11  C9   180.00   0.0  0
 P98  CONST_20  N8   C12  C11  C9     0.00   0.0  0
 P98  CONST_21  N8   C7   C10  C9     0.00   0.0  0
 P98  CONST_22  C7   N8   C12  C13  180.00   0.0  0
 P98  CONST_23  C3   C2   C1   C4     0.00   0.0  0
 P98  CONST_24  C20  N21  C17  C4   180.00   0.0  0
 P98  CONST_25  C3   C18  C17  C4     0.00   0.0  0
 P98  CONST_26  N19  C18  C17  C4   180.00   0.0  0
 P98  CONST_31  N21  C17  C4   C1   180.00   0.0  0
 P98  CONST_32  C18  C17  C4   C1     0.00   0.0  0
 P98  CONST_33  C18  C3   C2   C1     0.00   0.0  0
 P98  CONST_34  C12  C11  C9   C10    0.00   0.0  0
 P98  CONST_35  C12  N8   C7   C10    0.00   0.0  0
 P98  CONST_36  N21  C17  C18  C3   180.00   0.0  0
 P98  CONST_37  C20  N19  C18  C3   180.00   0.0  0
 P98  CONST_38  C22  N19  C18  C3     0.00   0.0  0
 P98  CONST_39  C7   C10  C9   C11    0.00   0.0  0
 P98  CONST_40  C7   N8   C12  C11    0.00   0.0  0
 P98  CONST_41  C2   C1   C4   C17    0.00   0.0  0
 P98  CONST_42  N19  C20  N21  C17    0.00   0.0  0
 P98  CONST_43  C2   C3   C18  C17    0.00   0.0  0
 P98  CONST_44  C20  N19  C18  C17    0.00   0.0  0
 P98  CONST_45  C22  N19  C18  C17  180.00   0.0  0
 P98  CONST_46  C20  N21  C17  C18    0.00   0.0  0
 P98  CONST_47  N21  C20  N19  C18    0.00   0.0  0
 P98  CONST_48  N21  C20  N19  C22  180.00   0.0  0
 P98  CONST_49  N19  C18  C3   C2   180.00   0.0  0
 P98  CONST_50  N19  C18  C17  N21    0.00   0.0  0
 P98  CONST_51  C6   C7   C10  C9   180.00   0.0  0
 P98  CONST_52  O5   C2   C1   C4   180.00   0.0  0
 P98  CONST_53  C6   C7   N8   C12  180.00   0.0  0
 P98  CONST_54  C28  C20  N21  C17  180.00   0.0  0
 P98  CONST_55  O5   C2   C3   C18  180.00   0.0  0
 P98  CONST_56  C28  C20  N19  C18  180.00   0.0  0
 P98  CONST_57  C28  C20  N19  C22    0.00   0.0  0
 P98  CONST_58  H10  C23  C24  C25  180.00   0.0  0
 P98  CONST_59  H11  C27  C26  C25  180.00   0.0  0
 P98  CONST_60  H8   C13  C14  C15  180.00   0.0  0
 P98  CONST_61  H6   C16  C15  C14  180.00   0.0  0
 P98  CONST_62  H5   C26  C25  C24  180.00   0.0  0
 P98  CONST_63  H4   C24  C25  C26  180.00   0.0  0
 P98  CONST_64  H3   C14  C15  C16  180.00   0.0  0
 P98  CONST_65  H7   C9   C11  C16    0.00   0.0  0
 P98  CONST_66  H2   C15  C14  C13  180.00   0.0  0
 P98  CONST_67  H1   C25  C24  C23  180.00   0.0  0
 P98  CONST_68  H14  C3   C2   C1   180.00   0.0  0
 P98  CONST_69  H12  C1   C2   C3   180.00   0.0  0
 P98  CONST_70  H13  C10  C9   C11  180.00   0.0  0
 P98  CONST_71  H9   C4   C17  C18  180.00   0.0  0
 P98  Var_01    O5   C6   C7   C10  -12.00  30.0  2
 P98  Var_02    C7   C6   O5   C2   175.13  30.0  3
 P98  Var_03    N21  C20  C28  C29  -31.49  30.0  2
 P98  Var_04    H15  C29  C28  C20   60.00  30.0  3
 P98  Var_05    H18  C30  C28  C20   58.45  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
 P98  plan-1  C25  0.020
 P98  plan-1  C24  0.020
 P98  plan-1  C26  0.020
 P98  plan-1  C23  0.020
 P98  plan-1  C27  0.020
 P98  plan-1  C22  0.020
 P98  plan-1  N19  0.020
 P98  plan-1  H1   0.020
 P98  plan-1  H4   0.020
 P98  plan-1  H5   0.020
 P98  plan-1  H10  0.020
 P98  plan-1  H11  0.020
 P98  plan-2  C4   0.020
 P98  plan-2  C1   0.020
 P98  plan-2  C3   0.020
 P98  plan-2  C17  0.020
 P98  plan-2  C18  0.020
 P98  plan-2  C22  0.020
 P98  plan-2  C2   0.020
 P98  plan-2  C20  0.020
 P98  plan-2  C28  0.020
 P98  plan-2  N21  0.020
 P98  plan-2  N19  0.020
 P98  plan-2  H9   0.020
 P98  plan-2  H12  0.020
 P98  plan-2  H14  0.020
 P98  plan-2  O5   0.020
 P98  plan-3  C15  0.020
 P98  plan-3  C14  0.020
 P98  plan-3  C16  0.020
 P98  plan-3  C9   0.020
 P98  plan-3  C13  0.020
 P98  plan-3  C10  0.020
 P98  plan-3  C11  0.020
 P98  plan-3  C12  0.020
 P98  plan-3  C7   0.020
 P98  plan-3  C6   0.020
 P98  plan-3  N8   0.020
 P98  plan-3  H3   0.020
 P98  plan-3  H6   0.020
 P98  plan-3  H7   0.020
 P98  plan-3  H8   0.020
 P98  plan-3  H13  0.020
 P98  plan-3  H2   0.020

