# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 21 20:01:06 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: 1-benzyl-2-phenyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C(n1c2ccccc2nc1c3ccccc3)c4ccccc4
#
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
 18F  18F  1-benzyl-2-phenyl-1H-benzimidazole  ligand  38  22  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_18F
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
 18F  CAR  C  CR16  0  -0.283  -0.6407  -2.0853  -0.7912
 18F  CAS  C  CR16  0  -0.241  -0.5597  -3.1987  -1.6130
 18F  CAT  C  CR16  0  -0.265   0.2097  -4.2928  -1.2327
 18F  CAU  C  CR16  0  -0.239   0.8991  -4.2635  -0.0294
 18F  CAV  C  CR16  0  -0.310   0.8185  -3.1440   0.7905
 18F  CAQ  C  CR6   0   0.134   0.0471  -2.0494   0.4198
 18F  CAP  C  CH2   0  -0.430  -0.0459  -0.8373   1.3115
 18F  NAE  N  NR5   0  -0.533   0.4287   0.3628   0.6510
 18F  CAD  C  CR56  0   0.350   1.7376   0.5778   0.2948
 18F  CAI  C  CR16  0  -0.305   2.9106  -0.1068   0.5932
 18F  CAH  C  CR16  0  -0.275   4.0811   0.4074   0.0621
 18F  CAG  C  CR16  0  -0.272   4.0804   1.5602  -0.7381
 18F  CAF  C  CR16  0  -0.337   2.9082   2.2329  -1.0317
 18F  CAC  C  CR56  0   0.128   1.7185   1.7277  -0.5075
 18F  NAB  N  N     0  -0.468   0.4317   2.1878  -0.6320
 18F  CAA  C  CR5   0   0.430  -0.3015   1.3599   0.0630
 18F  CAJ  C  CR6   0  -0.006  -1.7582   1.4899   0.1992
 18F  CAK  C  CR16  0  -0.291  -2.3760   1.4998   1.4493
 18F  CAL  C  CR16  0  -0.243  -3.7523   1.6433   1.5460
 18F  CAM  C  CR16  0  -0.252  -4.5214   1.7804   0.3979
 18F  CAN  C  CR16  0  -0.243  -3.9093   1.7839  -0.8488
 18F  CAO  C  CR16  0  -0.275  -2.5336   1.6401  -0.9494
 18F  H1   H  HCR6  0   0.249  -1.2503  -1.2422  -1.0963
 18F  H2   H  HCR6  0   0.259  -1.1028  -3.2176  -2.5489
 18F  H3   H  HCR6  0   0.259   0.2698  -5.1623  -1.8744
 18F  H4   H  HCR6  0   0.258   1.5022  -5.1095   0.2738
 18F  H5   H  HCR6  0   0.256   1.3553  -3.1280   1.7323
 18F  H6   H  HCH2  0   0.300  -1.0767  -0.6769   1.6215
 18F  H7   H  HCH2  0   0.289   0.5339  -0.9874   2.2236
 18F  H8   H  HCR6  0   0.264   2.9239  -0.9924   1.2146
 18F  H9   H  HCR6  0   0.257   5.0195  -0.0887   0.2718
 18F  H10  H  HCR6  0   0.254   5.0195   1.9269  -1.1313
 18F  H11  H  HCR6  0   0.255   2.9089   3.1205  -1.6513
 18F  H12  H  HCR6  0   0.273  -1.7817   1.4148   2.3504
 18F  H13  H  HCR6  0   0.265  -4.2237   1.6507   2.5201
 18F  H14  H  HCR6  0   0.264  -5.5953   1.8883   0.4748
 18F  H15  H  HCR6  0   0.264  -4.5037   1.8944  -1.7461
 18F  H16  H  HCR6  0   0.261  -2.0580   1.6418  -1.9219

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
 18F  CAF  CAG  aromatic  1.383  0.020  1.383
 18F  CAF  CAC  aromatic  1.395  0.020  1.395
 18F  CAG  CAH  aromatic  1.403  0.020  1.403
 18F  NAB  CAC  aromatic  1.372  0.020  1.372
 18F  NAB  CAA  aromatic  1.306  0.020  1.306
 18F  CAC  CAD  aromatic  1.402  0.020  1.402
 18F  CAK  CAL  aromatic  1.387  0.020  1.387
 18F  CAK  CAJ  aromatic  1.394  0.020  1.394
 18F  CAL  CAM  aromatic  1.389  0.020  1.389
 18F  CAH  CAI  aromatic  1.384  0.020  1.384
 18F  CAA  CAJ  single    1.469  0.020  1.469
 18F  CAA  NAE  aromatic  1.369  0.020  1.369
 18F  CAJ  CAO  aromatic  1.394  0.020  1.394
 18F  CAD  CAI  aromatic  1.390  0.020  1.390
 18F  CAD  NAE  aromatic  1.373  0.020  1.373
 18F  CAM  CAN  aromatic  1.389  0.020  1.389
 18F  NAE  CAP  single    1.450  0.020  1.450
 18F  CAO  CAN  aromatic  1.387  0.020  1.387
 18F  CAP  CAQ  single    1.508  0.020  1.508
 18F  CAV  CAU  aromatic  1.390  0.020  1.390
 18F  CAV  CAQ  aromatic  1.389  0.020  1.389
 18F  CAU  CAT  aromatic  1.387  0.020  1.387
 18F  CAQ  CAR  aromatic  1.393  0.020  1.393
 18F  CAT  CAS  aromatic  1.391  0.020  1.391
 18F  CAR  CAS  aromatic  1.386  0.020  1.386
 18F  CAR  H1   single    0.930  0.020  1.080
 18F  CAS  H2   single    0.930  0.020  1.080
 18F  CAT  H3   single    0.930  0.020  1.080
 18F  CAU  H4   single    0.930  0.020  1.080
 18F  CAV  H5   single    0.930  0.020  1.080
 18F  CAP  H6   single    0.970  0.020  1.090
 18F  CAP  H7   single    0.970  0.020  1.090
 18F  CAI  H8   single    0.930  0.020  1.080
 18F  CAH  H9   single    0.930  0.020  1.080
 18F  CAG  H10  single    0.930  0.020  1.080
 18F  CAF  H11  single    0.930  0.020  1.080
 18F  CAK  H12  single    0.930  0.020  1.080
 18F  CAL  H13  single    0.930  0.020  1.080
 18F  CAM  H14  single    0.930  0.020  1.080
 18F  CAN  H15  single    0.930  0.020  1.080
 18F  CAO  H16  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
 18F  H1   CAR  CAQ  120.15  3.000
 18F  H1   CAR  CAS  119.37  3.000
 18F  CAQ  CAR  CAS  120.48  3.000
 18F  H2   CAS  CAT  120.04  3.000
 18F  H2   CAS  CAR  119.83  3.000
 18F  CAT  CAS  CAR  120.14  3.000
 18F  H3   CAT  CAU  120.24  3.000
 18F  H3   CAT  CAS  120.04  3.000
 18F  CAU  CAT  CAS  119.71  3.000
 18F  H4   CAU  CAV  119.78  3.000
 18F  H4   CAU  CAT  120.23  3.000
 18F  CAV  CAU  CAT  119.99  3.000
 18F  H5   CAV  CAQ  119.68  3.000
 18F  H5   CAV  CAU  119.71  3.000
 18F  CAQ  CAV  CAU  120.62  3.000
 18F  CAP  CAQ  CAV  120.65  3.000
 18F  CAV  CAQ  CAR  119.06  3.000
 18F  CAP  CAQ  CAR  120.29  3.000
 18F  H7   CAP  H6   106.59  3.000
 18F  H7   CAP  NAE  108.71  3.000
 18F  H6   CAP  NAE  108.53  3.000
 18F  H7   CAP  CAQ  110.55  3.000
 18F  H6   CAP  CAQ  110.21  3.000
 18F  NAE  CAP  CAQ  112.08  3.000
 18F  CAA  NAE  CAD  106.44  3.000
 18F  CAD  NAE  CAP  124.03  3.000
 18F  CAA  NAE  CAP  128.62  3.000
 18F  CAC  CAD  CAI  122.55  3.000
 18F  CAI  CAD  NAE  132.16  3.000
 18F  CAC  CAD  NAE  105.29  3.000
 18F  H8   CAI  CAH  120.92  3.000
 18F  H8   CAI  CAD  122.45  3.000
 18F  CAH  CAI  CAD  116.62  3.000
 18F  H9   CAH  CAG  119.18  3.000
 18F  H9   CAH  CAI  119.25  3.000
 18F  CAG  CAH  CAI  121.56  3.000
 18F  H10  CAG  CAF  119.57  3.000
 18F  H10  CAG  CAH  119.02  3.000
 18F  CAF  CAG  CAH  121.40  3.000
 18F  H11  CAF  CAC  120.84  3.000
 18F  H11  CAF  CAG  121.32  3.000
 18F  CAC  CAF  CAG  117.84  3.000
 18F  NAB  CAC  CAF  130.12  3.000
 18F  NAB  CAC  CAD  109.85  3.000
 18F  CAF  CAC  CAD  120.03  3.000
 18F  CAA  NAB  CAC  105.41  3.000
 18F  CAJ  CAA  NAB  123.37  3.000
 18F  CAJ  CAA  NAE  123.63  3.000
 18F  NAB  CAA  NAE  113.00  3.000
 18F  CAO  CAJ  CAK  119.44  3.000
 18F  CAO  CAJ  CAA  119.00  3.000
 18F  CAK  CAJ  CAA  121.54  3.000
 18F  H12  CAK  CAL  119.64  3.000
 18F  H12  CAK  CAJ  120.16  3.000
 18F  CAL  CAK  CAJ  120.19  3.000
 18F  H13  CAL  CAM  120.15  3.000
 18F  H13  CAL  CAK  119.71  3.000
 18F  CAM  CAL  CAK  120.14  3.000
 18F  H14  CAM  CAN  120.06  3.000
 18F  H14  CAM  CAL  120.05  3.000
 18F  CAN  CAM  CAL  119.89  3.000
 18F  H15  CAN  CAO  119.70  3.000
 18F  H15  CAN  CAM  120.17  3.000
 18F  CAO  CAN  CAM  120.13  3.000
 18F  H16  CAO  CAN  120.05  3.000
 18F  H16  CAO  CAJ  119.73  3.000
 18F  CAN  CAO  CAJ  120.21  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
 18F  CONST_01  CAU  CAV  CAQ  CAR    0.00   0.0  0
 18F  CONST_02  CAU  CAT  CAS  CAR    0.00   0.0  0
 18F  CONST_03  CAV  CAU  CAT  CAS    0.00   0.0  0
 18F  CONST_04  CAV  CAQ  CAR  CAS    0.00   0.0  0
 18F  CONST_05  CAQ  CAV  CAU  CAT    0.00   0.0  0
 18F  CONST_06  CAQ  CAR  CAS  CAT    0.00   0.0  0
 18F  CONST_07  CAC  NAB  CAA  NAE    0.00   0.0  0
 18F  CONST_10  CAF  CAC  CAD  NAE  180.00   0.0  0
 18F  CONST_11  NAB  CAC  CAD  NAE    0.00   0.0  0
 18F  CONST_12  CAH  CAI  CAD  NAE  180.00   0.0  0
 18F  CONST_13  CAG  CAF  CAC  CAD    0.00   0.0  0
 18F  CONST_14  CAA  NAB  CAC  CAD    0.00   0.0  0
 18F  CONST_15  CAG  CAH  CAI  CAD    0.00   0.0  0
 18F  CONST_16  NAB  CAA  NAE  CAD    0.00   0.0  0
 18F  CONST_17  CAJ  CAA  NAE  CAD  180.00   0.0  0
 18F  CONST_18  CAF  CAG  CAH  CAI    0.00   0.0  0
 18F  CONST_19  CAF  CAC  CAD  CAI    0.00   0.0  0
 18F  CONST_20  NAB  CAC  CAD  CAI  180.00   0.0  0
 18F  CONST_21  CAA  NAE  CAD  CAI  180.00   0.0  0
 18F  CONST_22  CAC  CAF  CAG  CAH    0.00   0.0  0
 18F  CONST_23  CAC  CAD  CAI  CAH    0.00   0.0  0
 18F  CONST_24  NAB  CAC  CAF  CAG  180.00   0.0  0
 18F  CONST_25  CAA  NAB  CAC  CAF  180.00   0.0  0
 18F  CONST_26  CAJ  CAA  NAB  CAC  180.00   0.0  0
 18F  CONST_27  CAA  NAE  CAD  CAC    0.00   0.0  0
 18F  CONST_30  CAL  CAK  CAJ  CAA  180.00   0.0  0
 18F  CONST_31  CAN  CAO  CAJ  CAA  180.00   0.0  0
 18F  CONST_32  CAM  CAL  CAK  CAJ    0.00   0.0  0
 18F  CONST_33  CAM  CAN  CAO  CAJ    0.00   0.0  0
 18F  CONST_34  CAN  CAM  CAL  CAK    0.00   0.0  0
 18F  CONST_35  CAN  CAO  CAJ  CAK    0.00   0.0  0
 18F  CONST_36  CAO  CAJ  CAK  CAL    0.00   0.0  0
 18F  CONST_37  CAO  CAN  CAM  CAL    0.00   0.0  0
 18F  CONST_38  CAP  CAQ  CAR  CAS  180.00   0.0  0
 18F  CONST_39  CAP  CAQ  CAV  CAU  180.00   0.0  0
 18F  CONST_40  NAB  CAA  NAE  CAP  180.00   0.0  0
 18F  CONST_41  CAJ  CAA  NAE  CAP    0.00   0.0  0
 18F  CONST_42  CAC  CAD  NAE  CAP  180.00   0.0  0
 18F  CONST_43  CAI  CAD  NAE  CAP    0.00   0.0  0
 18F  CONST_44  H5   CAV  CAQ  CAR  180.00   0.0  0
 18F  CONST_45  H3   CAT  CAS  CAR  180.00   0.0  0
 18F  CONST_46  H4   CAU  CAT  CAS  180.00   0.0  0
 18F  CONST_47  H1   CAR  CAS  CAT  180.00   0.0  0
 18F  CONST_48  H2   CAS  CAT  CAU  180.00   0.0  0
 18F  CONST_49  H8   CAI  CAD  NAE    0.00   0.0  0
 18F  CONST_50  H11  CAF  CAC  CAD  180.00   0.0  0
 18F  CONST_51  H9   CAH  CAI  CAD  180.00   0.0  0
 18F  CONST_52  H10  CAG  CAH  CAI  180.00   0.0  0
 18F  CONST_53  H12  CAK  CAJ  CAA    0.00   0.0  0
 18F  CONST_54  H16  CAO  CAJ  CAA    0.00   0.0  0
 18F  CONST_55  H13  CAL  CAK  CAJ  180.00   0.0  0
 18F  CONST_56  H15  CAN  CAO  CAJ  180.00   0.0  0
 18F  CONST_57  H14  CAM  CAL  CAK  180.00   0.0  0
 18F  Var_01    NAE  CAP  CAQ  CAR  -59.79  30.0  2
 18F  Var_02    CAA  NAE  CAP  CAQ  100.34  30.0  2

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
 18F  plan-1  CAR  0.020
 18F  plan-1  CAS  0.020
 18F  plan-1  CAT  0.020
 18F  plan-1  CAU  0.020
 18F  plan-1  CAV  0.020
 18F  plan-1  CAQ  0.020
 18F  plan-1  CAP  0.020
 18F  plan-1  H1   0.020
 18F  plan-1  H2   0.020
 18F  plan-1  H3   0.020
 18F  plan-1  H4   0.020
 18F  plan-1  H5   0.020
 18F  plan-2  CAA  0.020
 18F  plan-2  CAJ  0.020
 18F  plan-2  CAK  0.020
 18F  plan-2  CAL  0.020
 18F  plan-2  CAM  0.020
 18F  plan-2  CAN  0.020
 18F  plan-2  CAO  0.020
 18F  plan-2  H12  0.020
 18F  plan-2  H13  0.020
 18F  plan-2  H14  0.020
 18F  plan-2  H15  0.020
 18F  plan-2  H16  0.020
 18F  plan-3  CAP  0.020
 18F  plan-3  NAE  0.020
 18F  plan-3  CAD  0.020
 18F  plan-3  CAI  0.020
 18F  plan-3  CAH  0.020
 18F  plan-3  CAG  0.020
 18F  plan-3  CAF  0.020
 18F  plan-3  CAC  0.020
 18F  plan-3  NAB  0.020
 18F  plan-3  CAA  0.020
 18F  plan-3  CAJ  0.020
 18F  plan-3  H8   0.020
 18F  plan-3  H9   0.020
 18F  plan-3  H10  0.020
 18F  plan-3  H11  0.020

