# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:53:59 2020
#   Inital geometry file: a 75 line input string
#   Ligand name: 1-[(4-fluorophenyl)methyl]benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(Cn2cnc3ccccc23)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
 GQP  GQP  1-[(4-fluorophenyl)methyl]benzimidazole  ligand  28  17  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GQP
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
 GQP  N1   N  N     0  -0.470   2.6873  -2.0927  -0.3765
 GQP  C4   C  CR56  0   0.346   1.7413  -0.1292   0.2862
 GQP  C5   C  CR56  0   0.120   2.7918  -0.7218  -0.4343
 GQP  C6   C  CR16  0  -0.322   3.7405   0.0815  -1.0668
 GQP  C7   C  CR15  0   0.104   1.6265  -2.3120   0.3445
 GQP  C10  C  CR16  0  -0.259  -1.7333  -0.8607  -0.3734
 GQP  C13  C  CR16  0  -0.399  -3.0901   1.2229   0.8681
 GQP  C1   C  CR16  0  -0.273   3.6042   1.4534  -0.9574
 GQP  C11  C  CR16  0  -0.398  -2.8019  -0.2599  -1.0196
 GQP  C12  C  CR6   0   0.518  -3.4631   0.7741  -0.3821
 GQP  C14  C  CR16  0  -0.289  -2.0134   0.6102   1.4963
 GQP  C2   C  CR16  0  -0.276   2.5473   2.0281  -0.2341
 GQP  C3   C  CR16  0  -0.295   1.5957   1.2493   0.4008
 GQP  C9   C  CR6   0   0.095  -1.3282  -0.4342   0.8886
 GQP  N2   N  NR5   0  -0.505   1.0102  -1.1818   0.7766
 GQP  H1   H  HCR6  0   0.255   4.5579  -0.3599  -1.6225
 GQP  H2   H  HCR5  0   0.293   1.2367  -3.2868   0.6018
 GQP  H3   H  HCH2  0   0.285   0.0572  -0.5739   2.5213
 GQP  H4   H  HCH2  0   0.293  -0.4444  -2.1243   1.8750
 GQP  H5   H  HCR6  0   0.263  -1.2125  -1.6715  -0.8687
 GQP  H6   H  HCR6  0   0.282  -3.6227   2.0358   1.3436
 GQP  H7   H  HCR6  0   0.253   4.3261   2.1006  -1.4381
 GQP  H8   H  HCR6  0   0.283  -3.1156  -0.5907  -2.0008
 GQP  H9   H  HCR6  0   0.270  -1.7086   0.9586   2.4755
 GQP  H10  H  HCR6  0   0.256   2.4740   3.1060  -0.1725
 GQP  H11  H  HCR6  0   0.269   0.7810   1.7006   0.9512
 GQP  C8   C  CH2   0  -0.387  -0.1782  -1.1037   1.5962
 GQP  F1   F  F     0  -0.315  -4.4996   1.3604  -1.0021

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
 GQP  C1   C6   aromatic  1.383  0.020  1.383
 GQP  C1   C2   aromatic  1.404  0.020  1.404
 GQP  C6   C5   aromatic  1.395  0.020  1.395
 GQP  C2   C3   aromatic  1.384  0.020  1.384
 GQP  C5   C4   aromatic  1.405  0.020  1.405
 GQP  C5   N1   aromatic  1.376  0.020  1.376
 GQP  C3   C4   aromatic  1.391  0.020  1.391
 GQP  C4   N2   aromatic  1.372  0.020  1.372
 GQP  C11  C10  aromatic  1.386  0.020  1.386
 GQP  C11  C12  aromatic  1.383  0.020  1.383
 GQP  N1   C7   aromatic  1.301  0.020  1.301
 GQP  C10  C9   aromatic  1.392  0.020  1.392
 GQP  F1   C12  single    1.343  0.020  1.343
 GQP  C12  C13  aromatic  1.380  0.020  1.380
 GQP  N2   C7   aromatic  1.358  0.020  1.358
 GQP  N2   C8   single    1.446  0.020  1.446
 GQP  C9   C8   single    1.507  0.020  1.507
 GQP  C9   C14  aromatic  1.389  0.020  1.389
 GQP  C13  C14  aromatic  1.389  0.020  1.389
 GQP  C6   H1   single    0.930  0.020  1.080
 GQP  C7   H2   single    0.930  0.020  1.080
 GQP  C8   H3   single    0.970  0.020  1.090
 GQP  C8   H4   single    0.970  0.020  1.090
 GQP  C10  H5   single    0.930  0.020  1.080
 GQP  C13  H6   single    0.930  0.020  1.080
 GQP  C1   H7   single    0.930  0.020  1.080
 GQP  C11  H8   single    0.930  0.020  1.080
 GQP  C14  H9   single    0.930  0.020  1.080
 GQP  C2   H10  single    0.930  0.020  1.080
 GQP  C3   H11  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
 GQP  C7   N1   C5   104.66  3.000
 GQP  N2   C4   C3   132.45  3.000
 GQP  N2   C4   C5   104.96  3.000
 GQP  C3   C4   C5   122.58  3.000
 GQP  C6   C5   C4   119.89  3.000
 GQP  C4   C5   N1   109.99  3.000
 GQP  C6   C5   N1   130.13  3.000
 GQP  H1   C6   C1   121.30  3.000
 GQP  H1   C6   C5   120.77  3.000
 GQP  C1   C6   C5   117.93  3.000
 GQP  H2   C7   N2   120.74  3.000
 GQP  H2   C7   N1   125.30  3.000
 GQP  N2   C7   N1   113.96  3.000
 GQP  H5   C10  C9   120.25  3.000
 GQP  H5   C10  C11  118.81  3.000
 GQP  C9   C10  C11  120.94  3.000
 GQP  H6   C13  C14  120.94  3.000
 GQP  H6   C13  C12  120.64  3.000
 GQP  C14  C13  C12  118.41  3.000
 GQP  H7   C1   C2   119.09  3.000
 GQP  H7   C1   C6   119.50  3.000
 GQP  C2   C1   C6   121.41  3.000
 GQP  H8   C11  C12  120.53  3.000
 GQP  H8   C11  C10  120.93  3.000
 GQP  C12  C11  C10  118.54  3.000
 GQP  F1   C12  C11  118.86  3.000
 GQP  F1   C12  C13  119.02  3.000
 GQP  C11  C12  C13  122.12  3.000
 GQP  H9   C14  C9   119.90  3.000
 GQP  H9   C14  C13  119.02  3.000
 GQP  C9   C14  C13  121.08  3.000
 GQP  H10  C2   C3   119.20  3.000
 GQP  H10  C2   C1   119.22  3.000
 GQP  C3   C2   C1   121.58  3.000
 GQP  H11  C3   C2   121.10  3.000
 GQP  H11  C3   C4   122.29  3.000
 GQP  C2   C3   C4   116.61  3.000
 GQP  C14  C9   C10  118.90  3.000
 GQP  C14  C9   C8   120.33  3.000
 GQP  C10  C9   C8   120.76  3.000
 GQP  C8   N2   C7   126.76  3.000
 GQP  C8   N2   C4   126.81  3.000
 GQP  C7   N2   C4   106.43  3.000
 GQP  H4   C8   H3   106.86  3.000
 GQP  H4   C8   N2   107.16  3.000
 GQP  H3   C8   N2   109.23  3.000
 GQP  H4   C8   C9   110.44  3.000
 GQP  H3   C8   C9   110.29  3.000
 GQP  N2   C8   C9   112.65  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
 GQP  CONST_01  C1   C6   C5   N1   180.00   0.0  0
 GQP  CONST_02  C3   C4   C5   N1   180.00   0.0  0
 GQP  CONST_03  N2   C4   C5   N1     0.00   0.0  0
 GQP  CONST_04  C4   N2   C7   N1     0.00   0.0  0
 GQP  CONST_05  C1   C6   C5   C4     0.00   0.0  0
 GQP  CONST_06  C7   N1   C5   C4     0.00   0.0  0
 GQP  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 GQP  CONST_08  C2   C1   C6   C5     0.00   0.0  0
 GQP  CONST_09  C2   C3   C4   C5     0.00   0.0  0
 GQP  CONST_10  C7   N2   C4   C5     0.00   0.0  0
 GQP  CONST_11  N2   C7   N1   C5     0.00   0.0  0
 GQP  CONST_12  C3   C2   C1   C6     0.00   0.0  0
 GQP  CONST_13  C3   C4   C5   C6     0.00   0.0  0
 GQP  CONST_14  N2   C4   C5   C6   180.00   0.0  0
 GQP  CONST_15  C7   N1   C5   C6   180.00   0.0  0
 GQP  CONST_16  C3   C4   N2   C7   180.00   0.0  0
 GQP  CONST_17  C13  C12  C11  C10    0.00   0.0  0
 GQP  CONST_18  C13  C14  C9   C10    0.00   0.0  0
 GQP  CONST_19  C14  C9   C10  C11    0.00   0.0  0
 GQP  CONST_20  C14  C13  C12  C11    0.00   0.0  0
 GQP  CONST_21  C9   C10  C11  C12    0.00   0.0  0
 GQP  CONST_22  C9   C14  C13  C12    0.00   0.0  0
 GQP  CONST_23  N2   C4   C3   C2   180.00   0.0  0
 GQP  CONST_24  C8   N2   C7   N1   180.00   0.0  0
 GQP  CONST_25  C8   N2   C4   C5   180.00   0.0  0
 GQP  CONST_26  C3   C4   N2   C8     0.00   0.0  0
 GQP  CONST_27  C11  C10  C9   C8   180.00   0.0  0
 GQP  CONST_28  C13  C14  C9   C8   180.00   0.0  0
 GQP  CONST_29  F1   C12  C11  C10  180.00   0.0  0
 GQP  CONST_30  F1   C12  C13  C14  180.00   0.0  0
 GQP  CONST_31  H1   C6   C5   N1     0.00   0.0  0
 GQP  CONST_32  H10  C2   C3   C4   180.00   0.0  0
 GQP  CONST_33  H2   C7   N2   C4   180.00   0.0  0
 GQP  CONST_34  H7   C1   C6   C5   180.00   0.0  0
 GQP  CONST_35  H11  C3   C4   C5   180.00   0.0  0
 GQP  CONST_36  H9   C14  C9   C10  180.00   0.0  0
 GQP  CONST_37  H8   C11  C12  C13  180.00   0.0  0
 GQP  CONST_38  H6   C13  C12  C11  180.00   0.0  0
 GQP  CONST_39  H5   C10  C11  C12  180.00   0.0  0
 GQP  Var_01    C9   C8   N2   C4    63.24  30.0  2
 GQP  Var_02    N2   C8   C9   C10   52.00  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
 GQP  plan-1  C10  0.020
 GQP  plan-1  C13  0.020
 GQP  plan-1  C11  0.020
 GQP  plan-1  C12  0.020
 GQP  plan-1  C14  0.020
 GQP  plan-1  C9   0.020
 GQP  plan-1  H5   0.020
 GQP  plan-1  H6   0.020
 GQP  plan-1  H8   0.020
 GQP  plan-1  H9   0.020
 GQP  plan-1  C8   0.020
 GQP  plan-1  F1   0.020
 GQP  plan-2  N1   0.020
 GQP  plan-2  C4   0.020
 GQP  plan-2  C5   0.020
 GQP  plan-2  C6   0.020
 GQP  plan-2  C7   0.020
 GQP  plan-2  C1   0.020
 GQP  plan-2  C2   0.020
 GQP  plan-2  C3   0.020
 GQP  plan-2  N2   0.020
 GQP  plan-2  H1   0.020
 GQP  plan-2  H2   0.020
 GQP  plan-2  H7   0.020
 GQP  plan-2  H10  0.020
 GQP  plan-2  H11  0.020
 GQP  plan-2  C8   0.020

