# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:23:20 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: 1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)-4-methyl-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc2n(Cc3c(F)cccc3F)c(nc12)c4c(F)cccc4F
#
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
 T50  T50  1-(2,6-difluorobenzyl)-2-(2,6-difluorophenyl)-4-methyl-1H-benzimidazole  ligand  41  27  .  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_T50
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
 T50  N1    N  NR5   0  -0.540   0.9933   0.0710  -0.7368
 T50  C2    C  CR5   0   0.482   0.3095   1.0279  -0.0463
 T50  N3    N  N     0  -0.447   1.0781   1.9569   0.4453
 T50  C4    C  CR6   0   0.012   3.5581   2.2655   0.3291
 T50  C5    C  CR16  0  -0.329   4.7006   1.6726  -0.1816
 T50  C6    C  CR16  0  -0.263   4.6582   0.4813  -0.9247
 T50  C7    C  CR16  0  -0.328   3.4696  -0.1696  -1.1928
 T50  C8    C  CR56  0   0.376   2.3182   0.4215  -0.6800
 T50  C9    C  CR56  0   0.090   2.3497   1.6088   0.0639
 T50  C17   C  CR6   0  -0.464  -1.1474   0.9729   0.1346
 T50  C18   C  CR6   0   0.578  -2.0311   1.2583  -0.8948
 T50  C4A   C  CH3   0  -0.726   3.5868   3.5321   1.1249
 T50  C19   C  CR16  0  -0.415  -3.4010   1.2157  -0.7396
 T50  C20   C  CR16  0  -0.223  -3.9087   0.8750   0.5056
 T50  C21   C  CR16  0  -0.413  -3.0673   0.5844   1.5710
 T50  C22   C  CR6   0   0.582  -1.7063   0.6441   1.3626
 T50  F1    F  F     0  -0.296  -1.5131   1.5867  -2.0842
 T50  F2    F  F     0  -0.292  -0.8751   0.3522   2.3659
 T50  C10   C  CH2   0  -0.371   0.4448  -1.1094  -1.3791
 T50  C11   C  CR6   0  -0.311  -0.4199  -1.9166  -0.4521
 T50  C12   C  CR6   0   0.571   0.0755  -2.4166   0.7447
 T50  C13   C  CR16  0  -0.416  -0.6852  -3.1396   1.6390
 T50  C14   C  CR16  0  -0.231  -2.0120  -3.3909   1.3194
 T50  C15   C  CR16  0  -0.410  -2.5563  -2.9297   0.1308
 T50  C16   C  CR6   0   0.561  -1.7487  -2.2083  -0.7256
 T50  F3    F  F     0  -0.300   1.3605  -2.1720   1.0334
 T50  F4    F  F     0  -0.305  -2.2757  -1.7589  -1.8722
 T50  H5    H  HCR6  0   0.246   5.6612   2.1405  -0.0032
 T50  H6    H  HCR6  0   0.255   5.5847   0.0633  -1.2961
 T50  H7    H  HCR6  0   0.267   3.4501  -1.0848  -1.7699
 T50  H4A1  H  HCH3  0   0.245   2.9866   4.3114   0.6527
 T50  H4A2  H  HCH3  0   0.244   3.1771   3.3800   2.1249
 T50  H4A3  H  HCH3  0   0.244   4.6031   3.9085   1.2314
 T50  H19   H  HCR6  0   0.290  -4.0538   1.4452  -1.5706
 T50  H20   H  HCR6  0   0.286  -4.9796   0.8328   0.6484
 T50  H21   H  HCR6  0   0.289  -3.4608   0.3120   2.5406
 T50  H101  H  HCH2  0   0.300  -0.1054  -0.8193  -2.2720
 T50  H102  H  HCH2  0   0.307   1.2852  -1.7110  -1.7241
 T50  H13   H  HCR6  0   0.287  -0.2492  -3.5015   2.5601
 T50  H14   H  HCR6  0   0.282  -2.6282  -3.9557   2.0051
 T50  H15   H  HCR6  0   0.286  -3.5881  -3.1236  -0.1279

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
 T50  N1   C2    aromatic  1.364  0.020  1.364
 T50  N1   C8    aromatic  1.372  0.020  1.372
 T50  N1   C10   single    1.452  0.020  1.452
 T50  C2   N3    aromatic  1.302  0.020  1.302
 T50  C2   C17   single    1.469  0.020  1.469
 T50  N3   C9    aromatic  1.372  0.020  1.372
 T50  C4   C5    aromatic  1.385  0.020  1.385
 T50  C4   C9    aromatic  1.401  0.020  1.401
 T50  C4   C4A   single    1.496  0.020  1.496
 T50  C5   C6    aromatic  1.405  0.020  1.405
 T50  C5   H5    single    0.930  0.020  1.080
 T50  C6   C7    aromatic  1.381  0.020  1.381
 T50  C6   H6    single    0.930  0.020  1.080
 T50  C7   C8    aromatic  1.392  0.020  1.392
 T50  C7   H7    single    0.930  0.020  1.080
 T50  C8   C9    aromatic  1.401  0.020  1.401
 T50  C17  C18   aromatic  1.386  0.020  1.386
 T50  C17  C22   aromatic  1.389  0.020  1.389
 T50  C18  C19   aromatic  1.379  0.020  1.379
 T50  C18  F1    single    1.338  0.020  1.338
 T50  C4A  H4A1  single    0.970  0.020  1.090
 T50  C4A  H4A2  single    0.970  0.020  1.090
 T50  C4A  H4A3  single    0.970  0.020  1.090
 T50  C19  C20   aromatic  1.387  0.020  1.387
 T50  C19  H19   single    0.930  0.020  1.080
 T50  C20  C21   aromatic  1.388  0.020  1.388
 T50  C20  H20   single    0.930  0.020  1.080
 T50  C21  C22   aromatic  1.378  0.020  1.378
 T50  C21  H21   single    0.930  0.020  1.080
 T50  C22  F2    single    1.335  0.020  1.335
 T50  C10  C11   single    1.503  0.020  1.503
 T50  C10  H101  single    0.970  0.020  1.090
 T50  C10  H102  single    0.970  0.020  1.090
 T50  C11  C12   aromatic  1.389  0.020  1.389
 T50  C11  C16   aromatic  1.388  0.020  1.388
 T50  C12  C13   aromatic  1.379  0.020  1.379
 T50  C12  F3    single    1.339  0.020  1.339
 T50  C13  C14   aromatic  1.388  0.020  1.388
 T50  C13  H13   single    0.930  0.020  1.080
 T50  C14  C15   aromatic  1.386  0.020  1.386
 T50  C14  H14   single    0.930  0.020  1.080
 T50  C15  C16   aromatic  1.381  0.020  1.381
 T50  C15  H15   single    0.930  0.020  1.080
 T50  C16  F4    single    1.340  0.020  1.340

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
 T50  C10   N1   C8    126.24  3.000
 T50  C10   N1   C2    127.24  3.000
 T50  C8    N1   C2    106.50  3.000
 T50  C17   C2   N3    124.45  3.000
 T50  C17   C2   N1    122.23  3.000
 T50  N3    C2   N1    113.31  3.000
 T50  C9    N3   C2    105.13  3.000
 T50  C4A   C4   C9    120.94  3.000
 T50  C4A   C4   C5    122.88  3.000
 T50  C9    C4   C5    116.18  3.000
 T50  H5    C5   C6    118.70  3.000
 T50  H5    C5   C4    119.07  3.000
 T50  C6    C5   C4    122.23  3.000
 T50  H6    C6   C7    119.21  3.000
 T50  H6    C6   C5    118.90  3.000
 T50  C7    C6   C5    121.88  3.000
 T50  H7    C7   C8    122.72  3.000
 T50  H7    C7   C6    121.17  3.000
 T50  C8    C7   C6    116.11  3.000
 T50  C9    C8   C7    122.45  3.000
 T50  C9    C8   N1    105.08  3.000
 T50  C7    C8   N1    132.47  3.000
 T50  C8    C9   C4    121.14  3.000
 T50  C8    C9   N3    109.97  3.000
 T50  C4    C9   N3    128.89  3.000
 T50  C22   C17  C18   116.67  3.000
 T50  C22   C17  C2    121.12  3.000
 T50  C18   C17  C2    122.21  3.000
 T50  F1    C18  C19   119.47  3.000
 T50  F1    C18  C17   117.63  3.000
 T50  C19   C18  C17   122.90  3.000
 T50  H4A3  C4A  H4A2  108.00  3.000
 T50  H4A3  C4A  H4A1  107.99  3.000
 T50  H4A2  C4A  H4A1  106.83  3.000
 T50  H4A3  C4A  C4    111.26  3.000
 T50  H4A2  C4A  C4    111.23  3.000
 T50  H4A1  C4A  C4    111.34  3.000
 T50  H19   C19  C20   121.40  3.000
 T50  H19   C19  C18   120.43  3.000
 T50  C20   C19  C18   118.17  3.000
 T50  H20   C20  C21   119.39  3.000
 T50  H20   C20  C19   119.39  3.000
 T50  C21   C20  C19   121.23  3.000
 T50  H21   C21  C22   120.39  3.000
 T50  H21   C21  C20   121.35  3.000
 T50  C22   C21  C20   118.25  3.000
 T50  F2    C22  C21   119.45  3.000
 T50  F2    C22  C17   117.75  3.000
 T50  C21   C22  C17   122.78  3.000
 T50  H102  C10  H101  106.10  3.000
 T50  H102  C10  C11   110.03  3.000
 T50  H101  C10  C11   111.01  3.000
 T50  H102  C10  N1    107.31  3.000
 T50  H101  C10  N1    109.72  3.000
 T50  C11   C10  N1    112.41  3.000
 T50  C16   C11  C12   115.84  3.000
 T50  C16   C11  C10   122.84  3.000
 T50  C12   C11  C10   121.32  3.000
 T50  F3    C12  C13   119.03  3.000
 T50  F3    C12  C11   117.54  3.000
 T50  C13   C12  C11   123.44  3.000
 T50  H13   C13  C14   121.41  3.000
 T50  H13   C13  C12   120.36  3.000
 T50  C14   C13  C12   118.23  3.000
 T50  H14   C14  C15   119.59  3.000
 T50  H14   C14  C13   119.57  3.000
 T50  C15   C14  C13   120.84  3.000
 T50  H15   C15  C16   120.23  3.000
 T50  H15   C15  C14   121.34  3.000
 T50  C16   C15  C14   118.43  3.000
 T50  F4    C16  C15   118.43  3.000
 T50  F4    C16  C11   118.35  3.000
 T50  C15   C16  C11   123.22  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
 T50  CONST_01  C9    N3   C2   N1     0.00   0.0  0
 T50  CONST_04  C6    C7   C8   N1   180.00   0.0  0
 T50  CONST_05  N3    C9   C8   N1     0.00   0.0  0
 T50  CONST_06  C4    C9   C8   N1   180.00   0.0  0
 T50  CONST_07  C7    C8   N1   C2   180.00   0.0  0
 T50  CONST_08  C9    C8   N1   C2     0.00   0.0  0
 T50  CONST_09  C4    C9   N3   C2   180.00   0.0  0
 T50  CONST_10  C8    C9   N3   C2     0.00   0.0  0
 T50  CONST_11  C19   C18  C17  C2   180.00   0.0  0
 T50  CONST_12  C21   C22  C17  C2   180.00   0.0  0
 T50  CONST_13  C8    N1   C2   N3     0.00   0.0  0
 T50  CONST_16  C5    C4   C9   N3   180.00   0.0  0
 T50  CONST_17  C7    C8   C9   N3   180.00   0.0  0
 T50  CONST_18  C7    C6   C5   C4     0.00   0.0  0
 T50  CONST_19  C7    C8   C9   C4     0.00   0.0  0
 T50  CONST_20  C8    C9   C4   C5     0.00   0.0  0
 T50  CONST_21  C8    C7   C6   C5     0.00   0.0  0
 T50  CONST_22  C9    C4   C5   C6     0.00   0.0  0
 T50  CONST_23  C9    C8   C7   C6     0.00   0.0  0
 T50  CONST_24  C17   C2   N1   C8   180.00   0.0  0
 T50  CONST_25  C17   C2   N3   C9   180.00   0.0  0
 T50  CONST_26  C20   C19  C18  C17    0.00   0.0  0
 T50  CONST_27  C20   C21  C22  C17    0.00   0.0  0
 T50  CONST_28  C21   C22  C17  C18    0.00   0.0  0
 T50  CONST_29  C21   C20  C19  C18    0.00   0.0  0
 T50  CONST_30  C22   C17  C18  C19    0.00   0.0  0
 T50  CONST_31  C22   C21  C20  C19    0.00   0.0  0
 T50  CONST_32  C14   C13  C12  C11    0.00   0.0  0
 T50  CONST_33  C14   C15  C16  C11    0.00   0.0  0
 T50  CONST_34  C15   C16  C11  C12    0.00   0.0  0
 T50  CONST_35  C15   C14  C13  C12    0.00   0.0  0
 T50  CONST_36  C16   C11  C12  C13    0.00   0.0  0
 T50  CONST_37  C16   C15  C14  C13    0.00   0.0  0
 T50  CONST_38  F1    C18  C17  C2     0.00   0.0  0
 T50  CONST_39  F2    C22  C17  C2     0.00   0.0  0
 T50  CONST_40  C10   N1   C2   N3   180.00   0.0  0
 T50  CONST_41  C4A   C4   C9   N3     0.00   0.0  0
 T50  CONST_42  C4A   C4   C5   C6   180.00   0.0  0
 T50  CONST_43  C10   N1   C8   C7     0.00   0.0  0
 T50  CONST_44  C4A   C4   C9   C8   180.00   0.0  0
 T50  CONST_45  C10   N1   C8   C9   180.00   0.0  0
 T50  CONST_46  C10   N1   C2   C17    0.00   0.0  0
 T50  CONST_47  F2    C22  C17  C18  180.00   0.0  0
 T50  CONST_48  F1    C18  C19  C20  180.00   0.0  0
 T50  CONST_49  F2    C22  C21  C20  180.00   0.0  0
 T50  CONST_50  F1    C18  C17  C22  180.00   0.0  0
 T50  CONST_51  C13   C12  C11  C10  180.00   0.0  0
 T50  CONST_52  C15   C16  C11  C10  180.00   0.0  0
 T50  CONST_53  F4    C16  C11  C12  180.00   0.0  0
 T50  CONST_54  F3    C12  C13  C14  180.00   0.0  0
 T50  CONST_55  F4    C16  C15  C14  180.00   0.0  0
 T50  CONST_56  F3    C12  C11  C16  180.00   0.0  0
 T50  CONST_57  H7    C7   C8   N1     0.00   0.0  0
 T50  CONST_58  H6    C6   C5   C4   180.00   0.0  0
 T50  CONST_59  H5    C5   C6   C7   180.00   0.0  0
 T50  CONST_60  H19   C19  C18  C17  180.00   0.0  0
 T50  CONST_61  H21   C21  C22  C17  180.00   0.0  0
 T50  CONST_62  H20   C20  C19  C18  180.00   0.0  0
 T50  CONST_63  H13   C13  C12  C11  180.00   0.0  0
 T50  CONST_64  H15   C15  C16  C11  180.00   0.0  0
 T50  CONST_65  H14   C14  C13  C12  180.00   0.0  0
 T50  Var_01    C12   C11  C10  N1   -57.73  30.0  2
 T50  Var_02    C11   C10  N1   C2   -51.85  30.0  2
 T50  Var_03    H4A1  C4A  C4   C5   120.97  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
 T50  plan-1  C2   0.020
 T50  plan-1  C17  0.020
 T50  plan-1  C18  0.020
 T50  plan-1  C19  0.020
 T50  plan-1  C20  0.020
 T50  plan-1  C21  0.020
 T50  plan-1  C22  0.020
 T50  plan-1  F1   0.020
 T50  plan-1  F2   0.020
 T50  plan-1  H19  0.020
 T50  plan-1  H20  0.020
 T50  plan-1  H21  0.020
 T50  plan-2  C10  0.020
 T50  plan-2  C11  0.020
 T50  plan-2  C12  0.020
 T50  plan-2  C13  0.020
 T50  plan-2  C14  0.020
 T50  plan-2  C15  0.020
 T50  plan-2  C16  0.020
 T50  plan-2  F3   0.020
 T50  plan-2  F4   0.020
 T50  plan-2  H13  0.020
 T50  plan-2  H14  0.020
 T50  plan-2  H15  0.020
 T50  plan-3  N1   0.020
 T50  plan-3  C2   0.020
 T50  plan-3  N3   0.020
 T50  plan-3  C4   0.020
 T50  plan-3  C5   0.020
 T50  plan-3  C6   0.020
 T50  plan-3  C7   0.020
 T50  plan-3  C8   0.020
 T50  plan-3  C9   0.020
 T50  plan-3  C17  0.020
 T50  plan-3  C4A  0.020
 T50  plan-3  C10  0.020
 T50  plan-3  H5   0.020
 T50  plan-3  H6   0.020
 T50  plan-3  H7   0.020

