# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 22:53:38 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 3-fluoranyl-~{N}-[1-(2-methyl-2-oxidanyl-propyl)benzimidazol-2-yl]-5-pyridin-3-yl-benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)Cn1c(NC(=O)c2cc(F)cc(c2)c3cccnc3)nc4ccccc14
#
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
 L1H  L1H  3-fluoranyl-~{N}-[1-(2-methyl-2-oxidanyl-propyl)benzimidazol-2-yl]-5-pyridin-3-yl-benzamide  ligand  51  30  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L1H
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
 L1H  C2   C  CR6   0   0.582   2.4301   1.6284   1.9111
 L1H  C3   C  CR16  0  -0.470   3.6544   1.2941   1.3720
 L1H  C4   C  CR6   0   0.126   3.7415   0.1952   0.5181
 L1H  C5   C  CR16  0  -0.345   2.5903  -0.5351   0.2340
 L1H  C6   C  CR6   0  -0.013   1.3646  -0.1714   0.7795
 L1H  C7   C  CR16  0  -0.473   1.2766   0.9224   1.6357
 L1H  C8   C  C     0   0.536   0.1727  -1.0074   0.4410
 L1H  O9   O  O     0  -0.431   0.2790  -2.1805   0.1534
 L1H  N10  N  NH1   0  -0.798  -1.0140  -0.3360   0.4624
 L1H  C11  C  CR5   0   0.682  -2.2522  -0.9188   0.3030
 L1H  C15  C  CR16  0  -0.273  -6.1211  -3.1029   0.1001
 L1H  C16  C  CR16  0  -0.277  -6.5258  -1.9326  -0.5559
 L1H  C17  C  CR16  0  -0.311  -5.6496  -0.8784  -0.7609
 L1H  C18  C  CR56  0   0.355  -4.3546  -1.0429  -0.2901
 L1H  C21  C  CT    0   0.204  -3.2215   2.2723  -0.0842
 L1H  C23  C  CH3   0  -0.685  -4.4146   2.1999   0.8596
 L1H  C27  C  CR16  0  -0.314   7.1733   0.3509  -1.0147
 L1H  C30  C  CR16  0  -0.096   5.3854  -1.5260  -0.2345
 L1H  F1   F  F     0  -0.308   2.3600   2.6699   2.7497
 L1H  N12  N  N     0  -0.476  -2.6111  -2.0924   0.7323
 L1H  C13  C  CR56  0   0.146  -3.9308  -2.2086   0.3664
 L1H  C14  C  CR16  0  -0.335  -4.8262  -3.2569   0.5668
 L1H  N19  N  NR5   0  -0.570  -3.2472  -0.2267  -0.3281
 L1H  C20  C  CH2   0  -0.343  -3.1552   1.0503  -1.0048
 L1H  C22  C  CH3   0  -0.666  -3.2906   3.5230  -0.9546
 L1H  O24  O  OH1   0  -0.681  -2.0025   2.2621   0.6560
 L1H  C25  C  CR6   0  -0.006   5.0383  -0.1851  -0.0681
 L1H  C26  C  CR16  0  -0.191   5.9702   0.7678  -0.4717
 L1H  C28  C  CR16  0  -0.067   7.4077  -1.0102  -1.1399
 L1H  N29  N  N     0  -0.397   6.5334  -1.9331  -0.7555
 L1H  H1   H  HCR6  0   0.288   4.5313   1.8716   1.6367
 L1H  H2   H  HCR6  0   0.270   2.6385  -1.3781  -0.4422
 L1H  H3   H  HCR6  0   0.284   0.3507   1.2097   2.1169
 L1H  H4   H  HNH1  0   0.449  -1.0278   0.6774   0.5675
 L1H  H5   H  HCR6  0   0.253  -6.8385  -3.9003   0.2439
 L1H  H6   H  HCR6  0   0.256  -7.5451  -1.8486  -0.9093
 L1H  H7   H  HCR6  0   0.265  -5.9709   0.0242  -1.2651
 L1H  H8   H  HCH3  0   0.248  -4.3671   1.3222   1.5047
 L1H  H9   H  HCH3  0   0.247  -4.4467   3.0858   1.4969
 L1H  H10  H  HCH3  0   0.235  -5.3521   2.1672   0.3040
 L1H  H11  H  HCR6  0   0.277   7.9142   1.0664  -1.3434
 L1H  H12  H  HCR6  0   0.266   4.7031  -2.3068   0.0866
 L1H  H13  H  HCR6  0   0.254  -4.5151  -4.1618   1.0729
 L1H  H14  H  HCH2  0   0.285  -3.9756   1.0976  -1.7200
 L1H  H15  H  HCH2  0   0.291  -2.2328   1.0775  -1.5905
 L1H  H16  H  HCH3  0   0.233  -4.2132   3.5453  -1.5354
 L1H  H17  H  HCH3  0   0.243  -3.2689   4.4218  -0.3360
 L1H  H18  H  HCH3  0   0.241  -2.4501   3.5684  -1.6492
 L1H  H19  H  HOH1  0   0.466  -2.0506   2.9106   1.3671
 L1H  H20  H  HCR6  0   0.275   5.7522   1.8246  -0.3807
 L1H  H21  H  HCR6  0   0.270   8.3372  -1.3688  -1.5667

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
 L1H  C27  C28  aromatic  1.387  0.020  1.387
 L1H  C27  C26  aromatic  1.384  0.020  1.384
 L1H  C28  N29  aromatic  1.328  0.020  1.328
 L1H  C22  C21  single    1.525  0.020  1.525
 L1H  C23  C21  single    1.523  0.020  1.523
 L1H  O24  C21  single    1.426  0.020  1.426
 L1H  C26  C25  aromatic  1.393  0.020  1.393
 L1H  C21  C20  single    1.531  0.020  1.531
 L1H  N29  C30  aromatic  1.325  0.020  1.325
 L1H  C25  C30  aromatic  1.395  0.020  1.395
 L1H  C25  C4   single    1.473  0.020  1.473
 L1H  C20  N19  single    1.448  0.020  1.448
 L1H  C4   C5   aromatic  1.393  0.020  1.393
 L1H  C4   C3   aromatic  1.394  0.020  1.394
 L1H  C5   C6   aromatic  1.390  0.020  1.390
 L1H  N19  C18  aromatic  1.376  0.020  1.376
 L1H  N19  C11  aromatic  1.366  0.020  1.366
 L1H  C3   C2   aromatic  1.379  0.020  1.379
 L1H  C17  C18  aromatic  1.388  0.020  1.388
 L1H  C17  C16  aromatic  1.386  0.020  1.386
 L1H  C18  C13  aromatic  1.403  0.020  1.403
 L1H  N10  C11  single    1.378  0.020  1.378
 L1H  N10  C8   single    1.364  0.020  1.364
 L1H  C16  C15  aromatic  1.401  0.020  1.401
 L1H  C11  N12  aromatic  1.300  0.020  1.300
 L1H  C6   C8   single    1.495  0.020  1.495
 L1H  C6   C7   aromatic  1.392  0.020  1.392
 L1H  C2   C7   aromatic  1.380  0.020  1.380
 L1H  C2   F1   single    1.339  0.020  1.339
 L1H  C13  N12  aromatic  1.374  0.020  1.374
 L1H  C13  C14  aromatic  1.393  0.020  1.393
 L1H  C8   O9   double    1.212  0.020  1.212
 L1H  C15  C14  aromatic  1.385  0.020  1.385
 L1H  C3   H1   single    0.930  0.020  1.080
 L1H  C5   H2   single    0.930  0.020  1.080
 L1H  C7   H3   single    0.930  0.020  1.080
 L1H  N10  H4   single    0.860  0.020  1.020
 L1H  C15  H5   single    0.930  0.020  1.080
 L1H  C16  H6   single    0.930  0.020  1.080
 L1H  C17  H7   single    0.930  0.020  1.080
 L1H  C23  H8   single    0.970  0.020  1.090
 L1H  C23  H9   single    0.970  0.020  1.090
 L1H  C23  H10  single    0.970  0.020  1.090
 L1H  C27  H11  single    0.930  0.020  1.080
 L1H  C30  H12  single    0.930  0.020  1.080
 L1H  C14  H13  single    0.930  0.020  1.080
 L1H  C20  H14  single    0.970  0.020  1.090
 L1H  C20  H15  single    0.970  0.020  1.090
 L1H  C22  H16  single    0.970  0.020  1.090
 L1H  C22  H17  single    0.970  0.020  1.090
 L1H  C22  H18  single    0.970  0.020  1.090
 L1H  O24  H19  single    0.850  0.020  0.980
 L1H  C26  H20  single    0.930  0.020  1.080
 L1H  C28  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
 L1H  F1   C2   C7   118.62  3.000
 L1H  F1   C2   C3   118.68  3.000
 L1H  C7   C2   C3   122.69  3.000
 L1H  H1   C3   C4   121.29  3.000
 L1H  H1   C3   C2   119.61  3.000
 L1H  C4   C3   C2   119.08  3.000
 L1H  C25  C4   C5   120.75  3.000
 L1H  C5   C4   C3   119.11  3.000
 L1H  C25  C4   C3   120.14  3.000
 L1H  H2   C5   C6   119.24  3.000
 L1H  H2   C5   C4   119.95  3.000
 L1H  C6   C5   C4   120.78  3.000
 L1H  C8   C6   C7   121.90  3.000
 L1H  C7   C6   C5   120.18  3.000
 L1H  C8   C6   C5   117.90  3.000
 L1H  H3   C7   C6   122.42  3.000
 L1H  H3   C7   C2   119.38  3.000
 L1H  C6   C7   C2   118.16  3.000
 L1H  N10  C8   O9   123.81  3.000
 L1H  O9   C8   C6   121.66  3.000
 L1H  N10  C8   C6   114.52  3.000
 L1H  H4   N10  C11  114.86  3.000
 L1H  H4   N10  C8   120.21  3.000
 L1H  C11  N10  C8   124.89  3.000
 L1H  N19  C11  N12  114.12  3.000
 L1H  N12  C11  N10  126.28  3.000
 L1H  N19  C11  N10  119.57  3.000
 L1H  H5   C15  C14  119.54  3.000
 L1H  H5   C15  C16  119.09  3.000
 L1H  C14  C15  C16  121.37  3.000
 L1H  H6   C16  C17  119.22  3.000
 L1H  H6   C16  C15  119.32  3.000
 L1H  C17  C16  C15  121.46  3.000
 L1H  H7   C17  C18  122.26  3.000
 L1H  H7   C17  C16  121.02  3.000
 L1H  C18  C17  C16  116.72  3.000
 L1H  N19  C18  C13  105.22  3.000
 L1H  C13  C18  C17  122.61  3.000
 L1H  N19  C18  C17  132.16  3.000
 L1H  O24  C21  C22  109.92  3.000
 L1H  O24  C21  C20  105.62  3.000
 L1H  C22  C21  C20  108.25  3.000
 L1H  C20  C21  C23  111.62  3.000
 L1H  O24  C21  C23  110.34  3.000
 L1H  C22  C21  C23  110.92  3.000
 L1H  H10  C23  H9   107.25  3.000
 L1H  H10  C23  H8   108.35  3.000
 L1H  H9   C23  H8   108.01  3.000
 L1H  H10  C23  C21  111.05  3.000
 L1H  H9   C23  C21  110.25  3.000
 L1H  H8   C23  C21  111.77  3.000
 L1H  H11  C27  C28  120.41  3.000
 L1H  H11  C27  C26  121.04  3.000
 L1H  C28  C27  C26  118.55  3.000
 L1H  H12  C30  N29  116.10  3.000
 L1H  H12  C30  C25  119.98  3.000
 L1H  N29  C30  C25  123.91  3.000
 L1H  C13  N12  C11  104.68  3.000
 L1H  C14  C13  N12  129.97  3.000
 L1H  C14  C13  C18  119.89  3.000
 L1H  N12  C13  C18  110.14  3.000
 L1H  H13  C14  C13  120.77  3.000
 L1H  H13  C14  C15  121.28  3.000
 L1H  C13  C14  C15  117.95  3.000
 L1H  C20  N19  C18  125.95  3.000
 L1H  C18  N19  C11  105.83  3.000
 L1H  C20  N19  C11  128.04  3.000
 L1H  H15  C20  H14  106.41  3.000
 L1H  H15  C20  N19  109.02  3.000
 L1H  H14  C20  N19  107.29  3.000
 L1H  H15  C20  C21  109.81  3.000
 L1H  H14  C20  C21  109.11  3.000
 L1H  N19  C20  C21  114.84  3.000
 L1H  H18  C22  H17  108.13  3.000
 L1H  H18  C22  H16  108.16  3.000
 L1H  H17  C22  H16  107.58  3.000
 L1H  H18  C22  C21  111.25  3.000
 L1H  H17  C22  C21  110.54  3.000
 L1H  H16  C22  C21  111.04  3.000
 L1H  H19  O24  C21  109.61  3.000
 L1H  C26  C25  C30  117.17  3.000
 L1H  C30  C25  C4   120.97  3.000
 L1H  C26  C25  C4   121.86  3.000
 L1H  H20  C26  C25  120.57  3.000
 L1H  H20  C26  C27  120.13  3.000
 L1H  C25  C26  C27  119.29  3.000
 L1H  H21  C28  N29  116.66  3.000
 L1H  H21  C28  C27  120.35  3.000
 L1H  N29  C28  C27  123.00  3.000
 L1H  C28  N29  C30  118.08  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
 L1H  CONST_01  C25  C4   C3   C2    180.00   0.0  0
 L1H  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 L1H  CONST_03  C5   C6   C7   C2      0.00   0.0  0
 L1H  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 L1H  CONST_07  C6   C7   C2   C3      0.00   0.0  0
 L1H  CONST_08  C27  C26  C25  C4    180.00   0.0  0
 L1H  CONST_09  N29  C30  C25  C4    180.00   0.0  0
 L1H  CONST_10  C7   C6   C5   C4      0.00   0.0  0
 L1H  CONST_11  C7   C2   C3   C4      0.00   0.0  0
 L1H  CONST_14  C25  C4   C5   C6    180.00   0.0  0
 L1H  CONST_15  C17  C18  N19  C11   180.00   0.0  0
 L1H  CONST_16  C13  C18  N19  C11     0.00   0.0  0
 L1H  CONST_17  C18  C13  N12  C11     0.00   0.0  0
 L1H  CONST_18  C14  C13  N12  C11   180.00   0.0  0
 L1H  CONST_19  C18  C17  C16  C15     0.00   0.0  0
 L1H  CONST_20  C18  C13  C14  C15     0.00   0.0  0
 L1H  CONST_21  N12  C13  C14  C15   180.00   0.0  0
 L1H  CONST_22  N19  C18  C17  C16   180.00   0.0  0
 L1H  CONST_23  C13  C18  C17  C16     0.00   0.0  0
 L1H  CONST_24  C13  C14  C15  C16     0.00   0.0  0
 L1H  CONST_25  N12  C13  C18  C17   180.00   0.0  0
 L1H  CONST_26  C14  C13  C18  C17     0.00   0.0  0
 L1H  CONST_27  C14  C15  C16  C17     0.00   0.0  0
 L1H  CONST_28  N12  C11  N19  C18     0.00   0.0  0
 L1H  CONST_29  C30  N29  C28  C27     0.00   0.0  0
 L1H  CONST_30  C30  C25  C26  C27     0.00   0.0  0
 L1H  CONST_31  N19  C18  C13  N12     0.00   0.0  0
 L1H  CONST_32  N19  C11  N12  C13     0.00   0.0  0
 L1H  CONST_33  N19  C18  C13  C14   180.00   0.0  0
 L1H  CONST_34  C28  C27  C26  C25     0.00   0.0  0
 L1H  CONST_35  C28  N29  C30  C25     0.00   0.0  0
 L1H  CONST_36  N29  C28  C27  C26     0.00   0.0  0
 L1H  CONST_37  N29  C30  C25  C26     0.00   0.0  0
 L1H  CONST_38  C8   C6   C7   C2    180.00   0.0  0
 L1H  CONST_39  C8   C6   C5   C4    180.00   0.0  0
 L1H  CONST_40  F1   C2   C3   C4    180.00   0.0  0
 L1H  CONST_41  F1   C2   C7   C6    180.00   0.0  0
 L1H  CONST_42  C18  N19  C11  N10   180.00   0.0  0
 L1H  CONST_43  C13  N12  C11  N10   180.00   0.0  0
 L1H  CONST_44  C20  N19  C18  C17     0.00   0.0  0
 L1H  CONST_45  C20  N19  C11  N12   180.00   0.0  0
 L1H  CONST_46  C20  N19  C18  C13   180.00   0.0  0
 L1H  CONST_47  H2   C5   C4   C3    180.00   0.0  0
 L1H  CONST_48  H3   C7   C2   C3    180.00   0.0  0
 L1H  CONST_49  H20  C26  C25  C4      0.00   0.0  0
 L1H  CONST_50  H12  C30  C25  C4      0.00   0.0  0
 L1H  CONST_51  H1   C3   C4   C5    180.00   0.0  0
 L1H  CONST_52  H7   C17  C16  C15   180.00   0.0  0
 L1H  CONST_53  H13  C14  C15  C16   180.00   0.0  0
 L1H  CONST_54  H5   C15  C16  C17   180.00   0.0  0
 L1H  CONST_55  H6   C16  C17  C18   180.00   0.0  0
 L1H  CONST_56  H21  C28  N29  C30   180.00   0.0  0
 L1H  CONST_57  H11  C27  C26  C25   180.00   0.0  0
 L1H  CONST_58  C11  N10  C8   C6    180.00   0.0  0
 L1H  CONST_62  C11  N10  C8   O9      0.00   0.0  0
 L1H  Var_01    N10  C8   C6   C5   -151.73  30.0  2
 L1H  Var_02    C21  C20  N19  C11   -81.89  30.0  1
 L1H  Var_03    N19  C20  C21  C23   -50.55  30.0  3
 L1H  Var_04    H16  C22  C21  C23   -58.15  30.0  3
 L1H  Var_05    H8   C23  C21  C20    60.49  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
 L1H  plan-1  C2   0.020
 L1H  plan-1  C3   0.020
 L1H  plan-1  C4   0.020
 L1H  plan-1  C5   0.020
 L1H  plan-1  C6   0.020
 L1H  plan-1  C7   0.020
 L1H  plan-1  C8   0.020
 L1H  plan-1  F1   0.020
 L1H  plan-1  C25  0.020
 L1H  plan-1  H1   0.020
 L1H  plan-1  H2   0.020
 L1H  plan-1  H3   0.020
 L1H  plan-2  C4   0.020
 L1H  plan-2  C27  0.020
 L1H  plan-2  C30  0.020
 L1H  plan-2  C25  0.020
 L1H  plan-2  C26  0.020
 L1H  plan-2  C28  0.020
 L1H  plan-2  N29  0.020
 L1H  plan-2  H11  0.020
 L1H  plan-2  H12  0.020
 L1H  plan-2  H20  0.020
 L1H  plan-2  H21  0.020
 L1H  plan-3  N10  0.020
 L1H  plan-3  C11  0.020
 L1H  plan-3  C15  0.020
 L1H  plan-3  C16  0.020
 L1H  plan-3  C17  0.020
 L1H  plan-3  C18  0.020
 L1H  plan-3  N12  0.020
 L1H  plan-3  C13  0.020
 L1H  plan-3  C14  0.020
 L1H  plan-3  N19  0.020
 L1H  plan-3  C20  0.020
 L1H  plan-3  H5   0.020
 L1H  plan-3  H6   0.020
 L1H  plan-3  H7   0.020
 L1H  plan-3  H13  0.020
 L1H  plan-4  C6   0.020
 L1H  plan-4  C8   0.020
 L1H  plan-4  O9   0.020
 L1H  plan-4  N10  0.020
 L1H  plan-4  C11  0.020
 L1H  plan-4  H4   0.020

