# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 16:20:48 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: ~{N}-[1-(2-methyl-2-oxidanyl-propyl)benzimidazol-2-yl]-2-phenyl-pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)Cn1c(NC(=O)c2ccnc(c2)c3ccccc3)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
 L1K  L1K  ~{N}-[1-(2-methyl-2-oxidanyl-propyl)benzimidazol-2-yl]-2-phenyl-pyridine-4-carboxamide  ligand  51  29  .  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_L1K
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
 L1K  C1   C  CH3   0  -0.676   2.3705  -2.2642   1.4512
 L1K  C2   C  CT    0   0.194   3.5041  -2.3385   0.4389
 L1K  C3   C  CH3   0  -0.679   3.6734  -3.7710  -0.0598
 L1K  C5   C  CH2   0  -0.350   3.2347  -1.4446  -0.7874
 L1K  C7   C  CR56  0   0.368   4.1522   0.8564  -0.3480
 L1K  C8   C  CR16  0  -0.309   5.5219   0.7383  -0.5484
 L1K  C11  C  CR16  0  -0.335   4.3358   3.2003   0.2415
 L1K  C12  C  CR56  0   0.145   3.5529   2.0668   0.0305
 L1K  N13  N  N     0  -0.468   2.1890   1.9179   0.1054
 L1K  C16  C  C     0   0.525  -0.3588   0.3908   0.4378
 L1K  C18  C  CR6   0   0.060  -1.5787  -0.4097   0.1037
 L1K  C19  C  CR16  0  -0.366  -1.5240  -1.7442  -0.2765
 L1K  C23  C  CR16  0  -0.359  -2.8195   0.1967   0.2285
 L1K  C24  C  CR6   0   0.073  -5.3159   0.0698   0.0058
 L1K  C27  C  CR16  0  -0.259  -7.8809   1.1777   0.1518
 L1K  O4   O  OH1   0  -0.659   4.6634  -1.8976   1.1188
 L1K  N6   N  NR5   0  -0.564   3.1121  -0.0361  -0.4802
 L1K  C9   C  CR16  0  -0.279   6.2843   1.8752  -0.3404
 L1K  C10  C  CR16  0  -0.273   5.7018   3.0882   0.0536
 L1K  C14  C  CR5   0   0.692   1.9785   0.6741  -0.2017
 L1K  N15  N  NH1   0  -0.777   0.7403   0.0656  -0.3029
 L1K  O17  O  O     0  -0.416  -0.3746   1.2446   1.2944
 L1K  C20  C  CR16  0  -0.055  -2.7216  -2.4007  -0.5164
 L1K  N21  N  N     0  -0.420  -3.9041  -1.8166  -0.4285
 L1K  C22  C  CR6   0   0.248  -3.9682  -0.5338  -0.0718
 L1K  C25  C  CR16  0  -0.282  -6.4354  -0.7465   0.1775
 L1K  C26  C  CR16  0  -0.239  -7.7052  -0.1966   0.2546
 L1K  C28  C  CR16  0  -0.238  -6.7752   1.9976  -0.0279
 L1K  C29  C  CR16  0  -0.319  -5.5033   1.4486  -0.1001
 L1K  H1   H  HCH3  0   0.221   1.4227  -2.5574   0.9998
 L1K  H2   H  HCH3  0   0.252   2.5639  -2.9478   2.2786
 L1K  H3   H  HCH3  0   0.242   2.2570  -1.2631   1.8699
 L1K  H4   H  HCH3  0   0.235   2.7676  -4.1327  -0.5473
 L1K  H5   H  HCH3  0   0.238   4.4906  -3.8490  -0.7811
 L1K  H6   H  HCH3  0   0.248   3.8939  -4.4387   0.7738
 L1K  H7   H  HCH2  0   0.284   4.0438  -1.5566  -1.5123
 L1K  H8   H  HCH2  0   0.268   2.3346  -1.7836  -1.3013
 L1K  H9   H  HCR6  0   0.260   5.9856  -0.1888  -0.8568
 L1K  H10  H  HCR6  0   0.255   3.8837   4.1380   0.5373
 L1K  H11  H  HCR6  0   0.270  -0.5961  -2.2939  -0.3634
 L1K  H12  H  HCR6  0   0.281  -2.8863   1.2242   0.5577
 L1K  H13  H  HCR6  0   0.261  -8.8733   1.6059   0.2081
 L1K  H14  H  HOH1  0   0.448   5.4395  -2.1123   0.5908
 L1K  H15  H  HCR6  0   0.256   7.3558   1.8244  -0.4820
 L1K  H16  H  HCR6  0   0.253   6.3359   3.9511   0.2093
 L1K  H17  H  HNH1  0   0.437   0.6202  -0.6026  -1.0498
 L1K  H18  H  HCR6  0   0.276  -2.7162  -3.4482  -0.7945
 L1K  H19  H  HCR6  0   0.255  -6.3077  -1.8175   0.2565
 L1K  H20  H  HCR6  0   0.260  -8.5606  -0.8442   0.3962
 L1K  H21  H  HCR6  0   0.262  -6.9010   3.0684  -0.1197
 L1K  H22  H  HCR6  0   0.256  -4.6602   2.1080  -0.2610

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
 L1K  C27  C26  aromatic  1.389  0.020  1.389
 L1K  C27  C28  aromatic  1.388  0.020  1.388
 L1K  O4   C2   single    1.414  0.020  1.414
 L1K  C26  C25  aromatic  1.386  0.020  1.386
 L1K  C3   C2   single    1.526  0.020  1.526
 L1K  C28  C29  aromatic  1.387  0.020  1.387
 L1K  C25  C24  aromatic  1.396  0.020  1.396
 L1K  C2   C1   single    1.522  0.020  1.522
 L1K  C2   C5   single    1.541  0.020  1.541
 L1K  C29  C24  aromatic  1.395  0.020  1.395
 L1K  C24  C22  single    1.479  0.020  1.479
 L1K  C5   N6   single    1.447  0.020  1.447
 L1K  C22  C23  aromatic  1.394  0.020  1.394
 L1K  C22  N21  aromatic  1.333  0.020  1.333
 L1K  N6   C7   aromatic  1.377  0.020  1.377
 L1K  N6   C14  aromatic  1.366  0.020  1.366
 L1K  C23  C18  aromatic  1.387  0.020  1.387
 L1K  C8   C7   aromatic  1.389  0.020  1.389
 L1K  C8   C9   aromatic  1.385  0.020  1.385
 L1K  N21  C20  aromatic  1.322  0.020  1.322
 L1K  C7   C12  aromatic  1.403  0.020  1.403
 L1K  N15  C14  single    1.383  0.020  1.383
 L1K  N15  C16  single    1.365  0.020  1.365
 L1K  C14  N13  aromatic  1.298  0.020  1.298
 L1K  C9   C10  aromatic  1.402  0.020  1.402
 L1K  C18  C16  single    1.497  0.020  1.497
 L1K  C18  C19  aromatic  1.389  0.020  1.389
 L1K  C20  C19  aromatic  1.387  0.020  1.387
 L1K  C16  O17  double    1.210  0.020  1.210
 L1K  C12  N13  aromatic  1.374  0.020  1.374
 L1K  C12  C11  aromatic  1.394  0.020  1.394
 L1K  C10  C11  aromatic  1.383  0.020  1.383
 L1K  C1   H1   single    0.970  0.020  1.090
 L1K  C1   H2   single    0.970  0.020  1.090
 L1K  C1   H3   single    0.970  0.020  1.090
 L1K  C3   H4   single    0.970  0.020  1.090
 L1K  C3   H5   single    0.970  0.020  1.090
 L1K  C3   H6   single    0.970  0.020  1.090
 L1K  C5   H7   single    0.970  0.020  1.090
 L1K  C5   H8   single    0.970  0.020  1.090
 L1K  C8   H9   single    0.930  0.020  1.080
 L1K  C11  H10  single    0.930  0.020  1.080
 L1K  C19  H11  single    0.930  0.020  1.080
 L1K  C23  H12  single    0.930  0.020  1.080
 L1K  C27  H13  single    0.930  0.020  1.080
 L1K  O4   H14  single    0.850  0.020  0.980
 L1K  C9   H15  single    0.930  0.020  1.080
 L1K  C10  H16  single    0.930  0.020  1.080
 L1K  N15  H17  single    0.860  0.020  1.020
 L1K  C20  H18  single    0.930  0.020  1.080
 L1K  C25  H19  single    0.930  0.020  1.080
 L1K  C26  H20  single    0.930  0.020  1.080
 L1K  C28  H21  single    0.930  0.020  1.080
 L1K  C29  H22  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
 L1K  H3   C1   H2   107.60  3.000
 L1K  H3   C1   H1   108.38  3.000
 L1K  H2   C1   H1   107.45  3.000
 L1K  H3   C1   C2   112.18  3.000
 L1K  H2   C1   C2   110.00  3.000
 L1K  H1   C1   C2   111.05  3.000
 L1K  O4   C2   C5   110.18  3.000
 L1K  C5   C2   C3   107.68  3.000
 L1K  O4   C2   C3   111.03  3.000
 L1K  C5   C2   C1   111.76  3.000
 L1K  C3   C2   C1   110.23  3.000
 L1K  O4   C2   C1   106.00  3.000
 L1K  H6   C3   H5   108.03  3.000
 L1K  H6   C3   H4   107.85  3.000
 L1K  H5   C3   H4   107.60  3.000
 L1K  H6   C3   C2   110.32  3.000
 L1K  H5   C3   C2   111.44  3.000
 L1K  H4   C3   C2   111.43  3.000
 L1K  H8   C5   H7   105.47  3.000
 L1K  H8   C5   N6   109.43  3.000
 L1K  H7   C5   N6   107.66  3.000
 L1K  H8   C5   C2   109.82  3.000
 L1K  H7   C5   C2   109.83  3.000
 L1K  N6   C5   C2   114.24  3.000
 L1K  N6   C7   C12  105.22  3.000
 L1K  C12  C7   C8   122.24  3.000
 L1K  N6   C7   C8   132.52  3.000
 L1K  H9   C8   C9   120.71  3.000
 L1K  H9   C8   C7   122.46  3.000
 L1K  C9   C8   C7   116.84  3.000
 L1K  H10  C11  C10  121.32  3.000
 L1K  H10  C11  C12  120.75  3.000
 L1K  C10  C11  C12  117.92  3.000
 L1K  N13  C12  C11  129.61  3.000
 L1K  C11  C12  C7   120.17  3.000
 L1K  N13  C12  C7   110.20  3.000
 L1K  C14  N13  C12  104.59  3.000
 L1K  O17  C16  N15  124.27  3.000
 L1K  O17  C16  C18  121.66  3.000
 L1K  N15  C16  C18  114.06  3.000
 L1K  C23  C18  C19  118.70  3.000
 L1K  C19  C18  C16  122.88  3.000
 L1K  C23  C18  C16  118.38  3.000
 L1K  H11  C19  C20  119.09  3.000
 L1K  H11  C19  C18  122.96  3.000
 L1K  C20  C19  C18  117.93  3.000
 L1K  H12  C23  C22  120.84  3.000
 L1K  H12  C23  C18  119.90  3.000
 L1K  C22  C23  C18  119.26  3.000
 L1K  C29  C24  C25  118.64  3.000
 L1K  C29  C24  C22  121.45  3.000
 L1K  C25  C24  C22  119.91  3.000
 L1K  H13  C27  C28  120.22  3.000
 L1K  H13  C27  C26  120.23  3.000
 L1K  C28  C27  C26  119.54  3.000
 L1K  H14  O4   C2   109.12  3.000
 L1K  C14  N6   C7   105.68  3.000
 L1K  C14  N6   C5   128.28  3.000
 L1K  C7   N6   C5   125.97  3.000
 L1K  H15  C9   C10  119.27  3.000
 L1K  H15  C9   C8   119.15  3.000
 L1K  C10  C9   C8   121.59  3.000
 L1K  H16  C10  C9   119.13  3.000
 L1K  H16  C10  C11  119.63  3.000
 L1K  C9   C10  C11  121.23  3.000
 L1K  N15  C14  N6   119.94  3.000
 L1K  N15  C14  N13  125.72  3.000
 L1K  N6   C14  N13  114.31  3.000
 L1K  H17  N15  C14  116.86  3.000
 L1K  H17  N15  C16  117.62  3.000
 L1K  C14  N15  C16  125.20  3.000
 L1K  H18  C20  N21  116.66  3.000
 L1K  H18  C20  C19  119.85  3.000
 L1K  N21  C20  C19  123.50  3.000
 L1K  C22  N21  C20  119.08  3.000
 L1K  N21  C22  C24  116.79  3.000
 L1K  N21  C22  C23  121.49  3.000
 L1K  C24  C22  C23  121.72  3.000
 L1K  H19  C25  C26  119.81  3.000
 L1K  H19  C25  C24  119.56  3.000
 L1K  C26  C25  C24  120.63  3.000
 L1K  H20  C26  C25  119.61  3.000
 L1K  H20  C26  C27  120.11  3.000
 L1K  C25  C26  C27  120.29  3.000
 L1K  H21  C28  C29  119.60  3.000
 L1K  H21  C28  C27  120.18  3.000
 L1K  C29  C28  C27  120.22  3.000
 L1K  H22  C29  C28  118.74  3.000
 L1K  H22  C29  C24  120.57  3.000
 L1K  C28  C29  C24  120.68  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
 L1K  CONST_01  N13  C14  N6   C7     0.00   0.0  0
 L1K  CONST_02  C10  C9   C8   C7     0.00   0.0  0
 L1K  CONST_03  C14  N13  C12  C7     0.00   0.0  0
 L1K  CONST_04  C10  C11  C12  C7     0.00   0.0  0
 L1K  CONST_05  C14  N6   C7   C8   180.00   0.0  0
 L1K  CONST_06  N13  C12  C7   C8   180.00   0.0  0
 L1K  CONST_07  C11  C12  C7   C8     0.00   0.0  0
 L1K  CONST_08  C11  C10  C9   C8     0.00   0.0  0
 L1K  CONST_09  N6   C7   C12  C11  180.00   0.0  0
 L1K  CONST_10  C14  N13  C12  C11  180.00   0.0  0
 L1K  CONST_11  C14  N6   C7   C12    0.00   0.0  0
 L1K  CONST_12  C9   C8   C7   C12    0.00   0.0  0
 L1K  CONST_13  N6   C14  N13  C12    0.00   0.0  0
 L1K  CONST_14  C9   C10  C11  C12    0.00   0.0  0
 L1K  CONST_15  N6   C7   C12  N13    0.00   0.0  0
 L1K  CONST_16  C10  C11  C12  N13  180.00   0.0  0
 L1K  CONST_17  C24  C22  C23  C18  180.00   0.0  0
 L1K  CONST_18  N21  C22  C23  C18    0.00   0.0  0
 L1K  CONST_19  N21  C20  C19  C18    0.00   0.0  0
 L1K  CONST_20  C22  C23  C18  C19    0.00   0.0  0
 L1K  CONST_21  C22  N21  C20  C19    0.00   0.0  0
 L1K  CONST_24  C20  N21  C22  C23    0.00   0.0  0
 L1K  CONST_25  C20  C19  C18  C23    0.00   0.0  0
 L1K  CONST_26  C27  C26  C25  C24    0.00   0.0  0
 L1K  CONST_27  C27  C28  C29  C24    0.00   0.0  0
 L1K  CONST_28  C20  N21  C22  C24  180.00   0.0  0
 L1K  CONST_29  C9   C8   C7   N6   180.00   0.0  0
 L1K  CONST_32  C26  C25  C24  C22  180.00   0.0  0
 L1K  CONST_33  C28  C29  C24  C22  180.00   0.0  0
 L1K  CONST_34  C28  C27  C26  C25    0.00   0.0  0
 L1K  CONST_35  C28  C29  C24  C25    0.00   0.0  0
 L1K  CONST_36  C29  C28  C27  C26    0.00   0.0  0
 L1K  CONST_37  C29  C24  C25  C26    0.00   0.0  0
 L1K  CONST_38  C8   C7   N6   C5     0.00   0.0  0
 L1K  CONST_39  C12  C7   N6   C5   180.00   0.0  0
 L1K  CONST_40  N13  C14  N6   C5   180.00   0.0  0
 L1K  CONST_41  N15  C14  N6   C7   180.00   0.0  0
 L1K  CONST_42  N15  C14  N13  C12  180.00   0.0  0
 L1K  CONST_43  C22  C23  C18  C16  180.00   0.0  0
 L1K  CONST_44  C20  C19  C18  C16  180.00   0.0  0
 L1K  CONST_45  H15  C9   C8   C7   180.00   0.0  0
 L1K  CONST_46  H10  C11  C12  C7   180.00   0.0  0
 L1K  CONST_47  H16  C10  C9   C8   180.00   0.0  0
 L1K  CONST_48  H9   C8   C7   C12  180.00   0.0  0
 L1K  CONST_49  H18  C20  C19  C18  180.00   0.0  0
 L1K  CONST_50  H12  C23  C18  C19  180.00   0.0  0
 L1K  CONST_51  H11  C19  C18  C23  180.00   0.0  0
 L1K  CONST_52  H20  C26  C25  C24  180.00   0.0  0
 L1K  CONST_53  H21  C28  C29  C24  180.00   0.0  0
 L1K  CONST_54  H19  C25  C26  C27  180.00   0.0  0
 L1K  CONST_55  H22  C29  C28  C27  180.00   0.0  0
 L1K  CONST_56  H13  C27  C26  C25  180.00   0.0  0
 L1K  CONST_57  C14  N15  C16  C18  180.00   0.0  0
 L1K  CONST_61  O17  C16  N15  C14    0.00   0.0  0
 L1K  Var_01    C7   N6   C5   C2    84.28  30.0  2
 L1K  Var_02    N15  C16  C18  C19   34.66  30.0  2
 L1K  Var_03    N6   C5   C2   C1    61.50  30.0  3
 L1K  Var_04    H4   C3   C2   C1    60.39  30.0  3
 L1K  Var_05    H1   C1   C2   C3   -61.67  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
 L1K  plan-1  C24  0.020
 L1K  plan-1  C27  0.020
 L1K  plan-1  C22  0.020
 L1K  plan-1  C25  0.020
 L1K  plan-1  C26  0.020
 L1K  plan-1  C28  0.020
 L1K  plan-1  C29  0.020
 L1K  plan-1  H13  0.020
 L1K  plan-1  H19  0.020
 L1K  plan-1  H20  0.020
 L1K  plan-1  H21  0.020
 L1K  plan-1  H22  0.020
 L1K  plan-2  C16  0.020
 L1K  plan-2  C18  0.020
 L1K  plan-2  C19  0.020
 L1K  plan-2  C23  0.020
 L1K  plan-2  C24  0.020
 L1K  plan-2  C20  0.020
 L1K  plan-2  N21  0.020
 L1K  plan-2  C22  0.020
 L1K  plan-2  H11  0.020
 L1K  plan-2  H12  0.020
 L1K  plan-2  H18  0.020
 L1K  plan-3  C5   0.020
 L1K  plan-3  C7   0.020
 L1K  plan-3  C8   0.020
 L1K  plan-3  C11  0.020
 L1K  plan-3  C12  0.020
 L1K  plan-3  N13  0.020
 L1K  plan-3  N6   0.020
 L1K  plan-3  C9   0.020
 L1K  plan-3  C10  0.020
 L1K  plan-3  C14  0.020
 L1K  plan-3  N15  0.020
 L1K  plan-3  H9   0.020
 L1K  plan-3  H10  0.020
 L1K  plan-3  H15  0.020
 L1K  plan-3  H16  0.020
 L1K  plan-4  C16  0.020
 L1K  plan-4  C18  0.020
 L1K  plan-4  C14  0.020
 L1K  plan-4  N15  0.020
 L1K  plan-4  O17  0.020
 L1K  plan-4  H17  0.020

