# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 01:42:36 2022
#   Inital geometry file: a 101 line input string
#   Ligand name: ~{N}-[1-(2-pyridin-2-ylethyl)benzimidazol-2-yl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1nc2ccccc2n1CCc3ccccn3
#
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
 05Y  05Y  "~{N}-[1-(2-pyridin-2-ylethyl)benzimidazol-2-yl]propanamide"  ligand  40  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_05Y
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
 05Y  C05  C  CH3   0  -0.662  -4.2312   0.6910   9.6140
 05Y  C06  C  CH2   0  -0.566  -4.8469   1.9592  10.2018
 05Y  C07  C  C     0   0.507  -6.0085   2.4467   9.3722
 05Y  C09  C  CR5   0   0.652  -4.6317   4.1618   8.2559
 05Y  C11  C  CR56  0   0.159  -2.6382   4.5433   7.6440
 05Y  C12  C  CR16  0  -0.330  -1.3157   4.4674   7.2118
 05Y  C13  C  CR16  0  -0.270  -0.6170   5.6514   7.0536
 05Y  C14  C  CR16  0  -0.274  -1.2126   6.8923   7.3217
 05Y  C15  C  CR16  0  -0.306  -2.5253   6.9872   7.7533
 05Y  C16  C  CR56  0   0.352  -3.2182   5.7935   7.9089
 05Y  C19  C  CH2   0  -0.509  -6.1354   7.1471   7.4307
 05Y  C20  C  CR6   0   0.214  -6.7045   6.1250   6.4910
 05Y  C22  C  CR16  0  -0.078  -6.3331   4.6731   4.7640
 05Y  C23  C  CR16  0  -0.316  -7.6201   4.1616   4.8281
 05Y  C24  C  CR16  0  -0.155  -8.4813   4.6812   5.7824
 05Y  C25  C  CR16  0  -0.334  -8.0177   5.6783   6.6269
 05Y  N08  N  NH1   0  -0.742  -5.8298   3.5521   8.5792
 05Y  N10  N  N     0  -0.470  -3.5565   3.5450   7.8584
 05Y  N17  N  NR5   0  -0.532  -4.4967   5.5173   8.3258
 05Y  N21  N  N     0  -0.403  -5.8812   5.6268   5.5700
 05Y  O26  O  O     0  -0.451  -7.0951   1.9040   9.4056
 05Y  H1   H  HCH3  0   0.241  -3.4421   0.3229  10.2684
 05Y  H2   H  HCH3  0   0.231  -4.9742  -0.0993   9.5113
 05Y  H3   H  HCH3  0   0.236  -3.7942   0.8847   8.6360
 05Y  H4   H  HCH2  0   0.257  -4.0811   2.7229  10.3264
 05Y  H5   H  HCH2  0   0.269  -5.2489   1.7422  11.1931
 05Y  H6   H  HCR6  0   0.253  -0.8539   3.5107   7.0041
 05Y  H7   H  HCR6  0   0.251   0.4109   5.6229   6.7165
 05Y  H8   H  HCR6  0   0.254  -0.6340   7.7967   7.1871
 05Y  H9   H  HCR6  0   0.269  -2.9801   7.9479   7.9583
 05Y  H10  H  HCH2  0   0.286  -5.0502   7.2556   9.2976
 05Y  H11  H  HCH2  0   0.284  -6.2697   5.9993   9.2686
 05Y  H12  H  HCH2  0   0.268  -5.3873   7.7473   6.9101
 05Y  H13  H  HCH2  0   0.271  -6.9158   7.8255   7.7788
 05Y  H14  H  HCR6  0   0.264  -5.6328   4.2956   4.0270
 05Y  H15  H  HCR6  0   0.271  -7.9344   3.3823   4.1479
 05Y  H16  H  HCR6  0   0.276  -9.4969   4.3173   5.8687
 05Y  H17  H  HCR6  0   0.272  -8.6613   6.1082   7.3840
 05Y  H18  H  HNH1  0   0.414  -6.6609   3.8648   8.0908
 05Y  C18  C  CH2   0  -0.351  -5.5076   6.4932   8.6659

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
 05Y  C22  N21  aromatic  1.328  0.020  1.328
 05Y  C22  C23  aromatic  1.386  0.020  1.386
 05Y  N21  C20  aromatic  1.332  0.020  1.332
 05Y  C23  C24  aromatic  1.387  0.020  1.387
 05Y  C20  C19  single    1.501  0.020  1.501
 05Y  C20  C25  aromatic  1.394  0.020  1.394
 05Y  C24  C25  aromatic  1.386  0.020  1.386
 05Y  C19  C18  single    1.532  0.020  1.532
 05Y  N10  C11  aromatic  1.373  0.020  1.373
 05Y  N10  C09  aromatic  1.302  0.020  1.302
 05Y  N08  C09  single    1.383  0.020  1.383
 05Y  N08  C07  single    1.372  0.020  1.372
 05Y  C12  C11  aromatic  1.393  0.020  1.393
 05Y  C12  C13  aromatic  1.384  0.020  1.384
 05Y  C11  C16  aromatic  1.403  0.020  1.403
 05Y  C09  N17  aromatic  1.364  0.020  1.364
 05Y  C13  C14  aromatic  1.402  0.020  1.402
 05Y  N17  C16  aromatic  1.373  0.020  1.373
 05Y  N17  C18  single    1.446  0.020  1.446
 05Y  C16  C15  aromatic  1.389  0.020  1.389
 05Y  C14  C15  aromatic  1.385  0.020  1.385
 05Y  O26  C07  double    1.215  0.020  1.215
 05Y  C07  C06  single    1.508  0.020  1.508
 05Y  C05  C06  single    1.527  0.020  1.527
 05Y  C05  H1   single    0.970  0.020  1.090
 05Y  C05  H2   single    0.970  0.020  1.090
 05Y  C05  H3   single    0.970  0.020  1.090
 05Y  C06  H4   single    0.970  0.020  1.090
 05Y  C06  H5   single    0.970  0.020  1.090
 05Y  C12  H6   single    0.930  0.020  1.080
 05Y  C13  H7   single    0.930  0.020  1.080
 05Y  C14  H8   single    0.930  0.020  1.080
 05Y  C15  H9   single    0.930  0.020  1.080
 05Y  C18  H10  single    0.970  0.020  1.090
 05Y  C18  H11  single    0.970  0.020  1.090
 05Y  C19  H12  single    0.970  0.020  1.090
 05Y  C19  H13  single    0.970  0.020  1.090
 05Y  C22  H14  single    0.930  0.020  1.080
 05Y  C23  H15  single    0.930  0.020  1.080
 05Y  C24  H16  single    0.930  0.020  1.080
 05Y  C25  H17  single    0.930  0.020  1.080
 05Y  N08  H18  single    0.860  0.020  1.020

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
 05Y  H3   C05  H2   108.55  3.000
 05Y  H3   C05  H1   108.01  3.000
 05Y  H2   C05  H1   107.78  3.000
 05Y  H3   C05  C06  111.09  3.000
 05Y  H2   C05  C06  111.32  3.000
 05Y  H1   C05  C06  109.97  3.000
 05Y  H5   C06  H4   107.13  3.000
 05Y  H5   C06  C07  106.27  3.000
 05Y  H4   C06  C07  112.21  3.000
 05Y  H5   C06  C05  109.45  3.000
 05Y  H4   C06  C05  110.06  3.000
 05Y  C07  C06  C05  111.54  3.000
 05Y  O26  C07  N08  119.49  3.000
 05Y  O26  C07  C06  121.95  3.000
 05Y  N08  C07  C06  118.55  3.000
 05Y  N17  C09  N10  113.88  3.000
 05Y  N17  C09  N08  120.80  3.000
 05Y  N10  C09  N08  125.32  3.000
 05Y  N10  C11  C16  109.98  3.000
 05Y  C16  C11  C12  119.95  3.000
 05Y  N10  C11  C12  130.06  3.000
 05Y  H6   C12  C13  121.26  3.000
 05Y  H6   C12  C11  120.83  3.000
 05Y  C13  C12  C11  117.91  3.000
 05Y  H7   C13  C14  119.10  3.000
 05Y  H7   C13  C12  119.51  3.000
 05Y  C14  C13  C12  121.39  3.000
 05Y  H8   C14  C15  119.23  3.000
 05Y  H8   C14  C13  119.26  3.000
 05Y  C15  C14  C13  121.52  3.000
 05Y  H9   C15  C16  122.14  3.000
 05Y  H9   C15  C14  121.20  3.000
 05Y  C16  C15  C14  116.67  3.000
 05Y  N17  C16  C15  132.19  3.000
 05Y  C15  C16  C11  122.57  3.000
 05Y  N17  C16  C11  105.25  3.000
 05Y  H13  C19  H12  107.49  3.000
 05Y  H13  C19  C20  110.61  3.000
 05Y  H12  C19  C20  109.62  3.000
 05Y  H13  C19  C18  107.54  3.000
 05Y  H12  C19  C18  109.78  3.000
 05Y  C20  C19  C18  111.69  3.000
 05Y  N21  C20  C25  122.00  3.000
 05Y  C25  C20  C19  120.97  3.000
 05Y  N21  C20  C19  116.96  3.000
 05Y  H14  C22  N21  116.28  3.000
 05Y  H14  C22  C23  120.16  3.000
 05Y  N21  C22  C23  123.56  3.000
 05Y  H15  C23  C24  121.51  3.000
 05Y  H15  C23  C22  120.45  3.000
 05Y  C24  C23  C22  118.04  3.000
 05Y  H16  C24  C25  120.47  3.000
 05Y  H16  C24  C23  120.78  3.000
 05Y  C25  C24  C23  118.75  3.000
 05Y  H17  C25  C24  120.84  3.000
 05Y  H17  C25  C20  120.07  3.000
 05Y  C24  C25  C20  119.09  3.000
 05Y  H18  N08  C09  117.50  3.000
 05Y  H18  N08  C07  114.85  3.000
 05Y  C09  N08  C07  127.11  3.000
 05Y  C11  N10  C09  104.81  3.000
 05Y  C18  N17  C16  125.93  3.000
 05Y  C18  N17  C09  127.86  3.000
 05Y  C16  N17  C09  106.06  3.000
 05Y  C22  N21  C20  118.55  3.000
 05Y  H11  C18  H10  106.85  3.000
 05Y  H11  C18  N17  108.24  3.000
 05Y  H10  C18  N17  108.36  3.000
 05Y  H11  C18  C19  110.65  3.000
 05Y  H10  C18  C19  109.91  3.000
 05Y  N17  C18  C19  112.64  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
 05Y  CONST_01  C12  C11  N10  C09   180.00   0.0  0
 05Y  CONST_02  C16  C11  N10  C09     0.00   0.0  0
 05Y  CONST_03  C11  C16  N17  C09     0.00   0.0  0
 05Y  CONST_04  C15  C16  N17  C09   180.00   0.0  0
 05Y  CONST_05  N17  C09  N10  C11     0.00   0.0  0
 05Y  CONST_06  C14  C13  C12  C11     0.00   0.0  0
 05Y  CONST_07  C14  C15  C16  C11     0.00   0.0  0
 05Y  CONST_08  N17  C16  C11  C12   180.00   0.0  0
 05Y  CONST_09  C15  C16  C11  C12     0.00   0.0  0
 05Y  CONST_10  C15  C14  C13  C12     0.00   0.0  0
 05Y  CONST_11  N10  C11  C12  C13   180.00   0.0  0
 05Y  CONST_12  C16  C11  C12  C13     0.00   0.0  0
 05Y  CONST_13  C16  C15  C14  C13     0.00   0.0  0
 05Y  CONST_14  N17  C16  C15  C14   180.00   0.0  0
 05Y  CONST_15  N10  C11  C16  C15   180.00   0.0  0
 05Y  CONST_16  N10  C09  N17  C16     0.00   0.0  0
 05Y  CONST_17  C23  C22  N21  C20     0.00   0.0  0
 05Y  CONST_18  C23  C24  C25  C20     0.00   0.0  0
 05Y  CONST_19  C25  C20  N21  C22     0.00   0.0  0
 05Y  CONST_20  C25  C24  C23  C22     0.00   0.0  0
 05Y  CONST_21  N21  C22  C23  C24     0.00   0.0  0
 05Y  CONST_22  N21  C20  C25  C24     0.00   0.0  0
 05Y  CONST_23  N17  C16  C11  N10     0.00   0.0  0
 05Y  CONST_24  N08  C09  N10  C11   180.00   0.0  0
 05Y  CONST_25  C18  N17  C16  C11   180.00   0.0  0
 05Y  CONST_26  C18  N17  C16  C15     0.00   0.0  0
 05Y  CONST_27  N08  C09  N17  C16   180.00   0.0  0
 05Y  CONST_28  N10  C09  N17  C18   180.00   0.0  0
 05Y  CONST_29  C22  N21  C20  C19   180.00   0.0  0
 05Y  CONST_30  C24  C25  C20  C19   180.00   0.0  0
 05Y  CONST_31  H7   C13  C12  C11   180.00   0.0  0
 05Y  CONST_32  H9   C15  C16  C11   180.00   0.0  0
 05Y  CONST_33  H8   C14  C13  C12   180.00   0.0  0
 05Y  CONST_34  H9   C15  C14  C13   180.00   0.0  0
 05Y  CONST_35  H6   C12  C13  C14   180.00   0.0  0
 05Y  CONST_36  H7   C13  C14  C15   180.00   0.0  0
 05Y  CONST_37  H6   C12  C11  C16   180.00   0.0  0
 05Y  CONST_38  H8   C14  C15  C16   180.00   0.0  0
 05Y  CONST_39  H14  C22  N21  C20   180.00   0.0  0
 05Y  CONST_40  H16  C24  C25  C20   180.00   0.0  0
 05Y  CONST_41  H16  C24  C23  C22   180.00   0.0  0
 05Y  CONST_42  H17  C25  C24  C23   180.00   0.0  0
 05Y  CONST_43  H14  C22  C23  C24   180.00   0.0  0
 05Y  CONST_44  H15  C23  C24  C25   180.00   0.0  0
 05Y  CONST_45  H6   C12  C11  N10     0.00   0.0  0
 05Y  CONST_46  H9   C15  C16  N17     0.00   0.0  0
 05Y  CONST_47  H15  C23  C22  N21   180.00   0.0  0
 05Y  CONST_48  H17  C25  C20  N21   180.00   0.0  0
 05Y  CONST_53  C09  N08  C07  C06     0.00   0.0  0
 05Y  CONST_54  O26  C07  N08  C09   180.00   0.0  0
 05Y  CONST_55  H18  N08  C07  C06   180.00   0.0  0
 05Y  CONST_56  H18  N08  C07  O26     0.00   0.0  0
 05Y  Var_01    C19  C18  N17  C09   -98.36  30.0  2
 05Y  Var_02    C19  C18  N17  C16    76.46  30.0  2
 05Y  Var_03    N21  C20  C19  C18   -88.41  30.0  3
 05Y  Var_04    C25  C20  C19  C18    88.60  30.0  3
 05Y  Var_05    N17  C18  C19  C20    55.62  30.0  3
 05Y  Var_06    H10  C18  N17  C09   139.83  30.0  2
 05Y  Var_07    H11  C18  N17  C09    24.31  30.0  2
 05Y  Var_08    H10  C18  N17  C16   -45.35  30.0  2
 05Y  Var_09    H11  C18  N17  C16  -160.87  30.0  2
 05Y  Var_10    H12  C19  C20  C25  -149.49  30.0  2
 05Y  Var_11    H13  C19  C20  C25   -31.14  30.0  2
 05Y  Var_12    H12  C19  C20  N21    33.49  30.0  2
 05Y  Var_13    H13  C19  C20  N21   151.85  30.0  2
 05Y  Var_14    H10  C18  C19  C20   176.54  30.0  3
 05Y  Var_15    H11  C18  C19  C20   -65.69  30.0  3
 05Y  Var_16    H12  C19  C18  N17   -66.19  30.0  2
 05Y  Var_17    H13  C19  C18  N17   177.15  30.0  2
 05Y  Var_18    N08  C07  C06  C05  -105.52  30.0  3
 05Y  Var_19    O26  C07  C06  C05    75.77  30.0  3
 05Y  Var_20    H1   C05  C06  C07  -176.06  30.0  3
 05Y  Var_21    H2   C05  C06  C07   -56.68  30.0  3
 05Y  Var_22    H3   C05  C06  C07    64.43  30.0  3
 05Y  Var_23    H4   C06  C07  N08    18.49  30.0  3
 05Y  Var_24    H5   C06  C07  N08   135.28  30.0  3
 05Y  Var_25    H4   C06  C07  O26  -160.22  30.0  3
 05Y  Var_26    H5   C06  C07  O26   -43.44  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
 05Y  plan-1  C19  0.020
 05Y  plan-1  C20  0.020
 05Y  plan-1  C22  0.020
 05Y  plan-1  C23  0.020
 05Y  plan-1  C24  0.020
 05Y  plan-1  C25  0.020
 05Y  plan-1  N21  0.020
 05Y  plan-1  H14  0.020
 05Y  plan-1  H15  0.020
 05Y  plan-1  H16  0.020
 05Y  plan-1  H17  0.020
 05Y  plan-2  C09  0.020
 05Y  plan-2  C11  0.020
 05Y  plan-2  C12  0.020
 05Y  plan-2  C13  0.020
 05Y  plan-2  C14  0.020
 05Y  plan-2  C15  0.020
 05Y  plan-2  C16  0.020
 05Y  plan-2  N08  0.020
 05Y  plan-2  N10  0.020
 05Y  plan-2  N17  0.020
 05Y  plan-2  H6   0.020
 05Y  plan-2  H7   0.020
 05Y  plan-2  H8   0.020
 05Y  plan-2  H9   0.020
 05Y  plan-2  C18  0.020
 05Y  plan-3  C06  0.020
 05Y  plan-3  C07  0.020
 05Y  plan-3  C09  0.020
 05Y  plan-3  N08  0.020
 05Y  plan-3  O26  0.020
 05Y  plan-3  H18  0.020

