# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 08:39:49 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc2[nH]c(CN3CCCCC3)nc2c1)c4ccc(cc4)C#N
#
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
 M8K  M8K  4-cyano-~{N}-[2-(piperidin-1-ylmethyl)-1~{H}-benzimidazol-5-yl]benzamide  ligand  48  27  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M8K
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
 M8K  N1   N  NH1   0  -0.755   2.2958  -0.0296   0.0516
 M8K  C2   C  CR16  0  -0.222   6.3138   1.3430  -0.0741
 M8K  N3   N  NR15  0  -0.678  -3.1569  -0.6187   0.3173
 M8K  C4   C  CR6   0  -0.032   4.6688  -0.4014   0.1670
 M8K  N4   N  NT    0  -0.430  -5.7463   0.1835  -0.4072
 M8K  C5   C  CR16  0  -0.255   5.6581  -1.3614  -0.0340
 M8K  C6   C  CR16  0  -0.226   6.9643  -0.9804  -0.2756
 M8K  O    O  O     0  -0.456   3.0752  -1.9499   0.9808
 M8K  C7   C  C     0   0.524   3.2754  -0.8753   0.4431
 M8K  C3   C  CR16  0  -0.280   5.0065   0.9499   0.1538
 M8K  C1   C  CR6   0   0.005   7.2908   0.3754  -0.2952
 M8K  C    C  CSP   0   0.062   8.6398   0.7752  -0.5383
 M8K  N    N  NS    0  -0.244   9.7284   1.0963  -0.7350
 M8K  C8   C  CR6   0   0.351   0.9105  -0.2496   0.2001
 M8K  C13  C  CR16  0  -0.425   0.0817   0.0887  -0.8588
 M8K  C12  C  CR56  0   0.146  -1.2913  -0.0743  -0.6981
 M8K  N2   N  N     0  -0.483  -2.3194   0.1948  -1.5704
 M8K  C14  C  CR5   0   0.423  -3.4047  -0.1431  -0.9275
 M8K  C11  C  CR56  0   0.339  -1.8021  -0.5850   0.5062
 M8K  C10  C  CR16  0  -0.307  -0.9783  -0.9238   1.5710
 M8K  C9   C  CR16  0  -0.309   0.3829  -0.7448   1.4059
 M8K  C15  C  CH2   0  -0.362  -4.7971  -0.0902  -1.4621
 M8K  C20  C  CH2   0  -0.286  -5.6895   1.5744   0.0190
 M8K  C19  C  CH2   0  -0.437  -6.5985   1.8204   1.2124
 M8K  C18  C  CH2   0  -0.442  -8.0292   1.4068   0.8942
 M8K  C17  C  CH2   0  -0.437  -8.0554  -0.0309   0.3909
 M8K  C16  C  CH2   0  -0.279  -7.0975  -0.2091  -0.7762
 M8K  H1   H  HNH1  0   0.419   2.5530   0.7395  -0.5480
 M8K  H3   H  HNR5  0   0.412  -3.8717  -0.8886   0.9760
 M8K  H5   H  HCR6  0   0.279   5.4071  -2.4129  -0.0100
 M8K  H6   H  HCR6  0   0.289   7.7278  -1.7271  -0.4441
 M8K  H7   H  HCR6  0   0.282   4.2640   1.7129   0.3468
 M8K  H8   H  HCR6  0   0.267   0.4903   0.4715  -1.7862
 M8K  H10  H  HCR6  0   0.270  -1.3748  -1.3044   2.5026
 M8K  H11  H  HCR6  0   0.267   1.0431  -0.9770   2.2281
 M8K  H12  H  HCH2  0   0.274  -5.0311  -1.0677  -1.8966
 M8K  H13  H  HCH2  0   0.234  -4.8290   0.6349  -2.2892
 M8K  H14  H  HCH2  0   0.242  -4.6596   1.8256   0.2840
 M8K  H15  H  HCH2  0   0.196  -5.9731   2.2504  -0.8071
 M8K  H16  H  HCH2  0   0.218  -6.2282   1.2477   2.0679
 M8K  H17  H  HCH2  0   0.232  -6.5498   2.8756   1.4892
 M8K  H18  H  HCH2  0   0.233  -8.6705   1.5211   1.7706
 M8K  H19  H  HCH2  0   0.212  -8.4335   2.0665   0.1189
 M8K  H20  H  HCH2  0   0.217  -7.7701  -0.7127   1.1977
 M8K  H21  H  HCH2  0   0.232  -9.0619  -0.3130   0.0746
 M8K  H22  H  HCH2  0   0.191  -7.4628   0.3755  -1.6381
 M8K  H23  H  HCH2  0   0.238  -7.0802  -1.2555  -1.0895
 M8K  H2   H  HCR6  0   0.290   6.5730   2.3924  -0.0760

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
 M8K  N    C    triple    1.152  0.020  1.152
 M8K  C    C1   single    1.428  0.020  1.428
 M8K  C2   C1   aromatic  1.393  0.020  1.393
 M8K  C2   C3   aromatic  1.384  0.020  1.384
 M8K  C1   C6   aromatic  1.395  0.020  1.395
 M8K  C3   C4   aromatic  1.393  0.020  1.393
 M8K  O    C7   double    1.218  0.020  1.218
 M8K  C6   C5   aromatic  1.382  0.020  1.382
 M8K  C4   C5   aromatic  1.393  0.020  1.393
 M8K  C4   C7   single    1.497  0.020  1.497
 M8K  C7   N1   single    1.352  0.020  1.352
 M8K  N1   C8   single    1.410  0.020  1.410
 M8K  C13  C8   aromatic  1.387  0.020  1.387
 M8K  C13  C12  aromatic  1.392  0.020  1.392
 M8K  C8   C9   aromatic  1.406  0.020  1.406
 M8K  N2   C12  aromatic  1.375  0.020  1.375
 M8K  N2   C14  aromatic  1.306  0.020  1.306
 M8K  C12  C11  aromatic  1.404  0.020  1.404
 M8K  C9   C10  aromatic  1.383  0.020  1.383
 M8K  C14  C15  single    1.492  0.020  1.492
 M8K  C14  N3   aromatic  1.355  0.020  1.355
 M8K  C11  C10  aromatic  1.388  0.020  1.388
 M8K  C11  N3   aromatic  1.368  0.020  1.368
 M8K  C15  N4   single    1.445  0.020  1.445
 M8K  N4   C16  single    1.455  0.020  1.455
 M8K  N4   C20  single    1.456  0.020  1.456
 M8K  C16  C17  single    1.520  0.020  1.520
 M8K  C17  C18  single    1.523  0.020  1.523
 M8K  C20  C19  single    1.520  0.020  1.520
 M8K  C18  C19  single    1.523  0.020  1.523
 M8K  N1   H1   single    0.860  0.020  1.020
 M8K  C2   H2   single    0.930  0.020  1.080
 M8K  N3   H3   single    0.860  0.020  1.020
 M8K  C5   H5   single    0.930  0.020  1.080
 M8K  C6   H6   single    0.930  0.020  1.080
 M8K  C3   H7   single    0.930  0.020  1.080
 M8K  C13  H8   single    0.930  0.020  1.080
 M8K  C10  H10  single    0.930  0.020  1.080
 M8K  C9   H11  single    0.930  0.020  1.080
 M8K  C15  H12  single    0.970  0.020  1.090
 M8K  C15  H13  single    0.970  0.020  1.090
 M8K  C20  H14  single    0.970  0.020  1.090
 M8K  C20  H15  single    0.970  0.020  1.090
 M8K  C19  H16  single    0.970  0.020  1.090
 M8K  C19  H17  single    0.970  0.020  1.090
 M8K  C18  H18  single    0.970  0.020  1.090
 M8K  C18  H19  single    0.970  0.020  1.090
 M8K  C17  H20  single    0.970  0.020  1.090
 M8K  C17  H21  single    0.970  0.020  1.090
 M8K  C16  H22  single    0.970  0.020  1.090
 M8K  C16  H23  single    0.970  0.020  1.090

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
 M8K  H1   N1   C8   115.60  3.000
 M8K  H1   N1   C7   117.66  3.000
 M8K  C8   N1   C7   125.70  3.000
 M8K  H2   C2   C1   120.39  3.000
 M8K  H2   C2   C3   120.17  3.000
 M8K  C1   C2   C3   119.44  3.000
 M8K  H3   N3   C11  128.17  3.000
 M8K  H3   N3   C14  124.34  3.000
 M8K  C11  N3   C14  107.40  3.000
 M8K  C3   C4   C7   122.30  3.000
 M8K  C7   C4   C5   117.99  3.000
 M8K  C3   C4   C5   119.67  3.000
 M8K  C16  N4   C20  111.61  3.000
 M8K  C20  N4   C15  111.66  3.000
 M8K  C16  N4   C15  111.95  3.000
 M8K  H5   C5   C6   119.43  3.000
 M8K  H5   C5   C4   120.13  3.000
 M8K  C6   C5   C4   120.43  3.000
 M8K  H6   C6   C1   120.26  3.000
 M8K  H6   C6   C5   120.29  3.000
 M8K  C1   C6   C5   119.46  3.000
 M8K  O    C7   C4   120.90  3.000
 M8K  C4   C7   N1   115.01  3.000
 M8K  O    C7   N1   124.09  3.000
 M8K  H7   C3   C4   121.06  3.000
 M8K  H7   C3   C2   118.51  3.000
 M8K  C4   C3   C2   120.41  3.000
 M8K  C    C1   C6   119.72  3.000
 M8K  C6   C1   C2   120.59  3.000
 M8K  C    C1   C2   119.69  3.000
 M8K  N    C    C1   180.00  3.000
 M8K  C9   C8   C13  121.10  3.000
 M8K  C9   C8   N1   120.91  3.000
 M8K  C13  C8   N1   117.94  3.000
 M8K  H8   C13  C12  120.81  3.000
 M8K  H8   C13  C8   120.97  3.000
 M8K  C12  C13  C8   118.21  3.000
 M8K  C11  C12  N2   110.07  3.000
 M8K  C11  C12  C13  120.03  3.000
 M8K  N2   C12  C13  129.90  3.000
 M8K  C14  N2   C12  104.98  3.000
 M8K  C15  C14  N2   126.15  3.000
 M8K  C15  C14  N3   120.79  3.000
 M8K  N2   C14  N3   113.02  3.000
 M8K  C10  C11  C12  122.05  3.000
 M8K  C10  C11  N3   133.43  3.000
 M8K  C12  C11  N3   104.52  3.000
 M8K  H10  C10  C9   120.61  3.000
 M8K  H10  C10  C11  121.93  3.000
 M8K  C9   C10  C11  117.45  3.000
 M8K  H11  C9   C10  118.89  3.000
 M8K  H11  C9   C8   119.95  3.000
 M8K  C10  C9   C8   121.15  3.000
 M8K  H13  C15  H12  106.48  3.000
 M8K  H13  C15  C14  108.64  3.000
 M8K  H12  C15  C14  108.05  3.000
 M8K  H13  C15  N4   113.88  3.000
 M8K  H12  C15  N4   108.57  3.000
 M8K  C14  C15  N4   110.98  3.000
 M8K  H15  C20  H14  106.42  3.000
 M8K  H15  C20  C19  109.55  3.000
 M8K  H14  C20  C19  109.63  3.000
 M8K  H15  C20  N4   110.85  3.000
 M8K  H14  C20  N4   109.11  3.000
 M8K  C19  C20  N4   111.17  3.000
 M8K  H17  C19  H16  107.01  3.000
 M8K  H17  C19  C18  110.93  3.000
 M8K  H16  C19  C18  109.82  3.000
 M8K  H17  C19  C20  109.19  3.000
 M8K  H16  C19  C20  109.07  3.000
 M8K  C18  C19  C20  110.71  3.000
 M8K  H19  C18  H18  106.76  3.000
 M8K  H19  C18  C17  109.16  3.000
 M8K  H18  C18  C17  110.72  3.000
 M8K  H19  C18  C19  109.33  3.000
 M8K  H18  C18  C19  110.83  3.000
 M8K  C17  C18  C19  109.97  3.000
 M8K  H21  C17  H20  107.04  3.000
 M8K  H21  C17  C16  109.15  3.000
 M8K  H20  C17  C16  109.18  3.000
 M8K  H21  C17  C18  110.81  3.000
 M8K  H20  C17  C18  109.87  3.000
 M8K  C16  C17  C18  110.69  3.000
 M8K  H23  C16  H22  106.78  3.000
 M8K  H23  C16  C17  110.02  3.000
 M8K  H22  C16  C17  109.20  3.000
 M8K  H23  C16  N4   108.46  3.000
 M8K  H22  C16  N4   111.26  3.000
 M8K  C17  C16  N4   111.03  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
 M8K  CONST_01  C5   C6   C1   C2     0.00   0.0  0
 M8K  CONST_02  C5   C4   C3   C2     0.00   0.0  0
 M8K  CONST_03  C12  N2   C14  N3     0.00   0.0  0
 M8K  CONST_04  C13  C12  C11  N3   180.00   0.0  0
 M8K  CONST_05  N2   C12  C11  N3     0.00   0.0  0
 M8K  CONST_06  C9   C10  C11  N3   180.00   0.0  0
 M8K  CONST_07  C1   C2   C3   C4     0.00   0.0  0
 M8K  CONST_08  C1   C6   C5   C4     0.00   0.0  0
 M8K  CONST_09  C3   C2   C1   C6     0.00   0.0  0
 M8K  CONST_10  C3   C4   C5   C6     0.00   0.0  0
 M8K  CONST_11  N2   C12  C13  C8   180.00   0.0  0
 M8K  CONST_12  C11  C12  C13  C8     0.00   0.0  0
 M8K  CONST_13  C11  C10  C9   C8     0.00   0.0  0
 M8K  CONST_14  C10  C9   C8   C13    0.00   0.0  0
 M8K  CONST_15  C14  N2   C12  C13  180.00   0.0  0
 M8K  CONST_16  C10  C11  C12  C13    0.00   0.0  0
 M8K  CONST_17  C9   C8   C13  C12    0.00   0.0  0
 M8K  CONST_18  C9   C10  C11  C12    0.00   0.0  0
 M8K  CONST_19  C14  N3   C11  C12    0.00   0.0  0
 M8K  CONST_20  C10  C11  C12  N2   180.00   0.0  0
 M8K  CONST_21  C11  N3   C14  N2     0.00   0.0  0
 M8K  CONST_22  C11  C12  N2   C14    0.00   0.0  0
 M8K  CONST_23  C10  C11  N3   C14  180.00   0.0  0
 M8K  CONST_24  C12  C13  C8   N1   180.00   0.0  0
 M8K  CONST_25  C10  C9   C8   N1   180.00   0.0  0
 M8K  CONST_26  C7   C4   C3   C2   180.00   0.0  0
 M8K  CONST_27  C    C1   C6   C5   180.00   0.0  0
 M8K  CONST_28  C7   C4   C5   C6   180.00   0.0  0
 M8K  CONST_29  C    C1   C2   C3   180.00   0.0  0
 M8K  CONST_30  C15  C14  N2   C12  180.00   0.0  0
 M8K  CONST_31  C15  C14  N3   C11  180.00   0.0  0
 M8K  CONST_32  H6   C6   C1   C2   180.00   0.0  0
 M8K  CONST_33  H10  C10  C11  N3     0.00   0.0  0
 M8K  CONST_34  H2   C2   C3   C4   180.00   0.0  0
 M8K  CONST_35  H7   C3   C4   C5   180.00   0.0  0
 M8K  CONST_36  H5   C5   C4   C3   180.00   0.0  0
 M8K  CONST_37  H11  C9   C8   C13  180.00   0.0  0
 M8K  CONST_38  H3   N3   C11  C12  180.00   0.0  0
 M8K  CONST_39  H8   C13  C12  N2     0.00   0.0  0
 M8K  CONST_40  C8   N1   C7   C4   180.00   0.0  0
 M8K  CONST_44  C8   N1   C7   O      0.00   0.0  0
 M8K  Var_01    C18  C17  C16  N4    56.55  30.0  1
 M8K  Var_02    C18  C19  C20  N4   -56.22  30.0  1
 M8K  Var_03    C17  C16  N4   C20  -59.20  30.0  1
 M8K  Var_04    C17  C18  C19  C20   53.53  30.0  1
 M8K  Var_05    C16  N4   C20  C19   59.07  30.0  1
 M8K  Var_06    C16  C17  C18  C19  -53.71  30.0  1
 M8K  Var_07    N4   C15  C14  N3    33.73  30.0  2
 M8K  Var_08    C3   C4   C7   N1    30.53  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
 M8K  plan-1  C2   0.020
 M8K  plan-1  C4   0.020
 M8K  plan-1  C5   0.020
 M8K  plan-1  C6   0.020
 M8K  plan-1  C7   0.020
 M8K  plan-1  C3   0.020
 M8K  plan-1  C1   0.020
 M8K  plan-1  C    0.020
 M8K  plan-1  N    0.020
 M8K  plan-1  H5   0.020
 M8K  plan-1  H6   0.020
 M8K  plan-1  H7   0.020
 M8K  plan-1  H2   0.020
 M8K  plan-2  N1   0.020
 M8K  plan-2  N3   0.020
 M8K  plan-2  C8   0.020
 M8K  plan-2  C13  0.020
 M8K  plan-2  C12  0.020
 M8K  plan-2  N2   0.020
 M8K  plan-2  C14  0.020
 M8K  plan-2  C11  0.020
 M8K  plan-2  C10  0.020
 M8K  plan-2  C9   0.020
 M8K  plan-2  C15  0.020
 M8K  plan-2  H3   0.020
 M8K  plan-2  H8   0.020
 M8K  plan-2  H10  0.020
 M8K  plan-2  H11  0.020
 M8K  plan-3  N1   0.020
 M8K  plan-3  C4   0.020
 M8K  plan-3  O    0.020
 M8K  plan-3  C7   0.020
 M8K  plan-3  C8   0.020
 M8K  plan-3  H1   0.020

