# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 20:58:08 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-iodanyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Ic1ccc(cc1)C(=O)Nc2ccc3nc(CN4CCCCC4)[nH]c3c2
#
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
 M82  M82  4-iodanyl-~{N}-[2-(piperidin-1-ylmethyl)-3~{H}-benzimidazol-5-yl]benzamide  ligand  47  26  .  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_M82
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
 M82  N1   N  NR15  0  -0.695   4.4544  -0.0763   1.3797
 M82  C2   C  CR16  0  -0.282  -3.0225   0.9247   0.8963
 M82  N3   N  NT    0  -0.410   7.7127  -0.3980   0.2374
 M82  C4   C  CR16  0  -0.256  -3.3985   0.0450  -1.3056
 M82  C5   C  CR16  0  -0.212  -4.7230  -0.2082  -0.9875
 M82  C6   C  C     0   0.524  -1.1197   0.8591  -0.7769
 M82  O    O  O     0  -0.458  -0.8273   1.0535  -1.9435
 M82  C3   C  CR6   0  -0.046  -2.5330   0.5988  -0.3659
 M82  C1   C  CR16  0  -0.209  -4.3502   0.6903   1.2236
 M82  C    C  CR6   0  -0.222  -5.1890   0.1182   0.2789
 M82  I    I  I     0   0.072  -7.1977  -0.2522   0.7690
 M82  N    N  NH1   0  -0.758  -0.2185   0.8495   0.2352
 M82  C7   C  CR6   0   0.349   1.1685   1.0532   0.1121
 M82  C12  C  CR16  0  -0.395   2.0053   0.2578   0.8822
 M82  C11  C  CR56  0   0.354   3.3677   0.5007   0.7857
 M82  C13  C  CR5   0   0.416   5.5642   0.5471   0.9004
 M82  N2   N  N     0  -0.459   5.2801   1.4874   0.0414
 M82  C10  C  CR56  0   0.130   3.9095   1.4848  -0.0562
 M82  C9   C  CR16  0  -0.340   3.0504   2.2767  -0.8165
 M82  C8   C  CR16  0  -0.302   1.6893   2.0598  -0.7230
 M82  C14  C  CH2   0  -0.365   6.9378   0.1484   1.3323
 M82  C19  C  CH2   0  -0.281   9.0959  -0.5928   0.6435
 M82  C18  C  CH2   0  -0.438   9.9489  -1.0771  -0.5187
 M82  C17  C  CH2   0  -0.441   9.3821  -2.3658  -1.0993
 M82  C16  C  CH2   0  -0.436   7.9170  -2.1631  -1.4614
 M82  C15  C  CH2   0  -0.289   7.1322  -1.6302  -0.2724
 M82  H1   H  HNR5  0   0.418   4.4446  -0.8248   2.0545
 M82  H4   H  HCR6  0   0.274  -3.0386  -0.2038  -2.2949
 M82  H5   H  HCR6  0   0.286  -5.3738  -0.6531  -1.7277
 M82  H6   H  HCR6  0   0.288  -4.7120   0.9621   2.2055
 M82  H7   H  HNH1  0   0.418  -0.5261   0.4853   1.1234
 M82  H8   H  HCR6  0   0.279   1.6069  -0.5193   1.5228
 M82  H10  H  HCR6  0   0.258   3.4378   3.0550  -1.4613
 M82  H11  H  HCR6  0   0.266   1.0180   2.6874  -1.2894
 M82  H12  H  HCH2  0   0.221   6.8581  -0.5525   2.1805
 M82  H13  H  HCH2  0   0.270   7.4502   1.0373   1.7090
 M82  H14  H  HCH2  0   0.237   9.4828   0.3565   1.0224
 M82  H15  H  HCH2  0   0.187   9.1697  -1.3202   1.4727
 M82  H16  H  HCH2  0   0.216   9.9751  -0.3034  -1.2921
 M82  H17  H  HCH2  0   0.232  10.9756  -1.2197  -0.1747
 M82  H18  H  HCH2  0   0.232   9.9565  -2.6844  -1.9719
 M82  H19  H  HCH2  0   0.211   9.4667  -3.1670  -0.3566
 M82  H20  H  HCH2  0   0.217   7.8376  -1.4525  -2.2898
 M82  H21  H  HCH2  0   0.232   7.4631  -3.0981  -1.7962
 M82  H22  H  HCH2  0   0.188   7.0899  -2.4042   0.5161
 M82  H23  H  HCH2  0   0.244   6.1012  -1.4412  -0.5806
 M82  H2   H  HCR6  0   0.276  -2.3889   1.3897   1.6412

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
 M82  I    C    single    2.101  0.020  2.101
 M82  C5   C    aromatic  1.388  0.020  1.388
 M82  C5   C4   aromatic  1.386  0.020  1.386
 M82  C    C1   aromatic  1.387  0.020  1.387
 M82  C4   C3   aromatic  1.392  0.020  1.392
 M82  C1   C2   aromatic  1.387  0.020  1.387
 M82  O    C6   double    1.218  0.020  1.218
 M82  C3   C2   aromatic  1.392  0.020  1.392
 M82  C3   C6   single    1.495  0.020  1.495
 M82  C6   N    single    1.355  0.020  1.355
 M82  N    C7   single    1.407  0.020  1.407
 M82  C12  C7   aromatic  1.388  0.020  1.388
 M82  C12  C11  aromatic  1.387  0.020  1.387
 M82  C7   C8   aromatic  1.408  0.020  1.408
 M82  N1   C11  aromatic  1.366  0.020  1.366
 M82  N1   C13  aromatic  1.360  0.020  1.360
 M82  C11  C10  aromatic  1.404  0.020  1.404
 M82  C8   C9   aromatic  1.381  0.020  1.381
 M82  C13  C14  single    1.494  0.020  1.494
 M82  C13  N2   aromatic  1.305  0.020  1.305
 M82  C10  C9   aromatic  1.394  0.020  1.394
 M82  C10  N2   aromatic  1.374  0.020  1.374
 M82  C14  N3   single    1.448  0.020  1.448
 M82  C15  N3   single    1.454  0.020  1.454
 M82  C15  C16  single    1.521  0.020  1.521
 M82  N3   C19  single    1.455  0.020  1.455
 M82  C16  C17  single    1.523  0.020  1.523
 M82  C19  C18  single    1.521  0.020  1.521
 M82  C17  C18  single    1.523  0.020  1.523
 M82  N1   H1   single    0.860  0.020  1.020
 M82  C2   H2   single    0.930  0.020  1.080
 M82  C4   H4   single    0.930  0.020  1.080
 M82  C5   H5   single    0.930  0.020  1.080
 M82  C1   H6   single    0.930  0.020  1.080
 M82  N    H7   single    0.860  0.020  1.020
 M82  C12  H8   single    0.930  0.020  1.080
 M82  C9   H10  single    0.930  0.020  1.080
 M82  C8   H11  single    0.930  0.020  1.080
 M82  C14  H12  single    0.970  0.020  1.090
 M82  C14  H13  single    0.970  0.020  1.090
 M82  C19  H14  single    0.970  0.020  1.090
 M82  C19  H15  single    0.970  0.020  1.090
 M82  C18  H16  single    0.970  0.020  1.090
 M82  C18  H17  single    0.970  0.020  1.090
 M82  C17  H18  single    0.970  0.020  1.090
 M82  C17  H19  single    0.970  0.020  1.090
 M82  C16  H20  single    0.970  0.020  1.090
 M82  C16  H21  single    0.970  0.020  1.090
 M82  C15  H22  single    0.970  0.020  1.090
 M82  C15  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
 M82  H1   N1   C13  125.75  3.000
 M82  H1   N1   C11  126.66  3.000
 M82  C13  N1   C11  107.59  3.000
 M82  H2   C2   C1   118.04  3.000
 M82  H2   C2   C3   121.23  3.000
 M82  C1   C2   C3   120.71  3.000
 M82  C15  N3   C19  111.34  3.000
 M82  C19  N3   C14  110.38  3.000
 M82  C15  N3   C14  111.78  3.000
 M82  H4   C4   C3   120.13  3.000
 M82  H4   C4   C5   119.07  3.000
 M82  C3   C4   C5   120.80  3.000
 M82  H5   C5   C    121.27  3.000
 M82  H5   C5   C4   119.56  3.000
 M82  C    C5   C4   119.16  3.000
 M82  N    C6   C3   114.97  3.000
 M82  N    C6   O    123.82  3.000
 M82  C3   C6   O    121.20  3.000
 M82  C6   C3   C4   118.13  3.000
 M82  C6   C3   C2   122.74  3.000
 M82  C4   C3   C2   119.10  3.000
 M82  H6   C1   C    121.33  3.000
 M82  H6   C1   C2   119.47  3.000
 M82  C    C1   C2   119.19  3.000
 M82  I    C    C1   119.48  3.000
 M82  C1   C    C5   121.02  3.000
 M82  I    C    C5   119.49  3.000
 M82  H7   N    C7   115.47  3.000
 M82  H7   N    C6   117.24  3.000
 M82  C7   N    C6   126.09  3.000
 M82  C8   C7   C12  121.06  3.000
 M82  C8   C7   N    121.33  3.000
 M82  C12  C7   N    117.57  3.000
 M82  H8   C12  C11  121.87  3.000
 M82  H8   C12  C7   121.18  3.000
 M82  C11  C12  C7   116.95  3.000
 M82  C10  C11  C12  122.92  3.000
 M82  C10  C11  N1   104.47  3.000
 M82  C12  C11  N1   132.60  3.000
 M82  C14  C13  N2   125.64  3.000
 M82  N2   C13  N1   112.62  3.000
 M82  C14  C13  N1   121.73  3.000
 M82  C10  N2   C13  105.22  3.000
 M82  C9   C10  N2   130.72  3.000
 M82  N2   C10  C11  110.10  3.000
 M82  C9   C10  C11  119.17  3.000
 M82  H10  C9   C8   120.39  3.000
 M82  H10  C9   C10  120.85  3.000
 M82  C8   C9   C10  118.76  3.000
 M82  H11  C8   C9   119.07  3.000
 M82  H11  C8   C7   119.80  3.000
 M82  C9   C8   C7   121.12  3.000
 M82  H13  C14  H12  106.59  3.000
 M82  H13  C14  C13  108.27  3.000
 M82  H12  C14  C13  108.99  3.000
 M82  H13  C14  N3   108.45  3.000
 M82  H12  C14  N3   112.35  3.000
 M82  C13  C14  N3   111.97  3.000
 M82  H15  C19  H14  106.72  3.000
 M82  H15  C19  C18  109.04  3.000
 M82  H14  C19  C18  110.06  3.000
 M82  H15  C19  N3   111.16  3.000
 M82  H14  C19  N3   108.49  3.000
 M82  C18  C19  N3   111.27  3.000
 M82  H17  C18  H16  107.00  3.000
 M82  H17  C18  C17  111.07  3.000
 M82  H16  C18  C17  109.74  3.000
 M82  H17  C18  C19  109.16  3.000
 M82  H16  C18  C19  109.17  3.000
 M82  C17  C18  C19  110.62  3.000
 M82  H19  C17  H18  106.72  3.000
 M82  H19  C17  C16  109.44  3.000
 M82  H18  C17  C16  110.79  3.000
 M82  H19  C17  C18  109.36  3.000
 M82  H18  C17  C18  110.84  3.000
 M82  C16  C17  C18  109.64  3.000
 M82  H21  C16  H20  107.09  3.000
 M82  H21  C16  C15  108.98  3.000
 M82  H20  C16  C15  109.08  3.000
 M82  H21  C16  C17  111.03  3.000
 M82  H20  C16  C17  109.65  3.000
 M82  C15  C16  C17  110.93  3.000
 M82  H23  C15  H22  106.63  3.000
 M82  H23  C15  C16  109.08  3.000
 M82  H22  C15  C16  109.38  3.000
 M82  H23  C15  N3   109.21  3.000
 M82  H22  C15  N3   111.00  3.000
 M82  C16  C15  N3   111.40  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
 M82  CONST_01  C7   C12  C11  N1    180.00   0.0  0
 M82  CONST_02  C9   C10  C11  N1    180.00   0.0  0
 M82  CONST_03  N2   C10  C11  N1      0.00   0.0  0
 M82  CONST_04  C10  N2   C13  N1      0.00   0.0  0
 M82  CONST_05  C5   C    C1   C2      0.00   0.0  0
 M82  CONST_06  C5   C4   C3   C2      0.00   0.0  0
 M82  CONST_07  C1   C    C5   C4      0.00   0.0  0
 M82  CONST_08  C1   C2   C3   C4      0.00   0.0  0
 M82  CONST_09  C    C5   C4   C3      0.00   0.0  0
 M82  CONST_10  C    C1   C2   C3      0.00   0.0  0
 M82  CONST_11  C10  C11  C12  C7      0.00   0.0  0
 M82  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 M82  CONST_13  C9   C8   C7   C12     0.00   0.0  0
 M82  CONST_14  C13  N1   C11  C12   180.00   0.0  0
 M82  CONST_15  C9   C10  C11  C12     0.00   0.0  0
 M82  CONST_16  N2   C10  C11  C12   180.00   0.0  0
 M82  CONST_17  C8   C7   C12  C11     0.00   0.0  0
 M82  CONST_18  N2   C13  N1   C11     0.00   0.0  0
 M82  CONST_19  C8   C9   C10  C11     0.00   0.0  0
 M82  CONST_20  C13  N2   C10  C11     0.00   0.0  0
 M82  CONST_21  C10  C11  N1   C13     0.00   0.0  0
 M82  CONST_22  C9   C10  N2   C13   180.00   0.0  0
 M82  CONST_23  C8   C9   C10  N2    180.00   0.0  0
 M82  CONST_24  I    C    C1   C2    180.00   0.0  0
 M82  CONST_25  I    C    C5   C4    180.00   0.0  0
 M82  CONST_26  C6   C3   C4   C5    180.00   0.0  0
 M82  CONST_27  C1   C2   C3   C6    180.00   0.0  0
 M82  CONST_28  C11  C12  C7   N     180.00   0.0  0
 M82  CONST_29  C9   C8   C7   N     180.00   0.0  0
 M82  CONST_30  C14  C13  N1   C11   180.00   0.0  0
 M82  CONST_31  C14  C13  N2   C10   180.00   0.0  0
 M82  CONST_32  H8   C12  C11  N1      0.00   0.0  0
 M82  CONST_33  H4   C4   C3   C2    180.00   0.0  0
 M82  CONST_34  H2   C2   C3   C4    180.00   0.0  0
 M82  CONST_35  H6   C1   C    C5    180.00   0.0  0
 M82  CONST_36  H5   C5   C4   C3    180.00   0.0  0
 M82  CONST_37  H10  C9   C8   C7    180.00   0.0  0
 M82  CONST_38  H11  C8   C7   C12   180.00   0.0  0
 M82  CONST_39  H1   N1   C11  C12     0.00   0.0  0
 M82  CONST_40  C7   N    C6   C3    180.00   0.0  0
 M82  CONST_44  C7   N    C6   O       0.00   0.0  0
 M82  Var_01    C17  C16  C15  N3     56.11  30.0  1
 M82  Var_02    C17  C18  C19  N3    -57.03  30.0  1
 M82  Var_03    C16  C15  N3   C19   -58.58  30.0  1
 M82  Var_04    C16  C17  C18  C19    53.95  30.0  1
 M82  Var_05    C15  N3   C19  C18    59.10  30.0  1
 M82  Var_06    C15  C16  C17  C18   -53.56  30.0  1
 M82  Var_07    N3   C14  C13  N1    114.99  30.0  2
 M82  Var_08    O    C6   C3   C2   -151.93  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
 M82  plan-1  C2   0.020
 M82  plan-1  C4   0.020
 M82  plan-1  C5   0.020
 M82  plan-1  C6   0.020
 M82  plan-1  C3   0.020
 M82  plan-1  C1   0.020
 M82  plan-1  C    0.020
 M82  plan-1  I    0.020
 M82  plan-1  H4   0.020
 M82  plan-1  H5   0.020
 M82  plan-1  H6   0.020
 M82  plan-1  H2   0.020
 M82  plan-2  N1   0.020
 M82  plan-2  N    0.020
 M82  plan-2  C7   0.020
 M82  plan-2  C12  0.020
 M82  plan-2  C11  0.020
 M82  plan-2  C13  0.020
 M82  plan-2  N2   0.020
 M82  plan-2  C10  0.020
 M82  plan-2  C9   0.020
 M82  plan-2  C8   0.020
 M82  plan-2  C14  0.020
 M82  plan-2  H1   0.020
 M82  plan-2  H8   0.020
 M82  plan-2  H10  0.020
 M82  plan-2  H11  0.020
 M82  plan-3  C6   0.020
 M82  plan-3  O    0.020
 M82  plan-3  C3   0.020
 M82  plan-3  N    0.020
 M82  plan-3  C7   0.020
 M82  plan-3  H7   0.020

