# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 07:14:48 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 2-{1-[2-(piperidin-1-yl)ethyl]-1H-benzimidazol-2-yl}thieno[3,2-b]pyridine-7-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1ccnc2cc(sc12)c3nc4ccccc4n3CCN5CCCCC5
#
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
 H61  H61  '2-{1-[2-(piperidin-1-yl)ethyl]-1H-benzimidazol-2-yl}thieno[3,2-b]pyridine-7-carboxylic acid'  ligand  50  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H61
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
 H61  C02  C  C      0   0.425   4.3238   0.1959  -0.6032
 H61  C04  C  CR6    0   0.006   3.7667   1.5661  -0.2567
 H61  C05  C  CR56   0  -0.223   2.3948   1.7622  -0.1386
 H61  C06  C  CR56   0   0.281   1.8792   3.0317   0.1775
 H61  C07  C  CR15   0  -0.213   0.4526   3.0279   0.2530
 H61  C08  C  CR5    0  -0.287  -0.0692   1.7973   0.0105
 H61  C09  C  CR5    0   0.489  -1.4976   1.5275  -0.0409
 H61  C11  C  CR56   0   0.139  -3.5876   1.8533  -0.3041
 H61  C12  C  CR16   0  -0.337  -4.8598   2.3693  -0.5579
 H61  C13  C  CR16   0  -0.271  -5.9435   1.5296  -0.3831
 H61  C14  C  CR16   0  -0.274  -5.7790   0.1994   0.0360
 H61  C15  C  CR16   0  -0.317  -4.5263  -0.3311   0.2882
 H61  C16  C  CR56   0   0.344  -3.4409   0.5202   0.1074
 H61  C19  C  CH2    0  -0.267  -1.2964  -1.8935  -0.3906
 H61  C21  C  CH2    0  -0.277  -0.9432  -4.1785  -0.9650
 H61  C22  C  CH2    0  -0.440  -0.4970  -5.5498  -0.4847
 H61  C23  C  CH2    0  -0.439   0.9465  -5.5113  -0.0019
 H61  C24  C  CH2    0  -0.436   1.1059  -4.4105   1.0373
 H61  C25  C  CH2    0  -0.291   0.6036  -3.0779   0.5034
 H61  C28  C  CR16   0  -0.088   3.9628   3.9094   0.2687
 H61  C29  C  CR16   0  -0.391   4.5558   2.6808  -0.0436
 H61  N10  N  N      0  -0.472  -2.3603   2.4499  -0.3891
 H61  N17  N  NR5    0  -0.559  -2.0920   0.3356   0.2762
 H61  N20  N  NT     0  -0.420  -0.7850  -3.1660   0.0697
 H61  N27  N  N      0  -0.435   2.6613   4.0972   0.3801
 H61  O01  O  OC    -1  -0.572   5.5557   0.0864  -0.6849
 H61  O03  O  O      0  -0.567   3.4567  -0.6852  -0.7701
 H61  S26  S  S2     0   0.238   1.1497   0.5893  -0.3392
 H61  H1   H  HCR5   0   0.266  -0.1398   3.9018   0.4822
 H61  H2   H  HCR6   0   0.256  -4.9892   3.3952  -0.8781
 H61  H3   H  HCR6   0   0.255  -6.9421   1.9013  -0.5710
 H61  H4   H  HCR6   0   0.257  -6.6528  -0.4257   0.1637
 H61  H5   H  HCR6   0   0.269  -4.4101  -1.3585   0.6090
 H61  H6   H  HCH2   0   0.279  -2.1653  -1.3289   1.5003
 H61  H7   H  HCH2   0   0.276  -0.5702  -0.6590   1.2633
 H61  H8   H  HCH2   0   0.247  -2.2675  -2.0665  -0.8626
 H61  H9   H  HCH2   0   0.205  -0.6521  -1.4411  -1.1636
 H61  H12  H  HCH2   0   0.215  -1.1484  -5.8749   0.3324
 H61  H13  H  HCH2   0   0.231  -0.6196  -6.2702  -1.2964
 H61  H14  H  HCH2   0   0.231   1.2417  -6.4789   0.4100
 H61  H15  H  HCH2   0   0.211   1.6124  -5.3148  -0.8489
 H61  H16  H  HCH2   0   0.215   0.5421  -4.6725   1.9380
 H61  H17  H  HCH2   0   0.231   2.1509  -4.3031   1.3363
 H61  H18  H  HCH2   0   0.234   0.6932  -2.3282   1.2917
 H61  H19  H  HCH2   0   0.196   1.2548  -2.7388  -0.3210
 H61  H20  H  HCR6   0   0.261   4.5914   4.7775   0.4347
 H61  H21  H  HCR6   0   0.264   5.6321   2.6077  -0.1173
 H61  C18  C  CH2    0  -0.363  -1.4991  -0.8998   0.7508
 H61  H10  H  HCH2   0   0.185  -0.3740  -3.9091  -1.8730
 H61  H11  H  HCH2   0   0.235  -1.9960  -4.2122  -1.2562

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
 H61  C21  C22  single    1.520  0.020  1.520
 H61  C21  N20  single    1.456  0.020  1.456
 H61  C22  C23  single    1.523  0.020  1.523
 H61  N20  C25  single    1.457  0.020  1.457
 H61  N20  C19  single    1.447  0.020  1.447
 H61  C23  C24  single    1.522  0.020  1.522
 H61  C25  C24  single    1.521  0.020  1.521
 H61  C19  C18  single    1.527  0.020  1.527
 H61  C18  N17  single    1.450  0.020  1.450
 H61  C15  C14  aromatic  1.384  0.020  1.384
 H61  C15  C16  aromatic  1.391  0.020  1.391
 H61  C14  C13  aromatic  1.404  0.020  1.404
 H61  C16  N17  aromatic  1.372  0.020  1.372
 H61  C16  C11  aromatic  1.403  0.020  1.403
 H61  N17  C09  aromatic  1.369  0.020  1.369
 H61  C13  C12  aromatic  1.382  0.020  1.382
 H61  C07  C06  aromatic  1.429  0.020  1.429
 H61  C07  C08  aromatic  1.358  0.020  1.358
 H61  N27  C06  aromatic  1.337  0.020  1.337
 H61  N27  C28  aromatic  1.320  0.020  1.320
 H61  C09  C08  single    1.455  0.020  1.455
 H61  C09  N10  aromatic  1.310  0.020  1.310
 H61  C11  C12  aromatic  1.396  0.020  1.396
 H61  C11  N10  aromatic  1.367  0.020  1.367
 H61  C06  C05  aromatic  1.406  0.020  1.406
 H61  C08  S26  aromatic  1.751  0.020  1.751
 H61  C28  C29  aromatic  1.400  0.020  1.400
 H61  C05  S26  aromatic  1.722  0.020  1.722
 H61  C05  C04  aromatic  1.391  0.020  1.391
 H61  C29  C04  aromatic  1.382  0.020  1.382
 H61  C04  C02  single    1.519  0.020  1.519
 H61  C02  O03  deloc     1.247  0.020  1.247
 H61  C02  O01  deloc     1.239  0.020  1.239
 H61  C07  H1   single    0.930  0.020  1.080
 H61  C12  H2   single    0.930  0.020  1.080
 H61  C13  H3   single    0.930  0.020  1.080
 H61  C14  H4   single    0.930  0.020  1.080
 H61  C15  H5   single    0.930  0.020  1.080
 H61  C18  H6   single    0.970  0.020  1.090
 H61  C18  H7   single    0.970  0.020  1.090
 H61  C19  H8   single    0.970  0.020  1.090
 H61  C19  H9   single    0.970  0.020  1.090
 H61  C21  H10  single    0.970  0.020  1.090
 H61  C21  H11  single    0.970  0.020  1.090
 H61  C22  H12  single    0.970  0.020  1.090
 H61  C22  H13  single    0.970  0.020  1.090
 H61  C23  H14  single    0.970  0.020  1.090
 H61  C23  H15  single    0.970  0.020  1.090
 H61  C24  H16  single    0.970  0.020  1.090
 H61  C24  H17  single    0.970  0.020  1.090
 H61  C25  H18  single    0.970  0.020  1.090
 H61  C25  H19  single    0.970  0.020  1.090
 H61  C28  H20  single    0.930  0.020  1.080
 H61  C29  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
 H61  O03  C02  O01  128.29  3.000
 H61  O01  C02  C04  117.33  3.000
 H61  O03  C02  C04  114.37  3.000
 H61  C29  C04  C05  115.87  3.000
 H61  C29  C04  C02  123.59  3.000
 H61  C05  C04  C02  120.54  3.000
 H61  S26  C05  C06  112.08  3.000
 H61  S26  C05  C04  127.38  3.000
 H61  C06  C05  C04  120.54  3.000
 H61  N27  C06  C07  125.33  3.000
 H61  N27  C06  C05  122.61  3.000
 H61  C07  C06  C05  112.07  3.000
 H61  H1   C07  C08  124.05  3.000
 H61  H1   C07  C06  123.83  3.000
 H61  C08  C07  C06  112.12  3.000
 H61  S26  C08  C09  123.26  3.000
 H61  S26  C08  C07  113.15  3.000
 H61  C09  C08  C07  123.47  3.000
 H61  N17  C09  N10  112.87  3.000
 H61  N10  C09  C08  121.70  3.000
 H61  N17  C09  C08  125.42  3.000
 H61  N10  C11  C16  109.82  3.000
 H61  N10  C11  C12  130.19  3.000
 H61  C16  C11  C12  119.99  3.000
 H61  H2   C12  C13  121.30  3.000
 H61  H2   C12  C11  120.87  3.000
 H61  C13  C12  C11  117.84  3.000
 H61  H3   C13  C14  119.04  3.000
 H61  H3   C13  C12  119.54  3.000
 H61  C14  C13  C12  121.43  3.000
 H61  H4   C14  C15  119.22  3.000
 H61  H4   C14  C13  119.20  3.000
 H61  C15  C14  C13  121.58  3.000
 H61  H5   C15  C16  122.38  3.000
 H61  H5   C15  C14  121.00  3.000
 H61  C16  C15  C14  116.62  3.000
 H61  N17  C16  C15  131.97  3.000
 H61  N17  C16  C11  105.47  3.000
 H61  C15  C16  C11  122.55  3.000
 H61  H9   C19  H8   106.33  3.000
 H61  H9   C19  N20  112.16  3.000
 H61  H8   C19  N20  108.19  3.000
 H61  H9   C19  C18  109.54  3.000
 H61  H8   C19  C18  107.92  3.000
 H61  N20  C19  C18  112.43  3.000
 H61  H11  C21  H10  106.55  3.000
 H61  H11  C21  N20  108.39  3.000
 H61  H10  C21  N20  111.00  3.000
 H61  H11  C21  C22  109.83  3.000
 H61  H10  C21  C22  109.17  3.000
 H61  N20  C21  C22  111.77  3.000
 H61  H13  C22  H12  106.98  3.000
 H61  H13  C22  C23  111.02  3.000
 H61  H12  C22  C23  109.58  3.000
 H61  H13  C22  C21  109.10  3.000
 H61  H12  C22  C21  109.22  3.000
 H61  C23  C22  C21  110.84  3.000
 H61  H15  C23  H14  106.64  3.000
 H61  H15  C23  C24  109.54  3.000
 H61  H14  C23  C24  110.78  3.000
 H61  H15  C23  C22  109.62  3.000
 H61  H14  C23  C22  110.70  3.000
 H61  C24  C23  C22  109.51  3.000
 H61  H17  C24  H16  106.93  3.000
 H61  H17  C24  C25  109.02  3.000
 H61  H16  C24  C25  109.18  3.000
 H61  H17  C24  C23  110.99  3.000
 H61  H16  C24  C23  109.56  3.000
 H61  C25  C24  C23  111.06  3.000
 H61  H19  C25  H18  106.25  3.000
 H61  H19  C25  N20  111.00  3.000
 H61  H18  C25  N20  109.55  3.000
 H61  H19  C25  C24  109.66  3.000
 H61  H18  C25  C24  108.73  3.000
 H61  N20  C25  C24  111.48  3.000
 H61  H20  C28  N27  116.41  3.000
 H61  H20  C28  C29  119.42  3.000
 H61  N27  C28  C29  124.17  3.000
 H61  H21  C29  C28  119.75  3.000
 H61  H21  C29  C04  120.22  3.000
 H61  C28  C29  C04  120.03  3.000
 H61  C11  N10  C09  105.51  3.000
 H61  C18  N17  C16  123.84  3.000
 H61  C16  N17  C09  106.33  3.000
 H61  C18  N17  C09  129.79  3.000
 H61  C25  N20  C21  110.92  3.000
 H61  C25  N20  C19  112.23  3.000
 H61  C21  N20  C19  110.31  3.000
 H61  C28  N27  C06  116.79  3.000
 H61  C08  S26  C05   90.58  3.000
 H61  H7   C18  H6   106.55  3.000
 H61  H7   C18  N17  108.34  3.000
 H61  H6   C18  N17  108.08  3.000
 H61  H7   C18  C19  112.51  3.000
 H61  H6   C18  C19  109.80  3.000
 H61  N17  C18  C19  111.35  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
 H61  CONST_01  C07  C06  C05  C04   180.00   0.0  0
 H61  CONST_02  N27  C06  C05  C04     0.00   0.0  0
 H61  CONST_03  C08  S26  C05  C04   180.00   0.0  0
 H61  CONST_04  N27  C28  C29  C04     0.00   0.0  0
 H61  CONST_05  C08  C07  C06  C05     0.00   0.0  0
 H61  CONST_06  C28  N27  C06  C05     0.00   0.0  0
 H61  CONST_07  C07  C08  S26  C05     0.00   0.0  0
 H61  CONST_08  C09  C08  S26  C05   180.00   0.0  0
 H61  CONST_09  C28  C29  C04  C05     0.00   0.0  0
 H61  CONST_10  C09  C08  C07  C06   180.00   0.0  0
 H61  CONST_11  S26  C08  C07  C06     0.00   0.0  0
 H61  CONST_12  C29  C28  N27  C06     0.00   0.0  0
 H61  CONST_13  C08  S26  C05  C06     0.00   0.0  0
 H61  CONST_14  C29  C04  C05  C06     0.00   0.0  0
 H61  CONST_15  C28  N27  C06  C07   180.00   0.0  0
 H61  CONST_16  S26  C05  C06  C07     0.00   0.0  0
 H61  CONST_19  N27  C06  C07  C08   180.00   0.0  0
 H61  CONST_20  C16  N17  C09  C08   180.00   0.0  0
 H61  CONST_21  C11  N10  C09  C08   180.00   0.0  0
 H61  CONST_22  C15  C16  N17  C09   180.00   0.0  0
 H61  CONST_23  C11  C16  N17  C09     0.00   0.0  0
 H61  CONST_24  C16  C11  N10  C09     0.00   0.0  0
 H61  CONST_25  C12  C11  N10  C09   180.00   0.0  0
 H61  CONST_26  C14  C15  C16  C11     0.00   0.0  0
 H61  CONST_27  C14  C13  C12  C11     0.00   0.0  0
 H61  CONST_28  N17  C09  N10  C11     0.00   0.0  0
 H61  CONST_29  C15  C14  C13  C12     0.00   0.0  0
 H61  CONST_30  C15  C16  C11  C12     0.00   0.0  0
 H61  CONST_31  N17  C16  C11  C12   180.00   0.0  0
 H61  CONST_32  C16  C15  C14  C13     0.00   0.0  0
 H61  CONST_33  C16  C11  C12  C13     0.00   0.0  0
 H61  CONST_34  N10  C11  C12  C13   180.00   0.0  0
 H61  CONST_35  N17  C16  C15  C14   180.00   0.0  0
 H61  CONST_36  N10  C11  C16  C15   180.00   0.0  0
 H61  CONST_37  N10  C09  N17  C16     0.00   0.0  0
 H61  CONST_38  S26  C05  C04  C29   180.00   0.0  0
 H61  CONST_40  N17  C16  C11  N10     0.00   0.0  0
 H61  CONST_42  S26  C05  C06  N27   180.00   0.0  0
 H61  CONST_43  C06  C05  C04  C02   180.00   0.0  0
 H61  CONST_44  S26  C05  C04  C02     0.00   0.0  0
 H61  CONST_45  C28  C29  C04  C02   180.00   0.0  0
 H61  CONST_46  C18  N17  C09  C08     0.00   0.0  0
 H61  CONST_47  C18  N17  C16  C11   180.00   0.0  0
 H61  CONST_48  C18  N17  C16  C15     0.00   0.0  0
 H61  CONST_49  N10  C09  N17  C18   180.00   0.0  0
 H61  CONST_50  H20  C28  C29  C04   180.00   0.0  0
 H61  CONST_51  H1   C07  C06  C05   180.00   0.0  0
 H61  CONST_52  H21  C29  C04  C05   180.00   0.0  0
 H61  CONST_53  H5   C15  C16  C11   180.00   0.0  0
 H61  CONST_54  H3   C13  C12  C11   180.00   0.0  0
 H61  CONST_55  H4   C14  C13  C12   180.00   0.0  0
 H61  CONST_56  H2   C12  C13  C14   180.00   0.0  0
 H61  Var_01    C24  C23  C22  C21    53.44  30.0  1
 H61  Var_02    C24  C25  N20  C21   -58.47  30.0  1
 H61  Var_03    C25  N20  C21  C22    58.63  30.0  1
 H61  Var_04    C25  C24  C23  C22   -53.57  30.0  1
 H61  Var_05    N20  C21  C22  C23   -56.60  30.0  1
 H61  Var_06    N20  C25  C24  C23    56.58  30.0  1
 H61  Var_07    O03  C02  C04  C05     0.44  30.0  2
 H61  Var_08    C19  C18  N17  C09   -98.26  30.0  2
 H61  Var_09    C21  N20  C19  C18   164.85  30.0  1
 H61  Var_10    N20  C19  C18  N17  -176.32  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
 H61  plan-1  C02  0.020
 H61  plan-1  C04  0.020
 H61  plan-1  C05  0.020
 H61  plan-1  C06  0.020
 H61  plan-1  C07  0.020
 H61  plan-1  C08  0.020
 H61  plan-1  C09  0.020
 H61  plan-1  C28  0.020
 H61  plan-1  C29  0.020
 H61  plan-1  N27  0.020
 H61  plan-1  S26  0.020
 H61  plan-1  H1   0.020
 H61  plan-1  H20  0.020
 H61  plan-1  H21  0.020
 H61  plan-2  C08  0.020
 H61  plan-2  C09  0.020
 H61  plan-2  C11  0.020
 H61  plan-2  C12  0.020
 H61  plan-2  C13  0.020
 H61  plan-2  C14  0.020
 H61  plan-2  C15  0.020
 H61  plan-2  C16  0.020
 H61  plan-2  N10  0.020
 H61  plan-2  N17  0.020
 H61  plan-2  H2   0.020
 H61  plan-2  H3   0.020
 H61  plan-2  H4   0.020
 H61  plan-2  H5   0.020
 H61  plan-2  C18  0.020
 H61  plan-3  C02  0.020
 H61  plan-3  C04  0.020
 H61  plan-3  O01  0.020
 H61  plan-3  O03  0.020

