# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 18:03:01 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 6-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12
#
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
 BH7  BH7  '6-({5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}amino)hexanoic acid'  ligand  50  24  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BH7
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
 BH7  N1    N  NH1    0  -0.661  -0.0987  -0.2086  -8.0493
 BH7  C2    C  CH1    0  -0.046   0.9483  -0.6899  -7.1858
 BH7  C3    C  CH1    0  -0.063   0.1518  -1.2041  -5.9498
 BH7  N4    N  NH1    0  -0.656  -1.1910  -0.7724  -6.2408
 BH7  C5    C  C      0   0.642  -1.3286  -0.2158  -7.4742
 BH7  C6    C  CH2    0  -0.570   1.9201   0.4044  -6.7282
 BH7  S7    S  S2     0  -0.024   1.2141   1.1218  -5.2226
 BH7  C8    C  CH1    0  -0.361   0.7310  -0.5527  -4.6875
 BH7  O9    O  O      0  -0.529  -2.3667   0.1898  -7.9742
 BH7  C10   C  CH2    0  -0.422  -0.2097  -0.5439  -3.4965
 BH7  C11   C  CH2    0  -0.419   0.4055   0.0597  -2.2401
 BH7  C12   C  CH2    0  -0.416  -0.5166  -0.0503  -1.0332
 BH7  C13   C  CH2    0  -0.574   0.0989   0.5733   0.2140
 BH7  C14   C  C      0   0.556  -0.7992   0.4618   1.4273
 BH7  O15   O  O      0  -0.512  -1.9979   0.7114   1.3730
 BH7  N16   N  NH1    0  -0.643  -0.1883   0.0930   2.5623
 BH7  C17   C  CH2    0  -0.237  -0.8664  -0.0415   3.8348
 BH7  C18   C  CH2    0  -0.467   0.1341  -0.0610   4.9793
 BH7  C19   C  CH2    0  -0.414  -0.5442  -0.2145   6.3342
 BH7  C20   C  CH2    0  -0.402   0.4461  -0.2252   7.4928
 BH7  C21   C  CH2    0  -0.580  -0.2329  -0.3628   8.8452
 BH7  C22   C  C      0   0.410   0.7005  -0.3789  10.0696
 BH7  O23   O  OC    -1  -0.634   0.1380  -0.3537  11.1852
 BH7  O24   O  O      0  -0.610   1.9295  -0.4250   9.8648
 BH7  HN1   H  HNH1   0   0.398   0.0889   0.3284  -8.8792
 BH7  H21A  H  HCH1   0   0.278   1.5113  -1.4925  -7.6666
 BH7  H31   H  HCH1   0   0.281   0.2068  -2.2921  -5.8523
 BH7  HN4   H  HNH1   0   0.400  -1.9900  -1.1383  -5.7514
 BH7  H61   H  HCH2   0   0.289   2.0598   1.1752  -7.4857
 BH7  H62   H  HCH2   0   0.275   2.8953  -0.0303  -6.5032
 BH7  H81   H  HCH1   0   0.275   1.6454  -1.0935  -4.4189
 BH7  H10   H  HCH2   0   0.240  -0.5006  -1.5801  -3.2915
 BH7  H11   H  HCH2   0   0.233  -1.1258  -0.0060  -3.7551
 BH7  H12   H  HCH2   0   0.222   0.6469   1.1130  -2.4159
 BH7  H13   H  HCH2   0   0.221   1.3556  -0.4391  -2.0214
 BH7  H14   H  HCH2   0   0.226  -0.7391  -1.1046  -0.8422
 BH7  H15   H  HCH2   0   0.226  -1.4705   0.4339  -1.2551
 BH7  H16   H  HCH2   0   0.263   0.2811   1.6386   0.0377
 BH7  H17   H  HCH2   0   0.245   1.0763   0.1259   0.4126
 BH7  H18   H  HNH1   0   0.397   0.7887  -0.1483   2.5261
 BH7  H19   H  HCH2   0   0.226  -1.4695  -0.9558   3.8524
 BH7  H20   H  HCH2   0   0.232  -1.5575   0.7941   3.9621
 BH7  H21   H  HCH2   0   0.226   0.7195   0.8641   4.9629
 BH7  H22   H  HCH2   0   0.224   0.8442  -0.8824   4.8330
 BH7  H23   H  HCH2   0   0.210  -1.1314  -1.1396   6.3458
 BH7  H24   H  HCH2   0   0.210  -1.2622   0.6011   6.4739
 BH7  H25   H  HCH2   0   0.202   1.0376   0.6953   7.4672
 BH7  H26   H  HCH2   0   0.203   1.1581  -1.0429   7.3509
 BH7  H27   H  HCH2   0   0.218  -0.8290  -1.2840   8.8637
 BH7  H28   H  HCH2   0   0.213  -0.9618   0.4450   8.9763

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
 BH7  N1   C2    single  1.440  0.020  1.440
 BH7  N1   C5    single  1.358  0.020  1.358
 BH7  N1   HN1   single  0.860  0.020  1.020
 BH7  C2   C3    single  1.558  0.020  1.558
 BH7  C2   C6    single  1.533  0.020  1.533
 BH7  C2   H21A  single  0.970  0.020  1.090
 BH7  C3   N4    single  1.440  0.020  1.440
 BH7  C3   C8    single  1.534  0.020  1.534
 BH7  C3   H31   single  0.970  0.020  1.090
 BH7  N4   C5    single  1.360  0.020  1.360
 BH7  N4   HN4   single  0.890  0.020  1.040
 BH7  C5   O9    double  1.222  0.020  1.222
 BH7  C6   S7    single  1.811  0.020  1.811
 BH7  C6   H61   single  0.970  0.020  1.090
 BH7  C6   H62   single  0.970  0.020  1.090
 BH7  S7   C8    single  1.823  0.020  1.823
 BH7  C8   C10   single  1.518  0.020  1.518
 BH7  C8   H81   single  0.970  0.020  1.090
 BH7  C10  C11   single  1.524  0.020  1.524
 BH7  C10  H10   single  0.970  0.020  1.090
 BH7  C10  H11   single  0.970  0.020  1.090
 BH7  C11  C12   single  1.523  0.020  1.523
 BH7  C11  H12   single  0.970  0.020  1.090
 BH7  C11  H13   single  0.970  0.020  1.090
 BH7  C12  C13   single  1.524  0.020  1.524
 BH7  C12  H14   single  0.970  0.020  1.090
 BH7  C12  H15   single  0.970  0.020  1.090
 BH7  C13  C14   single  1.514  0.020  1.514
 BH7  C13  H16   single  0.970  0.020  1.090
 BH7  C13  H17   single  0.970  0.020  1.090
 BH7  C14  O15   double  1.226  0.020  1.226
 BH7  C14  N16   single  1.341  0.020  1.341
 BH7  N16  C17   single  1.448  0.020  1.448
 BH7  N16  H18   single  0.860  0.020  1.020
 BH7  C17  C18   single  1.520  0.020  1.520
 BH7  C17  H19   single  0.970  0.020  1.090
 BH7  C17  H20   single  0.970  0.020  1.090
 BH7  C18  C19   single  1.523  0.020  1.523
 BH7  C18  H21   single  0.970  0.020  1.090
 BH7  C18  H22   single  0.970  0.020  1.090
 BH7  C19  C20   single  1.524  0.020  1.524
 BH7  C19  H23   single  0.970  0.020  1.090
 BH7  C19  H24   single  0.970  0.020  1.090
 BH7  C20  C21   single  1.520  0.020  1.520
 BH7  C20  H25   single  0.970  0.020  1.090
 BH7  C20  H26   single  0.970  0.020  1.090
 BH7  C21  C22   single  1.540  0.020  1.540
 BH7  C21  H27   single  0.970  0.020  1.090
 BH7  C21  H28   single  0.970  0.020  1.090
 BH7  C22  O23   deloc   1.250  0.020  1.250
 BH7  C22  O24   deloc   1.247  0.020  1.247

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
 BH7  HN1   N1   C5   121.41  3.000
 BH7  HN1   N1   C2   122.51  3.000
 BH7  C5    N1   C2   113.76  3.000
 BH7  H21A  C2   C6   109.22  3.000
 BH7  H21A  C2   C3   111.74  3.000
 BH7  C6    C2   C3   108.83  3.000
 BH7  H21A  C2   N1   110.89  3.000
 BH7  C6    C2   N1   113.66  3.000
 BH7  C3    C2   N1   102.38  3.000
 BH7  H31   C3   C8   109.27  3.000
 BH7  H31   C3   N4   111.28  3.000
 BH7  C8    C3   N4   113.02  3.000
 BH7  H31   C3   C2   111.93  3.000
 BH7  C8    C3   C2   108.65  3.000
 BH7  N4    C3   C2   102.56  3.000
 BH7  HN4   N4   C5   120.64  3.000
 BH7  HN4   N4   C3   122.23  3.000
 BH7  C5    N4   C3   113.59  3.000
 BH7  O9    C5   N4   126.37  3.000
 BH7  O9    C5   N1   126.49  3.000
 BH7  N4    C5   N1   107.14  3.000
 BH7  H62   C6   H61  108.10  3.000
 BH7  H62   C6   S7   109.56  3.000
 BH7  H61   C6   S7   110.35  3.000
 BH7  H62   C6   C2   110.10  3.000
 BH7  H61   C6   C2   112.24  3.000
 BH7  S7    C6   C2   106.48  3.000
 BH7  C8    S7   C6    89.05  3.000
 BH7  H81   C8   C10  109.13  3.000
 BH7  H81   C8   S7   107.70  3.000
 BH7  C10   C8   S7   112.91  3.000
 BH7  H81   C8   C3   107.89  3.000
 BH7  C10   C8   C3   114.47  3.000
 BH7  S7    C8   C3   104.39  3.000
 BH7  H11   C10  H10  106.68  3.000
 BH7  H11   C10  C11  109.78  3.000
 BH7  H10   C10  C11  109.12  3.000
 BH7  H11   C10  C8   109.67  3.000
 BH7  H10   C10  C8   107.82  3.000
 BH7  C11   C10  C8   113.52  3.000
 BH7  H13   C11  H12  106.20  3.000
 BH7  H13   C11  C12  109.52  3.000
 BH7  H12   C11  C12  109.29  3.000
 BH7  H13   C11  C10  109.55  3.000
 BH7  H12   C11  C10  109.74  3.000
 BH7  C12   C11  C10  112.36  3.000
 BH7  H15   C12  H14  106.56  3.000
 BH7  H15   C12  C13  109.72  3.000
 BH7  H14   C12  C13  109.48  3.000
 BH7  H15   C12  C11  109.61  3.000
 BH7  H14   C12  C11  109.33  3.000
 BH7  C13   C12  C11  111.99  3.000
 BH7  H17   C13  H16  106.18  3.000
 BH7  H17   C13  C14  110.77  3.000
 BH7  H16   C13  C14  107.42  3.000
 BH7  H17   C13  C12  110.02  3.000
 BH7  H16   C13  C12  109.48  3.000
 BH7  C14   C13  C12  112.72  3.000
 BH7  N16   C14  O15  122.62  3.000
 BH7  N16   C14  C13  115.38  3.000
 BH7  O15   C14  C13  121.99  3.000
 BH7  H18   N16  C17  117.62  3.000
 BH7  H18   N16  C14  118.53  3.000
 BH7  C17   N16  C14  123.79  3.000
 BH7  H20   C17  H19  106.77  3.000
 BH7  H20   C17  C18  109.80  3.000
 BH7  H19   C17  C18  109.85  3.000
 BH7  H20   C17  N16  109.13  3.000
 BH7  H19   C17  N16  110.45  3.000
 BH7  C18   C17  N16  110.76  3.000
 BH7  H22   C18  H21  106.56  3.000
 BH7  H22   C18  C19  109.38  3.000
 BH7  H21   C18  C19  109.67  3.000
 BH7  H22   C18  C17  109.61  3.000
 BH7  H21   C18  C17  109.25  3.000
 BH7  C19   C18  C17  112.20  3.000
 BH7  H24   C19  H23  106.01  3.000
 BH7  H24   C19  C20  109.52  3.000
 BH7  H23   C19  C20  109.52  3.000
 BH7  H24   C19  C18  109.29  3.000
 BH7  H23   C19  C18  109.46  3.000
 BH7  C20   C19  C18  112.80  3.000
 BH7  H26   C20  H25  105.90  3.000
 BH7  H26   C20  C21  109.80  3.000
 BH7  H25   C20  C21  109.78  3.000
 BH7  H26   C20  C19  109.25  3.000
 BH7  H25   C20  C19  109.11  3.000
 BH7  C21   C20  C19  112.76  3.000
 BH7  H28   C21  H27  104.80  3.000
 BH7  H28   C21  C22  108.41  3.000
 BH7  H27   C21  C22  107.89  3.000
 BH7  H28   C21  C20  109.69  3.000
 BH7  H27   C21  C20  109.49  3.000
 BH7  C22   C21  C20  115.97  3.000
 BH7  O24   C22  O23  126.23  3.000
 BH7  O24   C22  C21  117.86  3.000
 BH7  O23   C22  C21  115.91  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
 BH7  CONST_01  C3   N4   C5   N1      0.00   0.0  0
 BH7  CONST_02  N4   C5   N1   C2      0.00   0.0  0
 BH7  CONST_03  O9   C5   N1   C2    180.00   0.0  0
 BH7  CONST_04  O9   C5   N4   C3    180.00   0.0  0
 BH7  CONST_06  HN1  N1   C5   N4    180.00   0.0  0
 BH7  CONST_07  C17  N16  C14  C13   180.00   0.0  0
 BH7  CONST_08  C17  N16  C14  O15     0.00   0.0  0
 BH7  CONST_09  H18  N16  C14  C13     0.00   0.0  0
 BH7  Var_01    H61  C6   S7   C8    162.36  30.0  1
 BH7  Var_02    C12  C11  C10  C8   -175.20  30.0  3
 BH7  Var_03    C13  C12  C11  C10  -179.20  30.0  3
 BH7  Var_04    C14  C13  C12  C11  -179.47  30.0  3
 BH7  Var_05    O15  C14  C13  C12   -45.08  30.0  3
 BH7  Var_06    C18  C17  N16  C14  -163.10  30.0  3
 BH7  Var_07    C19  C18  C17  N16  -179.47  30.0  3
 BH7  Var_08    C20  C19  C18  C17  -179.57  30.0  3
 BH7  Var_09    C21  C20  C19  C18   179.36  30.0  3
 BH7  Var_10    C22  C21  C20  C19  -179.88  30.0  3
 BH7  Var_11    O23  C22  C21  C20   172.94  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BH7  chir_01  C2  N1  C3  C6   positiv
 BH7  chir_02  C3  N4  C8  C2   positiv
 BH7  chir_03  C8  S7  C3  C10  positiv

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
 BH7  plan-1  C13  0.020
 BH7  plan-1  C14  0.020
 BH7  plan-1  O15  0.020
 BH7  plan-1  N16  0.020
 BH7  plan-1  C17  0.020
 BH7  plan-1  H18  0.020
 BH7  plan-2  N1   0.020
 BH7  plan-2  C2   0.020
 BH7  plan-2  C3   0.020
 BH7  plan-2  N4   0.020
 BH7  plan-2  C5   0.020
 BH7  plan-2  O9   0.020
 BH7  plan-2  HN1  0.020
 BH7  plan-2  HN4  0.020
 BH7  plan-3  C21  0.020
 BH7  plan-3  C22  0.020
 BH7  plan-3  O23  0.020
 BH7  plan-3  O24  0.020

