# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 13:31:52 2021
#   Inital geometry file: a 132 line input string
#   Ligand name: 5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NC3CCN(CC3)c4ccncc4
#
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
 HL9  HL9  5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(1-pyridin-4-ylpiperidin-4-yl)pentanamide  ligand  57  28  .  2022-03-18  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HL9
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
 HL9  C01   C  CH1   0  -0.360  18.0540  28.0411  -10.4402
 HL9  C05   C  CR5   0   0.642  16.1684  28.4306   -7.5302
 HL9  C08   C  CR15  0  -0.065  17.2371  28.9768   -9.5418
 HL9  C10   C  CR15  0  -0.044  18.1315  29.4178   -8.3448
 HL9  C12   C  CH2   0  -0.570  19.4440  28.6248   -8.3874
 HL9  C14   C  CH2   0  -0.420  17.2302  27.1584  -11.3594
 HL9  C15   C  CH2   0  -0.427  18.0832  26.2734  -12.2617
 HL9  C16   C  CH2   0  -0.425  17.2504  25.5166  -13.2899
 HL9  C17   C  CH2   0  -0.568  18.0534  24.4728  -14.0668
 HL9  C18   C  CH1   0  -0.063  21.6879  25.2076  -14.8886
 HL9  C19   C  CH2   0  -0.453  22.7510  25.1578  -13.8010
 HL9  C20   C  CH2   0  -0.428  22.1792  24.4445  -16.1138
 HL9  C21   C  CH2   0  -0.312  23.5334  24.9587  -16.5855
 HL9  C22   C  CH2   0  -0.311  24.0853  25.6565  -14.3300
 HL9  C23   C  C     0   0.534  19.2252  25.1000  -14.7897
 HL9  C24   C  CR6   0   0.484  25.8195  24.6237  -15.7401
 HL9  C25   C  CR16  0  -0.430  26.3374  24.4010  -17.0307
 HL9  C26   C  CR16  0  -0.417  26.7575  24.4908  -14.6956
 HL9  C27   C  CR16  0  -0.077  28.0620  24.1463  -14.9807
 HL9  C28   C  CR16  0  -0.076  27.6666  24.0599  -17.1907
 HL9  N02   N  NR15  0  -0.661  17.3034  29.1028   -7.2107
 HL9  N06   N  NR15  0  -0.656  16.1374  28.3162   -8.8865
 HL9  N09   N  NH1   0  -0.634  20.4369  24.6906  -14.3788
 HL9  N11   N  NT    0  -0.515  24.5066  24.9163  -15.5088
 HL9  N13   N  N     0  -0.435  28.5440  23.9244  -16.2016
 HL9  O03   O  O     0  -0.528  15.3258  28.0157   -6.7493
 HL9  O07   O  O     0  -0.508  19.0679  25.9422  -15.6653
 HL9  S04   S  S2    0  -0.023  19.0896  27.0889   -9.2801
 HL9  H011  H  HCH1  0   0.275  18.7223  28.6632  -11.0461
 HL9  H081  H  HCR5  0   0.281  16.8908  29.8330  -10.1285
 HL9  H101  H  HCR5  0   0.278  18.3557  30.4860   -8.3792
 HL9  H122  H  HCH2  0   0.288  19.8249  28.4052   -7.3904
 HL9  H121  H  HCH2  0   0.274  20.2071  29.1907   -8.9244
 HL9  H142  H  HCH2  0   0.240  16.6049  27.8100  -11.9795
 HL9  H141  H  HCH2  0   0.234  16.5517  26.5353  -10.7707
 HL9  H151  H  HCH2  0   0.223  18.6462  25.5604  -11.6509
 HL9  H152  H  HCH2  0   0.226  18.8269  26.8955  -12.7698
 HL9  H162  H  HCH2  0   0.228  16.7945  26.2243  -13.9869
 HL9  H161  H  HCH2  0   0.234  16.4245  25.0046  -12.7888
 HL9  H171  H  HCH2  0   0.269  17.4118  23.9953  -14.8110
 HL9  H172  H  HCH2  0   0.243  18.3849  23.6855  -13.3859
 HL9  H181  H  HCH1  0   0.243  21.5254  26.2527  -15.1683
 HL9  H192  H  HCH2  0   0.254  22.4525  25.7750  -12.9508
 HL9  H191  H  HCH2  0   0.235  22.8668  24.1317  -13.4366
 HL9  H202  H  HCH2  0   0.250  21.4614  24.5367  -16.9312
 HL9  H201  H  HCH2  0   0.229  22.2635  23.3817  -15.8695
 HL9  H212  H  HCH2  0   0.264  23.8620  24.3332  -17.4114
 HL9  H211  H  HCH2  0   0.231  23.4344  25.9817  -16.9738
 HL9  H221  H  HCH2  0   0.269  24.8274  25.5809  -13.5423
 HL9  H222  H  HCH2  0   0.236  24.0031  26.7221  -14.5829
 HL9  H251  H  HCR6  0   0.270  25.7323  24.5053  -17.9188
 HL9  H261  H  HCR6  0   0.271  26.4850  24.6233  -13.6590
 HL9  H271  H  HCR6  0   0.255  28.7614  24.0373  -14.1583
 HL9  H281  H  HCR6  0   0.255  28.0417  23.8947  -18.1956
 HL9  H021  H  HNR5  0   0.399  17.6385  29.1516   -6.2633
 HL9  H061  H  HNR5  0   0.399  15.2675  28.1375   -9.3590
 HL9  H091  H  HNH1  0   0.396  20.4843  23.9763  -13.6699

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
 HL9  C28  C25   aromatic  1.382  0.020  1.382
 HL9  C28  N13   aromatic  1.329  0.020  1.329
 HL9  C25  C24   aromatic  1.408  0.020  1.408
 HL9  N13  C27   aromatic  1.331  0.020  1.331
 HL9  C21  C20   single    1.523  0.020  1.523
 HL9  C21  N11   single    1.452  0.020  1.452
 HL9  C24  N11   single    1.365  0.020  1.365
 HL9  C24  C26   aromatic  1.410  0.020  1.410
 HL9  C27  C26   aromatic  1.379  0.020  1.379
 HL9  C20  C18   single    1.525  0.020  1.525
 HL9  N11  C22   single    1.454  0.020  1.454
 HL9  O07  C23   double    1.225  0.020  1.225
 HL9  C18  N09   single    1.446  0.020  1.446
 HL9  C18  C19   single    1.522  0.020  1.522
 HL9  C22  C19   single    1.520  0.020  1.520
 HL9  C23  N09   single    1.343  0.020  1.343
 HL9  C23  C17   single    1.513  0.020  1.513
 HL9  C17  C16   single    1.529  0.020  1.529
 HL9  C16  C15   single    1.524  0.020  1.524
 HL9  C15  C14   single    1.525  0.020  1.525
 HL9  C14  C01   single    1.517  0.020  1.517
 HL9  C01  C08   single    1.533  0.020  1.533
 HL9  C01  S04   single    1.823  0.020  1.823
 HL9  N06  C08   single    1.441  0.020  1.441
 HL9  N06  C05   single    1.361  0.020  1.361
 HL9  C08  C10   single    1.558  0.020  1.558
 HL9  S04  C12   single    1.811  0.020  1.811
 HL9  C05  O03   double    1.221  0.020  1.221
 HL9  C05  N02   single    1.357  0.020  1.357
 HL9  C10  C12   single    1.534  0.020  1.534
 HL9  C10  N02   single    1.439  0.020  1.439
 HL9  C01  H011  single    0.970  0.020  1.090
 HL9  C08  H081  single    0.970  0.020  1.090
 HL9  C10  H101  single    0.970  0.020  1.090
 HL9  C12  H122  single    0.970  0.020  1.090
 HL9  C12  H121  single    0.970  0.020  1.090
 HL9  C14  H142  single    0.970  0.020  1.090
 HL9  C14  H141  single    0.970  0.020  1.090
 HL9  C15  H151  single    0.970  0.020  1.090
 HL9  C15  H152  single    0.970  0.020  1.090
 HL9  C16  H162  single    0.970  0.020  1.090
 HL9  C16  H161  single    0.970  0.020  1.090
 HL9  C17  H171  single    0.970  0.020  1.090
 HL9  C17  H172  single    0.970  0.020  1.090
 HL9  C18  H181  single    0.970  0.020  1.090
 HL9  C19  H192  single    0.970  0.020  1.090
 HL9  C19  H191  single    0.970  0.020  1.090
 HL9  C20  H202  single    0.970  0.020  1.090
 HL9  C20  H201  single    0.970  0.020  1.090
 HL9  C21  H212  single    0.970  0.020  1.090
 HL9  C21  H211  single    0.970  0.020  1.090
 HL9  C22  H221  single    0.970  0.020  1.090
 HL9  C22  H222  single    0.970  0.020  1.090
 HL9  C25  H251  single    0.930  0.020  1.080
 HL9  C26  H261  single    0.930  0.020  1.080
 HL9  C27  H271  single    0.930  0.020  1.080
 HL9  C28  H281  single    0.930  0.020  1.080
 HL9  N02  H021  single    0.860  0.020  1.020
 HL9  N06  H061  single    0.890  0.020  1.040
 HL9  N09  H091  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
 HL9  H011  C01  S04   107.57  3.000
 HL9  H011  C01  C14   109.05  3.000
 HL9  S04   C01  C14   112.95  3.000
 HL9  H011  C01  C08   107.61  3.000
 HL9  S04   C01  C08   104.39  3.000
 HL9  C14   C01  C08   114.88  3.000
 HL9  O03   C05  N06   126.34  3.000
 HL9  O03   C05  N02   126.49  3.000
 HL9  N06   C05  N02   107.17  3.000
 HL9  H081  C08  N06   111.17  3.000
 HL9  H081  C08  C10   111.85  3.000
 HL9  N06   C08  C10   102.62  3.000
 HL9  H081  C08  C01   109.39  3.000
 HL9  C10   C08  C01   108.49  3.000
 HL9  N06   C08  C01   113.17  3.000
 HL9  H101  C10  N02   110.92  3.000
 HL9  H101  C10  C12   109.21  3.000
 HL9  N02   C10  C12   113.64  3.000
 HL9  H101  C10  C08   111.75  3.000
 HL9  N02   C10  C08   102.31  3.000
 HL9  C12   C10  C08   108.88  3.000
 HL9  H121  C12  H122  108.08  3.000
 HL9  H121  C12  S04   109.51  3.000
 HL9  H122  C12  S04   110.39  3.000
 HL9  H121  C12  C10   110.11  3.000
 HL9  H122  C12  C10   112.20  3.000
 HL9  S04   C12  C10   106.53  3.000
 HL9  H141  C14  H142  106.83  3.000
 HL9  H141  C14  C15   109.57  3.000
 HL9  H142  C14  C15   109.24  3.000
 HL9  H141  C14  C01   110.02  3.000
 HL9  H142  C14  C01   107.87  3.000
 HL9  C15   C14  C01   113.10  3.000
 HL9  H152  C15  H151  106.24  3.000
 HL9  H152  C15  C16   109.89  3.000
 HL9  H151  C15  C16   109.51  3.000
 HL9  H152  C15  C14   108.96  3.000
 HL9  H151  C15  C14   109.60  3.000
 HL9  C16   C15  C14   112.44  3.000
 HL9  H161  C16  H162  106.28  3.000
 HL9  H161  C16  C17   108.05  3.000
 HL9  H162  C16  C17   109.70  3.000
 HL9  H161  C16  C15   109.64  3.000
 HL9  H162  C16  C15   109.67  3.000
 HL9  C17   C16  C15   113.25  3.000
 HL9  H172  C17  H171  106.73  3.000
 HL9  H172  C17  C23   111.19  3.000
 HL9  H171  C17  C23   108.09  3.000
 HL9  H172  C17  C16   109.56  3.000
 HL9  H171  C17  C16   109.64  3.000
 HL9  C23   C17  C16   111.50  3.000
 HL9  H181  C18  N09   107.64  3.000
 HL9  H181  C18  C20   108.70  3.000
 HL9  N09   C18  C20   112.52  3.000
 HL9  H181  C18  C19   108.52  3.000
 HL9  N09   C18  C19   109.91  3.000
 HL9  C20   C18  C19   109.44  3.000
 HL9  H191  C19  H192  107.42  3.000
 HL9  H191  C19  C22   109.30  3.000
 HL9  H192  C19  C22   109.00  3.000
 HL9  H191  C19  C18   110.02  3.000
 HL9  H192  C19  C18   110.30  3.000
 HL9  C22   C19  C18   110.73  3.000
 HL9  H201  C20  H202  107.46  3.000
 HL9  H201  C20  C21   109.18  3.000
 HL9  H202  C20  C21   108.91  3.000
 HL9  H201  C20  C18   109.37  3.000
 HL9  H202  C20  C18   110.34  3.000
 HL9  C21   C20  C18   111.49  3.000
 HL9  H211  C21  H212  107.13  3.000
 HL9  H211  C21  N11   110.47  3.000
 HL9  H212  C21  N11   110.12  3.000
 HL9  H211  C21  C20   110.10  3.000
 HL9  H212  C21  C20   108.05  3.000
 HL9  N11   C21  C20   110.87  3.000
 HL9  H222  C22  H221  106.62  3.000
 HL9  H222  C22  N11   109.20  3.000
 HL9  H221  C22  N11   110.78  3.000
 HL9  H222  C22  C19   109.45  3.000
 HL9  H221  C22  C19   108.97  3.000
 HL9  N11   C22  C19   111.68  3.000
 HL9  O07   C23  N09   122.96  3.000
 HL9  N09   C23  C17   115.22  3.000
 HL9  O07   C23  C17   121.80  3.000
 HL9  N11   C24  C26   122.32  3.000
 HL9  C26   C24  C25   114.79  3.000
 HL9  N11   C24  C25   122.88  3.000
 HL9  H251  C25  C28   117.89  3.000
 HL9  H251  C25  C24   122.17  3.000
 HL9  C28   C25  C24   119.93  3.000
 HL9  H261  C26  C27   117.89  3.000
 HL9  H261  C26  C24   122.11  3.000
 HL9  C27   C26  C24   119.98  3.000
 HL9  H271  C27  N13   116.43  3.000
 HL9  H271  C27  C26   118.56  3.000
 HL9  N13   C27  C26   125.01  3.000
 HL9  H281  C28  N13   116.45  3.000
 HL9  H281  C28  C25   118.51  3.000
 HL9  N13   C28  C25   125.03  3.000
 HL9  H021  N02  C10   122.67  3.000
 HL9  H021  N02  C05   121.61  3.000
 HL9  C10   N02  C05   113.83  3.000
 HL9  H061  N06  C08   121.86  3.000
 HL9  H061  N06  C05   120.18  3.000
 HL9  C08   N06  C05   113.41  3.000
 HL9  H091  N09  C23   118.28  3.000
 HL9  H091  N09  C18   117.43  3.000
 HL9  C23   N09  C18   124.29  3.000
 HL9  C24   N11  C22   121.67  3.000
 HL9  C22   N11  C21   113.08  3.000
 HL9  C24   N11  C21   121.69  3.000
 HL9  C28   N13  C27   115.25  3.000
 HL9  C12   S04  C01    88.96  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
 HL9  CONST_01  N13   C28  C25  C24     0.00   0.0  0
 HL9  CONST_02  N13   C27  C26  C24     0.00   0.0  0
 HL9  CONST_03  C27   N13  C28  C25     0.00   0.0  0
 HL9  CONST_04  C27   C26  C24  C25     0.00   0.0  0
 HL9  CONST_05  C28   C25  C24  C26     0.00   0.0  0
 HL9  CONST_06  C28   N13  C27  C26     0.00   0.0  0
 HL9  CONST_07  N11   C24  C26  C27   180.00   0.0  0
 HL9  CONST_08  N11   C24  C25  C28   180.00   0.0  0
 HL9  CONST_09  N02   C05  N06  C08     0.00   0.0  0
 HL9  CONST_10  N06   C05  N02  C10     0.00   0.0  0
 HL9  CONST_11  O03   C05  N06  C08   180.00   0.0  0
 HL9  CONST_12  O03   C05  N02  C10   180.00   0.0  0
 HL9  CONST_13  H281  C28  C25  C24   180.00   0.0  0
 HL9  CONST_14  H271  C27  C26  C24   180.00   0.0  0
 HL9  CONST_15  H261  C26  C24  C25   180.00   0.0  0
 HL9  CONST_16  H251  C25  C24  C26   180.00   0.0  0
 HL9  CONST_18  H021  N02  C05  N06   180.00   0.0  0
 HL9  CONST_19  C18   N09  C23  C17   180.00   0.0  0
 HL9  CONST_20  O07   C23  N09  C18     0.00   0.0  0
 HL9  CONST_21  H091  N09  C23  C17     0.00   0.0  0
 HL9  Var_01    C10   C12  S04  C01    40.11  30.0  1
 HL9  Var_02    N11   C21  C20  C18    55.23  30.0  1
 HL9  Var_03    N11   C22  C19  C18   -55.59  30.0  1
 HL9  Var_04    C21   N11  C22  C19    56.99  30.0  1
 HL9  Var_05    C25   C24  N11  C21     2.84  30.0  2
 HL9  Var_06    C16   C15  C14  C01  -173.23  30.0  2
 HL9  Var_07    C17   C16  C15  C14  -171.55  30.0  1
 HL9  Var_08    C23   C17  C16  C15   -58.13  30.0  2
 HL9  Var_09    O07   C23  C17  C16   -62.36  30.0  1

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
 HL9  chir_01  C01  C14  C08  S04  negativ
 HL9  chir_02  C08  N06  C10  C01  negativ
 HL9  chir_03  C10  N02  C08  C12  positiv
 HL9  chir_04  C18  C20  N09  C19  negativ

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
 HL9  plan-1  C24   0.020
 HL9  plan-1  C25   0.020
 HL9  plan-1  C26   0.020
 HL9  plan-1  C27   0.020
 HL9  plan-1  C28   0.020
 HL9  plan-1  N11   0.020
 HL9  plan-1  N13   0.020
 HL9  plan-1  H251  0.020
 HL9  plan-1  H261  0.020
 HL9  plan-1  H271  0.020
 HL9  plan-1  H281  0.020
 HL9  plan-2  C17   0.020
 HL9  plan-2  C18   0.020
 HL9  plan-2  C23   0.020
 HL9  plan-2  N09   0.020
 HL9  plan-2  O07   0.020
 HL9  plan-2  H091  0.020
 HL9  plan-3  C05   0.020
 HL9  plan-3  C08   0.020
 HL9  plan-3  C10   0.020
 HL9  plan-3  N02   0.020
 HL9  plan-3  N06   0.020
 HL9  plan-3  O03   0.020
 HL9  plan-3  H021  0.020
 HL9  plan-3  H061  0.020

