# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 19:42:32 2020
#   Inital geometry file: a 135 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}-[4-(2-azanylethylsulfamoyl)phenyl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCN[S](=O)(=O)c1ccc(NC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)cc1
#
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
 6IR  6IR  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}-[4-(2-azanylethylsulfamoyl)phenyl]pentanamide  ligand  56  29  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6IR
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
 6IR  C1   C  CR5   0   0.642   8.3764  -1.8577   0.4184
 6IR  N1   N  NR15  0  -0.661   9.1782  -0.8759  -0.0635
 6IR  O1   O  O     0  -0.529   8.5744  -3.0609   0.3441
 6IR  S1   S  S2    0  -0.024   6.5081   0.6702  -1.4495
 6IR  C2   C  CR15  0  -0.045   8.6605   0.4517   0.1372
 6IR  N2   N  NR15  0  -0.656   7.3108  -1.2515   1.0117
 6IR  O2   O  O     0  -0.456  -0.3421   0.1757   1.5393
 6IR  S2   S  S     0   1.373  -7.1171   0.5910   0.1340
 6IR  C3   C  CH2   0  -0.569   8.2315   1.1444  -1.1619
 6IR  N3   N  NH1   0  -0.751  -1.2297   1.2299  -0.2707
 6IR  O3   O  OS    0  -0.659  -7.4791   0.3223   1.5163
 6IR  C4   C  CR15  0  -0.065   7.3966   0.1872   1.0082
 6IR  N4   N  NC1   0  -0.727  -7.4734  -0.7670  -0.7254
 6IR  O4   O  OS    0  -0.659  -7.7409   1.6948  -0.5778
 6IR  C5   C  CH1   0  -0.360   6.1926   0.8592   0.3372
 6IR  N5   N  NH2   0  -0.800  -7.1249  -4.4541  -0.5640
 6IR  C6   C  CH2   0  -0.422   4.8435   0.3146   0.7658
 6IR  C7   C  CH2   0  -0.420   3.6634   1.0388   0.1302
 6IR  C8   C  CH2   0  -0.415   2.3269   0.5428   0.6668
 6IR  C9   C  CH2   0  -0.600   1.1593   1.2539   0.0030
 6IR  C10  C  C     0   0.567  -0.1933   0.8169   0.5180
 6IR  C11  C  CR6   0   0.397  -2.5957   1.0547  -0.0997
 6IR  C12  C  CR16  0  -0.342  -3.4253   1.5815  -1.0987
 6IR  C13  C  CR16  0  -0.222  -4.7959   1.4598  -1.0230
 6IR  C14  C  CR16  0  -0.307  -3.1804   0.4004   0.9882
 6IR  C15  C  CR16  0  -0.219  -4.5587   0.2805   1.0617
 6IR  C16  C  CR6   0  -0.224  -5.3661   0.8048   0.0636
 6IR  C27  C  CH2   0  -0.287  -6.9479  -2.0505  -0.2685
 6IR  C28  C  CH2   0  -0.294  -7.6405  -3.1759  -1.0216
 6IR  H1   H  HNR5  0   0.399   9.9480  -1.0724  -0.6807
 6IR  H2   H  HCR5  0   0.278   9.3868   1.0798   0.6574
 6IR  H3   H  HNR5  0   0.399   6.7635  -1.7476   1.6949
 6IR  H4   H  HCH2  0   0.289   8.8520   0.8508  -2.0080
 6IR  H5   H  HCH2  0   0.274   8.3010   2.2278  -1.0510
 6IR  H6   H  HNH1  0   0.422  -0.9701   1.7432  -1.1002
 6IR  H7   H  HCR5  0   0.281   7.5130   0.5782   2.0232
 6IR  H8   H  HNC1  0   0.409  -7.3602  -0.6146  -1.7232
 6IR  H9   H  HCH1  0   0.275   6.2366   1.9294   0.5674
 6IR  H10  H  HNH2  0   0.355  -7.6888  -5.1995  -0.9498
 6IR  H11  H  HNH2  0   0.345  -6.1923  -4.5975  -0.9308
 6IR  H13  H  HCH2  0   0.233   4.7846  -0.7537   0.5409
 6IR  H14  H  HCH2  0   0.240   4.7759   0.4074   1.8554
 6IR  H15  H  HCH2  0   0.222   3.7548   2.1150   0.3098
 6IR  H16  H  HCH2  0   0.223   3.6893   0.9084  -0.9565
 6IR  H17  H  HCH2  0   0.229   2.2457  -0.5350   0.5016
 6IR  H18  H  HCH2  0   0.230   2.2905   0.6945   1.7480
 6IR  H19  H  HCH2  0   0.282   1.2395   2.3354   0.1618
 6IR  H20  H  HCH2  0   0.268   1.1987   1.1127  -1.0814
 6IR  H21  H  HCR6  0   0.285  -2.9868   2.0936  -1.9464
 6IR  H22  H  HCR6  0   0.286  -5.4071   1.8805  -1.8102
 6IR  H23  H  HCR6  0   0.293  -2.5806  -0.0139   1.7802
 6IR  H24  H  HCR6  0   0.286  -4.9899  -0.2215   1.9170
 6IR  H25  H  HCH2  0   0.235  -5.8621  -2.1164  -0.4100
 6IR  H26  H  HCH2  0   0.258  -7.1521  -2.1562   0.7958
 6IR  H27  H  HCH2  0   0.206  -7.5274  -3.0124  -2.1027
 6IR  H28  H  HCH2  0   0.235  -8.7101  -3.1315  -0.8087

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
 6IR  C28  N5   single    1.452  0.020  1.452
 6IR  C28  C27  single    1.521  0.020  1.521
 6IR  C27  N4   single    1.460  0.020  1.460
 6IR  N4   S2   single    1.646  0.020  1.646
 6IR  O4   S2   double    1.454  0.020  1.454
 6IR  S2   O3   double    1.454  0.020  1.454
 6IR  S2   C16  single    1.765  0.020  1.765
 6IR  C13  C16  aromatic  1.391  0.020  1.391
 6IR  C13  C12  aromatic  1.378  0.020  1.378
 6IR  C16  C15  aromatic  1.387  0.020  1.387
 6IR  C12  C11  aromatic  1.401  0.020  1.401
 6IR  C15  C14  aromatic  1.385  0.020  1.385
 6IR  O2   C10  double    1.215  0.020  1.215
 6IR  C11  C14  aromatic  1.398  0.020  1.398
 6IR  C11  N3   single    1.388  0.020  1.388
 6IR  C10  N3   single    1.366  0.020  1.366
 6IR  C10  C9   single    1.512  0.020  1.512
 6IR  C9   C8   single    1.520  0.020  1.520
 6IR  C8   C7   single    1.523  0.020  1.523
 6IR  C7   C6   single    1.524  0.020  1.524
 6IR  C6   C5   single    1.517  0.020  1.517
 6IR  C5   C4   single    1.533  0.020  1.533
 6IR  C5   S1   single    1.824  0.020  1.824
 6IR  N2   C4   single    1.441  0.020  1.441
 6IR  N2   C1   single    1.362  0.020  1.362
 6IR  C4   C2   single    1.558  0.020  1.558
 6IR  S1   C3   single    1.810  0.020  1.810
 6IR  C1   O1   double    1.222  0.020  1.222
 6IR  C1   N1   single    1.356  0.020  1.356
 6IR  C2   C3   single    1.533  0.020  1.533
 6IR  C2   N1   single    1.439  0.020  1.439
 6IR  N1   H1   single    0.860  0.020  1.020
 6IR  C2   H2   single    0.970  0.020  1.090
 6IR  N2   H3   single    0.890  0.020  1.040
 6IR  C3   H4   single    0.970  0.020  1.090
 6IR  C3   H5   single    0.970  0.020  1.090
 6IR  N3   H6   single    0.860  0.020  1.020
 6IR  C4   H7   single    0.970  0.020  1.090
 6IR  N4   H8   single    0.890  0.020  1.040
 6IR  C5   H9   single    0.970  0.020  1.090
 6IR  N5   H10  single    0.890  0.020  1.040
 6IR  N5   H11  single    0.890  0.020  1.040
 6IR  C6   H13  single    0.970  0.020  1.090
 6IR  C6   H14  single    0.970  0.020  1.090
 6IR  C7   H15  single    0.970  0.020  1.090
 6IR  C7   H16  single    0.970  0.020  1.090
 6IR  C8   H17  single    0.970  0.020  1.090
 6IR  C8   H18  single    0.970  0.020  1.090
 6IR  C9   H19  single    0.970  0.020  1.090
 6IR  C9   H20  single    0.970  0.020  1.090
 6IR  C12  H21  single    0.930  0.020  1.080
 6IR  C13  H22  single    0.930  0.020  1.080
 6IR  C14  H23  single    0.930  0.020  1.080
 6IR  C15  H24  single    0.930  0.020  1.080
 6IR  C27  H25  single    0.970  0.020  1.090
 6IR  C27  H26  single    0.970  0.020  1.090
 6IR  C28  H27  single    0.970  0.020  1.090
 6IR  C28  H28  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
 6IR  N2   C1   O1   126.27  3.000
 6IR  O1   C1   N1   126.56  3.000
 6IR  N2   C1   N1   107.17  3.000
 6IR  H1   N1   C2   122.76  3.000
 6IR  H1   N1   C1   121.94  3.000
 6IR  C2   N1   C1   113.93  3.000
 6IR  C5   S1   C3    88.96  3.000
 6IR  H2   C2   C4   111.77  3.000
 6IR  H2   C2   C3   109.25  3.000
 6IR  C4   C2   C3   108.87  3.000
 6IR  H2   C2   N1   110.97  3.000
 6IR  C3   C2   N1   113.53  3.000
 6IR  C4   C2   N1   102.32  3.000
 6IR  H3   N2   C4   121.75  3.000
 6IR  H3   N2   C1   120.12  3.000
 6IR  C4   N2   C1   113.37  3.000
 6IR  C16  S2   O4   108.30  3.000
 6IR  C16  S2   N4   107.09  3.000
 6IR  O4   S2   N4   106.13  3.000
 6IR  C16  S2   O3   107.89  3.000
 6IR  O4   S2   O3   119.93  3.000
 6IR  N4   S2   O3   106.86  3.000
 6IR  H5   C3   H4   108.07  3.000
 6IR  H5   C3   C2   110.16  3.000
 6IR  H4   C3   C2   112.13  3.000
 6IR  H5   C3   S1   109.69  3.000
 6IR  H4   C3   S1   110.38  3.000
 6IR  C2   C3   S1   106.41  3.000
 6IR  H6   N3   C11  114.75  3.000
 6IR  H6   N3   C10  115.66  3.000
 6IR  C11  N3   C10  129.59  3.000
 6IR  H7   C4   C5   109.44  3.000
 6IR  H7   C4   N2   111.16  3.000
 6IR  C5   C4   N2   113.06  3.000
 6IR  H7   C4   C2   111.83  3.000
 6IR  N2   C4   C2   102.66  3.000
 6IR  C5   C4   C2   108.54  3.000
 6IR  H8   N4   C27  113.52  3.000
 6IR  H8   N4   S2   111.41  3.000
 6IR  C27  N4   S2   118.94  3.000
 6IR  H9   C5   C6   109.10  3.000
 6IR  H9   C5   C4   107.73  3.000
 6IR  C6   C5   C4   114.67  3.000
 6IR  H9   C5   S1   107.46  3.000
 6IR  C4   C5   S1   104.32  3.000
 6IR  C6   C5   S1   113.17  3.000
 6IR  H11  N5   H10  105.73  3.000
 6IR  H11  N5   C28  109.74  3.000
 6IR  H10  N5   C28  109.30  3.000
 6IR  H14  C6   H13  106.50  3.000
 6IR  H14  C6   C7   109.07  3.000
 6IR  H13  C6   C7   109.69  3.000
 6IR  H14  C6   C5   107.79  3.000
 6IR  H13  C6   C5   109.92  3.000
 6IR  C7   C6   C5   113.60  3.000
 6IR  H16  C7   H15  106.14  3.000
 6IR  H16  C7   C8   109.37  3.000
 6IR  H15  C7   C8   109.60  3.000
 6IR  H16  C7   C6   109.82  3.000
 6IR  H15  C7   C6   109.52  3.000
 6IR  C8   C7   C6   112.20  3.000
 6IR  H18  C8   H17  106.49  3.000
 6IR  H18  C8   C9   109.99  3.000
 6IR  H17  C8   C9   109.77  3.000
 6IR  H18  C8   C7   109.43  3.000
 6IR  H17  C8   C7   109.44  3.000
 6IR  C9   C8   C7   111.59  3.000
 6IR  H20  C9   H19  105.56  3.000
 6IR  H20  C9   C10  109.42  3.000
 6IR  H19  C9   C10  107.54  3.000
 6IR  H20  C9   C8   110.17  3.000
 6IR  H19  C9   C8   110.01  3.000
 6IR  C10  C9   C8   113.78  3.000
 6IR  C9   C10  N3   113.24  3.000
 6IR  C9   C10  O2   123.26  3.000
 6IR  N3   C10  O2   123.49  3.000
 6IR  C14  C11  C12  118.90  3.000
 6IR  C14  C11  N3   124.53  3.000
 6IR  C12  C11  N3   116.58  3.000
 6IR  H21  C12  C13  119.16  3.000
 6IR  H21  C12  C11  119.74  3.000
 6IR  C13  C12  C11  121.09  3.000
 6IR  H22  C13  C16  121.33  3.000
 6IR  H22  C13  C12  119.18  3.000
 6IR  C16  C13  C12  119.48  3.000
 6IR  H23  C14  C15  118.82  3.000
 6IR  H23  C14  C11  121.32  3.000
 6IR  C15  C14  C11  119.87  3.000
 6IR  H24  C15  C16  120.84  3.000
 6IR  H24  C15  C14  118.61  3.000
 6IR  C16  C15  C14  120.55  3.000
 6IR  C15  C16  C13  120.11  3.000
 6IR  C15  C16  S2   120.20  3.000
 6IR  C13  C16  S2   119.65  3.000
 6IR  H26  C27  H25  107.81  3.000
 6IR  H26  C27  C28  109.07  3.000
 6IR  H25  C27  C28  110.03  3.000
 6IR  H26  C27  N4   108.88  3.000
 6IR  H25  C27  N4   111.63  3.000
 6IR  C28  C27  N4   109.36  3.000
 6IR  H28  C28  H27  106.66  3.000
 6IR  H28  C28  C27  108.64  3.000
 6IR  H27  C28  C27  109.27  3.000
 6IR  H28  C28  N5   108.81  3.000
 6IR  H27  C28  N5   113.85  3.000
 6IR  C27  C28  N5   109.48  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
 6IR  CONST_01  C16  C13  C12  C11     0.00   0.0  0
 6IR  CONST_02  C16  C15  C14  C11     0.00   0.0  0
 6IR  CONST_03  C15  C16  C13  C12     0.00   0.0  0
 6IR  CONST_04  C15  C14  C11  C12     0.00   0.0  0
 6IR  CONST_05  C14  C15  C16  C13     0.00   0.0  0
 6IR  CONST_06  C14  C11  C12  C13     0.00   0.0  0
 6IR  CONST_07  C4   N2   C1   N1      0.00   0.0  0
 6IR  CONST_08  N2   C1   N1   C2      0.00   0.0  0
 6IR  CONST_09  C12  C13  C16  S2    180.00   0.0  0
 6IR  CONST_10  C14  C15  C16  S2    180.00   0.0  0
 6IR  CONST_11  C13  C12  C11  N3    180.00   0.0  0
 6IR  CONST_12  C15  C14  C11  N3    180.00   0.0  0
 6IR  CONST_13  C4   N2   C1   O1    180.00   0.0  0
 6IR  CONST_14  C2   N1   C1   O1    180.00   0.0  0
 6IR  CONST_15  H22  C13  C12  C11   180.00   0.0  0
 6IR  CONST_16  H24  C15  C14  C11   180.00   0.0  0
 6IR  CONST_17  H23  C14  C11  C12   180.00   0.0  0
 6IR  CONST_18  H21  C12  C11  C14   180.00   0.0  0
 6IR  CONST_20  H1   N1   C1   N2    180.00   0.0  0
 6IR  CONST_21  C12  C11  N3   C10   180.00   0.0  0
 6IR  CONST_22  C14  C11  N3   C10     0.00   0.0  0
 6IR  CONST_23  H6   N3   C11  C12     0.00   0.0  0
 6IR  CONST_24  C11  N3   C10  O2      0.00   0.0  0
 6IR  CONST_25  C11  N3   C10  C9    180.00   0.0  0
 6IR  Var_01    H4   C3   S1   C5    162.39  30.0  1
 6IR  Var_02    C13  C16  S2   O3   -160.54  30.0  2
 6IR  Var_03    C8   C7   C6   C5   -175.37  30.0  1
 6IR  Var_04    C27  N4   S2   C16    62.97  30.0  2
 6IR  Var_05    C8   C9   C10  O2     14.39  30.0  3
 6IR  Var_06    C28  C27  N4   S2    167.82  30.0  1
 6IR  Var_07    N5   C28  C27  N4   -179.70  30.0  2
 6IR  Var_08    C9   C8   C7   C6   -178.82  30.0  2
 6IR  Var_09    C10  C9   C8   C7   -178.93  30.0  1
 6IR  Var_10    H10  N5   C28  C27   170.70  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
 6IR  chir_01  C2  C4  C3  N1  positiv
 6IR  chir_02  C4  N2  C5  C2  positiv
 6IR  chir_03  C5  S1  C4  C6  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
 6IR  plan-1  S2   0.020
 6IR  plan-1  N3   0.020
 6IR  plan-1  C11  0.020
 6IR  plan-1  C12  0.020
 6IR  plan-1  C13  0.020
 6IR  plan-1  C14  0.020
 6IR  plan-1  C15  0.020
 6IR  plan-1  C16  0.020
 6IR  plan-1  H21  0.020
 6IR  plan-1  H22  0.020
 6IR  plan-1  H23  0.020
 6IR  plan-1  H24  0.020
 6IR  plan-2  O2   0.020
 6IR  plan-2  N3   0.020
 6IR  plan-2  C9   0.020
 6IR  plan-2  C10  0.020
 6IR  plan-2  C11  0.020
 6IR  plan-2  H6   0.020
 6IR  plan-3  C1   0.020
 6IR  plan-3  N1   0.020
 6IR  plan-3  O1   0.020
 6IR  plan-3  C2   0.020
 6IR  plan-3  N2   0.020
 6IR  plan-3  C4   0.020
 6IR  plan-3  H1   0.020
 6IR  plan-3  H3   0.020

