# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 18:34:10 2022
#   Inital geometry file: a 127 line input string
#   Ligand name: N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(cc1CCNC(=O)CCCC[C@@H]2SC[C@H]3NC(=O)N[C@H]23)[N](=O)=O
#
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
 V8M  V8M  N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aS)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide  ligand  52  28  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_V8M
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
 V8M  C10   C  CH2   0  -0.423  -23.4767  10.1058  -15.4969
 V8M  C13   C  C     0  -0.062  -20.6923  11.5837  -17.8440
 V8M  C15   C  CR5   0   0.640  -18.9845  12.9518  -17.0007
 V8M  C22   C  CR16  0  -0.320  -28.6798   4.6849  -16.9269
 V8M  C28   C  CR16  0  -0.329  -27.8381   2.1426  -16.2318
 V8M  C02   C  CR6   0   0.342  -27.4897   3.2375  -15.4370
 V8M  C03   C  CR6   0   0.015  -27.9164   4.5313  -15.7814
 V8M  C04   C  CH2   0  -0.567  -27.5205   5.7437  -14.9849
 V8M  C05   C  CH2   0  -0.274  -26.1453   6.2676  -15.4192
 V8M  C07   C  C     0   0.534  -26.0903   8.6552  -14.8526
 V8M  C09   C  CH2   0  -0.427  -24.6620  10.7225  -14.7647
 V8M  C11   C  CH2   0  -0.417  -22.6362  11.1527  -16.2181
 V8M  C12   C  CR15  0  -0.361  -21.5143  10.5592  -17.0503
 V8M  C18   C  C     0  -0.046  -19.3085  10.9534  -18.1855
 V8M  C19   C  CH2   0  -0.569  -19.1996   9.5903  -17.4930
 V8M  C23   C  CR6   0   0.244  -29.0173   3.5902  -17.7111
 V8M  C27   C  CR16  0  -0.267  -28.5976   2.3110  -17.3673
 V8M  N06   N  NH1   0  -0.626  -25.6887   7.3899  -14.6366
 V8M  N14   N  NR15  0  -0.658  -20.3288  12.7415  -17.0679
 V8M  N16   N  NR15  0  -0.661  -18.3884  11.9336  -17.6729
 V8M  N24   N  N     0   0.322  -29.8161   3.7834  -18.8983
 V8M  O21   O  O     0  -0.497  -26.8886   8.9529  -15.7315
 V8M  O25   O  O     0  -0.387  -30.1729   4.9071  -19.1746
 V8M  O26   O  O     0  -0.387  -30.0924   2.8111  -19.5653
 V8M  S20   S  S2    0  -0.025  -20.2822   9.6670  -16.0434
 V8M  H102  H  HCH2  0   0.222  -22.8569   9.5574  -14.7802
 V8M  H101  H  HCH2  0   0.225  -23.8292   9.3686  -16.2252
 V8M  H131  H  H     0   0.279  -21.2431  11.8681  -18.7452
 V8M  H221  H  HCR6  0   0.292  -29.0097   5.6782  -17.2003
 V8M  H281  H  HCR6  0   0.282  -27.5035   1.1540  -15.9460
 V8M  H042  H  HCH2  0   0.280  -28.2634   6.5273  -15.1367
 V8M  H041  H  HCH2  0   0.257  -27.5174   5.5471  -13.9083
 V8M  H052  H  HCH2  0   0.260  -25.3947   5.4818  -15.3284
 V8M  H051  H  HCH2  0   0.253  -26.1840   6.5480  -16.4728
 V8M  H091  H  HCH2  0   0.234  -24.3036  11.4970  -14.0818
 V8M  H092  H  HCH2  0   0.226  -25.3204  11.2229  -15.4793
 V8M  H112  H  HCH2  0   0.240  -23.2823  11.7310  -16.8873
 V8M  H111  H  HCH2  0   0.232  -22.2228  11.8585  -15.4932
 V8M  H121  H  HCR5  0   0.274  -21.9383   9.8447  -17.7645
 V8M  H181  H  H     0   0.276  -19.1782  10.8218  -19.2621
 V8M  H191  H  HCH2  0   0.289  -18.1770   9.3630  -17.1932
 V8M  H192  H  HCH2  0   0.274  -19.5410   8.7991  -18.1625
 V8M  H271  H  HCR6  0   0.295  -28.8565   1.4530  -17.9703
 V8M  H061  H  HNH1  0   0.402  -25.0521   7.2058  -13.8792
 V8M  H141  H  HNR5  0   0.397  -20.9714  13.4981  -16.9046
 V8M  H161  H  HNR5  0   0.397  -17.3968  11.7722  -17.6181
 V8M  H011  H  HOH1  0   0.486  -26.5701   3.7566  -13.8300
 V8M  O17   O  O     0  -0.517  -18.4249  13.8846  -16.4482
 V8M  C08   C  CH2   0  -0.563  -25.4649   9.7033  -13.9569
 V8M  O01   O  OH1   0  -0.600  -26.7447   2.9705  -14.3604
 V8M  H081  H  HCH2  0   0.268  -26.2720  10.2133  -13.4252
 V8M  H082  H  HCH2  0   0.245  -24.8234   9.2476  -13.1992

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
 V8M  C10  C09   single    1.524  0.020  1.524
 V8M  C10  C11   single    1.524  0.020  1.524
 V8M  C13  C12   single    1.535  0.020  1.535
 V8M  C13  C18   single    1.558  0.020  1.558
 V8M  C13  N14   single    1.440  0.020  1.440
 V8M  C15  N14   single    1.362  0.020  1.362
 V8M  C15  N16   single    1.358  0.020  1.358
 V8M  C15  O17   double    1.220  0.020  1.220
 V8M  C22  C03   aromatic  1.385  0.020  1.385
 V8M  C22  C23   aromatic  1.388  0.020  1.388
 V8M  C28  C02   aromatic  1.397  0.020  1.397
 V8M  C28  C27   aromatic  1.376  0.020  1.376
 V8M  C02  C03   aromatic  1.405  0.020  1.405
 V8M  C02  O01   single    1.336  0.020  1.336
 V8M  C03  C04   single    1.504  0.020  1.504
 V8M  C04  C05   single    1.534  0.020  1.534
 V8M  C05  N06   single    1.442  0.020  1.442
 V8M  C07  C08   single    1.514  0.020  1.514
 V8M  C07  N06   single    1.345  0.020  1.345
 V8M  C07  O21   double    1.224  0.020  1.224
 V8M  C08  C09   single    1.528  0.020  1.528
 V8M  C11  C12   single    1.518  0.020  1.518
 V8M  C12  S20   single    1.824  0.020  1.824
 V8M  C18  N16   single    1.439  0.020  1.439
 V8M  C19  S20   single    1.811  0.020  1.811
 V8M  C23  C27   aromatic  1.390  0.020  1.390
 V8M  C23  N24   single    1.444  0.020  1.444
 V8M  N24  O25   double    1.211  0.020  1.211
 V8M  N24  O26   double    1.211  0.020  1.211
 V8M  C10  H102  single    0.970  0.020  1.090
 V8M  C10  H101  single    0.970  0.020  1.090
 V8M  C13  H131  single    0.970  0.020  1.090
 V8M  C22  H221  single    0.930  0.020  1.080
 V8M  C28  H281  single    0.930  0.020  1.080
 V8M  C04  H042  single    0.970  0.020  1.090
 V8M  C04  H041  single    0.970  0.020  1.090
 V8M  C05  H052  single    0.970  0.020  1.090
 V8M  C05  H051  single    0.970  0.020  1.090
 V8M  C08  H081  single    0.970  0.020  1.090
 V8M  C08  H082  single    0.970  0.020  1.090
 V8M  C09  H091  single    0.970  0.020  1.090
 V8M  C09  H092  single    0.970  0.020  1.090
 V8M  C11  H112  single    0.970  0.020  1.090
 V8M  C11  H111  single    0.970  0.020  1.090
 V8M  C12  H121  single    0.970  0.020  1.090
 V8M  C18  H181  single    0.970  0.020  1.090
 V8M  C19  H191  single    0.970  0.020  1.090
 V8M  C19  H192  single    0.970  0.020  1.090
 V8M  C27  H271  single    0.930  0.020  1.080
 V8M  N06  H061  single    0.860  0.020  1.020
 V8M  N14  H141  single    0.890  0.020  1.040
 V8M  N16  H161  single    0.860  0.020  1.020
 V8M  O01  H011  single    0.850  0.020  0.980
 V8M  C18  C19   single    1.533  0.020  1.533

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
 V8M  H101  C10  H102  106.29  3.000
 V8M  H101  C10  C11   108.99  3.000
 V8M  H102  C10  C11   109.98  3.000
 V8M  H101  C10  C09   109.99  3.000
 V8M  H102  C10  C09   109.18  3.000
 V8M  C11   C10  C09   112.24  3.000
 V8M  H131  C13  N14   111.23  3.000
 V8M  H131  C13  C18   111.83  3.000
 V8M  N14   C13  C18   102.66  3.000
 V8M  H131  C13  C12   109.26  3.000
 V8M  N14   C13  C12   113.14  3.000
 V8M  C18   C13  C12   108.60  3.000
 V8M  O17   C15  N16   126.59  3.000
 V8M  O17   C15  N14   126.37  3.000
 V8M  N16   C15  N14   107.04  3.000
 V8M  H221  C22  C23   120.47  3.000
 V8M  H221  C22  C03   118.61  3.000
 V8M  C23   C22  C03   120.91  3.000
 V8M  H281  C28  C27   120.02  3.000
 V8M  H281  C28  C02   119.25  3.000
 V8M  C27   C28  C02   120.73  3.000
 V8M  O01   C02  C03   123.42  3.000
 V8M  O01   C02  C28   116.16  3.000
 V8M  C03   C02  C28   120.42  3.000
 V8M  C04   C03  C02   122.18  3.000
 V8M  C04   C03  C22   119.59  3.000
 V8M  C02   C03  C22   118.17  3.000
 V8M  H041  C04  H042  105.55  3.000
 V8M  H041  C04  C05   109.71  3.000
 V8M  H042  C04  C05   109.02  3.000
 V8M  H041  C04  C03   112.15  3.000
 V8M  H042  C04  C03   109.04  3.000
 V8M  C05   C04  C03   111.18  3.000
 V8M  H051  C05  H052  106.86  3.000
 V8M  H051  C05  N06   109.59  3.000
 V8M  H052  C05  N06   107.31  3.000
 V8M  H051  C05  C04   109.23  3.000
 V8M  H052  C05  C04   110.32  3.000
 V8M  N06   C05  C04   113.31  3.000
 V8M  O21   C07  N06   122.60  3.000
 V8M  O21   C07  C08   121.73  3.000
 V8M  N06   C07  C08   115.66  3.000
 V8M  H092  C09  H091  106.36  3.000
 V8M  H092  C09  C08   109.54  3.000
 V8M  H091  C09  C08   108.34  3.000
 V8M  H092  C09  C10   109.86  3.000
 V8M  H091  C09  C10   109.39  3.000
 V8M  C08   C09  C10   113.12  3.000
 V8M  H111  C11  H112  106.70  3.000
 V8M  H111  C11  C12   109.67  3.000
 V8M  H112  C11  C12   107.91  3.000
 V8M  H111  C11  C10   109.78  3.000
 V8M  H112  C11  C10   109.05  3.000
 V8M  C12   C11  C10   113.49  3.000
 V8M  H121  C12  S20   107.59  3.000
 V8M  H121  C12  C11   109.05  3.000
 V8M  S20   C12  C11   112.82  3.000
 V8M  H121  C12  C13   107.78  3.000
 V8M  S20   C12  C13   104.49  3.000
 V8M  C11   C12  C13   114.74  3.000
 V8M  H181  C18  N16   110.91  3.000
 V8M  H181  C18  C19   109.24  3.000
 V8M  N16   C18  C19   113.55  3.000
 V8M  C19   C18  C13   108.89  3.000
 V8M  H181  C18  C13   111.75  3.000
 V8M  N16   C18  C13   102.37  3.000
 V8M  H192  C19  H191  108.13  3.000
 V8M  H192  C19  S20   109.56  3.000
 V8M  H191  C19  S20   110.47  3.000
 V8M  H192  C19  C18   110.20  3.000
 V8M  H191  C19  C18   112.11  3.000
 V8M  S20   C19  C18   106.35  3.000
 V8M  N24   C23  C27   119.58  3.000
 V8M  N24   C23  C22   119.57  3.000
 V8M  C27   C23  C22   120.85  3.000
 V8M  H271  C27  C23   121.39  3.000
 V8M  H271  C27  C28   119.71  3.000
 V8M  C23   C27  C28   118.91  3.000
 V8M  H061  N06  C07   118.80  3.000
 V8M  H061  N06  C05   117.79  3.000
 V8M  C07   N06  C05   123.39  3.000
 V8M  H141  N14  C15   120.41  3.000
 V8M  H141  N14  C13   122.06  3.000
 V8M  C15   N14  C13   113.55  3.000
 V8M  H161  N16  C18   122.71  3.000
 V8M  H161  N16  C15   121.74  3.000
 V8M  C18   N16  C15   113.98  3.000
 V8M  O26   N24  O25   123.52  3.000
 V8M  O26   N24  C23   118.14  3.000
 V8M  O25   N24  C23   118.34  3.000
 V8M  C19   S20  C12    89.00  3.000
 V8M  H082  C08  H081  106.91  3.000
 V8M  H082  C08  C09   109.65  3.000
 V8M  H081  C08  C09   109.51  3.000
 V8M  H082  C08  C07   111.36  3.000
 V8M  H081  C08  C07   107.81  3.000
 V8M  C09   C08  C07   111.47  3.000
 V8M  H011  O01  C02   112.41  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
 V8M  CONST_01  C28   C02  C03  C22     0.00   0.0  0
 V8M  CONST_02  C28   C27  C23  C22     0.00   0.0  0
 V8M  CONST_03  C23   C27  C28  C02     0.00   0.0  0
 V8M  CONST_04  C23   C22  C03  C02     0.00   0.0  0
 V8M  CONST_05  C27   C23  C22  C03     0.00   0.0  0
 V8M  CONST_06  C27   C28  C02  C03     0.00   0.0  0
 V8M  CONST_07  N16   C15  N14  C13     0.00   0.0  0
 V8M  CONST_08  N14   C15  N16  C18     0.00   0.0  0
 V8M  CONST_09  O01   C02  C03  C22   180.00   0.0  0
 V8M  CONST_10  C04   C03  C02  C28   180.00   0.0  0
 V8M  CONST_11  N24   C23  C27  C28   180.00   0.0  0
 V8M  CONST_12  N24   C23  C22  C03   180.00   0.0  0
 V8M  CONST_13  C23   C22  C03  C04   180.00   0.0  0
 V8M  CONST_14  O01   C02  C28  C27   180.00   0.0  0
 V8M  CONST_15  O17   C15  N14  C13   180.00   0.0  0
 V8M  CONST_16  O17   C15  N16  C18   180.00   0.0  0
 V8M  CONST_17  H271  C27  C23  C22   180.00   0.0  0
 V8M  CONST_18  H221  C22  C03  C02   180.00   0.0  0
 V8M  CONST_19  H281  C28  C02  C03   180.00   0.0  0
 V8M  CONST_20  H161  N16  C15  N14   180.00   0.0  0
 V8M  CONST_22  O25   N24  C23  C22     0.00   0.0  0
 V8M  CONST_23  O26   N24  C23  C22   180.00   0.0  0
 V8M  CONST_24  O25   N24  C23  C27   180.00   0.0  0
 V8M  CONST_25  O26   N24  C23  C27     0.00   0.0  0
 V8M  CONST_26  C08   C07  N06  C05   180.00   0.0  0
 V8M  CONST_27  O21   C07  N06  C05     0.00   0.0  0
 V8M  CONST_28  H061  N06  C07  C08     0.00   0.0  0
 V8M  Var_01    C18   C19  S20  C12    40.70  30.0  1
 V8M  Var_02    C05   C04  C03  C22   -93.08  30.0  2
 V8M  Var_03    N06   C05  C04  C03  -176.96  30.0  3
 V8M  Var_04    C12   C11  C10  C09  -175.26  30.0  3
 V8M  Var_05    C07   C08  C09  C10   -63.12  30.0  2
 V8M  Var_06    C07   N06  C05  C04   -81.09  30.0  3
 V8M  Var_07    C11   C10  C09  C08  -176.12  30.0  2
 V8M  Var_08    N06   C07  C08  C09   118.24  30.0  2

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
 V8M  chir_01  C13  C12  C18  N14  positiv
 V8M  chir_02  C12  S20  C13  C11  positiv
 V8M  chir_03  C18  N16  C19  C13  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
 V8M  plan-1  C22   0.020
 V8M  plan-1  C28   0.020
 V8M  plan-1  C02   0.020
 V8M  plan-1  C03   0.020
 V8M  plan-1  C04   0.020
 V8M  plan-1  C23   0.020
 V8M  plan-1  C27   0.020
 V8M  plan-1  N24   0.020
 V8M  plan-1  H221  0.020
 V8M  plan-1  H281  0.020
 V8M  plan-1  H271  0.020
 V8M  plan-1  O01   0.020
 V8M  plan-2  C05   0.020
 V8M  plan-2  C07   0.020
 V8M  plan-2  N06   0.020
 V8M  plan-2  O21   0.020
 V8M  plan-2  H061  0.020
 V8M  plan-2  C08   0.020
 V8M  plan-3  C23   0.020
 V8M  plan-3  N24   0.020
 V8M  plan-3  O25   0.020
 V8M  plan-3  O26   0.020
 V8M  plan-4  C13   0.020
 V8M  plan-4  C15   0.020
 V8M  plan-4  C18   0.020
 V8M  plan-4  N14   0.020
 V8M  plan-4  N16   0.020
 V8M  plan-4  H141  0.020
 V8M  plan-4  H161  0.020
 V8M  plan-4  O17   0.020

