# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 16:05:14 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCC[C@@H]1SC[C@H]2[C@@H]1NC(=O)N2C(=O)OCc3ccccc3
#
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
 VHI  VHI  '5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid'  ligand  47  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_VHI
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
 VHI  N1    N  NR5    0  -0.600  -1.3227   1.1730  -0.3412
 VHI  S1    S  S2     0  -0.014   1.4840   1.0982   1.4356
 VHI  C2    C  CH1    0  -0.367   2.1291   1.4243  -0.2362
 VHI  N2    N  NR15   0  -0.659   0.3178   0.2832  -1.4974
 VHI  C3    C  CR5    0   0.695  -0.9285   0.0335  -1.0604
 VHI  O3    O  O      0  -0.472  -1.5844  -0.9627  -1.2611
 VHI  C4    C  CR15   0  -0.043   0.8752   1.5499  -1.1139
 VHI  C5    C  CR15   0  -0.091  -0.2675   2.1751  -0.2706
 VHI  C6    C  CH2    0  -0.565   0.2421   2.3841   1.1574
 VHI  C7    C  CH2    0  -0.426   3.1384   0.3933  -0.7049
 VHI  C8    C  CH2    0  -0.413   4.3848   0.3184   0.1698
 VHI  C9    C  CH2    0  -0.404   5.4682  -0.5672  -0.4351
 VHI  C10   C  CH2    0  -0.583   6.6876  -0.6924   0.4628
 VHI  C11   C  C      0   0.411   7.8496  -1.5393  -0.0853
 VHI  O11   O  O      0  -0.609   7.7406  -2.0065  -1.2360
 VHI  O12   O  OC    -1  -0.635   8.8258  -1.6872   0.6811
 VHI  C17   C  C      0   0.795  -2.5723   1.4799   0.1350
 VHI  O18   O  O2     0  -0.443  -3.4240   0.4770   0.0590
 VHI  O19   O  O      0  -0.495  -2.8323   2.5734   0.5835
 VHI  C20   C  CH2    0  -0.248  -4.7641   0.7369   0.5126
 VHI  C21   C  CR6    0   0.080  -5.5301  -0.5413   0.3676
 VHI  C22   C  CR16   0  -0.297  -5.7486  -1.3603   1.4701
 VHI  C23   C  CR16   0  -0.242  -6.4497  -2.5519   1.3363
 VHI  C24   C  CR16   0  -0.261  -6.9342  -2.9354   0.0934
 VHI  C25   C  CR16   0  -0.243  -6.7182  -2.1230  -1.0136
 VHI  C26   C  CR16   0  -0.281  -6.0202  -0.9323  -0.8759
 VHI  H2    H  HCH1   0   0.282   2.6129   2.4069  -0.2148
 VHI  HN2   H  HNR5   0   0.414   0.7942  -0.3728  -2.0940
 VHI  H4    H  HCR5   0   0.291   1.1111   2.1526  -1.9944
 VHI  H5    H  HCR5   0   0.303  -0.6111   3.1179  -0.6954
 VHI  H6    H  HCH2   0   0.297  -0.5464   2.3209   1.9034
 VHI  H6A   H  HCH2   0   0.283   0.7065   3.3680   1.2404
 VHI  H7    H  HCH2   0   0.231   2.6737  -0.5953  -0.7577
 VHI  H7A   H  HCH2   0   0.240   3.4332   0.6563  -1.7270
 VHI  H8    H  HCH2   0   0.213   4.7832   1.3268   0.3276
 VHI  H8A   H  HCH2   0   0.214   4.1170  -0.0601   1.1619
 VHI  H9    H  HCH2   0   0.204   5.0524  -1.5591  -0.6380
 VHI  H9A   H  HCH2   0   0.205   5.7598  -0.1589  -1.4068
 VHI  H10   H  HCH2   0   0.218   7.0764   0.3066   0.6950
 VHI  H10A  H  HCH2   0   0.216   6.3892  -1.1088   1.4319
 VHI  H20   H  HCH2   0   0.256  -4.7493   1.0642   1.5533
 VHI  H20A  H  HCH2   0   0.255  -5.2071   1.5318  -0.0904
 VHI  H22   H  HCR6   0   0.256  -5.3742  -1.0625   2.4425
 VHI  H23   H  HCR6   0   0.259  -6.6181  -3.1778   2.2031
 VHI  H24   H  HCR6   0   0.259  -7.4835  -3.8620  -0.0130
 VHI  H25   H  HCR6   0   0.259  -7.0975  -2.4166  -1.9838
 VHI  H26   H  HCR6   0   0.255  -5.8610  -0.2990  -1.7407

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
 VHI  N1   C3    single    1.404  0.020  1.404
 VHI  N1   C5    single    1.457  0.020  1.457
 VHI  N1   C17   single    1.372  0.020  1.372
 VHI  S1   C2    single    1.821  0.020  1.821
 VHI  S1   C6    single    1.809  0.020  1.809
 VHI  C2   C4    single    1.536  0.020  1.536
 VHI  C2   C7    single    1.517  0.020  1.517
 VHI  N2   C3    single    1.344  0.020  1.344
 VHI  N2   C4    single    1.436  0.020  1.436
 VHI  C3   O3    double    1.209  0.020  1.209
 VHI  C4   C5    single    1.552  0.020  1.552
 VHI  C5   C6    single    1.531  0.020  1.531
 VHI  C7   C8    single    1.525  0.020  1.525
 VHI  C8   C9    single    1.524  0.020  1.524
 VHI  C9   C10   single    1.520  0.020  1.520
 VHI  C10  C11   single    1.539  0.020  1.539
 VHI  C11  O11   deloc     1.247  0.020  1.247
 VHI  C11  O12   deloc     1.250  0.020  1.250
 VHI  C17  O18   single    1.318  0.020  1.318
 VHI  C17  O19   double    1.210  0.020  1.210
 VHI  O18  C20   single    1.438  0.020  1.438
 VHI  C20  C21   single    1.497  0.020  1.497
 VHI  C21  C22   aromatic  1.391  0.020  1.391
 VHI  C21  C26   aromatic  1.393  0.020  1.393
 VHI  C22  C23   aromatic  1.389  0.020  1.389
 VHI  C23  C24   aromatic  1.388  0.020  1.388
 VHI  C24  C25   aromatic  1.390  0.020  1.390
 VHI  C25  C26   aromatic  1.387  0.020  1.387
 VHI  C2   H2    single    0.970  0.020  1.090
 VHI  N2   HN2   single    0.860  0.020  1.020
 VHI  C4   H4    single    0.970  0.020  1.090
 VHI  C5   H5    single    0.970  0.020  1.090
 VHI  C6   H6    single    0.970  0.020  1.090
 VHI  C6   H6A   single    0.970  0.020  1.090
 VHI  C7   H7    single    0.970  0.020  1.090
 VHI  C7   H7A   single    0.970  0.020  1.090
 VHI  C8   H8    single    0.970  0.020  1.090
 VHI  C8   H8A   single    0.970  0.020  1.090
 VHI  C9   H9    single    0.970  0.020  1.090
 VHI  C9   H9A   single    0.970  0.020  1.090
 VHI  C10  H10   single    0.970  0.020  1.090
 VHI  C10  H10A  single    0.970  0.020  1.090
 VHI  C20  H20   single    0.970  0.020  1.090
 VHI  C20  H20A  single    0.970  0.020  1.090
 VHI  C22  H22   single    0.930  0.020  1.080
 VHI  C23  H23   single    0.930  0.020  1.080
 VHI  C24  H24   single    0.930  0.020  1.080
 VHI  C25  H25   single    0.930  0.020  1.080
 VHI  C26  H26   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
 VHI  C17   N1   C5   119.28  3.000
 VHI  C17   N1   C3   127.95  3.000
 VHI  C5    N1   C3   112.32  3.000
 VHI  C6    S1   C2    88.55  3.000
 VHI  H2    C2   C7   108.77  3.000
 VHI  H2    C2   C4   107.37  3.000
 VHI  C7    C2   C4   114.98  3.000
 VHI  H2    C2   S1   107.40  3.000
 VHI  C7    C2   S1   113.42  3.000
 VHI  C4    C2   S1   104.48  3.000
 VHI  HN2   N2   C4   123.33  3.000
 VHI  HN2   N2   C3   120.69  3.000
 VHI  C4    N2   C3   115.91  3.000
 VHI  O3    C3   N2   127.00  3.000
 VHI  O3    C3   N1   126.96  3.000
 VHI  N2    C3   N1   106.03  3.000
 VHI  H4    C4   C5   112.00  3.000
 VHI  H4    C4   N2   110.80  3.000
 VHI  C5    C4   N2   102.40  3.000
 VHI  H4    C4   C2   109.23  3.000
 VHI  C5    C4   C2   108.88  3.000
 VHI  N2    C4   C2   113.42  3.000
 VHI  H5    C5   C6   110.52  3.000
 VHI  H5    C5   C4   111.65  3.000
 VHI  C6    C5   C4   108.48  3.000
 VHI  H5    C5   N1   110.36  3.000
 VHI  C6    C5   N1   112.35  3.000
 VHI  C4    C5   N1   103.29  3.000
 VHI  H6A   C6   H6   107.99  3.000
 VHI  H6A   C6   C5   109.63  3.000
 VHI  H6    C6   C5   113.00  3.000
 VHI  H6A   C6   S1   109.70  3.000
 VHI  H6    C6   S1   110.54  3.000
 VHI  C5    C6   S1   105.96  3.000
 VHI  H7A   C7   H7   106.64  3.000
 VHI  H7A   C7   C8   109.09  3.000
 VHI  H7    C7   C8   109.31  3.000
 VHI  H7A   C7   C2   107.70  3.000
 VHI  H7    C7   C2   110.27  3.000
 VHI  C8    C7   C2   113.59  3.000
 VHI  H8A   C8   H8   106.05  3.000
 VHI  H8A   C8   C9   109.42  3.000
 VHI  H8    C8   C9   109.48  3.000
 VHI  H8A   C8   C7   109.68  3.000
 VHI  H8    C8   C7   109.55  3.000
 VHI  C9    C8   C7   112.45  3.000
 VHI  H9A   C9   H9   105.96  3.000
 VHI  H9A   C9   C10  109.99  3.000
 VHI  H9    C9   C10  109.86  3.000
 VHI  H9A   C9   C8   108.98  3.000
 VHI  H9    C9   C8   109.27  3.000
 VHI  C10   C9   C8   112.56  3.000
 VHI  H10A  C10  H10  104.79  3.000
 VHI  H10A  C10  C11  108.14  3.000
 VHI  H10   C10  C11  108.00  3.000
 VHI  H10A  C10  C9   109.59  3.000
 VHI  H10   C10  C9   109.54  3.000
 VHI  C11   C10  C9   116.16  3.000
 VHI  O12   C11  O11  126.15  3.000
 VHI  O12   C11  C10  115.88  3.000
 VHI  O11   C11  C10  117.97  3.000
 VHI  O19   C17  O18  124.76  3.000
 VHI  O19   C17  N1   121.76  3.000
 VHI  O18   C17  N1   113.48  3.000
 VHI  C20   O18  C17  116.51  3.000
 VHI  H20A  C20  H20  108.30  3.000
 VHI  H20A  C20  C21  111.13  3.000
 VHI  H20   C20  C21  110.82  3.000
 VHI  H20A  C20  O18  109.60  3.000
 VHI  H20   C20  O18  110.02  3.000
 VHI  C21   C20  O18  106.97  3.000
 VHI  C26   C21  C22  119.16  3.000
 VHI  C26   C21  C20  120.42  3.000
 VHI  C22   C21  C20  120.42  3.000
 VHI  H22   C22  C23  119.77  3.000
 VHI  H22   C22  C21  119.68  3.000
 VHI  C23   C22  C21  120.54  3.000
 VHI  H23   C23  C24  120.20  3.000
 VHI  H23   C23  C22  119.84  3.000
 VHI  C24   C23  C22  119.96  3.000
 VHI  H24   C24  C25  120.05  3.000
 VHI  H24   C24  C23  120.11  3.000
 VHI  C25   C24  C23  119.83  3.000
 VHI  H25   C25  C26  119.89  3.000
 VHI  H25   C25  C24  120.06  3.000
 VHI  C26   C25  C24  120.05  3.000
 VHI  H26   C26  C25  119.76  3.000
 VHI  H26   C26  C21  119.78  3.000
 VHI  C25   C26  C21  120.46  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
 VHI  CONST_01  C24  C23  C22  C21     0.00   0.0  0
 VHI  CONST_02  C24  C25  C26  C21     0.00   0.0  0
 VHI  CONST_03  C25  C26  C21  C22     0.00   0.0  0
 VHI  CONST_04  C25  C24  C23  C22     0.00   0.0  0
 VHI  CONST_05  C26  C21  C22  C23     0.00   0.0  0
 VHI  CONST_06  C26  C25  C24  C23     0.00   0.0  0
 VHI  CONST_07  C4   N2   C3   N1      0.00   0.0  0
 VHI  CONST_08  C5   N1   C3   N2      0.00   0.0  0
 VHI  CONST_09  C23  C22  C21  C20   180.00   0.0  0
 VHI  CONST_10  C25  C26  C21  C20   180.00   0.0  0
 VHI  CONST_11  C17  N1   C3   N2    180.00   0.0  0
 VHI  CONST_12  C5   N1   C3   O3    180.00   0.0  0
 VHI  CONST_13  C4   N2   C3   O3    180.00   0.0  0
 VHI  CONST_14  H23  C23  C22  C21   180.00   0.0  0
 VHI  CONST_15  H25  C25  C26  C21   180.00   0.0  0
 VHI  CONST_16  H26  C26  C21  C22   180.00   0.0  0
 VHI  CONST_17  H24  C24  C23  C22   180.00   0.0  0
 VHI  CONST_18  H22  C22  C23  C24   180.00   0.0  0
 VHI  CONST_19  HN2  N2   C3   N1    180.00   0.0  0
 VHI  CONST_20  C17  N1   C3   O3      0.00   0.0  0
 VHI  Var_01    C5   C6   S1   C2     42.64  30.0  1
 VHI  Var_02    O18  C17  N1   C3     10.67  30.0  2
 VHI  Var_03    C22  C21  C20  O18    99.92  30.0  2
 VHI  Var_04    C9   C8   C7   C2   -171.39  30.0  3
 VHI  Var_05    C21  C20  O18  C17  -178.50  30.0  3
 VHI  Var_06    C10  C9   C8   C7   -177.50  30.0  3
 VHI  Var_07    C11  C10  C9   C8   -178.43  30.0  3
 VHI  Var_08    O11  C11  C10  C9      3.25  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
 VHI  chir_01  C2  S1  C4  C7  positiv
 VHI  chir_02  C4  N2  C5  C2  negativ
 VHI  chir_03  C5  N1  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
 VHI  plan-1  C20  0.020
 VHI  plan-1  C21  0.020
 VHI  plan-1  C22  0.020
 VHI  plan-1  C23  0.020
 VHI  plan-1  C24  0.020
 VHI  plan-1  C25  0.020
 VHI  plan-1  C26  0.020
 VHI  plan-1  H22  0.020
 VHI  plan-1  H23  0.020
 VHI  plan-1  H24  0.020
 VHI  plan-1  H25  0.020
 VHI  plan-1  H26  0.020
 VHI  plan-2  N1   0.020
 VHI  plan-2  N2   0.020
 VHI  plan-2  C3   0.020
 VHI  plan-2  O3   0.020
 VHI  plan-2  C4   0.020
 VHI  plan-2  C5   0.020
 VHI  plan-2  C17  0.020
 VHI  plan-2  HN2  0.020
 VHI  plan-3  C10  0.020
 VHI  plan-3  C11  0.020
 VHI  plan-3  O11  0.020
 VHI  plan-3  O12  0.020
 VHI  plan-4  N1   0.020
 VHI  plan-4  C17  0.020
 VHI  plan-4  O18  0.020
 VHI  plan-4  O19  0.020

