# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Jun  1 00:06:09 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  48  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  -0.601  -1.3162   1.1506  -0.3314
 VHI  S1    S  S2    0  -0.013   1.4848   1.0586   1.4528
 VHI  C2    C  CH1   0  -0.369   2.1366   1.3741  -0.2183
 VHI  N2    N  NR15  0  -0.660   0.3205   0.2440  -1.4811
 VHI  C3    C  CR5   0   0.695  -0.9337   0.0107  -1.0563
 VHI  O3    O  O     0  -0.471  -1.6021  -0.9743  -1.2692
 VHI  C4    C  CR15  0  -0.044   0.8862   1.5076  -1.1000
 VHI  C5    C  CR15  0  -0.090  -0.2532   2.1444  -0.2609
 VHI  C6    C  CH2   0  -0.565   0.2551   2.3544   1.1671
 VHI  C7    C  CH2   0  -0.428   3.1353   0.3312  -0.6829
 VHI  C8    C  CH2   0  -0.418   4.3794   0.2494   0.1941
 VHI  C9    C  CH2   0  -0.420   5.4474  -0.6512  -0.4139
 VHI  C10   C  CH2   0  -0.582   6.6597  -0.7748   0.4936
 VHI  C11   C  C     0   0.550   7.7637  -1.6195  -0.0782
 VHI  O11   O  O     0  -0.446   7.7415  -2.1598  -1.1561
 VHI  O12   O  OH1   0  -0.598   8.7982  -1.7096   0.7539
 VHI  C17   C  C     0   0.795  -2.5640   1.4680   0.1437
 VHI  O18   O  O2    0  -0.443  -3.4226   0.4712   0.0700
 VHI  O19   O  O     0  -0.494  -2.8155   2.5642   0.5903
 VHI  C20   C  CH2   0  -0.248  -4.7616   0.7416   0.5207
 VHI  C21   C  CR6   0   0.080  -5.5361  -0.5314   0.3762
 VHI  C22   C  CR16  0  -0.297  -5.7612  -1.3483   1.4790
 VHI  C23   C  CR16  0  -0.242  -6.4695  -2.5357   1.3450
 VHI  C24   C  CR16  0  -0.261  -6.9547  -2.9169   0.1017
 VHI  C25   C  CR16  0  -0.243  -6.7319  -2.1067  -1.0057
 VHI  C26   C  CR16  0  -0.281  -6.0267  -0.9203  -0.8678
 VHI  H2    H  HCH1  0   0.283   2.6304   2.3517  -0.1992
 VHI  HN2   H  HNR5  0   0.414   0.7779  -0.4008  -2.1043
 VHI  H4    H  HCR5  0   0.292   1.1290   2.1061  -1.9816
 VHI  H5    H  HCR5  0   0.304  -0.5884   3.0885  -0.6896
 VHI  H6    H  HCH2  0   0.298  -0.5352   2.3009   1.9121
 VHI  H6A   H  HCH2  0   0.283   0.7279   3.3345   1.2476
 VHI  H7    H  HCH2  0   0.235   2.6607  -0.6527  -0.7312
 VHI  H7A   H  HCH2  0   0.244   3.4334   0.5872  -1.7056
 VHI  H8    H  HCH2  0   0.224   4.7904   1.2531   0.3449
 VHI  H8A   H  HCH2  0   0.225   4.1096  -0.1235   1.1872
 VHI  H9    H  HCH2  0   0.229   5.0245  -1.6410  -0.6058
 VHI  H9A   H  HCH2  0   0.230   5.7468  -0.2476  -1.3844
 VHI  H10   H  HCH2  0   0.277   7.0724   0.2136   0.7207
 VHI  H10A  H  HCH2  0   0.277   6.3734  -1.1990   1.4613
 VHI  HO12  H  HOH1  0   0.478   9.4930  -2.2566   0.3588
 VHI  H20   H  HCH2  0   0.256  -4.7456   1.0705   1.5609
 VHI  H20A  H  HCH2  0   0.256  -5.1978   1.5388  -0.0843
 VHI  H22   H  HCR6  0   0.256  -5.3866  -1.0520   2.4517
 VHI  H23   H  HCR6  0   0.259  -6.6431  -3.1601   2.2118
 VHI  H24   H  HCR6  0   0.259  -7.5091  -3.8404  -0.0051
 VHI  H25   H  HCR6  0   0.259  -7.1115  -2.3989  -1.9763
 VHI  H26   H  HCR6  0   0.255  -5.8621  -0.2886  -1.7327

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    1.345  0.020  1.345
 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    1.530  0.020  1.530
 VHI  C7   C8    single    1.524  0.020  1.524
 VHI  C8   C9    single    1.524  0.020  1.524
 VHI  C9   C10   single    1.519  0.020  1.519
 VHI  C10  C11   single    1.503  0.020  1.503
 VHI  C11  O11   double    1.206  0.020  1.206
 VHI  C11  O12   single    1.331  0.020  1.331
 VHI  C17  O18   single    1.318  0.020  1.318
 VHI  C17  O19   double    1.210  0.020  1.210
 VHI  O18  C20   single    1.439  0.020  1.439
 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  O12  HO12  single    0.850  0.020  0.980
 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   119.27  3.000
 VHI  C17   N1   C3   127.90  3.000
 VHI  C5    N1   C3   112.34  3.000
 VHI  C6    S1   C2    88.53  3.000
 VHI  H2    C2   C7   108.79  3.000
 VHI  H2    C2   C4   107.43  3.000
 VHI  C7    C2   C4   114.83  3.000
 VHI  H2    C2   S1   107.46  3.000
 VHI  C7    C2   S1   113.42  3.000
 VHI  C4    C2   S1   104.50  3.000
 VHI  HN2   N2   C4   123.30  3.000
 VHI  HN2   N2   C3   120.55  3.000
 VHI  C4    N2   C3   115.87  3.000
 VHI  O3    C3   N2   126.96  3.000
 VHI  O3    C3   N1   126.99  3.000
 VHI  N2    C3   N1   106.05  3.000
 VHI  H4    C4   C5   112.00  3.000
 VHI  H4    C4   N2   110.82  3.000
 VHI  C5    C4   N2   102.44  3.000
 VHI  H4    C4   C2   109.25  3.000
 VHI  C5    C4   C2   108.85  3.000
 VHI  N2    C4   C2   113.37  3.000
 VHI  H5    C5   C6   110.51  3.000
 VHI  H5    C5   C4   111.63  3.000
 VHI  C6    C5   C4   108.48  3.000
 VHI  H5    C5   N1   110.34  3.000
 VHI  C6    C5   N1   112.40  3.000
 VHI  C4    C5   N1   103.28  3.000
 VHI  H6A   C6   H6   107.98  3.000
 VHI  H6A   C6   C5   109.63  3.000
 VHI  H6    C6   C5   113.03  3.000
 VHI  H6A   C6   S1   109.70  3.000
 VHI  H6    C6   S1   110.52  3.000
 VHI  C5    C6   S1   105.95  3.000
 VHI  H7A   C7   H7   106.69  3.000
 VHI  H7A   C7   C8   109.11  3.000
 VHI  H7    C7   C8   109.35  3.000
 VHI  H7A   C7   C2   107.72  3.000
 VHI  H7    C7   C2   110.27  3.000
 VHI  C8    C7   C2   113.45  3.000
 VHI  H8A   C8   H8   106.25  3.000
 VHI  H8A   C8   C9   109.48  3.000
 VHI  H8    C8   C9   109.49  3.000
 VHI  H8A   C8   C7   109.82  3.000
 VHI  H8    C8   C7   109.66  3.000
 VHI  C9    C8   C7   111.98  3.000
 VHI  H9A   C9   H9   106.52  3.000
 VHI  H9A   C9   C10  109.99  3.000
 VHI  H9    C9   C10  109.87  3.000
 VHI  H9A   C9   C8   109.15  3.000
 VHI  H9    C9   C8   109.51  3.000
 VHI  C10   C9   C8   111.66  3.000
 VHI  H10A  C10  H10  105.37  3.000
 VHI  H10A  C10  C11  108.10  3.000
 VHI  H10   C10  C11  108.02  3.000
 VHI  H10A  C10  C9   110.54  3.000
 VHI  H10   C10  C9   110.56  3.000
 VHI  C11   C10  C9   113.87  3.000
 VHI  O12   C11  O11  122.89  3.000
 VHI  O12   C11  C10  111.79  3.000
 VHI  O11   C11  C10  125.33  3.000
 VHI  HO12  O12  C11  109.93  3.000
 VHI  O19   C17  O18  124.79  3.000
 VHI  O19   C17  N1   121.75  3.000
 VHI  O18   C17  N1   113.46  3.000
 VHI  C20   O18  C17  116.54  3.000
 VHI  H20A  C20  H20  108.31  3.000
 VHI  H20A  C20  C21  111.15  3.000
 VHI  H20   C20  C21  110.85  3.000
 VHI  H20A  C20  O18  109.61  3.000
 VHI  H20   C20  O18  109.98  3.000
 VHI  C21   C20  O18  106.94  3.000
 VHI  C26   C21  C22  119.16  3.000
 VHI  C26   C21  C20  120.39  3.000
 VHI  C22   C21  C20  120.44  3.000
 VHI  H22   C22  C23  119.78  3.000
 VHI  H22   C22  C21  119.68  3.000
 VHI  C23   C22  C21  120.54  3.000
 VHI  H23   C23  C24  120.19  3.000
 VHI  H23   C23  C22  119.85  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  119.90  3.000
 VHI  H25   C25  C24  120.05  3.000
 VHI  C26   C25  C24  120.05  3.000
 VHI  H26   C26  C25  119.77  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  CONST_21  HO12  O12  C11  C10   180.00   0.0  0
 VHI  Var_01    C5    C6   S1   C2     42.69  30.0  1
 VHI  Var_02    O18   C17  N1   C3     11.21  30.0  2
 VHI  Var_03    C22   C21  C20  O18    99.84  30.0  2
 VHI  Var_04    C9    C8   C7   C2   -171.42  30.0  3
 VHI  Var_05    C21   C20  O18  C17  -178.60  30.0  3
 VHI  Var_06    C10   C9   C8   C7   -177.57  30.0  3
 VHI  Var_07    C11   C10  C9   C8   -178.20  30.0  3
 VHI  Var_08    O11   C11  C10  C9      0.62  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-3  HO12  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

