# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 01:53:26 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(6S)-6-carboxy-6-(glycylamino)hexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)CCCC[C@H](NC(=O)CN)C(O)=O)C=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
 HE0  HE0  '(2R,4S)-2-[(1R)-1-{[(6S)-6-carboxy-6-(glycylamino)hexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  55  29  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HE0
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
 HE0  S1    S  S2     0  -0.024  -4.3418  -1.1399  -0.7253
 HE0  C2    C  CT     0  -0.192  -6.1586  -0.9141  -0.4882
 HE0  C3    C  CH1    0  -0.172  -6.2966   0.6040  -0.2338
 HE0  N4    N  NH1    0  -0.591  -5.1446   0.9613   0.5764
 HE0  C5    C  CH1    0  -0.205  -3.9069   0.4745   0.0146
 HE0  C6    C  CH1    0  -0.181  -2.8434   0.3268   1.1066
 HE0  C7    C  C1     0   0.183  -3.2673  -0.6765   2.1571
 HE0  N8    N  NH1    0  -0.641  -1.5632   0.0094   0.5427
 HE0  C9    C  C      0   0.569  -0.3989   0.3389   1.1409
 HE0  O10   O  O      0  -0.496  -0.3490   1.0551   2.1295
 HE0  C11   C  CH2    0  -0.584   0.8389  -0.2352   0.4905
 HE0  C12   C  CH2    0  -0.417   1.9969   0.7540   0.4383
 HE0  C13   C  CH2    0  -0.411   3.2429   0.1393  -0.1854
 HE0  C14   C  CH2    0  -0.452   4.3867   1.1377  -0.3127
 HE0  C15   C  CH1    0  -0.200   5.6587   0.5389  -0.9100
 HE0  C16   C  C      0   0.413   6.7016   1.6372  -1.2547
 HE0  O17   O  O      0  -0.594   7.8024   1.5911  -0.6808
 HE0  O18   O  OC    -1  -0.616   6.3212   2.4765  -2.0955
 HE0  N19   N  NH1    0  -0.617   6.1872  -0.4637  -0.0143
 HE0  C20   C  C      0   0.539   7.0806  -1.3841  -0.4022
 HE0  O21   O  O      0  -0.514   7.3297  -1.6337  -1.5746
 HE0  C22   C  CH2    0  -0.415   7.7904  -2.1030   0.7301
 HE0  N23   N  NH2    0  -0.795   8.2043  -3.4297   0.3227
 HE0  C24   C  CH3    0  -0.634  -6.8745  -1.4304  -1.7293
 HE0  C25   C  CH3    0  -0.625  -6.6242  -1.7033   0.7320
 HE0  C26   C  C      0   0.406  -6.4875   1.4384  -1.5229
 HE0  O27   O  OC    -1  -0.612  -7.6584   1.5152  -1.9432
 HE0  O28   O  O      0  -0.586  -5.4768   1.9663  -2.0259
 HE0  O29   O  O      0  -0.372  -2.5467  -1.5382   2.5898
 HE0  H3    H  HCH1   0   0.242  -7.1940   0.7439   0.3791
 HE0  HN4   H  HNH1   0   0.360  -5.0872   1.9662   0.6923
 HE0  H5    H  HCH1   0   0.278  -3.4996   1.1112  -0.7747
 HE0  H6    H  HCH1   0   0.299  -2.7706   1.2976   1.6129
 HE0  H7    H  H      0   0.207  -4.2927  -0.5331   2.5317
 HE0  HN8   H  HNH1   0   0.399  -1.5313  -0.6660  -0.2055
 HE0  H11   H  HCH2   0   0.268   1.1330  -1.1159   1.0721
 HE0  H11A  H  HCH2   0   0.249   0.6090  -0.5970  -0.5147
 HE0  H12   H  HCH2   0   0.224   1.6960   1.6360  -0.1355
 HE0  H12A  H  HCH2   0   0.225   2.2280   1.1033   1.4470
 HE0  H13   H  HCH2   0   0.218   3.5571  -0.7224   0.4117
 HE0  H13A  H  HCH2   0   0.213   3.0006  -0.2508  -1.1799
 HE0  H14   H  HCH2   0   0.234   4.0715   1.9670  -0.9481
 HE0  H14A  H  HCH2   0   0.217   4.6131   1.5732   0.6683
 HE0  H15   H  HCH1   0   0.235   5.3873   0.0411  -1.8456
 HE0  HN19  H  HNH1   0   0.385   6.1445  -0.2535   0.9714
 HE0  H22   H  HCH2   0   0.233   8.6157  -1.4440   1.0437
 HE0  H22A  H  HCH2   0   0.244   7.1269  -2.1824   1.5939
 HE0  HN23  H  HNH2   0   0.343   8.8584  -3.3562  -0.4452
 HE0  HN2A  H  HNH2   0   0.351   8.7112  -3.8642   1.0822
 HE0  H24   H  HCH3   0   0.232  -6.7314  -2.5082  -1.8210
 HE0  H24A  H  HCH3   0   0.236  -7.9455  -1.2426  -1.6533
 HE0  H24B  H  HCH3   0   0.238  -6.5103  -0.9648  -2.6429
 HE0  H25   H  HCH3   0   0.240  -6.1788  -1.3265   1.6513
 HE0  H25A  H  HCH3   0   0.230  -7.7101  -1.6275   0.8293
 HE0  H25B  H  HCH3   0   0.234  -6.3709  -2.7598   0.6380

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
 HE0  C5   S1    single  1.828  0.020  1.828
 HE0  S1   C2    single  1.846  0.020  1.846
 HE0  C3   C2    single  1.545  0.020  1.545
 HE0  C25  C2    single  1.526  0.020  1.526
 HE0  C2   C24   single  1.523  0.020  1.523
 HE0  N4   C3    single  1.453  0.020  1.453
 HE0  C3   C26   single  1.547  0.020  1.547
 HE0  C3   H3    single  0.970  0.020  1.090
 HE0  N4   C5    single  1.444  0.020  1.444
 HE0  N4   HN4   single  0.890  0.020  1.040
 HE0  C6   C5    single  1.531  0.020  1.531
 HE0  C5   H5    single  0.970  0.020  1.090
 HE0  C7   C6    single  1.513  0.020  1.513
 HE0  N8   C6    single  1.434  0.020  1.434
 HE0  C6   H6    single  0.970  0.020  1.090
 HE0  O29  C7    double  1.204  0.020  1.204
 HE0  C7   H7    single  0.930  0.020  1.080
 HE0  N8   C9    single  1.350  0.020  1.350
 HE0  N8   HN8   single  0.860  0.020  1.020
 HE0  C11  C9    single  1.512  0.020  1.512
 HE0  C9   O10   double  1.222  0.020  1.222
 HE0  C12  C11   single  1.524  0.020  1.524
 HE0  C11  H11   single  0.970  0.020  1.090
 HE0  C11  H11A  single  0.970  0.020  1.090
 HE0  C13  C12   single  1.523  0.020  1.523
 HE0  C12  H12   single  0.970  0.020  1.090
 HE0  C12  H12A  single  0.970  0.020  1.090
 HE0  C14  C13   single  1.524  0.020  1.524
 HE0  C13  H13   single  0.970  0.020  1.090
 HE0  C13  H13A  single  0.970  0.020  1.090
 HE0  C15  C14   single  1.528  0.020  1.528
 HE0  C14  H14   single  0.970  0.020  1.090
 HE0  C14  H14A  single  0.970  0.020  1.090
 HE0  C16  C15   single  1.553  0.020  1.553
 HE0  C15  N19   single  1.445  0.020  1.445
 HE0  C15  H15   single  0.970  0.020  1.090
 HE0  O17  C16   deloc   1.242  0.020  1.242
 HE0  C16  O18   deloc   1.248  0.020  1.248
 HE0  N19  C20   single  1.340  0.020  1.340
 HE0  N19  HN19  single  0.890  0.020  1.040
 HE0  O21  C20   double  1.224  0.020  1.224
 HE0  C20  C22   single  1.518  0.020  1.518
 HE0  C22  N23   single  1.448  0.020  1.448
 HE0  C22  H22   single  0.970  0.020  1.090
 HE0  C22  H22A  single  0.970  0.020  1.090
 HE0  N23  HN23  single  0.890  0.020  1.040
 HE0  N23  HN2A  single  0.890  0.020  1.040
 HE0  C24  H24   single  0.970  0.020  1.090
 HE0  C24  H24A  single  0.970  0.020  1.090
 HE0  C24  H24B  single  0.970  0.020  1.090
 HE0  C25  H25   single  0.970  0.020  1.090
 HE0  C25  H25A  single  0.970  0.020  1.090
 HE0  C25  H25B  single  0.970  0.020  1.090
 HE0  C26  O28   deloc   1.246  0.020  1.246
 HE0  C26  O27   deloc   1.246  0.020  1.246

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
 HE0  C5    S1   C2     94.25  3.000
 HE0  C25   C2   C24   109.44  3.000
 HE0  C24   C2   C3    115.16  3.000
 HE0  C25   C2   C3    110.44  3.000
 HE0  C24   C2   S1    108.45  3.000
 HE0  C25   C2   S1    109.86  3.000
 HE0  C3    C2   S1    103.25  3.000
 HE0  H3    C3   C26   107.23  3.000
 HE0  H3    C3   N4    107.82  3.000
 HE0  C26   C3   N4    115.45  3.000
 HE0  H3    C3   C2    106.90  3.000
 HE0  C26   C3   C2    113.80  3.000
 HE0  N4    C3   C2    105.22  3.000
 HE0  HN4   N4   C5    109.30  3.000
 HE0  HN4   N4   C3    110.65  3.000
 HE0  C5    N4   C3    112.32  3.000
 HE0  H5    C5   C6    108.20  3.000
 HE0  H5    C5   N4    113.83  3.000
 HE0  C6    C5   N4    110.51  3.000
 HE0  H5    C5   S1    108.11  3.000
 HE0  C6    C5   S1    111.63  3.000
 HE0  N4    C5   S1    104.56  3.000
 HE0  H6    C6   N8    108.54  3.000
 HE0  H6    C6   C7    106.55  3.000
 HE0  N8    C6   C7    112.10  3.000
 HE0  H6    C6   C5    106.84  3.000
 HE0  N8    C6   C5    111.15  3.000
 HE0  C7    C6   C5    111.37  3.000
 HE0  H7    C7   O29   121.90  3.000
 HE0  H7    C7   C6    114.25  3.000
 HE0  O29   C7   C6    123.81  3.000
 HE0  HN8   N8   C9    117.70  3.000
 HE0  HN8   N8   C6    117.91  3.000
 HE0  C9    N8   C6    122.80  3.000
 HE0  C11   C9   O10   122.50  3.000
 HE0  O10   C9   N8    122.47  3.000
 HE0  C11   C9   N8    115.02  3.000
 HE0  H11A  C11  H11   106.18  3.000
 HE0  H11A  C11  C12   110.08  3.000
 HE0  H11   C11  C12   109.63  3.000
 HE0  H11A  C11  C9    110.45  3.000
 HE0  H11   C11  C9    107.26  3.000
 HE0  C12   C11  C9    112.98  3.000
 HE0  H12A  C12  H12   106.54  3.000
 HE0  H12A  C12  C13   109.52  3.000
 HE0  H12   C12  C13   109.61  3.000
 HE0  H12A  C12  C11   109.68  3.000
 HE0  H12   C12  C11   109.40  3.000
 HE0  C13   C12  C11   111.94  3.000
 HE0  H13A  C13  H13   106.17  3.000
 HE0  H13A  C13  C14   108.88  3.000
 HE0  H13   C13  C14   110.25  3.000
 HE0  H13A  C13  C12   109.54  3.000
 HE0  H13   C13  C12   109.22  3.000
 HE0  C14   C13  C12   112.57  3.000
 HE0  H14A  C14  H14   106.18  3.000
 HE0  H14A  C14  C15   109.48  3.000
 HE0  H14   C14  C15   108.11  3.000
 HE0  H14A  C14  C13   109.90  3.000
 HE0  H14   C14  C13   109.26  3.000
 HE0  C15   C14  C13   113.63  3.000
 HE0  H15   C15  N19   107.77  3.000
 HE0  H15   C15  C16   107.37  3.000
 HE0  N19   C15  C16   112.50  3.000
 HE0  H15   C15  C14   107.83  3.000
 HE0  N19   C15  C14   109.53  3.000
 HE0  C16   C15  C14   111.63  3.000
 HE0  O18   C16  O17   127.34  3.000
 HE0  O18   C16  C15   114.87  3.000
 HE0  O17   C16  C15   117.79  3.000
 HE0  HN19  N19  C20   117.01  3.000
 HE0  HN19  N19  C15   116.47  3.000
 HE0  C20   N19  C15   122.76  3.000
 HE0  C22   C20  O21   121.52  3.000
 HE0  C22   C20  N19   114.91  3.000
 HE0  O21   C20  N19   123.56  3.000
 HE0  H22A  C22  H22   105.88  3.000
 HE0  H22A  C22  N23   109.24  3.000
 HE0  H22   C22  N23   114.45  3.000
 HE0  H22A  C22  C20   109.90  3.000
 HE0  H22   C22  C20   106.22  3.000
 HE0  N23   C22  C20   110.96  3.000
 HE0  HN2A  N23  HN23  106.10  3.000
 HE0  HN2A  N23  C22   109.00  3.000
 HE0  HN23  N23  C22   109.38  3.000
 HE0  H24B  C24  H24A  108.28  3.000
 HE0  H24B  C24  H24   107.95  3.000
 HE0  H24A  C24  H24   107.76  3.000
 HE0  H24B  C24  C2    112.45  3.000
 HE0  H24A  C24  C2    110.28  3.000
 HE0  H24   C24  C2    109.98  3.000
 HE0  H25B  C25  H25A  107.80  3.000
 HE0  H25B  C25  H25   108.24  3.000
 HE0  H25A  C25  H25   107.89  3.000
 HE0  H25B  C25  C2    111.18  3.000
 HE0  H25A  C25  C2    109.79  3.000
 HE0  H25   C25  C2    111.80  3.000
 HE0  O28   C26  O27   126.84  3.000
 HE0  O27   C26  C3    115.47  3.000
 HE0  O28   C26  C3    117.69  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
 HE0  CONST_01  C11   C9   N8   C6    180.00   0.0  0
 HE0  CONST_02  O10   C9   N8   C6      0.00   0.0  0
 HE0  CONST_03  O21   C20  N19  C15     0.00   0.0  0
 HE0  CONST_05  HN8   N8   C9   O10   180.00   0.0  0
 HE0  CONST_06  HN19  N19  C20  O21   180.00   0.0  0
 HE0  Var_01    C25   C2   S1   C5   -101.10  30.0  1
 HE0  Var_02    H25   C25  C2   S1     64.36  30.0  3
 HE0  Var_03    H24   C24  C2   S1     65.56  30.0  3
 HE0  Var_04    C12   C11  C9   N8    139.42  30.0  1
 HE0  Var_05    C13   C12  C11  C9    178.39  30.0  1
 HE0  Var_06    C14   C13  C12  C11   176.95  30.0  2
 HE0  Var_07    C15   C14  C13  C12   178.84  30.0  1
 HE0  Var_08    N23   C22  C20  N19   152.39  30.0  3
 HE0  Var_09    HN23  N23  C22  C20    61.73  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
 HE0  chir_01  C3   C2   N4   C26  negativ
 HE0  chir_02  C5   S1   N4   C6   negativ
 HE0  chir_03  C6   N8   C5   C7   negativ
 HE0  chir_04  C15  C14  C16  N19  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
 HE0  plan-1  C6    0.020
 HE0  plan-1  N8    0.020
 HE0  plan-1  C9    0.020
 HE0  plan-1  O10   0.020
 HE0  plan-1  C11   0.020
 HE0  plan-1  HN8   0.020
 HE0  plan-2  C15   0.020
 HE0  plan-2  N19   0.020
 HE0  plan-2  C20   0.020
 HE0  plan-2  O21   0.020
 HE0  plan-2  C22   0.020
 HE0  plan-2  HN19  0.020
 HE0  plan-3  C15   0.020
 HE0  plan-3  C16   0.020
 HE0  plan-3  O17   0.020
 HE0  plan-3  O18   0.020
 HE0  plan-4  C3    0.020
 HE0  plan-4  C26   0.020
 HE0  plan-4  O27   0.020
 HE0  plan-4  O28   0.020
 HE0  plan-5  C6    0.020
 HE0  plan-5  C7    0.020
 HE0  plan-5  O29   0.020
 HE0  plan-5  H7    0.020

