# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 06:21:22 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-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)[C@H](NC(=O)N2CCNC2=O)c3ccccc3)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
 59H  59H  '(2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-1,3-thiazolidine-4-carboxylic acid'  ligand  56  32  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_59H
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
 59H  N1   N  NH1    0  -0.628  -0.5579  -0.2184   0.0677
 59H  C3   C  C      0   0.409  -5.8396   1.1990   0.8196
 59H  N    N  NH1    0  -0.707   3.0304  -0.2230   0.1553
 59H  CA   C  CH1    0  -0.271   1.7737   0.3437  -0.2449
 59H  C    C  C      0   0.565   0.6793  -0.3577   0.5640
 59H  O    O  O      0  -0.473   0.9326  -0.9377   1.6063
 59H  CX1  C  C      0   0.169   1.6714   1.8361   0.0058
 59H  CX2  C  C1     0  -0.317   1.1088   2.6683  -0.9536
 59H  CX3  C  C1     0  -0.242   0.9725   4.0293  -0.7141
 59H  CX4  C  C1     0  -0.264   1.4031   4.5691   0.4900
 59H  CX5  C  C1     0  -0.240   1.9698   3.7406   1.4510
 59H  CX6  C  C1     0  -0.294   2.1009   2.3800   1.2120
 59H  OX1  O  O      0  -0.492   4.1814   0.7887  -1.4970
 59H  NX1  N  NR5    0  -0.607   5.2873  -0.5970  -0.0431
 59H  CX8  C  CH2    0  -0.341   5.2698  -1.5803   1.0336
 59H  CX9  C  CH2    0  -0.280   6.6876  -2.1462   0.9870
 59H  NX2  N  NR15   0  -0.666   7.4055  -1.0689   0.3480
 59H  CXA  C  CR5    0   0.698   6.6013  -0.2658  -0.3887
 59H  OX2  O  O      0  -0.481   6.9561   0.5885  -1.1705
 59H  CA1  C  CH1    0  -0.186  -1.7038  -0.8463   0.6660
 59H  C1   C  C1     0   0.185  -1.8632  -2.2772   0.1990
 59H  O1   O  O      0  -0.369  -1.0323  -2.8665  -0.4413
 59H  N3   N  NH1    0  -0.589  -4.0866  -0.6021   1.1430
 59H  CA3  C  CH1    0  -0.178  -5.3622  -0.2486   0.5421
 59H  CXC  C  CT     0  -0.194  -5.2092  -0.5995  -0.9547
 59H  CXD  C  CH1    0  -0.205  -2.9732  -0.0253   0.4259
 59H  S4   S  S2     0  -0.025  -3.4815  -0.0670  -1.3303
 59H  CXE  C  CH3    0  -0.628  -6.1512   0.1329  -1.8999
 59H  H1   H  HNH1   0   0.403  -0.6565   0.1442  -0.8692
 59H  H2   H  HNH1   0   0.417   3.0271  -0.7575   1.0108
 59H  H3   H  HCH1   0   0.305   1.6047   0.1543  -1.3095
 59H  H4   H  H      0   0.255   0.7843   2.2571  -1.9025
 59H  H5   H  H      0   0.259   0.5378   4.6672  -1.4729
 59H  H6   H  H      0   0.258   1.3021   5.6300   0.6781
 59H  H7   H  H      0   0.258   2.3122   4.1546   2.3904
 59H  H8   H  H      0   0.252   2.5497   1.7468   1.9682
 59H  H9   H  HCH2   0   0.272   5.0628  -1.1047   1.9960
 59H  H10  H  HCH2   0   0.280   4.5264  -2.3556   0.8571
 59H  H11  H  HCH2   0   0.266   7.0715  -2.3576   1.9827
 59H  H12  H  HCH2   0   0.254   6.7287  -3.0648   0.3963
 59H  H13  H  HNR5   0   0.408   8.3754  -1.1606   0.0922
 59H  H14  H  HCH1   0   0.307  -1.5513  -0.8850   1.7515
 59H  H15  H  H      0   0.212  -2.7970  -2.7579   0.5277
 59H  H16  H  HNH1   0   0.361  -4.0550  -0.2978   2.1091
 59H  H18  H  HCH1   0   0.246  -6.1258  -0.9206   0.9507
 59H  H20  H  HCH3   0   0.230  -6.3882  -2.4058  -1.0028
 59H  H21  H  HCH3   0   0.234  -5.0770  -2.3884  -2.1820
 59H  H22  H  HCH3   0   0.238  -4.7267  -2.6696  -0.4745
 59H  H23  H  HCH1   0   0.280  -2.7646   1.0135   0.6940
 59H  H24  H  HCH3   0   0.238  -6.0343   1.2131  -1.8525
 59H  H25  H  HCH3   0   0.229  -5.9641  -0.1812  -2.9279
 59H  H26  H  HCH3   0   0.235  -7.1864  -0.1084  -1.6603
 59H  O3   O  O      0  -0.586  -4.9867   2.0263   1.1934
 59H  CXB  C  CH3    0  -0.623  -5.3500  -2.1046  -1.1652
 59H  OXT  O  OC    -1  -0.609  -7.0597   1.4010   0.6667
 59H  CX7  C  C      0   0.772   4.1636   0.0540  -0.5281

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
 59H  O3   C3   deloc     1.246  0.020  1.246
 59H  O1   C1   double    1.203  0.020  1.203
 59H  C3   OXT  deloc     1.246  0.020  1.246
 59H  C3   CA3  single    1.549  0.020  1.549
 59H  OX1  CX7  double    1.216  0.020  1.216
 59H  CA3  N3   single    1.454  0.020  1.454
 59H  CA3  CXC  single    1.545  0.020  1.545
 59H  C1   CA1  single    1.514  0.020  1.514
 59H  CX6  CX5  aromatic  1.388  0.020  1.388
 59H  CX6  CX1  aromatic  1.391  0.020  1.391
 59H  CX8  NX1  single    1.458  0.020  1.458
 59H  CX8  CX9  single    1.527  0.020  1.527
 59H  CX5  CX4  aromatic  1.390  0.020  1.390
 59H  N3   CXD  single    1.444  0.020  1.444
 59H  CX7  NX1  single    1.386  0.020  1.386
 59H  CX7  N    single    1.352  0.020  1.352
 59H  N1   CA1  single    1.437  0.020  1.437
 59H  N1   C    single    1.340  0.020  1.340
 59H  CXB  CXC  single    1.526  0.020  1.526
 59H  CA   CX1  single    1.517  0.020  1.517
 59H  CA   N    single    1.435  0.020  1.435
 59H  CA   C    single    1.531  0.020  1.531
 59H  CX1  CX2  aromatic  1.389  0.020  1.389
 59H  CXC  CXE  single    1.522  0.020  1.522
 59H  CXC  S4   single    1.847  0.020  1.847
 59H  CA1  CXD  single    1.531  0.020  1.531
 59H  NX1  CXA  single    1.398  0.020  1.398
 59H  CX4  CX3  aromatic  1.388  0.020  1.388
 59H  C    O    double    1.219  0.020  1.219
 59H  CX9  NX2  single    1.444  0.020  1.444
 59H  CXD  S4   single    1.829  0.020  1.829
 59H  CX2  CX3  aromatic  1.389  0.020  1.389
 59H  CXA  NX2  single    1.354  0.020  1.354
 59H  CXA  OX2  double    1.211  0.020  1.211
 59H  N1   H1   single    0.860  0.020  1.020
 59H  N    H2   single    0.860  0.020  1.020
 59H  CA   H3   single    0.970  0.020  1.090
 59H  CX2  H4   single    0.930  0.020  1.080
 59H  CX3  H5   single    0.930  0.020  1.080
 59H  CX4  H6   single    0.930  0.020  1.080
 59H  CX5  H7   single    0.930  0.020  1.080
 59H  CX6  H8   single    0.930  0.020  1.080
 59H  CX8  H9   single    0.970  0.020  1.090
 59H  CX8  H10  single    0.970  0.020  1.090
 59H  CX9  H11  single    0.970  0.020  1.090
 59H  CX9  H12  single    0.970  0.020  1.090
 59H  NX2  H13  single    0.890  0.020  1.040
 59H  CA1  H14  single    0.970  0.020  1.090
 59H  C1   H15  single    0.930  0.020  1.080
 59H  N3   H16  single    0.890  0.020  1.040
 59H  CA3  H18  single    0.970  0.020  1.090
 59H  CXB  H20  single    0.970  0.020  1.090
 59H  CXB  H21  single    0.970  0.020  1.090
 59H  CXB  H22  single    0.970  0.020  1.090
 59H  CXD  H23  single    0.970  0.020  1.090
 59H  CXE  H24  single    0.970  0.020  1.090
 59H  CXE  H25  single    0.970  0.020  1.090
 59H  CXE  H26  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
 59H  H1   N1   CA1  117.74  3.000
 59H  H1   N1   C    118.10  3.000
 59H  CA1  N1   C    122.45  3.000
 59H  OXT  C3   O3   126.84  3.000
 59H  OXT  C3   CA3  115.54  3.000
 59H  O3   C3   CA3  117.60  3.000
 59H  H2   N    CX7  122.68  3.000
 59H  H2   N    CA   116.28  3.000
 59H  CX7  N    CA   120.80  3.000
 59H  H3   CA   CX1  108.70  3.000
 59H  H3   CA   C    108.92  3.000
 59H  CX1  CA   C    108.37  3.000
 59H  H3   CA   N    109.76  3.000
 59H  C    CA   N    107.32  3.000
 59H  CX1  CA   N    113.67  3.000
 59H  O    C    CA   121.40  3.000
 59H  O    C    N1   123.89  3.000
 59H  CA   C    N1   114.63  3.000
 59H  CX6  CX1  CX2  119.32  3.000
 59H  CX2  CX1  CA   120.18  3.000
 59H  CX6  CX1  CA   120.47  3.000
 59H  H4   CX2  CX3  119.57  3.000
 59H  H4   CX2  CX1  119.91  3.000
 59H  CX3  CX2  CX1  120.52  3.000
 59H  H5   CX3  CX4  120.23  3.000
 59H  H5   CX3  CX2  119.75  3.000
 59H  CX4  CX3  CX2  120.02  3.000
 59H  H6   CX4  CX5  120.15  3.000
 59H  H6   CX4  CX3  120.20  3.000
 59H  CX5  CX4  CX3  119.65  3.000
 59H  H7   CX5  CX6  119.65  3.000
 59H  H7   CX5  CX4  120.09  3.000
 59H  CX6  CX5  CX4  120.26  3.000
 59H  H8   CX6  CX5  119.46  3.000
 59H  H8   CX6  CX1  120.30  3.000
 59H  CX5  CX6  CX1  120.23  3.000
 59H  CXA  NX1  CX8  110.70  3.000
 59H  CXA  NX1  CX7  124.33  3.000
 59H  CX8  NX1  CX7  124.42  3.000
 59H  H10  CX8  H9   108.86  3.000
 59H  H10  CX8  CX9  111.42  3.000
 59H  H9   CX8  CX9  111.33  3.000
 59H  H10  CX8  NX1  111.64  3.000
 59H  H9   CX8  NX1  111.03  3.000
 59H  CX9  CX8  NX1  102.49  3.000
 59H  H12  CX9  H11  108.55  3.000
 59H  H12  CX9  NX2  111.67  3.000
 59H  H11  CX9  NX2  112.00  3.000
 59H  H12  CX9  CX8  111.27  3.000
 59H  H11  CX9  CX8  111.82  3.000
 59H  NX2  CX9  CX8  101.46  3.000
 59H  H13  NX2  CXA  119.17  3.000
 59H  H13  NX2  CX9  121.56  3.000
 59H  CXA  NX2  CX9  112.83  3.000
 59H  OX2  CXA  NX2  126.55  3.000
 59H  OX2  CXA  NX1  127.00  3.000
 59H  NX2  CXA  NX1  106.44  3.000
 59H  H14  CA1  CXD  106.82  3.000
 59H  H14  CA1  C1   106.66  3.000
 59H  CXD  CA1  C1   111.80  3.000
 59H  H14  CA1  N1   108.46  3.000
 59H  CXD  CA1  N1   111.20  3.000
 59H  C1   CA1  N1   111.62  3.000
 59H  H15  C1   O1   122.07  3.000
 59H  H15  C1   CA1  114.21  3.000
 59H  O1   C1   CA1  123.68  3.000
 59H  H16  N3   CXD  109.23  3.000
 59H  H16  N3   CA3  110.39  3.000
 59H  CXD  N3   CA3  111.96  3.000
 59H  H18  CA3  CXC  106.91  3.000
 59H  H18  CA3  N3   107.94  3.000
 59H  CXC  CA3  N3   104.98  3.000
 59H  H18  CA3  C3   106.94  3.000
 59H  CXC  CA3  C3   114.59  3.000
 59H  N3   CA3  C3   115.06  3.000
 59H  CXE  CXC  S4   108.30  3.000
 59H  S4   CXC  CXB  110.04  3.000
 59H  CXE  CXC  CXB  109.37  3.000
 59H  S4   CXC  CA3  102.96  3.000
 59H  CXE  CXC  CA3  115.54  3.000
 59H  CXB  CXC  CA3  110.39  3.000
 59H  H23  CXD  S4   108.08  3.000
 59H  H23  CXD  N3   113.88  3.000
 59H  S4   CXD  N3   104.68  3.000
 59H  H23  CXD  CA1  108.24  3.000
 59H  S4   CXD  CA1  111.65  3.000
 59H  N3   CXD  CA1  110.31  3.000
 59H  CXD  S4   CXC   94.09  3.000
 59H  H26  CXE  H25  107.84  3.000
 59H  H26  CXE  H24  108.21  3.000
 59H  H25  CXE  H24  107.98  3.000
 59H  H26  CXE  CXC  110.17  3.000
 59H  H25  CXE  CXC  109.90  3.000
 59H  H24  CXE  CXC  112.60  3.000
 59H  H22  CXB  H21  108.25  3.000
 59H  H22  CXB  H20  107.85  3.000
 59H  H21  CXB  H20  107.73  3.000
 59H  H22  CXB  CXC  111.81  3.000
 59H  H21  CXB  CXC  111.23  3.000
 59H  H20  CXB  CXC  109.81  3.000
 59H  NX1  CX7  OX1  123.41  3.000
 59H  NX1  CX7  N    113.97  3.000
 59H  OX1  CX7  N    122.60  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
 59H  CONST_01  CX4  CX5  CX6  CX1    0.00   0.0  0
 59H  CONST_02  CX4  CX3  CX2  CX1    0.00   0.0  0
 59H  CONST_03  CX5  CX6  CX1  CX2    0.00   0.0  0
 59H  CONST_04  CX5  CX4  CX3  CX2    0.00   0.0  0
 59H  CONST_05  CX6  CX5  CX4  CX3    0.00   0.0  0
 59H  CONST_06  CX6  CX1  CX2  CX3    0.00   0.0  0
 59H  CONST_08  CX9  NX2  CXA  NX1    0.00   0.0  0
 59H  CONST_09  NX2  CXA  NX1  CX8    0.00   0.0  0
 59H  CONST_12  CX5  CX6  CX1  CA   180.00   0.0  0
 59H  CONST_13  CX3  CX2  CX1  CA   180.00   0.0  0
 59H  CONST_14  CX9  CX8  NX1  CX7  180.00   0.0  0
 59H  CONST_15  NX2  CXA  NX1  CX7  180.00   0.0  0
 59H  CONST_16  OX2  CXA  NX1  CX8  180.00   0.0  0
 59H  CONST_17  OX2  CXA  NX2  CX9  180.00   0.0  0
 59H  CONST_18  H7   CX5  CX6  CX1  180.00   0.0  0
 59H  CONST_19  H5   CX3  CX2  CX1  180.00   0.0  0
 59H  CONST_20  H8   CX6  CX1  CX2  180.00   0.0  0
 59H  CONST_21  H6   CX4  CX3  CX2  180.00   0.0  0
 59H  CONST_22  H4   CX2  CX3  CX4  180.00   0.0  0
 59H  CONST_24  CX8  NX1  CX7  OX1  180.00   0.0  0
 59H  CONST_26  CX8  NX1  CX7  N      0.00   0.0  0
 59H  CONST_27  CXA  NX1  CX7  N    180.00   0.0  0
 59H  CONST_28  OX2  CXA  NX1  CX7    0.00   0.0  0
 59H  CONST_29  NX1  CX7  N    CA   180.00   0.0  0
 59H  CONST_30  H2   N    CX7  NX1    0.00   0.0  0
 59H  CONST_31  OX1  CX7  N    CA     0.00   0.0  0
 59H  CONST_32  CA1  N1   C    CA   180.00   0.0  0
 59H  CONST_33  CA1  N1   C    O      0.00   0.0  0
 59H  CONST_34  H1   N1   C    CA     0.00   0.0  0
 59H  Var_01    CXE  CXC  S4   CXD  140.90  30.0  1
 59H  Var_02    H11  CX9  CX8  NX1  142.82  30.0  1
 59H  Var_03    H20  CXB  CXC  CA3   70.57  30.0  3
 59H  Var_04    H24  CXE  CXC  CA3   59.50  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
 59H  chir_01  CA   CX1  N   C    negativ
 59H  chir_02  CA1  N1   C1  CXD  positiv
 59H  chir_03  CA3  N3   C3  CXC  negativ
 59H  chir_04  CXD  S4   N3  CA1  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
 59H  plan-1  C3   0.020
 59H  plan-1  CA3  0.020
 59H  plan-1  O3   0.020
 59H  plan-1  OXT  0.020
 59H  plan-2  CA1  0.020
 59H  plan-2  C1   0.020
 59H  plan-2  O1   0.020
 59H  plan-2  H15  0.020
 59H  plan-3  N1   0.020
 59H  plan-3  CA   0.020
 59H  plan-3  C    0.020
 59H  plan-3  O    0.020
 59H  plan-3  CA1  0.020
 59H  plan-3  H1   0.020
 59H  plan-4  CA   0.020
 59H  plan-4  CX1  0.020
 59H  plan-4  CX2  0.020
 59H  plan-4  CX3  0.020
 59H  plan-4  CX4  0.020
 59H  plan-4  CX5  0.020
 59H  plan-4  CX6  0.020
 59H  plan-4  H4   0.020
 59H  plan-4  H5   0.020
 59H  plan-4  H6   0.020
 59H  plan-4  H7   0.020
 59H  plan-4  H8   0.020
 59H  plan-5  N    0.020
 59H  plan-5  CA   0.020
 59H  plan-5  OX1  0.020
 59H  plan-5  NX1  0.020
 59H  plan-5  CX8  0.020
 59H  plan-5  CX9  0.020
 59H  plan-5  NX2  0.020
 59H  plan-5  CXA  0.020
 59H  plan-5  OX2  0.020
 59H  plan-5  H2   0.020
 59H  plan-5  H13  0.020
 59H  plan-5  CX7  0.020

