# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 04:51:22 2021
#   Inital geometry file: a 161 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN1CCN(C(=O)N[C@@H](C(=O)N[C@H](C=O)[C@@H]2N[C@@H](C(O)=O)C(C)(C)S2)c3ccccc3)C(=O)C1=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
 JPP  JPP  '(2R,4S)-2-[(1R)-1-{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  65  36  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JPP
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
 JPP  S    S  S2    0   0.039  -5.1416   5.3618  24.6907
 JPP  O01  O  O     0  -0.359  -2.7630   3.2128  20.7674
 JPP  O02  O  OH1   0  -0.587  -7.8748   5.4956  20.9162
 JPP  O03  O  O     0  -0.422  -7.2377   7.6301  21.0261
 JPP  O06  O  O     0  -0.463  -1.6656   5.7651  24.3667
 JPP  O04  O  O     0  -0.490   0.5947   8.9055  21.5038
 JPP  O05  O  O     0  -0.437   1.3906   7.6726  25.3124
 JPP  O    O  O     0  -0.462   3.4179   8.8796  26.5483
 JPP  N02  N  NR15  0  -0.578  -5.7193   4.6055  22.1966
 JPP  N03  N  NH1   0  -0.630  -2.8273   5.3253  22.4742
 JPP  N04  N  NH1   0  -0.702  -0.1325   7.5660  23.1624
 JPP  N01  N  NT    0  -0.589   1.9351   8.6740  23.3304
 JPP  N    N  NT    0  -0.453   4.4246   9.2599  24.5507
 JPP  C17  C  CR15  0  -0.259  -4.8936   4.1811  23.3005
 JPP  C19  C  CR5   0  -0.237  -6.3886   6.3543  23.7817
 JPP  C18  C  CR15  0  -0.156  -6.0224   6.0173  22.3066
 JPP  C20  C  CH1   0  -0.164  -3.4114   4.0915  22.9101
 JPP  C01  C  C1    0   0.185  -3.2948   3.0388  21.8313
 JPP  C02  C  CH3   0  -0.638  -7.7950   5.9039  24.1636
 JPP  C03  C  CH3   0  -0.626  -6.1746   7.8232  24.1095
 JPP  C04  C  C     0   0.539  -7.0965   6.4773  21.3445
 JPP  C21  C  C     0   0.579  -1.9643   6.0354  23.2187
 JPP  CA   C  CH1   0  -0.271  -1.3688   7.2523  22.5014
 JPP  C05  C  CR6   0   0.150  -2.3663   8.3960  22.5114
 JPP  C07  C  CR16  0  -0.319  -3.2314   8.5675  21.4364
 JPP  C08  C  CR16  0  -0.293  -2.4395   9.2728  23.5884
 JPP  C09  C  CH2   0  -0.306   2.9383   9.4996  22.6543
 JPP  C10  C  CH2   0  -0.313   4.3167   9.1073  23.1125
 JPP  C11  C  C     0   0.482   2.1406   8.3438  24.6361
 JPP  C12  C  CR16  0  -0.225  -4.1531   9.6052  21.4295
 JPP  C13  C  CR16  0  -0.241  -3.3520  10.3188  23.5766
 JPP  C14  C  C     0   0.483   3.4143   8.8734  25.3326
 JPP  C15  C  CH2   0  -0.319   5.7126   9.6238  25.1222
 JPP  C16  C  CR16  0  -0.261  -4.2093  10.4895  22.4974
 JPP  C    C  CH3   0  -0.664   6.6734   8.4475  25.1947
 JPP  H1   H  HOH1  0   0.490  -8.5675   5.8450  20.3345
 JPP  H2   H  HNR5  0   0.379  -6.5653   4.0520  22.1758
 JPP  H4   H  HNH1  0   0.405  -2.9167   5.5534  21.4957
 JPP  H5   H  HNH1  0   0.427   0.0370   7.1969  24.0902
 JPP  H6   H  HCR5  0   0.305  -5.2067   3.1848  23.6176
 JPP  H7   H  HCR5  0   0.298  -5.1303   6.5976  22.0579
 JPP  H8   H  HCH1  0   0.312  -2.8565   3.7158  23.7768
 JPP  H9   H  H     0   0.217  -3.7457   2.0698  22.1017
 JPP  H10  H  HCH3  0   0.252  -7.9470   6.0285  25.2354
 JPP  H11  H  HCH3  0   0.237  -8.5552   6.5036  23.6573
 JPP  H12  H  HCH3  0   0.237  -7.9743   4.8545  23.9290
 JPP  H13  H  HCH3  0   0.239  -6.3276   8.0096  25.1730
 JPP  H14  H  HCH3  0   0.255  -5.1671   8.1437  23.8488
 JPP  H15  H  HCH3  0   0.240  -6.8812   8.4460  23.5612
 JPP  H16  H  HCH1  0   0.308  -1.1683   6.9788  21.4611
 JPP  H17  H  HCR6  0   0.260  -3.1781   7.8982  20.5846
 JPP  H18  H  HCR6  0   0.249  -1.7709   9.1570  24.4323
 JPP  H19  H  HCH2  0   0.275   2.7522  10.5573  22.8517
 JPP  H20  H  HCH2  0   0.291   2.8612   9.3376  21.5844
 JPP  H21  H  HCH2  0   0.270   4.5554   8.0862  22.8009
 JPP  H22  H  HCH2  0   0.282   5.0382   9.7722  22.6407
 JPP  H23  H  HCR6  0   0.255  -4.8197   9.7254  20.5860
 JPP  H24  H  HCR6  0   0.258  -3.3942  11.0010  24.4157
 JPP  H25  H  HCH2  0   0.257   6.1304  10.4176  24.5016
 JPP  H26  H  HCH2  0   0.264   5.5465  10.0447  26.1116
 JPP  H27  H  HCR6  0   0.257  -4.9212  11.3044  22.4929
 JPP  H28  H  HCH3  0   0.242   7.6211   8.7705  25.6252
 JPP  H29  H  HCH3  0   0.235   6.2740   7.6500  25.8212
 JPP  H30  H  HCH3  0   0.235   6.8812   8.0357  24.2068
 JPP  C06  C  C     0   0.779   0.7493   8.3967  22.5968

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
 JPP  O03  C04  double    1.204  0.020  1.204
 JPP  O01  C01  double    1.202  0.020  1.202
 JPP  O02  C04  single    1.324  0.020  1.324
 JPP  C04  C18  single    1.514  0.020  1.514
 JPP  O04  C06  double    1.216  0.020  1.216
 JPP  C01  C20  single    1.512  0.020  1.512
 JPP  C18  N02  single    1.448  0.020  1.448
 JPP  C18  C19  single    1.557  0.020  1.557
 JPP  C07  C12  aromatic  1.388  0.020  1.388
 JPP  C07  C05  aromatic  1.390  0.020  1.390
 JPP  C12  C16  aromatic  1.388  0.020  1.388
 JPP  C09  C10  single    1.505  0.020  1.505
 JPP  C09  N01  single    1.465  0.020  1.465
 JPP  C03  C19  single    1.520  0.020  1.520
 JPP  N02  C17  single    1.442  0.020  1.442
 JPP  N03  C20  single    1.433  0.020  1.433
 JPP  N03  C21  single    1.343  0.020  1.343
 JPP  C06  N01  single    1.422  0.020  1.422
 JPP  C06  N04  single    1.337  0.020  1.337
 JPP  C10  N    single    1.450  0.020  1.450
 JPP  CA   C05  single    1.518  0.020  1.518
 JPP  CA   C21  single    1.533  0.020  1.533
 JPP  CA   N04  single    1.437  0.020  1.437
 JPP  C19  C02  single    1.525  0.020  1.525
 JPP  C19  S    single    1.835  0.020  1.835
 JPP  C20  C17  single    1.535  0.020  1.535
 JPP  C05  C08  aromatic  1.391  0.020  1.391
 JPP  N01  C11  single    1.362  0.020  1.362
 JPP  C16  C13  aromatic  1.389  0.020  1.389
 JPP  C21  O06  double    1.217  0.020  1.217
 JPP  C17  S    single    1.841  0.020  1.841
 JPP  C08  C13  aromatic  1.388  0.020  1.388
 JPP  N    C15  single    1.455  0.020  1.455
 JPP  N    C14  single    1.335  0.020  1.335
 JPP  C11  O05  double    1.213  0.020  1.213
 JPP  C11  C14  single    1.545  0.020  1.545
 JPP  C    C15  single    1.521  0.020  1.521
 JPP  C14  O    double    1.216  0.020  1.216
 JPP  O02  H1   single    0.850  0.020  0.980
 JPP  N02  H2   single    0.890  0.020  1.040
 JPP  N03  H4   single    0.860  0.020  1.020
 JPP  N04  H5   single    0.860  0.020  1.020
 JPP  C17  H6   single    0.970  0.020  1.090
 JPP  C18  H7   single    0.970  0.020  1.090
 JPP  C20  H8   single    0.970  0.020  1.090
 JPP  C01  H9   single    0.930  0.020  1.080
 JPP  C02  H10  single    0.970  0.020  1.090
 JPP  C02  H11  single    0.970  0.020  1.090
 JPP  C02  H12  single    0.970  0.020  1.090
 JPP  C03  H13  single    0.970  0.020  1.090
 JPP  C03  H14  single    0.970  0.020  1.090
 JPP  C03  H15  single    0.970  0.020  1.090
 JPP  CA   H16  single    0.970  0.020  1.090
 JPP  C07  H17  single    0.930  0.020  1.080
 JPP  C08  H18  single    0.930  0.020  1.080
 JPP  C09  H19  single    0.970  0.020  1.090
 JPP  C09  H20  single    0.970  0.020  1.090
 JPP  C10  H21  single    0.970  0.020  1.090
 JPP  C10  H22  single    0.970  0.020  1.090
 JPP  C12  H23  single    0.930  0.020  1.080
 JPP  C13  H24  single    0.930  0.020  1.080
 JPP  C15  H25  single    0.970  0.020  1.090
 JPP  C15  H26  single    0.970  0.020  1.090
 JPP  C16  H27  single    0.930  0.020  1.080
 JPP  C    H28  single    0.970  0.020  1.090
 JPP  C    H29  single    0.970  0.020  1.090
 JPP  C    H30  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
 JPP  C19  S    C17   93.69  3.000
 JPP  H1   O02  C04  110.29  3.000
 JPP  H2   N02  C18  111.11  3.000
 JPP  H2   N02  C17  109.49  3.000
 JPP  C18  N02  C17  110.39  3.000
 JPP  H4   N03  C21  118.38  3.000
 JPP  H4   N03  C20  116.97  3.000
 JPP  C21  N03  C20  123.27  3.000
 JPP  H5   N04  C06  120.23  3.000
 JPP  H5   N04  CA   119.08  3.000
 JPP  C06  N04  CA   120.57  3.000
 JPP  C11  N01  C09  118.41  3.000
 JPP  C11  N01  C06  124.96  3.000
 JPP  C09  N01  C06  116.30  3.000
 JPP  C15  N    C14  120.81  3.000
 JPP  C14  N    C10  119.62  3.000
 JPP  C15  N    C10  118.79  3.000
 JPP  H6   C17  C20  107.31  3.000
 JPP  H6   C17  N02  109.06  3.000
 JPP  C20  C17  N02  112.04  3.000
 JPP  H6   C17  S    109.11  3.000
 JPP  C20  C17  S    111.07  3.000
 JPP  N02  C17  S    108.19  3.000
 JPP  C03  C19  C02  111.17  3.000
 JPP  C02  C19  C18  112.97  3.000
 JPP  C03  C19  C18  112.36  3.000
 JPP  C02  C19  S    110.05  3.000
 JPP  C03  C19  S    108.67  3.000
 JPP  C18  C19  S    101.10  3.000
 JPP  H7   C18  C04  105.86  3.000
 JPP  H7   C18  C19  107.02  3.000
 JPP  C04  C18  C19  111.69  3.000
 JPP  H7   C18  N02  109.24  3.000
 JPP  C19  C18  N02  109.41  3.000
 JPP  C04  C18  N02  113.36  3.000
 JPP  H8   C20  C01  106.66  3.000
 JPP  H8   C20  C17  107.93  3.000
 JPP  C01  C20  C17  107.25  3.000
 JPP  H8   C20  N03  109.24  3.000
 JPP  C17  C20  N03  114.87  3.000
 JPP  C01  C20  N03  110.55  3.000
 JPP  H9   C01  C20  113.92  3.000
 JPP  H9   C01  O01  121.68  3.000
 JPP  C20  C01  O01  124.39  3.000
 JPP  H12  C02  H11  108.30  3.000
 JPP  H12  C02  H10  107.39  3.000
 JPP  H11  C02  H10  107.21  3.000
 JPP  H12  C02  C19  112.46  3.000
 JPP  H11  C02  C19  111.31  3.000
 JPP  H10  C02  C19  109.95  3.000
 JPP  H15  C03  H14  108.14  3.000
 JPP  H15  C03  H13  107.58  3.000
 JPP  H14  C03  H13  108.24  3.000
 JPP  H15  C03  C19  110.63  3.000
 JPP  H14  C03  C19  111.28  3.000
 JPP  H13  C03  C19  110.84  3.000
 JPP  C18  C04  O03  122.83  3.000
 JPP  C18  C04  O02  113.42  3.000
 JPP  O03  C04  O02  123.74  3.000
 JPP  CA   C21  N03  114.20  3.000
 JPP  CA   C21  O06  121.50  3.000
 JPP  N03  C21  O06  124.30  3.000
 JPP  H16  CA   C05  108.36  3.000
 JPP  H16  CA   C21  108.52  3.000
 JPP  C05  CA   C21  109.86  3.000
 JPP  H16  CA   N04  109.54  3.000
 JPP  C21  CA   N04  107.00  3.000
 JPP  C05  CA   N04  113.46  3.000
 JPP  C08  C05  C07  119.22  3.000
 JPP  C08  C05  CA   120.98  3.000
 JPP  C07  C05  CA   119.79  3.000
 JPP  H17  C07  C12  119.34  3.000
 JPP  H17  C07  C05  120.03  3.000
 JPP  C12  C07  C05  120.61  3.000
 JPP  H18  C08  C13  119.54  3.000
 JPP  H18  C08  C05  120.24  3.000
 JPP  C13  C08  C05  120.21  3.000
 JPP  H20  C09  H19  108.11  3.000
 JPP  H20  C09  C10  109.05  3.000
 JPP  H19  C09  C10  110.71  3.000
 JPP  H20  C09  N01  108.81  3.000
 JPP  H19  C09  N01  110.24  3.000
 JPP  C10  C09  N01  109.87  3.000
 JPP  H22  C10  H21  107.58  3.000
 JPP  H22  C10  C09  108.41  3.000
 JPP  H21  C10  C09  110.88  3.000
 JPP  H22  C10  N    108.44  3.000
 JPP  H21  C10  N    111.38  3.000
 JPP  C09  C10  N    110.04  3.000
 JPP  C14  C11  N01  118.24  3.000
 JPP  C14  C11  O05  116.62  3.000
 JPP  N01  C11  O05  125.13  3.000
 JPP  H23  C12  C16  120.29  3.000
 JPP  H23  C12  C07  119.74  3.000
 JPP  C16  C12  C07  119.96  3.000
 JPP  H24  C13  C16  120.06  3.000
 JPP  H24  C13  C08  119.61  3.000
 JPP  C16  C13  C08  120.33  3.000
 JPP  C11  C14  N    117.33  3.000
 JPP  C11  C14  O    117.06  3.000
 JPP  N    C14  O    125.60  3.000
 JPP  H26  C15  H25  107.12  3.000
 JPP  H26  C15  C    110.63  3.000
 JPP  H25  C15  C    110.37  3.000
 JPP  H26  C15  N    108.59  3.000
 JPP  H25  C15  N    107.31  3.000
 JPP  C    C15  N    112.61  3.000
 JPP  H27  C16  C13  120.13  3.000
 JPP  H27  C16  C12  120.22  3.000
 JPP  C13  C16  C12  119.65  3.000
 JPP  H30  C    H29  108.32  3.000
 JPP  H30  C    H28  107.71  3.000
 JPP  H29  C    H28  107.97  3.000
 JPP  H30  C    C15  111.68  3.000
 JPP  H29  C    C15  111.21  3.000
 JPP  H28  C    C15  109.81  3.000
 JPP  N01  C06  N04  116.94  3.000
 JPP  N04  C06  O04  123.82  3.000
 JPP  N01  C06  O04  119.24  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
 JPP  CONST_01  C16  C12  C07  C05    0.00   0.0  0
 JPP  CONST_02  C16  C13  C08  C05    0.00   0.0  0
 JPP  CONST_03  C13  C16  C12  C07    0.00   0.0  0
 JPP  CONST_04  C13  C08  C05  C07    0.00   0.0  0
 JPP  CONST_05  C12  C07  C05  C08    0.00   0.0  0
 JPP  CONST_06  C12  C16  C13  C08    0.00   0.0  0
 JPP  CONST_07  C14  C11  N01  C09    0.00   0.0  0
 JPP  CONST_08  C11  C14  N    C10    0.00   0.0  0
 JPP  CONST_09  C12  C07  C05  CA   180.00   0.0  0
 JPP  CONST_10  C13  C08  C05  CA   180.00   0.0  0
 JPP  CONST_11  C09  N01  C11  O05  180.00   0.0  0
 JPP  CONST_12  C10  N    C14  O    180.00   0.0  0
 JPP  CONST_13  C14  C11  N01  C06  180.00   0.0  0
 JPP  CONST_14  C15  N    C14  C11  180.00   0.0  0
 JPP  CONST_15  H23  C12  C07  C05  180.00   0.0  0
 JPP  CONST_16  H24  C13  C08  C05  180.00   0.0  0
 JPP  CONST_17  H27  C16  C12  C07  180.00   0.0  0
 JPP  CONST_18  H18  C08  C05  C07  180.00   0.0  0
 JPP  CONST_19  H17  C07  C05  C08  180.00   0.0  0
 JPP  CONST_20  C09  N01  C06  O04    0.00   0.0  0
 JPP  CONST_21  C11  N01  C06  O04  180.00   0.0  0
 JPP  CONST_22  C06  N01  C11  O05    0.00   0.0  0
 JPP  CONST_23  C15  N    C14  O      0.00   0.0  0
 JPP  CONST_24  C09  N01  C06  N04  180.00   0.0  0
 JPP  CONST_25  C11  N01  C06  N04    0.00   0.0  0
 JPP  CONST_26  CA   N04  C06  N01  180.00   0.0  0
 JPP  CONST_27  H5   N04  C06  N01    0.00   0.0  0
 JPP  CONST_28  H1   O02  C04  C18  180.00   0.0  0
 JPP  CONST_29  C20  N03  C21  O06    0.00   0.0  0
 JPP  CONST_30  CA   N04  C06  O04    0.00   0.0  0
 JPP  CONST_31  CA   C21  N03  C20  180.00   0.0  0
 JPP  CONST_32  H4   N03  C21  O06  180.00   0.0  0
 JPP  Var_01    N    C10  C09  N01  -58.32  30.0  1
 JPP  Var_02    N    C14  C11  N01  -20.14  30.0  1
 JPP  Var_03    C18  C19  S    C17  -23.42  30.0  1
 JPP  Var_04    C14  N    C10  C09   41.80  30.0  1
 JPP  Var_05    C11  N01  C09  C10   37.65  30.0  1
 JPP  Var_06    C    C15  N    C10  -77.70  30.0  3
 JPP  Var_07    H13  C03  C19  S    -62.47  30.0  3
 JPP  Var_08    H10  C02  C19  S     59.55  30.0  3
 JPP  Var_09    H28  C    C15  N    179.82  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
 JPP  chir_01  C17  N02  C20  S    negativ
 JPP  chir_02  C18  N02  C19  C04  positiv
 JPP  chir_03  C20  N03  C17  C01  negativ
 JPP  chir_04  CA   N04  C05  C21  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
 JPP  plan-1  O02  0.020
 JPP  plan-1  O03  0.020
 JPP  plan-1  C18  0.020
 JPP  plan-1  C04  0.020
 JPP  plan-1  H1   0.020
 JPP  plan-2  O01  0.020
 JPP  plan-2  C20  0.020
 JPP  plan-2  C01  0.020
 JPP  plan-2  H9   0.020
 JPP  plan-3  CA   0.020
 JPP  plan-3  C05  0.020
 JPP  plan-3  C07  0.020
 JPP  plan-3  C08  0.020
 JPP  plan-3  C12  0.020
 JPP  plan-3  C13  0.020
 JPP  plan-3  C16  0.020
 JPP  plan-3  H17  0.020
 JPP  plan-3  H18  0.020
 JPP  plan-3  H23  0.020
 JPP  plan-3  H24  0.020
 JPP  plan-3  H27  0.020
 JPP  plan-4  O04  0.020
 JPP  plan-4  O05  0.020
 JPP  plan-4  N04  0.020
 JPP  plan-4  N01  0.020
 JPP  plan-4  CA   0.020
 JPP  plan-4  C09  0.020
 JPP  plan-4  C11  0.020
 JPP  plan-4  C14  0.020
 JPP  plan-4  H5   0.020
 JPP  plan-4  C06  0.020
 JPP  plan-5  O06  0.020
 JPP  plan-5  N03  0.020
 JPP  plan-5  C20  0.020
 JPP  plan-5  C21  0.020
 JPP  plan-5  CA   0.020
 JPP  plan-5  H4   0.020
 JPP  plan-6  O    0.020
 JPP  plan-6  N    0.020
 JPP  plan-6  C10  0.020
 JPP  plan-6  C11  0.020
 JPP  plan-6  C14  0.020
 JPP  plan-6  C15  0.020

