# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 13:32:23 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(6S)-6-amino-6-carboxyhexanoyl]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](N)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
 HJ3  HJ3  '(2R,4S)-2-[(1R)-1-{[(6S)-6-amino-6-carboxyhexanoyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  50  25  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_HJ3
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
 HJ3  O11   O  O     0  -0.490   0.9169  -0.7519   2.0140
 HJ3  C10   C  C     0   0.575   0.8203  -0.6659   0.8004
 HJ3  CA1   C  CH2   0  -0.588   2.0121  -0.7407  -0.1252
 HJ3  CB1   C  CH2   0  -0.417   3.2744  -0.1338   0.4717
 HJ3  N9    N  NH1   0  -0.642  -0.3698  -0.4916   0.1820
 HJ3  C6    C  CH1   0  -0.203  -1.6149  -0.5705   0.8871
 HJ3  C7    C  C1    0   0.184  -2.0607  -2.0084   1.0808
 HJ3  O8    O  O     0  -0.357  -1.3626  -2.9596   0.8571
 HJ3  C5    C  CH1   0  -0.212  -2.6905   0.2569   0.1846
 HJ3  S1    S  S2    0  -0.014  -3.3568  -0.6304  -1.3126
 HJ3  N4    N  NH1   0  -0.560  -3.8088   0.5547   1.0366
 HJ3  C3    C  CH1   0  -0.220  -5.0251   0.7209   0.2755
 HJ3  C12   C  C     0   0.572  -5.0844   2.1173  -0.3150
 HJ3  O14   O  OH1   0  -0.587  -6.3239   2.5843  -0.3389
 HJ3  O13   O  O     0  -0.422  -4.1315   2.7328  -0.7190
 HJ3  C2    C  CT    0  -0.210  -5.1107  -0.3871  -0.8222
 HJ3  C16   C  CH3   0  -0.627  -5.6715  -1.6662  -0.2080
 HJ3  C15   C  CH3   0  -0.649  -5.9309  -0.0101  -2.0510
 HJ3  HA1   H  HCH2  0   0.273   2.1810  -1.7996  -0.3503
 HJ3  HA1A  H  HCH2  0   0.253   1.7791  -0.2627  -1.0802
 HJ3  C121  C  CH2   0  -0.412   4.4497  -0.2082  -0.4947
 HJ3  HB1   H  HCH2  0   0.225   3.0857   0.9103   0.7384
 HJ3  HB1A  H  HCH2  0   0.227   3.5319  -0.6500   1.3994
 HJ3  HN9   H  HNH1  0   0.403  -0.3908  -0.5318  -0.8258
 HJ3  H6    H  HCH1  0   0.317  -1.4746  -0.1427   1.8881
 HJ3  H7    H  H     0   0.196  -3.0777  -2.1330   1.4900
 HJ3  H5    H  HCH1  0   0.308  -2.2295   1.1769  -0.1702
 HJ3  HN4   H  HNH1  0   0.380  -3.9519  -0.1538   1.7440
 HJ3  H3    H  HCH1  0   0.314  -5.8722   0.6022   0.9540
 HJ3  HO14  H  HOH1  0   0.484  -6.3435   3.4580  -0.7591
 HJ3  H16   H  HCH3  0   0.232  -5.1409  -1.9625   0.6965
 HJ3  H16A  H  HCH3  0   0.244  -6.7229  -1.5284   0.0534
 HJ3  H16B  H  HCH3  0   0.252  -5.6050  -2.4932  -0.9143
 HJ3  H15   H  HCH3  0   0.254  -5.9441  -0.8372  -2.7607
 HJ3  H15A  H  HCH3  0   0.248  -6.9653   0.1950  -1.7714
 HJ3  H15B  H  HCH3  0   0.245  -5.5307   0.8588  -2.5725
 HJ3  C13   C  CH2   0  -0.431   5.7123   0.4083   0.0913
 HJ3  H18   H  HCH2  0   0.226   4.6417  -1.2487  -0.7649
 HJ3  H19   H  HCH2  0   0.215   4.1931   0.3109  -1.4246
 HJ3  H20   H  HCH2  0   0.240   5.5141   1.4493   0.3574
 HJ3  H21   H  HCH2  0   0.229   5.9784  -0.1046   1.0224
 HJ3  C14   C  CH1   0  -0.207   6.9076   0.3456  -0.8703
 HJ3  N3    N  NH2   0  -0.776   7.2451  -1.0240  -1.1749
 HJ3  H22   H  HCH1  0   0.265   6.6160   0.8426  -1.8017
 HJ3  C151  C  C     0   0.520   8.0648   1.1374  -0.2757
 HJ3  O6    O  O     0  -0.442   9.0500   0.6460   0.2166
 HJ3  H23   H  HOH1  0   0.480   8.6005   2.9222   0.0696
 HJ3  H24   H  HNH2  0   0.353   7.9960  -1.0628  -1.8519
 HJ3  H25   H  HNH2  0   0.343   7.5863  -1.4928  -0.3442
 HJ3  O5    O  OH1   0  -0.594   7.8626   2.4489  -0.3434

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
 HJ3  O11   C10   double  1.220  0.020  1.220
 HJ3  C10   CA1   single  1.511  0.020  1.511
 HJ3  CA1   CB1   single  1.523  0.020  1.523
 HJ3  CA1   HA1   single  0.970  0.020  1.090
 HJ3  CA1   HA1A  single  0.970  0.020  1.090
 HJ3  CB1   C121  single  1.523  0.020  1.523
 HJ3  CB1   HB1   single  0.970  0.020  1.090
 HJ3  CB1   HB1A  single  0.970  0.020  1.090
 HJ3  N9    C10   single  1.352  0.020  1.352
 HJ3  N9    HN9   single  0.890  0.020  1.040
 HJ3  C6    N9    single  1.433  0.020  1.433
 HJ3  C6    C5    single  1.528  0.020  1.528
 HJ3  C6    H6    single  0.970  0.020  1.090
 HJ3  C7    C6    single  1.518  0.020  1.518
 HJ3  C7    O8    double  1.201  0.020  1.201
 HJ3  C7    H7    single  0.930  0.020  1.080
 HJ3  C5    S1    single  1.864  0.020  1.864
 HJ3  C5    H5    single  0.970  0.020  1.090
 HJ3  S1    C2    single  1.837  0.020  1.837
 HJ3  N4    C5    single  1.437  0.020  1.437
 HJ3  N4    C3    single  1.444  0.020  1.444
 HJ3  N4    HN4   single  0.890  0.020  1.040
 HJ3  C3    C2    single  1.562  0.020  1.562
 HJ3  C3    H3    single  0.970  0.020  1.090
 HJ3  C12   C3    single  1.517  0.020  1.517
 HJ3  C12   O14   single  1.325  0.020  1.325
 HJ3  O14   HO14  single  0.850  0.020  0.980
 HJ3  O13   C12   double  1.204  0.020  1.204
 HJ3  C2    C15   single  1.525  0.020  1.525
 HJ3  C2    C16   single  1.526  0.020  1.526
 HJ3  C16   H16   single  0.970  0.020  1.090
 HJ3  C16   H16A  single  0.970  0.020  1.090
 HJ3  C16   H16B  single  0.970  0.020  1.090
 HJ3  C15   H15   single  0.970  0.020  1.090
 HJ3  C15   H15A  single  0.970  0.020  1.090
 HJ3  C15   H15B  single  0.970  0.020  1.090
 HJ3  C121  C13   single  1.522  0.020  1.522
 HJ3  C121  H18   single  0.970  0.020  1.090
 HJ3  C121  H19   single  0.970  0.020  1.090
 HJ3  C13   H20   single  0.970  0.020  1.090
 HJ3  C13   H21   single  0.970  0.020  1.090
 HJ3  C13   C14   single  1.535  0.020  1.535
 HJ3  C14   C151  single  1.523  0.020  1.523
 HJ3  C14   N3    single  1.443  0.020  1.443
 HJ3  C14   H22   single  0.970  0.020  1.090
 HJ3  O5    C151  single  1.329  0.020  1.329
 HJ3  C151  O6    double  1.206  0.020  1.206
 HJ3  O5    H23   single  0.850  0.020  0.980
 HJ3  N3    H24   single  0.890  0.020  1.040
 HJ3  N3    H25   single  0.890  0.020  1.040

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
 HJ3  N9    C10   CA1   114.86  3.000
 HJ3  N9    C10   O11   122.24  3.000
 HJ3  CA1   C10   O11   122.90  3.000
 HJ3  HA1A  CA1   HA1   106.02  3.000
 HJ3  HA1A  CA1   CB1   110.18  3.000
 HJ3  HA1   CA1   CB1   109.76  3.000
 HJ3  HA1A  CA1   C10   110.21  3.000
 HJ3  HA1   CA1   C10   107.18  3.000
 HJ3  CB1   CA1   C10   113.21  3.000
 HJ3  HB1A  CB1   HB1   106.54  3.000
 HJ3  HB1A  CB1   C121  109.50  3.000
 HJ3  HB1   CB1   C121  109.53  3.000
 HJ3  HB1A  CB1   CA1   109.87  3.000
 HJ3  HB1   CB1   CA1   109.45  3.000
 HJ3  C121  CB1   CA1   111.80  3.000
 HJ3  HN9   N9    C6    118.11  3.000
 HJ3  C6    N9    C10   122.17  3.000
 HJ3  HN9   N9    C10   118.03  3.000
 HJ3  H6    C6    C5    107.35  3.000
 HJ3  H6    C6    C7    106.88  3.000
 HJ3  C5    C6    C7    111.40  3.000
 HJ3  C7    C6    N9    111.72  3.000
 HJ3  H6    C6    N9    108.44  3.000
 HJ3  C5    C6    N9    110.83  3.000
 HJ3  H7    C7    O8    121.03  3.000
 HJ3  H7    C7    C6    115.15  3.000
 HJ3  O8    C7    C6    123.77  3.000
 HJ3  H5    C5    N4    110.34  3.000
 HJ3  N4    C5    S1    107.26  3.000
 HJ3  H5    C5    S1    106.98  3.000
 HJ3  N4    C5    C6    112.79  3.000
 HJ3  H5    C5    C6    108.02  3.000
 HJ3  S1    C5    C6    111.30  3.000
 HJ3  C2    S1    C5     93.66  3.000
 HJ3  HN4   N4    C3    109.27  3.000
 HJ3  HN4   N4    C5    112.31  3.000
 HJ3  C3    N4    C5    111.52  3.000
 HJ3  H3    C3    C2    108.48  3.000
 HJ3  H3    C3    C12   108.16  3.000
 HJ3  C2    C3    C12   112.16  3.000
 HJ3  C12   C3    N4    110.11  3.000
 HJ3  H3    C3    N4    108.27  3.000
 HJ3  C2    C3    N4    109.56  3.000
 HJ3  O13   C12   O14   123.66  3.000
 HJ3  O13   C12   C3    124.75  3.000
 HJ3  O14   C12   C3    111.59  3.000
 HJ3  HO14  O14   C12   110.14  3.000
 HJ3  C15   C2    C16   109.51  3.000
 HJ3  C16   C2    C3    109.39  3.000
 HJ3  C15   C2    C3    114.87  3.000
 HJ3  C16   C2    S1    110.32  3.000
 HJ3  C15   C2    S1    109.34  3.000
 HJ3  C3    C2    S1    103.25  3.000
 HJ3  H16B  C16   H16A  108.04  3.000
 HJ3  H16B  C16   H16   107.58  3.000
 HJ3  H16A  C16   H16   107.72  3.000
 HJ3  H16B  C16   C2    110.67  3.000
 HJ3  H16A  C16   C2    110.15  3.000
 HJ3  H16   C16   C2    112.53  3.000
 HJ3  H15B  C15   H15A  108.72  3.000
 HJ3  H15B  C15   H15   107.33  3.000
 HJ3  H15A  C15   H15   107.34  3.000
 HJ3  H15B  C15   C2    112.66  3.000
 HJ3  H15A  C15   C2    110.49  3.000
 HJ3  H15   C15   C2    110.10  3.000
 HJ3  H19   C121  H18   106.42  3.000
 HJ3  H19   C121  C13   109.22  3.000
 HJ3  H18   C121  C13   109.60  3.000
 HJ3  H19   C121  CB1   109.55  3.000
 HJ3  H18   C121  CB1   109.82  3.000
 HJ3  C13   C121  CB1   112.07  3.000
 HJ3  C14   C13   H21   108.90  3.000
 HJ3  C14   C13   H20   109.43  3.000
 HJ3  H21   C13   H20   106.45  3.000
 HJ3  C14   C13   C121  112.83  3.000
 HJ3  H21   C13   C121  109.81  3.000
 HJ3  H20   C13   C121  109.21  3.000
 HJ3  C151  C14   H22   107.36  3.000
 HJ3  H22   C14   N3    108.27  3.000
 HJ3  C151  C14   N3    113.46  3.000
 HJ3  H22   C14   C13   107.87  3.000
 HJ3  N3    C14   C13   110.67  3.000
 HJ3  C151  C14   C13   109.01  3.000
 HJ3  H25   N3    H24   106.32  3.000
 HJ3  H25   N3    C14   110.18  3.000
 HJ3  H24   N3    C14   110.56  3.000
 HJ3  O6    C151  O5    123.18  3.000
 HJ3  O6    C151  C14   124.63  3.000
 HJ3  O5    C151  C14   112.19  3.000
 HJ3  H23   O5    C151  110.16  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
 HJ3  CONST_01  HO14  O14   C12   C3    180.00   0.0  0
 HJ3  CONST_02  C6    N9    C10   O11     0.00   0.0  0
 HJ3  CONST_03  C6    N9    C10   CA1   180.00   0.0  0
 HJ3  CONST_04  HN9   N9    C10   O11   180.00   0.0  0
 HJ3  CONST_05  H23   O5    C151  C14   180.00   0.0  0
 HJ3  Var_01    C3    C2    S1    C5     15.39  30.0  1
 HJ3  Var_02    H15   C15   C2    S1     64.85  30.0  3
 HJ3  Var_03    H16   C16   C2    S1     61.58  30.0  3
 HJ3  Var_04    CB1   CA1   C10   O11   -33.77  30.0  3
 HJ3  Var_05    C121  CB1   CA1   C10  -179.18  30.0  3
 HJ3  Var_06    C13   C121  CB1   CA1   179.49  30.0  3
 HJ3  Var_07    C14   C13   C121  CB1  -179.86  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
 HJ3  chir_01  C6   N9   C5    C7   negativ
 HJ3  chir_02  C5   S1   N4    C6   negativ
 HJ3  chir_03  C3   N4   C2    C12  positiv
 HJ3  chir_04  C14  C13  C151  N3   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
 HJ3  plan-1  O11   0.020
 HJ3  plan-1  C10   0.020
 HJ3  plan-1  CA1   0.020
 HJ3  plan-1  N9    0.020
 HJ3  plan-1  C6    0.020
 HJ3  plan-1  HN9   0.020
 HJ3  plan-2  C3    0.020
 HJ3  plan-2  C12   0.020
 HJ3  plan-2  O14   0.020
 HJ3  plan-2  O13   0.020
 HJ3  plan-2  HO14  0.020
 HJ3  plan-3  C14   0.020
 HJ3  plan-3  C151  0.020
 HJ3  plan-3  O6    0.020
 HJ3  plan-3  H23   0.020
 HJ3  plan-3  O5    0.020
 HJ3  plan-4  C6    0.020
 HJ3  plan-4  C7    0.020
 HJ3  plan-4  O8    0.020
 HJ3  plan-4  H7    0.020

