# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 07:54:38 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(2S)-2-carboxy-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: CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)[C@@H](C(O)=O)c2ccccc2)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
 CB9  CB9  '(2R,4S)-2-[(1R)-1-{[(2S)-2-carboxy-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  46  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CB9
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
 CB9  C     C  C1    0   0.184  -0.6371  -1.9126   0.2623
 CB9  N     N  NH1   0  -0.626   0.5133   0.2289   0.0744
 CB9  O     O  O     0  -0.354   0.2763  -2.4709  -0.2818
 CB9  CA    C  CH1   0  -0.210  -0.6095  -0.4467   0.6571
 CB9  CB    C  CH1   0  -0.206  -1.9183   0.2585   0.3044
 CB9  OAD   O  O     0  -0.421  -4.0165   2.3972   0.4078
 CB9  CAJ   C  CR16  0  -0.263   6.4672  -1.2804   0.0574
 CB9  CAK   C  CR16  0  -0.242   5.7006  -1.2788  -1.0987
 CB9  CAL   C  CR16  0  -0.245   6.0538  -0.5387   1.1576
 CB9  CAM   C  CR16  0  -0.297   4.5266  -0.5382  -1.1527
 CB9  CAN   C  CR16  0  -0.285   4.8792   0.1967   1.1042
 CB9  NAP   N  NH1   0  -0.561  -2.9919  -0.0980   1.1898
 CB9  SAQ   S  S2    0  -0.014  -2.4700  -0.1542  -1.4268
 CB9  CAR   C  C     0   0.573  -4.7421   1.4423   0.5158
 CB9  CAS   C  C     0   0.596   2.9298   2.3998   0.3657
 CB9  CAT   C  C     0   0.606   1.7135   0.2738   0.6798
 CB9  CAU   C  CR6   0   0.164   4.1063   0.2037  -0.0548
 CB9  CAX   C  CH1   0  -0.221  -4.2746  -0.0012   0.5346
 CB9  CAY   C  CH1   0  -0.654   2.8082   0.9683  -0.1256
 CB9  CAZ   C  CT    0  -0.207  -4.1717  -0.6073  -0.9021
 CB9  H     H  H     0   0.201  -1.5504  -2.4590   0.5533
 CB9  HN    H  HNH1  0   0.411   0.4459   0.5162  -0.8903
 CB9  HA    H  HCH1  0   0.323  -0.5033  -0.4147   1.7482
 CB9  HB    H  HCH1  0   0.309  -1.7427   1.3319   0.3339
 CB9  HOAG  H  HOH1  0   0.484  -6.3389   2.4565   0.5733
 CB9  HOAH  H  HOH1  0   0.488   3.9963   3.9384   0.1059
 CB9  HAJ   H  HCR6  0   0.259   7.3835  -1.8546   0.1027
 CB9  HAK   H  HCR6  0   0.259   6.0139  -1.8529  -1.9610
 CB9  HAL   H  HCR6  0   0.259   6.6486  -0.5346   2.0618
 CB9  HAM   H  HCR6  0   0.259   3.9333  -0.5384  -2.0593
 CB9  HAN   H  HCR6  0   0.252   4.5739   0.7676   1.9723
 CB9  HNAP  H  HNH1  0   0.381  -2.8776  -1.0246   1.5791
 CB9  HAX   H  HCH1  0   0.315  -4.9989  -0.5866   1.1051
 CB9  HAY   H  HCH1  0   0.335   2.5109   1.0378  -1.1780
 CB9  CAA   C  CH3   0  -0.629  -4.3171  -2.1235  -0.8146
 CB9  CAB   C  CH3   0  -0.649  -5.1729  -0.0525  -1.9087
 CB9  OAE   O  O     0  -0.422   2.1721   2.9141   1.1462
 CB9  OAF   O  O     0  -0.460   1.9222  -0.1738   1.7904
 CB9  OAG   O  OH1   0  -0.587  -6.0590   1.5295   0.6287
 CB9  OAH   O  OH1   0  -0.579   3.9516   3.0190  -0.1990
 CB9  HAA   H  HCH3  0   0.252  -4.0664  -2.5929  -1.7653
 CB9  HAAA  H  HCH3  0   0.233  -3.6720  -2.5580  -0.0508
 CB9  HAAB  H  HCH3  0   0.245  -5.3476  -2.3870  -0.5667
 CB9  HAB   H  HCH3  0   0.248  -6.1937  -0.2654  -1.5880
 CB9  HABA  H  HCH3  0   0.245  -5.0682   1.0222  -2.0551
 CB9  HABB  H  HCH3  0   0.254  -5.0310  -0.5289  -2.8789

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
 CB9  C    O     double    1.201  0.020  1.201
 CB9  C    CA    single    1.518  0.020  1.518
 CB9  N    CA    single    1.434  0.020  1.434
 CB9  N    CAT   single    1.345  0.020  1.345
 CB9  CA   CB    single    1.528  0.020  1.528
 CB9  CB   NAP   single    1.437  0.020  1.437
 CB9  CB   SAQ   single    1.863  0.020  1.863
 CB9  CAA  CAZ   single    1.526  0.020  1.526
 CB9  CAB  CAZ   single    1.524  0.020  1.524
 CB9  OAD  CAR   double    1.204  0.020  1.204
 CB9  OAE  CAS   double    1.203  0.020  1.203
 CB9  OAF  CAT   double    1.216  0.020  1.216
 CB9  OAG  CAR   single    1.325  0.020  1.325
 CB9  OAH  CAS   single    1.322  0.020  1.322
 CB9  CAJ  CAK   aromatic  1.387  0.020  1.387
 CB9  CAJ  CAL   aromatic  1.390  0.020  1.390
 CB9  CAK  CAM   aromatic  1.389  0.020  1.389
 CB9  CAL  CAN   aromatic  1.387  0.020  1.387
 CB9  CAM  CAU   aromatic  1.390  0.020  1.390
 CB9  CAN  CAU   aromatic  1.393  0.020  1.393
 CB9  NAP  CAX   single    1.444  0.020  1.444
 CB9  SAQ  CAZ   single    1.838  0.020  1.838
 CB9  CAR  CAX   single    1.517  0.020  1.517
 CB9  CAS  CAY   single    1.518  0.020  1.518
 CB9  CAT  CAY   single    1.526  0.020  1.526
 CB9  CAU  CAY   single    1.508  0.020  1.508
 CB9  CAX  CAZ   single    1.563  0.020  1.563
 CB9  C    H     single    0.930  0.020  1.080
 CB9  N    HN    single    0.860  0.020  1.020
 CB9  CA   HA    single    0.970  0.020  1.090
 CB9  CB   HB    single    0.970  0.020  1.090
 CB9  CAA  HAA   single    0.970  0.020  1.090
 CB9  CAA  HAAA  single    0.970  0.020  1.090
 CB9  CAA  HAAB  single    0.970  0.020  1.090
 CB9  CAB  HAB   single    0.970  0.020  1.090
 CB9  CAB  HABA  single    0.970  0.020  1.090
 CB9  CAB  HABB  single    0.970  0.020  1.090
 CB9  OAG  HOAG  single    0.850  0.020  0.980
 CB9  OAH  HOAH  single    0.850  0.020  0.980
 CB9  CAJ  HAJ   single    0.930  0.020  1.080
 CB9  CAK  HAK   single    0.930  0.020  1.080
 CB9  CAL  HAL   single    0.930  0.020  1.080
 CB9  CAM  HAM   single    0.930  0.020  1.080
 CB9  CAN  HAN   single    0.930  0.020  1.080
 CB9  NAP  HNAP  single    0.890  0.020  1.040
 CB9  CAX  HAX   single    0.970  0.020  1.090
 CB9  CAY  HAY   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
 CB9  H     C    CA    115.12  3.000
 CB9  H     C    O     121.26  3.000
 CB9  CA    C    O     123.56  3.000
 CB9  HN    N    CAT   118.72  3.000
 CB9  HN    N    CA    118.06  3.000
 CB9  CAT   N    CA    122.11  3.000
 CB9  HA    CA   CB    107.41  3.000
 CB9  HA    CA   N     108.34  3.000
 CB9  CB    CA   N     111.06  3.000
 CB9  HA    CA   C     106.78  3.000
 CB9  CB    CA   C     111.72  3.000
 CB9  N     CA   C     111.30  3.000
 CB9  HB    CB   SAQ   106.95  3.000
 CB9  HB    CB   NAP   110.41  3.000
 CB9  SAQ   CB   NAP   107.24  3.000
 CB9  HB    CB   CA    108.10  3.000
 CB9  SAQ   CB   CA    111.46  3.000
 CB9  NAP   CB   CA    112.54  3.000
 CB9  HAJ   CAJ  CAL   120.12  3.000
 CB9  HAJ   CAJ  CAK   120.22  3.000
 CB9  CAL   CAJ  CAK   119.66  3.000
 CB9  HAK   CAK  CAM   119.77  3.000
 CB9  HAK   CAK  CAJ   120.23  3.000
 CB9  CAM   CAK  CAJ   120.00  3.000
 CB9  HAL   CAL  CAN   119.71  3.000
 CB9  HAL   CAL  CAJ   119.99  3.000
 CB9  CAN   CAL  CAJ   120.30  3.000
 CB9  HAM   CAM  CAU   119.70  3.000
 CB9  HAM   CAM  CAK   119.68  3.000
 CB9  CAU   CAM  CAK   120.62  3.000
 CB9  HAN   CAN  CAU   120.52  3.000
 CB9  HAN   CAN  CAL   119.17  3.000
 CB9  CAU   CAN  CAL   120.31  3.000
 CB9  HNAP  NAP  CAX   109.67  3.000
 CB9  HNAP  NAP  CB    112.34  3.000
 CB9  CAX   NAP  CB    111.57  3.000
 CB9  CAZ   SAQ  CB     93.64  3.000
 CB9  CAX   CAR  OAG   111.59  3.000
 CB9  CAX   CAR  OAD   124.74  3.000
 CB9  OAG   CAR  OAD   123.67  3.000
 CB9  CAY   CAS  OAH   111.43  3.000
 CB9  CAY   CAS  OAE   124.23  3.000
 CB9  OAH   CAS  OAE   124.32  3.000
 CB9  CAY   CAT  OAF   121.78  3.000
 CB9  CAY   CAT  N     114.69  3.000
 CB9  OAF   CAT  N     123.52  3.000
 CB9  CAY   CAU  CAN   121.28  3.000
 CB9  CAY   CAU  CAM   119.58  3.000
 CB9  CAN   CAU  CAM   119.12  3.000
 CB9  HAX   CAX  CAZ   108.42  3.000
 CB9  HAX   CAX  CAR   108.18  3.000
 CB9  CAZ   CAX  CAR   112.20  3.000
 CB9  HAX   CAX  NAP   108.43  3.000
 CB9  CAZ   CAX  NAP   109.44  3.000
 CB9  CAR   CAX  NAP   110.07  3.000
 CB9  HAY   CAY  CAU   108.10  3.000
 CB9  HAY   CAY  CAT   109.94  3.000
 CB9  CAU   CAY  CAT   111.21  3.000
 CB9  HAY   CAY  CAS   105.83  3.000
 CB9  CAU   CAY  CAS   113.19  3.000
 CB9  CAT   CAY  CAS   108.40  3.000
 CB9  CAX   CAZ  SAQ   103.17  3.000
 CB9  CAX   CAZ  CAB   115.01  3.000
 CB9  SAQ   CAZ  CAB   109.26  3.000
 CB9  CAX   CAZ  CAA   109.06  3.000
 CB9  SAQ   CAZ  CAA   110.47  3.000
 CB9  CAB   CAZ  CAA   109.69  3.000
 CB9  HAAB  CAA  HAAA  107.64  3.000
 CB9  HAAB  CAA  HAA   108.14  3.000
 CB9  HAAA  CAA  HAA   107.67  3.000
 CB9  HAAB  CAA  CAZ   110.04  3.000
 CB9  HAAA  CAA  CAZ   112.33  3.000
 CB9  HAA   CAA  CAZ   110.87  3.000
 CB9  HABB  CAB  HABA  107.39  3.000
 CB9  HABB  CAB  HAB   107.34  3.000
 CB9  HABA  CAB  HAB   108.77  3.000
 CB9  HABB  CAB  CAZ   110.08  3.000
 CB9  HABA  CAB  CAZ   112.62  3.000
 CB9  HAB   CAB  CAZ   110.45  3.000
 CB9  HOAG  OAG  CAR   110.18  3.000
 CB9  HOAH  OAH  CAS   110.21  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
 CB9  CONST_01  CAU   CAM  CAK  CAJ     0.00   0.0  0
 CB9  CONST_02  CAU   CAN  CAL  CAJ     0.00   0.0  0
 CB9  CONST_03  CAN   CAL  CAJ  CAK     0.00   0.0  0
 CB9  CONST_04  CAN   CAU  CAM  CAK     0.00   0.0  0
 CB9  CONST_05  CAM   CAK  CAJ  CAL     0.00   0.0  0
 CB9  CONST_06  CAM   CAU  CAN  CAL     0.00   0.0  0
 CB9  CONST_07  CAY   CAU  CAM  CAK   180.00   0.0  0
 CB9  CONST_08  CAY   CAU  CAN  CAL   180.00   0.0  0
 CB9  CONST_09  HAM   CAM  CAK  CAJ   180.00   0.0  0
 CB9  CONST_10  HAN   CAN  CAL  CAJ   180.00   0.0  0
 CB9  CONST_11  HAL   CAL  CAJ  CAK   180.00   0.0  0
 CB9  CONST_12  HAK   CAK  CAJ  CAL   180.00   0.0  0
 CB9  CONST_13  HAJ   CAJ  CAK  CAM   180.00   0.0  0
 CB9  CONST_14  HOAG  OAG  CAR  CAX   180.00   0.0  0
 CB9  CONST_15  OAF   CAT  N    CA      0.00   0.0  0
 CB9  CONST_16  CAY   CAT  N    CA    180.00   0.0  0
 CB9  CONST_17  HN    N    CAT  OAF   180.00   0.0  0
 CB9  CONST_18  HOAH  OAH  CAS  OAE     0.00   0.0  0
 CB9  Var_01    CAX   CAZ  SAQ  CB     15.79  30.0  1
 CB9  Var_02    HAA   CAA  CAZ  SAQ   -56.70  30.0  3
 CB9  Var_03    HAB   CAB  CAZ  SAQ  -177.03  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
 CB9  chir_01  CA   C    N    CB   negativ
 CB9  chir_02  CB   SAQ  NAP  CA   negativ
 CB9  chir_03  CAX  NAP  CAR  CAZ  negativ
 CB9  chir_04  CAY  CAS  CAT  CAU  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
 CB9  plan-1  CAJ   0.020
 CB9  plan-1  CAK   0.020
 CB9  plan-1  CAL   0.020
 CB9  plan-1  CAM   0.020
 CB9  plan-1  CAN   0.020
 CB9  plan-1  CAU   0.020
 CB9  plan-1  CAY   0.020
 CB9  plan-1  HAJ   0.020
 CB9  plan-1  HAK   0.020
 CB9  plan-1  HAL   0.020
 CB9  plan-1  HAM   0.020
 CB9  plan-1  HAN   0.020
 CB9  plan-2  N     0.020
 CB9  plan-2  CA    0.020
 CB9  plan-2  CAT   0.020
 CB9  plan-2  CAY   0.020
 CB9  plan-2  HN    0.020
 CB9  plan-2  OAF   0.020
 CB9  plan-3  OAD   0.020
 CB9  plan-3  CAR   0.020
 CB9  plan-3  CAX   0.020
 CB9  plan-3  HOAG  0.020
 CB9  plan-3  OAG   0.020
 CB9  plan-4  CAS   0.020
 CB9  plan-4  CAY   0.020
 CB9  plan-4  HOAH  0.020
 CB9  plan-4  OAE   0.020
 CB9  plan-4  OAH   0.020
 CB9  plan-5  C     0.020
 CB9  plan-5  O     0.020
 CB9  plan-5  CA    0.020
 CB9  plan-5  H     0.020

