# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 02:07:09 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  44  26  .  2021-08-07  2021-08-07  
;
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   0.183  -0.6792  -2.0240   0.2757
 CB9  N     N  NH1    0  -0.634   0.4885   0.1132   0.1309
 CB9  O     O  O      0  -0.361   0.2101  -2.5811  -0.3096
 CB9  CA    C  CH1    0  -0.194  -0.6343  -0.5684   0.7026
 CB9  CB    C  CR15   0  -0.209  -1.9360   0.1532   0.3631
 CB9  CAJ   C  C1     0  -0.273   6.6439  -1.0661   0.2843
 CB9  CAK   C  C1     0  -0.244   5.9414  -1.1597  -0.9081
 CB9  CAL   C  C1     0  -0.248   6.0934  -0.3607   1.3487
 CB9  CAM   C  C1     0  -0.319   4.6962  -0.5539  -1.0311
 CB9  CAN   C  C1     0  -0.289   4.8501   0.2406   1.2219
 CB9  NAP   N  NR15   0  -0.560  -3.0420  -0.2537   1.1771
 CB9  SAQ   S  S2     0  -0.052  -2.4184  -0.1614  -1.4116
 CB9  CAR   C  C      0   0.436  -4.7408   1.4827   0.6119
 CB9  CAS   C  C      0   0.455   2.8320   2.2969   0.3199
 CB9  CAT   C  C      0   0.611   1.7247   0.0536   0.6702
 CB9  CAU   C  C      0   0.184   4.1347   0.1522   0.0280
 CB9  CAX   C  CR15   0  -0.212  -4.3012   0.0069   0.4973
 CB9  CAY   C  CH1    0  -0.656   2.7838   0.7958  -0.1163
 CB9  CAZ   C  CR5    0  -0.199  -4.1784  -0.4796  -0.9838
 CB9  H     H  H      0   0.190  -1.5859  -2.5754   0.5829
 CB9  HN    H  HNH1   0   0.398   0.3788   0.5299  -0.7802
 CB9  HA    H  HCH1   0   0.307  -0.5356  -0.5622   1.7958
 CB9  HB    H  HCR5   0   0.297  -1.7820   1.2238   0.4649
 CB9  HAJ   H  H      0   0.251   7.6138  -1.5358   0.3859
 CB9  HAK   H  H      0   0.251   6.3596  -1.7047  -1.7449
 CB9  HAL   H  H      0   0.250   6.6364  -0.2801   2.2820
 CB9  HAM   H  H      0   0.246   4.1543  -0.6300  -1.9669
 CB9  HAN   H  H      0   0.241   4.4373   0.7922   2.0572
 CB9  HNAP  H  HNR5   0   0.355  -2.9858  -1.2406   1.3969
 CB9  HAX   H  HCR5   0   0.250  -5.0681  -0.6052   0.9790
 CB9  HAY   H  HCH1   0   0.269   2.5158   0.7773  -1.1778
 CB9  CAA   C  CH3    0  -0.624  -4.4550  -1.9795  -1.0608
 CB9  CAB   C  CH3    0  -0.635  -5.0807   0.2576  -1.9653
 CB9  OAF   O  O      0  -0.488   1.9481  -0.5338   1.7160
 CB9  OAG   O  OC    -1  -0.612  -5.9702   1.6698   0.6913
 CB9  OAH   O  OC    -1  -0.590   3.5796   3.0165  -0.3603
 CB9  HAA   H  HCH3   0   0.238  -4.2333  -2.3734  -2.0532
 CB9  HAAA  H  HCH3   0   0.224  -3.8587  -2.5431  -0.3422
 CB9  HAAB  H  HCH3   0   0.232  -5.5083  -2.1772  -0.8475
 CB9  HAB   H  HCH3   0   0.233  -6.1274   0.1292  -1.6868
 CB9  HABA  H  HCH3   0   0.238  -4.8624   1.3238  -1.9968
 CB9  HABB  H  HCH3   0   0.233  -4.9545  -0.1395  -2.9734
 CB9  OAE   O  O      0  -0.584   2.1336   2.6209   1.2945
 CB9  OAD   O  O      0  -0.585  -3.8531   2.3562   0.6055

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    1.202  0.020  1.202
 CB9  C    CA    single    1.518  0.020  1.518
 CB9  N    CA    single    1.433  0.020  1.433
 CB9  N    CAT   single    1.350  0.020  1.350
 CB9  CA   CB    single    1.527  0.020  1.527
 CB9  CB   NAP   single    1.432  0.020  1.432
 CB9  CB   SAQ   single    1.866  0.020  1.866
 CB9  CAA  CAZ   single    1.527  0.020  1.527
 CB9  CAB  CAZ   single    1.523  0.020  1.523
 CB9  OAD  CAR   deloc     1.245  0.020  1.245
 CB9  OAE  CAS   deloc     1.242  0.020  1.242
 CB9  OAF  CAT   double    1.220  0.020  1.220
 CB9  OAG  CAR   deloc     1.246  0.020  1.246
 CB9  OAH  CAS   deloc     1.241  0.020  1.241
 CB9  CAJ  CAK   aromatic  1.387  0.020  1.387
 CB9  CAJ  CAL   aromatic  1.391  0.020  1.391
 CB9  CAK  CAM   aromatic  1.390  0.020  1.390
 CB9  CAL  CAN   aromatic  1.387  0.020  1.387
 CB9  CAM  CAU   aromatic  1.391  0.020  1.391
 CB9  CAN  CAU   aromatic  1.395  0.020  1.395
 CB9  NAP  CAX   single    1.455  0.020  1.455
 CB9  SAQ  CAZ   single    1.839  0.020  1.839
 CB9  CAR  CAX   single    1.544  0.020  1.544
 CB9  CAS  CAY   single    1.564  0.020  1.564
 CB9  CAT  CAY   single    1.514  0.020  1.514
 CB9  CAU  CAY   single    1.503  0.020  1.503
 CB9  CAX  CAZ   single    1.564  0.020  1.564
 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  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    115.14  3.000
 CB9  H     C    O     120.76  3.000
 CB9  CA    C    O     124.04  3.000
 CB9  HN    N    CAT   118.62  3.000
 CB9  HN    N    CA    118.18  3.000
 CB9  CAT   N    CA    122.50  3.000
 CB9  HA    CA   CB    107.19  3.000
 CB9  HA    CA   N     108.92  3.000
 CB9  CB    CA   N     110.77  3.000
 CB9  HA    CA   C     106.75  3.000
 CB9  CB    CA   C     111.45  3.000
 CB9  N     CA   C     111.55  3.000
 CB9  HB    CB   SAQ   106.98  3.000
 CB9  HB    CB   NAP   109.64  3.000
 CB9  SAQ   CB   NAP   107.04  3.000
 CB9  HB    CB   CA    108.92  3.000
 CB9  SAQ   CB   CA    110.63  3.000
 CB9  NAP   CB   CA    113.43  3.000
 CB9  HAJ   CAJ  CAL   120.20  3.000
 CB9  HAJ   CAJ  CAK   120.34  3.000
 CB9  CAL   CAJ  CAK   119.46  3.000
 CB9  HAK   CAK  CAM   119.80  3.000
 CB9  HAK   CAK  CAJ   120.18  3.000
 CB9  CAM   CAK  CAJ   120.01  3.000
 CB9  HAL   CAL  CAN   119.74  3.000
 CB9  HAL   CAL  CAJ   119.93  3.000
 CB9  CAN   CAL  CAJ   120.32  3.000
 CB9  HAM   CAM  CAU   119.41  3.000
 CB9  HAM   CAM  CAK   119.57  3.000
 CB9  CAU   CAM  CAK   121.02  3.000
 CB9  HAN   CAN  CAU   119.81  3.000
 CB9  HAN   CAN  CAL   119.48  3.000
 CB9  CAU   CAN  CAL   120.70  3.000
 CB9  HNAP  NAP  CAX   108.91  3.000
 CB9  HNAP  NAP  CB    110.94  3.000
 CB9  CAX   NAP  CB    110.61  3.000
 CB9  CAZ   SAQ  CB     93.18  3.000
 CB9  CAX   CAR  OAG   115.41  3.000
 CB9  CAX   CAR  OAD   117.84  3.000
 CB9  OAG   CAR  OAD   126.74  3.000
 CB9  CAY   CAS  OAH   114.98  3.000
 CB9  CAY   CAS  OAE   116.87  3.000
 CB9  OAH   CAS  OAE   128.15  3.000
 CB9  CAY   CAT  OAF   123.59  3.000
 CB9  CAY   CAT  N     114.30  3.000
 CB9  OAF   CAT  N     122.10  3.000
 CB9  CAY   CAU  CAN   121.06  3.000
 CB9  CAY   CAU  CAM   120.45  3.000
 CB9  CAN   CAU  CAM   118.48  3.000
 CB9  HAX   CAX  CAZ   107.36  3.000
 CB9  HAX   CAX  CAR   107.62  3.000
 CB9  CAZ   CAX  CAR   112.95  3.000
 CB9  HAX   CAX  NAP   107.52  3.000
 CB9  CAZ   CAX  NAP   108.60  3.000
 CB9  CAR   CAX  NAP   112.52  3.000
 CB9  HAY   CAY  CAU   107.81  3.000
 CB9  HAY   CAY  CAT   108.91  3.000
 CB9  CAU   CAY  CAT   111.65  3.000
 CB9  HAY   CAY  CAS   107.11  3.000
 CB9  CAU   CAY  CAS   110.88  3.000
 CB9  CAT   CAY  CAS   110.32  3.000
 CB9  CAX   CAZ  SAQ   103.98  3.000
 CB9  CAX   CAZ  CAB   114.40  3.000
 CB9  SAQ   CAZ  CAB   109.47  3.000
 CB9  CAX   CAZ  CAA   109.82  3.000
 CB9  SAQ   CAZ  CAA   109.36  3.000
 CB9  CAB   CAZ  CAA   109.61  3.000
 CB9  HAAB  CAA  HAAA  107.76  3.000
 CB9  HAAB  CAA  HAA   107.96  3.000
 CB9  HAAA  CAA  HAA   107.57  3.000
 CB9  HAAB  CAA  CAZ   110.02  3.000
 CB9  HAAA  CAA  CAZ   112.04  3.000
 CB9  HAA   CAA  CAZ   111.33  3.000
 CB9  HABB  CAB  HABA  107.85  3.000
 CB9  HABB  CAB  HAB   107.71  3.000
 CB9  HABA  CAB  HAB   108.37  3.000
 CB9  HABB  CAB  CAZ   110.53  3.000
 CB9  HABA  CAB  CAZ   111.95  3.000
 CB9  HAB   CAB  CAZ   110.30  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  OAF  CAT  N    CA      0.00   0.0  0
 CB9  CONST_15  CAY  CAT  N    CA    180.00   0.0  0
 CB9  CONST_16  HN   N    CAT  OAF   180.00   0.0  0
 CB9  Var_01    CAX  CAZ  SAQ  CB     12.36  30.0  1
 CB9  Var_02    HAA  CAA  CAZ  SAQ   -58.10  30.0  3
 CB9  Var_03    HAB  CAB  CAZ  SAQ  -176.46  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  CAR  0.020
 CB9  plan-3  CAX  0.020
 CB9  plan-3  OAG  0.020
 CB9  plan-3  OAD  0.020
 CB9  plan-4  CAS  0.020
 CB9  plan-4  CAY  0.020
 CB9  plan-4  OAH  0.020
 CB9  plan-4  OAE  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

