# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 24 19:39:04 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-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](N)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
 XD1  XD1  '(2R,4S)-2-[(1R)-1-amino-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  27  14  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_XD1
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
 XD1  C     C  C1     0   0.179   2.6901  -0.4593   0.7876
 XD1  N     N  NH2    0  -0.777   3.1186   1.1347  -0.9880
 XD1  O     O  O      0  -0.372   3.6632  -1.0960   0.4772
 XD1  CA    C  CH1    0  -0.218   2.2649   0.8323   0.1343
 XD1  CB    C  CR15   0  -0.203   0.7660   0.8010  -0.1931
 XD1  OAE   O  OC    -1  -0.613  -3.5417   1.1395   0.1353
 XD1  OAF   O  O      0  -0.586  -1.8028   2.0997  -0.8710
 XD1  NAH   N  NR15   0  -0.560  -0.0972   0.8606   0.9488
 XD1  SAI   S  S2     0  -0.062   0.3341  -0.7569  -1.1269
 XD1  CAJ   C  C      0   0.432  -2.3250   1.2704  -0.1028
 XD1  CAM   C  CR15   0  -0.209  -1.3979   0.2864   0.6426
 XD1  CAN   C  CR5    0  -0.197  -1.1779  -1.0580  -0.1259
 XD1  HA    H  H      0   0.183   2.0521  -0.7914   1.6254
 XD1  HN    H  HNH2   0   0.344   3.0543   0.4107  -1.6933
 XD1  HNA   H  HNH2   0   0.358   2.8128   1.9940  -1.4262
 XD1  HAA   H  HCH1   0   0.287   2.3997   1.6143   0.8963
 XD1  HB    H  HCR5   0   0.286   0.5437   1.6302  -0.8607
 XD1  HAAA  H  HCH3   0   0.233  -3.2504  -1.5498  -0.4771
 XD1  HAAB  H  HCH3   0   0.236  -2.4846  -0.7213  -1.8362
 XD1  HAAC  H  HCH3   0   0.230  -2.1227  -2.4168  -1.5177
 XD1  HAB   H  HCH3   0   0.237  -0.6061  -3.0990   0.3585
 XD1  HABA  H  HCH3   0   0.222  -0.1362  -1.9339   1.5892
 XD1  HABB  H  HCH3   0   0.230  -1.8266  -2.4107   1.4307
 XD1  HNAH  H  HNR5   0   0.350   0.3024   0.3520   1.7273
 XD1  HAM   H  HCR5   0   0.248  -1.8801   0.0412   1.5926
 XD1  CAA   C  CH3    0  -0.634  -2.3258  -1.4539  -1.0469
 XD1  CAB   C  CH3    0  -0.623  -0.9159  -2.1865   0.8689

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
 XD1  O    C     double  1.204  0.020  1.204
 XD1  CA   C     single  1.509  0.020  1.509
 XD1  C    HA    single  0.930  0.020  1.080
 XD1  N    CA    single  1.442  0.020  1.442
 XD1  N    HN    single  0.890  0.020  1.040
 XD1  N    HNA   single  0.890  0.020  1.040
 XD1  CA   CB    single  1.535  0.020  1.535
 XD1  CA   HAA   single  0.970  0.020  1.090
 XD1  SAI  CB    single  1.867  0.020  1.867
 XD1  NAH  CB    single  1.433  0.020  1.433
 XD1  CB   HB    single  0.970  0.020  1.090
 XD1  CAN  CAA   single  1.524  0.020  1.524
 XD1  CAA  HAAA  single  0.970  0.020  1.090
 XD1  CAA  HAAB  single  0.970  0.020  1.090
 XD1  CAA  HAAC  single  0.970  0.020  1.090
 XD1  CAB  CAN   single  1.527  0.020  1.527
 XD1  CAB  HAB   single  0.970  0.020  1.090
 XD1  CAB  HABA  single  0.970  0.020  1.090
 XD1  CAB  HABB  single  0.970  0.020  1.090
 XD1  CAJ  OAE   deloc   1.247  0.020  1.247
 XD1  OAF  CAJ   deloc   1.245  0.020  1.245
 XD1  CAM  NAH   single  1.454  0.020  1.454
 XD1  NAH  HNAH  single  0.890  0.020  1.040
 XD1  CAN  SAI   single  1.838  0.020  1.838
 XD1  CAM  CAJ   single  1.544  0.020  1.544
 XD1  CAN  CAM   single  1.564  0.020  1.564
 XD1  CAM  HAM   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
 XD1  HA    C    CA    115.04  3.000
 XD1  HA    C    O     120.25  3.000
 XD1  CA    C    O     124.68  3.000
 XD1  HNA   N    HN    106.63  3.000
 XD1  HNA   N    CA    109.64  3.000
 XD1  HN    N    CA    110.76  3.000
 XD1  HAA   CA   CB    106.38  3.000
 XD1  HAA   CA   N     108.50  3.000
 XD1  CB    CA   N     114.61  3.000
 XD1  HAA   CA   C     105.90  3.000
 XD1  CB    CA   C     110.50  3.000
 XD1  N     CA   C     110.47  3.000
 XD1  HB    CB   SAI   106.38  3.000
 XD1  HB    CB   NAH   109.54  3.000
 XD1  SAI   CB   NAH   107.09  3.000
 XD1  HB    CB   CA    108.36  3.000
 XD1  NAH   CB   CA    114.68  3.000
 XD1  SAI   CB   CA    110.47  3.000
 XD1  HNAH  NAH  CAM   108.47  3.000
 XD1  HNAH  NAH  CB    110.75  3.000
 XD1  CAM   NAH  CB    110.77  3.000
 XD1  CAN   SAI  CB     93.13  3.000
 XD1  CAM   CAJ  OAF   118.07  3.000
 XD1  CAM   CAJ  OAE   115.28  3.000
 XD1  OAF   CAJ  OAE   126.66  3.000
 XD1  HAM   CAM  CAN   107.23  3.000
 XD1  HAM   CAM  CAJ   107.32  3.000
 XD1  CAN   CAM  CAJ   113.27  3.000
 XD1  HAM   CAM  NAH   107.46  3.000
 XD1  CAN   CAM  NAH   108.48  3.000
 XD1  CAJ   CAM  NAH   112.77  3.000
 XD1  CAM   CAN  SAI   104.03  3.000
 XD1  CAM   CAN  CAB   109.83  3.000
 XD1  SAI   CAN  CAB   109.55  3.000
 XD1  CAM   CAN  CAA   114.47  3.000
 XD1  SAI   CAN  CAA   109.45  3.000
 XD1  CAB   CAN  CAA   109.33  3.000
 XD1  HAAC  CAA  HAAB  107.95  3.000
 XD1  HAAC  CAA  HAAA  107.81  3.000
 XD1  HAAB  CAA  HAAA  108.33  3.000
 XD1  HAAC  CAA  CAN   110.48  3.000
 XD1  HAAB  CAA  CAN   111.91  3.000
 XD1  HAAA  CAA  CAN   110.23  3.000
 XD1  HABB  CAB  HABA  107.67  3.000
 XD1  HABB  CAB  HAB   107.79  3.000
 XD1  HABA  CAB  HAB   107.44  3.000
 XD1  HABB  CAB  CAN   110.08  3.000
 XD1  HABA  CAB  CAN   112.43  3.000
 XD1  HAB   CAB  CAN   111.24  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
 XD1  Var_01  CAM   CAN  SAI  CB     13.05  30.0  1
 XD1  Var_02  HAAA  CAA  CAN  SAI  -175.01  30.0  3
 XD1  Var_03  HAB   CAB  CAN  SAI   -57.43  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
 XD1  chir_01  CA   C    N    CB   negativ
 XD1  chir_02  CB   SAI  NAH  CA   negativ
 XD1  chir_03  CAM  NAH  CAJ  CAN  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
 XD1  plan-1  OAE  0.020
 XD1  plan-1  OAF  0.020
 XD1  plan-1  CAJ  0.020
 XD1  plan-1  CAM  0.020
 XD1  plan-2  C    0.020
 XD1  plan-2  O    0.020
 XD1  plan-2  CA   0.020
 XD1  plan-2  HA   0.020

