# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 00:31:15 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (2R,4S)-2-[(1R)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]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)c2cscc2)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
 XT8  XT8  '(2R,4S)-2-[(1R)-1-{[(2R)-2-carboxy-2-(thiophen-3-yl)acetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  41  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XT8
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
 XT8  C7   C  C1     0   0.177   0.6556  -0.5980  -1.8584
 XT8  O8   O  O      0  -0.365  -0.2350  -1.3603  -2.1299
 XT8  C6   C  CH1    0  -0.205   0.5835   0.4482  -0.7699
 XT8  C5   C  CR15   0  -0.185   1.8945   0.5256   0.0172
 XT8  S1   S  S2     0  -0.051   2.4129  -1.1812   0.5594
 XT8  C2   C  CR5    0  -0.197   4.1493  -0.9407   0.0057
 XT8  C10  C  CH3    0  -0.637   5.1004  -1.4919   1.0606
 XT8  C9   C  CH3    0  -0.627   4.3719  -1.6772  -1.3134
 XT8  C3   C  CR15   0  -0.209   4.2590   0.6018  -0.2201
 XT8  C11  C  C      0   0.433   4.7239   1.3624   1.0396
 XT8  O12  O  O      0  -0.586   3.8530   1.7379   1.8467
 XT8  O13  O  OC    -1  -0.613   5.9554   1.5267   1.1419
 XT8  N4   N  NR15   0  -0.564   2.9843   1.0870  -0.7250
 XT8  N14  N  NH1    0  -0.636  -0.5361   0.1997   0.0837
 XT8  C15  C  C      0   0.542  -1.3242   1.1680   0.5691
 XT8  O16  O  O      0  -0.501  -1.1501   2.3609   0.3533
 XT8  C17  C  CH1    0  -0.576  -2.5172   0.6845   1.3814
 XT8  C33  C  C      0   0.467  -2.3189  -0.6091   2.2261
 XT8  O33  O  OC    -1  -0.575  -2.7924  -0.5903   3.3684
 XT8  O32  O  O      0  -0.589  -1.7452  -1.5691   1.6633
 XT8  C28  C  CR5    0   0.195  -3.6870   0.4520   0.4595
 XT8  C32  C  CR15   0  -0.540  -3.6285  -0.1696  -0.7542
 XT8  S31  S  S2     0   0.206  -5.1761  -0.3011  -1.4791
 XT8  C30  C  CR15   0  -0.463  -5.9307   0.4759  -0.1521
 XT8  C29  C  CR15   0  -0.215  -5.0229   0.8195   0.8007
 XT8  H1   H  H      0   0.201   1.5903  -0.5980  -2.4438
 XT8  H2   H  HCH1   0   0.306   0.4453   1.4159  -1.2713
 XT8  H3   H  HCR5   0   0.291   1.7242   1.1033   0.9214
 XT8  H4   H  HCH3   0   0.232   5.0026  -2.5760   1.1338
 XT8  H5   H  HCH3   0   0.233   6.1339  -1.2686   0.7929
 XT8  H6   H  HCH3   0   0.237   4.9035  -1.0712   2.0453
 XT8  H7   H  HCH3   0   0.226   3.7523  -1.2800  -2.1185
 XT8  H8   H  HCH3   0   0.231   5.4153  -1.5854  -1.6255
 XT8  H9   H  HCH3   0   0.238   4.1416  -2.7385  -1.2161
 XT8  H10  H  HCR5   0   0.248   5.0063   0.7672  -1.0006
 XT8  H12  H  HNR5   0   0.355   2.9117   0.8551  -1.7081
 XT8  H14  H  HNH1   0   0.410  -0.7668  -0.7447   0.4099
 XT8  H15  H  HCH1   0   0.265  -2.7764   1.5015   2.0560
 XT8  H17  H  HCR5   0   0.284  -2.7581  -0.5572  -1.2630
 XT8  H18  H  HCR5   0   0.292  -6.9970   0.6407  -0.1451
 XT8  H19  H  HCR5   0   0.263  -5.2865   1.3231   1.7207

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
 XT8  C5   S1   single    1.864  0.020  1.864
 XT8  C5   N4   single    1.433  0.020  1.433
 XT8  C5   C6   single    1.531  0.020  1.531
 XT8  S1   C2   single    1.838  0.020  1.838
 XT8  C10  C2   single    1.524  0.020  1.524
 XT8  N4   C3   single    1.454  0.020  1.454
 XT8  O16  C15  double    1.225  0.020  1.225
 XT8  C6   C7   single    1.511  0.020  1.511
 XT8  C6   N14  single    1.430  0.020  1.430
 XT8  C2   C3   single    1.563  0.020  1.563
 XT8  C2   C9   single    1.527  0.020  1.527
 XT8  O12  C11  deloc     1.245  0.020  1.245
 XT8  C7   O8   double    1.203  0.020  1.203
 XT8  C3   C11  single    1.543  0.020  1.543
 XT8  C15  N14  single    1.340  0.020  1.340
 XT8  C15  C17  single    1.522  0.020  1.522
 XT8  C11  O13  deloc     1.247  0.020  1.247
 XT8  O32  C33  deloc     1.252  0.020  1.252
 XT8  C29  C30  aromatic  1.360  0.020  1.360
 XT8  C29  C28  aromatic  1.427  0.020  1.427
 XT8  C33  O33  deloc     1.237  0.020  1.237
 XT8  C33  C17  single    1.558  0.020  1.558
 XT8  C17  C28  single    1.507  0.020  1.507
 XT8  C30  S31  aromatic  1.713  0.020  1.713
 XT8  C28  C32  aromatic  1.365  0.020  1.365
 XT8  C32  S31  aromatic  1.714  0.020  1.714
 XT8  C7   H1   single    0.930  0.020  1.080
 XT8  C6   H2   single    0.970  0.020  1.090
 XT8  C5   H3   single    0.970  0.020  1.090
 XT8  C10  H4   single    0.970  0.020  1.090
 XT8  C10  H5   single    0.970  0.020  1.090
 XT8  C10  H6   single    0.970  0.020  1.090
 XT8  C9   H7   single    0.970  0.020  1.090
 XT8  C9   H8   single    0.970  0.020  1.090
 XT8  C9   H9   single    0.970  0.020  1.090
 XT8  C3   H10  single    0.970  0.020  1.090
 XT8  N4   H12  single    0.890  0.020  1.040
 XT8  N14  H14  single    0.860  0.020  1.020
 XT8  C17  H15  single    0.970  0.020  1.090
 XT8  C32  H17  single    0.930  0.020  1.080
 XT8  C30  H18  single    0.930  0.020  1.080
 XT8  C29  H19  single    0.930  0.020  1.080

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
 XT8  H1   C7   C6   115.00  3.000
 XT8  H1   C7   O8   120.50  3.000
 XT8  C6   C7   O8   124.45  3.000
 XT8  H2   C6   N14  109.09  3.000
 XT8  H2   C6   C5   107.33  3.000
 XT8  N14  C6   C5   111.86  3.000
 XT8  H2   C6   C7   106.68  3.000
 XT8  N14  C6   C7   110.30  3.000
 XT8  C5   C6   C7   111.37  3.000
 XT8  H3   C5   N4   109.99  3.000
 XT8  H3   C5   S1   106.76  3.000
 XT8  N4   C5   S1   107.32  3.000
 XT8  H3   C5   C6   108.70  3.000
 XT8  N4   C5   C6   113.87  3.000
 XT8  S1   C5   C6   109.96  3.000
 XT8  C2   S1   C5    93.17  3.000
 XT8  C3   C2   C9   109.94  3.000
 XT8  C9   C2   C10  109.42  3.000
 XT8  C3   C2   C10  114.41  3.000
 XT8  C9   C2   S1   109.56  3.000
 XT8  C3   C2   S1   103.83  3.000
 XT8  C10  C2   S1   109.49  3.000
 XT8  H6   C10  H5   108.32  3.000
 XT8  H6   C10  H4   107.88  3.000
 XT8  H5   C10  H4   107.75  3.000
 XT8  H6   C10  C2   111.93  3.000
 XT8  H5   C10  C2   110.34  3.000
 XT8  H4   C10  C2   110.48  3.000
 XT8  H9   C9   H8   108.00  3.000
 XT8  H9   C9   H7   107.48  3.000
 XT8  H8   C9   H7   107.51  3.000
 XT8  H9   C9   C2   111.20  3.000
 XT8  H8   C9   C2   110.21  3.000
 XT8  H7   C9   C2   112.28  3.000
 XT8  H10  C3   N4   107.51  3.000
 XT8  H10  C3   C11  107.60  3.000
 XT8  N4   C3   C11  112.52  3.000
 XT8  H10  C3   C2   107.49  3.000
 XT8  C11  C3   C2   112.94  3.000
 XT8  N4   C3   C2   108.53  3.000
 XT8  O13  C11  O12  126.72  3.000
 XT8  O13  C11  C3   115.44  3.000
 XT8  O12  C11  C3   117.84  3.000
 XT8  H12  N4   C3   108.87  3.000
 XT8  H12  N4   C5   111.01  3.000
 XT8  C3   N4   C5   110.86  3.000
 XT8  H14  N14  C15  114.71  3.000
 XT8  H14  N14  C6   121.75  3.000
 XT8  C15  N14  C6   123.46  3.000
 XT8  C17  C15  O16  120.99  3.000
 XT8  C17  C15  N14  115.14  3.000
 XT8  O16  C15  N14  123.82  3.000
 XT8  H15  C17  C28  108.02  3.000
 XT8  H15  C17  C33  108.47  3.000
 XT8  C28  C17  C33  107.60  3.000
 XT8  H15  C17  C15  106.16  3.000
 XT8  C28  C17  C15  109.32  3.000
 XT8  C33  C17  C15  116.97  3.000
 XT8  O32  C33  O33  127.04  3.000
 XT8  O33  C33  C17  116.08  3.000
 XT8  O32  C33  C17  116.83  3.000
 XT8  C29  C28  C32  111.72  3.000
 XT8  C32  C28  C17  125.51  3.000
 XT8  C29  C28  C17  122.72  3.000
 XT8  H17  C32  S31  120.06  3.000
 XT8  H17  C32  C28  128.08  3.000
 XT8  S31  C32  C28  111.86  3.000
 XT8  C30  S31  C32   92.02  3.000
 XT8  H18  C30  C29  128.06  3.000
 XT8  H18  C30  S31  120.64  3.000
 XT8  C29  C30  S31  111.30  3.000
 XT8  H19  C29  C30  123.42  3.000
 XT8  H19  C29  C28  123.48  3.000
 XT8  C30  C29  C28  113.10  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
 XT8  CONST_01  S31  C30  C29  C28    0.00   0.0  0
 XT8  CONST_02  C30  S31  C32  C28    0.00   0.0  0
 XT8  CONST_03  C30  C29  C28  C32    0.00   0.0  0
 XT8  CONST_04  C29  C30  S31  C32    0.00   0.0  0
 XT8  CONST_05  C29  C28  C32  S31    0.00   0.0  0
 XT8  CONST_06  C30  C29  C28  C17  180.00   0.0  0
 XT8  CONST_07  S31  C32  C28  C17  180.00   0.0  0
 XT8  CONST_08  H18  C30  C29  C28  180.00   0.0  0
 XT8  CONST_09  H19  C29  C28  C32  180.00   0.0  0
 XT8  CONST_10  H17  C32  S31  C30  180.00   0.0  0
 XT8  CONST_11  O16  C15  N14  C6     0.00   0.0  0
 XT8  CONST_12  C17  C15  N14  C6   180.00   0.0  0
 XT8  CONST_13  H14  N14  C15  O16  180.00   0.0  0
 XT8  Var_01    C3   C2   S1   C5    14.36  30.0  1
 XT8  Var_02    H4   C10  C2   S1    66.53  30.0  3
 XT8  Var_03    H7   C9   C2   S1    63.18  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
 XT8  chir_01  C6   C5   C7   N14  negativ
 XT8  chir_02  C5   S1   N4   C6   negativ
 XT8  chir_03  C3   N4   C2   C11  positiv
 XT8  chir_04  C17  C15  C33  C28  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
 XT8  plan-1  C17  0.020
 XT8  plan-1  C28  0.020
 XT8  plan-1  C32  0.020
 XT8  plan-1  S31  0.020
 XT8  plan-1  C30  0.020
 XT8  plan-1  C29  0.020
 XT8  plan-1  H17  0.020
 XT8  plan-1  H18  0.020
 XT8  plan-1  H19  0.020
 XT8  plan-2  C6   0.020
 XT8  plan-2  N14  0.020
 XT8  plan-2  C15  0.020
 XT8  plan-2  O16  0.020
 XT8  plan-2  C17  0.020
 XT8  plan-2  H14  0.020
 XT8  plan-3  C3   0.020
 XT8  plan-3  C11  0.020
 XT8  plan-3  O12  0.020
 XT8  plan-3  O13  0.020
 XT8  plan-4  C17  0.020
 XT8  plan-4  C33  0.020
 XT8  plan-4  O33  0.020
 XT8  plan-4  O32  0.020
 XT8  plan-5  C7   0.020
 XT8  plan-5  O8   0.020
 XT8  plan-5  C6   0.020
 XT8  plan-5  H1   0.020

