# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:55:21 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2R,4S)-2-[(1S)-1-carboxy-2-hydroxy-2-methylpropyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(O)[C@H]([C@@H]1N[C@@H](C(O)=O)C(C)(C)S1)C(O)=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
 AP3  AP3  '(2R,4S)-2-[(1S)-1-carboxy-2-hydroxy-2-methylpropyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  37  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AP3
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
 AP3  C1    C  C     0   0.554  -1.2915  -0.9219   1.8784
 AP3  O1    O  O     0  -0.444  -2.3398  -0.3225   1.8679
 AP3  OXT   O  OH1   0  -0.583  -1.1847  -2.1777   2.2927
 AP3  C2    C  CH1   0  -0.370   0.0305  -0.3412   1.4332
 AP3  C21   C  CT    0   0.216   0.6959   0.4955   2.5722
 AP3  O22   O  OH1   0  -0.659   1.8040   1.1914   2.0297
 AP3  C3    C  CH1   0  -0.159  -0.1747   0.4535   0.1325
 AP3  S4    S  S2    0   0.014   1.4001   0.6819  -0.7707
 AP3  C5    C  CT    0  -0.212   0.8661  -0.3100  -2.2167
 AP3  C51   C  CH3   0  -0.617   1.2278  -1.7810  -2.0293
 AP3  C52   C  CH3   0  -0.649   1.5436   0.2352  -3.4668
 AP3  C6    C  CH1   0  -0.166  -0.6667  -0.1491  -2.1721
 AP3  C8    C  C     0   0.536  -1.1377   1.1626  -2.7843
 AP3  O81   O  O     0  -0.423  -1.3205   2.1801  -2.1652
 AP3  O82   O  OH1   0  -0.590  -1.3542   1.0495  -4.0885
 AP3  N7    N  NH1   0  -0.599  -1.0274  -0.2910  -0.7845
 AP3  C9    C  CH3   0  -0.672   1.1620  -0.4238   3.6996
 AP3  C10   C  CH3   0  -0.672  -0.2277   1.5696   3.1355
 AP3  HXT   H  HOH1  0   0.480  -2.0499  -2.5039   2.5851
 AP3  H2    H  HCH1  0   0.274   0.7003  -1.1748   1.1999
 AP3  HOM   H  HOH1  0   0.447   2.4668   0.5504   1.7482
 AP3  H3    H  HCH1  0   0.271  -0.5687   1.4492   0.3496
 AP3  H511  H  HCH3  0   0.240   2.2998  -1.8935  -1.8689
 AP3  H512  H  HCH3  0   0.242   0.7075  -2.2147  -1.1769
 AP3  H513  H  HCH3  0   0.232   0.9576  -2.3515  -2.9210
 AP3  H521  H  HCH3  0   0.249   2.6191   0.0652  -3.4083
 AP3  H522  H  HCH3  0   0.246   1.1796  -0.2816  -4.3557
 AP3  H523  H  HCH3  0   0.243   1.3900   1.3055  -3.5989
 AP3  H6    H  HCH1  0   0.292  -1.1201  -0.9659  -2.7436
 AP3  HO    H  HOH1  0   0.481  -1.6310   1.9019  -4.4580
 AP3  HN7   H  HNH1  0   0.374  -2.0021  -0.0723  -0.6272
 AP3  H91   H  HCH3  0   0.242   1.6991   0.1553   4.4519
 AP3  H92   H  HCH3  0   0.234   0.3272  -0.9146   4.1989
 AP3  H93   H  HCH3  0   0.236   1.8305  -1.2032   3.3272
 AP3  H101  H  HCH3  0   0.234  -1.0361   1.1331   3.7183
 AP3  H102  H  HCH3  0   0.241   0.3406   2.2201   3.8019
 AP3  H103  H  HCH3  0   0.238  -0.6723   2.1930   2.3594

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
 AP3  C1   O1    double  1.208  0.020  1.208
 AP3  C1   OXT   single  1.327  0.020  1.327
 AP3  C1   C2    single  1.511  0.020  1.511
 AP3  OXT  HXT   single  0.850  0.020  0.980
 AP3  C2   C21   single  1.562  0.020  1.562
 AP3  C2   C3    single  1.538  0.020  1.538
 AP3  C2   H2    single  0.970  0.020  1.090
 AP3  C21  O22   single  1.416  0.020  1.416
 AP3  C21  C9    single  1.528  0.020  1.528
 AP3  C21  C10   single  1.524  0.020  1.524
 AP3  O22  HOM   single  0.850  0.020  0.980
 AP3  C3   S4    single  1.830  0.020  1.830
 AP3  C3   N7    single  1.457  0.020  1.457
 AP3  C3   H3    single  0.970  0.020  1.090
 AP3  S4   C5    single  1.833  0.020  1.833
 AP3  C5   C51   single  1.526  0.020  1.526
 AP3  C5   C52   single  1.523  0.020  1.523
 AP3  C5   C6    single  1.542  0.020  1.542
 AP3  C51  H511  single  0.970  0.020  1.090
 AP3  C51  H512  single  0.970  0.020  1.090
 AP3  C51  H513  single  0.970  0.020  1.090
 AP3  C52  H521  single  0.970  0.020  1.090
 AP3  C52  H522  single  0.970  0.020  1.090
 AP3  C52  H523  single  0.970  0.020  1.090
 AP3  C6   C8    single  1.522  0.020  1.522
 AP3  C6   N7    single  1.441  0.020  1.441
 AP3  C6   H6    single  0.970  0.020  1.090
 AP3  C8   O81   double  1.205  0.020  1.205
 AP3  C8   O82   single  1.327  0.020  1.327
 AP3  O82  HO    single  0.850  0.020  0.980
 AP3  N7   HN7   single  0.890  0.020  1.040
 AP3  C9   H91   single  0.970  0.020  1.090
 AP3  C9   H92   single  0.970  0.020  1.090
 AP3  C9   H93   single  0.970  0.020  1.090
 AP3  C10  H101  single  0.970  0.020  1.090
 AP3  C10  H102  single  0.970  0.020  1.090
 AP3  C10  H103  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
 AP3  C2    C1   OXT   112.67  3.000
 AP3  C2    C1   O1    124.48  3.000
 AP3  OXT   C1   O1    122.85  3.000
 AP3  HXT   OXT  C1    109.92  3.000
 AP3  H2    C2   C3    107.15  3.000
 AP3  H2    C2   C21   107.61  3.000
 AP3  C3    C2   C21   113.37  3.000
 AP3  H2    C2   C1    107.79  3.000
 AP3  C3    C2   C1    109.33  3.000
 AP3  C21   C2   C1    111.33  3.000
 AP3  C10   C21  C9    109.64  3.000
 AP3  C10   C21  O22   105.63  3.000
 AP3  C9    C21  O22   109.86  3.000
 AP3  C10   C21  C2    112.87  3.000
 AP3  C9    C21  C2    110.23  3.000
 AP3  O22   C21  C2    108.49  3.000
 AP3  HOM   O22  C21   108.85  3.000
 AP3  H3    C3   N7    112.32  3.000
 AP3  H3    C3   S4    107.13  3.000
 AP3  N7    C3   S4    104.88  3.000
 AP3  H3    C3   C2    110.55  3.000
 AP3  N7    C3   C2    110.27  3.000
 AP3  S4    C3   C2    111.54  3.000
 AP3  C5    S4   C3     94.08  3.000
 AP3  C6    C5   C52   115.39  3.000
 AP3  C6    C5   C51   109.43  3.000
 AP3  C52   C5   C51   109.90  3.000
 AP3  C6    C5   S4    102.14  3.000
 AP3  C52   C5   S4    108.92  3.000
 AP3  C51   C5   S4    110.83  3.000
 AP3  H513  C51  H512  108.23  3.000
 AP3  H513  C51  H511  108.03  3.000
 AP3  H512  C51  H511  108.28  3.000
 AP3  H513  C51  C5    110.15  3.000
 AP3  H512  C51  C5    111.52  3.000
 AP3  H511  C51  C5    110.53  3.000
 AP3  H523  C52  H522  108.64  3.000
 AP3  H523  C52  H521  107.39  3.000
 AP3  H522  C52  H521  107.39  3.000
 AP3  H523  C52  C5    112.87  3.000
 AP3  H522  C52  C5    110.54  3.000
 AP3  H521  C52  C5    109.82  3.000
 AP3  H6    C6   N7    109.00  3.000
 AP3  H6    C6   C8    107.74  3.000
 AP3  N7    C6   C8    113.25  3.000
 AP3  H6    C6   C5    108.58  3.000
 AP3  N7    C6   C5    105.46  3.000
 AP3  C8    C6   C5    112.70  3.000
 AP3  O82   C8   O81   123.52  3.000
 AP3  O82   C8   C6    111.86  3.000
 AP3  O81   C8   C6    124.60  3.000
 AP3  HO    O82  C8    110.26  3.000
 AP3  HN7   N7   C6    111.70  3.000
 AP3  HN7   N7   C3    110.84  3.000
 AP3  C6    N7   C3    114.17  3.000
 AP3  H93   C9   H92   107.69  3.000
 AP3  H93   C9   H91   108.22  3.000
 AP3  H92   C9   H91   107.48  3.000
 AP3  H93   C9   C21   111.38  3.000
 AP3  H92   C9   C21   112.06  3.000
 AP3  H91   C9   C21   109.86  3.000
 AP3  H103  C10  H102  107.84  3.000
 AP3  H103  C10  H101  107.92  3.000
 AP3  H102  C10  H101  107.39  3.000
 AP3  H103  C10  C21   112.76  3.000
 AP3  H102  C10  C21   109.28  3.000
 AP3  H101  C10  C21   111.43  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
 AP3  CONST_01  HO    O82  C8   C6  180.00   0.0  0
 AP3  CONST_02  HXT   OXT  C1   O1    0.00   0.0  0
 AP3  Var_01    C6    C5   S4   C3   26.61  30.0  1
 AP3  Var_02    H511  C51  C5   S4  -57.41  30.0  3
 AP3  Var_03    H521  C52  C5   S4   66.48  30.0  3
 AP3  Var_04    H91   C9   C21  C2  175.30  30.0  3
 AP3  Var_05    H101  C10  C21  C2   70.74  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
 AP3  chir_01  C2  C1  C21  C3  positiv
 AP3  chir_02  C3  S4  N7   C2  negativ
 AP3  chir_03  C6  N7  C8   C5  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
 AP3  plan-1  C1   0.020
 AP3  plan-1  O1   0.020
 AP3  plan-1  OXT  0.020
 AP3  plan-1  C2   0.020
 AP3  plan-1  HXT  0.020
 AP3  plan-2  C6   0.020
 AP3  plan-2  C8   0.020
 AP3  plan-2  O81  0.020
 AP3  plan-2  O82  0.020
 AP3  plan-2  HO   0.020

