# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 02:08:31 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-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)Cc2ccccc2)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
 PNK  PNK  '(2R,4S)-2-{(R)-carboxy[(phenylacetyl)amino]methyl}-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid'  ligand  42  24  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PNK
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
 PNK  C1    C  CH1    0  -0.142   0.2350  -1.0342   0.2136
 PNK  C2    C  C      0   0.407   0.2210  -2.3780   0.9941
 PNK  C3    C  C1     0  -0.297  -5.3652  -0.1542   0.4360
 PNK  C4    C  CH1    0  -0.236   1.5650  -0.3420   0.4706
 PNK  C5    C  CH1    0  -0.206   3.0545   1.3322  -0.2992
 PNK  C6    C  CT     0  -0.201   3.8632   0.1040  -0.8324
 PNK  C7    C  C1     0  -0.245  -6.4715  -0.0098  -0.3898
 PNK  C8    C  C1     0  -0.271  -6.5048   1.0006  -1.3428
 PNK  C9    C  C      0   0.430   3.6331   1.9265   1.0028
 PNK  C10   C  C1     0  -0.242  -5.4255   1.8661  -1.4605
 PNK  C11   C  C1     0  -0.296  -4.3213   1.7196  -0.6306
 PNK  C12   C  CH3    0  -0.625   3.7646   0.0600  -2.3571
 PNK  N1    N  NH1    0  -0.568   1.6596   0.9375  -0.1749
 PNK  O1    O  OC    -1  -0.616   4.4852   2.8241   0.8468
 PNK  O2    O  O      0  -0.586   3.2259   1.4759   2.0903
 PNK  O3    O  OC    -1  -0.597   0.5497  -3.3864   0.3443
 PNK  O4    O  O      0  -0.603  -0.0540  -2.3076   2.2036
 PNK  O5    O  O      0  -0.497  -2.4943  -1.5549   0.1731
 PNK  C16   C  C      0   0.142  -4.2785   0.7097   0.3270
 PNK  C15   C  CH2    0  -0.675  -3.0675   0.5381   1.1985
 PNK  N2    N  NH1    0  -0.639  -0.8131  -0.1369   0.6471
 PNK  S1    S  S2     0  -0.035   2.9888  -1.3597  -0.1430
 PNK  C13   C  CH3    0  -0.635   5.3269   0.0804  -0.4122
 PNK  H1    H  HCH1   0   0.224   0.1386  -1.2286  -0.8608
 PNK  H4    H  HCH1   0   0.274   1.7051  -0.2105   1.5410
 PNK  H5    H  HCH1   0   0.242   3.1094   2.1143  -1.0613
 PNK  H8    H  H      0   0.253  -7.3684   1.1155  -1.9850
 PNK  H10   H  H      0   0.254  -5.4424   2.6588  -2.1973
 PNK  H11   H  H      0   0.249  -3.4846   2.4017  -0.7286
 PNK  H12   H  HCH3   0   0.224   4.3196   0.8922  -2.7982
 PNK  H12A  H  HCH3   0   0.232   4.1789  -0.8668  -2.7563
 PNK  H12B  H  HCH3   0   0.225   2.7287   0.1290  -2.6930
 PNK  HN1   H  HNH1   0   0.350   1.2660   0.8616  -1.1076
 PNK  H15   H  HCH2   0   0.270  -2.5725   1.4974   1.3584
 PNK  H15A  H  HCH2   0   0.287  -3.3627   0.1713   2.1857
 PNK  HN2   H  HNH1   0   0.394  -0.5536   0.7736   0.9910
 PNK  H13   H  HCH3   0   0.234   5.4366   0.0297   0.6701
 PNK  H13A  H  HCH3   0   0.228   5.8347  -0.7861  -0.8394
 PNK  H13B  H  HCH3   0   0.227   5.8401   0.9752  -0.7674
 PNK  C14   C  C      0   0.566  -2.1028  -0.4856   0.6201
 PNK  H3    H  H      0   0.246  -5.3514  -0.9413   1.1795
 PNK  H7    H  H      0   0.253  -7.3106  -0.6860  -0.2875

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
 PNK  C1   C2    single    1.554  0.020  1.554
 PNK  C1   C4    single    1.521  0.020  1.521
 PNK  C1   N2    single    1.446  0.020  1.446
 PNK  C2   O3    deloc     1.244  0.020  1.244
 PNK  C2   O4    deloc     1.242  0.020  1.242
 PNK  C3   C7    aromatic  1.388  0.020  1.388
 PNK  C3   C16   aromatic  1.393  0.020  1.393
 PNK  C4   N1    single    1.436  0.020  1.436
 PNK  C4   S1    single    1.855  0.020  1.855
 PNK  C5   C6    single    1.564  0.020  1.564
 PNK  C5   C9    single    1.544  0.020  1.544
 PNK  C5   N1    single    1.455  0.020  1.455
 PNK  C6   C12   single    1.529  0.020  1.529
 PNK  C6   S1    single    1.839  0.020  1.839
 PNK  C6   C13   single    1.523  0.020  1.523
 PNK  C7   C8    aromatic  1.389  0.020  1.389
 PNK  C8   C10   aromatic  1.389  0.020  1.389
 PNK  C9   O1    deloc     1.247  0.020  1.247
 PNK  C9   O2    deloc     1.245  0.020  1.245
 PNK  C10  C11   aromatic  1.389  0.020  1.389
 PNK  C11  C16   aromatic  1.392  0.020  1.392
 PNK  O5   C14   double    1.223  0.020  1.223
 PNK  C16  C15   single    1.502  0.020  1.502
 PNK  C15  C14   single    1.521  0.020  1.521
 PNK  C14  N2    single    1.336  0.020  1.336
 PNK  C1   H1    single    0.970  0.020  1.090
 PNK  C3   H3    single    0.930  0.020  1.080
 PNK  C4   H4    single    0.970  0.020  1.090
 PNK  C5   H5    single    0.970  0.020  1.090
 PNK  C7   H7    single    0.930  0.020  1.080
 PNK  C8   H8    single    0.930  0.020  1.080
 PNK  C10  H10   single    0.930  0.020  1.080
 PNK  C11  H11   single    0.930  0.020  1.080
 PNK  C12  H12   single    0.970  0.020  1.090
 PNK  C12  H12A  single    0.970  0.020  1.090
 PNK  C12  H12B  single    0.970  0.020  1.090
 PNK  N1   HN1   single    0.890  0.020  1.040
 PNK  C15  H15   single    0.970  0.020  1.090
 PNK  C15  H15A  single    0.970  0.020  1.090
 PNK  N2   HN2   single    0.860  0.020  1.020
 PNK  C13  H13   single    0.970  0.020  1.090
 PNK  C13  H13A  single    0.970  0.020  1.090
 PNK  C13  H13B  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
 PNK  H1    C1   N2    109.88  3.000
 PNK  H1    C1   C4    108.85  3.000
 PNK  N2    C1   C4    107.50  3.000
 PNK  H1    C1   C2    109.76  3.000
 PNK  N2    C1   C2    112.30  3.000
 PNK  C4    C1   C2    108.45  3.000
 PNK  O4    C2   O3    127.80  3.000
 PNK  O4    C2   C1    116.23  3.000
 PNK  O3    C2   C1    115.87  3.000
 PNK  H3    C3   C16   119.65  3.000
 PNK  H3    C3   C7    119.63  3.000
 PNK  C16   C3   C7    120.72  3.000
 PNK  H4    C4   S1    107.04  3.000
 PNK  H4    C4   N1    109.04  3.000
 PNK  S1    C4   N1    106.83  3.000
 PNK  H4    C4   C1    109.51  3.000
 PNK  S1    C4   C1    111.45  3.000
 PNK  N1    C4   C1    112.77  3.000
 PNK  H5    C5   N1    107.56  3.000
 PNK  H5    C5   C9    107.08  3.000
 PNK  N1    C5   C9    113.06  3.000
 PNK  H5    C5   C6    107.34  3.000
 PNK  N1    C5   C6    108.16  3.000
 PNK  C9    C5   C6    113.33  3.000
 PNK  C13   C6   S1    109.95  3.000
 PNK  C13   C6   C12   109.68  3.000
 PNK  S1    C6   C12   108.68  3.000
 PNK  C13   C6   C5    114.52  3.000
 PNK  S1    C6   C5    104.56  3.000
 PNK  C12   C6   C5    109.23  3.000
 PNK  H7    C7   C8    120.04  3.000
 PNK  H7    C7   C3    119.78  3.000
 PNK  C8    C7   C3    120.19  3.000
 PNK  H8    C8   C10   120.25  3.000
 PNK  H8    C8   C7    120.22  3.000
 PNK  C10   C8   C7    119.53  3.000
 PNK  O2    C9   O1    126.36  3.000
 PNK  O2    C9   C5    118.33  3.000
 PNK  O1    C9   C5    115.31  3.000
 PNK  H10   C10  C11   119.76  3.000
 PNK  H10   C10  C8    120.14  3.000
 PNK  C11   C10  C8    120.10  3.000
 PNK  H11   C11  C16   119.66  3.000
 PNK  H11   C11  C10   119.55  3.000
 PNK  C16   C11  C10   120.79  3.000
 PNK  H12B  C12  H12A  107.55  3.000
 PNK  H12B  C12  H12   108.04  3.000
 PNK  H12A  C12  H12   107.84  3.000
 PNK  H12B  C12  C6    111.50  3.000
 PNK  H12A  C12  C6    111.41  3.000
 PNK  H12   C12  C6    110.35  3.000
 PNK  HN1   N1   C5    108.27  3.000
 PNK  HN1   N1   C4    108.71  3.000
 PNK  C5    N1   C4    110.08  3.000
 PNK  C15   C16  C11   120.45  3.000
 PNK  C15   C16  C3    120.87  3.000
 PNK  C11   C16  C3    118.67  3.000
 PNK  H15A  C15  H15   106.56  3.000
 PNK  H15A  C15  C14   106.78  3.000
 PNK  H15   C15  C14   111.08  3.000
 PNK  H15A  C15  C16   110.15  3.000
 PNK  H15   C15  C16   110.51  3.000
 PNK  C14   C15  C16   111.58  3.000
 PNK  HN2   N2   C14   119.43  3.000
 PNK  HN2   N2   C1    118.46  3.000
 PNK  C14   N2   C1    122.11  3.000
 PNK  C6    S1   C4     93.00  3.000
 PNK  H13B  C13  H13A  107.75  3.000
 PNK  H13B  C13  H13   108.32  3.000
 PNK  H13A  C13  H13   107.77  3.000
 PNK  H13B  C13  C6    110.46  3.000
 PNK  H13A  C13  C6    110.57  3.000
 PNK  H13   C13  C6    111.82  3.000
 PNK  N2    C14  C15   115.40  3.000
 PNK  N2    C14  O5    122.98  3.000
 PNK  C15   C14  O5    121.62  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
 PNK  CONST_01  C10  C8   C7   C3     0.00   0.0  0
 PNK  CONST_02  C10  C11  C16  C3     0.00   0.0  0
 PNK  CONST_03  C11  C16  C3   C7     0.00   0.0  0
 PNK  CONST_04  C11  C10  C8   C7     0.00   0.0  0
 PNK  CONST_05  C16  C3   C7   C8     0.00   0.0  0
 PNK  CONST_06  C16  C11  C10  C8     0.00   0.0  0
 PNK  CONST_07  C15  C16  C3   C7   180.00   0.0  0
 PNK  CONST_08  C15  C16  C11  C10  180.00   0.0  0
 PNK  CONST_09  H8   C8   C7   C3   180.00   0.0  0
 PNK  CONST_10  H11  C11  C16  C3   180.00   0.0  0
 PNK  CONST_11  H10  C10  C8   C7   180.00   0.0  0
 PNK  CONST_12  H3   C3   C7   C8   180.00   0.0  0
 PNK  CONST_13  H7   C7   C8   C10  180.00   0.0  0
 PNK  CONST_14  O5   C14  N2   C1     0.00   0.0  0
 PNK  CONST_15  C15  C14  N2   C1   180.00   0.0  0
 PNK  CONST_16  HN2  N2   C14  O5   180.00   0.0  0
 PNK  Var_01    C5   C6   S1   C4     9.36  30.0  1
 PNK  Var_02    C14  C15  C16  C3    84.14  30.0  2
 PNK  Var_03    H12  C12  C6   C5    69.34  30.0  3
 PNK  Var_04    H13  C13  C6   C5    61.40  30.0  3
 PNK  Var_05    C16  C15  C14  O5   -44.68  30.0  1

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
 PNK  chir_01  C1  C2  C4  N2  positiv
 PNK  chir_02  C4  S1  N1  C1  negativ
 PNK  chir_03  C5  N1  C6  C9  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
 PNK  plan-1  C3   0.020
 PNK  plan-1  C7   0.020
 PNK  plan-1  C8   0.020
 PNK  plan-1  C10  0.020
 PNK  plan-1  C11  0.020
 PNK  plan-1  C16  0.020
 PNK  plan-1  C15  0.020
 PNK  plan-1  H8   0.020
 PNK  plan-1  H10  0.020
 PNK  plan-1  H11  0.020
 PNK  plan-1  H3   0.020
 PNK  plan-1  H7   0.020
 PNK  plan-2  C1   0.020
 PNK  plan-2  O5   0.020
 PNK  plan-2  C15  0.020
 PNK  plan-2  N2   0.020
 PNK  plan-2  HN2  0.020
 PNK  plan-2  C14  0.020
 PNK  plan-3  C1   0.020
 PNK  plan-3  C2   0.020
 PNK  plan-3  O3   0.020
 PNK  plan-3  O4   0.020
 PNK  plan-4  C5   0.020
 PNK  plan-4  C9   0.020
 PNK  plan-4  O1   0.020
 PNK  plan-4  O2   0.020

