# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 23:03:44 2020
#   Inital geometry file: a 103 line input string
#   Ligand name: (2~{R},4~{S})-5,5-dimethyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-5-thiophen-2-yl-pentan-2-yl]-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](C=O)[C@H](O)CCc2sccc2
#
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
 PXH  PXH  '(2~{R},4~{S})-5,5-dimethyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-5-thiophen-2-yl-pentan-2-yl]-1,3-thiazolidine-4-carboxylic acid'  ligand  42  22  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PXH
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
 PXH  O8   O  O      0  -0.373   0.2122  -2.0686  -1.9838
 PXH  C7   C  C1     0   0.195  -0.0188  -1.7228  -0.8522
 PXH  N4   N  NH1    0  -0.572  -2.6120  -0.9476  -0.6015
 PXH  C3   C  CH1    0  -0.206  -3.9618  -0.5170  -0.2684
 PXH  C11  C  C      0   0.431  -4.5308  -1.2199   0.9828
 PXH  O13  O  OC    -1  -0.614  -5.7682  -1.3733   0.9886
 PXH  O12  O  O      0  -0.585  -3.7347  -1.5699   1.8741
 PXH  C2   C  CT     0  -0.202  -3.9481   1.0404  -0.1592
 PXH  C10  C  CH3    0  -0.634  -5.0354   1.6254   0.7336
 PXH  C9   C  CH3    0  -0.625  -4.0502   1.6544  -1.5557
 PXH  S1   S  S2     0  -0.030  -2.2995   1.4222   0.5575
 PXH  C5   C  CH1    0  -0.156  -1.6504  -0.2859   0.2384
 PXH  C6   C  CH1    0  -0.439  -0.2671  -0.3021  -0.4133
 PXH  C17  C  CH2    0  -0.493   3.3214   0.5257   0.9039
 PXH  C14  C  CH1    0   0.064   0.8357   0.1183   0.5783
 PXH  O14  O  OH1    0  -0.648   0.5280   1.3392   1.2066
 PXH  C1   C  CR5    0  -0.141   4.6805   0.4915   0.2852
 PXH  C4   C  CR15   0  -0.245   5.4773   1.5397  -0.0673
 PXH  C8   C  CR15   0  -0.182   6.7066   1.1394  -0.6633
 PXH  C12  C  CR15   0  -0.473   6.8255  -0.2121  -0.7574
 PXH  S13  S  S2     0   0.192   5.4426  -1.0038  -0.1196
 PXH  H1   H  H      0   0.193  -0.0528  -2.4598  -0.0286
 PXH  H2   H  HNH1   0   0.352  -2.4371  -0.6983  -1.5699
 PXH  H4   H  HCH1   0   0.245  -4.6067  -0.7834  -1.1102
 PXH  H6   H  HCH3   0   0.234  -4.9335   1.2986   1.7671
 PXH  H7   H  HCH3   0   0.228  -4.9899   2.7155   0.7226
 PXH  H8   H  HCH3   0   0.230  -6.0226   1.3304   0.3771
 PXH  H9   H  HCH3   0   0.226  -5.0414   1.4725  -1.9789
 PXH  H10  H  HCH3   0   0.234  -3.8914   2.7331  -1.5255
 PXH  H11  H  HCH3   0   0.223  -3.3114   1.2345  -2.2402
 PXH  H12  H  HCH1   0   0.276  -1.6077  -0.7935   1.1995
 PXH  H13  H  HCH1   0   0.264  -0.2580   0.3524  -1.2927
 PXH  H14  H  HCH2   0   0.245   2.2083   0.8496  -0.9213
 PXH  H15  H  HCH2   0   0.240   2.4316  -0.8358  -0.5037
 PXH  H16  H  HCH2   0   0.258   3.1525   1.5318   1.2893
 PXH  H17  H  HCH2   0   0.253   3.2863  -0.1487   1.7649
 PXH  H18  H  HCH1   0   0.237   0.8556  -0.6206   1.3882
 PXH  H19  H  HOH1   0   0.447   0.5175   2.0355   0.5398
 PXH  H20  H  HCR5   0   0.258   5.1923   2.5700   0.0968
 PXH  H21  H  HCR5   0   0.263   7.4664   1.8286  -1.0034
 PXH  H22  H  HCR5   0   0.291   7.6470  -0.7842  -1.1598
 PXH  C15  C  CH2    0  -0.460   2.2114   0.1483  -0.0798

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
 PXH  C8   C12  aromatic  1.360  0.020  1.360
 PXH  C8   C4   aromatic  1.424  0.020  1.424
 PXH  C12  S13  aromatic  1.716  0.020  1.716
 PXH  C4   C1   aromatic  1.363  0.020  1.363
 PXH  S13  C1   aromatic  1.727  0.020  1.727
 PXH  C1   C17  single    1.494  0.020  1.494
 PXH  C17  C15  single    1.530  0.020  1.530
 PXH  C15  C14  single    1.525  0.020  1.525
 PXH  C14  O14  single    1.407  0.020  1.407
 PXH  C14  C6   single    1.541  0.020  1.541
 PXH  O8   C7   double    1.206  0.020  1.206
 PXH  C7   C6   single    1.508  0.020  1.508
 PXH  C6   C5   single    1.529  0.020  1.529
 PXH  C5   N4   single    1.438  0.020  1.438
 PXH  C5   S1   single    1.855  0.020  1.855
 PXH  N4   C3   single    1.455  0.020  1.455
 PXH  S1   C2   single    1.838  0.020  1.838
 PXH  C3   C2   single    1.561  0.020  1.561
 PXH  C3   C11  single    1.544  0.020  1.544
 PXH  C2   C9   single    1.529  0.020  1.529
 PXH  C2   C10  single    1.524  0.020  1.524
 PXH  C11  O12  deloc     1.245  0.020  1.245
 PXH  C11  O13  deloc     1.247  0.020  1.247
 PXH  C7   H1   single    0.930  0.020  1.080
 PXH  N4   H2   single    0.890  0.020  1.040
 PXH  C3   H4   single    0.970  0.020  1.090
 PXH  C10  H6   single    0.970  0.020  1.090
 PXH  C10  H7   single    0.970  0.020  1.090
 PXH  C10  H8   single    0.970  0.020  1.090
 PXH  C9   H9   single    0.970  0.020  1.090
 PXH  C9   H10  single    0.970  0.020  1.090
 PXH  C9   H11  single    0.970  0.020  1.090
 PXH  C5   H12  single    0.970  0.020  1.090
 PXH  C6   H13  single    0.970  0.020  1.090
 PXH  C15  H14  single    0.970  0.020  1.090
 PXH  C15  H15  single    0.970  0.020  1.090
 PXH  C17  H16  single    0.970  0.020  1.090
 PXH  C17  H17  single    0.970  0.020  1.090
 PXH  C14  H18  single    0.970  0.020  1.090
 PXH  O14  H19  single    0.850  0.020  0.980
 PXH  C4   H20  single    0.930  0.020  1.080
 PXH  C8   H21  single    0.930  0.020  1.080
 PXH  C12  H22  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
 PXH  H1   C7   C6   113.97  3.000
 PXH  H1   C7   O8   120.92  3.000
 PXH  C6   C7   O8   125.11  3.000
 PXH  H2   N4   C5   109.21  3.000
 PXH  H2   N4   C3   107.79  3.000
 PXH  C5   N4   C3   110.51  3.000
 PXH  H4   C3   C2   107.58  3.000
 PXH  H4   C3   C11  107.20  3.000
 PXH  C2   C3   C11  113.63  3.000
 PXH  H4   C3   N4   107.38  3.000
 PXH  C11  C3   N4   113.12  3.000
 PXH  C2   C3   N4   107.64  3.000
 PXH  O12  C11  O13  126.62  3.000
 PXH  O13  C11  C3   115.19  3.000
 PXH  O12  C11  C3   118.19  3.000
 PXH  S1   C2   C9   109.43  3.000
 PXH  C9   C2   C10  109.48  3.000
 PXH  S1   C2   C10  109.38  3.000
 PXH  C10  C2   C3   114.69  3.000
 PXH  C9   C2   C3   109.64  3.000
 PXH  S1   C2   C3   104.03  3.000
 PXH  H8   C10  H7   107.74  3.000
 PXH  H8   C10  H6   108.30  3.000
 PXH  H7   C10  H6   107.79  3.000
 PXH  H8   C10  C2   110.52  3.000
 PXH  H7   C10  C2   110.36  3.000
 PXH  H6   C10  C2   111.98  3.000
 PXH  H11  C9   H10  107.42  3.000
 PXH  H11  C9   H9   107.88  3.000
 PXH  H10  C9   H9   107.89  3.000
 PXH  H11  C9   C2   111.92  3.000
 PXH  H10  C9   C2   111.24  3.000
 PXH  H9   C9   C2   110.33  3.000
 PXH  C5   S1   C2    93.18  3.000
 PXH  H12  C5   C6   109.64  3.000
 PXH  H12  C5   S1   106.94  3.000
 PXH  C6   C5   S1   113.55  3.000
 PXH  H12  C5   N4   109.12  3.000
 PXH  S1   C5   N4   106.87  3.000
 PXH  C6   C5   N4   110.55  3.000
 PXH  H13  C6   C14  110.32  3.000
 PXH  H13  C6   C5   110.07  3.000
 PXH  C14  C6   C5   111.72  3.000
 PXH  H13  C6   C7   109.13  3.000
 PXH  C5   C6   C7   106.44  3.000
 PXH  C14  C6   C7   109.05  3.000
 PXH  H17  C17  H16  106.59  3.000
 PXH  H17  C17  C1   109.94  3.000
 PXH  H16  C17  C1   107.96  3.000
 PXH  H17  C17  C15  109.30  3.000
 PXH  H16  C17  C15  110.02  3.000
 PXH  C1   C17  C15  112.84  3.000
 PXH  H18  C14  O14  105.00  3.000
 PXH  H18  C14  C15  108.39  3.000
 PXH  O14  C14  C15  111.89  3.000
 PXH  H18  C14  C6   107.72  3.000
 PXH  O14  C14  C6   111.56  3.000
 PXH  C15  C14  C6   111.90  3.000
 PXH  H19  O14  C14  108.68  3.000
 PXH  S13  C1   C4   110.33  3.000
 PXH  S13  C1   C17  121.24  3.000
 PXH  C4   C1   C17  128.42  3.000
 PXH  H20  C4   C8   123.99  3.000
 PXH  H20  C4   C1   122.63  3.000
 PXH  C8   C4   C1   113.38  3.000
 PXH  H21  C8   C12  123.41  3.000
 PXH  H21  C8   C4   124.02  3.000
 PXH  C12  C8   C4   112.58  3.000
 PXH  H22  C12  S13  120.49  3.000
 PXH  H22  C12  C8   128.26  3.000
 PXH  S13  C12  C8   111.24  3.000
 PXH  C12  S13  C1    92.48  3.000
 PXH  H15  C15  H14  106.19  3.000
 PXH  H15  C15  C14  109.34  3.000
 PXH  H14  C15  C14  109.97  3.000
 PXH  H15  C15  C17  108.96  3.000
 PXH  H14  C15  C17  109.75  3.000
 PXH  C14  C15  C17  112.44  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
 PXH  CONST_01  C12  C8   C4   C1     0.00   0.0  0
 PXH  CONST_02  C8   C12  S13  C1     0.00   0.0  0
 PXH  CONST_03  S13  C12  C8   C4     0.00   0.0  0
 PXH  CONST_04  C12  S13  C1   C4     0.00   0.0  0
 PXH  CONST_05  S13  C1   C4   C8     0.00   0.0  0
 PXH  CONST_06  C8   C4   C1   C17  180.00   0.0  0
 PXH  CONST_07  C12  S13  C1   C17  180.00   0.0  0
 PXH  CONST_08  H21  C8   C4   C1   180.00   0.0  0
 PXH  CONST_09  H22  C12  S13  C1   180.00   0.0  0
 PXH  CONST_10  H20  C4   C8   C12  180.00   0.0  0
 PXH  Var_01    C4   C1   C17  C15  106.60  30.0  2
 PXH  Var_02    H9   C9   C2   C3    68.91  30.0  3
 PXH  Var_03    H6   C10  C2   C3    62.54  30.0  3
 PXH  Var_04    C1   C17  C15  C14  177.14  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
 PXH  chir_01  C3   N4   C2  C11  positiv
 PXH  chir_02  C5   S1   N4  C6   negativ
 PXH  chir_03  C6   C5   C7  C14  positiv
 PXH  chir_04  C14  O14  C6  C15  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
 PXH  plan-1  C17  0.020
 PXH  plan-1  C1   0.020
 PXH  plan-1  C4   0.020
 PXH  plan-1  C8   0.020
 PXH  plan-1  C12  0.020
 PXH  plan-1  S13  0.020
 PXH  plan-1  H20  0.020
 PXH  plan-1  H21  0.020
 PXH  plan-1  H22  0.020
 PXH  plan-2  O8   0.020
 PXH  plan-2  C7   0.020
 PXH  plan-2  C6   0.020
 PXH  plan-2  H1   0.020
 PXH  plan-3  C3   0.020
 PXH  plan-3  C11  0.020
 PXH  plan-3  O13  0.020
 PXH  plan-3  O12  0.020

