# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 19:22:05 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-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
#
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
 PNM  PNM  '(2R,4S)-5,5-dimethyl-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-1,3-thiazolidine-4-carboxylic acid'  ligand  42  23  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_PNM
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
 PNM  O8    O  O      0  -0.354  -2.4786  -0.5558  -1.3279
 PNM  C7    C  C1     0   0.175  -2.2259  -1.2123  -0.3536
 PNM  N4    N  NH1    0  -0.598  -0.8204   0.5215   1.7572
 PNM  C3    C  CH1    0  -0.174  -0.2135   1.0079   2.9876
 PNM  C11   C  C      0   0.408  -1.1227   0.9164   4.2379
 PNM  O13   O  OC    -1  -0.610  -0.8195   1.6735   5.1801
 PNM  O12   O  O      0  -0.586  -2.0799   0.1202   4.1969
 PNM  C2    C  CT     0  -0.197   1.1206   0.2394   3.1109
 PNM  C10   C  CH3    0  -0.630   1.6952   0.1496   4.5182
 PNM  C9    C  CH3    0  -0.618   2.1692   0.8422   2.1786
 PNM  S1    S  S2     0   0.007   0.6767  -1.4572   2.5541
 PNM  C5    C  CH1    0  -0.220  -0.8340  -0.9255   1.6889
 PNM  C6    C  CH1    0  -0.187  -0.8363  -1.3900   0.2235
 PNM  N14   N  NH1    0  -0.610   0.1509  -0.6874  -0.5286
 PNM  C15   C  C      0   0.556   0.6634  -1.1376  -1.6828
 PNM  O16   O  O      0  -0.492   0.4164  -2.2422  -2.1417
 PNM  C17   C  CH2    0  -0.665   1.5803  -0.1652  -2.4038
 PNM  C18   C  CR6    0   0.130   0.9636   0.2304  -3.7180
 PNM  C19   C  CR16   0  -0.282   0.0922   1.3145  -3.7859
 PNM  C20   C  CR16   0  -0.243  -0.5139   1.6618  -4.9854
 PNM  C21   C  CR16   0  -0.269  -0.2592   0.9237  -6.1342
 PNM  C22   C  CR16   0  -0.242   0.6066  -0.1602  -6.0746
 PNM  C23   C  CR16   0  -0.303   1.2107  -0.5056  -4.8732
 PNM  HC7   H  H      0   0.207  -3.0145  -1.7515   0.2024
 PNM  H4    H  HNH1   0   0.364  -1.7675   0.8740   1.6774
 PNM  HC3   H  HCH1   0   0.244   0.0398   2.0660   2.8438
 PNM  H101  H  HCH3   0   0.229   2.6366  -0.4022   4.4992
 PNM  H102  H  HCH3   0   0.234   1.9013   1.1463   4.9083
 PNM  H103  H  HCH3   0   0.237   1.0245  -0.3556   5.2100
 PNM  HC91  H  HCH3   0   0.234   3.0452   0.1977   2.1000
 PNM  HC92  H  HCH3   0   0.226   1.7776   0.9997   1.1755
 PNM  HC93  H  HCH3   0   0.230   2.4975   1.8108   2.5636
 PNM  HC5   H  HCH1   0   0.277  -1.6883  -1.3798   2.1982
 PNM  HC6   H  HCH1   0   0.302  -0.6425  -2.4685   0.2106
 PNM  H14   H  HNH1   0   0.403   0.3057   0.2673  -0.2381
 PNM  H171  H  HCH2   0   0.269   1.7873   0.7206  -1.8001
 PNM  H172  H  HCH2   0   0.288   2.5361  -0.6673  -2.5667
 PNM  H19   H  HCR6   0   0.247  -0.1115   1.8955  -2.8939
 PNM  H20   H  HCR6   0   0.255  -1.1863   2.5093  -5.0227
 PNM  H21   H  HCR6   0   0.255  -0.7304   1.1932  -7.0706
 PNM  H22   H  HCR6   0   0.254   0.8118  -0.7401  -6.9654
 PNM  H23   H  HCR6   0   0.249   1.8890  -1.3491  -4.8369

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
 PNM  O8   C7    double    1.202  0.020  1.202
 PNM  C7   C6    single    1.515  0.020  1.515
 PNM  C7   HC7   single    0.930  0.020  1.080
 PNM  N4   C3    single    1.456  0.020  1.456
 PNM  N4   C5    single    1.449  0.020  1.449
 PNM  N4   H4    single    0.890  0.020  1.040
 PNM  C3   C11   single    1.549  0.020  1.549
 PNM  C3   C2    single    1.545  0.020  1.545
 PNM  C3   HC3   single    0.970  0.020  1.090
 PNM  C11  O13   deloc     1.246  0.020  1.246
 PNM  C11  O12   deloc     1.246  0.020  1.246
 PNM  C2   C10   single    1.523  0.020  1.523
 PNM  C2   C9    single    1.527  0.020  1.527
 PNM  C2   S1    single    1.840  0.020  1.840
 PNM  C10  H101  single    0.970  0.020  1.090
 PNM  C10  H102  single    0.970  0.020  1.090
 PNM  C10  H103  single    0.970  0.020  1.090
 PNM  C9   HC91  single    0.970  0.020  1.090
 PNM  C9   HC92  single    0.970  0.020  1.090
 PNM  C9   HC93  single    0.970  0.020  1.090
 PNM  S1   C5    single    1.820  0.020  1.820
 PNM  C5   C6    single    1.537  0.020  1.537
 PNM  C5   HC5   single    0.970  0.020  1.090
 PNM  C6   N14   single    1.426  0.020  1.426
 PNM  C6   HC6   single    0.970  0.020  1.090
 PNM  N14  C15   single    1.341  0.020  1.341
 PNM  N14  H14   single    0.860  0.020  1.020
 PNM  C15  O16   double    1.221  0.020  1.221
 PNM  C15  C17   single    1.519  0.020  1.519
 PNM  C17  C18   single    1.505  0.020  1.505
 PNM  C17  H171  single    0.970  0.020  1.090
 PNM  C17  H172  single    0.970  0.020  1.090
 PNM  C18  C19   aromatic  1.393  0.020  1.393
 PNM  C18  C23   aromatic  1.392  0.020  1.392
 PNM  C19  C20   aromatic  1.388  0.020  1.388
 PNM  C19  H19   single    0.930  0.020  1.080
 PNM  C20  C21   aromatic  1.389  0.020  1.389
 PNM  C20  H20   single    0.930  0.020  1.080
 PNM  C21  C22   aromatic  1.389  0.020  1.389
 PNM  C21  H21   single    0.930  0.020  1.080
 PNM  C22  C23   aromatic  1.388  0.020  1.388
 PNM  C22  H22   single    0.930  0.020  1.080
 PNM  C23  H23   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
 PNM  HC7   C7   C6    113.92  3.000
 PNM  HC7   C7   O8    121.62  3.000
 PNM  C6    C7   O8    124.45  3.000
 PNM  H4    N4   C5    109.56  3.000
 PNM  H4    N4   C3    109.87  3.000
 PNM  C5    N4   C3    112.18  3.000
 PNM  HC3   C3   C2    106.91  3.000
 PNM  HC3   C3   C11   107.35  3.000
 PNM  C2    C3   C11   114.41  3.000
 PNM  HC3   C3   N4    107.92  3.000
 PNM  C2    C3   N4    105.15  3.000
 PNM  C11   C3   N4    114.70  3.000
 PNM  O12   C11  O13   126.88  3.000
 PNM  O12   C11  C3    117.53  3.000
 PNM  O13   C11  C3    115.58  3.000
 PNM  S1    C2   C9    110.18  3.000
 PNM  S1    C2   C10   108.44  3.000
 PNM  C9    C2   C10   109.17  3.000
 PNM  S1    C2   C3    103.08  3.000
 PNM  C9    C2   C3    110.36  3.000
 PNM  C10   C2   C3    115.41  3.000
 PNM  H103  C10  H102  108.28  3.000
 PNM  H103  C10  H101  107.94  3.000
 PNM  H102  C10  H101  107.79  3.000
 PNM  H103  C10  C2    112.48  3.000
 PNM  H102  C10  C2    110.38  3.000
 PNM  H101  C10  C2    109.83  3.000
 PNM  HC93  C9   HC92  107.73  3.000
 PNM  HC93  C9   HC91  107.94  3.000
 PNM  HC92  C9   HC91  107.95  3.000
 PNM  HC93  C9   C2    109.95  3.000
 PNM  HC92  C9   C2    111.88  3.000
 PNM  HC91  C9   C2    111.24  3.000
 PNM  C5    S1   C2     94.28  3.000
 PNM  HC5   C5   C6    108.50  3.000
 PNM  HC5   C5   S1    107.80  3.000
 PNM  C6    C5   S1    111.47  3.000
 PNM  HC5   C5   N4    113.60  3.000
 PNM  C6    C5   N4    110.29  3.000
 PNM  S1    C5   N4    105.16  3.000
 PNM  HC6   C6   N14   110.87  3.000
 PNM  HC6   C6   C5    107.96  3.000
 PNM  N14   C6   C5    110.66  3.000
 PNM  HC6   C6   C7    105.85  3.000
 PNM  N14   C6   C7    112.10  3.000
 PNM  C5    C6   C7    109.21  3.000
 PNM  H14   N14  C15   120.43  3.000
 PNM  H14   N14  C6    114.85  3.000
 PNM  C15   N14  C6    123.58  3.000
 PNM  C17   C15  O16   121.52  3.000
 PNM  C17   C15  N14   115.12  3.000
 PNM  O16   C15  N14   123.36  3.000
 PNM  H172  C17  H171  106.83  3.000
 PNM  H172  C17  C18   110.45  3.000
 PNM  H171  C17  C18   110.33  3.000
 PNM  H172  C17  C15   107.75  3.000
 PNM  H171  C17  C15   111.81  3.000
 PNM  C18   C17  C15   109.61  3.000
 PNM  C23   C18  C19   118.83  3.000
 PNM  C23   C18  C17   120.87  3.000
 PNM  C19   C18  C17   120.25  3.000
 PNM  H19   C19  C20   119.67  3.000
 PNM  H19   C19  C18   119.65  3.000
 PNM  C20   C19  C18   120.68  3.000
 PNM  H20   C20  C21   120.09  3.000
 PNM  H20   C20  C19   119.80  3.000
 PNM  C21   C20  C19   120.11  3.000
 PNM  H21   C21  C22   120.19  3.000
 PNM  H21   C21  C20   120.23  3.000
 PNM  C22   C21  C20   119.58  3.000
 PNM  H22   C22  C23   119.76  3.000
 PNM  H22   C22  C21   120.06  3.000
 PNM  C23   C22  C21   120.18  3.000
 PNM  H23   C23  C22   119.69  3.000
 PNM  H23   C23  C18   119.68  3.000
 PNM  C22   C23  C18   120.62  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
 PNM  CONST_01  C21   C20  C19  C18     0.00   0.0  0
 PNM  CONST_02  C21   C22  C23  C18     0.00   0.0  0
 PNM  CONST_03  C22   C23  C18  C19     0.00   0.0  0
 PNM  CONST_04  C22   C21  C20  C19     0.00   0.0  0
 PNM  CONST_05  C23   C18  C19  C20     0.00   0.0  0
 PNM  CONST_06  C23   C22  C21  C20     0.00   0.0  0
 PNM  CONST_07  C20   C19  C18  C17   180.00   0.0  0
 PNM  CONST_08  C22   C23  C18  C17   180.00   0.0  0
 PNM  CONST_09  H20   C20  C19  C18   180.00   0.0  0
 PNM  CONST_10  H22   C22  C23  C18   180.00   0.0  0
 PNM  CONST_11  H23   C23  C18  C19   180.00   0.0  0
 PNM  CONST_12  H21   C21  C20  C19   180.00   0.0  0
 PNM  CONST_13  H19   C19  C20  C21   180.00   0.0  0
 PNM  CONST_14  O16   C15  N14  C6      0.00   0.0  0
 PNM  CONST_15  C17   C15  N14  C6    180.00   0.0  0
 PNM  CONST_16  H14   N14  C15  O16   180.00   0.0  0
 PNM  Var_01    C19   C18  C17  C15    88.23  30.0  2
 PNM  Var_02    H101  C10  C2   C3   -179.56  30.0  3
 PNM  Var_03    HC91  C9   C2   C3   -168.48  30.0  3
 PNM  Var_04    C18   C17  C15  N14  -115.30  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
 PNM  chir_01  C3  N4   C11  C2  negativ
 PNM  chir_02  C5  S1   N4   C6  negativ
 PNM  chir_03  C6  N14  C5   C7  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
 PNM  plan-1  C17  0.020
 PNM  plan-1  C18  0.020
 PNM  plan-1  C19  0.020
 PNM  plan-1  C20  0.020
 PNM  plan-1  C21  0.020
 PNM  plan-1  C22  0.020
 PNM  plan-1  C23  0.020
 PNM  plan-1  H19  0.020
 PNM  plan-1  H20  0.020
 PNM  plan-1  H21  0.020
 PNM  plan-1  H22  0.020
 PNM  plan-1  H23  0.020
 PNM  plan-2  C6   0.020
 PNM  plan-2  N14  0.020
 PNM  plan-2  C15  0.020
 PNM  plan-2  O16  0.020
 PNM  plan-2  C17  0.020
 PNM  plan-2  H14  0.020
 PNM  plan-3  C3   0.020
 PNM  plan-3  C11  0.020
 PNM  plan-3  O13  0.020
 PNM  plan-3  O12  0.020
 PNM  plan-4  O8   0.020
 PNM  plan-4  C7   0.020
 PNM  plan-4  C6   0.020
 PNM  plan-4  HC7  0.020

