# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 23 22:24:16 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  43  23  .  2021-08-20  2021-08-20  
;
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  -0.355  -4.0618   0.9136   0.4169
 PNM  C7    C  C1    0   0.181  -3.5197  -0.0624   0.8615
 PNM  N4    N  NH1   0  -0.591  -0.9725   0.5852   2.3679
 PNM  C3    C  CH1   0  -0.173   0.2679   0.5807   3.1015
 PNM  C11   C  C     0   0.540   0.1615  -0.0904   4.4638
 PNM  O13   O  OH1   0  -0.588   1.0098   0.4350   5.3364
 PNM  O12   O  O     0  -0.422  -0.6059  -0.9800   4.7309
 PNM  C2    C  CT    0  -0.206   1.2969  -0.1162   2.1803
 PNM  C10   C  CH3   0  -0.651   2.5006  -0.7212   2.8914
 PNM  C9    C  CH3   0  -0.623   1.7779   0.8652   1.1170
 PNM  S1    S  S2    0   0.041   0.3131  -1.4771   1.4312
 PNM  C5    C  CH1   0  -0.211  -1.2960  -0.6987   1.7804
 PNM  C6    C  CH1   0  -0.203  -2.1197  -0.5046   0.4961
 PNM  N14   N  NH1   0  -0.614  -1.4838   0.3925  -0.4112
 PNM  C15   C  C     0   0.571  -1.2488   0.1180  -1.7062
 PNM  O16   O  O     0  -0.479  -1.5925  -0.9195  -2.2471
 PNM  C17   C  CH2   0  -0.690  -0.5438   1.2277  -2.4682
 PNM  C18   C  CR6   0   0.147   0.4273   0.6812  -3.4739
 PNM  C19   C  CR16  0  -0.301   0.0210   0.3832  -4.7709
 PNM  C20   C  CR16  0  -0.243   0.9179  -0.1430  -5.6911
 PNM  C21   C  CR16  0  -0.269   2.2355  -0.3828  -5.3230
 PNM  C22   C  CR16  0  -0.243   2.6500  -0.0907  -4.0300
 PNM  C23   C  CR16  0  -0.294   1.7503   0.4378  -3.1142
 PNM  HC7   H  H     0   0.206  -4.0255  -0.7289   1.5820
 PNM  H4    H  HNH1  0   0.383  -1.7410   0.9596   2.9113
 PNM  HC3   H  HCH1  0   0.301   0.5924   1.6135   3.2602
 PNM  HXT   H  HOH1  0   0.483   0.9484  -0.0277   6.1862
 PNM  H101  H  HCH3  0   0.254   3.1577  -1.1956   2.1620
 PNM  H102  H  HCH3  0   0.249   3.0788   0.0554   3.3933
 PNM  H103  H  HCH3  0   0.246   2.2276  -1.4810   3.6229
 PNM  HC91  H  HCH3  0   0.246   2.3635   0.3489   0.3565
 PNM  HC92  H  HCH3  0   0.232   0.9489   1.3698   0.6264
 PNM  HC93  H  HCH3  0   0.240   2.4149   1.6259   1.5733
 PNM  HC5   H  HCH1  0   0.285  -1.8531  -1.3635   2.4480
 PNM  HC6   H  HCH1  0   0.312  -2.2353  -1.4861   0.0237
 PNM  H14   H  HNH1  0   0.405  -1.1532   1.2608  -0.0196
 PNM  H171  H  HCH2  0   0.300  -1.3207   1.8115  -2.9702
 PNM  H172  H  HCH2  0   0.272  -0.0412   1.9127  -1.7824
 PNM  H19   H  HCR6  0   0.248  -1.0034   0.5719  -5.0686
 PNM  H20   H  HCR6  0   0.254   0.5880  -0.3651  -6.6979
 PNM  H21   H  HCR6  0   0.255   2.9361  -0.7902  -6.0406
 PNM  H22   H  HCR6  0   0.255   3.6756  -0.2715  -3.7347
 PNM  H23   H  HCR6  0   0.250   2.0847   0.6674  -2.1087

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    1.513  0.020  1.513
 PNM  C7   HC7   single    0.930  0.020  1.080
 PNM  N4   C3    single    1.441  0.020  1.441
 PNM  N4   C5    single    1.449  0.020  1.449
 PNM  N4   H4    single    0.890  0.020  1.040
 PNM  C3   C11   single    1.522  0.020  1.522
 PNM  C3   C2    single    1.547  0.020  1.547
 PNM  C3   HC3   single    0.970  0.020  1.090
 PNM  C11  O13   single    1.326  0.020  1.326
 PNM  C11  O12   double    1.205  0.020  1.205
 PNM  O13  HXT   single    0.850  0.020  0.980
 PNM  C2   C10   single    1.523  0.020  1.523
 PNM  C2   C9    single    1.525  0.020  1.525
 PNM  C2   S1    single    1.839  0.020  1.839
 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    1.821  0.020  1.821
 PNM  C5   C6    single    1.538  0.020  1.538
 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    1.344  0.020  1.344
 PNM  N14  H14   single    0.860  0.020  1.020
 PNM  C15  O16   double    1.219  0.020  1.219
 PNM  C15  C17   single    1.520  0.020  1.520
 PNM  C17  C18   single    1.501  0.020  1.501
 PNM  C17  H171  single    0.970  0.020  1.090
 PNM  C17  H172  single    0.970  0.020  1.090
 PNM  C18  C19   aromatic  1.391  0.020  1.391
 PNM  C18  C23   aromatic  1.392  0.020  1.392
 PNM  C19  C20   aromatic  1.389  0.020  1.389
 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    113.89  3.000
 PNM  HC7   C7   O8    121.67  3.000
 PNM  C6    C7   O8    124.44  3.000
 PNM  H4    N4   C5    112.07  3.000
 PNM  H4    N4   C3    112.41  3.000
 PNM  C5    N4   C3    113.33  3.000
 PNM  HC3   C3   C2    108.32  3.000
 PNM  HC3   C3   C11   107.88  3.000
 PNM  C2    C3   C11   112.38  3.000
 PNM  HC3   C3   N4    109.04  3.000
 PNM  C2    C3   N4    105.72  3.000
 PNM  C11   C3   N4    113.37  3.000
 PNM  O12   C11  O13   123.66  3.000
 PNM  O12   C11  C3    124.64  3.000
 PNM  O13   C11  C3    111.69  3.000
 PNM  HXT   O13  C11   110.32  3.000
 PNM  S1    C2   C9    111.16  3.000
 PNM  S1    C2   C10   108.60  3.000
 PNM  C9    C2   C10   109.38  3.000
 PNM  S1    C2   C3    102.71  3.000
 PNM  C9    C2   C3    109.58  3.000
 PNM  C10   C2   C3    115.25  3.000
 PNM  H103  C10  H102  108.69  3.000
 PNM  H103  C10  H101  107.26  3.000
 PNM  H102  C10  H101  107.35  3.000
 PNM  H103  C10  C2    113.10  3.000
 PNM  H102  C10  C2    110.55  3.000
 PNM  H101  C10  C2    109.68  3.000
 PNM  HC93  C9   HC92  108.06  3.000
 PNM  HC93  C9   HC91  107.94  3.000
 PNM  HC92  C9   HC91  108.34  3.000
 PNM  HC93  C9   C2    109.93  3.000
 PNM  HC92  C9   C2    111.89  3.000
 PNM  HC91  C9   C2    110.56  3.000
 PNM  C5    S1   C2     94.49  3.000
 PNM  HC5   C5   C6    108.26  3.000
 PNM  HC5   C5   S1    107.88  3.000
 PNM  C6    C5   S1    111.53  3.000
 PNM  HC5   C5   N4    113.87  3.000
 PNM  C6    C5   N4    110.27  3.000
 PNM  S1    C5   N4    105.03  3.000
 PNM  HC6   C6   N14   109.66  3.000
 PNM  HC6   C6   C5    107.68  3.000
 PNM  N14   C6   C5    111.84  3.000
 PNM  HC6   C6   C7    105.56  3.000
 PNM  N14   C6   C7    112.49  3.000
 PNM  C5    C6   C7    109.32  3.000
 PNM  H14   N14  C15   119.52  3.000
 PNM  H14   N14  C6    116.16  3.000
 PNM  C15   N14  C6    124.23  3.000
 PNM  C17   C15  O16   121.98  3.000
 PNM  C17   C15  N14   114.52  3.000
 PNM  O16   C15  N14   123.48  3.000
 PNM  H172  C17  H171  106.28  3.000
 PNM  H172  C17  C18   110.58  3.000
 PNM  H171  C17  C18   110.26  3.000
 PNM  H172  C17  C15   110.90  3.000
 PNM  H171  C17  C15   106.88  3.000
 PNM  C18   C17  C15   111.73  3.000
 PNM  C23   C18  C19   118.73  3.000
 PNM  C23   C18  C17   120.35  3.000
 PNM  C19   C18  C17   120.90  3.000
 PNM  H19   C19  C20   119.65  3.000
 PNM  H19   C19  C18   119.67  3.000
 PNM  C20   C19  C18   120.68  3.000
 PNM  H20   C20  C21   120.01  3.000
 PNM  H20   C20  C19   119.82  3.000
 PNM  C21   C20  C19   120.17  3.000
 PNM  H21   C21  C22   120.21  3.000
 PNM  H21   C21  C20   120.21  3.000
 PNM  C22   C21  C20   119.57  3.000
 PNM  H22   C22  C23   119.84  3.000
 PNM  H22   C22  C21   120.11  3.000
 PNM  C23   C22  C21   120.05  3.000
 PNM  H23   C23  C22   119.51  3.000
 PNM  H23   C23  C18   119.70  3.000
 PNM  C22   C23  C18   120.79  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  HXT   O13  C11  C3    180.00   0.0  0
 PNM  CONST_15  O16   C15  N14  C6      0.00   0.0  0
 PNM  CONST_16  C17   C15  N14  C6    180.00   0.0  0
 PNM  CONST_17  H14   N14  C15  O16   180.00   0.0  0
 PNM  Var_01    C19   C18  C17  C15    88.94  30.0  2
 PNM  Var_02    H101  C10  C2   C3    179.38  30.0  3
 PNM  Var_03    HC91  C9   C2   C3   -169.95  30.0  3
 PNM  Var_04    C18   C17  C15  N14   143.47  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-3  HXT  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

