# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 23:09:31 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: (2~{S},4~{S})-4-(4-phenylphenyl)carbonyloxypyrrolidine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H]1C[C@@H](CN1)OC(=O)c2ccc(cc2)c3ccccc3
#
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
 TJ5  TJ5  "(2~{S},4~{S})-4-(4-phenylphenyl)carbonyloxypyrrolidine-2-carboxylic acid"  ligand  39  23  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TJ5
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
 TJ5  C10  C  C      0   0.598  121.6684  106.1385  107.0558
 TJ5  C13  C  CR16   0  -0.296  119.2326  105.5713  104.2556
 TJ5  C15  C  CR16   0  -0.294  121.4402  105.2431  103.3833
 TJ5  C17  C  CR6    0   0.089  119.4898  104.9812  101.8418
 TJ5  C20  C  CR16   0  -0.262  118.4047  104.4382   99.3179
 TJ5  C21  C  CR16   0  -0.237  119.5895  105.1538   99.4306
 TJ5  C22  C  CR16   0  -0.306  120.1275  105.4218  100.6805
 TJ5  C01  C  CH2    0  -0.460  125.1044  105.9538  108.2067
 TJ5  C02  C  CH1    0  -0.021  123.6495  106.3738  108.3499
 TJ5  C03  C  CH2    0  -0.317  123.7274  107.9126  108.5171
 TJ5  C05  C  CH1    0  -0.269  125.7649  107.2140  107.6282
 TJ5  C06  C  C      0   0.418  125.5819  107.2931  106.0921
 TJ5  C11  C  CR6    0  -0.105  121.1442  105.8178  105.7036
 TJ5  C12  C  CR16   0  -0.240  119.7664  105.8447  105.5016
 TJ5  C14  C  CR6    0   0.093  120.0601  105.2675  103.1726
 TJ5  C16  C  CR16   0  -0.253  121.9793  105.5132  104.6294
 TJ5  C18  C  CR16   0  -0.306  118.2981  104.2647  101.7156
 TJ5  C19  C  CR16   0  -0.237  117.7616  103.9942  100.4657
 TJ5  N04  N  NH1    0  -0.573  125.1252  108.3041  108.3574
 TJ5  O07  O  OC    -1  -0.593  124.9918  108.2777  105.6148
 TJ5  O08  O  O      0  -0.621  126.0701  106.3298  105.4630
 TJ5  O09  O  O2     0  -0.465  122.9798  106.0102  107.1286
 TJ5  O23  O  O      0  -0.447  120.9678  106.4785  107.9808
 TJ5  H1   H  HCR6   0   0.259  118.1596  105.6185  104.1209
 TJ5  H2   H  HCR6   0   0.260  122.1069  104.9906  102.5687
 TJ5  H3   H  HCR6   0   0.257  117.9853  104.2286   98.3425
 TJ5  H4   H  HCR6   0   0.258  120.0948  105.5113   98.5428
 TJ5  H5   H  HCR6   0   0.256  121.0415  105.9986  100.7507
 TJ5  H6   H  HCH2   0   0.242  125.2333  105.0516  107.6105
 TJ5  H7   H  HCH2   0   0.239  125.5069  105.7501  109.2022
 TJ5  H8   H  HCH1   0   0.255  123.1458  105.8858  109.1854
 TJ5  H9   H  HCH2   0   0.237  123.3497  108.2226  109.4913
 TJ5  H10  H  HCH2   0   0.228  123.1083  108.4022  107.7629
 TJ5  H11  H  HCH1   0   0.239  126.8392  107.2248  107.8354
 TJ5  H12  H  HCR6   0   0.261  119.1040  106.0890  106.3212
 TJ5  H13  H  HCR6   0   0.261  123.0530  105.4756  104.7549
 TJ5  H14  H  HCR6   0   0.256  117.7935  103.8953  102.5997
 TJ5  H15  H  HCR6   0   0.257  116.8412  103.4299  100.3891
 TJ5  H16  H  HNH1   0   0.339  125.5472  108.3485  109.2769

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
 TJ5  C20  C21  aromatic  1.389  0.020  1.389
 TJ5  C20  C19  aromatic  1.389  0.020  1.389
 TJ5  C21  C22  aromatic  1.387  0.020  1.387
 TJ5  C19  C18  aromatic  1.387  0.020  1.387
 TJ5  C22  C17  aromatic  1.396  0.020  1.396
 TJ5  C18  C17  aromatic  1.396  0.020  1.396
 TJ5  C17  C14  single    1.476  0.020  1.476
 TJ5  C14  C15  aromatic  1.396  0.020  1.396
 TJ5  C14  C13  aromatic  1.396  0.020  1.396
 TJ5  C15  C16  aromatic  1.384  0.020  1.384
 TJ5  C13  C12  aromatic  1.383  0.020  1.383
 TJ5  C16  C11  aromatic  1.394  0.020  1.394
 TJ5  O08  C06  deloc     1.250  0.020  1.250
 TJ5  O07  C06  deloc     1.243  0.020  1.243
 TJ5  C12  C11  aromatic  1.393  0.020  1.393
 TJ5  C11  C10  single    1.485  0.020  1.485
 TJ5  C06  C05  single    1.549  0.020  1.549
 TJ5  C10  O09  single    1.320  0.020  1.320
 TJ5  C10  O23  double    1.209  0.020  1.209
 TJ5  O09  C02  single    1.439  0.020  1.439
 TJ5  C05  C01  single    1.536  0.020  1.536
 TJ5  C05  N04  single    1.459  0.020  1.459
 TJ5  C01  C02  single    1.521  0.020  1.521
 TJ5  N04  C03  single    1.460  0.020  1.460
 TJ5  C03  C02  single    1.550  0.020  1.550
 TJ5  C13  H1   single    0.930  0.020  1.080
 TJ5  C15  H2   single    0.930  0.020  1.080
 TJ5  C20  H3   single    0.930  0.020  1.080
 TJ5  C21  H4   single    0.930  0.020  1.080
 TJ5  C22  H5   single    0.930  0.020  1.080
 TJ5  C01  H6   single    0.970  0.020  1.090
 TJ5  C01  H7   single    0.970  0.020  1.090
 TJ5  C02  H8   single    0.970  0.020  1.090
 TJ5  C03  H9   single    0.970  0.020  1.090
 TJ5  C03  H10  single    0.970  0.020  1.090
 TJ5  C05  H11  single    0.970  0.020  1.090
 TJ5  C12  H12  single    0.930  0.020  1.080
 TJ5  C16  H13  single    0.930  0.020  1.080
 TJ5  C18  H14  single    0.930  0.020  1.080
 TJ5  C19  H15  single    0.930  0.020  1.080
 TJ5  N04  H16  single    0.890  0.020  1.040

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
 TJ5  O23  C10  O09  124.12  3.000
 TJ5  O23  C10  C11  123.55  3.000
 TJ5  O09  C10  C11  112.33  3.000
 TJ5  H1   C13  C14  120.02  3.000
 TJ5  H1   C13  C12  119.09  3.000
 TJ5  C14  C13  C12  120.87  3.000
 TJ5  H2   C15  C16  118.89  3.000
 TJ5  H2   C15  C14  119.95  3.000
 TJ5  C16  C15  C14  121.15  3.000
 TJ5  C18  C17  C14  120.72  3.000
 TJ5  C14  C17  C22  120.82  3.000
 TJ5  C18  C17  C22  118.46  3.000
 TJ5  H3   C20  C19  120.23  3.000
 TJ5  H3   C20  C21  120.24  3.000
 TJ5  C19  C20  C21  119.53  3.000
 TJ5  H4   C21  C22  119.63  3.000
 TJ5  H4   C21  C20  120.13  3.000
 TJ5  C22  C21  C20  120.24  3.000
 TJ5  H5   C22  C21  119.26  3.000
 TJ5  H5   C22  C17  119.97  3.000
 TJ5  C21  C22  C17  120.76  3.000
 TJ5  H7   C01  H6   107.50  3.000
 TJ5  H7   C01  C05  109.73  3.000
 TJ5  H6   C01  C05  114.99  3.000
 TJ5  H7   C01  C02  108.55  3.000
 TJ5  H6   C01  C02  113.17  3.000
 TJ5  C05  C01  C02  102.73  3.000
 TJ5  H8   C02  O09  108.79  3.000
 TJ5  H8   C02  C03  112.63  3.000
 TJ5  O09  C02  C03  111.45  3.000
 TJ5  H8   C02  C01  112.97  3.000
 TJ5  C03  C02  C01  103.66  3.000
 TJ5  O09  C02  C01  107.18  3.000
 TJ5  H10  C03  H9   107.06  3.000
 TJ5  H10  C03  N04  110.31  3.000
 TJ5  H9   C03  N04  110.68  3.000
 TJ5  H10  C03  C02  110.01  3.000
 TJ5  H9   C03  C02  111.19  3.000
 TJ5  N04  C03  C02  107.61  3.000
 TJ5  H11  C05  N04  109.18  3.000
 TJ5  H11  C05  C06  107.66  3.000
 TJ5  N04  C05  C06  113.93  3.000
 TJ5  H11  C05  C01  111.04  3.000
 TJ5  N04  C05  C01  103.66  3.000
 TJ5  C06  C05  C01  111.39  3.000
 TJ5  O08  C06  O07  127.06  3.000
 TJ5  O07  C06  C05  118.51  3.000
 TJ5  O08  C06  C05  114.44  3.000
 TJ5  C16  C11  C12  119.01  3.000
 TJ5  C12  C11  C10  118.49  3.000
 TJ5  C16  C11  C10  122.49  3.000
 TJ5  H12  C12  C11  120.01  3.000
 TJ5  H12  C12  C13  119.41  3.000
 TJ5  C11  C12  C13  120.58  3.000
 TJ5  C17  C14  C15  120.97  3.000
 TJ5  C15  C14  C13  118.19  3.000
 TJ5  C17  C14  C13  120.84  3.000
 TJ5  H13  C16  C11  120.85  3.000
 TJ5  H13  C16  C15  118.96  3.000
 TJ5  C11  C16  C15  120.19  3.000
 TJ5  H14  C18  C19  119.28  3.000
 TJ5  H14  C18  C17  119.93  3.000
 TJ5  C19  C18  C17  120.78  3.000
 TJ5  H15  C19  C18  119.63  3.000
 TJ5  H15  C19  C20  120.14  3.000
 TJ5  C18  C19  C20  120.23  3.000
 TJ5  H16  N04  C05  107.68  3.000
 TJ5  H16  N04  C03  108.14  3.000
 TJ5  C05  N04  C03  105.90  3.000
 TJ5  C02  O09  C10  118.98  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
 TJ5  CONST_03  C16  C15  C14  C13    0.00   0.0  0
 TJ5  CONST_04  C16  C11  C12  C13    0.00   0.0  0
 TJ5  CONST_07  C12  C13  C14  C15    0.00   0.0  0
 TJ5  CONST_08  C12  C11  C16  C15    0.00   0.0  0
 TJ5  CONST_09  C20  C21  C22  C17    0.00   0.0  0
 TJ5  CONST_10  C20  C19  C18  C17    0.00   0.0  0
 TJ5  CONST_11  C16  C15  C14  C17  180.00   0.0  0
 TJ5  CONST_12  C12  C13  C14  C17  180.00   0.0  0
 TJ5  CONST_13  C18  C19  C20  C21    0.00   0.0  0
 TJ5  CONST_14  C18  C17  C22  C21    0.00   0.0  0
 TJ5  CONST_15  C14  C17  C22  C21  180.00   0.0  0
 TJ5  CONST_16  C19  C20  C21  C22    0.00   0.0  0
 TJ5  CONST_17  C19  C18  C17  C22    0.00   0.0  0
 TJ5  CONST_18  C14  C15  C16  C11    0.00   0.0  0
 TJ5  CONST_19  C14  C13  C12  C11    0.00   0.0  0
 TJ5  CONST_20  C19  C18  C17  C14  180.00   0.0  0
 TJ5  CONST_21  C15  C16  C11  C10  180.00   0.0  0
 TJ5  CONST_22  C13  C12  C11  C10  180.00   0.0  0
 TJ5  CONST_23  H2   C15  C14  C13  180.00   0.0  0
 TJ5  CONST_24  H1   C13  C14  C15  180.00   0.0  0
 TJ5  CONST_25  H4   C21  C22  C17  180.00   0.0  0
 TJ5  CONST_26  H15  C19  C18  C17  180.00   0.0  0
 TJ5  CONST_27  H2   C15  C14  C17    0.00   0.0  0
 TJ5  CONST_28  H1   C13  C14  C17    0.00   0.0  0
 TJ5  CONST_29  H5   C22  C21  C20  180.00   0.0  0
 TJ5  CONST_30  H14  C18  C19  C20  180.00   0.0  0
 TJ5  CONST_31  H15  C19  C20  C21  180.00   0.0  0
 TJ5  CONST_32  H3   C20  C21  C22  180.00   0.0  0
 TJ5  CONST_33  H14  C18  C17  C22  180.00   0.0  0
 TJ5  CONST_34  H2   C15  C16  C11  180.00   0.0  0
 TJ5  CONST_35  H1   C13  C12  C11  180.00   0.0  0
 TJ5  CONST_36  H13  C16  C11  C12  180.00   0.0  0
 TJ5  CONST_37  H5   C22  C17  C14    0.00   0.0  0
 TJ5  CONST_38  H14  C18  C17  C14    0.00   0.0  0
 TJ5  CONST_39  H13  C16  C15  C14  180.00   0.0  0
 TJ5  CONST_40  H12  C12  C13  C14  180.00   0.0  0
 TJ5  CONST_41  H12  C12  C11  C16  180.00   0.0  0
 TJ5  CONST_42  H3   C20  C19  C18  180.00   0.0  0
 TJ5  CONST_43  H5   C22  C17  C18  180.00   0.0  0
 TJ5  CONST_44  H4   C21  C20  C19  180.00   0.0  0
 TJ5  Var_01    C05  N04  C03  C02   20.88  30.0  1
 TJ5  Var_02    H16  N04  C03  C02  -94.32  30.0  1
 TJ5  Var_03    H9   C03  N04  C05  142.55  30.0  1
 TJ5  Var_04    H10  C03  N04  C05  -99.15  30.0  1
 TJ5  Var_05    C11  C10  O09  C02  175.81  30.0  1
 TJ5  Var_06    O09  C10  C11  C12  176.75  30.0  2
 TJ5  Var_07    O23  C10  C11  C12   -3.28  30.0  2
 TJ5  Var_08    O09  C10  C11  C16   -4.30  30.0  2
 TJ5  Var_09    O23  C10  C11  C16  175.67  30.0  2
 TJ5  Var_10    O23  C10  O09  C02   -4.16  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
 TJ5  chir_01  C02  O09  C01  C03  negativ
 TJ5  chir_02  C05  N04  C01  C06  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
 TJ5  plan-1  C17  0.020
 TJ5  plan-1  C20  0.020
 TJ5  plan-1  C21  0.020
 TJ5  plan-1  C22  0.020
 TJ5  plan-1  C14  0.020
 TJ5  plan-1  C18  0.020
 TJ5  plan-1  C19  0.020
 TJ5  plan-1  H3   0.020
 TJ5  plan-1  H4   0.020
 TJ5  plan-1  H5   0.020
 TJ5  plan-1  H14  0.020
 TJ5  plan-1  H15  0.020
 TJ5  plan-2  C10  0.020
 TJ5  plan-2  C13  0.020
 TJ5  plan-2  C15  0.020
 TJ5  plan-2  C17  0.020
 TJ5  plan-2  C11  0.020
 TJ5  plan-2  C12  0.020
 TJ5  plan-2  C14  0.020
 TJ5  plan-2  C16  0.020
 TJ5  plan-2  H1   0.020
 TJ5  plan-2  H2   0.020
 TJ5  plan-2  H12  0.020
 TJ5  plan-2  H13  0.020
 TJ5  plan-3  C05  0.020
 TJ5  plan-3  C06  0.020
 TJ5  plan-3  O07  0.020
 TJ5  plan-3  O08  0.020
 TJ5  plan-4  C10  0.020
 TJ5  plan-4  C11  0.020
 TJ5  plan-4  O09  0.020
 TJ5  plan-4  O23  0.020

