# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  2 09:41:04 2021
#   Inital geometry file: a 162 line input string
#   Ligand name: N~2~-{[2-(3-chlorophenyl)-2-methylpropoxy]carbonyl}-N-{(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)OCC(C)(C)c1cccc(Cl)c1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)S
#
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
 TKV  TKV  N~2~-{[2-(3-chlorophenyl)-2-methylpropoxy]carbonyl}-N-{(1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-1-sulfanylpropan-2-yl}-L-leucinamide  ligand  70  34  .  2022-07-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_TKV
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
 TKV  C01  C   CH3   0  -0.651  -24.0973  34.8996   -6.1478
 TKV  C02  C   CT    0  -0.196  -22.7821  35.1369   -6.8986
 TKV  C03  C   CH2   0  -0.157  -22.8122  36.5783   -7.4291
 TKV  C05  C   C     0   0.782  -20.6811  37.6195   -7.4073
 TKV  C07  C   CH1   0  -0.192  -18.3888  38.3707   -7.5174
 TKV  C08  C   CH2   0  -0.445  -17.1415  38.1433   -8.3706
 TKV  C09  C   CH1   0  -0.239  -16.6385  36.6974   -8.4099
 TKV  C10  C   CH3   0  -0.651  -15.4567  36.5994   -9.3694
 TKV  C11  C   CH3   0  -0.665  -16.2542  36.1857   -7.0260
 TKV  C12  C   C     0   0.578  -18.7211  39.8643   -7.4946
 TKV  C14  C   CH1   0  -0.112  -18.5309  41.8988   -6.1140
 TKV  C15  C   CH2   0  -0.437  -19.3295  42.0675   -4.8240
 TKV  C16  C   CR15  0  -0.428  -20.6510  41.3194   -4.8622
 TKV  C17  C   CR5   0   0.568  -21.4553  41.4476   -3.5803
 TKV  C19  C   CH2   0  -0.262  -22.9953  41.3442   -5.3470
 TKV  C20  C   CH2   0  -0.466  -21.6452  41.7462   -5.9400
 TKV  C22  C   CH1   0  -0.048  -17.2228  42.6851   -6.0895
 TKV  C26  C   CH3   0  -0.669  -22.7272  34.1602   -8.0747
 TKV  C27  C   CR6   0   0.144  -21.5794  34.9854   -5.9727
 TKV  C28  C   CR16  0  -0.231  -21.6048  35.5503   -4.6976
 TKV  C29  C   CR6   0  -0.020  -20.4931  35.4794   -3.8793
 TKV  C31  C   CR16  0  -0.239  -19.3257  34.8532   -4.2855
 TKV  C32  C   CR16  0  -0.238  -19.2986  34.2881   -5.5493
 TKV  C33  C   CR16  0  -0.295  -20.4071  34.3555   -6.3829
 TKV  N06  N   NH1   0  -0.665  -19.4974  37.6243   -8.0469
 TKV  N13  N   NH1   0  -0.623  -18.2925  40.5058   -6.3970
 TKV  N18  N   NR15  0  -0.630  -22.7536  41.4812   -3.9247
 TKV  O04  O   O2    0  -0.492  -21.5930  36.9057   -8.0856
 TKV  O21  O   O     0  -0.498  -21.0093  41.4894   -2.4442
 TKV  O24  O   O     0  -0.492  -19.3002  40.3985   -8.4262
 TKV  O25  O   O     0  -0.477  -20.8927  38.2018   -6.3669
 TKV  CL3  CL  CL    0  -0.142  -20.5603  36.2063   -2.3022
 TKV  S1   S   S2    0  -0.277  -16.0387  42.0284   -4.8251
 TKV  H1   H   HCH3  0   0.235  -24.2656  35.6263   -5.3532
 TKV  H2   H   HCH3  0   0.239  -24.9427  34.9709   -6.8343
 TKV  H3   H   HCH3  0   0.244  -24.1129  33.9037   -5.7042
 TKV  H4   H   HCH2  0   0.249  -23.0188  37.2867   -6.6244
 TKV  H5   H   HCH2  0   0.246  -23.6020  36.6769   -8.1772
 TKV  H6   H   HCH1  0   0.263  -18.1876  38.0364   -6.4948
 TKV  H7   H   HCH2  0   0.243  -16.3427  38.7832   -7.9814
 TKV  H8   H   HCH2  0   0.246  -17.3445  38.4900   -9.3891
 TKV  H9   H   HCH1  0   0.221  -17.4360  36.0553   -8.7999
 TKV  H10  H   HCH3  0   0.229  -15.0999  35.5717   -9.4508
 TKV  H11  H   HCH3  0   0.227  -15.7263  36.9383  -10.3710
 TKV  H12  H   HCH3  0   0.216  -14.6205  37.2126   -9.0244
 TKV  H13  H   HCH3  0   0.235  -17.1026  36.1666   -6.3414
 TKV  H14  H   HCH3  0   0.231  -15.8666  35.1674   -7.0841
 TKV  H15  H   HCH3  0   0.217  -15.4775  36.8133   -6.5822
 TKV  H16  H   HCH1  0   0.284  -19.1114  42.3054   -6.9452
 TKV  H17  H   HCH2  0   0.238  -18.7414  41.7085   -3.9750
 TKV  H18  H   HCH2  0   0.244  -19.5053  43.1351   -4.6591
 TKV  H19  H   HCR5  0   0.303  -20.4538  40.2473   -4.9876
 TKV  H20  H   HCH2  0   0.249  -23.8125  41.9877   -5.6709
 TKV  H21  H   HCH2  0   0.235  -23.2494  40.3126   -5.6083
 TKV  H22  H   HCH2  0   0.259  -21.4578  41.2732   -6.9017
 TKV  H23  H   HCH2  0   0.238  -21.6067  42.8304   -6.0798
 TKV  H24  H   HCH1  0   0.265  -17.4362  43.7218   -5.8080
 TKV  H25  H   HCH3  0   0.238  -22.6919  33.1276   -7.7241
 TKV  H26  H   HCH3  0   0.240  -23.6248  34.2711   -8.6850
 TKV  H27  H   HCH3  0   0.240  -21.8702  34.3228   -8.7278
 TKV  H28  H   HCR6  0   0.258  -22.4868  36.0606   -4.3362
 TKV  H29  H   HCR6  0   0.275  -18.4636  34.8063   -3.6341
 TKV  H30  H   HCR6  0   0.259  -18.3990  33.7939   -5.8926
 TKV  H31  H   HCR6  0   0.252  -20.3415  33.9037   -7.3623
 TKV  H32  H   HNH1  0   0.399  -19.4090  37.1613   -8.9368
 TKV  H33  H   HNH1  0   0.393  -17.8682  39.9623   -5.6604
 TKV  H34  H   HNR5  0   0.394  -23.4905  41.4293   -3.2389
 TKV  H36  H   HSH1  0   0.226  -16.4138  42.8089   -3.8058
 TKV  O23  O   OH1   0  -0.629  -16.6339  42.5753   -7.3389
 TKV  H35  H   HOH1  0   0.463  -15.8835  43.1773   -7.3853

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
 TKV  C10  C09  single    1.525  0.020  1.525
 TKV  C09  C08  single    1.531  0.020  1.531
 TKV  C09  C11  single    1.525  0.020  1.525
 TKV  C08  C07  single    1.528  0.020  1.528
 TKV  O24  C12  double    1.220  0.020  1.220
 TKV  C26  C02  single    1.530  0.020  1.530
 TKV  N06  C07  single    1.438  0.020  1.438
 TKV  N06  C05  single    1.345  0.020  1.345
 TKV  O23  C22  single    1.386  0.020  1.386
 TKV  C07  C12  single    1.530  0.020  1.530
 TKV  O04  C05  single    1.342  0.020  1.342
 TKV  O04  C03  single    1.423  0.020  1.423
 TKV  C12  N13  single    1.342  0.020  1.342
 TKV  C05  O25  double    1.211  0.020  1.211
 TKV  C02  C03  single    1.536  0.020  1.536
 TKV  C02  C01  single    1.533  0.020  1.533
 TKV  C02  C27  single    1.525  0.020  1.525
 TKV  C33  C27  aromatic  1.393  0.020  1.393
 TKV  C33  C32  aromatic  1.389  0.020  1.389
 TKV  N13  C14  single    1.441  0.020  1.441
 TKV  C14  C22  single    1.526  0.020  1.526
 TKV  C14  C15  single    1.527  0.020  1.527
 TKV  C20  C19  single    1.528  0.020  1.528
 TKV  C20  C16  single    1.527  0.020  1.527
 TKV  C27  C28  aromatic  1.395  0.020  1.395
 TKV  C19  N18  single    1.449  0.020  1.449
 TKV  C32  C31  aromatic  1.385  0.020  1.385
 TKV  C15  C16  single    1.519  0.020  1.519
 TKV  C16  C17  single    1.519  0.020  1.519
 TKV  C28  C29  aromatic  1.382  0.020  1.382
 TKV  N18  C17  single    1.344  0.020  1.344
 TKV  C31  C29  aromatic  1.386  0.020  1.386
 TKV  C17  O21  double    1.221  0.020  1.221
 TKV  C29  CL3  single    1.738  0.020  1.738
 TKV  C22  S1   single    1.853  0.020  1.853
 TKV  C01  H1   single    0.970  0.020  1.090
 TKV  C01  H2   single    0.970  0.020  1.090
 TKV  C01  H3   single    0.970  0.020  1.090
 TKV  C03  H4   single    0.970  0.020  1.090
 TKV  C03  H5   single    0.970  0.020  1.090
 TKV  C07  H6   single    0.970  0.020  1.090
 TKV  C08  H7   single    0.970  0.020  1.090
 TKV  C08  H8   single    0.970  0.020  1.090
 TKV  C09  H9   single    0.970  0.020  1.090
 TKV  C10  H10  single    0.970  0.020  1.090
 TKV  C10  H11  single    0.970  0.020  1.090
 TKV  C10  H12  single    0.970  0.020  1.090
 TKV  C11  H13  single    0.970  0.020  1.090
 TKV  C11  H14  single    0.970  0.020  1.090
 TKV  C11  H15  single    0.970  0.020  1.090
 TKV  C14  H16  single    0.970  0.020  1.090
 TKV  C15  H17  single    0.970  0.020  1.090
 TKV  C15  H18  single    0.970  0.020  1.090
 TKV  C16  H19  single    0.970  0.020  1.090
 TKV  C19  H20  single    0.970  0.020  1.090
 TKV  C19  H21  single    0.970  0.020  1.090
 TKV  C20  H22  single    0.970  0.020  1.090
 TKV  C20  H23  single    0.970  0.020  1.090
 TKV  C22  H24  single    0.970  0.020  1.090
 TKV  C26  H25  single    0.970  0.020  1.090
 TKV  C26  H26  single    0.970  0.020  1.090
 TKV  C26  H27  single    0.970  0.020  1.090
 TKV  C28  H28  single    0.930  0.020  1.080
 TKV  C31  H29  single    0.930  0.020  1.080
 TKV  C32  H30  single    0.930  0.020  1.080
 TKV  C33  H31  single    0.930  0.020  1.080
 TKV  N06  H32  single    0.860  0.020  1.020
 TKV  N13  H33  single    0.860  0.020  1.020
 TKV  N18  H34  single    0.860  0.020  1.020
 TKV  O23  H35  single    0.850  0.020  0.980
 TKV  S1   H36  single    1.200  0.020  1.300

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
 TKV  H3   C01  H2   107.72  3.000
 TKV  H3   C01  H1   108.07  3.000
 TKV  H2   C01  H1   107.18  3.000
 TKV  H3   C01  C02  110.67  3.000
 TKV  H2   C01  C02  110.27  3.000
 TKV  H1   C01  C02  112.73  3.000
 TKV  C27  C02  C26  112.02  3.000
 TKV  C27  C02  C03  108.56  3.000
 TKV  C26  C02  C03  109.53  3.000
 TKV  C27  C02  C01  111.33  3.000
 TKV  C03  C02  C01  107.31  3.000
 TKV  C26  C02  C01  107.97  3.000
 TKV  H5   C03  H4   108.02  3.000
 TKV  H5   C03  O04  106.43  3.000
 TKV  H4   C03  O04  110.66  3.000
 TKV  H5   C03  C02  109.60  3.000
 TKV  H4   C03  C02  110.98  3.000
 TKV  O04  C03  C02  111.00  3.000
 TKV  O25  C05  O04  124.84  3.000
 TKV  O25  C05  N06  124.09  3.000
 TKV  O04  C05  N06  111.06  3.000
 TKV  H6   C07  N06  109.11  3.000
 TKV  H6   C07  C12  108.91  3.000
 TKV  N06  C07  C12  110.17  3.000
 TKV  H6   C07  C08  109.03  3.000
 TKV  C12  C07  C08  109.32  3.000
 TKV  N06  C07  C08  110.28  3.000
 TKV  H8   C08  H7   106.32  3.000
 TKV  H8   C08  C09  109.63  3.000
 TKV  H7   C08  C09  108.74  3.000
 TKV  H8   C08  C07  108.72  3.000
 TKV  H7   C08  C07  108.06  3.000
 TKV  C09  C08  C07  115.02  3.000
 TKV  H9   C09  C11  108.05  3.000
 TKV  H9   C09  C10  107.60  3.000
 TKV  C11  C09  C10  110.74  3.000
 TKV  H9   C09  C08  108.87  3.000
 TKV  C11  C09  C08  112.11  3.000
 TKV  C10  C09  C08  109.35  3.000
 TKV  H12  C10  H11  107.73  3.000
 TKV  H12  C10  H10  107.57  3.000
 TKV  H11  C10  H10  107.75  3.000
 TKV  H12  C10  C09  110.99  3.000
 TKV  H11  C10  C09  111.47  3.000
 TKV  H10  C10  C09  111.15  3.000
 TKV  H15  C11  H14  107.76  3.000
 TKV  H15  C11  H13  107.95  3.000
 TKV  H14  C11  H13  107.07  3.000
 TKV  H15  C11  C09  110.79  3.000
 TKV  H14  C11  C09  110.76  3.000
 TKV  H13  C11  C09  112.32  3.000
 TKV  O24  C12  N13  124.54  3.000
 TKV  N13  C12  C07  114.18  3.000
 TKV  O24  C12  C07  121.27  3.000
 TKV  H16  C14  N13  107.35  3.000
 TKV  H16  C14  C22  106.01  3.000
 TKV  N13  C14  C22  111.06  3.000
 TKV  H16  C14  C15  108.90  3.000
 TKV  C22  C14  C15  112.20  3.000
 TKV  N13  C14  C15  111.06  3.000
 TKV  H18  C15  H17  106.85  3.000
 TKV  H18  C15  C16  110.15  3.000
 TKV  H17  C15  C16  109.01  3.000
 TKV  H18  C15  C14  108.61  3.000
 TKV  H17  C15  C14  109.78  3.000
 TKV  C16  C15  C14  112.30  3.000
 TKV  H19  C16  C20  108.03  3.000
 TKV  H19  C16  C17  105.91  3.000
 TKV  C20  C16  C17  103.14  3.000
 TKV  H19  C16  C15  109.13  3.000
 TKV  C17  C16  C15  113.45  3.000
 TKV  C20  C16  C15  116.52  3.000
 TKV  O21  C17  N18  126.19  3.000
 TKV  O21  C17  C16  126.49  3.000
 TKV  N18  C17  C16  107.30  3.000
 TKV  H21  C19  H20  108.16  3.000
 TKV  H21  C19  N18  111.24  3.000
 TKV  H20  C19  N18  111.17  3.000
 TKV  H21  C19  C20  111.13  3.000
 TKV  H20  C19  C20  113.07  3.000
 TKV  N18  C19  C20  102.04  3.000
 TKV  H23  C20  H22  108.17  3.000
 TKV  H23  C20  C19  109.96  3.000
 TKV  H22  C20  C19  112.39  3.000
 TKV  H23  C20  C16  110.14  3.000
 TKV  H22  C20  C16  112.96  3.000
 TKV  C19  C20  C16  103.16  3.000
 TKV  H24  C22  S1   106.54  3.000
 TKV  H24  C22  O23  112.93  3.000
 TKV  S1   C22  O23  108.40  3.000
 TKV  H24  C22  C14  108.95  3.000
 TKV  S1   C22  C14  112.09  3.000
 TKV  O23  C22  C14  107.99  3.000
 TKV  H27  C26  H26  107.25  3.000
 TKV  H27  C26  H25  107.96  3.000
 TKV  H26  C26  H25  107.61  3.000
 TKV  H27  C26  C02  113.19  3.000
 TKV  H26  C26  C02  109.61  3.000
 TKV  H25  C26  C02  111.00  3.000
 TKV  C33  C27  C28  117.89  3.000
 TKV  C28  C27  C02  120.02  3.000
 TKV  C33  C27  C02  121.99  3.000
 TKV  H28  C28  C29  118.84  3.000
 TKV  H28  C28  C27  120.76  3.000
 TKV  C29  C28  C27  120.39  3.000
 TKV  CL3  C29  C31  119.18  3.000
 TKV  CL3  C29  C28  119.00  3.000
 TKV  C31  C29  C28  121.82  3.000
 TKV  H29  C31  C32  121.09  3.000
 TKV  H29  C31  C29  120.97  3.000
 TKV  C32  C31  C29  117.94  3.000
 TKV  H30  C32  C33  119.69  3.000
 TKV  H30  C32  C31  119.48  3.000
 TKV  C33  C32  C31  120.83  3.000
 TKV  H31  C33  C32  118.38  3.000
 TKV  H31  C33  C27  120.48  3.000
 TKV  C32  C33  C27  121.14  3.000
 TKV  H32  N06  C07  119.77  3.000
 TKV  H32  N06  C05  119.72  3.000
 TKV  C07  N06  C05  120.34  3.000
 TKV  H33  N13  C14  116.54  3.000
 TKV  H33  N13  C12  118.29  3.000
 TKV  C14  N13  C12  124.75  3.000
 TKV  H34  N18  C19  122.75  3.000
 TKV  H34  N18  C17  122.05  3.000
 TKV  C19  N18  C17  114.23  3.000
 TKV  C05  O04  C03  118.12  3.000
 TKV  H36  S1   C22   97.70  3.000
 TKV  H35  O23  C22  108.96  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
 TKV  CONST_01  C31  C32  C33  C27     0.00   0.0  0
 TKV  CONST_02  C31  C29  C28  C27     0.00   0.0  0
 TKV  CONST_03  C32  C33  C27  C28     0.00   0.0  0
 TKV  CONST_04  C32  C31  C29  C28     0.00   0.0  0
 TKV  CONST_05  C33  C27  C28  C29     0.00   0.0  0
 TKV  CONST_06  C33  C32  C31  C29     0.00   0.0  0
 TKV  CONST_07  C19  N18  C17  C16     0.00   0.0  0
 TKV  CONST_08  C32  C33  C27  C02   180.00   0.0  0
 TKV  CONST_09  C29  C28  C27  C02   180.00   0.0  0
 TKV  CONST_10  CL3  C29  C28  C27   180.00   0.0  0
 TKV  CONST_11  CL3  C29  C31  C32   180.00   0.0  0
 TKV  CONST_12  O21  C17  N18  C19   180.00   0.0  0
 TKV  CONST_13  H30  C32  C33  C27   180.00   0.0  0
 TKV  CONST_14  H31  C33  C27  C28   180.00   0.0  0
 TKV  CONST_15  H29  C31  C29  C28   180.00   0.0  0
 TKV  CONST_16  H28  C28  C29  C31   180.00   0.0  0
 TKV  CONST_17  H34  N18  C17  C16   180.00   0.0  0
 TKV  CONST_18  C14  N13  C12  C07   180.00   0.0  0
 TKV  CONST_19  O24  C12  N13  C14     0.00   0.0  0
 TKV  CONST_20  H33  N13  C12  C07     0.00   0.0  0
 TKV  Var_01    N18  C19  C20  C16    30.29  30.0  1
 TKV  Var_02    C20  C19  N18  C17   -20.91  30.0  1
 TKV  Var_03    C33  C27  C02  C01   139.84  30.0  2
 TKV  Var_04    O04  C03  C02  C27    56.64  30.0  3
 TKV  Var_05    H25  C26  C02  C27    58.75  30.0  3
 TKV  Var_06    H1   C01  C02  C27    62.62  30.0  3
 TKV  Var_07    N06  C05  O04  C03   167.85  30.0  3
 TKV  Var_08    C10  C09  C08  C07   176.04  30.0  2
 TKV  Var_09    O04  C05  N06  C07   177.81  30.0  2
 TKV  Var_10    H10  C10  C09  C08  -177.71  30.0  3
 TKV  Var_11    H13  C11  C09  C08    62.33  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
 TKV  chir_01  C07  C08  N06  C12  positiv
 TKV  chir_02  C14  N13  C22  C15  positiv
 TKV  chir_03  C16  C17  C15  C20  positiv
 TKV  chir_04  C22  S1   O23  C14  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
 TKV  plan-1  C02  0.020
 TKV  plan-1  C27  0.020
 TKV  plan-1  C28  0.020
 TKV  plan-1  C29  0.020
 TKV  plan-1  C31  0.020
 TKV  plan-1  C32  0.020
 TKV  plan-1  C33  0.020
 TKV  plan-1  CL3  0.020
 TKV  plan-1  H28  0.020
 TKV  plan-1  H29  0.020
 TKV  plan-1  H30  0.020
 TKV  plan-1  H31  0.020
 TKV  plan-2  C07  0.020
 TKV  plan-2  C12  0.020
 TKV  plan-2  C14  0.020
 TKV  plan-2  N13  0.020
 TKV  plan-2  O24  0.020
 TKV  plan-2  H33  0.020
 TKV  plan-3  C16  0.020
 TKV  plan-3  C17  0.020
 TKV  plan-3  C19  0.020
 TKV  plan-3  N18  0.020
 TKV  plan-3  O21  0.020
 TKV  plan-3  H34  0.020
 TKV  plan-4  C05  0.020
 TKV  plan-4  N06  0.020
 TKV  plan-4  O04  0.020
 TKV  plan-4  O25  0.020

