# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 11:55:52 2020
#   Inital geometry file: a 162 line input string
#   Ligand name: N-[(2S)-2-(3,5-dichlorophenyl)-2-(ethylamino)acetyl]-3-methyl-L-valyl-N-[3-(methylsulfonyl)propyl]glycinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCN[C@H](C(=O)N[C@H](C(=O)NCC(=O)NCCC[S](C)(=O)=O)C(C)(C)C)c1cc(Cl)cc(Cl)c1
#
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
 3VK  3VK  N-[(2S)-2-(3,5-dichlorophenyl)-2-(ethylamino)acetyl]-3-methyl-L-valyl-N-[3-(methylsulfonyl)propyl]glycinamide  ligand  68  34  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3VK
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
 3VK  C1   C   CR16  0  -0.185  -3.4154   3.5909   0.0900
 3VK  C2   C   CR6   0  -0.028  -3.2986   2.9060  -1.1081
 3VK  C3   C   CR16  0  -0.259  -3.6958   1.5849  -1.2328
 3VK  C14  C   CH1   0  -0.179  -1.3738  -2.5136  -0.2974
 3VK  C15  C   C     0   0.579  -0.2507  -1.7752  -1.0220
 3VK  C18  C   CT    0  -0.091  -1.4340  -4.0269  -0.6418
 3VK  C19  C   CH3   0  -0.647  -2.5349  -4.6637   0.2103
 3VK  C20  C   CH3   0  -0.650  -1.7490  -4.2730  -2.1186
 3VK  C21  C   CH3   0  -0.656  -0.0969  -4.6830  -0.2938
 3VK  C22  C   CH2   0  -0.376   2.0424  -0.9745  -0.8533
 3VK  C23  C   C     0   0.528   3.1380  -0.9744   0.2013
 3VK  C25  C   CH2   0  -0.231   5.3872  -0.1994   0.7404
 3VK  C27  C   CH2   0  -0.489   6.5260   0.5218   0.0368
 3VK  C28  C   CH2   0  -0.612   7.7047   0.6692   0.9871
 3VK  C30  C   CH3   0  -0.787  10.3160   1.6054   1.4314
 3VK  C4   C   CR6   0   0.092  -4.2212   0.9242  -0.1299
 3VK  C5   C   CR16  0  -0.240  -4.3445   1.5869   1.0869
 3VK  C6   C   CR6   0  -0.025  -3.9441   2.9086   1.1754
 3VK  CL7  CL  CL    0  -0.114  -4.1001   3.7406   2.6848
 3VK  CL8  CL  CL    0  -0.112  -2.6447   3.7273  -2.4829
 3VK  C9   C   CH1   0  -0.247  -4.6131  -0.5303  -0.2436
 3VK  C10  C   C     0   0.555  -3.4452  -1.3443   0.3366
 3VK  N11  N   NH1   0  -0.589  -5.8180  -0.8009   0.4972
 3VK  O12  O   O     0  -0.470  -3.2955  -1.4815   1.5365
 3VK  N13  N   NH1   0  -0.629  -2.6097  -1.8315  -0.5949
 3VK  O17  O   O     0  -0.490  -0.3836  -1.3707  -2.1686
 3VK  N24  N   NH1   0  -0.646   4.2459  -0.3128  -0.1438
 3VK  O26  O   O     0  -0.491   3.0023  -1.5470   1.2728
 3VK  S29  S   S     0   1.195   9.0784   1.4698   0.1626
 3VK  O31  O   OS    0  -0.688   9.5738   0.5730  -0.8826
 3VK  O32  O   OS    0  -0.688   8.6625   2.8158  -0.2340
 3VK  C33  C   CH2   0  -0.283  -6.3344  -2.1456   0.2962
 3VK  C34  C   CH3   0  -0.676  -7.6423  -2.3355   1.0405
 3VK  H1   H   HCR6  0   0.302  -3.1075   4.6236   0.1754
 3VK  H2   H   HCR6  0   0.282  -3.6057   1.0750  -2.1832
 3VK  H3   H   HCH1  0   0.279  -1.2176  -2.4341   0.7805
 3VK  H4   H   HCH3  0   0.231  -3.5240  -4.2956  -0.0657
 3VK  H5   H   HCH3  0   0.235  -2.5379  -5.7455   0.0640
 3VK  H6   H   HCH3  0   0.229  -2.3875  -4.4694   1.2741
 3VK  H7   H   HCH3  0   0.234  -0.9699  -3.8952  -2.7801
 3VK  H8   H   HCH3  0   0.233  -1.8419  -5.3461  -2.2953
 3VK  H9   H   HCH3  0   0.224  -2.6958  -3.8181  -2.4147
 3VK  H10  H   HCH3  0   0.229   0.1757  -4.5192   0.7516
 3VK  H11  H   HCH3  0   0.239  -0.1625  -5.7608  -0.4489
 3VK  H12  H   HCH3  0   0.234   0.7221  -4.3170  -0.9153
 3VK  H13  H   HCH2  0   0.281   1.8338   0.0527  -1.1646
 3VK  H14  H   HCH2  0   0.285   2.4009  -1.5070  -1.7397
 3VK  H15  H   HCH2  0   0.248   5.7142  -1.1945   1.0496
 3VK  H16  H   HCH2  0   0.245   5.1068   0.3436   1.6472
 3VK  H17  H   HCH2  0   0.266   6.8257  -0.0426  -0.8486
 3VK  H18  H   HCH2  0   0.266   6.1916   1.5076  -0.2929
 3VK  H19  H   HCH2  0   0.303   7.4471   1.2782   1.8554
 3VK  H20  H   HCH2  0   0.303   8.0661  -0.2994   1.3366
 3VK  H21  H   HCH3  0   0.295  10.5909   0.6124   1.7790
 3VK  H22  H   HCH3  0   0.312  11.1800   2.0971   0.9865
 3VK  H23  H   HCH3  0   0.295   9.9316   2.2049   2.2534
 3VK  H24  H   HCR6  0   0.282  -4.7478   1.0709   1.9470
 3VK  H25  H   HCH1  0   0.259  -4.7141  -0.7721  -1.3149
 3VK  H26  H   HNH1  0   0.355  -6.5249  -0.1314   0.2146
 3VK  H28  H   HNH1  0   0.398  -2.8055  -1.6413  -1.5654
 3VK  H29  H   HNH1  0   0.403   0.9357  -1.9443   0.6345
 3VK  H30  H   HNH1  0   0.412   4.2712   0.1719  -1.0275
 3VK  H31  H   HCH2  0   0.201  -6.4778  -2.3785  -0.7695
 3VK  H32  H   HCH2  0   0.228  -5.6003  -2.8624   0.6730
 3VK  H33  H   HCH3  0   0.233  -8.0153  -3.3504   0.9052
 3VK  H34  H   HCH3  0   0.227  -7.5144  -2.1595   2.1087
 3VK  H35  H   HCH3  0   0.225  -8.4096  -1.6509   0.6741
 3VK  N16  N   NH1   0  -0.643   0.8684  -1.6006  -0.3124

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
 3VK  CL7  C6   single    1.731  0.020  1.731
 3VK  C6   C1   aromatic  1.387  0.020  1.387
 3VK  C6   C5   aromatic  1.384  0.020  1.384
 3VK  C34  C33  single    1.517  0.020  1.517
 3VK  C1   C2   aromatic  1.385  0.020  1.385
 3VK  C5   C4   aromatic  1.391  0.020  1.391
 3VK  N11  C33  single    1.454  0.020  1.454
 3VK  N11  C9   single    1.440  0.020  1.440
 3VK  C2   CL8  single    1.730  0.020  1.730
 3VK  C2   C3   aromatic  1.385  0.020  1.385
 3VK  C4   C3   aromatic  1.389  0.020  1.389
 3VK  C4   C9   single    1.511  0.020  1.511
 3VK  C9   C10  single    1.537  0.020  1.537
 3VK  O12  C10  double    1.217  0.020  1.217
 3VK  C10  N13  single    1.343  0.020  1.343
 3VK  N13  C14  single    1.443  0.020  1.443
 3VK  C14  C15  single    1.527  0.020  1.527
 3VK  C14  C18  single    1.553  0.020  1.553
 3VK  C20  C18  single    1.530  0.020  1.530
 3VK  O17  C15  double    1.223  0.020  1.223
 3VK  C15  N16  single    1.337  0.020  1.337
 3VK  C18  C21  single    1.530  0.020  1.530
 3VK  C18  C19  single    1.531  0.020  1.531
 3VK  N16  C22  single    1.436  0.020  1.436
 3VK  C22  C23  single    1.521  0.020  1.521
 3VK  O26  C23  double    1.223  0.020  1.223
 3VK  C23  N24  single    1.336  0.020  1.336
 3VK  N24  C25  single    1.448  0.020  1.448
 3VK  C25  C27  single    1.521  0.020  1.521
 3VK  C27  C28  single    1.521  0.020  1.521
 3VK  C28  S29  single    1.791  0.020  1.791
 3VK  S29  O32  double    1.464  0.020  1.464
 3VK  S29  O31  double    1.464  0.020  1.464
 3VK  S29  C30  single    1.778  0.020  1.778
 3VK  C1   H1   single    0.930  0.020  1.080
 3VK  C3   H2   single    0.930  0.020  1.080
 3VK  C14  H3   single    0.970  0.020  1.090
 3VK  C19  H4   single    0.970  0.020  1.090
 3VK  C19  H5   single    0.970  0.020  1.090
 3VK  C19  H6   single    0.970  0.020  1.090
 3VK  C20  H7   single    0.970  0.020  1.090
 3VK  C20  H8   single    0.970  0.020  1.090
 3VK  C20  H9   single    0.970  0.020  1.090
 3VK  C21  H10  single    0.970  0.020  1.090
 3VK  C21  H11  single    0.970  0.020  1.090
 3VK  C21  H12  single    0.970  0.020  1.090
 3VK  C22  H13  single    0.970  0.020  1.090
 3VK  C22  H14  single    0.970  0.020  1.090
 3VK  C25  H15  single    0.970  0.020  1.090
 3VK  C25  H16  single    0.970  0.020  1.090
 3VK  C27  H17  single    0.970  0.020  1.090
 3VK  C27  H18  single    0.970  0.020  1.090
 3VK  C28  H19  single    0.970  0.020  1.090
 3VK  C28  H20  single    0.970  0.020  1.090
 3VK  C30  H21  single    0.970  0.020  1.090
 3VK  C30  H22  single    0.970  0.020  1.090
 3VK  C30  H23  single    0.970  0.020  1.090
 3VK  C5   H24  single    0.930  0.020  1.080
 3VK  C9   H25  single    0.970  0.020  1.090
 3VK  N11  H26  single    0.890  0.020  1.040
 3VK  N13  H28  single    0.860  0.020  1.020
 3VK  N16  H29  single    0.860  0.020  1.020
 3VK  N24  H30  single    0.860  0.020  1.020
 3VK  C33  H31  single    0.970  0.020  1.090
 3VK  C33  H32  single    0.970  0.020  1.090
 3VK  C34  H33  single    0.970  0.020  1.090
 3VK  C34  H34  single    0.970  0.020  1.090
 3VK  C34  H35  single    0.970  0.020  1.090

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
 3VK  H1   C1   C6   121.11  3.000
 3VK  H1   C1   C2   121.12  3.000
 3VK  C6   C1   C2   117.77  3.000
 3VK  CL8  C2   C3   119.32  3.000
 3VK  C3   C2   C1   121.69  3.000
 3VK  CL8  C2   C1   118.99  3.000
 3VK  H2   C3   C4   120.30  3.000
 3VK  H2   C3   C2   120.30  3.000
 3VK  C4   C3   C2   119.39  3.000
 3VK  H3   C14  N13  106.95  3.000
 3VK  H3   C14  C18  107.18  3.000
 3VK  N13  C14  C18  112.44  3.000
 3VK  H3   C14  C15  109.15  3.000
 3VK  C18  C14  C15  113.23  3.000
 3VK  N13  C14  C15  107.68  3.000
 3VK  O17  C15  N16  123.06  3.000
 3VK  N16  C15  C14  115.28  3.000
 3VK  O17  C15  C14  121.66  3.000
 3VK  C21  C18  C20  109.30  3.000
 3VK  C21  C18  C19  108.88  3.000
 3VK  C20  C18  C19  108.80  3.000
 3VK  C19  C18  C14  108.04  3.000
 3VK  C21  C18  C14  109.49  3.000
 3VK  C20  C18  C14  112.26  3.000
 3VK  H6   C19  H5   107.90  3.000
 3VK  H6   C19  H4   108.00  3.000
 3VK  H5   C19  H4   107.33  3.000
 3VK  H6   C19  C18  111.80  3.000
 3VK  H5   C19  C18  109.85  3.000
 3VK  H4   C19  C18  111.77  3.000
 3VK  H9   C20  H8   106.98  3.000
 3VK  H9   C20  H7   108.12  3.000
 3VK  H8   C20  H7   107.67  3.000
 3VK  H9   C20  C18  111.93  3.000
 3VK  H8   C20  C18  109.39  3.000
 3VK  H7   C20  C18  112.52  3.000
 3VK  H12  C21  H11  107.19  3.000
 3VK  H12  C21  H10  107.90  3.000
 3VK  H11  C21  H10  107.40  3.000
 3VK  H12  C21  C18  112.50  3.000
 3VK  H11  C21  C18  109.81  3.000
 3VK  H10  C21  C18  111.81  3.000
 3VK  H14  C22  H13  106.80  3.000
 3VK  H14  C22  N16  111.14  3.000
 3VK  H13  C22  N16  111.15  3.000
 3VK  H14  C22  C23  109.01  3.000
 3VK  H13  C22  C23  109.56  3.000
 3VK  N16  C22  C23  109.13  3.000
 3VK  O26  C23  N24  123.41  3.000
 3VK  N24  C23  C22  114.73  3.000
 3VK  O26  C23  C22  121.86  3.000
 3VK  H16  C25  H15  107.13  3.000
 3VK  H16  C25  N24  110.07  3.000
 3VK  H15  C25  N24  109.72  3.000
 3VK  H16  C25  C27  109.89  3.000
 3VK  H15  C25  C27  109.81  3.000
 3VK  N24  C25  C27  110.17  3.000
 3VK  H18  C27  H17  107.81  3.000
 3VK  H18  C27  C28  109.78  3.000
 3VK  H17  C27  C28  110.12  3.000
 3VK  H18  C27  C25  109.78  3.000
 3VK  H17  C27  C25  109.61  3.000
 3VK  C28  C27  C25  109.71  3.000
 3VK  H20  C28  H19  108.57  3.000
 3VK  H20  C28  S29  106.87  3.000
 3VK  H19  C28  S29  107.33  3.000
 3VK  H20  C28  C27  111.76  3.000
 3VK  H19  C28  C27  111.61  3.000
 3VK  S29  C28  C27  110.49  3.000
 3VK  H23  C30  H22  109.90  3.000
 3VK  H23  C30  H21  110.56  3.000
 3VK  H22  C30  H21  110.02  3.000
 3VK  H23  C30  S29  109.60  3.000
 3VK  H22  C30  S29  107.17  3.000
 3VK  H21  C30  S29  109.54  3.000
 3VK  C9   C4   C5   120.11  3.000
 3VK  C9   C4   C3   119.76  3.000
 3VK  C5   C4   C3   120.10  3.000
 3VK  H24  C5   C6   120.86  3.000
 3VK  H24  C5   C4   120.10  3.000
 3VK  C6   C5   C4   119.03  3.000
 3VK  CL7  C6   C5   119.26  3.000
 3VK  C5   C6   C1   122.02  3.000
 3VK  CL7  C6   C1   118.72  3.000
 3VK  H25  C9   N11  112.45  3.000
 3VK  H25  C9   C10  108.67  3.000
 3VK  N11  C9   C10  110.00  3.000
 3VK  H25  C9   C4   107.94  3.000
 3VK  C10  C9   C4   106.52  3.000
 3VK  N11  C9   C4   111.05  3.000
 3VK  N13  C10  O12  124.50  3.000
 3VK  N13  C10  C9   113.77  3.000
 3VK  O12  C10  C9   121.69  3.000
 3VK  H26  N11  C33  108.93  3.000
 3VK  H26  N11  C9   108.42  3.000
 3VK  C33  N11  C9   113.56  3.000
 3VK  H28  N13  C10  118.59  3.000
 3VK  H28  N13  C14  117.00  3.000
 3VK  C10  N13  C14  124.17  3.000
 3VK  H30  N24  C25  118.54  3.000
 3VK  H30  N24  C23  119.04  3.000
 3VK  C25  N24  C23  122.32  3.000
 3VK  O32  S29  O31  117.79  3.000
 3VK  O31  S29  C30  108.71  3.000
 3VK  O32  S29  C30  108.73  3.000
 3VK  C30  S29  C28  103.86  3.000
 3VK  O31  S29  C28  108.33  3.000
 3VK  O32  S29  C28  108.53  3.000
 3VK  H32  C33  H31  106.42  3.000
 3VK  H32  C33  C34  109.14  3.000
 3VK  H31  C33  C34  109.66  3.000
 3VK  H32  C33  N11  108.67  3.000
 3VK  H31  C33  N11  112.08  3.000
 3VK  C34  C33  N11  110.74  3.000
 3VK  H35  C34  H34  108.06  3.000
 3VK  H35  C34  H33  107.57  3.000
 3VK  H34  C34  H33  108.19  3.000
 3VK  H35  C34  C33  111.27  3.000
 3VK  H34  C34  C33  111.06  3.000
 3VK  H33  C34  C33  110.54  3.000
 3VK  H29  N16  C22  116.56  3.000
 3VK  H29  N16  C15  120.62  3.000
 3VK  C22  N16  C15  122.77  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
 3VK  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 3VK  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 3VK  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 3VK  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 3VK  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 3VK  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 3VK  CONST_07  CL7  C6   C1   C2    180.00   0.0  0
 3VK  CONST_08  C9   C4   C3   C2    180.00   0.0  0
 3VK  CONST_09  CL7  C6   C5   C4    180.00   0.0  0
 3VK  CONST_10  CL8  C2   C3   C4    180.00   0.0  0
 3VK  CONST_11  CL8  C2   C1   C6    180.00   0.0  0
 3VK  CONST_12  C9   C4   C5   C6    180.00   0.0  0
 3VK  CONST_13  H24  C5   C6   C1    180.00   0.0  0
 3VK  CONST_14  H2   C3   C2   C1    180.00   0.0  0
 3VK  CONST_15  H1   C1   C2   C3    180.00   0.0  0
 3VK  CONST_16  C9   C10  N13  C14   180.00   0.0  0
 3VK  CONST_17  O12  C10  N13  C14     0.00   0.0  0
 3VK  CONST_18  C22  N16  C15  C14   180.00   0.0  0
 3VK  CONST_19  O17  C15  N16  C22     0.00   0.0  0
 3VK  CONST_20  C25  N24  C23  C22   180.00   0.0  0
 3VK  CONST_21  O26  C23  N24  C25     0.00   0.0  0
 3VK  CONST_22  H29  N16  C15  C14     0.00   0.0  0
 3VK  CONST_23  H30  N24  C23  C22     0.00   0.0  0
 3VK  CONST_24  H28  N13  C10  C9      0.00   0.0  0
 3VK  Var_01    C23  C22  N16  C15  -178.34  30.0  3
 3VK  Var_02    C27  C25  N24  C23   175.99  30.0  3
 3VK  Var_03    S29  C28  C27  C25   178.18  30.0  3
 3VK  Var_04    O32  S29  C28  C27    62.39  30.0  3
 3VK  Var_05    N24  C25  C27  C28   178.44  30.0  1
 3VK  Var_06    C34  C33  N11  C9   -176.77  30.0  3
 3VK  Var_07    O26  C23  C22  N16     6.00  30.0  3
 3VK  Var_08    H7   C20  C18  C14    63.90  30.0  3
 3VK  Var_09    H10  C21  C18  C14    55.82  30.0  3
 3VK  Var_10    H4   C19  C18  C14    66.48  30.0  3
 3VK  Var_11    H21  C30  S29  C28    61.15  30.0  3
 3VK  Var_12    H33  C34  C33  N11  -178.78  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
 3VK  chir_01  C14  N13  C15  C18  positiv
 3VK  chir_02  C9   N11  C10  C4   positiv

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
 3VK  plan-1  C1   0.020
 3VK  plan-1  C2   0.020
 3VK  plan-1  C3   0.020
 3VK  plan-1  C4   0.020
 3VK  plan-1  C5   0.020
 3VK  plan-1  C6   0.020
 3VK  plan-1  CL7  0.020
 3VK  plan-1  CL8  0.020
 3VK  plan-1  C9   0.020
 3VK  plan-1  H1   0.020
 3VK  plan-1  H2   0.020
 3VK  plan-1  H24  0.020
 3VK  plan-2  C14  0.020
 3VK  plan-2  C15  0.020
 3VK  plan-2  C22  0.020
 3VK  plan-2  O17  0.020
 3VK  plan-2  H29  0.020
 3VK  plan-2  N16  0.020
 3VK  plan-3  C22  0.020
 3VK  plan-3  C23  0.020
 3VK  plan-3  C25  0.020
 3VK  plan-3  N24  0.020
 3VK  plan-3  O26  0.020
 3VK  plan-3  H30  0.020
 3VK  plan-4  C14  0.020
 3VK  plan-4  C9   0.020
 3VK  plan-4  C10  0.020
 3VK  plan-4  O12  0.020
 3VK  plan-4  N13  0.020
 3VK  plan-4  H28  0.020

