# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 21:30:18 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(1~{H}-indol-3-yl)-~{N}-[2-(2,4,6-trimethylphenyl)ethyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(C)c(CCNC(=O)[C@@H](N)Cc2c[nH]c3ccccc23)c(C)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
 VSK  VSK  (2~{S})-2-azanyl-3-(1~{H}-indol-3-yl)-~{N}-[2-(2,4,6-trimethylphenyl)ethyl]propanamide  ligand  53  26  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VSK
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
 VSK  C1   C  CR16  0  -0.375  -5.3842   0.8898  -1.1026
 VSK  C10  C  CH1   0  -0.214  -1.7284   0.6938   0.4104
 VSK  C11  C  C     0   0.556  -0.3367   1.0418  -0.0966
 VSK  C12  C  CH2   0  -0.238   2.0623   0.5895   0.1413
 VSK  C13  C  CH2   0  -0.588   2.9191  -0.5092   0.7670
 VSK  C14  C  CR6   0   0.030   4.3638  -0.3759   0.3635
 VSK  C15  C  CR6   0   0.091   4.8273  -0.9912  -0.8086
 VSK  C16  C  CR16  0  -0.368   6.1576  -0.8377  -1.1832
 VSK  C17  C  CR6   0   0.123   7.0495  -0.0831  -0.4283
 VSK  C18  C  CR16  0  -0.376   6.5734   0.5202   0.7282
 VSK  C19  C  CR6   0   0.090   5.2477   0.3871   1.1353
 VSK  C2   C  CR56  0   0.017  -4.9645  -0.2248  -0.3651
 VSK  C20  C  CH3   0  -0.752   4.8011   1.0565   2.4056
 VSK  C21  C  CH3   0  -0.725   8.4769   0.0840  -0.8634
 VSK  C22  C  CH3   0  -0.751   3.9157  -1.8292  -1.6623
 VSK  C3   C  CR56  0   0.352  -5.9377  -1.0117   0.2924
 VSK  C4   C  CR16  0  -0.305  -7.2989  -0.7137   0.2366
 VSK  C5   C  CR16  0  -0.286  -7.6798   0.3937  -0.4956
 VSK  C6   C  CR16  0  -0.268  -6.7310   1.1880  -1.1618
 VSK  C7   C  CR15  0  -0.080  -3.9407  -1.9147   0.6831
 VSK  C8   C  CR5   0   0.010  -3.6878  -0.8233  -0.1013
 VSK  C9   C  CH2   0  -0.543  -2.3454  -0.3483  -0.5489
 VSK  N1   N  NR15  0  -0.684  -5.2808  -2.0269   0.9216
 VSK  N2   N  NH2   0  -0.789  -2.4811   1.9222   0.5657
 VSK  N3   N  NH1   0  -0.641   0.6769   0.4288   0.5278
 VSK  O1   O  O     0  -0.505  -0.1761   1.7972  -1.0469
 VSK  H1   H  HCR6  0   0.237  -4.6669   1.5109  -1.6250
 VSK  H2   H  HCH1  0   0.255  -1.6519   0.2283   1.3979
 VSK  H3   H  HCH2  0   0.240   2.4338   1.5730   0.4458
 VSK  H4   H  HCH2  0   0.243   2.1370   0.5483  -0.9468
 VSK  H5   H  HCH2  0   0.263   2.8204  -0.4646   1.8542
 VSK  H6   H  HCH2  0   0.263   2.5240  -1.4822   0.4667
 VSK  H7   H  HCR6  0   0.234   6.5062  -1.3212  -2.0900
 VSK  H8   H  HCR6  0   0.235   7.2498   1.1148   1.3330
 VSK  H9   H  HCH3  0   0.247   4.4662   0.3301   3.1493
 VSK  H10  H  HCH3  0   0.252   5.6140   1.6279   2.8513
 VSK  H11  H  HCH3  0   0.244   3.9717   1.7462   2.2394
 VSK  H12  H  HCH3  0   0.245   8.5515   0.7536  -1.7227
 VSK  H13  H  HCH3  0   0.241   9.0909   0.5032  -0.0669
 VSK  H14  H  HCH3  0   0.242   8.9185  -0.8677  -1.1609
 VSK  H15  H  HCH3  0   0.247   3.5496  -2.7049  -1.1224
 VSK  H16  H  HCH3  0   0.243   3.0376  -1.2737  -1.9958
 VSK  H17  H  HCH3  0   0.252   4.4335  -2.1841  -2.5519
 VSK  H18  H  HCR6  0   0.258  -8.0300  -1.3273   0.7477
 VSK  H19  H  HCR6  0   0.248  -8.7283   0.6548  -0.5585
 VSK  H20  H  HCR6  0   0.246  -7.0652   2.0485  -1.7271
 VSK  H21  H  HCR5  0   0.280  -3.2492  -2.6357   1.0913
 VSK  H22  H  HCH2  0   0.244  -2.4102   0.0898  -1.5498
 VSK  H23  H  HCH2  0   0.251  -1.6649  -1.2008  -0.6274
 VSK  H24  H  HNR5  0   0.408  -5.7114  -2.7640   1.4540
 VSK  H25  H  HNH2  0   0.341  -2.6077   2.3644  -0.3368
 VSK  H26  H  HNH2  0   0.358  -3.4062   1.7106   0.9182
 VSK  H28  H  HNH1  0   0.403   0.4781  -0.1222   1.3476

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
 VSK  C22  C15  single    1.504  0.020  1.504
 VSK  C15  C16  aromatic  1.391  0.020  1.391
 VSK  C15  C14  aromatic  1.403  0.020  1.403
 VSK  C16  C17  aromatic  1.391  0.020  1.391
 VSK  C13  C14  single    1.506  0.020  1.506
 VSK  C13  C12  single    1.527  0.020  1.527
 VSK  C14  C19  aromatic  1.400  0.020  1.400
 VSK  C17  C21  single    1.502  0.020  1.502
 VSK  C17  C18  aromatic  1.389  0.020  1.389
 VSK  C19  C18  aromatic  1.393  0.020  1.393
 VSK  C19  C20  single    1.504  0.020  1.504
 VSK  N3   C12  single    1.447  0.020  1.447
 VSK  N3   C11  single    1.339  0.020  1.339
 VSK  C10  N2   single    1.449  0.020  1.449
 VSK  C10  C11  single    1.522  0.020  1.522
 VSK  C10  C9   single    1.545  0.020  1.545
 VSK  C11  O1   double    1.225  0.020  1.225
 VSK  C6   C1   aromatic  1.381  0.020  1.381
 VSK  C6   C5   aromatic  1.405  0.020  1.405
 VSK  C1   C2   aromatic  1.401  0.020  1.401
 VSK  C5   C4   aromatic  1.381  0.020  1.381
 VSK  C2   C8   aromatic  1.435  0.020  1.435
 VSK  C2   C3   aromatic  1.414  0.020  1.414
 VSK  C9   C8   single    1.493  0.020  1.493
 VSK  C4   C3   aromatic  1.395  0.020  1.395
 VSK  C8   C7   aromatic  1.368  0.020  1.368
 VSK  C3   N1   aromatic  1.363  0.020  1.363
 VSK  C7   N1   aromatic  1.366  0.020  1.366
 VSK  C1   H1   single    0.930  0.020  1.080
 VSK  C10  H2   single    0.970  0.020  1.090
 VSK  C12  H3   single    0.970  0.020  1.090
 VSK  C12  H4   single    0.970  0.020  1.090
 VSK  C13  H5   single    0.970  0.020  1.090
 VSK  C13  H6   single    0.970  0.020  1.090
 VSK  C16  H7   single    0.930  0.020  1.080
 VSK  C18  H8   single    0.930  0.020  1.080
 VSK  C20  H9   single    0.970  0.020  1.090
 VSK  C20  H10  single    0.970  0.020  1.090
 VSK  C20  H11  single    0.970  0.020  1.090
 VSK  C21  H12  single    0.970  0.020  1.090
 VSK  C21  H13  single    0.970  0.020  1.090
 VSK  C21  H14  single    0.970  0.020  1.090
 VSK  C22  H15  single    0.970  0.020  1.090
 VSK  C22  H16  single    0.970  0.020  1.090
 VSK  C22  H17  single    0.970  0.020  1.090
 VSK  C4   H18  single    0.930  0.020  1.080
 VSK  C5   H19  single    0.930  0.020  1.080
 VSK  C6   H20  single    0.930  0.020  1.080
 VSK  C7   H21  single    0.930  0.020  1.080
 VSK  C9   H22  single    0.970  0.020  1.090
 VSK  C9   H23  single    0.970  0.020  1.090
 VSK  N1   H24  single    0.860  0.020  1.020
 VSK  N2   H25  single    0.890  0.020  1.040
 VSK  N2   H26  single    0.890  0.020  1.040
 VSK  N3   H28  single    0.860  0.020  1.020

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
 VSK  H1   C1   C6   120.09  3.000
 VSK  H1   C1   C2   120.79  3.000
 VSK  C6   C1   C2   119.12  3.000
 VSK  H2   C10  N2   107.47  3.000
 VSK  H2   C10  C9   107.54  3.000
 VSK  N2   C10  C9   115.53  3.000
 VSK  H2   C10  C11  109.51  3.000
 VSK  C9   C10  C11  108.22  3.000
 VSK  N2   C10  C11  108.48  3.000
 VSK  O1   C11  N3   123.03  3.000
 VSK  O1   C11  C10  121.31  3.000
 VSK  N3   C11  C10  115.61  3.000
 VSK  H4   C12  H3   106.74  3.000
 VSK  H4   C12  N3   109.12  3.000
 VSK  H3   C12  N3   110.51  3.000
 VSK  H4   C12  C13  110.06  3.000
 VSK  H3   C12  C13  110.00  3.000
 VSK  N3   C12  C13  110.35  3.000
 VSK  H6   C13  H5   106.10  3.000
 VSK  H6   C13  C14  110.62  3.000
 VSK  H5   C13  C14  110.47  3.000
 VSK  H6   C13  C12  108.98  3.000
 VSK  H5   C13  C12  109.12  3.000
 VSK  C14  C13  C12  111.39  3.000
 VSK  C19  C14  C15  119.42  3.000
 VSK  C19  C14  C13  120.42  3.000
 VSK  C15  C14  C13  120.14  3.000
 VSK  C22  C15  C16  119.24  3.000
 VSK  C16  C15  C14  119.52  3.000
 VSK  C22  C15  C14  121.23  3.000
 VSK  H7   C16  C17  119.29  3.000
 VSK  H7   C16  C15  118.89  3.000
 VSK  C17  C16  C15  121.81  3.000
 VSK  C21  C17  C18  121.26  3.000
 VSK  C18  C17  C16  117.89  3.000
 VSK  C21  C17  C16  120.84  3.000
 VSK  H8   C18  C19  118.87  3.000
 VSK  H8   C18  C17  119.25  3.000
 VSK  C19  C18  C17  121.88  3.000
 VSK  C20  C19  C18  119.14  3.000
 VSK  C20  C19  C14  121.39  3.000
 VSK  C18  C19  C14  119.46  3.000
 VSK  C8   C2   C3   107.15  3.000
 VSK  C3   C2   C1   118.79  3.000
 VSK  C8   C2   C1   134.06  3.000
 VSK  H11  C20  H10  107.33  3.000
 VSK  H11  C20  H9   106.92  3.000
 VSK  H10  C20  H9   107.41  3.000
 VSK  H11  C20  C19  112.23  3.000
 VSK  H10  C20  C19  110.95  3.000
 VSK  H9   C20  C19  111.73  3.000
 VSK  H14  C21  H13  107.88  3.000
 VSK  H14  C21  H12  107.02  3.000
 VSK  H13  C21  H12  107.51  3.000
 VSK  H14  C21  C17  111.52  3.000
 VSK  H13  C21  C17  111.51  3.000
 VSK  H12  C21  C17  111.18  3.000
 VSK  H17  C22  H16  107.39  3.000
 VSK  H17  C22  H15  107.58  3.000
 VSK  H16  C22  H15  106.83  3.000
 VSK  H17  C22  C15  110.92  3.000
 VSK  H16  C22  C15  112.19  3.000
 VSK  H15  C22  C15  111.67  3.000
 VSK  N1   C3   C4   130.39  3.000
 VSK  N1   C3   C2   107.31  3.000
 VSK  C4   C3   C2   122.30  3.000
 VSK  H18  C4   C5   121.22  3.000
 VSK  H18  C4   C3   121.27  3.000
 VSK  C5   C4   C3   117.50  3.000
 VSK  H19  C5   C6   119.35  3.000
 VSK  H19  C5   C4   119.43  3.000
 VSK  C6   C5   C4   121.21  3.000
 VSK  H20  C6   C5   119.24  3.000
 VSK  H20  C6   C1   119.69  3.000
 VSK  C5   C6   C1   121.07  3.000
 VSK  H21  C7   N1   120.51  3.000
 VSK  H21  C7   C8   129.17  3.000
 VSK  N1   C7   C8   110.32  3.000
 VSK  C9   C8   C7   126.32  3.000
 VSK  C7   C8   C2   105.89  3.000
 VSK  C9   C8   C2   127.77  3.000
 VSK  H23  C9   H22  106.45  3.000
 VSK  H23  C9   C8   109.45  3.000
 VSK  H22  C9   C8   110.39  3.000
 VSK  H23  C9   C10  108.78  3.000
 VSK  H22  C9   C10  108.76  3.000
 VSK  C8   C9   C10  112.81  3.000
 VSK  H24  N1   C7   124.93  3.000
 VSK  H24  N1   C3   125.71  3.000
 VSK  C7   N1   C3   109.33  3.000
 VSK  H26  N2   H25  106.69  3.000
 VSK  H26  N2   C10  109.56  3.000
 VSK  H25  N2   C10  109.85  3.000
 VSK  H28  N3   C12  117.83  3.000
 VSK  H28  N3   C11  118.71  3.000
 VSK  C12  N3   C11  123.31  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
 VSK  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 VSK  CONST_02  C7   C8   C2   C1    180.00   0.0  0
 VSK  CONST_03  C4   C3   C2   C1      0.00   0.0  0
 VSK  CONST_04  N1   C3   C2   C1    180.00   0.0  0
 VSK  CONST_05  C17  C16  C15  C14     0.00   0.0  0
 VSK  CONST_06  C17  C18  C19  C14     0.00   0.0  0
 VSK  CONST_07  C18  C17  C16  C15     0.00   0.0  0
 VSK  CONST_08  C18  C19  C14  C15     0.00   0.0  0
 VSK  CONST_09  C19  C14  C15  C16     0.00   0.0  0
 VSK  CONST_10  C19  C18  C17  C16     0.00   0.0  0
 VSK  CONST_11  C5   C6   C1   C2      0.00   0.0  0
 VSK  CONST_12  N1   C7   C8   C2      0.00   0.0  0
 VSK  CONST_13  C5   C4   C3   C2      0.00   0.0  0
 VSK  CONST_14  C7   N1   C3   C2      0.00   0.0  0
 VSK  CONST_15  C6   C1   C2   C3      0.00   0.0  0
 VSK  CONST_16  C7   C8   C2   C3      0.00   0.0  0
 VSK  CONST_17  C6   C5   C4   C3      0.00   0.0  0
 VSK  CONST_18  C8   C7   N1   C3      0.00   0.0  0
 VSK  CONST_19  C8   C2   C3   C4    180.00   0.0  0
 VSK  CONST_20  C7   N1   C3   C4    180.00   0.0  0
 VSK  CONST_21  N1   C3   C4   C5    180.00   0.0  0
 VSK  CONST_22  C8   C2   C1   C6    180.00   0.0  0
 VSK  CONST_23  N1   C3   C2   C8      0.00   0.0  0
 VSK  CONST_24  C9   C8   C2   C1      0.00   0.0  0
 VSK  CONST_25  C16  C15  C14  C13   180.00   0.0  0
 VSK  CONST_26  C18  C19  C14  C13   180.00   0.0  0
 VSK  CONST_27  C21  C17  C16  C15   180.00   0.0  0
 VSK  CONST_28  C20  C19  C14  C15   180.00   0.0  0
 VSK  CONST_29  C22  C15  C16  C17   180.00   0.0  0
 VSK  CONST_30  C20  C19  C18  C17   180.00   0.0  0
 VSK  CONST_31  C22  C15  C14  C19   180.00   0.0  0
 VSK  CONST_32  C21  C17  C18  C19   180.00   0.0  0
 VSK  CONST_33  C9   C8   C2   C3    180.00   0.0  0
 VSK  CONST_34  N1   C7   C8   C9    180.00   0.0  0
 VSK  CONST_35  H19  C5   C6   C1    180.00   0.0  0
 VSK  CONST_36  H7   C16  C15  C14   180.00   0.0  0
 VSK  CONST_37  H8   C18  C19  C14   180.00   0.0  0
 VSK  CONST_38  H20  C6   C1   C2    180.00   0.0  0
 VSK  CONST_39  H21  C7   C8   C2    180.00   0.0  0
 VSK  CONST_40  H18  C4   C3   C2    180.00   0.0  0
 VSK  CONST_41  H24  N1   C3   C2    180.00   0.0  0
 VSK  CONST_42  H1   C1   C2   C3    180.00   0.0  0
 VSK  CONST_43  C12  N3   C11  C10   180.00   0.0  0
 VSK  CONST_44  O1   C11  N3   C12     0.00   0.0  0
 VSK  CONST_45  H28  N3   C11  C10     0.00   0.0  0
 VSK  Var_01    C2   C8   C9   C10    86.13  30.0  2
 VSK  Var_02    C15  C14  C13  C12   -88.25  30.0  2
 VSK  Var_03    H15  C22  C15  C14   -62.77  30.0  2
 VSK  Var_04    H9   C20  C19  C14    61.89  30.0  2
 VSK  Var_05    H12  C21  C17  C16    72.87  30.0  2
 VSK  Var_06    N3   C12  C13  C14   179.18  30.0  3
 VSK  Var_07    C13  C12  N3   C11  -164.22  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
 VSK  chir_01  C10  N2  C11  C9  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
 VSK  plan-1  C13  0.020
 VSK  plan-1  C14  0.020
 VSK  plan-1  C15  0.020
 VSK  plan-1  C16  0.020
 VSK  plan-1  C17  0.020
 VSK  plan-1  C18  0.020
 VSK  plan-1  C19  0.020
 VSK  plan-1  C20  0.020
 VSK  plan-1  C21  0.020
 VSK  plan-1  C22  0.020
 VSK  plan-1  H7   0.020
 VSK  plan-1  H8   0.020
 VSK  plan-2  C1   0.020
 VSK  plan-2  C2   0.020
 VSK  plan-2  C3   0.020
 VSK  plan-2  C4   0.020
 VSK  plan-2  C5   0.020
 VSK  plan-2  C6   0.020
 VSK  plan-2  C7   0.020
 VSK  plan-2  C8   0.020
 VSK  plan-2  C9   0.020
 VSK  plan-2  N1   0.020
 VSK  plan-2  H1   0.020
 VSK  plan-2  H18  0.020
 VSK  plan-2  H19  0.020
 VSK  plan-2  H20  0.020
 VSK  plan-2  H21  0.020
 VSK  plan-2  H24  0.020
 VSK  plan-3  C10  0.020
 VSK  plan-3  C11  0.020
 VSK  plan-3  C12  0.020
 VSK  plan-3  N3   0.020
 VSK  plan-3  O1   0.020
 VSK  plan-3  H28  0.020

