# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:26:57 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-2-amino-N-{(1S)-1-cyclohexyl-2-[(4-methylphenyl)amino]-2-oxoethyl}-4-(methylselanyl)butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se]CC[C@H](N)C(=O)N[C@@H](C1CCCCC1)C(=O)Nc2ccc(C)cc2
#
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
 2QW  2QW  (2S)-2-amino-N-{(1S)-1-cyclohexyl-2-[(4-methylphenyl)amino]-2-oxoethyl}-4-(methylselanyl)butanamide  ligand  57  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2QW
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
 2QW  O1   O   O     0  -0.460   1.2422   0.5558  -1.0369
 2QW  C7   C   C     0  -0.435   1.8868  -2.7761  -1.4474
 2QW  C6   C   CR16  0  -0.222   1.8096  -2.5809   0.0668
 2QW  C1   C   CH2   0  -0.424  -3.1562   0.1830   0.4128
 2QW  N1   N   NH1   0  -0.626  -0.3415  -1.3300   0.0488
 2QW  C5   C   CH1   0  -0.236   1.0331  -1.3094   0.4717
 2QW  C3   C   CH3   0  -0.802  -6.5585   2.3800  -1.1192
 2QW  C2   C   CH2   0  -0.569  -4.4384   0.5141  -0.3328
 2QW  C12  C   C     0   0.555   1.7073  -0.0603  -0.0959
 2QW  N2   N   NH1   0  -0.740   2.8667   0.2519   0.5268
 2QW  C13  C   CR6   0   0.355   3.7523   1.3045   0.2542
 2QW  C19  C   CR16  0  -0.292   3.8247   1.9657  -0.9713
 2QW  C18  C   CR16  0  -0.288   4.7549   2.9792  -1.1514
 2QW  C16  C   CR6   0   0.084   5.6341   3.3672  -0.1439
 2QW  C17  C   CH3   0  -0.721   6.6110   4.4870  -0.3529
 2QW  C15  C   CR16  0  -0.291   5.5564   2.6881   1.0689
 2QW  C14  C   CR16  0  -0.331   4.6318   1.6770   1.2697
 2QW  C11  C   C     0  -0.417   1.2159  -3.8185   0.7383
 2QW  C10  C   C     0  -0.432   2.0044  -5.0757   0.3849
 2QW  C9   C   C     0  -0.430   2.0805  -5.2721  -1.1250
 2QW  C8   C   C     0  -0.429   2.6656  -4.0391  -1.8047
 2QW  O    O   O     0  -0.491  -1.2760  -1.7168   2.0748
 2QW  C    C   CH1   0  -0.224  -2.7586  -1.2890   0.2303
 2QW  N    N   NH2   0  -0.775  -3.7773  -2.1618   0.7686
 2QW  SE   SE  SE    0   0.017  -4.8876   2.4109  -0.1122
 2QW  H1   H   H     0   0.214   0.8726  -2.8562  -1.8535
 2QW  H2   H   H     0   0.236   2.3536  -1.9130  -1.9294
 2QW  H3   H   HCR6  0   0.230   2.8329  -2.4581   0.4443
 2QW  H5   H   HCH2  0   0.242  -3.2719   0.3889   1.4816
 2QW  H6   H   HNH1  0   0.398  -0.5283  -1.1043  -0.9158
 2QW  H7   H   HCH1  0   0.292   1.0414  -1.2477   1.5633
 2QW  H8   H   HCH3  0   0.262  -6.3826   2.0720  -2.1490
 2QW  H9   H   HCH3  0   0.262  -7.2774   1.7056  -0.6560
 2QW  H10  H   HCH3  0   0.269  -6.9729   3.3876  -1.1211
 2QW  H11  H   HCH2  0   0.257  -4.3235   0.3054  -1.3991
 2QW  H12  H   HCH2  0   0.266  -5.2664  -0.0870   0.0429
 2QW  H13  H   HNH1  0   0.418   3.0855  -0.2791   1.3567
 2QW  H14  H   HCR6  0   0.271   3.1750   1.6978  -1.7889
 2QW  H15  H   HCR6  0   0.250   4.7946   3.4761  -2.1138
 2QW  H16  H   HCH3  0   0.247   6.1253   5.4589  -0.2421
 2QW  H17  H   HCH3  0   0.243   7.4265   4.4471   0.3685
 2QW  H18  H   HCH3  0   0.243   7.0460   4.4593  -1.3522
 2QW  H19  H   HCR6  0   0.251   6.2281   2.9511   1.8775
 2QW  H20  H   HCR6  0   0.267   4.5952   1.1692   2.2267
 2QW  H21  H   H     0   0.230   1.1935  -3.6784   1.8222
 2QW  H22  H   H     0   0.217   0.1777  -3.9460   0.4138
 2QW  H23  H   H     0   0.211   3.0188  -4.9948   0.7902
 2QW  H24  H   H     0   0.229   1.5475  -5.9463   0.8612
 2QW  H25  H   H     0   0.227   2.6789  -6.1545  -1.3649
 2QW  H26  H   H     0   0.209   1.0750  -5.4605  -1.5175
 2QW  H27  H   H     0   0.230   2.6755  -4.1707  -2.8892
 2QW  H28  H   H     0   0.212   3.7097  -3.9173  -1.4969
 2QW  H29  H   HCH1  0   0.254  -2.6767  -1.4884  -0.8431
 2QW  H30  H   HNH2  0   0.353  -3.5671  -3.1250   0.5393
 2QW  H31  H   HNH2  0   0.343  -3.7695  -2.1042   1.7804
 2QW  C4   C   C     0   0.540  -1.3867  -1.4809   0.8809
 2QW  H4   H   HCH2  0   0.246  -2.3383   0.8150   0.0551

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
 2QW  C17  C16  single    1.501  0.020  1.501
 2QW  C18  C16  aromatic  1.392  0.020  1.392
 2QW  C18  C19  aromatic  1.387  0.020  1.387
 2QW  C16  C15  aromatic  1.392  0.020  1.392
 2QW  C19  C13  aromatic  1.394  0.020  1.394
 2QW  C15  C14  aromatic  1.385  0.020  1.385
 2QW  C13  C14  aromatic  1.394  0.020  1.394
 2QW  C13  N2   single    1.402  0.020  1.402
 2QW  N2   C12  single    1.353  0.020  1.353
 2QW  C10  C11  single    1.526  0.020  1.526
 2QW  C10  C9   single    1.525  0.020  1.525
 2QW  C11  C6   single    1.528  0.020  1.528
 2QW  C9   C8   single    1.525  0.020  1.525
 2QW  C12  C5   single    1.529  0.020  1.529
 2QW  C12  O1   double    1.217  0.020  1.217
 2QW  C5   C6   single    1.544  0.020  1.544
 2QW  C5   N1   single    1.438  0.020  1.438
 2QW  C6   C7   single    1.529  0.020  1.529
 2QW  O    C4   double    1.222  0.020  1.222
 2QW  C7   C8   single    1.526  0.020  1.526
 2QW  N1   C4   single    1.344  0.020  1.344
 2QW  C4   C    single    1.530  0.020  1.530
 2QW  C    N    single    1.446  0.020  1.446
 2QW  C    C1   single    1.536  0.020  1.536
 2QW  C1   C2   single    1.520  0.020  1.520
 2QW  SE   C3   single    1.951  0.020  1.951
 2QW  SE   C2   single    1.962  0.020  1.962
 2QW  C7   H1   single    0.970  0.020  1.090
 2QW  C7   H2   single    0.970  0.020  1.090
 2QW  C6   H3   single    0.970  0.020  1.090
 2QW  C1   H4   single    0.970  0.020  1.090
 2QW  C1   H5   single    0.970  0.020  1.090
 2QW  N1   H6   single    0.860  0.020  1.020
 2QW  C5   H7   single    0.970  0.020  1.090
 2QW  C3   H8   single    0.970  0.020  1.090
 2QW  C3   H9   single    0.970  0.020  1.090
 2QW  C3   H10  single    0.970  0.020  1.090
 2QW  C2   H11  single    0.970  0.020  1.090
 2QW  C2   H12  single    0.970  0.020  1.090
 2QW  N2   H13  single    0.860  0.020  1.020
 2QW  C19  H14  single    0.930  0.020  1.080
 2QW  C18  H15  single    0.930  0.020  1.080
 2QW  C17  H16  single    0.970  0.020  1.090
 2QW  C17  H17  single    0.970  0.020  1.090
 2QW  C17  H18  single    0.970  0.020  1.090
 2QW  C15  H19  single    0.930  0.020  1.080
 2QW  C14  H20  single    0.930  0.020  1.080
 2QW  C11  H21  single    0.970  0.020  1.090
 2QW  C11  H22  single    0.970  0.020  1.090
 2QW  C10  H23  single    0.970  0.020  1.090
 2QW  C10  H24  single    0.970  0.020  1.090
 2QW  C9   H25  single    0.970  0.020  1.090
 2QW  C9   H26  single    0.970  0.020  1.090
 2QW  C8   H27  single    0.970  0.020  1.090
 2QW  C8   H28  single    0.970  0.020  1.090
 2QW  C    H29  single    0.970  0.020  1.090
 2QW  N    H30  single    0.890  0.020  1.040
 2QW  N    H31  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
 2QW  H2   C7   H1   106.83  3.000
 2QW  H2   C7   C8   109.41  3.000
 2QW  H1   C7   C8   108.97  3.000
 2QW  H2   C7   C6   110.95  3.000
 2QW  H1   C7   C6   109.25  3.000
 2QW  C8   C7   C6   111.31  3.000
 2QW  H3   C6   C11  107.56  3.000
 2QW  H3   C6   C5   106.65  3.000
 2QW  C11  C6   C5   110.88  3.000
 2QW  H3   C6   C7   107.93  3.000
 2QW  C5   C6   C7   112.98  3.000
 2QW  C11  C6   C7   110.58  3.000
 2QW  H5   C1   H4   106.85  3.000
 2QW  H5   C1   C    108.89  3.000
 2QW  H4   C1   C    108.75  3.000
 2QW  H5   C1   C2   110.42  3.000
 2QW  H4   C1   C2   110.15  3.000
 2QW  C    C1   C2   111.65  3.000
 2QW  H6   N1   C4   118.25  3.000
 2QW  H6   N1   C5   117.08  3.000
 2QW  C4   N1   C5   124.24  3.000
 2QW  H7   C5   C12  108.74  3.000
 2QW  H7   C5   N1   107.55  3.000
 2QW  C12  C5   N1   108.91  3.000
 2QW  H7   C5   C6   107.73  3.000
 2QW  N1   C5   C6   113.06  3.000
 2QW  C12  C5   C6   110.72  3.000
 2QW  H10  C3   H9   108.80  3.000
 2QW  H10  C3   H8   108.75  3.000
 2QW  H9   C3   H8   109.49  3.000
 2QW  H10  C3   SE   108.18  3.000
 2QW  H9   C3   SE   110.83  3.000
 2QW  H8   C3   SE   110.74  3.000
 2QW  H12  C2   H11  108.12  3.000
 2QW  H12  C2   SE   108.69  3.000
 2QW  H11  C2   SE   108.57  3.000
 2QW  H12  C2   C1   110.59  3.000
 2QW  H11  C2   C1   110.40  3.000
 2QW  SE   C2   C1   110.40  3.000
 2QW  N2   C12  C5   113.31  3.000
 2QW  C5   C12  O1   122.15  3.000
 2QW  N2   C12  O1   124.52  3.000
 2QW  H13  N2   C13  114.70  3.000
 2QW  H13  N2   C12  116.29  3.000
 2QW  C13  N2   C12  128.69  3.000
 2QW  C14  C13  C19  118.73  3.000
 2QW  C14  C13  N2   117.22  3.000
 2QW  C19  C13  N2   124.02  3.000
 2QW  H14  C19  C18  119.15  3.000
 2QW  H14  C19  C13  121.16  3.000
 2QW  C18  C19  C13  119.69  3.000
 2QW  H15  C18  C16  119.45  3.000
 2QW  H15  C18  C19  118.34  3.000
 2QW  C16  C18  C19  122.21  3.000
 2QW  C15  C16  C17  121.44  3.000
 2QW  C15  C16  C18  117.34  3.000
 2QW  C17  C16  C18  121.21  3.000
 2QW  H18  C17  H17  107.90  3.000
 2QW  H18  C17  H16  107.04  3.000
 2QW  H17  C17  H16  107.35  3.000
 2QW  H18  C17  C16  111.62  3.000
 2QW  H17  C17  C16  111.57  3.000
 2QW  H16  C17  C16  111.13  3.000
 2QW  H19  C15  C14  118.87  3.000
 2QW  H19  C15  C16  119.81  3.000
 2QW  C14  C15  C16  121.31  3.000
 2QW  H20  C14  C15  119.51  3.000
 2QW  H20  C14  C13  119.78  3.000
 2QW  C15  C14  C13  120.71  3.000
 2QW  H22  C11  H21  106.81  3.000
 2QW  H22  C11  C10  108.99  3.000
 2QW  H21  C11  C10  110.24  3.000
 2QW  H22  C11  C6   109.41  3.000
 2QW  H21  C11  C6   109.87  3.000
 2QW  C10  C11  C6   111.40  3.000
 2QW  H24  C10  H23  106.55  3.000
 2QW  H24  C10  C9   110.49  3.000
 2QW  H23  C10  C9   109.26  3.000
 2QW  H24  C10  C11  109.85  3.000
 2QW  H23  C10  C11  109.39  3.000
 2QW  C9   C10  C11  111.19  3.000
 2QW  H26  C9   H25  106.56  3.000
 2QW  H26  C9   C8   109.36  3.000
 2QW  H25  C9   C8   110.18  3.000
 2QW  H26  C9   C10  109.33  3.000
 2QW  H25  C9   C10  110.41  3.000
 2QW  C8   C9   C10  110.88  3.000
 2QW  H28  C8   H27  106.48  3.000
 2QW  H28  C8   C9   109.30  3.000
 2QW  H27  C8   C9   110.40  3.000
 2QW  H28  C8   C7   109.18  3.000
 2QW  H27  C8   C7   109.67  3.000
 2QW  C9   C8   C7   111.66  3.000
 2QW  H29  C    N    107.93  3.000
 2QW  H29  C    C4   109.09  3.000
 2QW  N    C    C4   113.43  3.000
 2QW  H29  C    C1   108.09  3.000
 2QW  N    C    C1   110.61  3.000
 2QW  C4   C    C1   107.56  3.000
 2QW  H31  N    H30  106.19  3.000
 2QW  H31  N    C    109.39  3.000
 2QW  H30  N    C    110.11  3.000
 2QW  C2   SE   C3    97.05  3.000
 2QW  C    C4   O    121.39  3.000
 2QW  C    C4   N1   114.81  3.000
 2QW  O    C4   N1   123.77  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
 2QW  CONST_01  C16  C18  C19  C13     0.00   0.0  0
 2QW  CONST_02  C16  C15  C14  C13     0.00   0.0  0
 2QW  CONST_03  C15  C16  C18  C19     0.00   0.0  0
 2QW  CONST_04  C15  C14  C13  C19     0.00   0.0  0
 2QW  CONST_05  C14  C15  C16  C18     0.00   0.0  0
 2QW  CONST_06  C14  C13  C19  C18     0.00   0.0  0
 2QW  CONST_07  C18  C19  C13  N2    180.00   0.0  0
 2QW  CONST_08  C15  C14  C13  N2    180.00   0.0  0
 2QW  CONST_09  C17  C16  C18  C19   180.00   0.0  0
 2QW  CONST_10  C14  C15  C16  C17   180.00   0.0  0
 2QW  CONST_11  H15  C18  C19  C13   180.00   0.0  0
 2QW  CONST_12  H19  C15  C14  C13   180.00   0.0  0
 2QW  CONST_13  H20  C14  C13  C19   180.00   0.0  0
 2QW  CONST_14  H14  C19  C18  C16   180.00   0.0  0
 2QW  CONST_18  C13  N2   C12  O1      0.00   0.0  0
 2QW  CONST_19  C13  N2   C12  C5    180.00   0.0  0
 2QW  CONST_20  O    C4   N1   C5      0.00   0.0  0
 2QW  CONST_21  C    C4   N1   C5    180.00   0.0  0
 2QW  CONST_22  H6   N1   C4   O     180.00   0.0  0
 2QW  Var_01    C10  C9   C8   C7    -55.21  30.0  1
 2QW  Var_02    C9   C10  C11  C6    -56.26  30.0  1
 2QW  Var_03    C9   C8   C7   C6     55.39  30.0  1
 2QW  Var_04    C8   C9   C10  C11    55.48  30.0  1
 2QW  Var_05    H16  C17  C16  C18    79.45  30.0  2
 2QW  Var_06    SE   C2   C1   C    -178.58  30.0  3
 2QW  Var_07    H11  C2   SE   C3     61.02  30.0  3
 2QW  Var_08    H8   C3   SE   C2    -60.27  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
 2QW  chir_01  C6  C11  C5  C7   positiv
 2QW  chir_02  C5  N1   C6  C12  negativ
 2QW  chir_03  C   N    C4  C1   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
 2QW  plan-1  N2   0.020
 2QW  plan-1  C13  0.020
 2QW  plan-1  C19  0.020
 2QW  plan-1  C18  0.020
 2QW  plan-1  C16  0.020
 2QW  plan-1  C17  0.020
 2QW  plan-1  C15  0.020
 2QW  plan-1  C14  0.020
 2QW  plan-1  H14  0.020
 2QW  plan-1  H15  0.020
 2QW  plan-1  H19  0.020
 2QW  plan-1  H20  0.020
 2QW  plan-2  O1   0.020
 2QW  plan-2  C5   0.020
 2QW  plan-2  C12  0.020
 2QW  plan-2  N2   0.020
 2QW  plan-2  C13  0.020
 2QW  plan-2  H13  0.020
 2QW  plan-3  N1   0.020
 2QW  plan-3  C5   0.020
 2QW  plan-3  O    0.020
 2QW  plan-3  C    0.020
 2QW  plan-3  H6   0.020
 2QW  plan-3  C4   0.020

