# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:10:20 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{S})-2-[(2,3-dimethylphenyl)methylcarbamoylamino]-4-methyl-~{N}-oxidanyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)NCc1cccc(C)c1C)C(=O)NO
#
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
 E8G  E8G  (2~{S})-2-[(2,3-dimethylphenyl)methylcarbamoylamino]-4-methyl-~{N}-oxidanyl-pentanamide  ligand  47  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E8G
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
 E8G  CD1  C  CH3   0  -0.750  -3.4103   1.7745   0.9084
 E8G  CG1  C  CR6   0   0.034  -4.0653   0.5587   0.3154
 E8G  C3   C  CR6   0   0.084  -5.2700   0.1009   0.8728
 E8G  C4   C  CH3   0  -0.736  -5.8825   0.8093   2.0465
 E8G  C5   C  CR16  0  -0.311  -5.8970  -1.0177   0.3329
 E8G  C6   C  CR16  0  -0.246  -5.3490  -1.6916  -0.7475
 E8G  CG2  C  CR16  0  -0.315  -4.1561  -1.2464  -1.2911
 E8G  CB   C  CR6   0   0.035  -3.5094  -0.1273  -0.7721
 E8G  CA   C  CH2   0  -0.339  -2.2005   0.2894  -1.3904
 E8G  N    N  NH1   0  -0.676  -1.1053  -0.0354  -0.4974
 E8G  C10  C  C     0   0.754   0.1832   0.1745  -0.8682
 E8G  O    O  O     0  -0.546   0.4809   0.7486  -1.9105
 E8G  N2   N  NH1   0  -0.691   1.1126  -0.3117   0.0015
 E8G  C11  C  CH1   0  -0.193   2.5242  -0.0778  -0.1876
 E8G  C12  C  CH2   0  -0.408   2.9830   1.2657   0.3917
 E8G  C13  C  CH1   0  -0.253   4.4658   1.5930   0.2056
 E8G  C14  C  CH3   0  -0.657   4.8462   1.7121  -1.2673
 E8G  C15  C  CH3   0  -0.649   4.8021   2.8859   0.9427
 E8G  C16  C  C     0   0.526   3.2563  -1.2210   0.5035
 E8G  O2   O  O     0  -0.470   3.0389  -1.5173   1.6650
 E8G  N3   N  NH1   0  -0.372   4.1751  -1.8222  -0.2668
 E8G  O3   O  OH1   0  -0.539   4.8309  -2.9247   0.1861
 E8G  H1   H  HCH3  0   0.248  -3.0994   1.5911   1.9393
 E8G  H2   H  HCH3  0   0.259  -2.5288   2.0927   0.3590
 E8G  H3   H  HCH3  0   0.244  -4.1028   2.6180   0.9374
 E8G  H4   H  HCH3  0   0.244  -6.1352   1.8443   1.8069
 E8G  H5   H  HCH3  0   0.250  -6.7953   0.3133   2.3720
 E8G  H6   H  HCH3  0   0.244  -5.1989   0.8438   2.8974
 E8G  H7   H  HCR6  0   0.245  -6.8281  -1.3634   0.7662
 E8G  H8   H  HCR6  0   0.251  -5.8477  -2.5593  -1.1598
 E8G  H9   H  HCR6  0   0.247  -3.7180  -1.7733  -2.1304
 E8G  H10  H  HCH2  0   0.253  -2.0811  -0.2164  -2.3528
 E8G  H11  H  HCH2  0   0.246  -2.1957   1.3610  -1.6034
 E8G  H12  H  HNH1  0   0.394  -1.2997  -0.6746   0.2566
 E8G  H13  H  HNH1  0   0.391   0.8197  -0.5898   0.9260
 E8G  H14  H  HCH1  0   0.267   2.7192  -0.0977  -1.2613
 E8G  H15  H  HCH2  0   0.237   2.3845   2.0504  -0.0812
 E8G  H16  H  HCH2  0   0.232   2.7352   1.2814   1.4575
 E8G  H17  H  HCH1  0   0.224   5.0662   0.7924   0.6530
 E8G  H18  H  HCH3  0   0.219   4.2524   2.4887  -1.7555
 E8G  H19  H  HCH3  0   0.233   5.8978   1.9808  -1.3773
 E8G  H20  H  HCH3  0   0.221   4.6921   0.7857  -1.8223
 E8G  H21  H  HCH3  0   0.227   4.5579   2.8174   2.0040
 E8G  H22  H  HCH3  0   0.228   5.8648   3.1200   0.8597
 E8G  H23  H  HCH3  0   0.216   4.2450   3.7284   0.5259
 E8G  H24  H  HNH1  0   0.419   4.2299  -1.6738  -1.2641
 E8G  H25  H  HOH1  0   0.480   5.6796  -2.6140   0.5282

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
 E8G  O3   N3   single    1.360  0.020  1.360
 E8G  O2   C16  double    1.218  0.020  1.218
 E8G  N3   C16  single    1.341  0.020  1.341
 E8G  C16  C11  single    1.523  0.020  1.523
 E8G  C15  C13  single    1.526  0.020  1.526
 E8G  C11  C12  single    1.533  0.020  1.533
 E8G  C11  N2   single    1.443  0.020  1.443
 E8G  C12  C13  single    1.530  0.020  1.530
 E8G  C14  C13  single    1.526  0.020  1.526
 E8G  N2   C10  single    1.363  0.020  1.363
 E8G  O    C10  double    1.227  0.020  1.227
 E8G  C10  N    single    1.357  0.020  1.357
 E8G  N    CA   single    1.450  0.020  1.450
 E8G  CA   CB   single    1.506  0.020  1.506
 E8G  CB   CG2  aromatic  1.393  0.020  1.393
 E8G  CB   CG1  aromatic  1.401  0.020  1.401
 E8G  CG2  C6   aromatic  1.384  0.020  1.384
 E8G  C6   C5   aromatic  1.386  0.020  1.386
 E8G  CG1  CD1  single    1.503  0.020  1.503
 E8G  CG1  C3   aromatic  1.404  0.020  1.404
 E8G  C5   C3   aromatic  1.391  0.020  1.391
 E8G  C3   C4   single    1.501  0.020  1.501
 E8G  CD1  H1   single    0.970  0.020  1.090
 E8G  CD1  H2   single    0.970  0.020  1.090
 E8G  CD1  H3   single    0.970  0.020  1.090
 E8G  C4   H4   single    0.970  0.020  1.090
 E8G  C4   H5   single    0.970  0.020  1.090
 E8G  C4   H6   single    0.970  0.020  1.090
 E8G  C5   H7   single    0.930  0.020  1.080
 E8G  C6   H8   single    0.930  0.020  1.080
 E8G  CG2  H9   single    0.930  0.020  1.080
 E8G  CA   H10  single    0.970  0.020  1.090
 E8G  CA   H11  single    0.970  0.020  1.090
 E8G  N    H12  single    0.860  0.020  1.020
 E8G  N2   H13  single    0.860  0.020  1.020
 E8G  C11  H14  single    0.970  0.020  1.090
 E8G  C12  H15  single    0.970  0.020  1.090
 E8G  C12  H16  single    0.970  0.020  1.090
 E8G  C13  H17  single    0.970  0.020  1.090
 E8G  C14  H18  single    0.970  0.020  1.090
 E8G  C14  H19  single    0.970  0.020  1.090
 E8G  C14  H20  single    0.970  0.020  1.090
 E8G  C15  H21  single    0.970  0.020  1.090
 E8G  C15  H22  single    0.970  0.020  1.090
 E8G  C15  H23  single    0.970  0.020  1.090
 E8G  N3   H24  single    0.860  0.020  1.020
 E8G  O3   H25  single    0.850  0.020  0.980

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
 E8G  H3   CD1  H2   107.56  3.000
 E8G  H3   CD1  H1   106.57  3.000
 E8G  H2   CD1  H1   107.19  3.000
 E8G  H3   CD1  CG1  111.04  3.000
 E8G  H2   CD1  CG1  113.02  3.000
 E8G  H1   CD1  CG1  111.14  3.000
 E8G  CB   CG1  C3   119.27  3.000
 E8G  C3   CG1  CD1  118.75  3.000
 E8G  CB   CG1  CD1  121.97  3.000
 E8G  C5   C3   C4   119.92  3.000
 E8G  C4   C3   CG1  120.43  3.000
 E8G  C5   C3   CG1  119.65  3.000
 E8G  H6   C4   H5   107.83  3.000
 E8G  H6   C4   H4   106.61  3.000
 E8G  H5   C4   H4   107.66  3.000
 E8G  H6   C4   C3   111.63  3.000
 E8G  H5   C4   C3   111.15  3.000
 E8G  H4   C4   C3   111.72  3.000
 E8G  H7   C5   C6   119.75  3.000
 E8G  H7   C5   C3   119.24  3.000
 E8G  C6   C5   C3   121.01  3.000
 E8G  H8   C6   CG2  120.35  3.000
 E8G  H8   C6   C5   120.29  3.000
 E8G  CG2  C6   C5   119.36  3.000
 E8G  H9   CG2  CB   119.44  3.000
 E8G  H9   CG2  C6   119.75  3.000
 E8G  CB   CG2  C6   120.81  3.000
 E8G  CA   CB   CG2  118.21  3.000
 E8G  CG2  CB   CG1  119.90  3.000
 E8G  CA   CB   CG1  121.87  3.000
 E8G  H11  CA   H10  106.36  3.000
 E8G  H11  CA   N    109.66  3.000
 E8G  H10  CA   N    110.85  3.000
 E8G  H11  CA   CB   110.80  3.000
 E8G  H10  CA   CB   109.15  3.000
 E8G  N    CA   CB   109.97  3.000
 E8G  H12  N    C10  119.06  3.000
 E8G  H12  N    CA   117.22  3.000
 E8G  C10  N    CA   120.94  3.000
 E8G  N2   C10  O    122.95  3.000
 E8G  O    C10  N    122.34  3.000
 E8G  N2   C10  N    114.71  3.000
 E8G  H13  N2   C11  116.65  3.000
 E8G  H13  N2   C10  119.03  3.000
 E8G  C11  N2   C10  121.71  3.000
 E8G  H14  C11  C16  110.29  3.000
 E8G  H14  C11  C12  109.52  3.000
 E8G  C16  C11  C12  110.02  3.000
 E8G  H14  C11  N2   107.50  3.000
 E8G  C12  C11  N2   112.66  3.000
 E8G  C16  C11  N2   106.80  3.000
 E8G  H16  C12  H15  106.66  3.000
 E8G  H16  C12  C13  109.57  3.000
 E8G  H15  C12  C13  108.92  3.000
 E8G  H16  C12  C11  108.22  3.000
 E8G  H15  C12  C11  107.54  3.000
 E8G  C13  C12  C11  115.57  3.000
 E8G  H17  C13  C15  107.52  3.000
 E8G  H17  C13  C14  108.33  3.000
 E8G  C15  C13  C14  110.19  3.000
 E8G  H17  C13  C12  108.97  3.000
 E8G  C14  C13  C12  112.07  3.000
 E8G  C15  C13  C12  109.64  3.000
 E8G  H20  C14  H19  107.10  3.000
 E8G  H20  C14  H18  107.42  3.000
 E8G  H19  C14  H18  107.68  3.000
 E8G  H20  C14  C13  112.93  3.000
 E8G  H19  C14  C13  110.91  3.000
 E8G  H18  C14  C13  110.56  3.000
 E8G  H23  C15  H22  107.58  3.000
 E8G  H23  C15  H21  107.78  3.000
 E8G  H22  C15  H21  107.78  3.000
 E8G  H23  C15  C13  110.90  3.000
 E8G  H22  C15  C13  111.08  3.000
 E8G  H21  C15  C13  111.55  3.000
 E8G  N3   C16  O2   124.11  3.000
 E8G  N3   C16  C11  113.90  3.000
 E8G  O2   C16  C11  121.96  3.000
 E8G  H24  N3   O3   114.95  3.000
 E8G  H24  N3   C16  122.58  3.000
 E8G  O3   N3   C16  120.15  3.000
 E8G  H25  O3   N3   106.30  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
 E8G  CONST_01  C6   CG2  CB   CG1     0.00   0.0  0
 E8G  CONST_02  C6   C5   C3   CG1     0.00   0.0  0
 E8G  CONST_03  CG2  CB   CG1  C3      0.00   0.0  0
 E8G  CONST_04  CG2  C6   C5   C3      0.00   0.0  0
 E8G  CONST_05  CB   CG2  C6   C5      0.00   0.0  0
 E8G  CONST_06  CB   CG1  C3   C5      0.00   0.0  0
 E8G  CONST_07  CG2  CB   CG1  CD1   180.00   0.0  0
 E8G  CONST_08  C5   C3   CG1  CD1   180.00   0.0  0
 E8G  CONST_09  CA   CB   CG1  C3    180.00   0.0  0
 E8G  CONST_10  CB   CG1  C3   C4    180.00   0.0  0
 E8G  CONST_11  C6   C5   C3   C4    180.00   0.0  0
 E8G  CONST_12  CA   CB   CG2  C6    180.00   0.0  0
 E8G  CONST_13  H9   CG2  CB   CG1   180.00   0.0  0
 E8G  CONST_14  H7   C5   C3   CG1   180.00   0.0  0
 E8G  CONST_15  H8   C6   C5   C3    180.00   0.0  0
 E8G  CONST_16  O    C10  N    CA      0.00   0.0  0
 E8G  CONST_17  C11  N2   C10  O       0.00   0.0  0
 E8G  CONST_18  O3   N3   C16  C11   180.00   0.0  0
 E8G  CONST_19  O3   N3   C16  O2      0.00   0.0  0
 E8G  CONST_20  N2   C10  N    CA    180.00   0.0  0
 E8G  CONST_21  C11  N2   C10  N     180.00   0.0  0
 E8G  CONST_22  H13  N2   C10  O     180.00   0.0  0
 E8G  CONST_23  H12  N    C10  O     180.00   0.0  0
 E8G  CONST_24  H24  N3   C16  C11     0.00   0.0  0
 E8G  Var_01    N    CA   CB   CG1    71.82  30.0  3
 E8G  Var_02    H4   C4   C3   CG1    61.28  30.0  2
 E8G  Var_03    H1   CD1  CG1  C3     63.99  30.0  2
 E8G  Var_04    C10  N    CA   CB    176.16  30.0  2
 E8G  Var_05    C15  C13  C12  C11  -174.63  30.0  3
 E8G  Var_06    H21  C15  C13  C12    57.39  30.0  3
 E8G  Var_07    H18  C14  C13  C12    58.58  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
 E8G  chir_01  C11  C16  C12  N2  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
 E8G  plan-1  CD1  0.020
 E8G  plan-1  CG1  0.020
 E8G  plan-1  C3   0.020
 E8G  plan-1  C4   0.020
 E8G  plan-1  C5   0.020
 E8G  plan-1  C6   0.020
 E8G  plan-1  CG2  0.020
 E8G  plan-1  CB   0.020
 E8G  plan-1  CA   0.020
 E8G  plan-1  H7   0.020
 E8G  plan-1  H8   0.020
 E8G  plan-1  H9   0.020
 E8G  plan-2  CA   0.020
 E8G  plan-2  N    0.020
 E8G  plan-2  C10  0.020
 E8G  plan-2  O    0.020
 E8G  plan-2  N2   0.020
 E8G  plan-2  C11  0.020
 E8G  plan-2  H12  0.020
 E8G  plan-2  H13  0.020
 E8G  plan-3  C11  0.020
 E8G  plan-3  C16  0.020
 E8G  plan-3  O2   0.020
 E8G  plan-3  N3   0.020
 E8G  plan-3  O3   0.020
 E8G  plan-3  H24  0.020

