# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:13:48 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{R})-2-[(3,4-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)NCc1ccc(C)c(C)c1)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
 E8R  E8R  (2~{R})-2-[(3,4-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_E8R
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
 E8R  C1   C  CH3   0  -0.734   6.9101  -0.2828  -0.9924
 E8R  C2   C  CR6   0   0.054   5.5393   0.1655  -0.5793
 E8R  CD1  C  CR16  0  -0.285   5.0076   1.3538  -1.0637
 E8R  CG1  C  CR16  0  -0.314   3.7396   1.7847  -0.6911
 E8R  CB   C  CR6   0   0.070   2.9748   1.0279   0.1830
 E8R  CA   C  CH2   0  -0.320   1.5942   1.4674   0.5887
 E8R  N    N  NH1   0  -0.677   0.6008   0.5578   0.0579
 E8R  C7   C  C     0   0.753  -0.6518   0.4865   0.5705
 E8R  O    O  O     0  -0.544  -0.9892   1.0658   1.5981
 E8R  N2   N  NH1   0  -0.681  -1.5176  -0.3176  -0.1120
 E8R  C8   C  CH1   0  -0.197  -2.9157  -0.2943   0.2228
 E8R  C9   C  CH2   0  -0.447  -3.6933  -1.2337  -0.7004
 E8R  C10  C  CH1   0  -0.234  -3.2834  -2.7059  -0.6215
 E8R  C11  C  CH3   0  -0.663  -3.4866  -3.2868   0.7738
 E8R  C12  C  CH3   0  -0.652  -4.0730  -3.5051  -1.6538
 E8R  C13  C  C     0   0.526  -3.4798   1.1206   0.0783
 E8R  O2   O  O     0  -0.472  -3.1518   1.8679  -0.8230
 E8R  N3   N  NH1   0  -0.373  -4.4274   1.4051   0.9889
 E8R  O3   O  OH1   0  -0.543  -4.9626   2.6573   1.0440
 E8R  CG2  C  CR16  0  -0.332   3.5066  -0.1649   0.6701
 E8R  C15  C  CR6   0   0.088   4.7720  -0.6072   0.3082
 E8R  C16  C  CH3   0  -0.735   5.3125  -1.8951   0.8569
 E8R  H1   H  HCH3  0   0.244   7.5933  -0.3202  -0.1411
 E8R  H2   H  HCH3  0   0.242   6.8932  -1.2854  -1.4245
 E8R  H3   H  HCH3  0   0.250   7.3406   0.3909  -1.7318
 E8R  H4   H  HCR6  0   0.245   5.5932   1.9555  -1.7490
 E8R  H5   H  HCR6  0   0.248   3.3494   2.7145  -1.0879
 E8R  H6   H  HCH2  0   0.255   1.5093   1.4760   1.6757
 E8R  H7   H  HCH2  0   0.243   1.4206   2.4933   0.2473
 E8R  H8   H  HNH1  0   0.393   0.7754   0.1838  -0.8614
 E8R  H9   H  HNH1  0   0.393  -1.2797  -0.5969  -1.0511
 E8R  H10  H  HCH1  0   0.266  -3.0451  -0.6269   1.2563
 E8R  H11  H  HCH2  0   0.247  -4.7559  -1.1486  -0.4532
 E8R  H12  H  HCH2  0   0.244  -3.5877  -0.8799  -1.7318
 E8R  H13  H  HCH1  0   0.223  -2.2210  -2.7894  -0.8751
 E8R  H14  H  HCH3  0   0.216  -4.5295  -3.1942   1.0878
 E8R  H15  H  HCH3  0   0.232  -3.2291  -4.3468   0.7925
 E8R  H16  H  HCH3  0   0.231  -2.8696  -2.7939   1.5264
 E8R  H17  H  HCH3  0   0.227  -3.8883  -3.1438  -2.6668
 E8R  H18  H  HCH3  0   0.229  -3.8019  -4.5614  -1.6244
 E8R  H19  H  HCH3  0   0.215  -5.1470  -3.4337  -1.4656
 E8R  H20  H  HNH1  0   0.414  -4.5290   0.8685   1.8387
 E8R  H21  H  HOH1  0   0.478  -5.8075   2.6082   0.5788
 E8R  H22  H  HCR6  0   0.241   2.9162  -0.7647   1.3549
 E8R  H23  H  HCH3  0   0.242   6.2618  -1.7450   1.3749
 E8R  H24  H  HCH3  0   0.250   4.6172  -2.3486   1.5620
 E8R  H25  H  HCH3  0   0.243   5.5010  -2.6214   0.0628

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
 E8R  C1   C2   single    1.500  0.020  1.500
 E8R  C2   CD1  aromatic  1.389  0.020  1.389
 E8R  C2   C15  aromatic  1.405  0.020  1.405
 E8R  CD1  CG1  aromatic  1.390  0.020  1.390
 E8R  C16  C15  single    1.501  0.020  1.501
 E8R  C11  C10  single    1.525  0.020  1.525
 E8R  C15  CG2  aromatic  1.388  0.020  1.388
 E8R  C10  C9   single    1.530  0.020  1.530
 E8R  C10  C12  single    1.526  0.020  1.526
 E8R  CG1  CB   aromatic  1.386  0.020  1.386
 E8R  C9   C8   single    1.530  0.020  1.530
 E8R  CG2  CB   aromatic  1.394  0.020  1.394
 E8R  CB   CA   single    1.505  0.020  1.505
 E8R  N2   C8   single    1.438  0.020  1.438
 E8R  N2   C7   single    1.365  0.020  1.365
 E8R  C8   C13  single    1.530  0.020  1.530
 E8R  N    C7   single    1.355  0.020  1.355
 E8R  N    CA   single    1.448  0.020  1.448
 E8R  C7   O    double    1.227  0.020  1.227
 E8R  C13  O2   double    1.216  0.020  1.216
 E8R  C13  N3   single    1.345  0.020  1.345
 E8R  N3   O3   single    1.363  0.020  1.363
 E8R  C1   H1   single    0.970  0.020  1.090
 E8R  C1   H2   single    0.970  0.020  1.090
 E8R  C1   H3   single    0.970  0.020  1.090
 E8R  CD1  H4   single    0.930  0.020  1.080
 E8R  CG1  H5   single    0.930  0.020  1.080
 E8R  CA   H6   single    0.970  0.020  1.090
 E8R  CA   H7   single    0.970  0.020  1.090
 E8R  N    H8   single    0.860  0.020  1.020
 E8R  N2   H9   single    0.890  0.020  1.040
 E8R  C8   H10  single    0.970  0.020  1.090
 E8R  C9   H11  single    0.970  0.020  1.090
 E8R  C9   H12  single    0.970  0.020  1.090
 E8R  C10  H13  single    0.970  0.020  1.090
 E8R  C11  H14  single    0.970  0.020  1.090
 E8R  C11  H15  single    0.970  0.020  1.090
 E8R  C11  H16  single    0.970  0.020  1.090
 E8R  C12  H17  single    0.970  0.020  1.090
 E8R  C12  H18  single    0.970  0.020  1.090
 E8R  C12  H19  single    0.970  0.020  1.090
 E8R  N3   H20  single    0.890  0.020  1.040
 E8R  O3   H21  single    0.850  0.020  0.980
 E8R  CG2  H22  single    0.930  0.020  1.080
 E8R  C16  H23  single    0.970  0.020  1.090
 E8R  C16  H24  single    0.970  0.020  1.090
 E8R  C16  H25  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
 E8R  H3   C1   H2   107.79  3.000
 E8R  H3   C1   H1   107.64  3.000
 E8R  H2   C1   H1   106.65  3.000
 E8R  H3   C1   C2   111.31  3.000
 E8R  H2   C1   C2   111.67  3.000
 E8R  H1   C1   C2   111.54  3.000
 E8R  C15  C2   CD1  118.80  3.000
 E8R  C15  C2   C1   120.58  3.000
 E8R  CD1  C2   C1   120.62  3.000
 E8R  H4   CD1  CG1  119.35  3.000
 E8R  H4   CD1  C2   119.26  3.000
 E8R  CG1  CD1  C2   121.39  3.000
 E8R  H5   CG1  CB   120.05  3.000
 E8R  H5   CG1  CD1  119.75  3.000
 E8R  CB   CG1  CD1  120.20  3.000
 E8R  CG2  CB   CA   120.39  3.000
 E8R  CA   CB   CG1  121.11  3.000
 E8R  CG2  CB   CG1  118.49  3.000
 E8R  H7   CA   H6   106.93  3.000
 E8R  H7   CA   N    111.44  3.000
 E8R  H6   CA   N    108.48  3.000
 E8R  H7   CA   CB   109.58  3.000
 E8R  H6   CA   CB   110.03  3.000
 E8R  N    CA   CB   110.32  3.000
 E8R  H8   N    C7   119.06  3.000
 E8R  H8   N    CA   116.66  3.000
 E8R  C7   N    CA   121.91  3.000
 E8R  N2   C7   O    121.51  3.000
 E8R  O    C7   N    123.10  3.000
 E8R  N2   C7   N    115.35  3.000
 E8R  H9   N2   C8   116.80  3.000
 E8R  H9   N2   C7   118.65  3.000
 E8R  C8   N2   C7   119.40  3.000
 E8R  H10  C8   C13  109.09  3.000
 E8R  H10  C8   C9   108.87  3.000
 E8R  C13  C8   C9   108.87  3.000
 E8R  H10  C8   N2   109.28  3.000
 E8R  C13  C8   N2   110.58  3.000
 E8R  C9   C8   N2   110.11  3.000
 E8R  H12  C9   H11  106.33  3.000
 E8R  H12  C9   C10  109.48  3.000
 E8R  H11  C9   C10  108.86  3.000
 E8R  H12  C9   C8   108.71  3.000
 E8R  H11  C9   C8   108.03  3.000
 E8R  C10  C9   C8   115.06  3.000
 E8R  H13  C10  C12  107.78  3.000
 E8R  H13  C10  C11  108.18  3.000
 E8R  C12  C10  C11  110.53  3.000
 E8R  H13  C10  C9   108.73  3.000
 E8R  C12  C10  C9   109.29  3.000
 E8R  C11  C10  C9   112.21  3.000
 E8R  H16  C11  H15  107.08  3.000
 E8R  H16  C11  H14  107.65  3.000
 E8R  H15  C11  H14  107.61  3.000
 E8R  H16  C11  C10  112.57  3.000
 E8R  H15  C11  C10  110.75  3.000
 E8R  H14  C11  C10  110.96  3.000
 E8R  H19  C12  H18  107.63  3.000
 E8R  H19  C12  H17  107.74  3.000
 E8R  H18  C12  H17  107.68  3.000
 E8R  H19  C12  C10  110.97  3.000
 E8R  H18  C12  C10  111.12  3.000
 E8R  H17  C12  C10  111.54  3.000
 E8R  N3   C13  O2   124.19  3.000
 E8R  N3   C13  C8   113.05  3.000
 E8R  O2   C13  C8   122.61  3.000
 E8R  H20  N3   O3   114.49  3.000
 E8R  H20  N3   C13  121.88  3.000
 E8R  O3   N3   C13  119.90  3.000
 E8R  H21  O3   N3   106.10  3.000
 E8R  H22  CG2  C15  118.96  3.000
 E8R  H22  CG2  CB   119.08  3.000
 E8R  C15  CG2  CB   121.95  3.000
 E8R  C16  C15  CG2  120.42  3.000
 E8R  CG2  C15  C2   119.16  3.000
 E8R  C16  C15  C2   120.42  3.000
 E8R  H25  C16  H24  107.70  3.000
 E8R  H25  C16  H23  106.63  3.000
 E8R  H24  C16  H23  107.77  3.000
 E8R  H25  C16  C15  111.52  3.000
 E8R  H24  C16  C15  111.35  3.000
 E8R  H23  C16  C15  111.63  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
 E8R  CONST_01  CB   CG1  CD1  C2     0.00   0.0  0
 E8R  CONST_02  CB   CG2  C15  C2     0.00   0.0  0
 E8R  CONST_03  CG2  C15  C2   CD1    0.00   0.0  0
 E8R  CONST_04  CG2  CB   CG1  CD1    0.00   0.0  0
 E8R  CONST_05  C15  C2   CD1  CG1    0.00   0.0  0
 E8R  CONST_06  C15  CG2  CB   CG1    0.00   0.0  0
 E8R  CONST_07  CG1  CD1  C2   C1   180.00   0.0  0
 E8R  CONST_08  CG2  C15  C2   C1   180.00   0.0  0
 E8R  CONST_09  C16  C15  C2   CD1  180.00   0.0  0
 E8R  CONST_10  CA   CB   CG1  CD1  180.00   0.0  0
 E8R  CONST_11  C16  C15  CG2  CB   180.00   0.0  0
 E8R  CONST_12  C15  CG2  CB   CA   180.00   0.0  0
 E8R  CONST_13  H5   CG1  CD1  C2   180.00   0.0  0
 E8R  CONST_14  H22  CG2  C15  C2   180.00   0.0  0
 E8R  CONST_15  H4   CD1  CG1  CB   180.00   0.0  0
 E8R  CONST_16  O    C7   N    CA     0.00   0.0  0
 E8R  CONST_17  C8   N2   C7   O      0.00   0.0  0
 E8R  CONST_18  O3   N3   C13  C8   180.00   0.0  0
 E8R  CONST_19  O3   N3   C13  O2     0.00   0.0  0
 E8R  CONST_20  N2   C7   N    CA   180.00   0.0  0
 E8R  CONST_21  C8   N2   C7   N    180.00   0.0  0
 E8R  CONST_22  H9   N2   C7   O    180.00   0.0  0
 E8R  CONST_23  H8   N    C7   O    180.00   0.0  0
 E8R  Var_01    N    CA   CB   CG1  112.79  30.0  2
 E8R  Var_02    H23  C16  C15  C2    56.92  30.0  2
 E8R  Var_03    H1   C1   C2   CD1  116.22  30.0  2
 E8R  Var_04    C7   N    CA   CB   160.66  30.0  1
 E8R  Var_05    C11  C10  C9   C8    60.68  30.0  2
 E8R  Var_06    H14  C11  C10  C9    58.06  30.0  3
 E8R  Var_07    H17  C12  C10  C9    59.74  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
 E8R  chir_01  C8  C9  N2  C13  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
 E8R  plan-1  C1   0.020
 E8R  plan-1  C2   0.020
 E8R  plan-1  CD1  0.020
 E8R  plan-1  CG1  0.020
 E8R  plan-1  CB   0.020
 E8R  plan-1  CA   0.020
 E8R  plan-1  CG2  0.020
 E8R  plan-1  C15  0.020
 E8R  plan-1  C16  0.020
 E8R  plan-1  H4   0.020
 E8R  plan-1  H5   0.020
 E8R  plan-1  H22  0.020
 E8R  plan-2  CA   0.020
 E8R  plan-2  N    0.020
 E8R  plan-2  C7   0.020
 E8R  plan-2  O    0.020
 E8R  plan-2  N2   0.020
 E8R  plan-2  C8   0.020
 E8R  plan-2  H8   0.020
 E8R  plan-2  H9   0.020
 E8R  plan-3  C8   0.020
 E8R  plan-3  C13  0.020
 E8R  plan-3  O2   0.020
 E8R  plan-3  N3   0.020
 E8R  plan-3  O3   0.020
 E8R  plan-3  H20  0.020

