# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 10:28:06 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2~{S})-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
 E8F  E8F  (2~{S})-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_E8F
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
 E8F  C1   C  CH3   0  -0.736   6.8347   1.0043  -0.6186
 E8F  C2   C  CR6   0   0.052   5.4886   0.4859  -0.2066
 E8F  CD1  C  CR16  0  -0.284   4.6146   1.2835   0.5281
 E8F  CG1  C  CR16  0  -0.291   3.3669   0.8218   0.9176
 E8F  CB   C  CR6   0   0.067   2.9609  -0.4639   0.5772
 E8F  CA   C  CH2   0  -0.315   1.6053  -0.9747   0.9831
 E8F  N    N  NH1   0  -0.679   0.5662  -0.2270   0.3061
 E8F  C7   C  C     0   0.755  -0.7274  -0.2879   0.7072
 E8F  O    O  O     0  -0.544  -1.0807  -0.8542   1.7363
 E8F  N2   N  NH1   0  -0.679  -1.6178   0.3702  -0.0899
 E8F  C8   C  CH1   0  -0.208  -3.0280   0.2064   0.1324
 E8F  C9   C  CH2   0  -0.445  -3.8175   1.0657  -0.8579
 E8F  C10  C  CH1   0  -0.233  -3.5534   2.5708  -0.7576
 E8F  C11  C  CH3   0  -0.653  -4.3258   3.2958  -1.8552
 E8F  C12  C  CH3   0  -0.663  -3.9191   3.1263   0.6143
 E8F  C13  C  C     0   0.530  -3.4414  -1.2550  -0.0440
 E8F  O2   O  O     0  -0.473  -2.9480  -1.9808  -0.8860
 E8F  N3   N  NH1   0  -0.372  -4.4137  -1.6351   0.8007
 E8F  O3   O  OH1   0  -0.543  -5.0694  -2.8136   0.6097
 E8F  CG2  C  CR16  0  -0.354   3.8308  -1.2600  -0.1581
 E8F  C15  C  CR6   0   0.091   5.0881  -0.8107  -0.5535
 E8F  C16  C  CH3   0  -0.738   5.9966  -1.7026  -1.3474
 E8F  H1   H  HCH3  0   0.244   7.6433   0.4201  -0.1738
 E8F  H2   H  HCH3  0   0.242   6.9713   0.9522  -1.7009
 E8F  H3   H  HCH3  0   0.250   6.9710   2.0415  -0.3159
 E8F  H4   H  HCR6  0   0.245   4.9178   2.2870   0.8031
 E8F  H5   H  HCR6  0   0.247   2.7103   1.4641   1.4926
 E8F  H6   H  HCH2  0   0.242   1.5341  -2.0456   0.7660
 E8F  H7   H  HCH2  0   0.253   1.4737  -0.8599   2.0600
 E8F  H8   H  HNH1  0   0.393   0.7784   0.1051  -0.6213
 E8F  H9   H  HNH1  0   0.392  -1.3312   0.6372  -1.0189
 E8F  H10  H  HCH1  0   0.270  -3.2687   0.5280   1.1497
 E8F  H11  H  HCH2  0   0.245  -3.5968   0.7226  -1.8744
 E8F  H12  H  HCH2  0   0.245  -4.8845   0.8828  -0.6969
 E8F  H13  H  HCH1  0   0.224  -2.4865   2.7503  -0.9242
 E8F  H14  H  HCH3  0   0.216  -5.4023   3.1453  -1.7427
 E8F  H15  H  HCH3  0   0.229  -4.1379   4.3700  -1.8223
 E8F  H16  H  HCH3  0   0.227  -4.0424   2.9387  -2.8466
 E8F  H17  H  HCH3  0   0.231  -3.3197   2.6872   1.4130
 E8F  H18  H  HCH3  0   0.233  -3.7617   4.2054   0.6503
 E8F  H19  H  HCH3  0   0.216  -4.9706   2.9373   0.8445
 E8F  H20  H  HNH1  0   0.414  -4.8710  -0.9920   1.4309
 E8F  H21  H  HOH1  0   0.479  -4.6510  -3.4520   1.2015
 E8F  H22  H  HCR6  0   0.242   3.5216  -2.2627  -0.4345
 E8F  H23  H  HCH3  0   0.244   6.9307  -1.9011  -0.8173
 E8F  H24  H  HCH3  0   0.251   5.5262  -2.6616  -1.5587
 E8F  H25  H  HCH3  0   0.243   6.2697  -1.2488  -2.3026

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
 E8F  C16  C15  single    1.500  0.020  1.500
 E8F  C1   C2   single    1.500  0.020  1.500
 E8F  C15  C2   aromatic  1.401  0.020  1.401
 E8F  C15  CG2  aromatic  1.393  0.020  1.393
 E8F  C2   CD1  aromatic  1.393  0.020  1.393
 E8F  CG2  CB   aromatic  1.390  0.020  1.390
 E8F  CD1  CG1  aromatic  1.386  0.020  1.386
 E8F  CB   CG1  aromatic  1.391  0.020  1.391
 E8F  CB   CA   single    1.505  0.020  1.505
 E8F  CA   N    single    1.448  0.020  1.448
 E8F  N    C7   single    1.356  0.020  1.356
 E8F  C7   O    double    1.227  0.020  1.227
 E8F  C7   N2   single    1.364  0.020  1.364
 E8F  N2   C8   single    1.437  0.020  1.437
 E8F  C8   C13  single    1.529  0.020  1.529
 E8F  C8   C9   single    1.530  0.020  1.530
 E8F  O2   C13  double    1.216  0.020  1.216
 E8F  C13  N3   single    1.343  0.020  1.343
 E8F  C9   C10  single    1.531  0.020  1.531
 E8F  N3   O3   single    1.362  0.020  1.362
 E8F  C12  C10  single    1.525  0.020  1.525
 E8F  C10  C11  single    1.525  0.020  1.525
 E8F  C1   H1   single    0.970  0.020  1.090
 E8F  C1   H2   single    0.970  0.020  1.090
 E8F  C1   H3   single    0.970  0.020  1.090
 E8F  CD1  H4   single    0.930  0.020  1.080
 E8F  CG1  H5   single    0.930  0.020  1.080
 E8F  CA   H6   single    0.970  0.020  1.090
 E8F  CA   H7   single    0.970  0.020  1.090
 E8F  N    H8   single    0.860  0.020  1.020
 E8F  N2   H9   single    0.890  0.020  1.040
 E8F  C8   H10  single    0.970  0.020  1.090
 E8F  C9   H11  single    0.970  0.020  1.090
 E8F  C9   H12  single    0.970  0.020  1.090
 E8F  C10  H13  single    0.970  0.020  1.090
 E8F  C11  H14  single    0.970  0.020  1.090
 E8F  C11  H15  single    0.970  0.020  1.090
 E8F  C11  H16  single    0.970  0.020  1.090
 E8F  C12  H17  single    0.970  0.020  1.090
 E8F  C12  H18  single    0.970  0.020  1.090
 E8F  C12  H19  single    0.970  0.020  1.090
 E8F  N3   H20  single    0.860  0.020  1.020
 E8F  O3   H21  single    0.850  0.020  0.980
 E8F  CG2  H22  single    0.930  0.020  1.080
 E8F  C16  H23  single    0.970  0.020  1.090
 E8F  C16  H24  single    0.970  0.020  1.090
 E8F  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
 E8F  H3   C1   H2   107.77  3.000
 E8F  H3   C1   H1   107.67  3.000
 E8F  H2   C1   H1   106.58  3.000
 E8F  H3   C1   C2   111.42  3.000
 E8F  H2   C1   C2   111.59  3.000
 E8F  H1   C1   C2   111.57  3.000
 E8F  C15  C2   CD1  118.77  3.000
 E8F  CD1  C2   C1   120.66  3.000
 E8F  C15  C2   C1   120.56  3.000
 E8F  H4   CD1  CG1  119.27  3.000
 E8F  H4   CD1  C2   119.25  3.000
 E8F  CG1  CD1  C2   121.48  3.000
 E8F  H5   CG1  CB   120.07  3.000
 E8F  H5   CG1  CD1  119.80  3.000
 E8F  CB   CG1  CD1  120.13  3.000
 E8F  CG2  CB   CA   120.81  3.000
 E8F  CA   CB   CG1  120.73  3.000
 E8F  CG2  CB   CG1  118.46  3.000
 E8F  H7   CA   H6   106.91  3.000
 E8F  H7   CA   N    108.70  3.000
 E8F  H6   CA   N    111.44  3.000
 E8F  H7   CA   CB   109.83  3.000
 E8F  H6   CA   CB   109.70  3.000
 E8F  N    CA   CB   110.18  3.000
 E8F  H8   N    C7   119.21  3.000
 E8F  H8   N    CA   116.70  3.000
 E8F  C7   N    CA   121.54  3.000
 E8F  N2   C7   O    121.66  3.000
 E8F  N2   C7   N    115.36  3.000
 E8F  O    C7   N    122.94  3.000
 E8F  H9   N2   C8   116.85  3.000
 E8F  H9   N2   C7   118.73  3.000
 E8F  C8   N2   C7   119.68  3.000
 E8F  H10  C8   C13  109.20  3.000
 E8F  H10  C8   C9   108.86  3.000
 E8F  C13  C8   C9   108.81  3.000
 E8F  H10  C8   N2   109.05  3.000
 E8F  C9   C8   N2   110.01  3.000
 E8F  C13  C8   N2   110.88  3.000
 E8F  H12  C9   H11  106.30  3.000
 E8F  H12  C9   C10  108.83  3.000
 E8F  H11  C9   C10  109.50  3.000
 E8F  H12  C9   C8   108.29  3.000
 E8F  H11  C9   C8   108.71  3.000
 E8F  C10  C9   C8   114.86  3.000
 E8F  H13  C10  C12  108.12  3.000
 E8F  H13  C10  C11  107.82  3.000
 E8F  C12  C10  C11  110.66  3.000
 E8F  H13  C10  C9   108.62  3.000
 E8F  C11  C10  C9   109.43  3.000
 E8F  C12  C10  C9   112.07  3.000
 E8F  H16  C11  H15  107.75  3.000
 E8F  H16  C11  H14  107.72  3.000
 E8F  H15  C11  H14  107.59  3.000
 E8F  H16  C11  C10  111.51  3.000
 E8F  H15  C11  C10  111.04  3.000
 E8F  H14  C11  C10  111.06  3.000
 E8F  H19  C12  H18  107.63  3.000
 E8F  H19  C12  H17  107.76  3.000
 E8F  H18  C12  H17  107.14  3.000
 E8F  H19  C12  C10  110.93  3.000
 E8F  H18  C12  C10  110.82  3.000
 E8F  H17  C12  C10  112.35  3.000
 E8F  N3   C13  O2   124.07  3.000
 E8F  N3   C13  C8   113.18  3.000
 E8F  O2   C13  C8   122.73  3.000
 E8F  H20  N3   O3   114.87  3.000
 E8F  H20  N3   C13  122.69  3.000
 E8F  O3   N3   C13  120.35  3.000
 E8F  H21  O3   N3   106.10  3.000
 E8F  H22  CG2  C15  118.89  3.000
 E8F  H22  CG2  CB   119.07  3.000
 E8F  C15  CG2  CB   122.04  3.000
 E8F  C16  C15  CG2  120.34  3.000
 E8F  CG2  C15  C2   119.12  3.000
 E8F  C16  C15  C2   120.54  3.000
 E8F  H25  C16  H24  107.71  3.000
 E8F  H25  C16  H23  106.63  3.000
 E8F  H24  C16  H23  107.67  3.000
 E8F  H25  C16  C15  111.54  3.000
 E8F  H24  C16  C15  111.38  3.000
 E8F  H23  C16  C15  111.66  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
 E8F  CONST_01  CB   CG2  C15  C2      0.00   0.0  0
 E8F  CONST_02  CB   CG1  CD1  C2      0.00   0.0  0
 E8F  CONST_03  CG2  C15  C2   CD1     0.00   0.0  0
 E8F  CONST_04  CG2  CB   CG1  CD1     0.00   0.0  0
 E8F  CONST_05  C15  C2   CD1  CG1     0.00   0.0  0
 E8F  CONST_06  C15  CG2  CB   CG1     0.00   0.0  0
 E8F  CONST_07  CG2  C15  C2   C1    180.00   0.0  0
 E8F  CONST_08  CG1  CD1  C2   C1    180.00   0.0  0
 E8F  CONST_09  C16  C15  C2   CD1   180.00   0.0  0
 E8F  CONST_10  CA   CB   CG1  CD1   180.00   0.0  0
 E8F  CONST_11  C16  C15  CG2  CB    180.00   0.0  0
 E8F  CONST_12  C15  CG2  CB   CA    180.00   0.0  0
 E8F  CONST_13  H22  CG2  C15  C2    180.00   0.0  0
 E8F  CONST_14  H5   CG1  CD1  C2    180.00   0.0  0
 E8F  CONST_15  H4   CD1  CG1  CB    180.00   0.0  0
 E8F  CONST_16  O    C7   N    CA      0.00   0.0  0
 E8F  CONST_17  C8   N2   C7   O       0.00   0.0  0
 E8F  CONST_18  O3   N3   C13  C8    180.00   0.0  0
 E8F  CONST_19  O3   N3   C13  O2      0.00   0.0  0
 E8F  CONST_20  N2   C7   N    CA    180.00   0.0  0
 E8F  CONST_21  C8   N2   C7   N     180.00   0.0  0
 E8F  CONST_22  H8   N    C7   O     180.00   0.0  0
 E8F  CONST_23  H9   N2   C7   O     180.00   0.0  0
 E8F  CONST_24  H20  N3   C13  C8      0.00   0.0  0
 E8F  Var_01    N    CA   CB   CG1    65.88  30.0  2
 E8F  Var_02    H23  C16  C15  C2     61.33  30.0  2
 E8F  Var_03    H1   C1   C2   CD1   117.44  30.0  2
 E8F  Var_04    C7   N    CA   CB   -165.47  30.0  3
 E8F  Var_05    C12  C10  C9   C8    -60.67  30.0  3
 E8F  Var_06    H17  C12  C10  C9     62.50  30.0  3
 E8F  Var_07    H14  C11  C10  C9     61.64  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
 E8F  chir_01  C8  N2  C13  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
 E8F  plan-1  C1   0.020
 E8F  plan-1  C2   0.020
 E8F  plan-1  CD1  0.020
 E8F  plan-1  CG1  0.020
 E8F  plan-1  CB   0.020
 E8F  plan-1  CA   0.020
 E8F  plan-1  CG2  0.020
 E8F  plan-1  C15  0.020
 E8F  plan-1  C16  0.020
 E8F  plan-1  H4   0.020
 E8F  plan-1  H5   0.020
 E8F  plan-1  H22  0.020
 E8F  plan-2  CA   0.020
 E8F  plan-2  N    0.020
 E8F  plan-2  C7   0.020
 E8F  plan-2  O    0.020
 E8F  plan-2  N2   0.020
 E8F  plan-2  C8   0.020
 E8F  plan-2  H8   0.020
 E8F  plan-2  H9   0.020
 E8F  plan-3  C8   0.020
 E8F  plan-3  C13  0.020
 E8F  plan-3  O2   0.020
 E8F  plan-3  N3   0.020
 E8F  plan-3  O3   0.020
 E8F  plan-3  H20  0.020

