# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 13:30:25 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: (2~{R})-4-methyl-2-[(3-methylphenyl)methylcarbamoylamino]-~{N}-oxidanyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](NC(=O)NCc1cccc(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
 8N3  8N3  (2~{R})-4-methyl-2-[(3-methylphenyl)methylcarbamoylamino]-~{N}-oxidanyl-pentanamide  ligand  44  21  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8N3
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
 8N3  C1   C  CH3   0  -0.724   5.5778   2.0682  -0.5734
 8N3  C2   C  CR6   0   0.115   5.0928   0.7240  -0.1121
 8N3  C3   C  CR16  0  -0.316   5.8833  -0.0884   0.6996
 8N3  CD1  C  CR16  0  -0.226   5.4187  -1.3211   1.1339
 8N3  CG1  C  CR16  0  -0.328   4.1544  -1.7608   0.7646
 8N3  CB   C  CR6   0   0.089   3.3508  -0.9690  -0.0477
 8N3  CA   C  CH2   0  -0.319   1.9788  -1.4342  -0.4585
 8N3  N    N  NH1   0  -0.679   0.9676  -0.5229   0.0315
 8N3  C8   C  C     0   0.754  -0.2732  -0.4707  -0.5130
 8N3  O    O  O     0  -0.543  -0.5821  -1.0747  -1.5351
 8N3  N2   N  NH1   0  -0.680  -1.1583   0.3435   0.1308
 8N3  C9   C  CH1   0  -0.198  -2.5506   0.2951  -0.2249
 8N3  C10  C  CH2   0  -0.447  -3.3510   1.2556   0.6565
 8N3  C11  C  CH1   0  -0.234  -2.9559   2.7288   0.5336
 8N3  C12  C  CH3   0  -0.663  -3.1490   3.2583  -0.8834
 8N3  C13  C  CH3   0  -0.651  -3.7677   3.5529   1.5284
 8N3  C14  C  C     0   0.526  -3.1026  -1.1200  -0.0418
 8N3  O2   O  O     0  -0.472  -2.7689  -1.8392   0.8800
 8N3  N3   N  NH1   0  -0.373  -4.0469  -1.4390  -0.9440
 8N3  O3   O  OH1   0  -0.543  -4.5717  -2.6969  -0.9614
 8N3  CG2  C  CR16  0  -0.331   3.8301   0.2657  -0.4767
 8N3  H1   H  HCH3  0   0.248   5.0750   2.8728  -0.0334
 8N3  H2   H  HCH3  0   0.244   6.6486   2.1848  -0.4119
 8N3  H3   H  HCH3  0   0.245   5.3786   2.2209  -1.6344
 8N3  H4   H  HCR6  0   0.247   6.8712   0.2460   0.9932
 8N3  H5   H  HCR6  0   0.254   6.0420  -1.9404   1.7661
 8N3  H6   H  HCR6  0   0.251   3.7931  -2.7223   1.1090
 8N3  H7   H  HCH2  0   0.258   1.9107  -1.4728  -1.5461
 8N3  H8   H  HCH2  0   0.245   1.8122  -2.4533  -0.0940
 8N3  H9   H  HNH1  0   0.393   1.1122  -0.1402   0.9525
 8N3  H10  H  HNH1  0   0.393  -0.9379   0.6516   1.0652
 8N3  H11  H  HCH1  0   0.267  -2.6667   0.5938  -1.2704
 8N3  H12  H  HCH2  0   0.247  -4.4093   1.1511   0.3986
 8N3  H13  H  HCH2  0   0.244  -3.2558   0.9358   1.7001
 8N3  H14  H  HCH1  0   0.224  -1.8978   2.8326   0.7975
 8N3  H15  H  HCH3  0   0.216  -4.1858   3.1367  -1.2077
 8N3  H16  H  HCH3  0   0.233  -2.9089   4.3213  -0.9360
 8N3  H17  H  HCH3  0   0.231  -2.5134   2.7509  -1.6103
 8N3  H18  H  HCH3  0   0.227  -3.5918   3.2278   2.5551
 8N3  H19  H  HCH3  0   0.229  -3.5080   4.6107   1.4668
 8N3  H20  H  HCH3  0   0.215  -4.8383   3.4628   1.3291
 8N3  H21  H  HNH1  0   0.414  -4.1563  -0.9279  -1.8083
 8N3  H22  H  HOH1  0   0.478  -5.4162  -2.6418  -0.4961
 8N3  H23  H  HCR6  0   0.243   3.2057   0.8836  -1.1139

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
 8N3  C13  C11  single    1.526  0.020  1.526
 8N3  C12  C11  single    1.525  0.020  1.525
 8N3  CD1  CG1  aromatic  1.389  0.020  1.389
 8N3  CD1  C3   aromatic  1.387  0.020  1.387
 8N3  CG1  CB   aromatic  1.390  0.020  1.390
 8N3  C11  C10  single    1.530  0.020  1.530
 8N3  C3   C2   aromatic  1.394  0.020  1.394
 8N3  C10  C9   single    1.530  0.020  1.530
 8N3  CB   CA   single    1.506  0.020  1.506
 8N3  CB   CG2  aromatic  1.392  0.020  1.392
 8N3  C2   CG2  aromatic  1.392  0.020  1.392
 8N3  C2   C1   single    1.502  0.020  1.502
 8N3  O    C8   double    1.227  0.020  1.227
 8N3  C8   N2   single    1.364  0.020  1.364
 8N3  C8   N    single    1.356  0.020  1.356
 8N3  N2   C9   single    1.438  0.020  1.438
 8N3  CA   N    single    1.447  0.020  1.447
 8N3  C9   C14  single    1.530  0.020  1.530
 8N3  C14  O2   double    1.216  0.020  1.216
 8N3  C14  N3   single    1.344  0.020  1.344
 8N3  N3   O3   single    1.363  0.020  1.363
 8N3  C1   H1   single    0.970  0.020  1.090
 8N3  C1   H2   single    0.970  0.020  1.090
 8N3  C1   H3   single    0.970  0.020  1.090
 8N3  C3   H4   single    0.930  0.020  1.080
 8N3  CD1  H5   single    0.930  0.020  1.080
 8N3  CG1  H6   single    0.930  0.020  1.080
 8N3  CA   H7   single    0.970  0.020  1.090
 8N3  CA   H8   single    0.970  0.020  1.090
 8N3  N    H9   single    0.860  0.020  1.020
 8N3  N2   H10  single    0.890  0.020  1.040
 8N3  C9   H11  single    0.970  0.020  1.090
 8N3  C10  H12  single    0.970  0.020  1.090
 8N3  C10  H13  single    0.970  0.020  1.090
 8N3  C11  H14  single    0.970  0.020  1.090
 8N3  C12  H15  single    0.970  0.020  1.090
 8N3  C12  H16  single    0.970  0.020  1.090
 8N3  C12  H17  single    0.970  0.020  1.090
 8N3  C13  H18  single    0.970  0.020  1.090
 8N3  C13  H19  single    0.970  0.020  1.090
 8N3  C13  H20  single    0.970  0.020  1.090
 8N3  N3   H21  single    0.890  0.020  1.040
 8N3  O3   H22  single    0.850  0.020  0.980
 8N3  CG2  H23  single    0.930  0.020  1.080

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
 8N3  H3   C1   H2   107.99  3.000
 8N3  H3   C1   H1   107.10  3.000
 8N3  H2   C1   H1   107.50  3.000
 8N3  H3   C1   C2   111.43  3.000
 8N3  H2   C1   C2   111.58  3.000
 8N3  H1   C1   C2   111.04  3.000
 8N3  CG2  C2   C3   118.36  3.000
 8N3  CG2  C2   C1   120.48  3.000
 8N3  C3   C2   C1   121.15  3.000
 8N3  H4   C3   CD1  119.66  3.000
 8N3  H4   C3   C2   119.66  3.000
 8N3  CD1  C3   C2   120.68  3.000
 8N3  H5   CD1  CG1  119.90  3.000
 8N3  H5   CD1  C3   119.90  3.000
 8N3  CG1  CD1  C3   120.20  3.000
 8N3  H6   CG1  CB   119.90  3.000
 8N3  H6   CG1  CD1  120.01  3.000
 8N3  CB   CG1  CD1  120.09  3.000
 8N3  CG2  CB   CA   120.24  3.000
 8N3  CG2  CB   CG1  119.09  3.000
 8N3  CA   CB   CG1  120.68  3.000
 8N3  H8   CA   H7   106.83  3.000
 8N3  H8   CA   N    111.54  3.000
 8N3  H7   CA   N    108.45  3.000
 8N3  H8   CA   CB   109.59  3.000
 8N3  H7   CA   CB   109.87  3.000
 8N3  N    CA   CB   110.48  3.000
 8N3  H9   N    C8   118.93  3.000
 8N3  H9   N    CA   116.64  3.000
 8N3  C8   N    CA   121.86  3.000
 8N3  N2   C8   O    121.58  3.000
 8N3  N2   C8   N    115.29  3.000
 8N3  O    C8   N    123.09  3.000
 8N3  H10  N2   C9   116.83  3.000
 8N3  H10  N2   C8   118.55  3.000
 8N3  C9   N2   C8   119.44  3.000
 8N3  H11  C9   C14  109.19  3.000
 8N3  H11  C9   C10  108.89  3.000
 8N3  C14  C9   C10  108.84  3.000
 8N3  H11  C9   N2   109.28  3.000
 8N3  C14  C9   N2   110.54  3.000
 8N3  C10  C9   N2   110.06  3.000
 8N3  H13  C10  H12  106.30  3.000
 8N3  H13  C10  C11  109.58  3.000
 8N3  H12  C10  C11  108.83  3.000
 8N3  H13  C10  C9   108.66  3.000
 8N3  H12  C10  C9   108.08  3.000
 8N3  C11  C10  C9   115.03  3.000
 8N3  H14  C11  C13  107.80  3.000
 8N3  H14  C11  C12  108.25  3.000
 8N3  C13  C11  C12  110.54  3.000
 8N3  H14  C11  C10  108.74  3.000
 8N3  C12  C11  C10  112.10  3.000
 8N3  C13  C11  C10  109.28  3.000
 8N3  H17  C12  H16  107.02  3.000
 8N3  H17  C12  H15  107.65  3.000
 8N3  H16  C12  H15  107.62  3.000
 8N3  H17  C12  C11  112.58  3.000
 8N3  H16  C12  C11  110.81  3.000
 8N3  H15  C12  C11  110.93  3.000
 8N3  H20  C13  H19  107.63  3.000
 8N3  H20  C13  H18  107.75  3.000
 8N3  H19  C13  H18  107.68  3.000
 8N3  H20  C13  C11  110.97  3.000
 8N3  H19  C13  C11  111.12  3.000
 8N3  H18  C13  C11  111.52  3.000
 8N3  N3   C14  O2   124.14  3.000
 8N3  N3   C14  C9   113.12  3.000
 8N3  O2   C14  C9   122.60  3.000
 8N3  H21  N3   O3   114.48  3.000
 8N3  H21  N3   C14  122.02  3.000
 8N3  O3   N3   C14  119.86  3.000
 8N3  H22  O3   N3   106.14  3.000
 8N3  H23  CG2  CB   119.20  3.000
 8N3  H23  CG2  C2   119.23  3.000
 8N3  CB   CG2  C2   121.58  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
 8N3  CONST_01  CG1  CD1  C3   C2      0.00   0.0  0
 8N3  CONST_02  CG1  CB   CG2  C2      0.00   0.0  0
 8N3  CONST_03  CB   CG1  CD1  C3      0.00   0.0  0
 8N3  CONST_04  CB   CG2  C2   C3      0.00   0.0  0
 8N3  CONST_05  CG2  CB   CG1  CD1     0.00   0.0  0
 8N3  CONST_06  CG2  C2   C3   CD1     0.00   0.0  0
 8N3  CONST_07  CD1  C3   C2   C1    180.00   0.0  0
 8N3  CONST_08  CB   CG2  C2   C1    180.00   0.0  0
 8N3  CONST_09  CA   CB   CG2  C2    180.00   0.0  0
 8N3  CONST_10  CA   CB   CG1  CD1   180.00   0.0  0
 8N3  CONST_11  H5   CD1  C3   C2    180.00   0.0  0
 8N3  CONST_12  H6   CG1  CD1  C3    180.00   0.0  0
 8N3  CONST_13  H23  CG2  C2   C3    180.00   0.0  0
 8N3  CONST_14  H4   C3   CD1  CG1   180.00   0.0  0
 8N3  CONST_15  O    C8   N    CA      0.00   0.0  0
 8N3  CONST_16  C9   N2   C8   O       0.00   0.0  0
 8N3  CONST_17  O3   N3   C14  C9    180.00   0.0  0
 8N3  CONST_18  O3   N3   C14  O2      0.00   0.0  0
 8N3  CONST_19  N2   C8   N    CA    180.00   0.0  0
 8N3  CONST_20  C9   N2   C8   N     180.00   0.0  0
 8N3  CONST_21  H10  N2   C8   O     180.00   0.0  0
 8N3  CONST_22  H9   N    C8   O     180.00   0.0  0
 8N3  Var_01    N    CA   CB   CG1   118.66  30.0  2
 8N3  Var_02    H1   C1   C2   C3   -105.76  30.0  2
 8N3  Var_03    C8   N    CA   CB    159.79  30.0  3
 8N3  Var_04    C13  C11  C10  C9   -176.34  30.0  1
 8N3  Var_05    H18  C13  C11  C10    59.78  30.0  3
 8N3  Var_06    H15  C12  C11  C10    57.69  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
 8N3  chir_01  C9  C10  N2  C14  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
 8N3  plan-1  C1   0.020
 8N3  plan-1  C2   0.020
 8N3  plan-1  C3   0.020
 8N3  plan-1  CD1  0.020
 8N3  plan-1  CG1  0.020
 8N3  plan-1  CB   0.020
 8N3  plan-1  CA   0.020
 8N3  plan-1  CG2  0.020
 8N3  plan-1  H4   0.020
 8N3  plan-1  H5   0.020
 8N3  plan-1  H6   0.020
 8N3  plan-1  H23  0.020
 8N3  plan-2  CA   0.020
 8N3  plan-2  N    0.020
 8N3  plan-2  C8   0.020
 8N3  plan-2  O    0.020
 8N3  plan-2  N2   0.020
 8N3  plan-2  C9   0.020
 8N3  plan-2  H9   0.020
 8N3  plan-2  H10  0.020
 8N3  plan-3  C9   0.020
 8N3  plan-3  C14  0.020
 8N3  plan-3  O2   0.020
 8N3  plan-3  N3   0.020
 8N3  plan-3  O3   0.020
 8N3  plan-3  H21  0.020

