# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 06:39:41 2020
#   Inital geometry file: a 101 line input string
#   Ligand name: (2~{R})-4-methyl-2-[(2-methylphenyl)carbamoylamino]-~{N}-oxidanyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@@H](NC(=O)Nc1ccccc1C)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
 8KR  8KR  (2~{R})-4-methyl-2-[(2-methylphenyl)carbamoylamino]-~{N}-oxidanyl-pentanamide  ligand  41  20  .  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_8KR
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
 8KR  O1   O  O     0  -0.520   0.6653   0.6604   1.6012
 8KR  C1   C  C     0   0.732   0.5245   0.5682   0.3904
 8KR  N    N  NH1   0  -0.782   1.5796   0.4756  -0.4844
 8KR  CA   C  CR6   0   0.301   2.9258   0.3756  -0.1048
 8KR  C    C  CR16  0  -0.278   3.4696   1.2217   0.8595
 8KR  C4   C  CR16  0  -0.276   4.8082   1.1183   1.2063
 8KR  CD1  C  CR16  0  -0.256   5.6207   0.1858   0.5783
 8KR  CG1  C  CR16  0  -0.309   5.0804  -0.6413  -0.3959
 8KR  CB   C  CR6   0   0.058   3.7360  -0.5715  -0.7478
 8KR  CG2  C  CH3   0  -0.750   3.1683  -1.4939  -1.7873
 8KR  N2   N  NH1   0  -0.689  -0.6869   0.5464  -0.2132
 8KR  C9   C  CH1   0  -0.201  -1.9093   0.6398   0.5389
 8KR  C10  C  CH2   0  -0.421  -2.2945  -0.6880   1.2166
 8KR  C11  C  CH1   0  -0.231  -2.3415  -1.9343   0.3322
 8KR  C12  C  CH3   0  -0.652  -2.5319  -3.1632   1.2179
 8KR  C13  C  CH3   0  -0.670  -3.4248  -1.8913  -0.7417
 8KR  C14  C  C     0   0.521  -2.9813   1.2224  -0.3825
 8KR  O2   O  O     0  -0.465  -2.7784   1.4940  -1.5520
 8KR  N3   N  NH1   0  -0.373  -4.1670   1.3998   0.2253
 8KR  O3   O  OH1   0  -0.538  -5.1533   2.0830  -0.4194
 8KR  H1   H  HNH1  0   0.403   1.3675   0.2405  -1.4412
 8KR  H2   H  HCR6  0   0.259   2.8512   1.9709   1.3313
 8KR  H3   H  HCR6  0   0.253   5.2163   1.7788   1.9606
 8KR  H4   H  HCR6  0   0.252   6.6672   0.1036   0.8410
 8KR  H5   H  HCR6  0   0.248   5.7127  -1.3699  -0.8891
 8KR  H6   H  HCH3  0   0.247   2.8212  -0.9538  -2.6722
 8KR  H7   H  HCH3  0   0.259   3.9167  -2.2092  -2.1238
 8KR  H8   H  HCH3  0   0.249   2.3163  -2.0582  -1.4025
 8KR  H9   H  HNH1  0   0.396  -0.7623   0.5618  -1.2191
 8KR  H10  H  HCH1  0   0.297  -1.7730   1.3744   1.3406
 8KR  H11  H  HCH2  0   0.247  -1.5517  -0.8513   1.9999
 8KR  H12  H  HCH2  0   0.226  -3.2500  -0.5707   1.7377
 8KR  H13  H  HCH1  0   0.222  -1.3714  -2.0293  -0.1668
 8KR  H14  H  HCH3  0   0.214  -3.4906  -3.1240   1.7413
 8KR  H15  H  HCH3  0   0.227  -2.5193  -4.0799   0.6261
 8KR  H16  H  HCH3  0   0.225  -1.7463  -3.2432   1.9714
 8KR  H17  H  HCH3  0   0.228  -3.2355  -1.1333  -1.5008
 8KR  H18  H  HCH3  0   0.232  -3.4807  -2.8493  -1.2620
 8KR  H19  H  HCH3  0   0.215  -4.4072  -1.6947  -0.3064
 8KR  H20  H  HNH1  0   0.418  -4.2694   1.3651   1.2298
 8KR  H21  H  HOH1  0   0.479  -5.7623   1.4143  -0.7579

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
 8KR  O3   N3   single    1.362  0.020  1.362
 8KR  N3   C14  single    1.344  0.020  1.344
 8KR  O2   C14  double    1.218  0.020  1.218
 8KR  C14  C9   single    1.529  0.020  1.529
 8KR  C    C4   aromatic  1.387  0.020  1.387
 8KR  C    CA   aromatic  1.393  0.020  1.393
 8KR  C4   CD1  aromatic  1.387  0.020  1.387
 8KR  O1   C1   double    1.222  0.020  1.222
 8KR  C9   N2   single    1.438  0.020  1.438
 8KR  C9   C10  single    1.540  0.020  1.540
 8KR  C1   N    single    1.374  0.020  1.374
 8KR  C1   N2   single    1.354  0.020  1.354
 8KR  N    CA   single    1.402  0.020  1.402
 8KR  CA   CB   aromatic  1.402  0.020  1.402
 8KR  CD1  CG1  aromatic  1.387  0.020  1.387
 8KR  C10  C11  single    1.529  0.020  1.529
 8KR  CB   CG1  aromatic  1.391  0.020  1.391
 8KR  CB   CG2  single    1.501  0.020  1.501
 8KR  C11  C12  single    1.527  0.020  1.527
 8KR  C11  C13  single    1.526  0.020  1.526
 8KR  N    H1   single    0.860  0.020  1.020
 8KR  C    H2   single    0.930  0.020  1.080
 8KR  C4   H3   single    0.930  0.020  1.080
 8KR  CD1  H4   single    0.930  0.020  1.080
 8KR  CG1  H5   single    0.930  0.020  1.080
 8KR  CG2  H6   single    0.970  0.020  1.090
 8KR  CG2  H7   single    0.970  0.020  1.090
 8KR  CG2  H8   single    0.970  0.020  1.090
 8KR  N2   H9   single    0.860  0.020  1.020
 8KR  C9   H10  single    0.970  0.020  1.090
 8KR  C10  H11  single    0.970  0.020  1.090
 8KR  C10  H12  single    0.970  0.020  1.090
 8KR  C11  H13  single    0.970  0.020  1.090
 8KR  C12  H14  single    0.970  0.020  1.090
 8KR  C12  H15  single    0.970  0.020  1.090
 8KR  C12  H16  single    0.970  0.020  1.090
 8KR  C13  H17  single    0.970  0.020  1.090
 8KR  C13  H18  single    0.970  0.020  1.090
 8KR  C13  H19  single    0.970  0.020  1.090
 8KR  N3   H20  single    0.890  0.020  1.040
 8KR  O3   H21  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
 8KR  N2   C1   N    113.73  3.000
 8KR  N2   C1   O1   123.09  3.000
 8KR  N    C1   O1   123.18  3.000
 8KR  H1   N    CA   116.25  3.000
 8KR  H1   N    C1   117.30  3.000
 8KR  CA   N    C1   124.74  3.000
 8KR  CB   CA   C    120.13  3.000
 8KR  CB   CA   N    118.60  3.000
 8KR  C    CA   N    121.24  3.000
 8KR  H2   C    C4   119.69  3.000
 8KR  H2   C    CA   120.01  3.000
 8KR  C4   C    CA   120.30  3.000
 8KR  H3   C4   CD1  120.32  3.000
 8KR  H3   C4   C    119.52  3.000
 8KR  CD1  C4   C    120.15  3.000
 8KR  H4   CD1  CG1  120.12  3.000
 8KR  H4   CD1  C4   120.50  3.000
 8KR  CG1  CD1  C4   119.38  3.000
 8KR  H5   CG1  CB   118.84  3.000
 8KR  H5   CG1  CD1  119.56  3.000
 8KR  CB   CG1  CD1  121.60  3.000
 8KR  CG2  CB   CG1  120.64  3.000
 8KR  CG2  CB   CA   120.93  3.000
 8KR  CG1  CB   CA   118.43  3.000
 8KR  H8   CG2  H7   107.80  3.000
 8KR  H8   CG2  H6   107.02  3.000
 8KR  H7   CG2  H6   107.02  3.000
 8KR  H8   CG2  CB   111.63  3.000
 8KR  H7   CG2  CB   110.97  3.000
 8KR  H6   CG2  CB   112.15  3.000
 8KR  H9   N2   C9   117.19  3.000
 8KR  H9   N2   C1   120.74  3.000
 8KR  C9   N2   C1   121.77  3.000
 8KR  H10  C9   C14  105.82  3.000
 8KR  H10  C9   C10  106.69  3.000
 8KR  C14  C9   C10  114.74  3.000
 8KR  H10  C9   N2   108.68  3.000
 8KR  C10  C9   N2   112.75  3.000
 8KR  C14  C9   N2   107.79  3.000
 8KR  H12  C10  H11  105.57  3.000
 8KR  H12  C10  C11  109.62  3.000
 8KR  H11  C10  C11  108.30  3.000
 8KR  H12  C10  C9   109.60  3.000
 8KR  H11  C10  C9   105.94  3.000
 8KR  C11  C10  C9   117.13  3.000
 8KR  H13  C11  C13  108.10  3.000
 8KR  H13  C11  C12  107.76  3.000
 8KR  C13  C11  C12  110.03  3.000
 8KR  H13  C11  C10  107.88  3.000
 8KR  C13  C11  C10  113.95  3.000
 8KR  C12  C11  C10  108.93  3.000
 8KR  H16  C12  H15  107.73  3.000
 8KR  H16  C12  H14  107.66  3.000
 8KR  H15  C12  H14  107.45  3.000
 8KR  H16  C12  C11  111.70  3.000
 8KR  H15  C12  C11  111.11  3.000
 8KR  H14  C12  C11  111.00  3.000
 8KR  H19  C13  H18  107.57  3.000
 8KR  H19  C13  H17  107.98  3.000
 8KR  H18  C13  H17  106.71  3.000
 8KR  H19  C13  C11  111.29  3.000
 8KR  H18  C13  C11  110.31  3.000
 8KR  H17  C13  C11  112.75  3.000
 8KR  N3   C14  O2   123.49  3.000
 8KR  O2   C14  C9   123.16  3.000
 8KR  N3   C14  C9   113.35  3.000
 8KR  H20  N3   O3   114.49  3.000
 8KR  H20  N3   C14  122.30  3.000
 8KR  O3   N3   C14  119.40  3.000
 8KR  H21  O3   N3   105.97  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
 8KR  CONST_01  CD1  C4   C    CA     0.00   0.0  0
 8KR  CONST_02  CD1  CG1  CB   CA     0.00   0.0  0
 8KR  CONST_03  CG1  CD1  C4   C      0.00   0.0  0
 8KR  CONST_04  CG1  CB   CA   C      0.00   0.0  0
 8KR  CONST_05  CB   CA   C    C4     0.00   0.0  0
 8KR  CONST_06  CB   CG1  CD1  C4     0.00   0.0  0
 8KR  CONST_07  C4   C    CA   N    180.00   0.0  0
 8KR  CONST_08  CG1  CB   CA   N    180.00   0.0  0
 8KR  CONST_09  CG2  CB   CA   C    180.00   0.0  0
 8KR  CONST_10  CG2  CB   CG1  CD1  180.00   0.0  0
 8KR  CONST_11  H3   C4   C    CA   180.00   0.0  0
 8KR  CONST_12  H5   CG1  CB   CA   180.00   0.0  0
 8KR  CONST_13  H4   CD1  C4   C    180.00   0.0  0
 8KR  CONST_14  H2   C    C4   CD1  180.00   0.0  0
 8KR  CONST_18  CA   N    C1   O1     0.00   0.0  0
 8KR  CONST_19  N2   C1   N    CA   180.00   0.0  0
 8KR  CONST_20  C9   N2   C1   O1     0.00   0.0  0
 8KR  CONST_21  O3   N3   C14  C9   180.00   0.0  0
 8KR  CONST_22  O3   N3   C14  O2     0.00   0.0  0
 8KR  CONST_23  C9   N2   C1   N    180.00   0.0  0
 8KR  CONST_24  H9   N2   C1   O1   180.00   0.0  0
 8KR  CONST_25  H20  N3   C14  C9     0.00   0.0  0
 8KR  Var_01    H6   CG2  CB   CA    64.68  30.0  2
 8KR  Var_02    C12  C11  C10  C9   171.58  30.0  3
 8KR  Var_03    H14  C12  C11  C10   63.40  30.0  3
 8KR  Var_04    H17  C13  C11  C10   67.21  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
 8KR  chir_01  C9  C14  N2  C10  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
 8KR  plan-1  N    0.020
 8KR  plan-1  CA   0.020
 8KR  plan-1  C    0.020
 8KR  plan-1  C4   0.020
 8KR  plan-1  CD1  0.020
 8KR  plan-1  CG1  0.020
 8KR  plan-1  CB   0.020
 8KR  plan-1  CG2  0.020
 8KR  plan-1  H2   0.020
 8KR  plan-1  H3   0.020
 8KR  plan-1  H4   0.020
 8KR  plan-1  H5   0.020
 8KR  plan-2  O1   0.020
 8KR  plan-2  C1   0.020
 8KR  plan-2  N    0.020
 8KR  plan-2  CA   0.020
 8KR  plan-2  N2   0.020
 8KR  plan-2  C9   0.020
 8KR  plan-2  H1   0.020
 8KR  plan-2  H9   0.020
 8KR  plan-3  C9   0.020
 8KR  plan-3  C14  0.020
 8KR  plan-3  O2   0.020
 8KR  plan-3  N3   0.020
 8KR  plan-3  O3   0.020
 8KR  plan-3  H20  0.020

