# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 09:10:43 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2~{S})-2-[[(2~{S},3~{R})-3-azanyl-2-oxidanyl-4-phenyl-butanoyl]amino]-4-methyl-~{N}-oxidanyl-pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](NC(=O)[C@@H](O)[C@H](N)Cc1ccccc1)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
 8KO  8KO  (2~{S})-2-[[(2~{S},3~{R})-3-azanyl-2-oxidanyl-4-phenyl-butanoyl]amino]-4-methyl-~{N}-oxidanyl-pentanamide  ligand  48  23  .  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_8KO
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
 8KO  N    N  NH2   0  -0.785  -1.6803   0.8882   1.2837
 8KO  CA   C  CH1   0  -0.102  -1.5019  -0.4243   0.6992
 8KO  CB   C  CH2   0  -0.532  -2.7877  -1.2609   0.5629
 8KO  CG   C  CR6   0   0.139  -3.8282  -0.5506  -0.2530
 8KO  CD2  C  CR16  0  -0.322  -4.8338   0.1988   0.3543
 8KO  CE2  C  CR16  0  -0.240  -5.7636   0.8968  -0.4064
 8KO  CZ   C  CR16  0  -0.274  -5.6997   0.8590  -1.7928
 8KO  CE1  C  CR16  0  -0.239  -4.7017   0.1156  -2.4112
 8KO  CD1  C  CR16  0  -0.306  -3.7762  -0.5805  -1.6462
 8KO  C    C  CH1   0  -0.071  -0.4498  -1.1943   1.5138
 8KO  O    O  OH1   0  -0.668  -0.8281  -1.3321   2.8534
 8KO  C10  C  C     0   0.537   0.8940  -0.4782   1.4271
 8KO  O2   O  O     0  -0.488   1.3524   0.1317   2.3817
 8KO  N2   N  NH1   0  -0.635   1.5273  -0.5768   0.2506
 8KO  C11  C  CH1   0  -0.217   2.7415   0.1418  -0.0361
 8KO  C12  C  CH2   0  -0.448   3.3293  -0.3383  -1.3638
 8KO  C13  C  CH1   0  -0.238   3.7358  -1.8146  -1.3883
 8KO  C14  C  CH3   0  -0.652   4.1751  -2.1942  -2.7986
 8KO  C15  C  CH3   0  -0.660   4.8370  -2.1240  -0.3798
 8KO  C16  C  C     0   0.534   2.4562   1.6405  -0.1275
 8KO  O3   O  O     0  -0.460   1.4663   2.0879  -0.6703
 8KO  N3   N  NH1   0  -0.371   3.4187   2.3914   0.4350
 8KO  O4   O  OH1   0  -0.542   3.4519   3.7343   0.2132
 8KO  H1   H  HNH2  0   0.354  -2.1918   1.4865   0.6490
 8KO  H2   H  HNH2  0   0.339  -2.2405   0.8246   2.1257
 8KO  H4   H  HCH1  0   0.244  -1.0994  -0.2778  -0.3084
 8KO  H5   H  HCH2  0   0.245  -2.5374  -2.2165   0.0941
 8KO  H6   H  HCH2  0   0.249  -3.1799  -1.4873   1.5580
 8KO  H7   H  HCR6  0   0.245  -4.8974   0.2307   1.4359
 8KO  H8   H  HCR6  0   0.253  -6.5400   1.4685   0.0860
 8KO  H9   H  HCR6  0   0.253  -6.4241   1.4004  -2.3874
 8KO  H10  H  HCR6  0   0.253  -4.6455   0.0758  -3.4918
 8KO  H11  H  HCR6  0   0.245  -3.0021  -1.1580  -2.1392
 8KO  H12  H  HCH1  0   0.258  -0.3388  -2.1971   1.0837
 8KO  H13  H  HOH1  0   0.444  -0.4082  -0.6127   3.3443
 8KO  H14  H  HNH1  0   0.406   1.0674  -1.0484  -0.5125
 8KO  H15  H  HCH1  0   0.276   3.4609  -0.0422   0.7672
 8KO  H16  H  HCH2  0   0.249   2.5999  -0.1445  -2.1571
 8KO  H17  H  HCH3  0   0.230   4.4469  -3.2492  -2.8547
 8KO  H18  H  HCH3  0   0.228   3.3808  -2.0159  -3.5253
 8KO  H19  H  HCH3  0   0.217   5.0456  -1.6111  -3.1082
 8KO  H20  H  HCH3  0   0.234   5.1306  -3.1730  -0.4382
 8KO  H21  H  HCH3  0   0.217   5.7262  -1.5202  -0.5778
 8KO  H22  H  HCH3  0   0.230   4.5269  -1.9340   0.6489
 8KO  H23  H  HNH1  0   0.416   4.2844   1.9969   0.7741
 8KO  H24  H  HOH1  0   0.479   3.0581   4.1446   0.9938
 8KO  H3   H  HCH2  0   0.250   4.2064   0.2736  -1.5958
 8KO  H25  H  HCH1  0   0.224   2.8615  -2.4249  -1.1370

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
 8KO  C14  C13  single    1.525  0.020  1.525
 8KO  C13  C15  single    1.525  0.020  1.525
 8KO  C13  C12  single    1.531  0.020  1.531
 8KO  C12  C11  single    1.529  0.020  1.529
 8KO  O    C    single    1.399  0.020  1.399
 8KO  O2   C10  double    1.222  0.020  1.222
 8KO  C10  N2   single    1.340  0.020  1.340
 8KO  C10  C    single    1.525  0.020  1.525
 8KO  C11  N2   single    1.440  0.020  1.440
 8KO  C11  C16  single    1.528  0.020  1.528
 8KO  C    CA   single    1.537  0.020  1.537
 8KO  C16  N3   single    1.344  0.020  1.344
 8KO  C16  O3   double    1.214  0.020  1.214
 8KO  N    CA   single    1.448  0.020  1.448
 8KO  N3   O4   single    1.362  0.020  1.362
 8KO  CA   CB   single    1.540  0.020  1.540
 8KO  CB   CG   single    1.501  0.020  1.501
 8KO  CG   CD1  aromatic  1.395  0.020  1.395
 8KO  CG   CD2  aromatic  1.393  0.020  1.393
 8KO  CD1  CE1  aromatic  1.388  0.020  1.388
 8KO  CD2  CE2  aromatic  1.389  0.020  1.389
 8KO  CE1  CZ   aromatic  1.390  0.020  1.390
 8KO  CE2  CZ   aromatic  1.388  0.020  1.388
 8KO  N    H1   single    0.890  0.020  1.040
 8KO  N    H2   single    0.890  0.020  1.040
 8KO  CA   H4   single    0.970  0.020  1.090
 8KO  CB   H5   single    0.970  0.020  1.090
 8KO  CB   H6   single    0.970  0.020  1.090
 8KO  CD2  H7   single    0.930  0.020  1.080
 8KO  CE2  H8   single    0.930  0.020  1.080
 8KO  CZ   H9   single    0.930  0.020  1.080
 8KO  CE1  H10  single    0.930  0.020  1.080
 8KO  CD1  H11  single    0.930  0.020  1.080
 8KO  C    H12  single    0.970  0.020  1.090
 8KO  O    H13  single    0.850  0.020  0.980
 8KO  N2   H14  single    0.860  0.020  1.020
 8KO  C11  H15  single    0.970  0.020  1.090
 8KO  C12  H16  single    0.970  0.020  1.090
 8KO  C14  H17  single    0.970  0.020  1.090
 8KO  C14  H18  single    0.970  0.020  1.090
 8KO  C14  H19  single    0.970  0.020  1.090
 8KO  C15  H20  single    0.970  0.020  1.090
 8KO  C15  H21  single    0.970  0.020  1.090
 8KO  C15  H22  single    0.970  0.020  1.090
 8KO  N3   H23  single    0.860  0.020  1.020
 8KO  O4   H24  single    0.850  0.020  0.980
 8KO  C12  H3   single    0.970  0.020  1.090
 8KO  C13  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
 8KO  H2   N    H1   106.21  3.000
 8KO  H2   N    CA   110.29  3.000
 8KO  H1   N    CA   110.20  3.000
 8KO  H4   CA   C    107.64  3.000
 8KO  H4   CA   CB   107.35  3.000
 8KO  C    CA   CB   110.25  3.000
 8KO  H4   CA   N    107.19  3.000
 8KO  CB   CA   N    115.17  3.000
 8KO  C    CA   N    108.94  3.000
 8KO  H6   CB   H5   106.94  3.000
 8KO  H6   CB   CG   110.12  3.000
 8KO  H5   CB   CG   109.83  3.000
 8KO  H6   CB   CA   109.36  3.000
 8KO  H5   CB   CA   108.76  3.000
 8KO  CG   CB   CA   111.70  3.000
 8KO  CD1  CG   CD2  118.29  3.000
 8KO  CD2  CG   CB   121.19  3.000
 8KO  CD1  CG   CB   120.46  3.000
 8KO  H7   CD2  CE2  119.49  3.000
 8KO  H7   CD2  CG   119.54  3.000
 8KO  CE2  CD2  CG   120.97  3.000
 8KO  H8   CE2  CZ   120.11  3.000
 8KO  H8   CE2  CD2  119.74  3.000
 8KO  CZ   CE2  CD2  120.15  3.000
 8KO  H9   CZ   CE1  120.25  3.000
 8KO  H9   CZ   CE2  120.27  3.000
 8KO  CE1  CZ   CE2  119.47  3.000
 8KO  H10  CE1  CD1  119.80  3.000
 8KO  H10  CE1  CZ   120.07  3.000
 8KO  CD1  CE1  CZ   120.13  3.000
 8KO  H11  CD1  CE1  119.51  3.000
 8KO  H11  CD1  CG   119.49  3.000
 8KO  CE1  CD1  CG   121.00  3.000
 8KO  H12  C    C10  108.53  3.000
 8KO  H12  C    O    108.23  3.000
 8KO  C10  C    O    109.81  3.000
 8KO  H12  C    CA   108.63  3.000
 8KO  C10  C    CA   109.73  3.000
 8KO  O    C    CA   111.82  3.000
 8KO  H13  O    C    107.19  3.000
 8KO  N2   C10  O2   123.05  3.000
 8KO  N2   C10  C    115.58  3.000
 8KO  O2   C10  C    121.37  3.000
 8KO  H14  N2   C11  117.87  3.000
 8KO  H14  N2   C10  118.92  3.000
 8KO  C11  N2   C10  122.46  3.000
 8KO  H15  C11  C16  109.36  3.000
 8KO  H15  C11  C12  109.39  3.000
 8KO  C16  C11  C12  109.13  3.000
 8KO  H15  C11  N2   108.93  3.000
 8KO  C16  C11  N2   110.12  3.000
 8KO  C12  C11  N2   109.90  3.000
 8KO  H3   C12  H16  106.33  3.000
 8KO  H3   C12  C13  108.84  3.000
 8KO  H16  C12  C13  109.62  3.000
 8KO  H3   C12  C11  108.46  3.000
 8KO  H16  C12  C11  108.50  3.000
 8KO  C13  C12  C11  114.75  3.000
 8KO  H25  C13  C15  108.15  3.000
 8KO  H25  C13  C14  107.66  3.000
 8KO  C15  C13  C14  110.67  3.000
 8KO  H25  C13  C12  108.76  3.000
 8KO  C15  C13  C12  112.13  3.000
 8KO  C14  C13  C12  109.35  3.000
 8KO  H19  C14  H18  107.70  3.000
 8KO  H19  C14  H17  107.65  3.000
 8KO  H18  C14  H17  107.77  3.000
 8KO  H19  C14  C13  111.02  3.000
 8KO  H18  C14  C13  111.43  3.000
 8KO  H17  C14  C13  111.10  3.000
 8KO  H22  C15  H21  107.82  3.000
 8KO  H22  C15  H20  107.12  3.000
 8KO  H21  C15  H20  107.61  3.000
 8KO  H22  C15  C13  112.52  3.000
 8KO  H21  C15  C13  110.83  3.000
 8KO  H20  C15  C13  110.73  3.000
 8KO  N3   C16  O3   124.40  3.000
 8KO  O3   C16  C11  122.69  3.000
 8KO  N3   C16  C11  112.90  3.000
 8KO  H23  N3   O4   114.77  3.000
 8KO  H23  N3   C16  122.42  3.000
 8KO  O4   N3   C16  120.02  3.000
 8KO  H24  O4   N3   106.10  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
 8KO  CONST_01  CZ   CE1  CD1  CG      0.00   0.0  0
 8KO  CONST_02  CZ   CE2  CD2  CG      0.00   0.0  0
 8KO  CONST_03  CE1  CD1  CG   CD2     0.00   0.0  0
 8KO  CONST_04  CE1  CZ   CE2  CD2     0.00   0.0  0
 8KO  CONST_05  CD1  CG   CD2  CE2     0.00   0.0  0
 8KO  CONST_06  CD1  CE1  CZ   CE2     0.00   0.0  0
 8KO  CONST_07  CE1  CD1  CG   CB    180.00   0.0  0
 8KO  CONST_08  CE2  CD2  CG   CB    180.00   0.0  0
 8KO  CONST_09  H10  CE1  CD1  CG    180.00   0.0  0
 8KO  CONST_10  H8   CE2  CD2  CG    180.00   0.0  0
 8KO  CONST_11  H11  CD1  CG   CD2   180.00   0.0  0
 8KO  CONST_12  H9   CZ   CE2  CD2   180.00   0.0  0
 8KO  CONST_13  H7   CD2  CE2  CZ    180.00   0.0  0
 8KO  CONST_14  C11  N2   C10  C     180.00   0.0  0
 8KO  CONST_15  C11  N2   C10  O2      0.00   0.0  0
 8KO  CONST_16  O4   N3   C16  C11   180.00   0.0  0
 8KO  CONST_17  O4   N3   C16  O3      0.00   0.0  0
 8KO  CONST_18  H14  N2   C10  C       0.00   0.0  0
 8KO  CONST_19  H23  N3   C16  C11     0.00   0.0  0
 8KO  Var_01    CD1  CG   CB   CA     81.48  30.0  2
 8KO  Var_02    C14  C13  C12  C11   174.52  30.0  1
 8KO  Var_03    H17  C14  C13  C12  -178.52  30.0  3
 8KO  Var_04    H20  C15  C13  C12  -178.22  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
 8KO  chir_01  CA   C   N    CB   positiv
 8KO  chir_02  C    O   CA   C10  negativ
 8KO  chir_03  C11  N2  C12  C16  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
 8KO  plan-1  CB   0.020
 8KO  plan-1  CG   0.020
 8KO  plan-1  CD2  0.020
 8KO  plan-1  CE2  0.020
 8KO  plan-1  CZ   0.020
 8KO  plan-1  CE1  0.020
 8KO  plan-1  CD1  0.020
 8KO  plan-1  H7   0.020
 8KO  plan-1  H8   0.020
 8KO  plan-1  H9   0.020
 8KO  plan-1  H10  0.020
 8KO  plan-1  H11  0.020
 8KO  plan-2  C    0.020
 8KO  plan-2  C10  0.020
 8KO  plan-2  O2   0.020
 8KO  plan-2  N2   0.020
 8KO  plan-2  C11  0.020
 8KO  plan-2  H14  0.020
 8KO  plan-3  C11  0.020
 8KO  plan-3  C16  0.020
 8KO  plan-3  O3   0.020
 8KO  plan-3  N3   0.020
 8KO  plan-3  O4   0.020
 8KO  plan-3  H23  0.020

