# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 05:25:11 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (2~{S})-2-azanyl-6-[[(6~{S})-6-sulfanyloctanoyl]amino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](S)CCCCC(=O)NCCCC[C@H](N)C(O)=O
#
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
 XOK  XOK  '(2~{S})-2-azanyl-6-[[(6~{S})-6-sulfanyloctanoyl]amino]hexanoic acid'  L-peptide  47  20  .  2017-07-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_XOK
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
 XOK  O    O  O      0  -0.603  91.5181   2.5121  123.8802
 XOK  N    N  NH2    0  -0.816  91.2572   2.5251  126.5387
 XOK  CA   C  CH1    0  -0.220  92.5627   2.1616  126.0022
 XOK  C    C  C      0   0.413  92.4966   1.9974  124.4602
 XOK  CB   C  CH2    0  -0.392  93.0974   0.9145  126.7036
 XOK  CG   C  CH2    0  -0.431  93.2785   1.1167  128.2028
 XOK  CD   C  CH2    0  -0.480  93.9666  -0.0472  128.9133
 XOK  CE   C  CH2    0  -0.267  93.2589  -1.3888  128.7943
 XOK  NZ   N  NH1    0  -0.638  91.9213  -1.3281  129.3479
 XOK  C1   C  C      0   0.556  91.0192  -2.3108  129.1971
 XOK  O1   O  O      0  -0.503  91.2477  -3.3153  128.5344
 XOK  C2   C  CH2    0  -0.573  89.6988  -2.1021  129.9095
 XOK  C3   C  CH2    0  -0.413  88.5030  -2.4934  129.0491
 XOK  C4   C  CH2    0  -0.415  87.1792  -2.3373  129.7861
 XOK  C5   C  CH2    0  -0.415  85.9965  -2.7244  128.9055
 XOK  C6   C  CH1    0  -0.358  84.6377  -2.7191  129.5977
 XOK  C7   C  CH2    0  -0.397  83.5121  -3.2194  128.6953
 XOK  C8   C  CH3    0  -0.672  83.6356  -4.6945  128.3304
 XOK  S6   S  S2     0  -0.256  84.2999  -1.0003  130.1503
 XOK  OXT  O  OC    -1  -0.605  93.4506   1.4050  123.9194
 XOK  H4   H  HCH1   0   0.190  93.3062   2.9626  126.1709
 XOK  H5   H  HCH2   0   0.200  92.4081   0.0841  126.5175
 XOK  H6   H  HCH2   0   0.203  94.0552   0.6379  126.2582
 XOK  H7   H  HCH2   0   0.217  93.8805   2.0162  128.3700
 XOK  H8   H  HCH2   0   0.212  92.3098   1.3203  128.6688
 XOK  H9   H  HCH2   0   0.232  94.0955   0.1973  129.9724
 XOK  H10  H  HCH2   0   0.234  94.9740  -0.1746  128.5079
 XOK  H11  H  HCH2   0   0.234  93.1988  -1.6943  127.7483
 XOK  H12  H  HCH2   0   0.238  93.8486  -2.1541  129.3088
 XOK  H13  H  HNH1   0   0.398  91.6942  -0.5578  129.9563
 XOK  H14  H  HCH2   0   0.260  89.7119  -2.7180  130.8150
 XOK  H15  H  HCH2   0   0.245  89.5978  -1.0668  130.2448
 XOK  H16  H  HCH2   0   0.224  88.4877  -1.8771  128.1449
 XOK  H17  H  HCH2   0   0.224  88.6150  -3.5280  128.7172
 XOK  H18  H  HCH2   0   0.217  87.1830  -2.9640  130.6843
 XOK  H19  H  HCH2   0   0.221  87.0776  -1.3050  130.1328
 XOK  H20  H  HCH2   0   0.243  86.1722  -3.7340  128.5238
 XOK  H21  H  HCH2   0   0.225  85.9557  -2.0699  128.0276
 XOK  H22  H  HCH1   0   0.259  84.6886  -3.3472  130.4921
 XOK  H23  H  HCH2   0   0.231  82.5573  -3.0648  129.2040
 XOK  H24  H  HCH2   0   0.222  83.4829  -2.6060  127.7906
 XOK  H25  H  HCH3   0   0.235  82.7596  -5.0222  127.7703
 XOK  H26  H  HCH3   0   0.225  84.5097  -4.8987  127.7123
 XOK  H27  H  HCH3   0   0.221  83.7061  -5.3177  129.2239
 XOK  H28  H  HSH1   0   0.216  83.0925  -1.2227  130.6833
 XOK  H    H  HNH2   0   0.329  91.3645   3.1113  127.3555
 XOK  H2   H  HNH2   0   0.332  90.7829   3.0805  125.8384

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
 XOK  O   C    deloc   1.231  0.020  1.231
 XOK  C   CA   single  1.525  0.021  1.525
 XOK  CA  CB   single  1.530  0.020  1.530
 XOK  CA  N    single  1.458  0.019  1.458
 XOK  CB  CG   single  1.524  0.020  1.524
 XOK  O1  C1   double  1.225  0.020  1.225
 XOK  CE  CD   single  1.521  0.020  1.521
 XOK  CE  NZ   single  1.449  0.020  1.449
 XOK  CG  CD   single  1.527  0.020  1.527
 XOK  C1  NZ   single  1.343  0.020  1.343
 XOK  C1  C2   single  1.515  0.020  1.515
 XOK  S6  C6   single  1.837  0.020  1.837
 XOK  C3  C2   single  1.524  0.020  1.524
 XOK  C3  C4   single  1.523  0.020  1.523
 XOK  C5  C6   single  1.525  0.020  1.525
 XOK  C5  C4   single  1.525  0.020  1.525
 XOK  C7  C6   single  1.527  0.020  1.527
 XOK  C7  C8   single  1.525  0.020  1.525
 XOK  C   OXT  deloc   1.246  0.020  1.246
 XOK  N   H    single  0.860  0.020  0.860
 XOK  N   H2   single  0.890  0.020  1.040
 XOK  CA  H4   single  0.970  0.020  1.090
 XOK  CB  H5   single  0.970  0.020  1.090
 XOK  CB  H6   single  0.970  0.020  1.090
 XOK  CG  H7   single  0.970  0.020  1.090
 XOK  CG  H8   single  0.970  0.020  1.090
 XOK  CD  H9   single  0.970  0.020  1.090
 XOK  CD  H10  single  0.970  0.020  1.090
 XOK  CE  H11  single  0.970  0.020  1.090
 XOK  CE  H12  single  0.970  0.020  1.090
 XOK  NZ  H13  single  0.860  0.020  1.020
 XOK  C2  H14  single  0.970  0.020  1.090
 XOK  C2  H15  single  0.970  0.020  1.090
 XOK  C3  H16  single  0.970  0.020  1.090
 XOK  C3  H17  single  0.970  0.020  1.090
 XOK  C4  H18  single  0.970  0.020  1.090
 XOK  C4  H19  single  0.970  0.020  1.090
 XOK  C5  H20  single  0.970  0.020  1.090
 XOK  C5  H21  single  0.970  0.020  1.090
 XOK  C6  H22  single  0.970  0.020  1.090
 XOK  C7  H23  single  0.970  0.020  1.090
 XOK  C7  H24  single  0.970  0.020  1.090
 XOK  C8  H25  single  0.970  0.020  1.090
 XOK  C8  H26  single  0.970  0.020  1.090
 XOK  C8  H27  single  0.970  0.020  1.090
 XOK  S6  H28  single  1.200  0.020  1.300

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
 XOK  H2   N   H    106.90  3.000
 XOK  H2   N   CA   107.57  3.000
 XOK  H    N   CA   114.00  3.000
 XOK  H4   CA  CB   106.61  3.000
 XOK  H4   CA  C    104.88  3.000
 XOK  CB   CA  C    110.10  1.900
 XOK  H4   CA  N    111.43  3.000
 XOK  CB   CA  N    110.50  1.700
 XOK  C    CA  N    111.00  2.800
 XOK  OXT  C   CA   116.66  3.000
 XOK  OXT  C   O    126.46  3.000
 XOK  CA   C   O    120.80  1.700
 XOK  H6   CB  H5   106.89  3.000
 XOK  H6   CB  CG   109.31  3.000
 XOK  H5   CB  CG   110.04  3.000
 XOK  H6   CB  CA   109.06  3.000
 XOK  H5   CB  CA   108.71  3.000
 XOK  CG   CB  CA   112.66  3.000
 XOK  H8   CG  H7   105.59  3.000
 XOK  H8   CG  CD   110.04  3.000
 XOK  H7   CG  CD   107.89  3.000
 XOK  H8   CG  CB   109.79  3.000
 XOK  H7   CG  CB   108.93  3.000
 XOK  CD   CG  CB   114.22  3.000
 XOK  H10  CD  H9   106.04  3.000
 XOK  H10  CD  CE   107.27  3.000
 XOK  H9   CD  CE   109.11  3.000
 XOK  H10  CD  CG   109.35  3.000
 XOK  H9   CD  CG   109.44  3.000
 XOK  CE   CD  CG   115.21  3.000
 XOK  H12  CE  H11  106.52  3.000
 XOK  H12  CE  NZ   110.30  3.000
 XOK  H11  CE  NZ   109.09  3.000
 XOK  H12  CE  CD   109.22  3.000
 XOK  H11  CE  CD   110.33  3.000
 XOK  NZ   CE  CD   111.26  3.000
 XOK  H13  NZ  C1   118.43  3.000
 XOK  H13  NZ  CE   118.09  3.000
 XOK  C1   NZ  CE   123.15  3.000
 XOK  C2   C1  O1   122.01  3.000
 XOK  C2   C1  NZ   115.60  3.000
 XOK  O1   C1  NZ   122.39  3.000
 XOK  H15  C2  H14  106.27  3.000
 XOK  H15  C2  C3   110.12  3.000
 XOK  H14  C2  C3   109.37  3.000
 XOK  H15  C2  C1   110.81  3.000
 XOK  H14  C2  C1   107.51  3.000
 XOK  C3   C2  C1   112.52  3.000
 XOK  H17  C3  H16  106.49  3.000
 XOK  H17  C3  C4   109.47  3.000
 XOK  H16  C3  C4   109.27  3.000
 XOK  H17  C3  C2   109.53  3.000
 XOK  H16  C3  C2   109.43  3.000
 XOK  C4   C3  C2   112.48  3.000
 XOK  H19  C4  H18  106.29  3.000
 XOK  H19  C4  C5   110.53  3.000
 XOK  H18  C4  C5   109.34  3.000
 XOK  H19  C4  C3   109.32  3.000
 XOK  H18  C4  C3   109.58  3.000
 XOK  C5   C4  C3   111.64  3.000
 XOK  H21  C5  H20  106.13  3.000
 XOK  H21  C5  C6   109.17  3.000
 XOK  H20  C5  C6   107.74  3.000
 XOK  H21  C5  C4   109.88  3.000
 XOK  H20  C5  C4   108.14  3.000
 XOK  C6   C5  C4   115.35  3.000
 XOK  H22  C6  S6   107.45  3.000
 XOK  H22  C6  C7   109.23  3.000
 XOK  S6   C6  C7   110.42  3.000
 XOK  H22  C6  C5   109.12  3.000
 XOK  C7   C6  C5   112.80  3.000
 XOK  S6   C6  C5   107.68  3.000
 XOK  H24  C7  H23  106.41  3.000
 XOK  H24  C7  C8   110.30  3.000
 XOK  H23  C7  C8   108.61  3.000
 XOK  H24  C7  C6   108.95  3.000
 XOK  H23  C7  C6   108.82  3.000
 XOK  C8   C7  C6   113.50  3.000
 XOK  H27  C8  H26  107.78  3.000
 XOK  H27  C8  H25  107.50  3.000
 XOK  H26  C8  H25  107.26  3.000
 XOK  H27  C8  C7   111.21  3.000
 XOK  H26  C8  C7   112.46  3.000
 XOK  H25  C8  C7   110.41  3.000
 XOK  H28  S6  C6    97.48  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
 XOK  CONST_01  O1   C1  NZ  CE     0.00   0.0  0
 XOK  CONST_02  C2   C1  NZ  CE   180.00   0.0  0
 XOK  CONST_03  H13  NZ  C1  O1   180.00   0.0  0
 XOK  Var_01    CD   CG  CB  CA  -173.06  30.0  3
 XOK  Var_02    CE   CD  CG  CB   -59.08  30.0  3
 XOK  Var_03    NZ   CE  CD  CG   -59.77  30.0  2
 XOK  Var_04    C1   NZ  CE  CD   170.05  30.0  3
 XOK  Var_05    C3   C2  C1  NZ   137.38  30.0  3
 XOK  Var_06    C4   C3  C2  C1   177.65  30.0  1
 XOK  Var_07    C5   C4  C3  C2   179.61  30.0  3
 XOK  Var_08    C6   C5  C4  C3   174.78  30.0  1
 XOK  Var_09    H25  C8  C7  C6   174.41  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
 XOK  chir_01  CA  C   CB  N   positiv
 XOK  chir_02  C6  S6  C5  C7  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
 XOK  plan-1  CE   0.020
 XOK  plan-1  NZ   0.020
 XOK  plan-1  C1   0.020
 XOK  plan-1  O1   0.020
 XOK  plan-1  C2   0.020
 XOK  plan-1  H13  0.020
 XOK  plan-2  O    0.020
 XOK  plan-2  CA   0.020
 XOK  plan-2  C    0.020
 XOK  plan-2  OXT  0.020

