# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 05:41:56 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2,4-bis(oxidanyl)butanoyl]amino]propanoylamino]ethyl] (2~{R})-2-methyl-3-oxidanylidene-pentanethioate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)[C@@H](C)C(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO
#
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
 8H6  8H6  '~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2,4-bis(oxidanyl)butanoyl]amino]propanoylamino]ethyl] (2~{R})-2-methyl-3-oxidanylidene-pentanethioate'  ligand  56  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8H6
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
 8H6  O1   O  OH1   0  -0.671   8.1730  -1.4899  -0.1645
 8H6  O17  O  O     0  -0.502   3.8755  -0.2018  -1.1962
 8H6  C5   C  C     0   0.511   4.4036   0.6433  -0.4803
 8H6  C4   C  CH1   0  -0.032   5.7294   1.2763  -0.9102
 8H6  C3   C  CT    0  -0.142   6.9766   0.5863  -0.2870
 8H6  C15  C  CH3   0  -0.670   6.9651   0.7464   1.2355
 8H6  C2   C  CH2   0  -0.131   6.9925  -0.8981  -0.6586
 8H6  C14  C  CH3   0  -0.643   8.2179   1.2902  -0.8448
 8H6  O16  O  OH1   0  -0.663   5.7686   1.2877  -2.3112
 8H6  C7   C  CH2   0  -0.283   2.6571   0.5138   1.2291
 8H6  C8   C  CH2   0  -0.591   1.4148   1.1735   0.6390
 8H6  C9   C  C     0   0.567   0.1398   0.5855   1.2018
 8H6  O18  O  O     0  -0.497   0.0578  -0.5843   1.5491
 8H6  N10  N  NH1   0  -0.634  -0.8978   1.4383   1.2737
 8H6  C11  C  CH2   0  -0.290  -2.2169   1.0421   1.7009
 8H6  C12  C  CH2   0  -0.565  -2.9895   0.3651   0.5707
 8H6  S13  S  S2    0   0.024  -4.6380  -0.0787   1.1858
 8H6  C19  C  C     0   0.270  -5.3383  -0.8761  -0.2135
 8H6  O24  O  O     0  -0.370  -4.7644  -1.0201  -1.2615
 8H6  C20  C  CH1   0  -0.469  -6.7527  -1.3799   0.0318
 8H6  C26  C  CH3   0  -0.646  -6.7886  -2.8988  -0.0950
 8H6  C21  C  C     0   0.424  -7.6598  -0.6748  -0.9768
 8H6  O25  O  O     0  -0.379  -8.0138  -1.2223  -1.9907
 8H6  C22  C  CH2   0  -0.552  -8.0654   0.7262  -0.6119
 8H6  C23  C  CH3   0  -0.664  -8.8074   1.4750  -1.7025
 8H6  H1   H  HOH1  0   0.453   8.1627  -2.4184  -0.4121
 8H6  H2   H  HCH1  0   0.250   5.7508   2.3203  -0.5754
 8H6  H3   H  HCH3  0   0.227   6.8453   1.7943   1.5236
 8H6  H4   H  HCH3  0   0.230   6.1674   0.1731   1.7096
 8H6  H5   H  HCH3  0   0.244   7.9091   0.4059   1.6599
 8H6  H6   H  HCH2  0   0.198   6.9303  -1.0034  -1.7498
 8H6  H7   H  HCH2  0   0.201   6.1081  -1.3928  -0.2355
 8H6  H8   H  HCH3  0   0.234   9.1241   0.8996  -0.3837
 8H6  H9   H  HCH3  0   0.231   8.3085   1.1649  -1.9235
 8H6  H10  H  HCH3  0   0.222   8.1789   2.3618  -0.6353
 8H6  H11  H  HOH1  0   0.443   5.2685   0.5189  -2.6157
 8H6  H12  H  HNH1  0   0.408   4.3300   1.8035   1.1773
 8H6  H13  H  HCH2  0   0.254   2.6324  -0.5609   1.0588
 8H6  H14  H  HCH2  0   0.266   2.6922   0.6687   2.3068
 8H6  H15  H  HCH2  0   0.264   1.4496   2.2531   0.7999
 8H6  H16  H  HCH2  0   0.284   1.3989   1.0198  -0.4441
 8H6  H17  H  HNH1  0   0.407  -0.7731   2.3839   0.9515
 8H6  H18  H  HCH2  0   0.260  -2.1392   0.3759   2.5605
 8H6  H19  H  HCH2  0   0.272  -2.7398   1.9389   2.0312
 8H6  H20  H  HCH2  0   0.291  -3.0939   1.0399  -0.2781
 8H6  H21  H  HCH2  0   0.293  -2.4802  -0.5408   0.2454
 8H6  H22  H  HCH1  0   0.298  -7.0688  -1.0853   1.0375
 8H6  H23  H  HCH3  0   0.249  -6.1199  -3.3552   0.6342
 8H6  H24  H  HCH3  0   0.254  -7.7946  -3.2669   0.1014
 8H6  H25  H  HCH3  0   0.243  -6.4909  -3.2274  -1.0883
 8H6  H26  H  HCH2  0   0.280  -8.6768   0.6504   0.2944
 8H6  H27  H  HCH2  0   0.263  -7.1717   1.2743  -0.2933
 8H6  H28  H  HCH3  0   0.239  -9.0708   2.4736  -1.3568
 8H6  H29  H  HCH3  0   0.232  -8.1989   1.5832  -2.5998
 8H6  H30  H  HCH3  0   0.233  -9.7293   0.9667  -1.9816
 8H6  N6   N  NH1   0  -0.623   3.8801   1.0544   0.6764

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
 8H6  O1   C2   single  1.410  0.020  1.410
 8H6  C2   C3   single  1.530  0.020  1.530
 8H6  C26  C20  single  1.525  0.020  1.525
 8H6  C23  C22  single  1.517  0.020  1.517
 8H6  C3   C15  single  1.531  0.020  1.531
 8H6  C3   C14  single  1.532  0.020  1.532
 8H6  C3   C4   single  1.556  0.020  1.556
 8H6  C20  C21  single  1.529  0.020  1.529
 8H6  C20  C19  single  1.521  0.020  1.521
 8H6  C22  C21  single  1.503  0.020  1.503
 8H6  S13  C19  single  1.756  0.020  1.756
 8H6  S13  C12  single  1.815  0.020  1.815
 8H6  C21  O25  double  1.205  0.020  1.205
 8H6  C4   O16  single  1.402  0.020  1.402
 8H6  C4   C5   single  1.531  0.020  1.531
 8H6  C19  O24  double  1.203  0.020  1.203
 8H6  C12  C11  single  1.527  0.020  1.527
 8H6  C7   N6   single  1.447  0.020  1.447
 8H6  C7   C8   single  1.525  0.020  1.525
 8H6  C5   N6   single  1.335  0.020  1.335
 8H6  C5   O17  double  1.227  0.020  1.227
 8H6  N10  C11  single  1.442  0.020  1.442
 8H6  N10  C9   single  1.345  0.020  1.345
 8H6  C9   C8   single  1.513  0.020  1.513
 8H6  C9   O18  double  1.223  0.020  1.223
 8H6  O1   H1   single  0.850  0.020  0.980
 8H6  C4   H2   single  0.970  0.020  1.090
 8H6  C15  H3   single  0.970  0.020  1.090
 8H6  C15  H4   single  0.970  0.020  1.090
 8H6  C15  H5   single  0.970  0.020  1.090
 8H6  C2   H6   single  0.970  0.020  1.090
 8H6  C2   H7   single  0.970  0.020  1.090
 8H6  C14  H8   single  0.970  0.020  1.090
 8H6  C14  H9   single  0.970  0.020  1.090
 8H6  C14  H10  single  0.970  0.020  1.090
 8H6  O16  H11  single  0.850  0.020  0.980
 8H6  N6   H12  single  0.860  0.020  1.020
 8H6  C7   H13  single  0.970  0.020  1.090
 8H6  C7   H14  single  0.970  0.020  1.090
 8H6  C8   H15  single  0.970  0.020  1.090
 8H6  C8   H16  single  0.970  0.020  1.090
 8H6  N10  H17  single  0.860  0.020  1.020
 8H6  C11  H18  single  0.970  0.020  1.090
 8H6  C11  H19  single  0.970  0.020  1.090
 8H6  C12  H20  single  0.970  0.020  1.090
 8H6  C12  H21  single  0.970  0.020  1.090
 8H6  C20  H22  single  0.970  0.020  1.090
 8H6  C26  H23  single  0.970  0.020  1.090
 8H6  C26  H24  single  0.970  0.020  1.090
 8H6  C26  H25  single  0.970  0.020  1.090
 8H6  C22  H26  single  0.970  0.020  1.090
 8H6  C22  H27  single  0.970  0.020  1.090
 8H6  C23  H28  single  0.970  0.020  1.090
 8H6  C23  H29  single  0.970  0.020  1.090
 8H6  C23  H30  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
 8H6  H1   O1   C2   107.84  3.000
 8H6  N6   C5   C4   117.11  3.000
 8H6  N6   C5   O17  123.30  3.000
 8H6  C4   C5   O17  119.59  3.000
 8H6  H2   C4   O16  107.27  3.000
 8H6  H2   C4   C3   106.52  3.000
 8H6  O16  C4   C3   112.43  3.000
 8H6  H2   C4   C5   108.96  3.000
 8H6  O16  C4   C5   107.95  3.000
 8H6  C3   C4   C5   113.48  3.000
 8H6  C14  C3   C2   110.42  3.000
 8H6  C14  C3   C15  108.67  3.000
 8H6  C2   C3   C15  110.06  3.000
 8H6  C14  C3   C4   107.45  3.000
 8H6  C15  C3   C4   110.24  3.000
 8H6  C2   C3   C4   109.96  3.000
 8H6  H5   C15  H4   107.46  3.000
 8H6  H5   C15  H3   106.97  3.000
 8H6  H4   C15  H3   108.01  3.000
 8H6  H5   C15  C3   110.37  3.000
 8H6  H4   C15  C3   112.51  3.000
 8H6  H3   C15  C3   111.29  3.000
 8H6  H7   C2   H6   107.10  3.000
 8H6  H7   C2   C3   109.58  3.000
 8H6  H6   C2   C3   109.50  3.000
 8H6  H7   C2   O1   110.50  3.000
 8H6  H6   C2   O1   110.82  3.000
 8H6  C3   C2   O1   109.32  3.000
 8H6  H10  C14  H9   107.79  3.000
 8H6  H10  C14  H8   107.47  3.000
 8H6  H9   C14  H8   107.98  3.000
 8H6  H10  C14  C3   110.61  3.000
 8H6  H9   C14  C3   112.02  3.000
 8H6  H8   C14  C3   110.80  3.000
 8H6  H11  O16  C4   107.10  3.000
 8H6  H14  C7   H13  107.22  3.000
 8H6  H14  C7   C8   110.33  3.000
 8H6  H13  C7   C8   110.37  3.000
 8H6  H14  C7   N6   107.31  3.000
 8H6  H13  C7   N6   109.17  3.000
 8H6  C8   C7   N6   112.27  3.000
 8H6  H16  C8   H15  106.57  3.000
 8H6  H16  C8   C9   107.54  3.000
 8H6  H15  C8   C9   110.87  3.000
 8H6  H16  C8   C7   109.52  3.000
 8H6  H15  C8   C7   110.16  3.000
 8H6  C9   C8   C7   111.99  3.000
 8H6  N10  C9   O18  122.66  3.000
 8H6  O18  C9   C8   122.27  3.000
 8H6  N10  C9   C8   115.07  3.000
 8H6  H17  N10  C11  117.78  3.000
 8H6  H17  N10  C9   118.88  3.000
 8H6  C11  N10  C9   123.18  3.000
 8H6  H19  C11  H18  107.35  3.000
 8H6  H19  C11  C12  110.27  3.000
 8H6  H18  C11  C12  110.40  3.000
 8H6  H19  C11  N10  107.62  3.000
 8H6  H18  C11  N10  109.64  3.000
 8H6  C12  C11  N10  111.43  3.000
 8H6  H21  C12  H20  109.11  3.000
 8H6  H21  C12  S13  108.82  3.000
 8H6  H20  C12  S13  109.18  3.000
 8H6  H21  C12  C11  110.68  3.000
 8H6  H20  C12  C11  110.52  3.000
 8H6  S13  C12  C11  108.49  3.000
 8H6  C19  S13  C12  101.72  3.000
 8H6  C20  C19  O24  122.97  3.000
 8H6  O24  C19  S13  123.92  3.000
 8H6  C20  C19  S13  113.11  3.000
 8H6  H22  C20  C21  108.10  3.000
 8H6  H22  C20  C26  109.74  3.000
 8H6  C21  C20  C26  113.00  3.000
 8H6  H22  C20  C19  109.12  3.000
 8H6  C21  C20  C19  107.01  3.000
 8H6  C26  C20  C19  109.78  3.000
 8H6  H25  C26  H24  108.38  3.000
 8H6  H25  C26  H23  108.46  3.000
 8H6  H24  C26  H23  107.74  3.000
 8H6  H25  C26  C20  111.74  3.000
 8H6  H24  C26  C20  110.09  3.000
 8H6  H23  C26  C20  110.32  3.000
 8H6  C22  C21  O25  123.24  3.000
 8H6  O25  C21  C20  121.31  3.000
 8H6  C22  C21  C20  115.45  3.000
 8H6  H27  C22  H26  104.43  3.000
 8H6  H27  C22  C23  111.17  3.000
 8H6  H26  C22  C23  110.85  3.000
 8H6  H27  C22  C21  108.46  3.000
 8H6  H26  C22  C21  106.66  3.000
 8H6  C23  C22  C21  114.68  3.000
 8H6  H30  C23  H29  107.95  3.000
 8H6  H30  C23  H28  107.73  3.000
 8H6  H29  C23  H28  107.79  3.000
 8H6  H30  C23  C22  111.58  3.000
 8H6  H29  C23  C22  111.59  3.000
 8H6  H28  C23  C22  110.04  3.000
 8H6  H12  N6   C7   117.74  3.000
 8H6  H12  N6   C5   119.01  3.000
 8H6  C7   N6   C5   123.20  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
 8H6  CONST_01  C7   N6   C5   O17     0.00   0.0  0
 8H6  CONST_02  C7   N6   C5   C4    180.00   0.0  0
 8H6  CONST_03  C11  N10  C9   C8    180.00   0.0  0
 8H6  CONST_04  C11  N10  C9   O18     0.00   0.0  0
 8H6  CONST_05  H12  N6   C5   O17   180.00   0.0  0
 8H6  CONST_06  H17  N10  C9   C8      0.00   0.0  0
 8H6  Var_01    C15  C3   C2   O1    -62.32  30.0  3
 8H6  Var_02    C8   C7   N6   C5    -83.32  30.0  1
 8H6  Var_03    C9   C8   C7   N6    178.92  30.0  3
 8H6  Var_04    N10  C9   C8   C7    149.43  30.0  1
 8H6  Var_05    C12  C11  N10  C9    -80.37  30.0  3
 8H6  Var_06    S13  C12  C11  N10  -179.26  30.0  1
 8H6  Var_07    C20  C19  S13  C12   179.30  30.0  3
 8H6  Var_08    C23  C22  C21  C20   172.19  30.0  1
 8H6  Var_09    H3   C15  C3   C4    -52.43  30.0  3
 8H6  Var_10    H8   C14  C3   C4    175.61  30.0  3
 8H6  Var_11    H28  C23  C22  C21   179.54  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
 8H6  chir_01  C4   C3   O16  C5   negativ
 8H6  chir_02  C20  C26  C21  C19  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
 8H6  plan-1  O17  0.020
 8H6  plan-1  C5   0.020
 8H6  plan-1  C4   0.020
 8H6  plan-1  C7   0.020
 8H6  plan-1  H12  0.020
 8H6  plan-1  N6   0.020
 8H6  plan-2  C8   0.020
 8H6  plan-2  C9   0.020
 8H6  plan-2  O18  0.020
 8H6  plan-2  N10  0.020
 8H6  plan-2  C11  0.020
 8H6  plan-2  H17  0.020
 8H6  plan-3  C20  0.020
 8H6  plan-3  C21  0.020
 8H6  plan-3  O25  0.020
 8H6  plan-3  C22  0.020
 8H6  plan-4  S13  0.020
 8H6  plan-4  C19  0.020
 8H6  plan-4  O24  0.020
 8H6  plan-4  C20  0.020

