# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:23:24 2022
#   Inital geometry file: a 149 line input string
#   Ligand name: (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3,17-dithia-7,10,14,19,20-pentaazatricyclo[14.2.1.1~2,5~]icosa-1(18),2(20),16(19)-triene-6,9,13-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1NC(=O)[C@]2(C)CSC(=N2)c3csc(CNC(=O)C[C@H](NC1=O)\C=C\CCS)n3
#
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
 L6G  L6G  (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3,17-dithia-7,10,14,19,20-pentaazatricyclo[14.2.1.1~2,5~]icosa-1(18),2(20),16(19)-triene-6,9,13-trione  ligand  61  32  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L6G
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
 L6G  C1   C  CH2   0  -0.550  -2.4168  -1.2058   2.5542
 L6G  C2   C  CH2   0  -0.485  -3.2429   0.0163   2.1580
 L6G  C3   C  C1    0  -0.193  -2.7082   0.5589   0.8719
 L6G  C4   C  C1    0  -0.198  -3.3447   0.5048  -0.2905
 L6G  C5   C  CH1   0  -0.132  -2.7842   0.9294  -1.6203
 L6G  C6   C  C     0   0.554  -1.0242   2.6472  -1.4488
 L6G  C7   C  CH1   0  -0.197   0.4345   2.9114  -1.0615
 L6G  C8   C  CH1   0  -0.228   1.4282   2.7853  -2.2348
 L6G  C9   C  CH3   0  -0.691   1.5514   1.3776  -2.8064
 L6G  C10  C  CH3   0  -0.662   1.1023   3.7922  -3.3321
 L6G  C11  C  C     0   0.579   1.4472   2.4880   1.1606
 L6G  C12  C  CR5   0  -0.067   1.4903   1.4321   2.2960
 L6G  C13  C  CH3   0  -0.649   0.6069   1.9348   3.4323
 L6G  C14  C  CH2   0  -0.575   2.9375   1.2045   2.7642
 L6G  C15  C  CR5   0   0.061   1.9027  -0.5744   1.3407
 L6G  C16  C  CR5   0   0.329   1.6428  -1.7109   0.4590
 L6G  C17  C  CR15  0  -0.535   2.2873  -2.9059   0.4906
 L6G  C18  C  CR5   0   0.059   0.6381  -2.6260  -1.2638
 L6G  C19  C  CH2   0  -0.354  -0.2244  -2.8011  -2.4821
 L6G  C20  C  C     0   0.536  -2.2558  -1.4682  -2.2517
 L6G  C21  C  CH2   0  -0.572  -2.9427  -0.1864  -2.6697
 L6G  N1   N  NH1   0  -0.657  -1.4026   1.3522  -1.5254
 L6G  N2   N  NH1   0  -0.661   0.7894   2.0797   0.0665
 L6G  N3   N  N     0  -0.360   0.9801   0.1858   1.7582
 L6G  N4   N  N     0  -0.385   0.7118  -1.5630  -0.5379
 L6G  N5   N  NH1   0  -0.627  -1.0245  -1.6504  -2.7759
 L6G  O1   O  O     0  -0.471  -1.7846   3.5748  -1.6652
 L6G  O2   O  O     0  -0.476   1.9365   3.5937   1.3092
 L6G  O3   O  O     0  -0.465  -2.7620  -2.2633  -1.4794
 L6G  S1   S  S2    0  -0.265  -3.0102  -1.8450   4.1566
 L6G  S2   S  S2    0   0.080   3.5652  -0.1127   1.6809
 L6G  S3   S  S2    0   0.272   1.6976  -3.9030  -0.7629
 L6G  H1   H  HCH2  0   0.268  -2.5062  -1.9753   1.7874
 L6G  H2   H  HCH2  0   0.277  -1.3647  -0.9320   2.6363
 L6G  H3   H  HCH2  0   0.247  -4.2967  -0.2544   2.0578
 L6G  H4   H  HCH2  0   0.243  -3.1727   0.7715   2.9466
 L6G  H5   H  H     0   0.220  -1.6977   0.9510   0.9254
 L6G  H6   H  H     0   0.242  -4.3519   0.0999  -0.3285
 L6G  H7   H  HCH1  0   0.289  -3.3583   1.7795  -1.9939
 L6G  H8   H  HCH1  0   0.289   0.4628   3.9485  -0.7240
 L6G  H9   H  HCH1  0   0.249   2.3980   3.0574  -1.8057
 L6G  H10  H  HCH3  0   0.215   0.6641   1.0922  -3.3755
 L6G  H11  H  HCH3  0   0.251   2.3963   1.3308  -3.4939
 L6G  H12  H  HCH3  0   0.230   1.7250   0.6231  -2.0366
 L6G  H13  H  HCH3  0   0.225   0.1589   3.5581  -3.8283
 L6G  H14  H  HCH3  0   0.235   1.0301   4.8068  -2.9378
 L6G  H15  H  HCH3  0   0.238   1.8822   3.7853  -4.0938
 L6G  H16  H  HCH3  0   0.248  -0.4065   2.1262   3.0778
 L6G  H17  H  HCH3  0   0.251   0.5539   1.1851   4.2212
 L6G  H18  H  HCH3  0   0.249   1.0015   2.8572   3.8556
 L6G  H19  H  HCH2  0   0.304   3.5581   2.0931   2.6735
 L6G  H20  H  HCH2  0   0.305   2.9656   0.8587   3.7978
 L6G  H22  H  HCR5  0   0.322   3.0461  -3.2429   1.1798
 L6G  H23  H  HCH2  0   0.303   0.4176  -3.0053  -3.3398
 L6G  H24  H  HCH2  0   0.288  -0.8612  -3.6776  -2.3516
 L6G  H25  H  HCH2  0   0.285  -4.0059  -0.3955  -2.7911
 L6G  H26  H  HCH2  0   0.275  -2.5708   0.1791  -3.6285
 L6G  H27  H  HNH1  0   0.398  -0.7267   0.6194  -1.3523
 L6G  H28  H  HNH1  0   0.411   0.4653   1.1244   0.1052
 L6G  H31  H  HNH1  0   0.410  -0.6733  -0.9953  -3.4541
 L6G  H32  H  HSH1  0   0.221  -2.0932  -2.8048   4.3185

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
 L6G  C10  C8   single    1.525  0.020  1.525
 L6G  C8   C9   single    1.524  0.020  1.524
 L6G  C8   C7   single    1.543  0.020  1.543
 L6G  O2   C11  double    1.218  0.020  1.218
 L6G  O1   C6   double    1.219  0.020  1.219
 L6G  C7   C6   single    1.532  0.020  1.532
 L6G  C7   N2   single    1.446  0.020  1.446
 L6G  C6   N1   single    1.351  0.020  1.351
 L6G  C11  N2   single    1.340  0.020  1.340
 L6G  C11  C12  single    1.551  0.020  1.551
 L6G  C14  C12  single    1.538  0.020  1.538
 L6G  C14  S2   single    1.817  0.020  1.817
 L6G  N1   C5   single    1.448  0.020  1.448
 L6G  C12  C13  single    1.525  0.020  1.525
 L6G  C12  N3   single    1.450  0.020  1.450
 L6G  S2   C15  single    1.759  0.020  1.759
 L6G  C2   C3   single    1.495  0.020  1.495
 L6G  C2   C1   single    1.527  0.020  1.527
 L6G  C4   C3   double    1.326  0.020  1.326
 L6G  C4   C5   single    1.504  0.020  1.504
 L6G  C5   C21  single    1.540  0.020  1.540
 L6G  S1   C1   single    1.824  0.020  1.824
 L6G  C15  N3   double    1.266  0.020  1.266
 L6G  C15  C16  single    1.462  0.020  1.462
 L6G  O3   C20  double    1.218  0.020  1.218
 L6G  C16  N4   aromatic  1.372  0.020  1.372
 L6G  C16  C17  aromatic  1.358  0.020  1.358
 L6G  C21  C20  single    1.513  0.020  1.513
 L6G  C20  N5   single    1.351  0.020  1.351
 L6G  N4   C18  aromatic  1.289  0.020  1.289
 L6G  C17  S3   aromatic  1.707  0.020  1.707
 L6G  C18  S3   aromatic  1.733  0.020  1.733
 L6G  C18  C19  single    1.503  0.020  1.503
 L6G  N5   C19  single    1.432  0.020  1.432
 L6G  C1   H1   single    0.970  0.020  1.090
 L6G  C1   H2   single    0.970  0.020  1.090
 L6G  C2   H3   single    0.970  0.020  1.090
 L6G  C2   H4   single    0.970  0.020  1.090
 L6G  C3   H5   single    0.930  0.020  1.080
 L6G  C4   H6   single    0.930  0.020  1.080
 L6G  C5   H7   single    0.970  0.020  1.090
 L6G  C7   H8   single    0.970  0.020  1.090
 L6G  C8   H9   single    0.970  0.020  1.090
 L6G  C9   H10  single    0.970  0.020  1.090
 L6G  C9   H11  single    0.970  0.020  1.090
 L6G  C9   H12  single    0.970  0.020  1.090
 L6G  C10  H13  single    0.970  0.020  1.090
 L6G  C10  H14  single    0.970  0.020  1.090
 L6G  C10  H15  single    0.970  0.020  1.090
 L6G  C13  H16  single    0.970  0.020  1.090
 L6G  C13  H17  single    0.970  0.020  1.090
 L6G  C13  H18  single    0.970  0.020  1.090
 L6G  C14  H19  single    0.970  0.020  1.090
 L6G  C14  H20  single    0.970  0.020  1.090
 L6G  C17  H22  single    0.930  0.020  1.080
 L6G  C19  H23  single    0.970  0.020  1.090
 L6G  C19  H24  single    0.970  0.020  1.090
 L6G  C21  H25  single    0.970  0.020  1.090
 L6G  C21  H26  single    0.970  0.020  1.090
 L6G  N1   H27  single    0.860  0.020  1.020
 L6G  N2   H28  single    0.860  0.020  1.020
 L6G  N5   H31  single    0.860  0.020  1.020
 L6G  S1   H32  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
 L6G  H2   C1   H1   108.02  3.000
 L6G  H2   C1   S1   109.62  3.000
 L6G  H1   C1   S1   110.11  3.000
 L6G  H2   C1   C2   109.91  3.000
 L6G  H1   C1   C2   109.76  3.000
 L6G  S1   C1   C2   109.41  3.000
 L6G  H4   C2   H3   107.40  3.000
 L6G  H4   C2   C3   110.28  3.000
 L6G  H3   C2   C3   110.86  3.000
 L6G  H4   C2   C1   109.31  3.000
 L6G  H3   C2   C1   110.32  3.000
 L6G  C3   C2   C1   108.67  3.000
 L6G  H5   C3   C4   120.32  3.000
 L6G  H5   C3   C2   114.95  3.000
 L6G  C4   C3   C2   124.58  3.000
 L6G  H6   C4   C5   114.82  3.000
 L6G  H6   C4   C3   119.40  3.000
 L6G  C5   C4   C3   125.76  3.000
 L6G  H7   C5   N1   107.27  3.000
 L6G  H7   C5   C21  106.08  3.000
 L6G  N1   C5   C21  110.76  3.000
 L6G  H7   C5   C4   109.04  3.000
 L6G  C21  C5   C4   111.07  3.000
 L6G  N1   C5   C4   112.34  3.000
 L6G  O1   C6   N1   122.99  3.000
 L6G  N1   C6   C7   116.50  3.000
 L6G  O1   C6   C7   120.51  3.000
 L6G  H8   C7   N2   107.40  3.000
 L6G  H8   C7   C8   107.23  3.000
 L6G  N2   C7   C8   112.85  3.000
 L6G  H8   C7   C6   105.48  3.000
 L6G  N2   C7   C6   109.37  3.000
 L6G  C8   C7   C6   114.01  3.000
 L6G  H9   C8   C10  107.90  3.000
 L6G  H9   C8   C9   107.75  3.000
 L6G  C10  C8   C9   110.93  3.000
 L6G  H9   C8   C7   104.61  3.000
 L6G  C9   C8   C7   114.38  3.000
 L6G  C10  C8   C7   110.84  3.000
 L6G  H12  C9   H11  106.96  3.000
 L6G  H12  C9   H10  108.43  3.000
 L6G  H11  C9   H10  106.84  3.000
 L6G  H12  C9   C8   112.74  3.000
 L6G  H11  C9   C8   109.80  3.000
 L6G  H10  C9   C8   111.78  3.000
 L6G  H15  C10  H14  107.80  3.000
 L6G  H15  C10  H13  107.41  3.000
 L6G  H14  C10  H13  107.86  3.000
 L6G  H15  C10  C8   110.23  3.000
 L6G  H14  C10  C8   111.61  3.000
 L6G  H13  C10  C8   111.74  3.000
 L6G  O2   C11  N2   124.97  3.000
 L6G  N2   C11  C12  113.82  3.000
 L6G  O2   C11  C12  121.16  3.000
 L6G  N3   C12  C14  108.47  3.000
 L6G  N3   C12  C13  110.85  3.000
 L6G  C14  C12  C13  111.54  3.000
 L6G  N3   C12  C11  107.69  3.000
 L6G  C13  C12  C11  107.75  3.000
 L6G  C14  C12  C11  110.47  3.000
 L6G  H18  C13  H17  108.60  3.000
 L6G  H18  C13  H16  108.33  3.000
 L6G  H17  C13  H16  108.11  3.000
 L6G  H18  C13  C12  111.04  3.000
 L6G  H17  C13  C12  109.93  3.000
 L6G  H16  C13  C12  110.74  3.000
 L6G  H20  C14  H19  108.87  3.000
 L6G  H20  C14  S2   109.05  3.000
 L6G  H19  C14  S2   110.20  3.000
 L6G  H20  C14  C12  111.09  3.000
 L6G  H19  C14  C12  112.99  3.000
 L6G  S2   C14  C12  104.53  3.000
 L6G  S2   C15  N3   117.86  3.000
 L6G  N3   C15  C16  122.42  3.000
 L6G  S2   C15  C16  119.27  3.000
 L6G  N4   C16  C17  115.71  3.000
 L6G  C17  C16  C15  125.86  3.000
 L6G  N4   C16  C15  118.37  3.000
 L6G  H22  C17  S3   121.98  3.000
 L6G  H22  C17  C16  128.56  3.000
 L6G  S3   C17  C16  109.45  3.000
 L6G  S3   C18  N4   114.19  3.000
 L6G  S3   C18  C19  119.95  3.000
 L6G  N4   C18  C19  125.82  3.000
 L6G  H24  C19  H23  106.69  3.000
 L6G  H24  C19  N5   110.12  3.000
 L6G  H23  C19  N5   108.54  3.000
 L6G  H24  C19  C18  109.36  3.000
 L6G  H23  C19  C18  108.75  3.000
 L6G  N5   C19  C18  113.16  3.000
 L6G  O3   C20  N5   122.46  3.000
 L6G  N5   C20  C21  114.89  3.000
 L6G  O3   C20  C21  122.63  3.000
 L6G  H26  C21  H25  107.38  3.000
 L6G  H26  C21  C20  111.82  3.000
 L6G  H25  C21  C20  108.12  3.000
 L6G  H26  C21  C5   108.71  3.000
 L6G  H25  C21  C5   108.38  3.000
 L6G  C20  C21  C5   112.26  3.000
 L6G  H27  N1   C6   119.81  3.000
 L6G  H27  N1   C5   115.92  3.000
 L6G  C6   N1   C5   123.42  3.000
 L6G  H28  N2   C11  114.49  3.000
 L6G  H28  N2   C7   119.70  3.000
 L6G  C11  N2   C7   125.60  3.000
 L6G  C15  N3   C12  112.45  3.000
 L6G  C18  N4   C16  111.04  3.000
 L6G  H31  N5   C20  119.47  3.000
 L6G  H31  N5   C19  117.81  3.000
 L6G  C20  N5   C19  122.55  3.000
 L6G  H32  S1   C1    97.75  3.000
 L6G  C15  S2   C14   88.80  3.000
 L6G  C18  S3   C17   89.60  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
 L6G  CONST_01  S3   C18  N4   C16     0.00   0.0  0
 L6G  CONST_02  C18  S3   C17  C16     0.00   0.0  0
 L6G  CONST_03  C18  N4   C16  C17     0.00   0.0  0
 L6G  CONST_04  N4   C18  S3   C17     0.00   0.0  0
 L6G  CONST_05  S3   C17  C16  N4      0.00   0.0  0
 L6G  CONST_06  C7   C6   N1   C5    180.00   0.0  0
 L6G  CONST_07  C12  C11  N2   C7    180.00   0.0  0
 L6G  CONST_08  C21  C20  N5   C19   180.00   0.0  0
 L6G  CONST_09  O1   C6   N1   C5      0.00   0.0  0
 L6G  CONST_10  O2   C11  N2   C7      0.00   0.0  0
 L6G  CONST_11  O3   C20  N5   C19     0.00   0.0  0
 L6G  CONST_12  H22  C17  C16  C15     0.00   0.0  0
 L6G  CONST_13  H27  N1   C6   C7      0.00   0.0  0
 L6G  CONST_14  H28  N2   C11  C12     0.00   0.0  0
 L6G  CONST_15  H31  N5   C20  C21     0.00   0.0  0
 L6G  Var_01    N5   C20  C21  C5    -97.45  30.0  1
 L6G  Var_02    S2   C15  N3   C12     8.31  30.0  1
 L6G  Var_03    N3   C15  S2   C14     8.74  30.0  1
 L6G  Var_04    C20  N5   C19  C18   -88.62  30.0  1
 L6G  Var_05    N5   C19  C18  N4     -1.42  30.0  1
 L6G  Var_06    H19  C14  S2   C15  -142.56  30.0  1
 L6G  Var_07    C5   C4   C3   C2   -174.18   0.0  2
 L6G  Var_08    H13  C10  C8   C7    -68.00  30.0  3
 L6G  Var_09    H10  C9   C8   C7     72.18  30.0  3
 L6G  Var_10    C4   C3   C2   C1    110.45  30.0  3
 L6G  Var_11    S1   C1   C2   C3    177.75  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
 L6G  chir_01  C5   N1   C4   C21  positiv
 L6G  chir_02  C7   N2   C6   C8   positiv
 L6G  chir_03  C12  C11  C14  N3   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
 L6G  plan-1  C2   0.020
 L6G  plan-1  C3   0.020
 L6G  plan-1  C4   0.020
 L6G  plan-1  C5   0.020
 L6G  plan-1  H5   0.020
 L6G  plan-1  H6   0.020
 L6G  plan-2  C15  0.020
 L6G  plan-2  C16  0.020
 L6G  plan-2  C17  0.020
 L6G  plan-2  C18  0.020
 L6G  plan-2  C19  0.020
 L6G  plan-2  N4   0.020
 L6G  plan-2  S3   0.020
 L6G  plan-2  H22  0.020
 L6G  plan-3  C7   0.020
 L6G  plan-3  C11  0.020
 L6G  plan-3  C12  0.020
 L6G  plan-3  N2   0.020
 L6G  plan-3  O2   0.020
 L6G  plan-3  H28  0.020
 L6G  plan-4  C19  0.020
 L6G  plan-4  C20  0.020
 L6G  plan-4  C21  0.020
 L6G  plan-4  N5   0.020
 L6G  plan-4  O3   0.020
 L6G  plan-4  H31  0.020
 L6G  plan-5  C5   0.020
 L6G  plan-5  C6   0.020
 L6G  plan-5  C7   0.020
 L6G  plan-5  N1   0.020
 L6G  plan-5  O1   0.020
 L6G  plan-5  H27  0.020

