# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 00:58:53 2020
#   Inital geometry file: a 135 line input string
#   Ligand name: (3~{R},6~{S})-1,4-dimethyl-6-[(4-nitro-1~{H}-indol-3-yl)methyl]-3-oxidanyl-3-(phenylmethyl)piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](Cc2c[nH]c3cccc(c23)[N+]([O-])=O)C(=O)N(C)[C@@](O)(Cc4ccccc4)C1=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
 C8B  C8B  (3~{R},6~{S})-1,4-dimethyl-6-[(4-nitro-1~{H}-indol-3-yl)methyl]-3-oxidanyl-3-(phenylmethyl)piperazine-2,5-dione  ligand  53  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_C8B
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
 C8B  C1   C  C      0   0.531  -1.6046  -0.3324  -1.2793
 C8B  C2   C  CT     0   0.316  -2.4375  -1.2853  -0.4009
 C8B  C3   C  CH2    0  -0.562  -2.9063  -0.5669   0.8813
 C8B  C4   C  CR6    0   0.175  -3.7259   0.6679   0.6410
 C8B  C5   C  CR16   0  -0.303  -5.1006   0.5898   0.4338
 C8B  C6   C  CR16   0  -0.243  -5.8511   1.7373   0.2180
 C8B  C12  C  CH2    0  -0.564   0.8905  -0.6356   1.0698
 C8B  C13  C  CR5    0   0.061   1.7123   0.6011   0.9182
 C8B  C14  C  CR56   0   0.062   3.0383   0.8271   0.4124
 C8B  C11  C  CH1    0  -0.209   0.4396  -1.2472  -0.2746
 C8B  O5   O  OH1    0  -0.631  -3.5795  -1.6484  -1.0915
 C8B  O4   O  O     -1  -0.381   4.7119  -1.9878  -0.8789
 C8B  C8   C  CR16   0  -0.247  -3.8679   3.0735   0.4182
 C8B  C9   C  CR16   0  -0.293  -3.1235   1.9226   0.6346
 C8B  C10  C  C      0   0.548  -0.3285  -2.5217   0.0081
 C8B  C15  C  CR6    0   0.076   4.1183   0.0696  -0.0816
 C8B  C16  C  CR16   0  -0.291   5.2533   0.6711  -0.5938
 C8B  C17  C  CR16   0  -0.293   5.3779   2.0600  -0.6006
 C8B  N4   N  N      1   0.326   4.1253  -1.3744  -0.0159
 C8B  O3   O  O      0  -0.384   3.5652  -1.9005   0.9198
 C8B  C18  C  CR16   0  -0.272   4.3626   2.8582  -0.1145
 C8B  C19  C  CR56   0   0.363   3.2171   2.2368   0.3655
 C8B  N3   N  NR15   0  -0.674   2.0827   2.8142   0.8434
 C8B  C20  C  CR15   0  -0.063   1.1935   1.8463   1.1635
 C8B  N1   N  NT     0  -0.457  -0.2751  -0.3162  -1.1229
 C8B  O1   O  O      0  -0.468  -2.1807   0.3836  -2.0783
 C8B  N2   N  NT     0  -0.494  -1.6705  -2.4819  -0.0473
 C8B  C7   C  CR16   0  -0.270  -5.2369   2.9834   0.2054
 C8B  H1   H  HCH2   0   0.284  -3.4844  -1.2909   1.4617
 C8B  H2   H  HCH2   0   0.274  -2.0341  -0.3191   1.4886
 C8B  H3   H  HCR6   0   0.245  -5.5925  -0.3747   0.4484
 C8B  H4   H  HCR6   0   0.253  -6.9196   1.6585   0.0635
 C8B  H5   H  HCH2   0   0.282   1.4078  -1.4045   1.6386
 C8B  H6   H  HCH2   0   0.266   0.0023  -0.3721   1.6473
 C8B  H7   H  HCH1   0   0.288   1.3236  -1.5656  -0.8304
 C8B  H8   H  HOH1   0   0.460  -3.3536  -1.9371  -1.9839
 C8B  H9   H  HCH3   0   0.259   0.2409   0.3843  -3.0406
 C8B  H10  H  HCH3   0   0.253   0.3138   1.6104  -1.7636
 C8B  H11  H  HCH3   0   0.250   1.5497   0.3618  -1.8599
 C8B  H12  H  HCR6   0   0.253  -3.3792   4.0394   0.4197
 C8B  H13  H  HCR6   0   0.235  -2.0559   2.0057   0.8037
 C8B  H14  H  HCR6   0   0.290   6.0698   0.0669  -0.9622
 C8B  H15  H  HCR6   0   0.274   6.2834   2.5074  -0.9848
 C8B  H16  H  HCH3   0   0.254  -2.3593  -4.4539  -0.3571
 C8B  H17  H  HCH3   0   0.251  -1.9775  -4.0456   1.3212
 C8B  H18  H  HCH3   0   0.259  -3.4403  -3.4178   0.5679
 C8B  H19  H  HCR6   0   0.283   4.4494   3.9369  -0.1143
 C8B  H20  H  HNR5   0   0.422   1.9224   3.8042   0.9324
 C8B  H21  H  HCR5   0   0.297   0.2198   2.1022   1.5508
 C8B  H22  H  HCR6   0   0.254  -5.8230   3.8779   0.0383
 C8B  C21  C  CH3    0  -0.528   0.4915   0.5612  -1.9950
 C8B  O2   O  O      0  -0.484   0.2880  -3.5243   0.3320
 C8B  C22  C  CH3    0  -0.535  -2.3987  -3.6648   0.3935

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
 C8B  C8   C7   aromatic  1.388  0.020  1.388
 C8B  C8   C9   aromatic  1.388  0.020  1.388
 C8B  O3   N4   double    1.211  0.020  1.211
 C8B  C7   C6   aromatic  1.389  0.020  1.389
 C8B  C9   C4   aromatic  1.392  0.020  1.392
 C8B  O4   N4   single    1.210  0.020  1.210
 C8B  N4   C15  single    1.445  0.020  1.445
 C8B  C6   C5   aromatic  1.388  0.020  1.388
 C8B  C4   C5   aromatic  1.392  0.020  1.392
 C8B  C4   C3   single    1.501  0.020  1.501
 C8B  C16  C15  aromatic  1.383  0.020  1.383
 C8B  C16  C17  aromatic  1.395  0.020  1.395
 C8B  C15  C14  aromatic  1.409  0.020  1.409
 C8B  C3   C2   single    1.543  0.020  1.543
 C8B  O1   C1   double    1.218  0.020  1.218
 C8B  C17  C18  aromatic  1.380  0.020  1.380
 C8B  C1   C2   single    1.540  0.020  1.540
 C8B  C1   N1   single    1.339  0.020  1.339
 C8B  C12  C13  single    1.493  0.020  1.493
 C8B  C12  C11  single    1.544  0.020  1.544
 C8B  C21  N1   single    1.455  0.020  1.455
 C8B  C14  C13  aromatic  1.437  0.020  1.437
 C8B  C14  C19  aromatic  1.422  0.020  1.422
 C8B  C2   O5   single    1.383  0.020  1.383
 C8B  C2   N2   single    1.465  0.020  1.465
 C8B  N1   C11  single    1.448  0.020  1.448
 C8B  C13  C20  aromatic  1.371  0.020  1.371
 C8B  C18  C19  aromatic  1.389  0.020  1.389
 C8B  C11  C10  single    1.515  0.020  1.515
 C8B  C19  N3   aromatic  1.360  0.020  1.360
 C8B  N2   C10  single    1.344  0.020  1.344
 C8B  N2   C22  single    1.457  0.020  1.457
 C8B  C10  O2   double    1.221  0.020  1.221
 C8B  C20  N3   aromatic  1.353  0.020  1.353
 C8B  C3   H1   single    0.970  0.020  1.090
 C8B  C3   H2   single    0.970  0.020  1.090
 C8B  C5   H3   single    0.930  0.020  1.080
 C8B  C6   H4   single    0.930  0.020  1.080
 C8B  C12  H5   single    0.970  0.020  1.090
 C8B  C12  H6   single    0.970  0.020  1.090
 C8B  C11  H7   single    0.970  0.020  1.090
 C8B  O5   H8   single    0.850  0.020  0.980
 C8B  C21  H9   single    0.970  0.020  1.090
 C8B  C21  H10  single    0.970  0.020  1.090
 C8B  C21  H11  single    0.970  0.020  1.090
 C8B  C8   H12  single    0.930  0.020  1.080
 C8B  C9   H13  single    0.930  0.020  1.080
 C8B  C16  H14  single    0.930  0.020  1.080
 C8B  C17  H15  single    0.930  0.020  1.080
 C8B  C22  H16  single    0.970  0.020  1.090
 C8B  C22  H17  single    0.970  0.020  1.090
 C8B  C22  H18  single    0.970  0.020  1.090
 C8B  C18  H19  single    0.930  0.020  1.080
 C8B  N3   H20  single    0.860  0.020  1.020
 C8B  C20  H21  single    0.930  0.020  1.080
 C8B  C7   H22  single    0.930  0.020  1.080

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
 C8B  O1   C1   N1   122.64  3.000
 C8B  N1   C1   C2   118.54  3.000
 C8B  O1   C1   C2   118.82  3.000
 C8B  N2   C2   O5   109.78  3.000
 C8B  N2   C2   C3   109.81  3.000
 C8B  O5   C2   C3   106.64  3.000
 C8B  N2   C2   C1   111.10  3.000
 C8B  O5   C2   C1   108.91  3.000
 C8B  C3   C2   C1   110.50  3.000
 C8B  H2   C3   H1   106.12  3.000
 C8B  H2   C3   C4   109.79  3.000
 C8B  H1   C3   C4   109.93  3.000
 C8B  H2   C3   C2   108.99  3.000
 C8B  H1   C3   C2   107.07  3.000
 C8B  C4   C3   C2   114.57  3.000
 C8B  C9   C4   C5   118.50  3.000
 C8B  C5   C4   C3   121.10  3.000
 C8B  C9   C4   C3   120.39  3.000
 C8B  H3   C5   C6   119.53  3.000
 C8B  H3   C5   C4   119.77  3.000
 C8B  C6   C5   C4   120.70  3.000
 C8B  H4   C6   C7   120.02  3.000
 C8B  H4   C6   C5   119.72  3.000
 C8B  C7   C6   C5   120.26  3.000
 C8B  H6   C12  H5   106.31  3.000
 C8B  H6   C12  C11  108.58  3.000
 C8B  H5   C12  C11  108.32  3.000
 C8B  H6   C12  C13  107.56  3.000
 C8B  H5   C12  C13  112.15  3.000
 C8B  C11  C12  C13  113.61  3.000
 C8B  C20  C13  C14  105.62  3.000
 C8B  C20  C13  C12  121.74  3.000
 C8B  C14  C13  C12  132.39  3.000
 C8B  C19  C14  C15  115.17  3.000
 C8B  C19  C14  C13  106.47  3.000
 C8B  C15  C14  C13  138.27  3.000
 C8B  H7   C11  N1   106.79  3.000
 C8B  H7   C11  C10  105.08  3.000
 C8B  N1   C11  C10  113.57  3.000
 C8B  H7   C11  C12  108.80  3.000
 C8B  C10  C11  C12  108.59  3.000
 C8B  N1   C11  C12  113.54  3.000
 C8B  H8   O5   C2   110.30  3.000
 C8B  H12  C8   C7   120.22  3.000
 C8B  H12  C8   C9   119.84  3.000
 C8B  C7   C8   C9   119.94  3.000
 C8B  H13  C9   C8   119.28  3.000
 C8B  H13  C9   C4   119.64  3.000
 C8B  C8   C9   C4   121.08  3.000
 C8B  N2   C10  O2   122.66  3.000
 C8B  O2   C10  C11  118.98  3.000
 C8B  N2   C10  C11  118.28  3.000
 C8B  N4   C15  C16  116.57  3.000
 C8B  C16  C15  C14  121.68  3.000
 C8B  N4   C15  C14  121.67  3.000
 C8B  H14  C16  C17  119.20  3.000
 C8B  H14  C16  C15  120.22  3.000
 C8B  C17  C16  C15  120.55  3.000
 C8B  H15  C17  C18  120.15  3.000
 C8B  H15  C17  C16  119.27  3.000
 C8B  C18  C17  C16  120.57  3.000
 C8B  O3   N4   C15  117.84  3.000
 C8B  C15  N4   O4   118.43  3.000
 C8B  O3   N4   O4   123.71  3.000
 C8B  H19  C18  C19  120.80  3.000
 C8B  H19  C18  C17  121.17  3.000
 C8B  C19  C18  C17  118.02  3.000
 C8B  N3   C19  C18  128.29  3.000
 C8B  N3   C19  C14  107.74  3.000
 C8B  C18  C19  C14  123.97  3.000
 C8B  H20  N3   C20  125.31  3.000
 C8B  H20  N3   C19  125.55  3.000
 C8B  C20  N3   C19  109.13  3.000
 C8B  H21  C20  N3   120.57  3.000
 C8B  H21  C20  C13  128.40  3.000
 C8B  N3   C20  C13  111.03  3.000
 C8B  C21  N1   C11  118.59  3.000
 C8B  C11  N1   C1   123.42  3.000
 C8B  C21  N1   C1   117.41  3.000
 C8B  C22  N2   C10  117.55  3.000
 C8B  C22  N2   C2   118.33  3.000
 C8B  C10  N2   C2   123.86  3.000
 C8B  H22  C7   C8   120.26  3.000
 C8B  H22  C7   C6   120.21  3.000
 C8B  C8   C7   C6   119.52  3.000
 C8B  H11  C21  H10  108.05  3.000
 C8B  H11  C21  H9   108.30  3.000
 C8B  H10  C21  H9   108.83  3.000
 C8B  H11  C21  N1   109.16  3.000
 C8B  H10  C21  N1   111.56  3.000
 C8B  H9   C21  N1   110.85  3.000
 C8B  H18  C22  H17  108.33  3.000
 C8B  H18  C22  H16  108.08  3.000
 C8B  H17  C22  H16  108.66  3.000
 C8B  H18  C22  N2   110.10  3.000
 C8B  H17  C22  N2   110.41  3.000
 C8B  H16  C22  N2   111.18  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
 C8B  CONST_01  C7   C8   C9   C4     0.00   0.0  0
 C8B  CONST_02  C7   C6   C5   C4     0.00   0.0  0
 C8B  CONST_03  C8   C7   C6   C5     0.00   0.0  0
 C8B  CONST_04  C8   C9   C4   C5     0.00   0.0  0
 C8B  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 C8B  CONST_06  C9   C4   C5   C6     0.00   0.0  0
 C8B  CONST_07  C16  C15  C14  C13  180.00   0.0  0
 C8B  CONST_08  C18  C19  C14  C13  180.00   0.0  0
 C8B  CONST_09  N3   C19  C14  C13    0.00   0.0  0
 C8B  CONST_10  C19  N3   C20  C13    0.00   0.0  0
 C8B  CONST_11  C17  C16  C15  C14    0.00   0.0  0
 C8B  CONST_12  N3   C20  C13  C14    0.00   0.0  0
 C8B  CONST_13  C17  C18  C19  C14    0.00   0.0  0
 C8B  CONST_14  C20  N3   C19  C14    0.00   0.0  0
 C8B  CONST_15  C18  C17  C16  C15    0.00   0.0  0
 C8B  CONST_16  C20  C13  C14  C15  180.00   0.0  0
 C8B  CONST_17  C18  C19  C14  C15    0.00   0.0  0
 C8B  CONST_18  N3   C19  C14  C15  180.00   0.0  0
 C8B  CONST_19  C19  C14  C15  C16    0.00   0.0  0
 C8B  CONST_20  C19  C18  C17  C16    0.00   0.0  0
 C8B  CONST_21  N3   C19  C18  C17  180.00   0.0  0
 C8B  CONST_22  C20  N3   C19  C18  180.00   0.0  0
 C8B  CONST_23  C20  C13  C14  C19    0.00   0.0  0
 C8B  CONST_24  C11  N1   C1   C2     0.00   0.0  0
 C8B  CONST_25  C11  C10  N2   C2     0.00   0.0  0
 C8B  CONST_26  C8   C9   C4   C3   180.00   0.0  0
 C8B  CONST_27  C6   C5   C4   C3   180.00   0.0  0
 C8B  CONST_28  C15  C14  C13  C12    0.00   0.0  0
 C8B  CONST_29  C19  C14  C13  C12  180.00   0.0  0
 C8B  CONST_30  N3   C20  C13  C12  180.00   0.0  0
 C8B  CONST_31  N4   C15  C14  C13    0.00   0.0  0
 C8B  CONST_32  N4   C15  C16  C17  180.00   0.0  0
 C8B  CONST_33  C19  C14  C15  N4   180.00   0.0  0
 C8B  CONST_34  C21  N1   C1   C2   180.00   0.0  0
 C8B  CONST_35  O2   C10  N2   C2   180.00   0.0  0
 C8B  CONST_36  O1   C1   N1   C11  180.00   0.0  0
 C8B  CONST_37  C22  N2   C10  C11  180.00   0.0  0
 C8B  CONST_38  H12  C8   C9   C4   180.00   0.0  0
 C8B  CONST_39  H4   C6   C5   C4   180.00   0.0  0
 C8B  CONST_40  H22  C7   C6   C5   180.00   0.0  0
 C8B  CONST_41  H13  C9   C4   C5   180.00   0.0  0
 C8B  CONST_42  H20  N3   C20  C13  180.00   0.0  0
 C8B  CONST_43  H14  C16  C15  C14  180.00   0.0  0
 C8B  CONST_44  H21  C20  C13  C14  180.00   0.0  0
 C8B  CONST_45  H19  C18  C19  C14  180.00   0.0  0
 C8B  CONST_46  H3   C5   C4   C9   180.00   0.0  0
 C8B  CONST_47  H15  C17  C16  C15  180.00   0.0  0
 C8B  CONST_52  O1   C1   N1   C21    0.00   0.0  0
 C8B  CONST_53  C22  N2   C10  O2     0.00   0.0  0
 C8B  Var_01    C9   C4   C3   C2   -95.42  30.0  3
 C8B  Var_02    C11  C12  C13  C14  -68.80  30.0  2
 C8B  Var_03    H9   C21  N1   C1   -52.38  30.0  3
 C8B  Var_04    H16  C22  N2   C2   109.41  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
 C8B  chir_01  C2   C1  O5   N2   negativ
 C8B  chir_02  C11  N1  C12  C10  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
 C8B  plan-1  C3   0.020
 C8B  plan-1  C4   0.020
 C8B  plan-1  C5   0.020
 C8B  plan-1  C6   0.020
 C8B  plan-1  C8   0.020
 C8B  plan-1  C9   0.020
 C8B  plan-1  C7   0.020
 C8B  plan-1  H3   0.020
 C8B  plan-1  H4   0.020
 C8B  plan-1  H12  0.020
 C8B  plan-1  H13  0.020
 C8B  plan-1  H22  0.020
 C8B  plan-2  C12  0.020
 C8B  plan-2  C13  0.020
 C8B  plan-2  C14  0.020
 C8B  plan-2  C15  0.020
 C8B  plan-2  C16  0.020
 C8B  plan-2  C17  0.020
 C8B  plan-2  N4   0.020
 C8B  plan-2  C18  0.020
 C8B  plan-2  C19  0.020
 C8B  plan-2  N3   0.020
 C8B  plan-2  C20  0.020
 C8B  plan-2  H14  0.020
 C8B  plan-2  H15  0.020
 C8B  plan-2  H19  0.020
 C8B  plan-2  H20  0.020
 C8B  plan-2  H21  0.020
 C8B  plan-3  O4   0.020
 C8B  plan-3  C15  0.020
 C8B  plan-3  N4   0.020
 C8B  plan-3  O3   0.020
 C8B  plan-4  C1   0.020
 C8B  plan-4  C2   0.020
 C8B  plan-4  C11  0.020
 C8B  plan-4  N1   0.020
 C8B  plan-4  O1   0.020
 C8B  plan-4  C21  0.020
 C8B  plan-5  C2   0.020
 C8B  plan-5  C11  0.020
 C8B  plan-5  C10  0.020
 C8B  plan-5  N2   0.020
 C8B  plan-5  O2   0.020
 C8B  plan-5  C22  0.020

