# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 03:14:23 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (3~{S},6~{S})-1,4-dimethyl-3-[(4-nitro-1~{H}-indol-3-yl)methyl]-6-(phenylmethyl)piperazine-2,5-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1[C@@H](Cc2ccccc2)C(=O)N(C)[C@@H](Cc3c[nH]c4cccc(c34)[N+]([O-])=O)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
 C8H  C8H  (3~{S},6~{S})-1,4-dimethyl-3-[(4-nitro-1~{H}-indol-3-yl)methyl]-6-(phenylmethyl)piperazine-2,5-dione  ligand  52  30  .  2022-07-24  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_C8H
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
 C8H  C1   C  C      0   0.573  -1.6864  -0.3409  -1.2782
 C8H  C2   C  CH1    0  -0.224  -2.4512  -1.3616  -0.4591
 C8H  C3   C  CH2    0  -0.545  -2.9917  -0.7647   0.8586
 C8H  C4   C  CR6    0   0.166  -3.9233   0.3938   0.6496
 C8H  C5   C  CR16   0  -0.313  -5.2402   0.1750   0.2524
 C8H  C6   C  CR16   0  -0.240  -6.1035   1.2398   0.0375
 C8H  C7   C  CR16   0  -0.271  -5.6612   2.5439   0.2232
 C8H  C12  C  CH2    0  -0.563   0.7716  -0.6416   1.0320
 C8H  C13  C  CR5    0   0.062   1.5684   0.6143   0.9073
 C8H  C14  C  CR56   0   0.069   2.8957   0.8713   0.4198
 C8H  C10  C  C      0   0.555  -0.3598  -2.5710  -0.0641
 C8H  N2   N  NT     0  -0.453  -1.6907  -2.5728  -0.2239
 C8H  C22  C  CH3    0  -0.534  -2.4312  -3.7870   0.0708
 C8H  C8   C  CR16   0  -0.245  -4.3526   2.7723   0.6267
 C8H  C9   C  CR16   0  -0.301  -3.4923   1.7031   0.8360
 C8H  O1   O  O      0  -0.483  -2.2929   0.4506  -1.9826
 C8H  N1   N  NT     0  -0.451  -0.3480  -0.3582  -1.1913
 C8H  C21  C  CH3    0  -0.527   0.4033   0.5567  -2.0351
 C8H  C11  C  CH1    0  -0.212   0.3744  -1.2672  -0.3227
 C8H  C15  C  CR6    0   0.075   3.9936   0.1419  -0.0773
 C8H  N4   N  N      1   0.326   4.0253  -1.3024  -0.0395
 C8H  O3   O  O      0  -0.381   4.6322  -1.8890  -0.9073
 C8H  O4   O  O     -1  -0.383   3.4639  -1.8563   0.8793
 C8H  C20  C  CR15   0  -0.065   1.0267   1.8457   1.1739
 C8H  N3   N  NR15   0  -0.676   1.9060   2.8337   0.8852
 C8H  C19  C  CR56   0   0.360   3.0534   2.2839   0.4065
 C8H  C18  C  CR16   0  -0.272   4.1940   2.9338  -0.0468
 C8H  C17  C  CR16   0  -0.293   5.2269   2.1628  -0.5395
 C8H  C16  C  CR16   0  -0.291   5.1243   0.7724  -0.5640
 C8H  H1   H  HCH1   0   0.299  -3.3090  -1.6376  -1.0765
 C8H  H2   H  HCH2   0   0.283  -3.5158  -1.5652   1.3866
 C8H  H3   H  HCH2   0   0.267  -2.1597  -0.4682   1.5007
 C8H  H4   H  HCR6   0   0.248  -5.5978  -0.8392   0.1130
 C8H  H5   H  HCR6   0   0.255  -7.1240   1.0506  -0.2701
 C8H  H6   H  HCR6   0   0.254  -6.3338   3.3758   0.0594
 C8H  H7   H  HCH2   0   0.280   1.2895  -1.3969   1.6192
 C8H  H8   H  HCH2   0   0.264  -0.1399  -0.3995   1.5821
 C8H  H9   H  HCH3   0   0.262  -1.9736  -4.6426  -0.4205
 C8H  H10  H  HCH3   0   0.251  -2.4795  -3.9854   1.1423
 C8H  H11  H  HCH3   0   0.253  -3.4456  -3.6797  -0.3056
 C8H  H12  H  HCR6   0   0.254  -3.9998   3.7841   0.7797
 C8H  H13  H  HCR6   0   0.246  -2.4723   1.8938   1.1498
 C8H  H14  H  HCH3   0   0.257   0.1035   0.4526  -3.0775
 C8H  H15  H  HCH3   0   0.251   0.2638   1.5946  -1.7345
 C8H  H16  H  HCH3   0   0.247   1.4611   0.3221  -1.9610
 C8H  H17  H  HCH1   0   0.288   1.2808  -1.5594  -0.8563
 C8H  H18  H  HCR5   0   0.300   0.0444   2.0791   1.5543
 C8H  H19  H  HNR5   0   0.421   1.7396   3.8197   1.0027
 C8H  H20  H  HCR6   0   0.282   4.2634   4.0136  -0.0211
 C8H  H21  H  HCR6   0   0.274   6.1291   2.6328  -0.9042
 C8H  H22  H  HCR6   0   0.290   5.9544   0.1892  -0.9358
 C8H  O2   O  O      0  -0.488   0.2698  -3.5554   0.2913

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
 C8H  C8   C9   aromatic  1.388  0.020  1.388
 C8H  C8   C7   aromatic  1.388  0.020  1.388
 C8H  O3   N4   double    1.211  0.020  1.211
 C8H  C9   C4   aromatic  1.391  0.020  1.391
 C8H  C7   C6   aromatic  1.389  0.020  1.389
 C8H  O4   N4   single    1.211  0.020  1.211
 C8H  N4   C15  single    1.445  0.020  1.445
 C8H  C4   C3   single    1.501  0.020  1.501
 C8H  C4   C5   aromatic  1.393  0.020  1.393
 C8H  C6   C5   aromatic  1.388  0.020  1.388
 C8H  C3   C2   single    1.544  0.020  1.544
 C8H  O1   C1   double    1.221  0.020  1.221
 C8H  C16  C15  aromatic  1.383  0.020  1.383
 C8H  C16  C17  aromatic  1.394  0.020  1.394
 C8H  C15  C14  aromatic  1.409  0.020  1.409
 C8H  C21  N1   single    1.454  0.020  1.454
 C8H  C1   C2   single    1.516  0.020  1.516
 C8H  C1   N1   single    1.341  0.020  1.341
 C8H  C2   N2   single    1.449  0.020  1.449
 C8H  N1   C11  single    1.450  0.020  1.450
 C8H  C17  C18  aromatic  1.380  0.020  1.380
 C8H  C12  C13  single    1.493  0.020  1.493
 C8H  C12  C11  single    1.544  0.020  1.544
 C8H  C14  C13  aromatic  1.437  0.020  1.437
 C8H  C14  C19  aromatic  1.421  0.020  1.421
 C8H  C13  C20  aromatic  1.371  0.020  1.371
 C8H  N2   C22  single    1.452  0.020  1.452
 C8H  N2   C10  single    1.340  0.020  1.340
 C8H  C11  C10  single    1.518  0.020  1.518
 C8H  C18  C19  aromatic  1.389  0.020  1.389
 C8H  C10  O2   double    1.221  0.020  1.221
 C8H  C19  N3   aromatic  1.359  0.020  1.359
 C8H  C20  N3   aromatic  1.354  0.020  1.354
 C8H  C2   H1   single    0.970  0.020  1.090
 C8H  C3   H2   single    0.970  0.020  1.090
 C8H  C3   H3   single    0.970  0.020  1.090
 C8H  C5   H4   single    0.930  0.020  1.080
 C8H  C6   H5   single    0.930  0.020  1.080
 C8H  C7   H6   single    0.930  0.020  1.080
 C8H  C12  H7   single    0.970  0.020  1.090
 C8H  C12  H8   single    0.970  0.020  1.090
 C8H  C22  H9   single    0.970  0.020  1.090
 C8H  C22  H10  single    0.970  0.020  1.090
 C8H  C22  H11  single    0.970  0.020  1.090
 C8H  C8   H12  single    0.930  0.020  1.080
 C8H  C9   H13  single    0.930  0.020  1.080
 C8H  C21  H14  single    0.970  0.020  1.090
 C8H  C21  H15  single    0.970  0.020  1.090
 C8H  C21  H16  single    0.970  0.020  1.090
 C8H  C11  H17  single    0.970  0.020  1.090
 C8H  C20  H18  single    0.930  0.020  1.080
 C8H  N3   H19  single    0.860  0.020  1.020
 C8H  C18  H20  single    0.930  0.020  1.080
 C8H  C17  H21  single    0.930  0.020  1.080
 C8H  C16  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
 C8H  N1   C1   O1   122.78  3.000
 C8H  N1   C1   C2   117.36  3.000
 C8H  O1   C1   C2   119.85  3.000
 C8H  H1   C2   N2   107.02  3.000
 C8H  H1   C2   C3   107.76  3.000
 C8H  N2   C2   C3   111.61  3.000
 C8H  H1   C2   C1   105.12  3.000
 C8H  N2   C2   C1   112.69  3.000
 C8H  C3   C2   C1   112.17  3.000
 C8H  H3   C3   H2   106.27  3.000
 C8H  H3   C3   C4   110.20  3.000
 C8H  H2   C3   C4   109.57  3.000
 C8H  H3   C3   C2   109.88  3.000
 C8H  H2   C3   C2   107.27  3.000
 C8H  C4   C3   C2   113.37  3.000
 C8H  C9   C4   C5   118.62  3.000
 C8H  C5   C4   C3   120.35  3.000
 C8H  C9   C4   C3   121.02  3.000
 C8H  H4   C5   C6   119.51  3.000
 C8H  H4   C5   C4   119.69  3.000
 C8H  C6   C5   C4   120.79  3.000
 C8H  H5   C6   C7   120.14  3.000
 C8H  H5   C6   C5   119.76  3.000
 C8H  C7   C6   C5   120.09  3.000
 C8H  H6   C7   C8   120.22  3.000
 C8H  H6   C7   C6   120.22  3.000
 C8H  C8   C7   C6   119.56  3.000
 C8H  H8   C12  H7   106.22  3.000
 C8H  H8   C12  C11  108.49  3.000
 C8H  H7   C12  C11  108.35  3.000
 C8H  H8   C12  C13  107.53  3.000
 C8H  H7   C12  C13  112.03  3.000
 C8H  C11  C12  C13  113.89  3.000
 C8H  C20  C13  C14  105.68  3.000
 C8H  C20  C13  C12  121.89  3.000
 C8H  C14  C13  C12  132.21  3.000
 C8H  C19  C14  C15  115.14  3.000
 C8H  C19  C14  C13  106.46  3.000
 C8H  C15  C14  C13  138.32  3.000
 C8H  C11  C10  N2   117.45  3.000
 C8H  C11  C10  O2   119.50  3.000
 C8H  N2   C10  O2   123.05  3.000
 C8H  C22  N2   C10  118.89  3.000
 C8H  C10  N2   C2   122.62  3.000
 C8H  C22  N2   C2   117.65  3.000
 C8H  H11  C22  H10  108.46  3.000
 C8H  H11  C22  H9   108.28  3.000
 C8H  H10  C22  H9   108.62  3.000
 C8H  H11  C22  N2   108.84  3.000
 C8H  H10  C22  N2   111.96  3.000
 C8H  H9   C22  N2   110.58  3.000
 C8H  H12  C8   C9   119.78  3.000
 C8H  H12  C8   C7   120.14  3.000
 C8H  C9   C8   C7   120.08  3.000
 C8H  H13  C9   C8   119.42  3.000
 C8H  H13  C9   C4   119.74  3.000
 C8H  C8   C9   C4   120.85  3.000
 C8H  C11  N1   C21  118.99  3.000
 C8H  C11  N1   C1   122.96  3.000
 C8H  C21  N1   C1   118.03  3.000
 C8H  H16  C21  H15  108.17  3.000
 C8H  H16  C21  H14  108.22  3.000
 C8H  H15  C21  H14  108.64  3.000
 C8H  H16  C21  N1   109.14  3.000
 C8H  H15  C21  N1   111.91  3.000
 C8H  H14  C21  N1   110.67  3.000
 C8H  H17  C11  N1   106.78  3.000
 C8H  H17  C11  C10  104.76  3.000
 C8H  N1   C11  C10  113.54  3.000
 C8H  H17  C11  C12  108.89  3.000
 C8H  C10  C11  C12  108.84  3.000
 C8H  N1   C11  C12  113.56  3.000
 C8H  C16  C15  N4   116.54  3.000
 C8H  C16  C15  C14  121.69  3.000
 C8H  N4   C15  C14  121.69  3.000
 C8H  O4   N4   O3   123.69  3.000
 C8H  O4   N4   C15  117.83  3.000
 C8H  O3   N4   C15  118.46  3.000
 C8H  H18  C20  N3   120.58  3.000
 C8H  H18  C20  C13  128.49  3.000
 C8H  N3   C20  C13  110.93  3.000
 C8H  H19  N3   C19  125.22  3.000
 C8H  H19  N3   C20  125.62  3.000
 C8H  C19  N3   C20  109.16  3.000
 C8H  C18  C19  N3   128.23  3.000
 C8H  N3   C19  C14  107.76  3.000
 C8H  C18  C19  C14  124.00  3.000
 C8H  H20  C18  C17  121.19  3.000
 C8H  H20  C18  C19  120.78  3.000
 C8H  C17  C18  C19  118.02  3.000
 C8H  H21  C17  C16  119.29  3.000
 C8H  H21  C17  C18  120.16  3.000
 C8H  C16  C17  C18  120.55  3.000
 C8H  H22  C16  C17  119.19  3.000
 C8H  H22  C16  C15  120.21  3.000
 C8H  C17  C16  C15  120.57  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
 C8H  CONST_01  C7   C8   C9   C4      0.00   0.0  0
 C8H  CONST_02  C7   C6   C5   C4      0.00   0.0  0
 C8H  CONST_03  C8   C9   C4   C5      0.00   0.0  0
 C8H  CONST_04  C8   C7   C6   C5      0.00   0.0  0
 C8H  CONST_05  C9   C8   C7   C6      0.00   0.0  0
 C8H  CONST_06  C9   C4   C5   C6      0.00   0.0  0
 C8H  CONST_07  C16  C15  C14  C13   180.00   0.0  0
 C8H  CONST_08  C18  C19  C14  C13   180.00   0.0  0
 C8H  CONST_09  N3   C19  C14  C13     0.00   0.0  0
 C8H  CONST_10  C19  N3   C20  C13     0.00   0.0  0
 C8H  CONST_11  C17  C16  C15  C14     0.00   0.0  0
 C8H  CONST_12  N3   C20  C13  C14     0.00   0.0  0
 C8H  CONST_13  C17  C18  C19  C14     0.00   0.0  0
 C8H  CONST_14  C20  N3   C19  C14     0.00   0.0  0
 C8H  CONST_15  C18  C17  C16  C15     0.00   0.0  0
 C8H  CONST_16  C20  C13  C14  C15   180.00   0.0  0
 C8H  CONST_17  C18  C19  C14  C15     0.00   0.0  0
 C8H  CONST_18  N3   C19  C14  C15   180.00   0.0  0
 C8H  CONST_19  C19  C14  C13  C20     0.00   0.0  0
 C8H  CONST_20  C18  C19  N3   C20   180.00   0.0  0
 C8H  CONST_21  C17  C18  C19  N3    180.00   0.0  0
 C8H  CONST_22  C16  C15  C14  C19     0.00   0.0  0
 C8H  CONST_23  C16  C17  C18  C19     0.00   0.0  0
 C8H  CONST_24  C11  N1   C1   C2      0.00   0.0  0
 C8H  CONST_25  C11  C10  N2   C2      0.00   0.0  0
 C8H  CONST_26  C8   C9   C4   C3    180.00   0.0  0
 C8H  CONST_27  C6   C5   C4   C3    180.00   0.0  0
 C8H  CONST_28  C15  C14  C13  C12     0.00   0.0  0
 C8H  CONST_29  C19  C14  C13  C12   180.00   0.0  0
 C8H  CONST_30  N3   C20  C13  C12   180.00   0.0  0
 C8H  CONST_31  N4   C15  C14  C13     0.00   0.0  0
 C8H  CONST_32  C17  C16  C15  N4    180.00   0.0  0
 C8H  CONST_33  C19  C14  C15  N4    180.00   0.0  0
 C8H  CONST_34  C21  N1   C1   C2    180.00   0.0  0
 C8H  CONST_35  O2   C10  N2   C2    180.00   0.0  0
 C8H  CONST_36  C11  C10  N2   C22   180.00   0.0  0
 C8H  CONST_37  C11  N1   C1   O1    180.00   0.0  0
 C8H  CONST_38  H12  C8   C9   C4    180.00   0.0  0
 C8H  CONST_39  H5   C6   C5   C4    180.00   0.0  0
 C8H  CONST_40  H13  C9   C4   C5    180.00   0.0  0
 C8H  CONST_41  H6   C7   C6   C5    180.00   0.0  0
 C8H  CONST_42  H4   C5   C6   C7    180.00   0.0  0
 C8H  CONST_43  H19  N3   C20  C13   180.00   0.0  0
 C8H  CONST_44  H22  C16  C15  C14   180.00   0.0  0
 C8H  CONST_45  H18  C20  C13  C14   180.00   0.0  0
 C8H  CONST_46  H20  C18  C19  C14   180.00   0.0  0
 C8H  CONST_47  H21  C17  C16  C15   180.00   0.0  0
 C8H  CONST_52  C22  N2   C10  O2      0.00   0.0  0
 C8H  CONST_53  C21  N1   C1   O1      0.00   0.0  0
 C8H  Var_01    C9   C4   C3   C2   -102.13  30.0  3
 C8H  Var_02    C11  C12  C13  C14   -67.46  30.0  2
 C8H  Var_03    H14  C21  N1   C1    -52.64  30.0  3
 C8H  Var_04    H9   C22  N2   C2    140.71  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
 C8H  chir_01  C2   C3  C1   N2   negativ
 C8H  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
 C8H  plan-1  C3   0.020
 C8H  plan-1  C4   0.020
 C8H  plan-1  C5   0.020
 C8H  plan-1  C6   0.020
 C8H  plan-1  C7   0.020
 C8H  plan-1  C8   0.020
 C8H  plan-1  C9   0.020
 C8H  plan-1  H4   0.020
 C8H  plan-1  H5   0.020
 C8H  plan-1  H6   0.020
 C8H  plan-1  H12  0.020
 C8H  plan-1  H13  0.020
 C8H  plan-2  C12  0.020
 C8H  plan-2  C13  0.020
 C8H  plan-2  C14  0.020
 C8H  plan-2  C15  0.020
 C8H  plan-2  N4   0.020
 C8H  plan-2  C20  0.020
 C8H  plan-2  N3   0.020
 C8H  plan-2  C19  0.020
 C8H  plan-2  C18  0.020
 C8H  plan-2  C17  0.020
 C8H  plan-2  C16  0.020
 C8H  plan-2  H18  0.020
 C8H  plan-2  H19  0.020
 C8H  plan-2  H20  0.020
 C8H  plan-2  H21  0.020
 C8H  plan-2  H22  0.020
 C8H  plan-3  C15  0.020
 C8H  plan-3  N4   0.020
 C8H  plan-3  O3   0.020
 C8H  plan-3  O4   0.020
 C8H  plan-4  C2   0.020
 C8H  plan-4  C10  0.020
 C8H  plan-4  N2   0.020
 C8H  plan-4  C22  0.020
 C8H  plan-4  C11  0.020
 C8H  plan-4  O2   0.020
 C8H  plan-5  C1   0.020
 C8H  plan-5  C2   0.020
 C8H  plan-5  O1   0.020
 C8H  plan-5  N1   0.020
 C8H  plan-5  C21  0.020
 C8H  plan-5  C11  0.020

