# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:29:48 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3S,5R)-3,5-bis(6-bromo-1H-indol-3-yl)piperazin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccc2c([nH]cc2[C@@H]3CNC(=O)[C@@H](N3)c4c[nH]c5cc(Br)ccc45)c1
#
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
 09C  09C  (3S,5R)-3,5-bis(6-bromo-1H-indol-3-yl)piperazin-2-one  ligand  43  27  .  2021-08-03  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_09C
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
 09C  C1    C   C     0   0.541   1.1153   1.9121  -0.9466
 09C  N1    N   NH1   0  -0.604  -0.0388  -0.2923  -0.5968
 09C  O1    O   O     0  -0.489   2.1275   2.5952  -1.0123
 09C  C2    C   CH1   0  -0.310   1.1457   0.5041  -0.3366
 09C  N2    N   NH1   0  -0.633  -0.0831   2.3620  -1.3481
 09C  N3    N   NR15  0  -0.691  -3.7682  -2.1903  -0.7834
 09C  N4    N   NR15  0  -0.692   3.7995  -1.6638  -1.7129
 09C  C3    C   CR16  0  -0.240  -5.8193   1.1465   0.4234
 09C  C4    C   CR16  0  -0.246   5.5888   0.7676   1.0579
 09C  C5    C   CR16  0  -0.380  -4.4494   1.1334   0.2533
 09C  C6    C   CR16  0  -0.362   4.2447   0.8441   0.7549
 09C  C7    C   CR15  0  -0.080  -2.4839  -1.7254  -0.7974
 09C  C8    C   CR15  0  -0.083   2.5038  -1.2382  -1.6426
 09C  C9    C   CR16  0  -0.273  -5.9907  -1.1949  -0.2440
 09C  C10   C   CR16  0  -0.276   5.9203  -1.0321  -0.5593
 09C  C11   C   CH2   0  -0.241  -1.3366   1.6325  -1.3351
 09C  C12   C   CH1   0  -0.207  -1.2508   0.4695  -0.3517
 09C  C13   C   CR6   0  -0.141  -6.5678  -0.0124   0.1692
 09C  C14   C   CR6   0  -0.139   6.4044  -0.1639   0.3962
 09C  C15   C   CR5   0   0.019  -2.4575  -0.4081  -0.4361
 09C  C16   C   CR5   0   0.027   2.3918  -0.2241  -0.7330
 09C  C17   C   CR56  0   0.365  -4.6066  -1.1879  -0.4057
 09C  C18   C   CR56  0   0.365   4.5582  -0.9443  -0.8422
 09C  C19   C   CR56  0   0.045  -3.8166  -0.0394  -0.1721
 09C  C20   C   CR56  0   0.048   3.7048  -0.0189  -0.2031
 09C  HA    H   HCH1  0   0.291   1.1896   0.6748   0.7482
 09C  HAE   H   HCR6  0   0.269   6.0110   1.4297   1.8016
 09C  HAF   H   HCR6  0   0.255  -3.8838   2.0330   0.4614
 09C  HAG   H   HCR6  0   0.248   3.6218   1.5706   1.2589
 09C  HAH   H   HCR5  0   0.285  -1.6709  -2.3820  -1.0624
 09C  HAI   H   HCR5  0   0.284   1.7556  -1.7129  -2.2573
 09C  HAJ   H   HCR6  0   0.284  -6.5736  -2.0862  -0.4352
 09C  HAK   H   HCR6  0   0.283   6.5547  -1.7483  -1.0648
 09C  H1AL  H   HCH2  0   0.253  -2.1336   2.3270  -1.0678
 09C  H2AL  H   HCH2  0   0.237  -1.5657   1.2444  -2.3335
 09C  H12   H   HNH1  0   0.355  -0.0434  -0.5904  -1.5676
 09C  H13   H   HNH1  0   0.397  -0.0949   3.2856  -1.7566
 09C  H14   H   HNR5  0   0.414  -4.0424  -3.1312  -1.0118
 09C  H15   H   HNR5  0   0.414   4.1264  -2.4134  -2.2996
 09C  H16   H   HCH1  0   0.262  -1.1761   0.8813   0.6626
 09C  HAD   H   HCR6  0   0.271  -6.3089   2.0521   0.7544
 09C  BR1   BR  BR    0  -0.062  -8.4443   0.0518   0.4090
 09C  BR2   BR  BR    0  -0.065   8.2453  -0.2247   0.8361

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
 09C  C1   C2    single    1.535  0.020  1.535
 09C  C1   O1    double    1.223  0.020  1.223
 09C  N1   C2    single    1.451  0.020  1.451
 09C  C2   C16   single    1.497  0.020  1.497
 09C  C2   HA    single    0.970  0.020  1.090
 09C  N2   C1    single    1.342  0.020  1.342
 09C  N3   C7    aromatic  1.366  0.020  1.366
 09C  N4   C18   aromatic  1.361  0.020  1.361
 09C  BR1  C13   single    1.893  0.020  1.893
 09C  C3   C5    aromatic  1.381  0.020  1.381
 09C  C3   HAD   single    0.930  0.020  1.080
 09C  C4   HAE   single    0.930  0.020  1.080
 09C  C5   C19   aromatic  1.399  0.020  1.399
 09C  C5   HAF   single    0.930  0.020  1.080
 09C  C6   C4    aromatic  1.380  0.020  1.380
 09C  C6   HAG   single    0.930  0.020  1.080
 09C  C7   HAH   single    0.930  0.020  1.080
 09C  C8   N4    aromatic  1.366  0.020  1.366
 09C  C8   C16   aromatic  1.367  0.020  1.367
 09C  C8   HAI   single    0.930  0.020  1.080
 09C  C9   C17   aromatic  1.394  0.020  1.394
 09C  C9   HAJ   single    0.930  0.020  1.080
 09C  C10  C14   aromatic  1.379  0.020  1.379
 09C  C10  HAK   single    0.930  0.020  1.080
 09C  C11  C12   single    1.525  0.020  1.525
 09C  C11  N2    single    1.450  0.020  1.450
 09C  C11  H1AL  single    0.970  0.020  1.090
 09C  C11  H2AL  single    0.970  0.020  1.090
 09C  C12  N1    single    1.452  0.020  1.452
 09C  C13  C3    aromatic  1.403  0.020  1.403
 09C  C13  C9    aromatic  1.379  0.020  1.379
 09C  C14  C4    aromatic  1.404  0.020  1.404
 09C  C14  BR2   single    1.894  0.020  1.894
 09C  C15  C7    aromatic  1.366  0.020  1.366
 09C  C15  C12   single    1.494  0.020  1.494
 09C  C16  C20   aromatic  1.431  0.020  1.431
 09C  C17  C19   aromatic  1.413  0.020  1.413
 09C  C17  N3    aromatic  1.360  0.020  1.360
 09C  C18  C20   aromatic  1.412  0.020  1.412
 09C  C18  C10   aromatic  1.394  0.020  1.394
 09C  C19  C15   aromatic  1.433  0.020  1.433
 09C  C20  C6    aromatic  1.398  0.020  1.398
 09C  N1   H12   single    0.890  0.020  1.040
 09C  N2   H13   single    0.860  0.020  1.020
 09C  N3   H14   single    0.860  0.020  1.020
 09C  N4   H15   single    0.860  0.020  1.020
 09C  C12  H16   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
 09C  N2    C1   C2    116.38  3.000
 09C  N2    C1   O1    122.41  3.000
 09C  C2    C1   O1    121.16  3.000
 09C  H12   N1   C12   108.14  3.000
 09C  H12   N1   C2    109.65  3.000
 09C  C12   N1   C2    111.30  3.000
 09C  HA    C2   C16   107.68  3.000
 09C  HA    C2   N1    107.15  3.000
 09C  C16   C2   N1    111.42  3.000
 09C  HA    C2   C1    104.51  3.000
 09C  C16   C2   C1    110.95  3.000
 09C  N1    C2   C1    114.59  3.000
 09C  H13   N2   C11   116.97  3.000
 09C  H13   N2   C1    115.99  3.000
 09C  C11   N2   C1    126.92  3.000
 09C  H14   N3   C17   125.73  3.000
 09C  H14   N3   C7    124.90  3.000
 09C  C17   N3   C7    109.36  3.000
 09C  H15   N4   C18   125.85  3.000
 09C  H15   N4   C8    124.77  3.000
 09C  C18   N4   C8    109.35  3.000
 09C  HAD   C3   C13   120.38  3.000
 09C  C13   C3   C5    119.95  3.000
 09C  HAD   C3   C5    119.67  3.000
 09C  HAE   C4   C14   120.23  3.000
 09C  C14   C4   C6    119.95  3.000
 09C  HAE   C4   C6    119.82  3.000
 09C  HAF   C5   C19   121.24  3.000
 09C  HAF   C5   C3    119.13  3.000
 09C  C19   C5   C3    119.63  3.000
 09C  HAG   C6   C20   120.77  3.000
 09C  C20   C6   C4    119.50  3.000
 09C  HAG   C6   C4    119.73  3.000
 09C  HAH   C7   C15   129.62  3.000
 09C  C15   C7   N3    110.10  3.000
 09C  HAH   C7   N3    120.28  3.000
 09C  HAI   C8   C16   130.47  3.000
 09C  HAI   C8   N4    119.45  3.000
 09C  C16   C8   N4    110.08  3.000
 09C  HAJ   C9   C17   121.25  3.000
 09C  HAJ   C9   C13   122.26  3.000
 09C  C17   C9   C13   116.49  3.000
 09C  HAK   C10  C18   121.31  3.000
 09C  C18   C10  C14   116.37  3.000
 09C  HAK   C10  C14   122.32  3.000
 09C  H2AL  C11  H1AL  107.23  3.000
 09C  H2AL  C11  C12   109.23  3.000
 09C  H1AL  C11  C12   111.63  3.000
 09C  H2AL  C11  N2    110.53  3.000
 09C  H1AL  C11  N2    108.27  3.000
 09C  C12   C11  N2    109.92  3.000
 09C  H16   C12  C15   109.12  3.000
 09C  H16   C12  C11   108.28  3.000
 09C  C15   C12  C11   111.46  3.000
 09C  H16   C12  N1    107.22  3.000
 09C  C15   C12  N1    110.87  3.000
 09C  C11   C12  N1    109.76  3.000
 09C  C9    C13  C3    122.64  3.000
 09C  C9    C13  BR1   118.81  3.000
 09C  C3    C13  BR1   118.55  3.000
 09C  C10   C14  C4    122.71  3.000
 09C  C4    C14  BR2   118.46  3.000
 09C  C10   C14  BR2   118.82  3.000
 09C  C19   C15  C12   127.19  3.000
 09C  C19   C15  C7    106.17  3.000
 09C  C12   C15  C7    126.64  3.000
 09C  C20   C16  C8    106.12  3.000
 09C  C20   C16  C2    126.60  3.000
 09C  C8    C16  C2    127.26  3.000
 09C  C19   C17  C9    122.69  3.000
 09C  C19   C17  N3    107.47  3.000
 09C  C9    C17  N3    129.84  3.000
 09C  C20   C18  C10   122.69  3.000
 09C  C10   C18  N4    129.90  3.000
 09C  C20   C18  N4    107.41  3.000
 09C  C17   C19  C15   106.90  3.000
 09C  C15   C19  C5    134.50  3.000
 09C  C17   C19  C5    118.60  3.000
 09C  C18   C20  C16   107.05  3.000
 09C  C18   C20  C6    118.78  3.000
 09C  C16   C20  C6    134.17  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
 09C  CONST_01  C19  C15  C7   N3     0.00   0.0  0
 09C  CONST_02  C13  C9   C17  N3   180.00   0.0  0
 09C  CONST_03  C5   C19  C17  N3   180.00   0.0  0
 09C  CONST_04  C15  C19  C17  N3     0.00   0.0  0
 09C  CONST_05  C16  C20  C18  N4     0.00   0.0  0
 09C  CONST_06  C6   C20  C18  N4   180.00   0.0  0
 09C  CONST_07  C14  C10  C18  N4   180.00   0.0  0
 09C  CONST_08  C20  C16  C8   N4     0.00   0.0  0
 09C  CONST_09  C17  C19  C5   C3     0.00   0.0  0
 09C  CONST_10  C15  C19  C5   C3   180.00   0.0  0
 09C  CONST_11  C17  C9   C13  C3     0.00   0.0  0
 09C  CONST_12  C16  C20  C6   C4   180.00   0.0  0
 09C  CONST_13  C18  C20  C6   C4     0.00   0.0  0
 09C  CONST_14  C18  C10  C14  C4     0.00   0.0  0
 09C  CONST_15  C9   C13  C3   C5     0.00   0.0  0
 09C  CONST_16  C9   C17  C19  C5     0.00   0.0  0
 09C  CONST_17  C7   C15  C19  C5   180.00   0.0  0
 09C  CONST_18  C10  C14  C4   C6     0.00   0.0  0
 09C  CONST_19  C8   C16  C20  C6   180.00   0.0  0
 09C  CONST_20  C10  C18  C20  C6     0.00   0.0  0
 09C  CONST_21  C9   C17  N3   C7   180.00   0.0  0
 09C  CONST_22  C19  C17  N3   C7     0.00   0.0  0
 09C  CONST_23  C17  C19  C15  C7     0.00   0.0  0
 09C  CONST_24  C20  C18  N4   C8     0.00   0.0  0
 09C  CONST_25  C10  C18  N4   C8   180.00   0.0  0
 09C  CONST_26  C18  C20  C16  C8     0.00   0.0  0
 09C  CONST_27  C15  C19  C17  C9   180.00   0.0  0
 09C  CONST_28  C16  C20  C18  C10  180.00   0.0  0
 09C  CONST_29  C19  C5   C3   C13    0.00   0.0  0
 09C  CONST_30  C19  C17  C9   C13    0.00   0.0  0
 09C  CONST_31  C20  C18  C10  C14    0.00   0.0  0
 09C  CONST_32  C20  C6   C4   C14    0.00   0.0  0
 09C  CONST_33  C17  N3   C7   C15    0.00   0.0  0
 09C  CONST_34  C18  N4   C8   C16    0.00   0.0  0
 09C  CONST_35  N4   C8   C16  C2   180.00   0.0  0
 09C  CONST_36  C18  C20  C16  C2   180.00   0.0  0
 09C  CONST_37  C6   C20  C16  C2     0.00   0.0  0
 09C  CONST_38  C12  C15  C7   N3   180.00   0.0  0
 09C  CONST_39  C12  C15  C19  C5     0.00   0.0  0
 09C  CONST_40  C17  C19  C15  C12  180.00   0.0  0
 09C  CONST_41  C11  N2   C1   C2     0.00   0.0  0
 09C  CONST_42  C5   C3   C13  BR1  180.00   0.0  0
 09C  CONST_43  C17  C9   C13  BR1  180.00   0.0  0
 09C  CONST_44  C18  C10  C14  BR2  180.00   0.0  0
 09C  CONST_45  C6   C4   C14  BR2  180.00   0.0  0
 09C  CONST_46  C11  N2   C1   O1   180.00   0.0  0
 09C  CONST_47  HAI  C8   C16  C2     0.00   0.0  0
 09C  CONST_48  HAJ  C9   C17  N3     0.00   0.0  0
 09C  CONST_49  HAK  C10  C18  N4     0.00   0.0  0
 09C  CONST_50  H14  N3   C17  C9     0.00   0.0  0
 09C  CONST_51  HAD  C3   C13  C9   180.00   0.0  0
 09C  CONST_52  HAE  C4   C14  C10  180.00   0.0  0
 09C  CONST_53  H15  N4   C18  C10    0.00   0.0  0
 09C  CONST_54  HAH  C7   C15  C12    0.00   0.0  0
 09C  CONST_55  HAF  C5   C3   C13  180.00   0.0  0
 09C  CONST_56  HAG  C6   C4   C14  180.00   0.0  0
 09C  CONST_57  H13  N2   C1   C2   180.00   0.0  0
 09C  Var_01    C12  C11  N2   C1    20.64  30.0  1

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
 09C  chir_01  C2   C1  N1   C16  negativ
 09C  chir_02  C12  N1  C11  C15  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
 09C  plan-1  N3   0.020
 09C  plan-1  C3   0.020
 09C  plan-1  C5   0.020
 09C  plan-1  C7   0.020
 09C  plan-1  C9   0.020
 09C  plan-1  C12  0.020
 09C  plan-1  C13  0.020
 09C  plan-1  C15  0.020
 09C  plan-1  C17  0.020
 09C  plan-1  C19  0.020
 09C  plan-1  HAF  0.020
 09C  plan-1  HAH  0.020
 09C  plan-1  HAJ  0.020
 09C  plan-1  H14  0.020
 09C  plan-1  HAD  0.020
 09C  plan-1  BR1  0.020
 09C  plan-2  C2   0.020
 09C  plan-2  N4   0.020
 09C  plan-2  C4   0.020
 09C  plan-2  C6   0.020
 09C  plan-2  C8   0.020
 09C  plan-2  C10  0.020
 09C  plan-2  C14  0.020
 09C  plan-2  C16  0.020
 09C  plan-2  C18  0.020
 09C  plan-2  C20  0.020
 09C  plan-2  HAE  0.020
 09C  plan-2  HAG  0.020
 09C  plan-2  HAI  0.020
 09C  plan-2  HAK  0.020
 09C  plan-2  H15  0.020
 09C  plan-2  BR2  0.020
 09C  plan-3  C1   0.020
 09C  plan-3  O1   0.020
 09C  plan-3  C2   0.020
 09C  plan-3  N2   0.020
 09C  plan-3  C11  0.020
 09C  plan-3  H13  0.020

