# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:35:41 2022
#   Inital geometry file: a 94 line input string
#   Ligand name: (2Z,3E)-2,3'-biindole-2',3(1H,1'H)-dione 3-oxime
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O/N=C1/C(Nc2ccccc12)=C3/C(=O)Nc4ccccc34
#
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
 IXM  IXM  '(2Z,3E)-2,3'-biindole-2',3(1H,1'H)-dione 3-oxime'  ligand  32  21  .  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_IXM
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
 IXM  C1   C  CR56  0   0.023  -2.5867   0.5286  -0.0024
 IXM  C2   C  CR5   0   0.079  -1.1831   0.9348  -0.0103
 IXM  C3   C  CR56  0   0.371  -2.5797  -0.8697  -0.0355
 IXM  N4   N  NR15  0  -0.802  -1.2776  -1.3209  -0.0618
 IXM  C5   C  CR16  0  -0.322  -3.7451  -1.6143  -0.0395
 IXM  C7   C  CR16  0  -0.253  -4.9465  -0.9155  -0.0086
 IXM  C9   C  CR16  0  -0.263  -4.9757   0.4759   0.0252
 IXM  C11  C  CR16  0  -0.311  -3.7958   1.2121   0.0283
 IXM  C13  C  CR5   0   0.422  -0.3744  -0.3079  -0.0502
 IXM  C14  C  CR5   0  -0.168   0.9813  -0.5288  -0.0751
 IXM  C15  C  CR5   0   0.540   1.4823  -1.9166  -0.1165
 IXM  N16  N  NR15  0  -0.763   2.8409  -1.8389  -0.1325
 IXM  C17  C  CR56  0   0.369   3.2748  -0.5287  -0.1081
 IXM  C18  C  CR56  0   0.004   2.1566   0.3301  -0.0713
 IXM  C19  C  CR16  0  -0.309   4.5774  -0.0727  -0.1159
 IXM  C20  C  CR16  0  -0.278   4.7848   1.3030  -0.0865
 IXM  C21  C  CR16  0  -0.254   3.7039   2.1750  -0.0508
 IXM  C22  C  CR16  0  -0.420   2.3947   1.7014  -0.0426
 IXM  O23  O  O     0  -0.497   0.8423  -2.9660  -0.1349
 IXM  N24  N  N     0  -0.108  -0.6368   2.0883   0.0094
 IXM  O39  O  OH1   0  -0.507  -1.5207   3.0937   0.0426
 IXM  HN4  H  HNR5  0   0.429  -0.9825  -2.2893  -0.0910
 IXM  HC5  H  HCR6  0   0.273  -3.7244  -2.6956  -0.0650
 IXM  HC7  H  HCR6  0   0.268  -5.8764  -1.4690  -0.0113
 IXM  HC9  H  HCR6  0   0.261  -5.9257   0.9921   0.0494
 IXM  H11  H  HCR6  0   0.266  -3.8381   2.2900   0.0534
 IXM  H16  H  HNR5  0   0.410   3.4452  -2.6449  -0.1692
 IXM  H19  H  HCR6  0   0.264   5.4083  -0.7659  -0.1438
 IXM  H20  H  HCR6  0   0.255   5.7954   1.6902  -0.0912
 IXM  H21  H  HCR6  0   0.249   3.8764   3.2432  -0.0301
 IXM  H22  H  HCR6  0   0.276   1.5751   2.3989  -0.0155
 IXM  H39  H  HOH1  0   0.494  -0.9864   3.8974   0.0538

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
 IXM  C1   C2   single    1.461  0.020  1.461
 IXM  C1   C3   aromatic  1.399  0.020  1.399
 IXM  C1   C11  aromatic  1.389  0.020  1.389
 IXM  C2   C13  single    1.483  0.020  1.483
 IXM  C2   N24  double    1.277  0.020  1.277
 IXM  C3   N4   single    1.378  0.020  1.378
 IXM  C3   C5   aromatic  1.383  0.020  1.383
 IXM  N4   C13  single    1.357  0.020  1.357
 IXM  N4   HN4  single    0.860  0.020  1.020
 IXM  C5   C7   aromatic  1.390  0.020  1.390
 IXM  C5   HC5  single    0.930  0.020  1.080
 IXM  C7   C9   aromatic  1.392  0.020  1.392
 IXM  C7   HC7  single    0.930  0.020  1.080
 IXM  C9   C11  aromatic  1.391  0.020  1.391
 IXM  C9   HC9  single    0.930  0.020  1.080
 IXM  C11  H11  single    0.930  0.020  1.080
 IXM  C13  C14  double    1.374  0.020  1.374
 IXM  C14  C15  single    1.476  0.020  1.476
 IXM  C14  C18  single    1.456  0.020  1.456
 IXM  C15  N16  single    1.361  0.020  1.361
 IXM  C15  O23  double    1.229  0.020  1.229
 IXM  N16  C17  single    1.380  0.020  1.380
 IXM  N16  H16  single    0.860  0.020  1.020
 IXM  C17  C18  aromatic  1.410  0.020  1.410
 IXM  C17  C19  aromatic  1.380  0.020  1.380
 IXM  C18  C22  aromatic  1.392  0.020  1.392
 IXM  C19  C20  aromatic  1.391  0.020  1.391
 IXM  C19  H19  single    0.930  0.020  1.080
 IXM  C20  C21  aromatic  1.389  0.020  1.389
 IXM  C20  H20  single    0.930  0.020  1.080
 IXM  C21  C22  aromatic  1.392  0.020  1.392
 IXM  C21  H21  single    0.930  0.020  1.080
 IXM  C22  H22  single    0.930  0.020  1.080
 IXM  N24  O39  single    1.339  0.020  1.339
 IXM  O39  H39  single    0.850  0.020  0.980

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
 IXM  C11  C1   C3   119.78  3.000
 IXM  C11  C1   C2   134.38  3.000
 IXM  C3   C1   C2   105.84  3.000
 IXM  N24  C2   C13  121.61  3.000
 IXM  N24  C2   C1   131.47  3.000
 IXM  C13  C2   C1   106.92  3.000
 IXM  C5   C3   N4   128.30  3.000
 IXM  C5   C3   C1   122.28  3.000
 IXM  N4   C3   C1   109.42  3.000
 IXM  HN4  N4   C13  121.33  3.000
 IXM  HN4  N4   C3   126.08  3.000
 IXM  C13  N4   C3   112.60  3.000
 IXM  HC5  C5   C7   121.30  3.000
 IXM  HC5  C5   C3   121.47  3.000
 IXM  C7   C5   C3   117.23  3.000
 IXM  HC7  C7   C9   119.56  3.000
 IXM  HC7  C7   C5   119.04  3.000
 IXM  C9   C7   C5   121.40  3.000
 IXM  HC9  C9   C11  119.50  3.000
 IXM  HC9  C9   C7   119.74  3.000
 IXM  C11  C9   C7   120.76  3.000
 IXM  H11  C11  C9   119.71  3.000
 IXM  H11  C11  C1   121.74  3.000
 IXM  C9   C11  C1   118.54  3.000
 IXM  C14  C13  N4   122.45  3.000
 IXM  C14  C13  C2   132.32  3.000
 IXM  N4   C13  C2   105.23  3.000
 IXM  C18  C14  C15  106.31  3.000
 IXM  C18  C14  C13  134.57  3.000
 IXM  C15  C14  C13  119.12  3.000
 IXM  O23  C15  N16  124.63  3.000
 IXM  O23  C15  C14  128.78  3.000
 IXM  N16  C15  C14  106.58  3.000
 IXM  H16  N16  C17  124.82  3.000
 IXM  H16  N16  C15  123.59  3.000
 IXM  C17  N16  C15  111.58  3.000
 IXM  C19  C17  C18  123.17  3.000
 IXM  C19  C17  N16  127.61  3.000
 IXM  C18  C17  N16  109.22  3.000
 IXM  C22  C18  C17  117.69  3.000
 IXM  C22  C18  C14  136.00  3.000
 IXM  C17  C18  C14  106.30  3.000
 IXM  H19  C19  C20  121.29  3.000
 IXM  H19  C19  C17  120.86  3.000
 IXM  C20  C19  C17  117.85  3.000
 IXM  H20  C20  C21  120.13  3.000
 IXM  H20  C20  C19  119.52  3.000
 IXM  C21  C20  C19  120.35  3.000
 IXM  H21  C21  C22  119.04  3.000
 IXM  H21  C21  C20  119.75  3.000
 IXM  C22  C21  C20  121.21  3.000
 IXM  H22  C22  C21  119.72  3.000
 IXM  H22  C22  C18  120.56  3.000
 IXM  C21  C22  C18  119.72  3.000
 IXM  O39  N24  C2   113.35  3.000
 IXM  H39  O39  N24  105.07  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
 IXM  CONST_01  C7   C5   C3   C1      0.00  0.0  0
 IXM  CONST_02  C7   C9   C11  C1      0.00  0.0  0
 IXM  CONST_03  C9   C11  C1   C3      0.00  0.0  0
 IXM  CONST_04  C9   C7   C5   C3      0.00  0.0  0
 IXM  CONST_05  C11  C1   C3   C5      0.00  0.0  0
 IXM  CONST_06  C11  C9   C7   C5      0.00  0.0  0
 IXM  CONST_07  C21  C22  C18  C17     0.00  0.0  0
 IXM  CONST_08  C21  C20  C19  C17     0.00  0.0  0
 IXM  CONST_09  C20  C19  C17  C18     0.00  0.0  0
 IXM  CONST_10  C20  C21  C22  C18     0.00  0.0  0
 IXM  CONST_11  C22  C18  C17  C19     0.00  0.0  0
 IXM  CONST_12  C22  C21  C20  C19     0.00  0.0  0
 IXM  CONST_13  C17  N16  C15  C14     0.00  0.0  0
 IXM  CONST_14  O23  C15  N16  C17   180.00  0.0  0
 IXM  CONST_15  HC5  C5   C3   C1    180.00  0.0  0
 IXM  CONST_16  HC9  C9   C11  C1    180.00  0.0  0
 IXM  CONST_17  H11  C11  C1   C2      0.00  0.0  0
 IXM  CONST_18  HC7  C7   C5   C3    180.00  0.0  0
 IXM  CONST_19  H22  C22  C18  C14     0.00  0.0  0
 IXM  CONST_20  H19  C19  C17  N16     0.00  0.0  0
 IXM  CONST_21  H20  C20  C19  C17   180.00  0.0  0
 IXM  CONST_22  H21  C21  C22  C18   180.00  0.0  0
 IXM  CONST_23  H16  N16  C15  C14   180.00  0.0  0
 IXM  CONST_24  O39  N24  C2   C1      0.00  0.0  0
 IXM  CONST_25  O39  N24  C2   C13   180.00  0.0  0
 IXM  Var_01    C15  C14  C13  C2   -179.88  0.0  2

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
 IXM  plan-1  C1   0.020
 IXM  plan-1  C2   0.020
 IXM  plan-1  C3   0.020
 IXM  plan-1  N4   0.020
 IXM  plan-1  C5   0.020
 IXM  plan-1  C7   0.020
 IXM  plan-1  C9   0.020
 IXM  plan-1  C11  0.020
 IXM  plan-1  C13  0.020
 IXM  plan-1  C14  0.020
 IXM  plan-1  C15  0.020
 IXM  plan-1  N16  0.020
 IXM  plan-1  C17  0.020
 IXM  plan-1  C18  0.020
 IXM  plan-1  C19  0.020
 IXM  plan-1  C20  0.020
 IXM  plan-1  C21  0.020
 IXM  plan-1  C22  0.020
 IXM  plan-1  O23  0.020
 IXM  plan-1  N24  0.020
 IXM  plan-1  O39  0.020
 IXM  plan-1  HN4  0.020
 IXM  plan-1  HC5  0.020
 IXM  plan-1  HC7  0.020
 IXM  plan-1  HC9  0.020
 IXM  plan-1  H11  0.020
 IXM  plan-1  H16  0.020
 IXM  plan-1  H19  0.020
 IXM  plan-1  H20  0.020
 IXM  plan-1  H21  0.020
 IXM  plan-1  H22  0.020

