# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 16:22:45 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: N-{4-[(1E)-N-(N-hydroxycarbamimidoyl)ethanehydrazonoyl]phenyl}-7-nitro-1H-indole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=N\NC(=N)NO)/c1ccc(NC(=O)c2[nH]c3c(cccc3[N+]([O-])=O)c2)cc1
#
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
 XK9  XK9  N-{4-[(1E)-N-(N-hydroxycarbamimidoyl)ethanehydrazonoyl]phenyl}-7-nitro-1H-indole-2-carboxamide  ligand  46  29  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XK9
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
 XK9  O3    O  O     -1  -0.380  -6.4148   3.2718   0.6787
 XK9  N7    N  N      1   0.346  -5.5710   2.4116   0.5900
 XK9  O2    O  O      0  -0.407  -4.4177   2.5652   0.9403
 XK9  C3    C  CR6    0   0.220  -5.9325   1.1338   0.0423
 XK9  C2    C  CR16   0  -0.313  -7.2388   0.9010  -0.3529
 XK9  C4    C  CR56   0   0.377  -4.9795   0.1139  -0.1033
 XK9  N1    N  NR15   0  -0.729  -3.6584   0.0426   0.1768
 XK9  C8    C  CR5    0   0.221  -3.1929  -1.2148  -0.1389
 XK9  C7    C  CR15   0  -0.368  -4.2152  -1.9653  -0.6409
 XK9  C5    C  CR56   0   0.041  -5.3720  -1.1379  -0.6385
 XK9  C6    C  CR16   0  -0.308  -6.6924  -1.3507  -1.0337
 XK9  C1    C  CR16   0  -0.270  -7.6138  -0.3308  -0.8880
 XK9  C9    C  C      0   0.519  -1.7956  -1.6609   0.0307
 XK9  O1    O  O      0  -0.449  -1.5366  -2.8493   0.0854
 XK9  N2    N  NH1    0  -0.762  -0.8736  -0.6667   0.0986
 XK9  C10   C  CR6    0   0.371   0.5094  -0.7911   0.2656
 XK9  C15   C  CR16   0  -0.331   1.2952   0.3133  -0.0791
 XK9  C14   C  CR16   0  -0.273   2.6651   0.2836   0.0693
 XK9  C13   C  CR6    0   0.043   3.3139  -0.8485   0.5751
 XK9  C12   C  CR16   0  -0.314   2.5183  -1.9374   0.9237
 XK9  C11   C  CR16   0  -0.287   1.1383  -1.9230   0.7758
 XK9  C16   C  C      0   0.198   4.7840  -0.8920   0.7135
 XK9  C17   C  CH3    0  -0.784   5.4059  -2.0386   1.4574
 XK9  N3    N  N      0  -0.205   5.4260   0.0624   0.1558
 XK9  N4    N  NH1    0  -0.541   6.7598   0.0871   0.1763
 XK9  C18   C  C      0   0.573   7.4335   1.1921  -0.2912
 XK9  N6    N  N      0  -0.661   6.8439   2.2556  -0.6511
 XK9  N5    N  NH1    0  -0.406   8.8092   0.9611  -0.2359
 XK9  OBC   O  OH1    0  -0.556   9.5946   1.9388  -0.7961
 XK9  H2    H  HCR6   0   0.302  -7.9798   1.6800  -0.2479
 XK9  H1    H  HCR6   0   0.277  -8.6413  -0.4809  -1.1875
 XK9  HA    H  HNR5   0   0.425  -3.1485   0.7628   0.6625
 XK9  H7    H  HCR5   0   0.274  -4.1473  -2.9819  -0.9926
 XK9  H6    H  HCR6   0   0.276  -6.9910  -2.3054  -1.4464
 XK9  HB    H  HNH1   0   0.419  -1.1792   0.2622  -0.1502
 XK9  H15   H  HCR6   0   0.272   0.8237   1.2065  -0.4722
 XK9  H11   H  HCR6   0   0.279   0.5758  -2.7946   1.0669
 XK9  H14   H  HCR6   0   0.260   3.2441   1.1525  -0.2128
 XK9  H12   H  HCR6   0   0.258   2.9642  -2.8411   1.3160
 XK9  H171  H  HCH3   0   0.273   5.5039  -2.9181   0.8172
 XK9  H172  H  HCH3   0   0.260   6.3956  -1.8078   1.8497
 XK9  H173  H  HCH3   0   0.267   4.7997  -2.3261   2.3143
 XK9  H4    H  HNH1   0   0.402   7.2882  -0.6450   0.6316
 XK9  H5    H  HNH1   0   0.396   9.1019   0.0373  -0.5343
 XK9  HBC   H  HOH1   0   0.467   9.5020   1.8810  -1.7587
 XK9  H6A   H  H      0   0.331   7.5161   2.9337  -0.9892

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
 XK9  O3   N7    single    1.208  0.020  1.208
 XK9  N7   O2    double    1.215  0.020  1.215
 XK9  N7   C3    single    1.436  0.020  1.436
 XK9  C3   C2    aromatic  1.385  0.020  1.385
 XK9  C3   C4    aromatic  1.403  0.020  1.403
 XK9  C2   C1    aromatic  1.394  0.020  1.394
 XK9  C4   N1    aromatic  1.352  0.020  1.352
 XK9  C4   C5    aromatic  1.417  0.020  1.417
 XK9  N1   C8    aromatic  1.377  0.020  1.377
 XK9  C8   C7    aromatic  1.364  0.020  1.364
 XK9  C8   C9    single    1.477  0.020  1.477
 XK9  C7   C5    aromatic  1.422  0.020  1.422
 XK9  C5   C6    aromatic  1.395  0.020  1.395
 XK9  C6   C1    aromatic  1.382  0.020  1.382
 XK9  C9   O1    double    1.218  0.020  1.218
 XK9  C9   N2    single    1.358  0.020  1.358
 XK9  N2   C10   single    1.399  0.020  1.399
 XK9  C10  C15   aromatic  1.399  0.020  1.399
 XK9  C10  C11   aromatic  1.392  0.020  1.392
 XK9  C15  C14   aromatic  1.378  0.020  1.378
 XK9  C14  C13   aromatic  1.399  0.020  1.399
 XK9  C13  C12   aromatic  1.393  0.020  1.393
 XK9  C13  C16   single    1.477  0.020  1.477
 XK9  C12  C11   aromatic  1.388  0.020  1.388
 XK9  C16  C17   single    1.502  0.020  1.502
 XK9  C16  N3    double    1.278  0.020  1.278
 XK9  N3   N4    single    1.334  0.020  1.334
 XK9  N4   C18   single    1.376  0.020  1.376
 XK9  C18  N6    double    1.268  0.020  1.268
 XK9  C18  N5    single    1.396  0.020  1.396
 XK9  N5   OBC   single    1.374  0.020  1.374
 XK9  C2   H2    single    0.930  0.020  1.080
 XK9  C1   H1    single    0.930  0.020  1.080
 XK9  N1   HA    single    0.860  0.020  1.020
 XK9  C7   H7    single    0.930  0.020  1.080
 XK9  C6   H6    single    0.930  0.020  1.080
 XK9  N2   HB    single    0.860  0.020  1.020
 XK9  C15  H15   single    0.930  0.020  1.080
 XK9  C11  H11   single    0.930  0.020  1.080
 XK9  C14  H14   single    0.930  0.020  1.080
 XK9  C12  H12   single    0.930  0.020  1.080
 XK9  C17  H171  single    0.970  0.020  1.090
 XK9  C17  H172  single    0.970  0.020  1.090
 XK9  C17  H173  single    0.970  0.020  1.090
 XK9  N4   H4    single    0.860  0.020  1.020
 XK9  N5   H5    single    0.890  0.020  1.040
 XK9  OBC  HBC   single    0.850  0.020  0.980
 XK9  N6   H6A   single    0.890  0.020  1.040

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
 XK9  C3    N7   O2    117.47  3.000
 XK9  C3    N7   O3    119.05  3.000
 XK9  O2    N7   O3    123.48  3.000
 XK9  C4    C3   C2    119.27  3.000
 XK9  C4    C3   N7    121.01  3.000
 XK9  C2    C3   N7    119.73  3.000
 XK9  H2    C2   C1    119.34  3.000
 XK9  H2    C2   C3    119.87  3.000
 XK9  C1    C2   C3    120.79  3.000
 XK9  C5    C4   N1    107.59  3.000
 XK9  C5    C4   C3    119.55  3.000
 XK9  N1    C4   C3    132.86  3.000
 XK9  HA    N1   C8    126.31  3.000
 XK9  HA    N1   C4    123.82  3.000
 XK9  C8    N1   C4    109.31  3.000
 XK9  C9    C8   C7    125.82  3.000
 XK9  C9    C8   N1    124.69  3.000
 XK9  C7    C8   N1    109.48  3.000
 XK9  H7    C7   C5    126.90  3.000
 XK9  H7    C7   C8    126.30  3.000
 XK9  C5    C7   C8    106.79  3.000
 XK9  C6    C5   C7    132.91  3.000
 XK9  C6    C5   C4    120.27  3.000
 XK9  C7    C5   C4    106.82  3.000
 XK9  H6    C6   C1    120.48  3.000
 XK9  H6    C6   C5    120.26  3.000
 XK9  C1    C6   C5    119.26  3.000
 XK9  H1    C1   C6    120.14  3.000
 XK9  H1    C1   C2    119.00  3.000
 XK9  C6    C1   C2    120.87  3.000
 XK9  N2    C9   O1    124.62  3.000
 XK9  N2    C9   C8    115.29  3.000
 XK9  O1    C9   C8    120.09  3.000
 XK9  HB    N2   C10   114.26  3.000
 XK9  HB    N2   C9    117.14  3.000
 XK9  C10   N2   C9    127.76  3.000
 XK9  C11   C10  C15   118.60  3.000
 XK9  C11   C10  N2    124.26  3.000
 XK9  C15   C10  N2    117.12  3.000
 XK9  H15   C15  C14   119.29  3.000
 XK9  H15   C15  C10   119.72  3.000
 XK9  C14   C15  C10   120.99  3.000
 XK9  H14   C14  C13   119.73  3.000
 XK9  H14   C14  C15   119.12  3.000
 XK9  C13   C14  C15   121.14  3.000
 XK9  C16   C13  C12   121.46  3.000
 XK9  C16   C13  C14   121.27  3.000
 XK9  C12   C13  C14   117.26  3.000
 XK9  H12   C12  C11   117.22  3.000
 XK9  H12   C12  C13   120.56  3.000
 XK9  C11   C12  C13   122.22  3.000
 XK9  H11   C11  C12   118.81  3.000
 XK9  H11   C11  C10   121.40  3.000
 XK9  C12   C11  C10   119.79  3.000
 XK9  N3    C16  C17   125.32  3.000
 XK9  N3    C16  C13   115.91  3.000
 XK9  C17   C16  C13   118.75  3.000
 XK9  H173  C17  H172  106.17  3.000
 XK9  H173  C17  H171  107.39  3.000
 XK9  H172  C17  H171  107.47  3.000
 XK9  H173  C17  C16   111.17  3.000
 XK9  H172  C17  C16   113.13  3.000
 XK9  H171  C17  C16   111.20  3.000
 XK9  N4    N3   C16   120.61  3.000
 XK9  H4    N4   C18   118.59  3.000
 XK9  H4    N4   N3    121.06  3.000
 XK9  C18   N4   N3    119.94  3.000
 XK9  N5    C18  N6    127.46  3.000
 XK9  N5    C18  N4    109.64  3.000
 XK9  N6    C18  N4    122.84  3.000
 XK9  H6A   N6   C18   110.34  3.000
 XK9  H5    N5   OBC   111.30  3.000
 XK9  H5    N5   C18   115.06  3.000
 XK9  OBC   N5   C18   115.44  3.000
 XK9  HBC   OBC  N5    107.95  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
 XK9  CONST_01  C6    C1   C2   C3      0.00   0.0  0
 XK9  CONST_02  C8    N1   C4   C3    180.00   0.0  0
 XK9  CONST_03  C7    C5   C4   C3    180.00   0.0  0
 XK9  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 XK9  CONST_05  N1    C4   C3   C2    180.00   0.0  0
 XK9  CONST_06  C5    C4   C3   C2      0.00   0.0  0
 XK9  CONST_07  C5    C6   C1   C2      0.00   0.0  0
 XK9  CONST_08  C1    C2   C3   C4      0.00   0.0  0
 XK9  CONST_09  C7    C8   N1   C4      0.00   0.0  0
 XK9  CONST_10  C8    C7   C5   C4      0.00   0.0  0
 XK9  CONST_11  C1    C6   C5   C4      0.00   0.0  0
 XK9  CONST_12  C7    C5   C4   N1      0.00   0.0  0
 XK9  CONST_13  C6    C5   C4   N1    180.00   0.0  0
 XK9  CONST_14  C5    C7   C8   N1      0.00   0.0  0
 XK9  CONST_15  C5    C4   N1   C8      0.00   0.0  0
 XK9  CONST_16  C6    C5   C7   C8    180.00   0.0  0
 XK9  CONST_17  C1    C6   C5   C7    180.00   0.0  0
 XK9  CONST_18  C13   C14  C15  C10     0.00   0.0  0
 XK9  CONST_19  C13   C12  C11  C10     0.00   0.0  0
 XK9  CONST_20  C12   C11  C10  C15     0.00   0.0  0
 XK9  CONST_21  C12   C13  C14  C15     0.00   0.0  0
 XK9  CONST_22  C11   C10  C15  C14     0.00   0.0  0
 XK9  CONST_23  C11   C12  C13  C14     0.00   0.0  0
 XK9  CONST_24  C1    C2   C3   N7    180.00   0.0  0
 XK9  CONST_25  N1    C4   C3   N7      0.00   0.0  0
 XK9  CONST_26  C5    C4   C3   N7    180.00   0.0  0
 XK9  CONST_27  C9    C8   N1   C4    180.00   0.0  0
 XK9  CONST_28  C9    C8   C7   C5    180.00   0.0  0
 XK9  CONST_29  C14   C15  C10  N2    180.00   0.0  0
 XK9  CONST_30  C12   C11  C10  N2    180.00   0.0  0
 XK9  CONST_31  C16   C13  C14  C15   180.00   0.0  0
 XK9  CONST_32  C16   C13  C12  C11   180.00   0.0  0
 XK9  CONST_33  H1    C1   C2   C3    180.00   0.0  0
 XK9  CONST_34  HA    N1   C4   C3      0.00   0.0  0
 XK9  CONST_35  H6    C6   C1   C2    180.00   0.0  0
 XK9  CONST_36  H2    C2   C3   C4    180.00   0.0  0
 XK9  CONST_37  H7    C7   C5   C4    180.00   0.0  0
 XK9  CONST_38  H14   C14  C15  C10   180.00   0.0  0
 XK9  CONST_39  H12   C12  C11  C10   180.00   0.0  0
 XK9  CONST_40  H11   C11  C10  C15   180.00   0.0  0
 XK9  CONST_41  H15   C15  C14  C13   180.00   0.0  0
 XK9  CONST_42  C10   N2   C9   C8    180.00   0.0  0
 XK9  CONST_43  C2    C3   N7   O3      0.00   0.0  0
 XK9  CONST_44  C4    C3   N7   O3    180.00   0.0  0
 XK9  CONST_45  C2    C3   N7   O2    180.00   0.0  0
 XK9  CONST_46  C4    C3   N7   O2      0.00   0.0  0
 XK9  CONST_49  HB    N2   C10  C15     0.00   0.0  0
 XK9  CONST_50  C10   N2   C9   O1      0.00   0.0  0
 XK9  CONST_51  N6    C18  N4   N3      0.00   0.0  0
 XK9  CONST_52  N5    C18  N4   N3    180.00   0.0  0
 XK9  CONST_53  OBC   N5   C18  N4    180.00   0.0  0
 XK9  CONST_54  OBC   N5   C18  N6      0.00   0.0  0
 XK9  CONST_55  H6A   N6   C18  N4    180.00   0.0  0
 XK9  CONST_57  H4    N4   C18  N6    180.00   0.0  0
 XK9  Var_01    O1    C9   C8   N1    159.71  30.0  2
 XK9  Var_02    C17   C16  C13  C14   170.51  30.0  2
 XK9  Var_03    H171  C17  C16  C13    81.85  30.0  3
 XK9  Var_04    C18   N4   N3   C16  -172.56  30.0  3

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
 XK9  plan-1  N2   0.020
 XK9  plan-1  C10  0.020
 XK9  plan-1  C15  0.020
 XK9  plan-1  C14  0.020
 XK9  plan-1  C13  0.020
 XK9  plan-1  C12  0.020
 XK9  plan-1  C11  0.020
 XK9  plan-1  C16  0.020
 XK9  plan-1  H15  0.020
 XK9  plan-1  H11  0.020
 XK9  plan-1  H14  0.020
 XK9  plan-1  H12  0.020
 XK9  plan-2  C13  0.020
 XK9  plan-2  C16  0.020
 XK9  plan-2  C17  0.020
 XK9  plan-2  N3   0.020
 XK9  plan-2  N4   0.020
 XK9  plan-3  N7   0.020
 XK9  plan-3  C3   0.020
 XK9  plan-3  C2   0.020
 XK9  plan-3  C4   0.020
 XK9  plan-3  N1   0.020
 XK9  plan-3  C8   0.020
 XK9  plan-3  C7   0.020
 XK9  plan-3  C5   0.020
 XK9  plan-3  C6   0.020
 XK9  plan-3  C1   0.020
 XK9  plan-3  C9   0.020
 XK9  plan-3  H2   0.020
 XK9  plan-3  H1   0.020
 XK9  plan-3  HA   0.020
 XK9  plan-3  H7   0.020
 XK9  plan-3  H6   0.020
 XK9  plan-4  C8   0.020
 XK9  plan-4  C9   0.020
 XK9  plan-4  O1   0.020
 XK9  plan-4  N2   0.020
 XK9  plan-4  C10  0.020
 XK9  plan-4  HB   0.020
 XK9  plan-5  O3   0.020
 XK9  plan-5  N7   0.020
 XK9  plan-5  O2   0.020
 XK9  plan-5  C3   0.020
 XK9  plan-6  N3   0.020
 XK9  plan-6  N4   0.020
 XK9  plan-6  C18  0.020
 XK9  plan-6  N6   0.020
 XK9  plan-6  N5   0.020
 XK9  plan-6  OBC  0.020
 XK9  plan-6  H4   0.020
 XK9  plan-6  H5   0.020
 XK9  plan-6  H6A  0.020

