# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:04:36 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 2-(4-aminophenyl)-5-methoxy-3H-indol-3-one 1-oxide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2c(c1)C(=O)C(=[N+]2[O-])c3ccc(N)cc3
#
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
 3ZU  3ZU  '2-(4-aminophenyl)-5-methoxy-3H-indol-3-one 1-oxide'  ligand  32  20  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3ZU
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
 3ZU  C1   C  CH3    0  -0.442   6.3231  -0.1021  -0.0596
 3ZU  O1   O  O2     0  -0.462   5.1450  -0.8660  -0.2475
 3ZU  C2   C  CR16   0  -0.388   3.7886   1.0828   0.1950
 3ZU  C3   C  CR16   0  -0.273   2.5129   1.6434   0.3259
 3ZU  C4   C  CR56   0   0.337   1.4501   0.8048   0.1441
 3ZU  C5   C  CR5    0   0.152  -0.6927   0.0385   0.0092
 3ZU  C6   C  CR5    0   0.294   0.2245  -1.0907  -0.2734
 3ZU  C7   C  CR6    0   0.324  -4.9686  -0.1266  -0.0044
 3ZU  C8   C  CR56   0  -0.015   1.5966  -0.5358  -0.1539
 3ZU  C9   C  CR16   0  -0.404   2.8346  -1.1027  -0.2882
 3ZU  C10  C  CR6    0   0.412   3.9561  -0.2677  -0.1076
 3ZU  N1   N  NR5    1  -0.119   0.0489   1.1118   0.2314
 3ZU  O2   O  O     -1  -0.474  -0.3189   2.2692   0.4981
 3ZU  N2   N  NH2    0  -0.854  -6.3312  -0.1758   0.0358
 3ZU  C11  C  CR16   0  -0.314  -4.2948   1.0447  -0.3835
 3ZU  C12  C  CR16   0  -0.277  -2.9176   1.1109  -0.3679
 3ZU  C13  C  CR6    0   0.047  -2.1386   0.0075   0.0105
 3ZU  C14  C  CR16   0  -0.296  -2.8155  -1.1628   0.3832
 3ZU  C15  C  CR16   0  -0.313  -4.1924  -1.2308   0.3801
 3ZU  H1   H  HCH3   0   0.236   6.4032   0.7063  -0.7903
 3ZU  H2   H  HCH3   0   0.236   6.3749   0.3205   0.9464
 3ZU  H3   H  HCH3   0   0.266   7.1562  -0.7857  -0.1983
 3ZU  H4   H  HCR6   0   0.299   4.6441   1.7285   0.3340
 3ZU  H5   H  HCR6   0   0.290   2.3922   2.6924   0.5572
 3ZU  H7   H  HCR6   0   0.286   2.9639  -2.1523  -0.5207
 3ZU  H9   H  HNH2   0   0.388  -6.8388   0.5204  -0.4845
 3ZU  H10  H  HNH2   0   0.388  -6.7647  -1.0839   0.0242
 3ZU  H11  H  HCR6   0   0.261  -4.8642   1.9125  -0.6942
 3ZU  H12  H  HCR6   0   0.257  -2.4472   2.0310  -0.6808
 3ZU  H13  H  HCR6   0   0.255  -2.2630  -2.0359   0.6999
 3ZU  H14  H  HCR6   0   0.262  -4.6806  -2.1478   0.6870
 3ZU  O3   O  O      0  -0.356  -0.0795  -2.2219  -0.5639

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
 3ZU  N2   C7   single    1.364  0.020  1.364
 3ZU  C7   C11  aromatic  1.403  0.020  1.403
 3ZU  C7   C15  aromatic  1.403  0.020  1.403
 3ZU  C11  C12  aromatic  1.379  0.020  1.379
 3ZU  O2   N1   single    1.243  0.020  1.243
 3ZU  C15  C14  aromatic  1.379  0.020  1.379
 3ZU  C12  C13  aromatic  1.403  0.020  1.403
 3ZU  C14  C13  aromatic  1.402  0.020  1.402
 3ZU  C13  C5   single    1.446  0.020  1.446
 3ZU  N1   C5   double    1.323  0.020  1.323
 3ZU  N1   C4   single    1.437  0.020  1.437
 3ZU  C5   C6   single    1.482  0.020  1.482
 3ZU  C4   C3   aromatic  1.366  0.020  1.366
 3ZU  C4   C8   aromatic  1.381  0.020  1.381
 3ZU  C6   O3   double    1.207  0.020  1.207
 3ZU  C6   C8   single    1.485  0.020  1.485
 3ZU  C3   C2   aromatic  1.400  0.020  1.400
 3ZU  C8   C9   aromatic  1.368  0.020  1.368
 3ZU  C2   C10  aromatic  1.394  0.020  1.394
 3ZU  C9   C10  aromatic  1.410  0.020  1.410
 3ZU  C10  O1   single    1.338  0.020  1.338
 3ZU  O1   C1   single    1.417  0.020  1.417
 3ZU  C1   H1   single    0.970  0.020  1.090
 3ZU  C1   H2   single    0.970  0.020  1.090
 3ZU  C1   H3   single    0.970  0.020  1.090
 3ZU  C2   H4   single    0.930  0.020  1.080
 3ZU  C3   H5   single    0.930  0.020  1.080
 3ZU  C9   H7   single    0.930  0.020  1.080
 3ZU  N2   H9   single    0.890  0.020  1.040
 3ZU  N2   H10  single    0.890  0.020  1.040
 3ZU  C11  H11  single    0.930  0.020  1.080
 3ZU  C12  H12  single    0.930  0.020  1.080
 3ZU  C14  H13  single    0.930  0.020  1.080
 3ZU  C15  H14  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
 3ZU  H3   C1   H2   108.94  3.000
 3ZU  H3   C1   H1   108.90  3.000
 3ZU  H2   C1   H1   109.03  3.000
 3ZU  H3   C1   O1   106.35  3.000
 3ZU  H2   C1   O1   111.73  3.000
 3ZU  H1   C1   O1   111.79  3.000
 3ZU  C10  O1   C1   118.94  3.000
 3ZU  H4   C2   C10  120.77  3.000
 3ZU  H4   C2   C3   118.04  3.000
 3ZU  C10  C2   C3   121.19  3.000
 3ZU  H5   C3   C4   122.50  3.000
 3ZU  H5   C3   C2   120.70  3.000
 3ZU  C4   C3   C2   116.80  3.000
 3ZU  N1   C4   C8   108.90  3.000
 3ZU  C8   C4   C3   122.82  3.000
 3ZU  N1   C4   C3   128.27  3.000
 3ZU  C13  C5   N1   125.28  3.000
 3ZU  N1   C5   C6   107.65  3.000
 3ZU  C13  C5   C6   127.06  3.000
 3ZU  O3   C6   C8   127.05  3.000
 3ZU  C8   C6   C5   105.77  3.000
 3ZU  O3   C6   C5   127.17  3.000
 3ZU  C15  C7   C11  117.72  3.000
 3ZU  C15  C7   N2   121.07  3.000
 3ZU  C11  C7   N2   121.17  3.000
 3ZU  C9   C8   C6   132.32  3.000
 3ZU  C9   C8   C4   121.29  3.000
 3ZU  C6   C8   C4   106.39  3.000
 3ZU  H7   C9   C10  120.44  3.000
 3ZU  H7   C9   C8   122.06  3.000
 3ZU  C10  C9   C8   117.50  3.000
 3ZU  C9   C10  C2   120.40  3.000
 3ZU  C9   C10  O1   115.37  3.000
 3ZU  C2   C10  O1   124.23  3.000
 3ZU  O2   N1   C5   128.69  3.000
 3ZU  C5   N1   C4   111.28  3.000
 3ZU  O2   N1   C4   120.03  3.000
 3ZU  H10  N2   H9   113.64  3.000
 3ZU  H10  N2   C7   117.55  3.000
 3ZU  H9   N2   C7   117.62  3.000
 3ZU  H11  C11  C12  119.32  3.000
 3ZU  H11  C11  C7   119.58  3.000
 3ZU  C12  C11  C7   121.10  3.000
 3ZU  H12  C12  C13  120.43  3.000
 3ZU  H12  C12  C11  118.22  3.000
 3ZU  C13  C12  C11  121.33  3.000
 3ZU  C14  C13  C12  117.39  3.000
 3ZU  C14  C13  C5   120.05  3.000
 3ZU  C12  C13  C5   122.56  3.000
 3ZU  H13  C14  C15  118.13  3.000
 3ZU  H13  C14  C13  120.35  3.000
 3ZU  C15  C14  C13  121.51  3.000
 3ZU  H14  C15  C14  119.42  3.000
 3ZU  H14  C15  C7   119.63  3.000
 3ZU  C14  C15  C7   120.94  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
 3ZU  CONST_01  C8   C4   C3   C2      0.00   0.0  0
 3ZU  CONST_02  C8   C9   C10  C2      0.00   0.0  0
 3ZU  CONST_03  C9   C8   C4   C3      0.00   0.0  0
 3ZU  CONST_04  C9   C10  C2   C3      0.00   0.0  0
 3ZU  CONST_05  C10  C2   C3   C4      0.00   0.0  0
 3ZU  CONST_06  C10  C9   C8   C4      0.00   0.0  0
 3ZU  CONST_07  C13  C12  C11  C7      0.00   0.0  0
 3ZU  CONST_08  C13  C14  C15  C7      0.00   0.0  0
 3ZU  CONST_09  C14  C15  C7   C11     0.00   0.0  0
 3ZU  CONST_10  C14  C13  C12  C11     0.00   0.0  0
 3ZU  CONST_11  C15  C7   C11  C12     0.00   0.0  0
 3ZU  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 3ZU  CONST_13  C11  C12  C13  C5    180.00   0.0  0
 3ZU  CONST_14  C15  C14  C13  C5    180.00   0.0  0
 3ZU  CONST_15  C3   C2   C10  O1    180.00   0.0  0
 3ZU  CONST_16  C8   C9   C10  O1    180.00   0.0  0
 3ZU  CONST_17  C12  C11  C7   N2    180.00   0.0  0
 3ZU  CONST_18  C14  C15  C7   N2    180.00   0.0  0
 3ZU  CONST_19  H7   C9   C10  C2    180.00   0.0  0
 3ZU  CONST_20  H4   C2   C3   C4    180.00   0.0  0
 3ZU  CONST_21  H12  C12  C13  C5      0.00   0.0  0
 3ZU  CONST_22  H13  C14  C13  C5      0.00   0.0  0
 3ZU  CONST_23  H5   C3   C4   C8    180.00   0.0  0
 3ZU  CONST_24  H14  C15  C7   C11   180.00   0.0  0
 3ZU  CONST_25  H11  C11  C12  C13   180.00   0.0  0
 3ZU  Var_01    C12  C13  C5   C6   -147.51  30.0  2
 3ZU  Var_02    C2   C10  O1   C1      1.06  30.0  2
 3ZU  Var_03    H1   C1   O1   C10   -62.49  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
 3ZU  plan-1  C5   0.020
 3ZU  plan-1  C7   0.020
 3ZU  plan-1  N2   0.020
 3ZU  plan-1  C11  0.020
 3ZU  plan-1  C12  0.020
 3ZU  plan-1  C13  0.020
 3ZU  plan-1  C14  0.020
 3ZU  plan-1  C15  0.020
 3ZU  plan-1  H11  0.020
 3ZU  plan-1  H12  0.020
 3ZU  plan-1  H13  0.020
 3ZU  plan-1  H14  0.020
 3ZU  plan-2  O1   0.020
 3ZU  plan-2  C2   0.020
 3ZU  plan-2  C3   0.020
 3ZU  plan-2  C4   0.020
 3ZU  plan-2  C5   0.020
 3ZU  plan-2  C6   0.020
 3ZU  plan-2  C8   0.020
 3ZU  plan-2  C9   0.020
 3ZU  plan-2  C10  0.020
 3ZU  plan-2  N1   0.020
 3ZU  plan-2  O2   0.020
 3ZU  plan-2  C13  0.020
 3ZU  plan-2  H4   0.020
 3ZU  plan-2  H5   0.020
 3ZU  plan-2  H7   0.020
 3ZU  plan-2  O3   0.020
 3ZU  plan-3  C7   0.020
 3ZU  plan-3  N2   0.020
 3ZU  plan-3  H9   0.020
 3ZU  plan-3  H10  0.020

