# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 01:25:28 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: 5-methoxy-2-(4-methoxyphenyl)-3H-indol-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)C2=Nc3ccc(OC)cc3C2=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
 3ZV  3ZV  5-methoxy-2-(4-methoxyphenyl)-3H-indol-3-one  ligand  33  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 PERFECT
;

data_comp_3ZV
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
 3ZV  C5   C  CH3   0  -0.467   6.6901   0.2735   0.0800
 3ZV  O4   O  O2    0  -0.415   5.5693  -0.5837   0.0510
 3ZV  C6   C  CR16  0  -0.342   4.0807   1.3271   0.0317
 3ZV  C7   C  CR16  0  -0.396   2.7710   1.8204   0.0196
 3ZV  C8   C  CR56  0   0.445   1.7337   0.9203   0.0178
 3ZV  C10  C  CR5   0   0.088  -0.2942   0.0851   0.0059
 3ZV  C11  C  CR5   0   0.361   0.6785  -1.1060   0.0228
 3ZV  C13  C  CR6   0   0.427  -4.5549  -0.0547  -0.0289
 3ZV  C15  C  CH3   0  -0.444  -6.6868   0.9823   0.0036
 3ZV  C1   C  CR56  0  -0.068   1.9997  -0.4462   0.0265
 3ZV  C2   C  CR16  0  -0.336   3.2713  -0.9556   0.0376
 3ZV  C3   C  CR6   0   0.368   4.3400  -0.0416   0.0406
 3ZV  N9   N  N     0  -0.453   0.3493   1.1955   0.0062
 3ZV  O14  O  O2    0  -0.426  -5.8863  -0.1818  -0.0452
 3ZV  C16  C  CR16  0  -0.322  -3.8784   1.1673  -0.0011
 3ZV  C17  C  CR16  0  -0.243  -2.4972   1.1854   0.0112
 3ZV  C18  C  CR6   0   0.038  -1.7458   0.0068  -0.0043
 3ZV  C19  C  CR16  0  -0.281  -2.4387  -1.2113  -0.0315
 3ZV  C20  C  CR16  0  -0.359  -3.8172  -1.2407  -0.0438
 3ZV  H1   H  HCH3  0   0.209   6.6989   0.9063   0.9711
 3ZV  H2   H  HCH3  0   0.239   7.5682  -0.3658   0.1013
 3ZV  H3   H  HCH3  0   0.182   6.7446   0.9090  -0.8076
 3ZV  H4   H  HCR6  0   0.306   4.8891   2.0444   0.0346
 3ZV  H5   H  HCR6  0   0.274   2.5954   2.8877   0.0119
 3ZV  H6   H  HCH3  0   0.262  -7.7196   0.6462   0.0037
 3ZV  H7   H  HCH3  0   0.139  -6.5080   1.5641   0.9108
 3ZV  H8   H  HCH3  0   0.179  -6.5276   1.6248  -0.8657
 3ZV  H9   H  HCR6  0   0.284   3.4595  -2.0223   0.0432
 3ZV  H10  H  HCR6  0   0.286  -4.4123   2.1075   0.0109
 3ZV  H11  H  HCR6  0   0.249  -1.9860   2.1385   0.0345
 3ZV  H12  H  HCR6  0   0.285  -1.9011  -2.1476  -0.0428
 3ZV  H13  H  HCR6  0   0.274  -4.3398  -2.1883  -0.0643
 3ZV  O12  O  O     0  -0.342   0.4245  -2.2788   0.0292

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
 3ZV  C15  O14  single    1.414  0.020  1.414
 3ZV  C16  C17  aromatic  1.381  0.020  1.381
 3ZV  C16  C13  aromatic  1.397  0.020  1.397
 3ZV  C17  C18  aromatic  1.398  0.020  1.398
 3ZV  O14  C13  single    1.338  0.020  1.338
 3ZV  C13  C20  aromatic  1.397  0.020  1.397
 3ZV  N9   C10  double    1.283  0.020  1.283
 3ZV  N9   C8   single    1.412  0.020  1.412
 3ZV  C18  C10  single    1.454  0.020  1.454
 3ZV  C18  C19  aromatic  1.402  0.020  1.402
 3ZV  C10  C11  single    1.538  0.020  1.538
 3ZV  C8   C7   aromatic  1.373  0.020  1.373
 3ZV  C8   C1   aromatic  1.392  0.020  1.392
 3ZV  C7   C6   aromatic  1.400  0.020  1.400
 3ZV  C11  C1   single    1.477  0.020  1.477
 3ZV  C11  O12  double    1.200  0.020  1.200
 3ZV  C20  C19  aromatic  1.379  0.020  1.379
 3ZV  C1   C2   aromatic  1.370  0.020  1.370
 3ZV  C6   C3   aromatic  1.393  0.020  1.393
 3ZV  C2   C3   aromatic  1.406  0.020  1.406
 3ZV  C3   O4   single    1.344  0.020  1.344
 3ZV  O4   C5   single    1.411  0.020  1.411
 3ZV  C5   H1   single    0.970  0.020  1.090
 3ZV  C5   H2   single    0.970  0.020  1.090
 3ZV  C5   H3   single    0.970  0.020  1.090
 3ZV  C6   H4   single    0.930  0.020  1.080
 3ZV  C7   H5   single    0.930  0.020  1.080
 3ZV  C15  H6   single    0.970  0.020  1.090
 3ZV  C15  H7   single    0.970  0.020  1.090
 3ZV  C15  H8   single    0.970  0.020  1.090
 3ZV  C2   H9   single    0.930  0.020  1.080
 3ZV  C16  H10  single    0.930  0.020  1.080
 3ZV  C17  H11  single    0.930  0.020  1.080
 3ZV  C19  H12  single    0.930  0.020  1.080
 3ZV  C20  H13  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
 3ZV  H3   C5   H2   108.53  3.000
 3ZV  H3   C5   H1   108.96  3.000
 3ZV  H2   C5   H1   108.55  3.000
 3ZV  H3   C5   O4   112.09  3.000
 3ZV  H2   C5   O4   106.55  3.000
 3ZV  H1   C5   O4   112.01  3.000
 3ZV  C3   O4   C5   118.80  3.000
 3ZV  H4   C6   C3   120.85  3.000
 3ZV  H4   C6   C7   117.78  3.000
 3ZV  C3   C6   C7   121.37  3.000
 3ZV  H5   C7   C8   121.60  3.000
 3ZV  H5   C7   C6   119.99  3.000
 3ZV  C8   C7   C6   118.41  3.000
 3ZV  N9   C8   C1   112.26  3.000
 3ZV  C1   C8   C7   119.93  3.000
 3ZV  N9   C8   C7   127.81  3.000
 3ZV  C18  C10  N9   123.18  3.000
 3ZV  C18  C10  C11  126.15  3.000
 3ZV  N9   C10  C11  110.67  3.000
 3ZV  O12  C11  C1   128.75  3.000
 3ZV  O12  C11  C10  128.54  3.000
 3ZV  C1   C11  C10  102.70  3.000
 3ZV  C20  C13  C16  119.16  3.000
 3ZV  C20  C13  O14  116.41  3.000
 3ZV  C16  C13  O14  124.43  3.000
 3ZV  H8   C15  H7   108.89  3.000
 3ZV  H8   C15  H6   108.70  3.000
 3ZV  H7   C15  H6   108.68  3.000
 3ZV  H8   C15  O14  111.98  3.000
 3ZV  H7   C15  O14  112.00  3.000
 3ZV  H6   C15  O14  106.48  3.000
 3ZV  C2   C1   C11  131.63  3.000
 3ZV  C2   C1   C8   122.85  3.000
 3ZV  C11  C1   C8   105.52  3.000
 3ZV  H9   C2   C3   120.53  3.000
 3ZV  H9   C2   C1   121.84  3.000
 3ZV  C3   C2   C1   117.63  3.000
 3ZV  C2   C3   C6   119.81  3.000
 3ZV  C2   C3   O4   115.67  3.000
 3ZV  C6   C3   O4   124.53  3.000
 3ZV  C10  N9   C8   108.85  3.000
 3ZV  C15  O14  C13  119.01  3.000
 3ZV  H10  C16  C17  118.83  3.000
 3ZV  H10  C16  C13  121.45  3.000
 3ZV  C17  C16  C13  119.73  3.000
 3ZV  H11  C17  C18  119.28  3.000
 3ZV  H11  C17  C16  118.96  3.000
 3ZV  C18  C17  C16  121.75  3.000
 3ZV  C19  C18  C17  117.85  3.000
 3ZV  C19  C18  C10  122.72  3.000
 3ZV  C17  C18  C10  119.42  3.000
 3ZV  H12  C19  C20  118.63  3.000
 3ZV  H12  C19  C18  120.51  3.000
 3ZV  C20  C19  C18  120.86  3.000
 3ZV  H13  C20  C19  120.10  3.000
 3ZV  H13  C20  C13  119.25  3.000
 3ZV  C19  C20  C13  120.65  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
 3ZV  CONST_01  C1   C8   C7   C6      0.00   0.0  0
 3ZV  CONST_02  C1   C2   C3   C6      0.00   0.0  0
 3ZV  CONST_03  C2   C1   C8   C7      0.00   0.0  0
 3ZV  CONST_04  C2   C3   C6   C7      0.00   0.0  0
 3ZV  CONST_05  C3   C6   C7   C8      0.00   0.0  0
 3ZV  CONST_06  C3   C2   C1   C8      0.00   0.0  0
 3ZV  CONST_07  C18  C17  C16  C13     0.00   0.0  0
 3ZV  CONST_08  C18  C19  C20  C13     0.00   0.0  0
 3ZV  CONST_09  C19  C18  C17  C16     0.00   0.0  0
 3ZV  CONST_10  C19  C20  C13  C16     0.00   0.0  0
 3ZV  CONST_11  C20  C13  C16  C17     0.00   0.0  0
 3ZV  CONST_12  C20  C19  C18  C17     0.00   0.0  0
 3ZV  CONST_13  C16  C17  C18  C10   180.00   0.0  0
 3ZV  CONST_14  C20  C19  C18  C10   180.00   0.0  0
 3ZV  CONST_15  C7   C6   C3   O4    180.00   0.0  0
 3ZV  CONST_16  C1   C2   C3   O4    180.00   0.0  0
 3ZV  CONST_17  C17  C16  C13  O14   180.00   0.0  0
 3ZV  CONST_18  C19  C20  C13  O14   180.00   0.0  0
 3ZV  CONST_19  H9   C2   C3   C6    180.00   0.0  0
 3ZV  CONST_20  H4   C6   C7   C8    180.00   0.0  0
 3ZV  CONST_21  H11  C17  C18  C10     0.00   0.0  0
 3ZV  CONST_22  H12  C19  C18  C10     0.00   0.0  0
 3ZV  CONST_23  H5   C7   C8   C1    180.00   0.0  0
 3ZV  CONST_24  H13  C20  C13  C16   180.00   0.0  0
 3ZV  CONST_25  H10  C16  C17  C18   180.00   0.0  0
 3ZV  Var_01    C17  C18  C10  C11   178.55  30.0  3
 3ZV  Var_02    C6   C3   O4   C5      1.24  30.0  1
 3ZV  Var_03    C16  C13  O14  C15    -1.74  30.0  2
 3ZV  Var_04    H6   C15  O14  C13  -178.68  30.0  3
 3ZV  Var_05    H1   C5   O4   C3     60.47  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
 3ZV  plan-1  C10  0.020
 3ZV  plan-1  C13  0.020
 3ZV  plan-1  O14  0.020
 3ZV  plan-1  C16  0.020
 3ZV  plan-1  C17  0.020
 3ZV  plan-1  C18  0.020
 3ZV  plan-1  C19  0.020
 3ZV  plan-1  C20  0.020
 3ZV  plan-1  H10  0.020
 3ZV  plan-1  H11  0.020
 3ZV  plan-1  H12  0.020
 3ZV  plan-1  H13  0.020
 3ZV  plan-2  O4   0.020
 3ZV  plan-2  C6   0.020
 3ZV  plan-2  C7   0.020
 3ZV  plan-2  C8   0.020
 3ZV  plan-2  C10  0.020
 3ZV  plan-2  C11  0.020
 3ZV  plan-2  C1   0.020
 3ZV  plan-2  C2   0.020
 3ZV  plan-2  C3   0.020
 3ZV  plan-2  N9   0.020
 3ZV  plan-2  C18  0.020
 3ZV  plan-2  H4   0.020
 3ZV  plan-2  H5   0.020
 3ZV  plan-2  H9   0.020
 3ZV  plan-2  O12  0.020

