# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 06:21:56 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 1-[(4-methoxyphenyl)methyl]-~{N}-oxidanyl-indole-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Cn2ccc3ccc(cc23)C(=O)NO)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
 GKW  GKW  1-[(4-methoxyphenyl)methyl]-~{N}-oxidanyl-indole-6-carboxamide  ligand  38  22  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GKW
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
 GKW  C01  C  CH3   0  -0.437   5.0515   2.1955   1.6527
 GKW  O02  O  O2    0  -0.470   4.2715   2.4475   0.5007
 GKW  C03  C  CR6   0   0.374   3.5426   1.4404  -0.0159
 GKW  C04  C  CR16  0  -0.331   2.7850   1.7387  -1.1486
 GKW  C05  C  CR16  0  -0.294   2.0050   0.7604  -1.7398
 GKW  C06  C  CR6   0   0.092   1.9588  -0.5336  -1.2293
 GKW  C07  C  CH2   0  -0.405   1.1113  -1.5919  -1.8883
 GKW  N08  N  NR5   0  -0.518   0.2073  -2.2410  -0.9646
 GKW  C09  C  CR15  0  -0.017   0.3327  -3.5131  -0.4806
 GKW  C10  C  CR15  0  -0.429  -0.6501  -3.7762   0.4308
 GKW  C11  C  CR56  0   0.057  -1.4372  -2.5921   0.5275
 GKW  C12  C  CR16  0  -0.333  -2.5715  -2.2273   1.2604
 GKW  C13  C  CR16  0  -0.302  -3.0912  -0.9595   1.1080
 GKW  C14  C  CR6   0  -0.077  -2.5047  -0.0285   0.2261
 GKW  C15  C  C     0   0.495  -3.0597   1.3396   0.0232
 GKW  O16  O  O     0  -0.476  -2.9270   1.9527  -1.0246
 GKW  N17  N  NH1   0  -0.383  -3.6886   1.8555   1.0953
 GKW  O18  O  OH1   0  -0.540  -4.3564   3.0356   0.9975
 GKW  C19  C  CR16  0  -0.323  -1.3926  -0.3751  -0.5260
 GKW  C20  C  CR56  0   0.404  -0.8673  -1.6495  -0.3594
 GKW  C21  C  CR16  0  -0.268   2.7185  -0.8198  -0.1026
 GKW  C22  C  CR16  0  -0.369   3.5037   0.1487   0.5079
 GKW  H1   H  HCH3  0   0.229   4.4361   1.8990   2.5063
 GKW  H2   H  HCH3  0   0.229   5.8041   1.4227   1.4754
 GKW  H3   H  HCH3  0   0.260   5.5573   3.1272   1.8931
 GKW  H4   H  HCR6  0   0.263   2.8060   2.7414  -1.5571
 GKW  H5   H  HCR6  0   0.257   1.4213   1.0143  -2.6175
 GKW  H6   H  HCH2  0   0.278   0.5376  -1.1543  -2.7080
 GKW  H7   H  HCH2  0   0.287   1.7347  -2.3711  -2.3292
 GKW  H8   H  HCR5  0   0.292   1.1282  -4.1498  -0.8362
 GKW  H9   H  HCR5  0   0.252  -0.7929  -4.7032   0.9624
 GKW  H10  H  HCR6  0   0.255  -3.0449  -2.9306   1.9333
 GKW  H11  H  HCR6  0   0.253  -3.9864  -0.6990   1.6580
 GKW  H12  H  HNH1  0   0.421  -3.7478   1.3988   1.9930
 GKW  H13  H  HOH1  0   0.477  -3.7163   3.7324   1.1964
 GKW  H14  H  HCR6  0   0.265  -0.9518   0.3362  -1.2119
 GKW  H15  H  HCR6  0   0.255   2.7070  -1.8170   0.3224
 GKW  H16  H  HCR6  0   0.280   4.0751  -0.1216   1.3856

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
 GKW  C12  C13  aromatic  1.379  0.020  1.379
 GKW  C12  C11  aromatic  1.399  0.020  1.399
 GKW  C10  C11  aromatic  1.425  0.020  1.425
 GKW  C10  C09  aromatic  1.366  0.020  1.366
 GKW  C13  C14  aromatic  1.410  0.020  1.410
 GKW  C11  C20  aromatic  1.414  0.020  1.414
 GKW  C09  N08  aromatic  1.367  0.020  1.367
 GKW  N17  O18  single    1.359  0.020  1.359
 GKW  N17  C15  single    1.346  0.020  1.346
 GKW  C20  N08  aromatic  1.368  0.020  1.368
 GKW  C20  C19  aromatic  1.389  0.020  1.389
 GKW  C14  C19  aromatic  1.387  0.020  1.387
 GKW  C14  C15  single    1.490  0.020  1.490
 GKW  N08  C07  single    1.446  0.020  1.446
 GKW  C15  O16  double    1.221  0.020  1.221
 GKW  C07  C06  single    1.508  0.020  1.508
 GKW  C06  C21  aromatic  1.389  0.020  1.389
 GKW  C06  C05  aromatic  1.392  0.020  1.392
 GKW  C21  C22  aromatic  1.388  0.020  1.388
 GKW  C05  C04  aromatic  1.384  0.020  1.384
 GKW  C22  C03  aromatic  1.394  0.020  1.394
 GKW  C04  C03  aromatic  1.395  0.020  1.395
 GKW  C03  O02  single    1.346  0.020  1.346
 GKW  O02  C01  single    1.414  0.020  1.414
 GKW  C01  H1   single    0.970  0.020  1.090
 GKW  C01  H2   single    0.970  0.020  1.090
 GKW  C01  H3   single    0.970  0.020  1.090
 GKW  C04  H4   single    0.930  0.020  1.080
 GKW  C05  H5   single    0.930  0.020  1.080
 GKW  C07  H6   single    0.970  0.020  1.090
 GKW  C07  H7   single    0.970  0.020  1.090
 GKW  C09  H8   single    0.930  0.020  1.080
 GKW  C10  H9   single    0.930  0.020  1.080
 GKW  C12  H10  single    0.930  0.020  1.080
 GKW  C13  H11  single    0.930  0.020  1.080
 GKW  N17  H12  single    0.860  0.020  1.020
 GKW  O18  H13  single    0.850  0.020  0.980
 GKW  C19  H14  single    0.930  0.020  1.080
 GKW  C21  H15  single    0.930  0.020  1.080
 GKW  C22  H16  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
 GKW  H3   C01  H2   108.75  3.000
 GKW  H3   C01  H1   108.76  3.000
 GKW  H2   C01  H1   108.81  3.000
 GKW  H3   C01  O02  106.50  3.000
 GKW  H2   C01  O02  111.95  3.000
 GKW  H1   C01  O02  111.96  3.000
 GKW  C03  O02  C01  118.55  3.000
 GKW  C22  C03  C04  119.20  3.000
 GKW  C04  C03  O02  116.46  3.000
 GKW  C22  C03  O02  124.33  3.000
 GKW  H4   C04  C05  120.29  3.000
 GKW  H4   C04  C03  119.59  3.000
 GKW  C05  C04  C03  120.12  3.000
 GKW  H5   C05  C06  119.79  3.000
 GKW  H5   C05  C04  118.93  3.000
 GKW  C06  C05  C04  121.29  3.000
 GKW  C21  C06  C07  121.17  3.000
 GKW  C21  C06  C05  118.10  3.000
 GKW  C07  C06  C05  120.73  3.000
 GKW  H7   C07  H6   106.44  3.000
 GKW  H7   C07  N08  107.14  3.000
 GKW  H6   C07  N08  109.33  3.000
 GKW  H7   C07  C06  110.90  3.000
 GKW  H6   C07  C06  110.01  3.000
 GKW  N08  C07  C06  112.79  3.000
 GKW  C20  N08  C09  108.53  3.000
 GKW  C20  N08  C07  125.42  3.000
 GKW  C09  N08  C07  125.91  3.000
 GKW  H8   C09  C10  129.53  3.000
 GKW  H8   C09  N08  120.00  3.000
 GKW  C10  C09  N08  110.46  3.000
 GKW  H9   C10  C11  127.43  3.000
 GKW  H9   C10  C09  126.16  3.000
 GKW  C11  C10  C09  106.42  3.000
 GKW  C20  C11  C12  118.79  3.000
 GKW  C20  C11  C10  106.78  3.000
 GKW  C12  C11  C10  134.43  3.000
 GKW  H10  C12  C13  120.09  3.000
 GKW  H10  C12  C11  120.73  3.000
 GKW  C13  C12  C11  119.18  3.000
 GKW  H11  C13  C14  120.19  3.000
 GKW  H11  C13  C12  118.49  3.000
 GKW  C14  C13  C12  121.30  3.000
 GKW  C19  C14  C15  117.02  3.000
 GKW  C15  C14  C13  122.44  3.000
 GKW  C19  C14  C13  120.52  3.000
 GKW  N17  C15  O16  122.81  3.000
 GKW  O16  C15  C14  122.50  3.000
 GKW  N17  C15  C14  114.68  3.000
 GKW  H12  N17  O18  115.35  3.000
 GKW  H12  N17  C15  124.24  3.000
 GKW  O18  N17  C15  120.33  3.000
 GKW  H13  O18  N17  106.60  3.000
 GKW  H14  C19  C20  121.69  3.000
 GKW  H14  C19  C14  120.42  3.000
 GKW  C20  C19  C14  117.89  3.000
 GKW  C19  C20  C11  122.31  3.000
 GKW  C19  C20  N08  129.87  3.000
 GKW  C11  C20  N08  107.81  3.000
 GKW  H15  C21  C22  118.38  3.000
 GKW  H15  C21  C06  120.13  3.000
 GKW  C22  C21  C06  121.50  3.000
 GKW  H16  C22  C21  118.77  3.000
 GKW  H16  C22  C03  121.44  3.000
 GKW  C21  C22  C03  119.79  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
 GKW  CONST_01  C06  C21  C22  C03     0.00   0.0  0
 GKW  CONST_02  C06  C05  C04  C03     0.00   0.0  0
 GKW  CONST_03  C21  C06  C05  C04     0.00   0.0  0
 GKW  CONST_04  C21  C22  C03  C04     0.00   0.0  0
 GKW  CONST_05  C22  C21  C06  C05     0.00   0.0  0
 GKW  CONST_06  C22  C03  C04  C05     0.00   0.0  0
 GKW  CONST_07  C11  C10  C09  N08     0.00   0.0  0
 GKW  CONST_08  C12  C11  C20  N08   180.00   0.0  0
 GKW  CONST_09  C10  C11  C20  N08     0.00   0.0  0
 GKW  CONST_10  C14  C19  C20  N08   180.00   0.0  0
 GKW  CONST_11  C12  C11  C10  C09   180.00   0.0  0
 GKW  CONST_12  C20  C11  C10  C09     0.00   0.0  0
 GKW  CONST_13  C11  C20  N08  C09     0.00   0.0  0
 GKW  CONST_14  C19  C20  N08  C09   180.00   0.0  0
 GKW  CONST_15  C13  C12  C11  C10   180.00   0.0  0
 GKW  CONST_16  C19  C20  C11  C10   180.00   0.0  0
 GKW  CONST_17  C20  N08  C09  C10     0.00   0.0  0
 GKW  CONST_18  C14  C13  C12  C11     0.00   0.0  0
 GKW  CONST_19  C14  C19  C20  C11     0.00   0.0  0
 GKW  CONST_20  C19  C14  C13  C12     0.00   0.0  0
 GKW  CONST_21  C19  C20  C11  C12     0.00   0.0  0
 GKW  CONST_22  C20  C11  C12  C13     0.00   0.0  0
 GKW  CONST_23  C20  C19  C14  C13     0.00   0.0  0
 GKW  CONST_24  C21  C22  C03  O02   180.00   0.0  0
 GKW  CONST_25  C05  C04  C03  O02   180.00   0.0  0
 GKW  CONST_26  C07  C06  C05  C04   180.00   0.0  0
 GKW  CONST_27  C10  C09  N08  C07   180.00   0.0  0
 GKW  CONST_28  C11  C20  N08  C07   180.00   0.0  0
 GKW  CONST_29  C19  C20  N08  C07     0.00   0.0  0
 GKW  CONST_30  C22  C21  C06  C07   180.00   0.0  0
 GKW  CONST_31  C15  C14  C13  C12   180.00   0.0  0
 GKW  CONST_32  C20  C19  C14  C15   180.00   0.0  0
 GKW  CONST_33  H15  C21  C22  C03   180.00   0.0  0
 GKW  CONST_34  H5   C05  C04  C03   180.00   0.0  0
 GKW  CONST_35  H16  C22  C03  C04   180.00   0.0  0
 GKW  CONST_36  H4   C04  C05  C06   180.00   0.0  0
 GKW  CONST_37  H9   C10  C09  N08   180.00   0.0  0
 GKW  CONST_38  H14  C19  C20  N08     0.00   0.0  0
 GKW  CONST_39  H10  C12  C11  C10     0.00   0.0  0
 GKW  CONST_40  H11  C13  C12  C11   180.00   0.0  0
 GKW  CONST_41  H8   C09  C10  C11   180.00   0.0  0
 GKW  CONST_42  O18  N17  C15  C14   180.00   0.0  0
 GKW  CONST_43  H12  N17  C15  C14     0.00   0.0  0
 GKW  CONST_44  O18  N17  C15  O16     0.00   0.0  0
 GKW  Var_01    N08  C07  C06  C05  -126.76  30.0  3
 GKW  Var_02    C09  N08  C07  C06  -107.12  30.0  2
 GKW  Var_03    C22  C03  O02  C01    -0.18  30.0  2
 GKW  Var_04    N17  C15  C14  C13    30.11  30.0  2
 GKW  Var_05    H1   C01  O02  C03   -61.66  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
 GKW  plan-1  O02  0.020
 GKW  plan-1  C03  0.020
 GKW  plan-1  C04  0.020
 GKW  plan-1  C05  0.020
 GKW  plan-1  C06  0.020
 GKW  plan-1  C07  0.020
 GKW  plan-1  C21  0.020
 GKW  plan-1  C22  0.020
 GKW  plan-1  H4   0.020
 GKW  plan-1  H5   0.020
 GKW  plan-1  H15  0.020
 GKW  plan-1  H16  0.020
 GKW  plan-2  C07  0.020
 GKW  plan-2  N08  0.020
 GKW  plan-2  C09  0.020
 GKW  plan-2  C10  0.020
 GKW  plan-2  C11  0.020
 GKW  plan-2  C12  0.020
 GKW  plan-2  C13  0.020
 GKW  plan-2  C14  0.020
 GKW  plan-2  C15  0.020
 GKW  plan-2  C19  0.020
 GKW  plan-2  C20  0.020
 GKW  plan-2  H8   0.020
 GKW  plan-2  H9   0.020
 GKW  plan-2  H10  0.020
 GKW  plan-2  H11  0.020
 GKW  plan-2  H14  0.020
 GKW  plan-3  C14  0.020
 GKW  plan-3  C15  0.020
 GKW  plan-3  O16  0.020
 GKW  plan-3  N17  0.020
 GKW  plan-3  O18  0.020
 GKW  plan-3  H12  0.020

