# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 16:07:45 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: ~{N}-oxidanyl-1-(phenylmethyl)pyrrolo[2,3-b]pyridine-4-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1ccnc2n(Cc3ccccc3)ccc12
#
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
 EYL  EYL  ~{N}-oxidanyl-1-(phenylmethyl)pyrrolo[2,3-b]pyridine-4-carboxamide  ligand  33  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EYL
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
 EYL  C4   C  CH2   0  -0.394   0.6116   -9.1373  10.4981
 EYL  C6   C  CR16  0  -0.285   2.7330   -9.8317  11.6715
 EYL  C8   C  CR16  0  -0.265   4.7484  -10.3122  10.4466
 EYL  C2   C  CR56  0   0.029   0.3237   -5.9447  12.2480
 EYL  C1   C  CR6   0  -0.019   0.6164   -4.5797  12.1829
 EYL  C11  C  CR15  0   0.014  -0.2199   -8.0773  12.6204
 EYL  C10  C  CR16  0  -0.308   2.7573   -9.6277   9.2827
 EYL  C9   C  CR16  0  -0.238   4.0907  -10.0188   9.2608
 EYL  C7   C  CR16  0  -0.238   4.0654  -10.2164  11.6535
 EYL  C14  C  CR16  0  -0.387   1.2125   -4.1096  11.0208
 EYL  C13  C  CR16  0  -0.080   1.5104   -4.9919   9.9779
 EYL  C12  C  CR15  0  -0.470  -0.2582   -6.8387  13.1923
 EYL  O    O  O     0  -0.454  -0.7966   -3.8452  13.9453
 EYL  C    C  C     0   0.480   0.2339   -3.6862  13.3163
 EYL  N    N  NH1   0  -0.370   1.1389   -2.7305  13.5875
 EYL  O1   O  OH1   0  -0.534   0.8539   -1.7535  14.4881
 EYL  N2   N  N     0  -0.419   1.2638   -6.2918  10.0154
 EYL  C3   C  CR56  0   0.506   0.6919   -6.7248  11.1244
 EYL  N1   N  NR5   0  -0.505   0.3436   -8.0184  11.3742
 EYL  C5   C  CR6   0   0.120   2.0665   -9.5354  10.4848
 EYL  H1   H  HCH2  0   0.280   0.2810   -8.8844   9.4902
 EYL  H2   H  HCH2  0   0.286  -0.0085   -9.9684  10.8372
 EYL  H3   H  HCR6  0   0.253   2.2103   -9.7638  12.6187
 EYL  H4   H  HCR6  0   0.255   5.7881  -10.6125  10.4330
 EYL  H5   H  HCR5  0   0.296  -0.5669   -9.0217  13.0105
 EYL  H7   H  HCR6  0   0.253   2.2507   -9.3917   8.3543
 EYL  H8   H  HCR6  0   0.255   4.6162  -10.0866   8.3170
 EYL  H9   H  HCR6  0   0.255   4.5716  -10.4446  12.5827
 EYL  H10  H  HCR6  0   0.272   1.4336   -3.0590  10.8856
 EYL  H11  H  HCR6  0   0.262   1.9682   -4.6112   9.0724
 EYL  H12  H  HCR5  0   0.250  -0.6635   -6.6052  14.1618
 EYL  H14  H  HNH1  0   0.423   1.9981   -2.6097  13.0704
 EYL  H15  H  HOH1  0   0.477   1.1925   -2.0594  15.3410

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
 EYL  C9   C10  aromatic  1.390  0.020  1.390
 EYL  C9   C8   aromatic  1.387  0.020  1.387
 EYL  C10  C5   aromatic  1.390  0.020  1.390
 EYL  C8   C7   aromatic  1.390  0.020  1.390
 EYL  C5   C4   single    1.508  0.020  1.508
 EYL  C5   C6   aromatic  1.393  0.020  1.393
 EYL  C4   N1   single    1.446  0.020  1.446
 EYL  N2   C13  aromatic  1.324  0.020  1.324
 EYL  N2   C3   aromatic  1.321  0.020  1.321
 EYL  C13  C14  aromatic  1.398  0.020  1.398
 EYL  C7   C6   aromatic  1.387  0.020  1.387
 EYL  N1   C3   aromatic  1.363  0.020  1.363
 EYL  N1   C11  aromatic  1.369  0.020  1.369
 EYL  C3   C2   aromatic  1.417  0.020  1.417
 EYL  C14  C1   aromatic  1.388  0.020  1.388
 EYL  C11  C12  aromatic  1.365  0.020  1.365
 EYL  C2   C1   aromatic  1.397  0.020  1.397
 EYL  C2   C12  aromatic  1.425  0.020  1.425
 EYL  C1   C    single    1.493  0.020  1.493
 EYL  N    C    single    1.344  0.020  1.344
 EYL  N    O1   single    1.359  0.020  1.359
 EYL  C    O    double    1.218  0.020  1.218
 EYL  C4   H1   single    0.970  0.020  1.090
 EYL  C4   H2   single    0.970  0.020  1.090
 EYL  C6   H3   single    0.930  0.020  1.080
 EYL  C8   H4   single    0.930  0.020  1.080
 EYL  C11  H5   single    0.930  0.020  1.080
 EYL  C10  H7   single    0.930  0.020  1.080
 EYL  C9   H8   single    0.930  0.020  1.080
 EYL  C7   H9   single    0.930  0.020  1.080
 EYL  C14  H10  single    0.930  0.020  1.080
 EYL  C13  H11  single    0.930  0.020  1.080
 EYL  C12  H12  single    0.930  0.020  1.080
 EYL  N    H14  single    0.860  0.020  1.020
 EYL  O1   H15  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
 EYL  H2   C4   H1   106.95  3.000
 EYL  H2   C4   C5   110.48  3.000
 EYL  H1   C4   C5   110.22  3.000
 EYL  H2   C4   N1   107.20  3.000
 EYL  H1   C4   N1   108.92  3.000
 EYL  C5   C4   N1   112.85  3.000
 EYL  H3   C6   C5   120.03  3.000
 EYL  H3   C6   C7   119.47  3.000
 EYL  C5   C6   C7   120.51  3.000
 EYL  H4   C8   C7   120.13  3.000
 EYL  H4   C8   C9   120.23  3.000
 EYL  C7   C8   C9   119.64  3.000
 EYL  C3   C2   C12  106.64  3.000
 EYL  C12  C2   C1   136.83  3.000
 EYL  C3   C2   C1   116.52  3.000
 EYL  C    C1   C14  122.87  3.000
 EYL  C    C1   C2   119.70  3.000
 EYL  C14  C1   C2   117.37  3.000
 EYL  H5   C11  N1   119.94  3.000
 EYL  H5   C11  C12  129.33  3.000
 EYL  N1   C11  C12  110.73  3.000
 EYL  H7   C10  C5   119.62  3.000
 EYL  H7   C10  C9   119.76  3.000
 EYL  C5   C10  C9   120.62  3.000
 EYL  H8   C9   C10  119.81  3.000
 EYL  H8   C9   C8   120.12  3.000
 EYL  C10  C9   C8   120.06  3.000
 EYL  H9   C7   C8   120.07  3.000
 EYL  H9   C7   C6   119.77  3.000
 EYL  C8   C7   C6   120.16  3.000
 EYL  H10  C14  C13  118.42  3.000
 EYL  H10  C14  C1   121.42  3.000
 EYL  C13  C14  C1   120.15  3.000
 EYL  H11  C13  N2   116.58  3.000
 EYL  H11  C13  C14  119.44  3.000
 EYL  N2   C13  C14  123.98  3.000
 EYL  H12  C12  C11  125.79  3.000
 EYL  H12  C12  C2   127.93  3.000
 EYL  C11  C12  C2   106.28  3.000
 EYL  N    C    O    123.96  3.000
 EYL  O    C    C1   122.06  3.000
 EYL  N    C    C1   113.97  3.000
 EYL  H14  N    O1   115.57  3.000
 EYL  H14  N    C    123.68  3.000
 EYL  O1   N    C    120.25  3.000
 EYL  H15  O1   N    106.47  3.000
 EYL  C3   N2   C13  115.24  3.000
 EYL  N1   C3   N2   125.15  3.000
 EYL  N1   C3   C2   108.12  3.000
 EYL  N2   C3   C2   126.73  3.000
 EYL  C3   N1   C11  108.23  3.000
 EYL  C11  N1   C4   126.48  3.000
 EYL  C3   N1   C4   125.17  3.000
 EYL  C10  C5   C6   119.02  3.000
 EYL  C6   C5   C4   120.67  3.000
 EYL  C10  C5   C4   120.31  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
 EYL  CONST_01  C9   C10  C5   C6      0.00   0.0  0
 EYL  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 EYL  CONST_03  C5   C10  C9   C8      0.00   0.0  0
 EYL  CONST_04  C5   C6   C7   C8      0.00   0.0  0
 EYL  CONST_05  C13  N2   C3   C2      0.00   0.0  0
 EYL  CONST_06  C11  N1   C3   C2      0.00   0.0  0
 EYL  CONST_07  C13  C14  C1   C2      0.00   0.0  0
 EYL  CONST_08  N1   C11  C12  C2      0.00   0.0  0
 EYL  CONST_09  N2   C13  C14  C1      0.00   0.0  0
 EYL  CONST_10  N2   C3   C2   C1      0.00   0.0  0
 EYL  CONST_11  N1   C3   C2   C1    180.00   0.0  0
 EYL  CONST_12  C11  C12  C2   C1    180.00   0.0  0
 EYL  CONST_13  N2   C3   N1   C11   180.00   0.0  0
 EYL  CONST_14  C3   C2   C12  C11     0.00   0.0  0
 EYL  CONST_15  C7   C8   C9   C10     0.00   0.0  0
 EYL  CONST_16  C7   C6   C5   C10     0.00   0.0  0
 EYL  CONST_17  C3   N2   C13  C14     0.00   0.0  0
 EYL  CONST_18  C3   C2   C1   C14     0.00   0.0  0
 EYL  CONST_19  C12  C2   C1   C14   180.00   0.0  0
 EYL  CONST_20  N1   C3   N2   C13   180.00   0.0  0
 EYL  CONST_21  C3   N1   C11  C12     0.00   0.0  0
 EYL  CONST_22  N2   C3   C2   C12   180.00   0.0  0
 EYL  CONST_23  N1   C3   C2   C12     0.00   0.0  0
 EYL  CONST_24  C9   C10  C5   C4    180.00   0.0  0
 EYL  CONST_25  C7   C6   C5   C4    180.00   0.0  0
 EYL  CONST_26  N2   C3   N1   C4      0.00   0.0  0
 EYL  CONST_27  C2   C3   N1   C4    180.00   0.0  0
 EYL  CONST_28  C12  C11  N1   C4    180.00   0.0  0
 EYL  CONST_29  C    C1   C14  C13   180.00   0.0  0
 EYL  CONST_30  C    C1   C2   C12     0.00   0.0  0
 EYL  CONST_31  C3   C2   C1   C     180.00   0.0  0
 EYL  CONST_32  H7   C10  C5   C6    180.00   0.0  0
 EYL  CONST_33  H4   C8   C7   C6    180.00   0.0  0
 EYL  CONST_34  H3   C6   C7   C8    180.00   0.0  0
 EYL  CONST_35  H10  C14  C1   C2    180.00   0.0  0
 EYL  CONST_36  H5   C11  C12  C2    180.00   0.0  0
 EYL  CONST_37  H11  C13  C14  C1    180.00   0.0  0
 EYL  CONST_38  H12  C12  C2   C1      0.00   0.0  0
 EYL  CONST_39  H9   C7   C8   C9    180.00   0.0  0
 EYL  CONST_40  H8   C9   C8   C7    180.00   0.0  0
 EYL  CONST_41  O1   N    C    C1    180.00   0.0  0
 EYL  CONST_42  H14  N    C    C1      0.00   0.0  0
 EYL  CONST_43  O1   N    C    O       0.00   0.0  0
 EYL  Var_01    N1   C4   C5   C6     54.44  30.0  2
 EYL  Var_02    C5   C4   N1   C11  -102.70  30.0  2
 EYL  Var_03    N    C    C1   C2    141.94  30.0  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
 EYL  plan-1  C4   0.020
 EYL  plan-1  C6   0.020
 EYL  plan-1  C8   0.020
 EYL  plan-1  C10  0.020
 EYL  plan-1  C9   0.020
 EYL  plan-1  C7   0.020
 EYL  plan-1  C5   0.020
 EYL  plan-1  H3   0.020
 EYL  plan-1  H4   0.020
 EYL  plan-1  H7   0.020
 EYL  plan-1  H8   0.020
 EYL  plan-1  H9   0.020
 EYL  plan-2  C4   0.020
 EYL  plan-2  C2   0.020
 EYL  plan-2  C1   0.020
 EYL  plan-2  C11  0.020
 EYL  plan-2  C14  0.020
 EYL  plan-2  C13  0.020
 EYL  plan-2  C12  0.020
 EYL  plan-2  C    0.020
 EYL  plan-2  N2   0.020
 EYL  plan-2  C3   0.020
 EYL  plan-2  N1   0.020
 EYL  plan-2  H5   0.020
 EYL  plan-2  H10  0.020
 EYL  plan-2  H11  0.020
 EYL  plan-2  H12  0.020
 EYL  plan-3  C1   0.020
 EYL  plan-3  O    0.020
 EYL  plan-3  C    0.020
 EYL  plan-3  N    0.020
 EYL  plan-3  O1   0.020
 EYL  plan-3  H14  0.020

