# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 16:54:32 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: 1-[(3-methoxyphenyl)methyl]-~{N}-oxidanyl-pyrrolo[2,3-b]pyridine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(Cn2ccc3cc(cnc23)C(=O)NO)c1
#
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
 EYF  EYF  1-[(3-methoxyphenyl)methyl]-~{N}-oxidanyl-pyrrolo[2,3-b]pyridine-5-carboxamide  ligand  37  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EYF
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
 EYF  C8   C  CH3   0  -0.437   3.7800  -11.8917   7.6243
 EYF  C5   C  CR6   0   0.105   1.9480   -9.9986  10.8960
 EYF  C6   C  CR16  0  -0.429   2.5307  -10.6186   9.7912
 EYF  N1   N  N     0  -0.422   1.0410   -6.6761  10.7208
 EYF  C2   C  CR16  0  -0.080   1.2100   -5.3755  10.8685
 EYF  C4   C  CH2   0  -0.353   0.4988   -9.5856  10.7852
 EYF  O    O  O     0  -0.452   1.1362   -2.5301  10.9626
 EYF  N    N  NH1   0  -0.387   1.1177   -2.6311  13.2266
 EYF  O1   O  OH1   0  -0.536   1.5136   -1.3294  13.3359
 EYF  C1   C  CR6   0  -0.175   0.7675   -4.6417  11.9837
 EYF  C15  C  CR16  0  -0.255   0.0821   -5.2957  13.0013
 EYF  C14  C  CR56  0   0.047  -0.1183   -6.6636  12.8716
 EYF  C3   C  CR56  0   0.496   0.3942   -7.2780  11.7061
 EYF  C13  C  CR15  0  -0.440  -0.7444   -7.6928  13.6365
 EYF  C12  C  CR15  0   0.003  -0.5857   -8.8453  12.9270
 EYF  N2   N  NR5   0  -0.514   0.0942   -8.6029  11.7582
 EYF  C11  C  CR16  0  -0.324   2.6850   -9.8127  12.0549
 EYF  C10  C  CR16  0  -0.224   4.0050  -10.2521  12.1023
 EYF  C9   C  CR16  0  -0.349   4.5901  -10.8716  11.0153
 EYF  C7   C  CR6   0   0.399   3.8488  -11.0593   9.8455
 EYF  O2   O  O2    0  -0.468   4.4870  -11.6638   8.8259
 EYF  H1   H  HCH3  0   0.259   4.4721  -12.3887   6.9488
 EYF  H2   H  HCH3  0   0.227   2.9125  -12.5397   7.7757
 EYF  H3   H  HCH3  0   0.228   3.4467  -10.9593   7.1610
 EYF  H4   H  HCR6  0   0.275   1.9360  -10.7440   8.8944
 EYF  H5   H  HCR6  0   0.264   1.7351   -4.8652  10.0700
 EYF  H6   H  HCH2  0   0.278   0.2990   -9.1944   9.7865
 EYF  H7   H  HCH2  0   0.290  -0.1448  -10.4581  10.9110
 EYF  H8   H  HNH1  0   0.414   1.3749   -3.1957  14.0247
 EYF  H9   H  HOH1  0   0.476   0.7108   -0.8252  13.5207
 EYF  H10  H  HCR6  0   0.271  -0.3077   -4.7623  13.8599
 EYF  H11  H  HCR5  0   0.256  -1.2469   -7.5932  14.5847
 EYF  H13  H  HCR5  0   0.296  -0.9106   -9.8469  13.1626
 EYF  H15  H  HCR6  0   0.249   2.2501   -9.3321  12.9217
 EYF  H16  H  HCR6  0   0.256   4.5849  -10.1078  13.0049
 EYF  H17  H  HCR6  0   0.259   5.6178  -11.2103  11.0586
 EYF  C    C  C     0   0.495   1.0318   -3.1768  11.9880

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
 EYF  C8   O2   single    1.413  0.020  1.413
 EYF  O2   C7   single    1.346  0.020  1.346
 EYF  C7   C6   aromatic  1.391  0.020  1.391
 EYF  C7   C9   aromatic  1.398  0.020  1.398
 EYF  C6   C5   aromatic  1.395  0.020  1.395
 EYF  C9   C10  aromatic  1.381  0.020  1.381
 EYF  C4   C5   single    1.511  0.020  1.511
 EYF  C4   N2   single    1.441  0.020  1.441
 EYF  C5   C11  aromatic  1.386  0.020  1.386
 EYF  N1   C2   aromatic  1.320  0.020  1.320
 EYF  N1   C3   aromatic  1.323  0.020  1.323
 EYF  C2   C1   aromatic  1.406  0.020  1.406
 EYF  N2   C3   aromatic  1.359  0.020  1.359
 EYF  N2   C12  aromatic  1.374  0.020  1.374
 EYF  C3   C14  aromatic  1.414  0.020  1.414
 EYF  O    C    double    1.217  0.020  1.217
 EYF  C10  C11  aromatic  1.392  0.020  1.392
 EYF  C1   C    single    1.489  0.020  1.489
 EYF  C1   C15  aromatic  1.390  0.020  1.390
 EYF  C    N    single    1.356  0.020  1.356
 EYF  C12  C13  aromatic  1.363  0.020  1.363
 EYF  C14  C13  aromatic  1.427  0.020  1.427
 EYF  C14  C15  aromatic  1.389  0.020  1.389
 EYF  O1   N    single    1.365  0.020  1.365
 EYF  C8   H1   single    0.970  0.020  1.090
 EYF  C8   H2   single    0.970  0.020  1.090
 EYF  C8   H3   single    0.970  0.020  1.090
 EYF  C6   H4   single    0.930  0.020  1.080
 EYF  C2   H5   single    0.930  0.020  1.080
 EYF  C4   H6   single    0.970  0.020  1.090
 EYF  C4   H7   single    0.970  0.020  1.090
 EYF  N    H8   single    0.890  0.020  1.040
 EYF  O1   H9   single    0.850  0.020  0.980
 EYF  C15  H10  single    0.930  0.020  1.080
 EYF  C13  H11  single    0.930  0.020  1.080
 EYF  C12  H13  single    0.930  0.020  1.080
 EYF  C11  H15  single    0.930  0.020  1.080
 EYF  C10  H16  single    0.930  0.020  1.080
 EYF  C9   H17  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
 EYF  H3   C8   H2   108.80  3.000
 EYF  H3   C8   H1   108.70  3.000
 EYF  H2   C8   H1   108.67  3.000
 EYF  H3   C8   O2   112.05  3.000
 EYF  H2   C8   O2   112.02  3.000
 EYF  H1   C8   O2   106.48  3.000
 EYF  C11  C5   C4   122.32  3.000
 EYF  C11  C5   C6   119.99  3.000
 EYF  C4   C5   C6   117.66  3.000
 EYF  H4   C6   C7   121.06  3.000
 EYF  H4   C6   C5   118.55  3.000
 EYF  C7   C6   C5   120.39  3.000
 EYF  C3   N1   C2   115.31  3.000
 EYF  H5   C2   C1   119.42  3.000
 EYF  H5   C2   N1   116.35  3.000
 EYF  C1   C2   N1   124.23  3.000
 EYF  H7   C4   H6   106.50  3.000
 EYF  H7   C4   N2   107.57  3.000
 EYF  H6   C4   N2   108.79  3.000
 EYF  H7   C4   C5   109.80  3.000
 EYF  H6   C4   C5   109.92  3.000
 EYF  N2   C4   C5   113.97  3.000
 EYF  H8   N    O1   113.30  3.000
 EYF  H8   N    C    120.83  3.000
 EYF  O1   N    C    118.37  3.000
 EYF  H9   O1   N    105.79  3.000
 EYF  C15  C1   C    123.25  3.000
 EYF  C15  C1   C2   119.35  3.000
 EYF  C    C1   C2   117.38  3.000
 EYF  H10  C15  C14  120.47  3.000
 EYF  H10  C15  C1   121.73  3.000
 EYF  C14  C15  C1   117.78  3.000
 EYF  C13  C14  C3   106.71  3.000
 EYF  C13  C14  C15  136.37  3.000
 EYF  C3   C14  C15  116.92  3.000
 EYF  N2   C3   C14  108.17  3.000
 EYF  C14  C3   N1   126.39  3.000
 EYF  N2   C3   N1   125.43  3.000
 EYF  H11  C13  C12  126.19  3.000
 EYF  H11  C13  C14  127.55  3.000
 EYF  C12  C13  C14  106.25  3.000
 EYF  H13  C12  N2   119.91  3.000
 EYF  H13  C12  C13  129.52  3.000
 EYF  N2   C12  C13  110.57  3.000
 EYF  C12  N2   C3   108.29  3.000
 EYF  C12  N2   C4   126.38  3.000
 EYF  C3   N2   C4   125.23  3.000
 EYF  H15  C11  C10  119.60  3.000
 EYF  H15  C11  C5   121.04  3.000
 EYF  C10  C11  C5   119.37  3.000
 EYF  H16  C10  C9   119.28  3.000
 EYF  H16  C10  C11  119.62  3.000
 EYF  C9   C10  C11  121.10  3.000
 EYF  H17  C9   C7   119.66  3.000
 EYF  H17  C9   C10  120.72  3.000
 EYF  C7   C9   C10  119.62  3.000
 EYF  O2   C7   C9   116.28  3.000
 EYF  C9   C7   C6   119.53  3.000
 EYF  O2   C7   C6   124.19  3.000
 EYF  C7   O2   C8   118.65  3.000
 EYF  C1   C    N    114.19  3.000
 EYF  N    C    O    123.40  3.000
 EYF  C1   C    O    122.40  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
 EYF  CONST_01  C9   C7   C6   C5      0.00   0.0  0
 EYF  CONST_02  C9   C10  C11  C5      0.00   0.0  0
 EYF  CONST_03  C10  C9   C7   C6      0.00   0.0  0
 EYF  CONST_04  C10  C11  C5   C6      0.00   0.0  0
 EYF  CONST_05  C15  C1   C2   N1      0.00   0.0  0
 EYF  CONST_06  C12  N2   C3   N1    180.00   0.0  0
 EYF  CONST_07  C13  C14  C3   N1    180.00   0.0  0
 EYF  CONST_08  C15  C14  C3   N1      0.00   0.0  0
 EYF  CONST_09  N2   C3   N1   C2    180.00   0.0  0
 EYF  CONST_10  C14  C3   N1   C2      0.00   0.0  0
 EYF  CONST_11  C14  C15  C1   C2      0.00   0.0  0
 EYF  CONST_12  C3   N1   C2   C1      0.00   0.0  0
 EYF  CONST_13  C3   C14  C15  C1      0.00   0.0  0
 EYF  CONST_14  C13  C14  C15  C1    180.00   0.0  0
 EYF  CONST_15  N2   C3   C14  C15   180.00   0.0  0
 EYF  CONST_16  C12  C13  C14  C15   180.00   0.0  0
 EYF  CONST_17  C12  N2   C3   C14     0.00   0.0  0
 EYF  CONST_18  N2   C12  C13  C14     0.00   0.0  0
 EYF  CONST_19  C13  C12  N2   C3      0.00   0.0  0
 EYF  CONST_20  C12  C13  C14  C3      0.00   0.0  0
 EYF  CONST_21  N2   C3   C14  C13     0.00   0.0  0
 EYF  CONST_22  C7   C6   C5   C11     0.00   0.0  0
 EYF  CONST_23  C7   C9   C10  C11     0.00   0.0  0
 EYF  CONST_24  O2   C7   C6   C5    180.00   0.0  0
 EYF  CONST_25  C    C1   C2   N1    180.00   0.0  0
 EYF  CONST_26  C4   N2   C3   N1      0.00   0.0  0
 EYF  CONST_27  C7   C6   C5   C4    180.00   0.0  0
 EYF  CONST_28  C10  C11  C5   C4    180.00   0.0  0
 EYF  CONST_29  C14  C3   N2   C4    180.00   0.0  0
 EYF  CONST_30  C13  C12  N2   C4    180.00   0.0  0
 EYF  CONST_31  C14  C15  C1   C     180.00   0.0  0
 EYF  CONST_32  O2   C7   C9   C10   180.00   0.0  0
 EYF  CONST_33  H16  C10  C11  C5    180.00   0.0  0
 EYF  CONST_34  H17  C9   C7   C6    180.00   0.0  0
 EYF  CONST_35  H15  C11  C5   C6    180.00   0.0  0
 EYF  CONST_36  H10  C15  C1   C2    180.00   0.0  0
 EYF  CONST_37  H5   C2   C1   C15   180.00   0.0  0
 EYF  CONST_38  H11  C13  C14  C15     0.00   0.0  0
 EYF  CONST_39  H13  C12  C13  C14   180.00   0.0  0
 EYF  CONST_40  H4   C6   C5   C11   180.00   0.0  0
 EYF  CONST_41  C1   C    N    O1    180.00   0.0  0
 EYF  CONST_43  O1   N    C    O       0.00   0.0  0
 EYF  Var_01    C3   N2   C4   C5     76.30  30.0  2
 EYF  Var_02    N2   C4   C5   C6   -161.38  30.0  2
 EYF  Var_03    C6   C7   O2   C8     -1.06  30.0  2
 EYF  Var_04    O    C    C1   C2     27.61  30.0  2
 EYF  Var_05    H1   C8   O2   C7   -179.66  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
 EYF  plan-1  C5   0.020
 EYF  plan-1  C6   0.020
 EYF  plan-1  C4   0.020
 EYF  plan-1  C11  0.020
 EYF  plan-1  C10  0.020
 EYF  plan-1  C9   0.020
 EYF  plan-1  C7   0.020
 EYF  plan-1  O2   0.020
 EYF  plan-1  H4   0.020
 EYF  plan-1  H15  0.020
 EYF  plan-1  H16  0.020
 EYF  plan-1  H17  0.020
 EYF  plan-2  N1   0.020
 EYF  plan-2  C2   0.020
 EYF  plan-2  C4   0.020
 EYF  plan-2  C1   0.020
 EYF  plan-2  C15  0.020
 EYF  plan-2  C14  0.020
 EYF  plan-2  C3   0.020
 EYF  plan-2  C13  0.020
 EYF  plan-2  C12  0.020
 EYF  plan-2  N2   0.020
 EYF  plan-2  H5   0.020
 EYF  plan-2  H10  0.020
 EYF  plan-2  H11  0.020
 EYF  plan-2  H13  0.020
 EYF  plan-2  C    0.020
 EYF  plan-3  O    0.020
 EYF  plan-3  N    0.020
 EYF  plan-3  O1   0.020
 EYF  plan-3  C1   0.020
 EYF  plan-3  H8   0.020
 EYF  plan-3  C    0.020

