# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 19:26:19 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 5-[5-(1H-indol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-1,3,4-oxadiazol-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1oc(nn1)c2c[nH]c3ncc(cc23)c4c[nH]c5ccccc45
#
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
 499  499  5-[5-(1H-indol-3-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]-1,3,4-oxadiazol-2-amine  ligand  36  24  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_499
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
 499  C1   C  CR5   0   0.413  -3.4662  -0.4281  -0.0267
 499  C2   C  CR5   0  -0.147  -2.7023   0.7831  -0.0074
 499  C3   C  CR15  0  -0.004  -3.1849   2.0670  -0.0972
 499  C11  C  CR56  0   0.357   4.3196  -1.2742   0.3145
 499  C12  C  CR16  0  -0.303   5.6445  -1.4576  -0.0778
 499  C13  C  CR16  0  -0.284   6.1851  -0.5312  -0.9473
 499  C14  C  CR16  0  -0.267   5.4242   0.5496  -1.4228
 499  C15  C  CR16  0  -0.384   4.1129   0.7285  -1.0286
 499  C16  C  CR56  0   0.033   3.5401  -0.1852  -0.1347
 499  C    C  CR5   0   0.621  -5.1869  -1.6510  -0.1351
 499  O    O  O     0  -0.436  -4.8162  -0.3609  -0.1445
 499  N2   N  N     0  -0.332  -3.0623  -1.6437   0.0517
 499  N1   N  N     0  -0.369  -4.1779  -2.4510  -0.0244
 499  C8   C  CR56  0   0.050  -1.2789   0.8891   0.1095
 499  C4   C  CR56  0   0.473  -0.9792   2.2653   0.0818
 499  N3   N  NR15  0  -0.663  -2.1555   2.9473  -0.0459
 499  C7   C  CR16  0  -0.320  -0.2113   0.0060   0.2186
 499  C6   C  CR6   0  -0.030   1.0716   0.5363   0.3129
 499  C5   C  CR16  0  -0.140   1.2203   1.9373   0.2854
 499  N4   N  N     0  -0.413   0.2250   2.8000   0.1656
 499  C9   C  CR5   0  -0.019   2.2408  -0.3293   0.4638
 499  N5   N  NR15  0  -0.683   3.5335  -2.0305   1.1342
 499  C10  C  CR15  0  -0.070   2.2971  -1.4701   1.2225
 499  H1   H  HCR5  0   0.307  -4.2005   2.4149  -0.1964
 499  H2   H  HCR6  0   0.261   6.2263  -2.2957   0.2848
 499  H3   H  HCR6  0   0.251   7.2112  -0.6429  -1.2723
 499  H4   H  HCR6  0   0.248   5.8757   1.2509  -2.1124
 499  H5   H  HCR6  0   0.244   3.5409   1.5617  -1.4168
 499  H6   H  HNH2  0   0.412  -7.1092  -1.2728  -0.6222
 499  H7   H  HNH2  0   0.410  -6.7259  -2.8998  -0.3746
 499  H8   H  HNR5  0   0.421  -2.2492   3.9501  -0.0821
 499  H9   H  HCR6  0   0.255  -0.3682  -1.0652   0.2191
 499  H10  H  HCR6  0   0.256   2.2106   2.3679   0.3847
 499  H11  H  HNR5  0   0.413   3.8196  -2.8691   1.6112
 499  H12  H  HCR5  0   0.288   1.5342  -1.9166   1.8408
 499  N    N  NH2   0  -0.849  -6.5006  -1.9389  -0.1729

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
 499  N1   N2   aromatic  1.379  0.020  1.379
 499  N1   C    aromatic  1.292  0.020  1.292
 499  N2   C1   aromatic  1.283  0.020  1.283
 499  N    C    single    1.345  0.020  1.345
 499  C    O    aromatic  1.342  0.020  1.342
 499  C1   O    aromatic  1.357  0.020  1.357
 499  C1   C2   single    1.432  0.020  1.432
 499  C2   C3   aromatic  1.375  0.020  1.375
 499  C2   C8   aromatic  1.432  0.020  1.432
 499  C3   N3   aromatic  1.355  0.020  1.355
 499  C8   C7   aromatic  1.390  0.020  1.390
 499  C8   C4   aromatic  1.409  0.020  1.409
 499  N3   C4   aromatic  1.366  0.020  1.366
 499  C7   C6   aromatic  1.391  0.020  1.391
 499  C4   N4   aromatic  1.320  0.020  1.320
 499  C6   C5   aromatic  1.409  0.020  1.409
 499  C6   C9   single    1.463  0.020  1.463
 499  N4   C5   aromatic  1.323  0.020  1.323
 499  C10  C9   aromatic  1.371  0.020  1.371
 499  C10  N5   aromatic  1.360  0.020  1.360
 499  C9   C16  aromatic  1.438  0.020  1.438
 499  N5   C11  aromatic  1.364  0.020  1.364
 499  C16  C11  aromatic  1.413  0.020  1.413
 499  C16  C15  aromatic  1.401  0.020  1.401
 499  C11  C12  aromatic  1.394  0.020  1.394
 499  C15  C14  aromatic  1.381  0.020  1.381
 499  C12  C13  aromatic  1.381  0.020  1.381
 499  C14  C13  aromatic  1.405  0.020  1.405
 499  C3   H1   single    0.930  0.020  1.080
 499  C12  H2   single    0.930  0.020  1.080
 499  C13  H3   single    0.930  0.020  1.080
 499  C14  H4   single    0.930  0.020  1.080
 499  C15  H5   single    0.930  0.020  1.080
 499  N    H6   single    0.890  0.020  1.040
 499  N    H7   single    0.890  0.020  1.040
 499  N3   H8   single    0.860  0.020  1.020
 499  C7   H9   single    0.930  0.020  1.080
 499  C5   H10  single    0.930  0.020  1.080
 499  N5   H11  single    0.860  0.020  1.020
 499  C10  H12  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
 499  N2   C1   O    111.43  3.000
 499  O    C1   C2   119.34  3.000
 499  N2   C1   C2   129.23  3.000
 499  C8   C2   C3   106.57  3.000
 499  C8   C2   C1   126.43  3.000
 499  C3   C2   C1   127.00  3.000
 499  H1   C3   N3   120.61  3.000
 499  H1   C3   C2   129.66  3.000
 499  N3   C3   C2   109.72  3.000
 499  N5   C11  C16  107.48  3.000
 499  C16  C11  C12  122.44  3.000
 499  N5   C11  C12  130.07  3.000
 499  H2   C12  C13  121.32  3.000
 499  H2   C12  C11  121.22  3.000
 499  C13  C12  C11  117.46  3.000
 499  H3   C13  C14  119.44  3.000
 499  H3   C13  C12  119.41  3.000
 499  C14  C13  C12  121.15  3.000
 499  H4   C14  C15  119.61  3.000
 499  H4   C14  C13  119.22  3.000
 499  C15  C14  C13  121.16  3.000
 499  H5   C15  C16  120.98  3.000
 499  H5   C15  C14  119.94  3.000
 499  C16  C15  C14  119.08  3.000
 499  C9   C16  C15  134.47  3.000
 499  C15  C16  C11  118.69  3.000
 499  C9   C16  C11  106.80  3.000
 499  N1   C    O    112.33  3.000
 499  O    C    N    118.36  3.000
 499  N1   C    N    129.22  3.000
 499  C    O    C1   103.09  3.000
 499  N1   N2   C1   107.25  3.000
 499  N2   N1   C    105.90  3.000
 499  C7   C8   C4   117.31  3.000
 499  C4   C8   C2   106.39  3.000
 499  C7   C8   C2   136.29  3.000
 499  N4   C4   N3   126.11  3.000
 499  N4   C4   C8   126.05  3.000
 499  N3   C4   C8   107.84  3.000
 499  H8   N3   C4   125.47  3.000
 499  H8   N3   C3   125.05  3.000
 499  C4   N3   C3   109.47  3.000
 499  H9   C7   C6   120.71  3.000
 499  H9   C7   C8   121.16  3.000
 499  C6   C7   C8   118.13  3.000
 499  C9   C6   C5   120.40  3.000
 499  C9   C6   C7   121.23  3.000
 499  C5   C6   C7   118.35  3.000
 499  H10  C5   N4   115.88  3.000
 499  H10  C5   C6   119.30  3.000
 499  N4   C5   C6   124.81  3.000
 499  C5   N4   C4   115.34  3.000
 499  C10  C9   C6   125.61  3.000
 499  C10  C9   C16  106.06  3.000
 499  C6   C9   C16  128.33  3.000
 499  H11  N5   C10  124.81  3.000
 499  H11  N5   C11  125.65  3.000
 499  C10  N5   C11  109.53  3.000
 499  H12  C10  N5   120.63  3.000
 499  H12  C10  C9   129.23  3.000
 499  N5   C10  C9   110.13  3.000
 499  H7   N    H6   113.96  3.000
 499  H7   N    C    115.35  3.000
 499  H6   N    C    117.43  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
 499  CONST_01  C    N1   N2   C1     0.00  0.0  0
 499  CONST_02  N1   C    O    C1     0.00  0.0  0
 499  CONST_03  N3   C3   C2   C1   180.00  0.0  0
 499  CONST_04  C7   C8   C2   C1     0.00  0.0  0
 499  CONST_05  C4   C8   C2   C1   180.00  0.0  0
 499  CONST_06  N1   N2   C1   C2   180.00  0.0  0
 499  CONST_07  C    O    C1   C2   180.00  0.0  0
 499  CONST_08  C4   N3   C3   C2     0.00  0.0  0
 499  CONST_09  C6   C7   C8   C2   180.00  0.0  0
 499  CONST_10  N3   C4   C8   C2     0.00  0.0  0
 499  CONST_11  N4   C4   C8   C2   180.00  0.0  0
 499  CONST_12  N2   C1   C2   C3   180.00  0.0  0
 499  CONST_13  O    C1   C2   C3     0.00  0.0  0
 499  CONST_14  C7   C8   C2   C3   180.00  0.0  0
 499  CONST_15  C4   C8   C2   C3     0.00  0.0  0
 499  CONST_16  C8   C4   N3   C3     0.00  0.0  0
 499  CONST_17  N4   C4   N3   C3   180.00  0.0  0
 499  CONST_18  C9   C10  N5   C11    0.00  0.0  0
 499  CONST_19  C6   C9   C16  C11  180.00  0.0  0
 499  CONST_20  C10  C9   C16  C11    0.00  0.0  0
 499  CONST_21  C14  C15  C16  C11    0.00  0.0  0
 499  CONST_22  C14  C13  C12  C11    0.00  0.0  0
 499  CONST_23  C10  N5   C11  C12  180.00  0.0  0
 499  CONST_24  C9   C16  C11  C12  180.00  0.0  0
 499  CONST_25  C15  C16  C11  C12    0.00  0.0  0
 499  CONST_26  C15  C14  C13  C12    0.00  0.0  0
 499  CONST_27  N5   C11  C12  C13  180.00  0.0  0
 499  CONST_28  C16  C11  C12  C13    0.00  0.0  0
 499  CONST_29  C16  C15  C14  C13    0.00  0.0  0
 499  CONST_30  C9   C16  C15  C14  180.00  0.0  0
 499  CONST_31  C6   C9   C16  C15    0.00  0.0  0
 499  CONST_32  C10  C9   C16  C15  180.00  0.0  0
 499  CONST_33  N5   C11  C16  C15  180.00  0.0  0
 499  CONST_36  N5   C10  C9   C16    0.00  0.0  0
 499  CONST_37  C10  N5   C11  C16    0.00  0.0  0
 499  CONST_38  N2   C1   O    C      0.00  0.0  0
 499  CONST_39  N2   N1   C    O      0.00  0.0  0
 499  CONST_40  N1   N2   C1   O      0.00  0.0  0
 499  CONST_41  C8   C2   C1   O    180.00  0.0  0
 499  CONST_42  C8   C2   C1   N2     0.00  0.0  0
 499  CONST_43  N3   C3   C2   C8     0.00  0.0  0
 499  CONST_44  C5   C6   C7   C8     0.00  0.0  0
 499  CONST_45  C9   C6   C7   C8   180.00  0.0  0
 499  CONST_46  C5   N4   C4   C8     0.00  0.0  0
 499  CONST_47  C6   C7   C8   C4     0.00  0.0  0
 499  CONST_48  C6   C5   N4   C4     0.00  0.0  0
 499  CONST_49  C7   C8   C4   N3   180.00  0.0  0
 499  CONST_50  C5   N4   C4   N3   180.00  0.0  0
 499  CONST_51  N4   C4   C8   C7     0.00  0.0  0
 499  CONST_52  N4   C5   C6   C7     0.00  0.0  0
 499  CONST_54  N5   C10  C9   C6   180.00  0.0  0
 499  CONST_56  C9   C6   C5   N4   180.00  0.0  0
 499  CONST_57  N5   C11  C16  C9     0.00  0.0  0
 499  CONST_58  N    C    O    C1   180.00  0.0  0
 499  CONST_59  N2   N1   C    N    180.00  0.0  0
 499  CONST_60  H1   C3   C2   C1     0.00  0.0  0
 499  CONST_61  H8   N3   C3   C2   180.00  0.0  0
 499  CONST_62  H9   C7   C8   C2     0.00  0.0  0
 499  CONST_63  H12  C10  N5   C11  180.00  0.0  0
 499  CONST_64  H5   C15  C16  C11  180.00  0.0  0
 499  CONST_65  H3   C13  C12  C11  180.00  0.0  0
 499  CONST_66  H11  N5   C11  C12    0.00  0.0  0
 499  CONST_67  H4   C14  C13  C12  180.00  0.0  0
 499  CONST_68  H2   C12  C13  C14  180.00  0.0  0
 499  CONST_69  H10  C5   N4   C4   180.00  0.0  0
 499  CONST_71  H7   N    C    O    180.00  0.0  0

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
 499  plan-1  C1   0.020
 499  plan-1  C2   0.020
 499  plan-1  C    0.020
 499  plan-1  O    0.020
 499  plan-1  N2   0.020
 499  plan-1  N1   0.020
 499  plan-1  N    0.020
 499  plan-2  C1   0.020
 499  plan-2  C2   0.020
 499  plan-2  C3   0.020
 499  plan-2  C8   0.020
 499  plan-2  C4   0.020
 499  plan-2  N3   0.020
 499  plan-2  C7   0.020
 499  plan-2  C6   0.020
 499  plan-2  C5   0.020
 499  plan-2  N4   0.020
 499  plan-2  C9   0.020
 499  plan-2  H1   0.020
 499  plan-2  H8   0.020
 499  plan-2  H9   0.020
 499  plan-2  H10  0.020
 499  plan-3  C11  0.020
 499  plan-3  C12  0.020
 499  plan-3  C13  0.020
 499  plan-3  C14  0.020
 499  plan-3  C15  0.020
 499  plan-3  C16  0.020
 499  plan-3  C6   0.020
 499  plan-3  C9   0.020
 499  plan-3  N5   0.020
 499  plan-3  C10  0.020
 499  plan-3  H2   0.020
 499  plan-3  H3   0.020
 499  plan-3  H4   0.020
 499  plan-3  H5   0.020
 499  plan-3  H11  0.020
 499  plan-3  H12  0.020
 499  plan-4  C    0.020
 499  plan-4  H6   0.020
 499  plan-4  H7   0.020
 499  plan-4  N    0.020

