# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 13:24:16 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: ~{N}-ethyl-4-[(3~{S})-3-methylmorpholin-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCNC(=O)c1[nH]c2nccc(N3CCOC[C@@H]3C)c2c1
#
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
 8XT  8XT  ~{N}-ethyl-4-[(3~{S})-3-methylmorpholin-4-yl]-1~{H}-pyrrolo[2,3-b]pyridine-2-carboxamide  ligand  41  21  .  2022-07-24  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_8XT
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
 8XT  C1   C  CH3   0  -0.693   6.7053  -0.2125   0.3849
 8XT  C2   C  CH2   0  -0.266   5.5299  -1.1698   0.3238
 8XT  C3   C  C     0   0.526   3.1350  -0.9922  -0.1784
 8XT  C7   C  CR6   0   0.409  -1.5447   0.9519  -0.2933
 8XT  C8   C  CH1   0  -0.157  -2.4231  -1.0894   0.7232
 8XT  C9   C  CH3   0  -0.663  -2.8079  -0.5739   2.1076
 8XT  C10  C  CH2   0  -0.180  -3.2798  -2.2650   0.2770
 8XT  C11  C  CH2   0  -0.185  -4.6618  -0.9149  -0.9893
 8XT  C12  C  CH2   0  -0.343  -3.8644   0.3284  -0.6402
 8XT  C13  C  CR16  0  -0.455  -1.8621   2.3094  -0.3870
 8XT  C14  C  CR16  0  -0.083  -0.8629   3.2843  -0.3853
 8XT  C15  C  CR56  0   0.446   0.7338   1.7543  -0.2243
 8XT  N1   N  NH1   0  -0.651   4.2835  -0.4326   0.2369
 8XT  O1   O  O     0  -0.488   3.0429  -2.1621  -0.5281
 8XT  C4   C  CR5   0   0.240   1.9517  -0.1100  -0.2041
 8XT  C5   C  CR15  0  -0.431   0.6454  -0.5141  -0.2368
 8XT  N4   N  NR15  0  -0.729   1.9992   1.2623  -0.1791
 8XT  C6   C  CR56  0  -0.038  -0.1601   0.6612  -0.2289
 8XT  N2   N  NT    0  -0.512  -2.4994  -0.0393  -0.3017
 8XT  N3   N  N     0  -0.445   0.4343   3.0462  -0.2973
 8XT  O2   O  O2    0  -0.478  -4.6123  -1.8819   0.0330
 8XT  H1   H  HCH3  0   0.233   6.6474   0.4348   1.2613
 8XT  H2   H  HCH3  0   0.244   7.6384  -0.7705   0.4476
 8XT  H3   H  HCH3  0   0.235   6.7457   0.4169  -0.5042
 8XT  H4   H  HCH2  0   0.244   5.6149  -1.8135  -0.5514
 8XT  H5   H  HCH2  0   0.237   5.5283  -1.8230   1.2014
 8XT  H6   H  HCH1  0   0.266  -1.4012  -1.4588   0.7723
 8XT  H7   H  HCH3  0   0.239  -2.6852  -1.3646   2.8486
 8XT  H8   H  HCH3  0   0.237  -2.1691   0.2587   2.4053
 8XT  H9   H  HCH3  0   0.233  -3.8429  -0.2354   2.1514
 8XT  H10  H  HCH2  0   0.218  -2.8372  -2.7128  -0.6244
 8XT  H11  H  HCH2  0   0.241  -3.2935  -3.0272   1.0576
 8XT  H12  H  HCH2  0   0.245  -5.7075  -0.6439  -1.1401
 8XT  H13  H  HCH2  0   0.207  -4.2824  -1.3347  -1.9315
 8XT  H14  H  HCH2  0   0.265  -3.8567   0.9744  -1.5192
 8XT  H15  H  HCH2  0   0.231  -4.3604   0.8845   0.1663
 8XT  H16  H  HCR6  0   0.276  -2.8879   2.6440  -0.4346
 8XT  H17  H  HCR6  0   0.256  -1.1569   4.3266  -0.4448
 8XT  H18  H  HNH1  0   0.398   4.2545   0.4567   0.7107
 8XT  H19  H  HCR5  0   0.261   0.3284  -1.5434  -0.2648
 8XT  H20  H  HNR5  0   0.411   2.8210   1.8359  -0.2857

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
 8XT  C1   C2   single    1.517  0.020  1.517
 8XT  C2   N1   single    1.451  0.020  1.451
 8XT  N1   C3   single    1.343  0.020  1.343
 8XT  O1   C3   double    1.224  0.020  1.224
 8XT  C3   C4   single    1.476  0.020  1.476
 8XT  C4   N4   aromatic  1.373  0.020  1.373
 8XT  C4   C5   aromatic  1.368  0.020  1.368
 8XT  N4   C15  aromatic  1.358  0.020  1.358
 8XT  C5   C6   aromatic  1.425  0.020  1.425
 8XT  C15  C6   aromatic  1.412  0.020  1.412
 8XT  C15  N3   aromatic  1.328  0.020  1.328
 8XT  C9   C8   single    1.527  0.020  1.527
 8XT  C6   C7   aromatic  1.416  0.020  1.416
 8XT  N3   C14  aromatic  1.322  0.020  1.322
 8XT  C8   C10  single    1.521  0.020  1.521
 8XT  C8   N2   single    1.469  0.020  1.469
 8XT  C7   N2   single    1.376  0.020  1.376
 8XT  C7   C13  aromatic  1.397  0.020  1.397
 8XT  C14  C13  aromatic  1.396  0.020  1.396
 8XT  C10  O2   single    1.408  0.020  1.408
 8XT  N2   C12  single    1.454  0.020  1.454
 8XT  O2   C11  single    1.408  0.020  1.408
 8XT  C12  C11  single    1.518  0.020  1.518
 8XT  C1   H1   single    0.970  0.020  1.090
 8XT  C1   H2   single    0.970  0.020  1.090
 8XT  C1   H3   single    0.970  0.020  1.090
 8XT  C2   H4   single    0.970  0.020  1.090
 8XT  C2   H5   single    0.970  0.020  1.090
 8XT  C8   H6   single    0.970  0.020  1.090
 8XT  C9   H7   single    0.970  0.020  1.090
 8XT  C9   H8   single    0.970  0.020  1.090
 8XT  C9   H9   single    0.970  0.020  1.090
 8XT  C10  H10  single    0.970  0.020  1.090
 8XT  C10  H11  single    0.970  0.020  1.090
 8XT  C11  H12  single    0.970  0.020  1.090
 8XT  C11  H13  single    0.970  0.020  1.090
 8XT  C12  H14  single    0.970  0.020  1.090
 8XT  C12  H15  single    0.970  0.020  1.090
 8XT  C13  H16  single    0.930  0.020  1.080
 8XT  C14  H17  single    0.930  0.020  1.080
 8XT  N1   H18  single    0.860  0.020  1.020
 8XT  C5   H19  single    0.930  0.020  1.080
 8XT  N4   H20  single    0.860  0.020  1.020

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
 8XT  H3   C1   H2   108.12  3.000
 8XT  H3   C1   H1   108.33  3.000
 8XT  H2   C1   H1   107.66  3.000
 8XT  H3   C1   C2   111.11  3.000
 8XT  H2   C1   C2   110.05  3.000
 8XT  H1   C1   C2   111.44  3.000
 8XT  H5   C2   H4   106.96  3.000
 8XT  H5   C2   N1   110.50  3.000
 8XT  H4   C2   N1   108.61  3.000
 8XT  H5   C2   C1   110.22  3.000
 8XT  H4   C2   C1   110.16  3.000
 8XT  N1   C2   C1   110.33  3.000
 8XT  C4   C3   O1   120.38  3.000
 8XT  C4   C3   N1   116.22  3.000
 8XT  O1   C3   N1   123.40  3.000
 8XT  N2   C7   C6   122.05  3.000
 8XT  N2   C7   C13  122.80  3.000
 8XT  C6   C7   C13  115.12  3.000
 8XT  H6   C8   N2   108.84  3.000
 8XT  H6   C8   C10  106.25  3.000
 8XT  N2   C8   C10  108.57  3.000
 8XT  H6   C8   C9   108.09  3.000
 8XT  N2   C8   C9   112.22  3.000
 8XT  C10  C8   C9   112.64  3.000
 8XT  H9   C9   H8   107.95  3.000
 8XT  H9   C9   H7   107.74  3.000
 8XT  H8   C9   H7   107.59  3.000
 8XT  H9   C9   C8   112.37  3.000
 8XT  H8   C9   C8   110.95  3.000
 8XT  H7   C9   C8   110.06  3.000
 8XT  H11  C10  H10  107.88  3.000
 8XT  H11  C10  O2   107.59  3.000
 8XT  H10  C10  O2   110.47  3.000
 8XT  H11  C10  C8   109.70  3.000
 8XT  H10  C10  C8   109.18  3.000
 8XT  O2   C10  C8   111.93  3.000
 8XT  H13  C11  H12  107.90  3.000
 8XT  H13  C11  O2   110.37  3.000
 8XT  H12  C11  O2   107.74  3.000
 8XT  H13  C11  C12  109.19  3.000
 8XT  H12  C11  C12  109.39  3.000
 8XT  O2   C11  C12  112.16  3.000
 8XT  H15  C12  H14  107.16  3.000
 8XT  H15  C12  N2   112.41  3.000
 8XT  H14  C12  N2   109.31  3.000
 8XT  H15  C12  C11  110.28  3.000
 8XT  H14  C12  C11  107.67  3.000
 8XT  N2   C12  C11  109.86  3.000
 8XT  H16  C13  C14  117.61  3.000
 8XT  H16  C13  C7   121.31  3.000
 8XT  C14  C13  C7   121.06  3.000
 8XT  H17  C14  N3   116.28  3.000
 8XT  H17  C14  C13  118.49  3.000
 8XT  N3   C14  C13  125.22  3.000
 8XT  N3   C15  C6   127.59  3.000
 8XT  N3   C15  N4   124.35  3.000
 8XT  C6   C15  N4   108.02  3.000
 8XT  H18  N1   C3   119.22  3.000
 8XT  H18  N1   C2   116.42  3.000
 8XT  C3   N1   C2   122.78  3.000
 8XT  N4   C4   C5   109.19  3.000
 8XT  C5   C4   C3   126.11  3.000
 8XT  N4   C4   C3   124.69  3.000
 8XT  H19  C5   C6   128.45  3.000
 8XT  H19  C5   C4   124.33  3.000
 8XT  C6   C5   C4   107.22  3.000
 8XT  H20  N4   C4   126.51  3.000
 8XT  H20  N4   C15  123.36  3.000
 8XT  C4   N4   C15  109.21  3.000
 8XT  C5   C6   C15  106.30  3.000
 8XT  C15  C6   C7   117.40  3.000
 8XT  C5   C6   C7   136.20  3.000
 8XT  C12  N2   C8   113.08  3.000
 8XT  C12  N2   C7   118.08  3.000
 8XT  C8   N2   C7   118.32  3.000
 8XT  C15  N3   C14  113.59  3.000
 8XT  C11  O2   C10  110.24  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
 8XT  CONST_01  C4   C5   C6   C7   180.00   0.0  0
 8XT  CONST_02  N4   C15  C6   C7   180.00   0.0  0
 8XT  CONST_03  N3   C15  C6   C7     0.00   0.0  0
 8XT  CONST_04  N3   C14  C13  C7     0.00   0.0  0
 8XT  CONST_05  C5   C6   C7   C13  180.00   0.0  0
 8XT  CONST_06  C15  C6   C7   C13    0.00   0.0  0
 8XT  CONST_07  C15  N3   C14  C13    0.00   0.0  0
 8XT  CONST_08  N4   C15  N3   C14  180.00   0.0  0
 8XT  CONST_09  C6   C15  N3   C14    0.00   0.0  0
 8XT  CONST_10  C6   C7   C13  C14    0.00   0.0  0
 8XT  CONST_11  C5   C4   N4   C15    0.00   0.0  0
 8XT  CONST_12  C4   C5   C6   C15    0.00   0.0  0
 8XT  CONST_13  C6   C15  N4   C4     0.00   0.0  0
 8XT  CONST_14  N3   C15  N4   C4   180.00   0.0  0
 8XT  CONST_15  N4   C15  C6   C5     0.00   0.0  0
 8XT  CONST_16  N3   C15  C6   C5   180.00   0.0  0
 8XT  CONST_17  C6   C5   C4   N4     0.00   0.0  0
 8XT  CONST_18  N2   C7   C13  C14  180.00   0.0  0
 8XT  CONST_19  N2   C7   C6   C15  180.00   0.0  0
 8XT  CONST_20  N2   C7   C6   C5     0.00   0.0  0
 8XT  CONST_21  C15  N4   C4   C3   180.00   0.0  0
 8XT  CONST_22  C6   C5   C4   C3   180.00   0.0  0
 8XT  CONST_23  H19  C5   C6   C7     0.00   0.0  0
 8XT  CONST_24  H17  C14  C13  C7   180.00   0.0  0
 8XT  CONST_25  H20  N4   C4   C5   180.00   0.0  0
 8XT  CONST_26  H16  C13  C7   C6   180.00   0.0  0
 8XT  CONST_27  C4   C3   N1   C2   180.00   0.0  0
 8XT  CONST_28  H18  N1   C3   C4     0.00   0.0  0
 8XT  CONST_29  O1   C3   N1   C2     0.00   0.0  0
 8XT  Var_01    C11  C12  N2   C7   163.58  30.0  1
 8XT  Var_02    C6   C7   N2   C8    49.87  30.0  2
 8XT  Var_03    C12  C11  O2   C10  -59.21  30.0  1
 8XT  Var_04    O2   C11  C12  N2    54.66  30.0  1
 8XT  Var_05    H10  C10  O2   C11  -61.28  30.0  1
 8XT  Var_06    N4   C4   C3   N1    17.68  30.0  2
 8XT  Var_07    C3   N1   C2   C1   161.94  30.0  3
 8XT  Var_08    H1   C1   C2   N1    60.78  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 8XT  chir_01  C8  C9  C10  N2  negativ

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
 8XT  plan-1  C3   0.020
 8XT  plan-1  C7   0.020
 8XT  plan-1  C13  0.020
 8XT  plan-1  C14  0.020
 8XT  plan-1  C15  0.020
 8XT  plan-1  C4   0.020
 8XT  plan-1  C5   0.020
 8XT  plan-1  N4   0.020
 8XT  plan-1  C6   0.020
 8XT  plan-1  N2   0.020
 8XT  plan-1  N3   0.020
 8XT  plan-1  H16  0.020
 8XT  plan-1  H17  0.020
 8XT  plan-1  H19  0.020
 8XT  plan-1  H20  0.020
 8XT  plan-2  C2   0.020
 8XT  plan-2  C3   0.020
 8XT  plan-2  N1   0.020
 8XT  plan-2  O1   0.020
 8XT  plan-2  C4   0.020
 8XT  plan-2  H18  0.020

