# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:22:51 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: 4-[[(1~{S},3~{R})-5-oxidanyl-2-adamantyl]amino]-1~{H}-pyrrolo[2,3-b]pyridine-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)c1cnc2[nH]ccc2c1N[C@@H]3[C@@H]4CC5C[C@H]3CC(O)(C5)C4
#
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
 9T6  9T6  4-[[(1~{S},3~{R})-5-oxidanyl-2-adamantyl]amino]-1~{H}-pyrrolo[2,3-b]pyridine-5-carboxamide  ligand  46  24  .  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_9T6
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
 9T6  C9   C  CR15  0  -0.452   1.7438   2.3622   0.2821
 9T6  C3   C  CR16  0  -0.110   3.7093  -1.1840  -0.3036
 9T6  C8   C  CR15  0   0.001   2.7887   3.1268  -0.1418
 9T6  C5   C  CR56  0  -0.034   2.1449   0.9976   0.1293
 9T6  C2   C  CR6   0  -0.220   2.4048  -1.3701   0.1861
 9T6  C1   C  CR6   0   0.311   1.5796  -0.2507   0.4213
 9T6  C6   C  CR56  0   0.471   3.4663   1.0240  -0.3729
 9T6  C10  C  C     0   0.489   1.9365  -2.7528   0.4821
 9T6  C19  C  CH2   0  -0.431  -1.8154   1.8241   0.8581
 9T6  C23  C  CH2   0  -0.418  -2.5573  -0.3651   1.7892
 9T6  C22  C  CH2   0  -0.455  -4.1133   0.9717   0.3636
 9T6  C15  C  CH2   0  -0.455  -2.3940   1.0343  -1.4419
 9T6  C16  C  CH2   0  -0.443  -3.1355  -1.1432  -0.5142
 9T6  C21  C  CH1   0  -0.250  -3.0085   1.0488   1.4201
 9T6  C14  C  CH1   0  -0.268  -1.2843   1.1192  -0.3900
 9T6  C17  C  CH1   0  -0.304  -2.0273  -1.0681   0.5377
 9T6  C18  C  CH1   0  -0.048  -0.8293  -0.3024  -0.0447
 9T6  C20  C  CT    0   0.254  -3.5939   0.2632  -0.8900
 9T6  N4   N  N     0  -0.431   4.2545  -0.0197  -0.5931
 9T6  N7   N  NR15  0  -0.665   3.8203   2.3215  -0.5427
 9T6  N12  N  NH2   0  -0.801   2.3980  -3.7167  -0.3279
 9T6  N13  N  NH1   0  -0.681   0.2832  -0.3611   0.9221
 9T6  O11  O  O     0  -0.496   1.1832  -3.0010   1.4222
 9T6  O24  O  OH1   0  -0.687  -4.6118   0.1279  -1.8651
 9T6  H1   H  HCR5  0   0.269   0.8150   2.7369   0.6760
 9T6  H2   H  HCR6  0   0.262   4.3504  -2.0473  -0.4477
 9T6  H3   H  HCR5  0   0.290   2.8843   4.1994  -0.1824
 9T6  H4   H  HCH2  0   0.226  -2.1113   2.8476   0.6079
 9T6  H5   H  HCH2  0   0.233  -1.0335   1.8968   1.6184
 9T6  H6   H  HCH2  0   0.234  -1.7901  -0.3231   2.5666
 9T6  H7   H  HCH2  0   0.228  -3.3936  -0.9373   2.2022
 9T6  H8   H  HCH2  0   0.229  -4.9809   0.4299   0.7549
 9T6  H9   H  HCH2  0   0.225  -4.4555   1.9806   0.1025
 9T6  H10  H  HCH2  0   0.230  -2.7024   2.0453  -1.7311
 9T6  H11  H  HCH2  0   0.232  -2.0282   0.5408  -2.3486
 9T6  H12  H  HCH2  0   0.234  -2.7777  -1.6687  -1.4064
 9T6  H13  H  HCH2  0   0.234  -3.9796  -1.7184  -0.1190
 9T6  H14  H  HCH1  0   0.230  -3.3908   1.5571   2.3098
 9T6  H15  H  HCH1  0   0.247  -0.4522   1.6807  -0.8182
 9T6  H16  H  HCH1  0   0.239  -1.7092  -2.0863   0.7861
 9T6  H17  H  HCH1  0   0.228  -0.5296  -0.8058  -0.9764
 9T6  H18  H  HNR5  0   0.413   4.7130   2.6389  -0.8840
 9T6  H19  H  HNH2  0   0.413   2.8967  -3.5172  -1.1772
 9T6  H20  H  HNH2  0   0.406   2.1276  -4.6736  -0.1678
 9T6  H21  H  HNH1  0   0.383   0.2177  -1.2399   1.4221
 9T6  H22  H  HOH1  0   0.438  -4.9191   1.0106  -2.0988

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
 9T6  N7   C6   aromatic  1.356  0.020  1.356
 9T6  N7   C8   aromatic  1.369  0.020  1.369
 9T6  N4   C6   aromatic  1.326  0.020  1.326
 9T6  N4   C3   aromatic  1.318  0.020  1.318
 9T6  C6   C5   aromatic  1.414  0.020  1.414
 9T6  C3   C2   aromatic  1.406  0.020  1.406
 9T6  C8   C9   aromatic  1.362  0.020  1.362
 9T6  C5   C9   aromatic  1.431  0.020  1.431
 9T6  C5   C1   aromatic  1.401  0.020  1.401
 9T6  N12  C10  single    1.341  0.020  1.341
 9T6  C2   C1   aromatic  1.410  0.020  1.410
 9T6  C2   C10  single    1.490  0.020  1.490
 9T6  C1   N13  single    1.394  0.020  1.394
 9T6  C10  O11  double    1.230  0.020  1.230
 9T6  N13  C18  single    1.475  0.020  1.475
 9T6  C17  C16  single    1.530  0.020  1.530
 9T6  C17  C18  single    1.536  0.020  1.536
 9T6  C17  C23  single    1.530  0.020  1.530
 9T6  C16  C20  single    1.526  0.020  1.526
 9T6  C18  C14  single    1.532  0.020  1.532
 9T6  C23  C21  single    1.529  0.020  1.529
 9T6  C20  O24  single    1.416  0.020  1.416
 9T6  C20  C15  single    1.529  0.020  1.529
 9T6  C20  C22  single    1.531  0.020  1.531
 9T6  C14  C15  single    1.531  0.020  1.531
 9T6  C14  C19  single    1.529  0.020  1.529
 9T6  C21  C22  single    1.531  0.020  1.531
 9T6  C21  C19  single    1.530  0.020  1.530
 9T6  C9   H1   single    0.930  0.020  1.080
 9T6  C3   H2   single    0.930  0.020  1.080
 9T6  C8   H3   single    0.930  0.020  1.080
 9T6  C19  H4   single    0.970  0.020  1.090
 9T6  C19  H5   single    0.970  0.020  1.090
 9T6  C23  H6   single    0.970  0.020  1.090
 9T6  C23  H7   single    0.970  0.020  1.090
 9T6  C22  H8   single    0.970  0.020  1.090
 9T6  C22  H9   single    0.970  0.020  1.090
 9T6  C15  H10  single    0.970  0.020  1.090
 9T6  C15  H11  single    0.970  0.020  1.090
 9T6  C16  H12  single    0.970  0.020  1.090
 9T6  C16  H13  single    0.970  0.020  1.090
 9T6  C21  H14  single    0.970  0.020  1.090
 9T6  C14  H15  single    0.970  0.020  1.090
 9T6  C17  H16  single    0.970  0.020  1.090
 9T6  C18  H17  single    0.970  0.020  1.090
 9T6  N7   H18  single    0.860  0.020  1.020
 9T6  N12  H19  single    0.860  0.020  1.020
 9T6  N12  H20  single    0.860  0.020  1.020
 9T6  N13  H21  single    0.890  0.020  1.040
 9T6  O24  H22  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
 9T6  H1   C9   C5   127.82  3.000
 9T6  H1   C9   C8   125.48  3.000
 9T6  C5   C9   C8   106.68  3.000
 9T6  H2   C3   N4   115.43  3.000
 9T6  H2   C3   C2   119.30  3.000
 9T6  N4   C3   C2   125.27  3.000
 9T6  H3   C8   N7   120.52  3.000
 9T6  H3   C8   C9   129.67  3.000
 9T6  N7   C8   C9   109.82  3.000
 9T6  C6   C5   C1   117.89  3.000
 9T6  C1   C5   C9   135.60  3.000
 9T6  C6   C5   C9   106.39  3.000
 9T6  C10  C2   C1   121.31  3.000
 9T6  C10  C2   C3   118.94  3.000
 9T6  C1   C2   C3   119.73  3.000
 9T6  N13  C1   C2   122.76  3.000
 9T6  N13  C1   C5   121.37  3.000
 9T6  C2   C1   C5   115.87  3.000
 9T6  N7   C6   N4   125.25  3.000
 9T6  N4   C6   C5   126.85  3.000
 9T6  N7   C6   C5   107.85  3.000
 9T6  O11  C10  N12  121.83  3.000
 9T6  O11  C10  C2   122.13  3.000
 9T6  N12  C10  C2   116.04  3.000
 9T6  H5   C19  H4   106.88  3.000
 9T6  H5   C19  C14  110.49  3.000
 9T6  H4   C19  C14  109.78  3.000
 9T6  H5   C19  C21  109.64  3.000
 9T6  H4   C19  C21  110.31  3.000
 9T6  C14  C19  C21  109.71  3.000
 9T6  H7   C23  H6   106.74  3.000
 9T6  H7   C23  C17  109.46  3.000
 9T6  H6   C23  C17  110.87  3.000
 9T6  H7   C23  C21  110.43  3.000
 9T6  H6   C23  C21  110.07  3.000
 9T6  C17  C23  C21  109.25  3.000
 9T6  H9   C22  H8   107.03  3.000
 9T6  H9   C22  C20  109.67  3.000
 9T6  H8   C22  C20  109.41  3.000
 9T6  H9   C22  C21  110.07  3.000
 9T6  H8   C22  C21  110.49  3.000
 9T6  C20  C22  C21  110.10  3.000
 9T6  H11  C15  H10  106.93  3.000
 9T6  H11  C15  C20  109.49  3.000
 9T6  H10  C15  C20  109.86  3.000
 9T6  H11  C15  C14  110.58  3.000
 9T6  H10  C15  C14  109.52  3.000
 9T6  C20  C15  C14  110.41  3.000
 9T6  H13  C16  H12  107.08  3.000
 9T6  H13  C16  C20  109.96  3.000
 9T6  H12  C16  C20  109.85  3.000
 9T6  H13  C16  C17  109.63  3.000
 9T6  H12  C16  C17  110.30  3.000
 9T6  C20  C16  C17  109.98  3.000
 9T6  H14  C21  C22  109.42  3.000
 9T6  H14  C21  C23  109.67  3.000
 9T6  C22  C21  C23  109.45  3.000
 9T6  H14  C21  C19  109.63  3.000
 9T6  C22  C21  C19  109.57  3.000
 9T6  C23  C21  C19  109.09  3.000
 9T6  H15  C14  C18  109.84  3.000
 9T6  H15  C14  C15  108.16  3.000
 9T6  C18  C14  C15  108.58  3.000
 9T6  H15  C14  C19  110.37  3.000
 9T6  C15  C14  C19  109.55  3.000
 9T6  C18  C14  C19  110.31  3.000
 9T6  H16  C17  C18  108.83  3.000
 9T6  H16  C17  C16  108.70  3.000
 9T6  C18  C17  C16  109.18  3.000
 9T6  H16  C17  C23  110.02  3.000
 9T6  C18  C17  C23  110.56  3.000
 9T6  C16  C17  C23  109.51  3.000
 9T6  H17  C18  N13  109.35  3.000
 9T6  H17  C18  C17  107.78  3.000
 9T6  N13  C18  C17  108.65  3.000
 9T6  H17  C18  C14  108.33  3.000
 9T6  C17  C18  C14  108.44  3.000
 9T6  N13  C18  C14  114.12  3.000
 9T6  O24  C20  C16  107.30  3.000
 9T6  O24  C20  C15  111.33  3.000
 9T6  C16  C20  C15  108.53  3.000
 9T6  C15  C20  C22  109.17  3.000
 9T6  O24  C20  C22  111.36  3.000
 9T6  C16  C20  C22  109.07  3.000
 9T6  C6   N4   C3   114.39  3.000
 9T6  H18  N7   C6   125.14  3.000
 9T6  H18  N7   C8   125.59  3.000
 9T6  C6   N7   C8   109.25  3.000
 9T6  H20  N12  H19  117.14  3.000
 9T6  H20  N12  C10  119.64  3.000
 9T6  H19  N12  C10  122.59  3.000
 9T6  H21  N13  C18  108.01  3.000
 9T6  H21  N13  C1   107.82  3.000
 9T6  C18  N13  C1   117.56  3.000
 9T6  H22  O24  C20  107.98  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
 9T6  CONST_01  C6   N7   C8   C9     0.00   0.0  0
 9T6  CONST_02  N7   C6   C5   C9     0.00   0.0  0
 9T6  CONST_03  N4   C6   C5   C9   180.00   0.0  0
 9T6  CONST_04  C2   C1   C5   C9   180.00   0.0  0
 9T6  CONST_05  N7   C6   N4   C3   180.00   0.0  0
 9T6  CONST_06  C5   C6   N4   C3     0.00   0.0  0
 9T6  CONST_07  C5   C1   C2   C3     0.00   0.0  0
 9T6  CONST_08  N4   C6   N7   C8   180.00   0.0  0
 9T6  CONST_09  C5   C6   N7   C8     0.00   0.0  0
 9T6  CONST_10  C6   C5   C9   C8     0.00   0.0  0
 9T6  CONST_11  C1   C5   C9   C8   180.00   0.0  0
 9T6  CONST_12  N7   C8   C9   C5     0.00   0.0  0
 9T6  CONST_13  C6   N4   C3   C2     0.00   0.0  0
 9T6  CONST_14  C6   C5   C1   C2     0.00   0.0  0
 9T6  CONST_15  N7   C6   C5   C1   180.00   0.0  0
 9T6  CONST_16  N4   C6   C5   C1     0.00   0.0  0
 9T6  CONST_17  N4   C3   C2   C1     0.00   0.0  0
 9T6  CONST_18  N13  C1   C5   C9     0.00   0.0  0
 9T6  CONST_19  N13  C1   C2   C3   180.00   0.0  0
 9T6  CONST_20  C10  C2   C1   C5   180.00   0.0  0
 9T6  CONST_21  N13  C1   C5   C6   180.00   0.0  0
 9T6  CONST_22  N4   C3   C2   C10  180.00   0.0  0
 9T6  CONST_25  H18  N7   C8   C9   180.00   0.0  0
 9T6  CONST_26  H3   C8   C9   C5   180.00   0.0  0
 9T6  CONST_27  H1   C9   C5   C1     0.00   0.0  0
 9T6  CONST_28  H2   C3   C2   C1   180.00   0.0  0
 9T6  CONST_30  H19  N12  C10  C2     0.00   0.0  0
 9T6  CONST_31  H20  N12  C10  C2   180.00   0.0  0
 9T6  Var_01    N12  C10  C2   C3   -34.62  30.0  2

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
 9T6  chir_01  C21  C23  C22  C19  positiv
 9T6  chir_02  C14  C18  C15  C19  negativ
 9T6  chir_03  C17  C16  C18  C23  negativ
 9T6  chir_04  C18  N13  C17  C14  negativ
 9T6  chir_05  C20  C16  C15  C22  positiv

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
 9T6  plan-1  C9   0.020
 9T6  plan-1  C3   0.020
 9T6  plan-1  C8   0.020
 9T6  plan-1  C5   0.020
 9T6  plan-1  C2   0.020
 9T6  plan-1  C1   0.020
 9T6  plan-1  C6   0.020
 9T6  plan-1  C10  0.020
 9T6  plan-1  N4   0.020
 9T6  plan-1  N7   0.020
 9T6  plan-1  N13  0.020
 9T6  plan-1  H1   0.020
 9T6  plan-1  H2   0.020
 9T6  plan-1  H3   0.020
 9T6  plan-1  H18  0.020
 9T6  plan-2  C2   0.020
 9T6  plan-2  C10  0.020
 9T6  plan-2  N12  0.020
 9T6  plan-2  O11  0.020
 9T6  plan-2  H19  0.020
 9T6  plan-2  H20  0.020
 9T6  plan-3  C1   0.020
 9T6  plan-3  C18  0.020
 9T6  plan-3  N13  0.020
 9T6  plan-3  H21  0.020

