# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 10:59:06 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1[nH]nc2cc(ccc12)c3cncc(Cl)c3N4CCC5(CCNC5=O)CC4
#
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
 5XG  5XG  8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one  ligand  49  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5XG
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
 5XG  C2   C   CR5   0   0.506  -4.0645  -2.2977   0.1554
 5XG  C5   C   CR56  0   0.263  -3.3148  -0.3264   0.8720
 5XG  C6   C   CR16  0  -0.344  -2.5392   0.8593   0.8558
 5XG  C7   C   CR6   0   0.029  -1.6576   1.0522  -0.1746
 5XG  C8   C   CR16  0  -0.292  -1.5209   0.0909  -1.2244
 5XG  C11  C   CR6   0  -0.071  -0.8676   2.3010  -0.2505
 5XG  C12  C   CR16  0  -0.095  -1.5288   3.5157  -0.3603
 5XG  N13  N   N     0  -0.408  -0.9252   4.6865  -0.5277
 5XG  C15  C   CR6   0  -0.195   1.1560   3.5334  -0.4435
 5XG  C17  C   CR6   0   0.496   0.5431   2.2852  -0.2774
 5XG  C19  C   CH2   0  -0.309   2.3480   0.7203  -0.9537
 5XG  C21  C   CT    0  -0.265   2.2178  -1.6153   0.0314
 5XG  C23  C   CH2   0  -0.262   4.3183  -2.8106   0.1433
 5XG  O26  O   O     0  -0.487   1.0108  -3.5897  -0.7748
 5XG  C27  C   CH2   0  -0.423   1.0498  -1.1360   0.8876
 5XG  N1   N   NH2   0  -0.845  -4.4052  -3.4328  -0.5210
 5XG  N3   N   NR15  0  -0.478  -4.6388  -1.9014   1.2948
 5XG  N4   N   N     0  -0.356  -4.2161  -0.7104   1.7690
 5XG  C9   C   CR16  0  -0.274  -2.2599  -1.0567  -1.2337
 5XG  C10  C   CR56  0  -0.142  -3.1633  -1.2763  -0.1761
 5XG  C14  C   CR16  0  -0.052   0.3953   4.6860  -0.5769
 5XG  CL1  CL  CL    0  -0.105   2.8746   3.7158  -0.3799
 5XG  N18  N   NT    0  -0.511   1.2184   1.0913  -0.1281
 5XG  C20  C   CH2   0  -0.413   2.2904  -0.7723  -1.2541
 5XG  C22  C   CH2   0  -0.458   3.5616  -1.6415   0.7740
 5XG  N24  N   NH1   0  -0.622   3.2411  -3.6778  -0.2816
 5XG  C25  C   C     0   0.578   2.0464  -3.0747  -0.3856
 5XG  C28  C   CH2   0  -0.312   1.1087   0.3632   1.1242
 5XG  H1   H   HCR6  0   0.251  -2.6336   1.5883   1.6517
 5XG  H2   H   HCR6  0   0.241  -0.8202   0.2899  -2.0237
 5XG  H3   H   HCR6  0   0.264  -2.6135   3.5297  -0.3447
 5XG  H4   H   HCH2  0   0.258   2.3035   1.2725  -1.8927
 5XG  H5   H   HCH2  0   0.220   3.3083   0.9687  -0.4860
 5XG  H6   H   HCH2  0   0.235   4.9280  -2.4917  -0.7074
 5XG  H7   H   HCH2  0   0.253   4.9739  -3.3158   0.8520
 5XG  H8   H   HCH2  0   0.263   0.1081  -1.3870   0.3970
 5XG  H9   H   HCH2  0   0.235   1.0637  -1.6490   1.8529
 5XG  H10  H   HNH2  0   0.396  -4.8219  -4.1700   0.0266
 5XG  H11  H   HNH2  0   0.398  -3.6867  -3.7896  -1.1312
 5XG  H12  H   HNR5  0   0.420  -5.3428  -2.4095   1.8083
 5XG  H13  H   HCR6  0   0.249  -2.1512  -1.7742  -2.0378
 5XG  H14  H   HCR6  0   0.280   0.8901   5.6431  -0.7024
 5XG  H15  H   HCH2  0   0.245   1.4144  -0.9770  -1.8747
 5XG  H16  H   HCH2  0   0.245   3.1720  -1.0443  -1.8418
 5XG  H17  H   HCH2  0   0.254   4.1268  -0.7125   0.7092
 5XG  H18  H   HCH2  0   0.250   3.3931  -1.8443   1.8346
 5XG  H19  H   HNH1  0   0.394   3.4003  -4.6131  -0.6229
 5XG  H20  H   HCH2  0   0.262   0.2143   0.6875   1.6534
 5XG  H21  H   HCH2  0   0.233   1.9614   0.6098   1.7742

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
 5XG  N1   C2   single    1.365  0.020  1.365
 5XG  C2   N3   aromatic  1.336  0.020  1.336
 5XG  C2   C10  aromatic  1.402  0.020  1.402
 5XG  N3   N4   aromatic  1.350  0.020  1.350
 5XG  C10  C9   aromatic  1.408  0.020  1.408
 5XG  C10  C5   aromatic  1.423  0.020  1.423
 5XG  C9   C8   aromatic  1.365  0.020  1.365
 5XG  N4   C5   aromatic  1.328  0.020  1.328
 5XG  C5   C6   aromatic  1.417  0.020  1.417
 5XG  C8   C7   aromatic  1.430  0.020  1.430
 5XG  C6   C7   aromatic  1.370  0.020  1.370
 5XG  C7   C11  single    1.480  0.020  1.480
 5XG  C12  C11  aromatic  1.387  0.020  1.387
 5XG  C12  N13  aromatic  1.328  0.020  1.328
 5XG  C11  C17  aromatic  1.411  0.020  1.411
 5XG  N13  C14  aromatic  1.321  0.020  1.321
 5XG  C19  N18  single    1.447  0.020  1.447
 5XG  C19  C20  single    1.524  0.020  1.524
 5XG  C17  N18  single    1.380  0.020  1.380
 5XG  C17  C15  aromatic  1.400  0.020  1.400
 5XG  N18  C28  single    1.453  0.020  1.453
 5XG  C22  C21  single    1.536  0.020  1.536
 5XG  C22  C23  single    1.529  0.020  1.529
 5XG  C20  C21  single    1.539  0.020  1.539
 5XG  C14  C15  aromatic  1.387  0.020  1.387
 5XG  C15  CL1  single    1.729  0.020  1.729
 5XG  C28  C27  single    1.519  0.020  1.519
 5XG  C21  C27  single    1.525  0.020  1.525
 5XG  C21  C25  single    1.527  0.020  1.527
 5XG  C23  N24  single    1.447  0.020  1.447
 5XG  C25  N24  single    1.342  0.020  1.342
 5XG  C25  O26  double    1.220  0.020  1.220
 5XG  C6   H1   single    0.930  0.020  1.080
 5XG  C8   H2   single    0.930  0.020  1.080
 5XG  C12  H3   single    0.930  0.020  1.080
 5XG  C19  H4   single    0.970  0.020  1.090
 5XG  C19  H5   single    0.970  0.020  1.090
 5XG  C23  H6   single    0.970  0.020  1.090
 5XG  C23  H7   single    0.970  0.020  1.090
 5XG  C27  H8   single    0.970  0.020  1.090
 5XG  C27  H9   single    0.970  0.020  1.090
 5XG  N1   H10  single    0.890  0.020  1.040
 5XG  N1   H11  single    0.890  0.020  1.040
 5XG  N3   H12  single    0.860  0.020  1.020
 5XG  C9   H13  single    0.930  0.020  1.080
 5XG  C14  H14  single    0.930  0.020  1.080
 5XG  C20  H15  single    0.970  0.020  1.090
 5XG  C20  H16  single    0.970  0.020  1.090
 5XG  C22  H17  single    0.970  0.020  1.090
 5XG  C22  H18  single    0.970  0.020  1.090
 5XG  N24  H19  single    0.860  0.020  1.020
 5XG  C28  H20  single    0.970  0.020  1.090
 5XG  C28  H21  single    0.970  0.020  1.090

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
 5XG  C10  C2   N3   105.18  3.000
 5XG  C10  C2   N1   130.49  3.000
 5XG  N3   C2   N1   124.21  3.000
 5XG  C10  C5   N4   112.13  3.000
 5XG  N4   C5   C6   128.39  3.000
 5XG  C10  C5   C6   119.48  3.000
 5XG  H1   C6   C7   120.93  3.000
 5XG  H1   C6   C5   120.46  3.000
 5XG  C7   C6   C5   118.60  3.000
 5XG  C11  C7   C8   118.60  3.000
 5XG  C11  C7   C6   120.07  3.000
 5XG  C8   C7   C6   121.27  3.000
 5XG  H2   C8   C9   120.03  3.000
 5XG  H2   C8   C7   118.74  3.000
 5XG  C9   C8   C7   121.23  3.000
 5XG  C17  C11  C12  119.00  3.000
 5XG  C17  C11  C7   121.69  3.000
 5XG  C12  C11  C7   119.24  3.000
 5XG  H3   C12  N13  116.42  3.000
 5XG  H3   C12  C11  119.12  3.000
 5XG  N13  C12  C11  124.43  3.000
 5XG  C14  N13  C12  117.30  3.000
 5XG  CL1  C15  C14  117.44  3.000
 5XG  CL1  C15  C17  121.63  3.000
 5XG  C14  C15  C17  120.80  3.000
 5XG  N18  C17  C15  124.75  3.000
 5XG  C15  C17  C11  115.45  3.000
 5XG  N18  C17  C11  119.80  3.000
 5XG  H5   C19  H4   106.76  3.000
 5XG  H5   C19  C20  109.82  3.000
 5XG  H4   C19  C20  108.95  3.000
 5XG  H5   C19  N18  112.46  3.000
 5XG  H4   C19  N18  109.24  3.000
 5XG  C20  C19  N18  109.51  3.000
 5XG  C25  C21  C22  102.35  3.000
 5XG  C25  C21  C20  107.50  3.000
 5XG  C22  C21  C20  111.84  3.000
 5XG  C25  C21  C27  111.56  3.000
 5XG  C20  C21  C27  109.44  3.000
 5XG  C22  C21  C27  113.83  3.000
 5XG  H7   C23  H6   107.79  3.000
 5XG  H7   C23  N24  111.17  3.000
 5XG  H6   C23  N24  111.18  3.000
 5XG  H7   C23  C22  112.58  3.000
 5XG  H6   C23  C22  111.94  3.000
 5XG  N24  C23  C22  102.18  3.000
 5XG  H9   C27  H8   107.46  3.000
 5XG  H9   C27  C28  108.97  3.000
 5XG  H8   C27  C28  109.30  3.000
 5XG  H9   C27  C21  109.78  3.000
 5XG  H8   C27  C21  109.64  3.000
 5XG  C28  C27  C21  111.58  3.000
 5XG  H11  N1   H10  111.38  3.000
 5XG  H11  N1   C2   114.62  3.000
 5XG  H10  N1   C2   116.24  3.000
 5XG  H12  N3   N4   118.96  3.000
 5XG  H12  N3   C2   125.78  3.000
 5XG  N4   N3   C2   115.26  3.000
 5XG  N3   N4   C5   103.32  3.000
 5XG  H13  C9   C10  121.24  3.000
 5XG  H13  C9   C8   120.51  3.000
 5XG  C10  C9   C8   118.25  3.000
 5XG  C9   C10  C5   121.17  3.000
 5XG  C5   C10  C2   104.11  3.000
 5XG  C9   C10  C2   134.72  3.000
 5XG  H14  C14  C15  119.61  3.000
 5XG  H14  C14  N13  117.38  3.000
 5XG  C15  C14  N13  123.00  3.000
 5XG  C28  N18  C19  114.97  3.000
 5XG  C28  N18  C17  119.34  3.000
 5XG  C19  N18  C17  122.82  3.000
 5XG  H16  C20  H15  107.11  3.000
 5XG  H16  C20  C21  110.52  3.000
 5XG  H15  C20  C21  109.51  3.000
 5XG  H16  C20  C19  108.60  3.000
 5XG  H15  C20  C19  109.02  3.000
 5XG  C21  C20  C19  111.95  3.000
 5XG  H18  C22  H17  107.21  3.000
 5XG  H18  C22  C23  109.56  3.000
 5XG  H17  C22  C23  111.77  3.000
 5XG  H18  C22  C21  109.73  3.000
 5XG  H17  C22  C21  114.25  3.000
 5XG  C23  C22  C21  104.28  3.000
 5XG  H19  N24  C25  122.08  3.000
 5XG  H19  N24  C23  122.54  3.000
 5XG  C25  N24  C23  114.59  3.000
 5XG  N24  C25  O26  126.18  3.000
 5XG  O26  C25  C21  125.84  3.000
 5XG  N24  C25  C21  107.96  3.000
 5XG  H21  C28  H20  106.43  3.000
 5XG  H21  C28  N18  109.78  3.000
 5XG  H20  C28  N18  109.38  3.000
 5XG  H21  C28  C27  110.08  3.000
 5XG  H20  C28  C27  109.75  3.000
 5XG  N18  C28  C27  111.30  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
 5XG  CONST_01  C5   N4   N3   C2      0.00   0.0  0
 5XG  CONST_02  C8   C9   C10  C2    180.00   0.0  0
 5XG  CONST_03  N4   C5   C10  C2      0.00   0.0  0
 5XG  CONST_04  C6   C5   C10  C2    180.00   0.0  0
 5XG  CONST_05  N3   C2   C10  C5      0.00   0.0  0
 5XG  CONST_06  C8   C9   C10  C5      0.00   0.0  0
 5XG  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 5XG  CONST_08  C11  C7   C6   C5    180.00   0.0  0
 5XG  CONST_09  C9   C10  C5   C6      0.00   0.0  0
 5XG  CONST_10  N3   N4   C5   C6    180.00   0.0  0
 5XG  CONST_11  C9   C8   C7   C6      0.00   0.0  0
 5XG  CONST_14  C10  C9   C8   C7      0.00   0.0  0
 5XG  CONST_15  C10  C5   C6   C7      0.00   0.0  0
 5XG  CONST_16  N4   C5   C6   C7    180.00   0.0  0
 5XG  CONST_17  N13  C12  C11  C7    180.00   0.0  0
 5XG  CONST_18  C15  C17  C11  C7    180.00   0.0  0
 5XG  CONST_21  C9   C8   C7   C11   180.00   0.0  0
 5XG  CONST_22  C14  N13  C12  C11     0.00   0.0  0
 5XG  CONST_23  C14  C15  C17  C11     0.00   0.0  0
 5XG  CONST_24  C15  C17  C11  C12     0.00   0.0  0
 5XG  CONST_25  C15  C14  N13  C12     0.00   0.0  0
 5XG  CONST_26  C17  C11  C12  N13     0.00   0.0  0
 5XG  CONST_27  C17  C15  C14  N13     0.00   0.0  0
 5XG  CONST_28  C9   C10  C2   N3    180.00   0.0  0
 5XG  CONST_29  C10  C5   N4   N3      0.00   0.0  0
 5XG  CONST_30  C10  C2   N3   N4      0.00   0.0  0
 5XG  CONST_31  C9   C10  C5   N4    180.00   0.0  0
 5XG  CONST_32  N18  C17  C11  C7      0.00   0.0  0
 5XG  CONST_33  N18  C17  C11  C12   180.00   0.0  0
 5XG  CONST_34  N18  C17  C15  C14   180.00   0.0  0
 5XG  CONST_35  C23  N24  C25  C21     0.00   0.0  0
 5XG  CONST_36  N1   C2   C10  C5    180.00   0.0  0
 5XG  CONST_37  CL1  C15  C17  C11   180.00   0.0  0
 5XG  CONST_38  CL1  C15  C14  N13   180.00   0.0  0
 5XG  CONST_39  N4   N3   C2   N1    180.00   0.0  0
 5XG  CONST_40  C9   C10  C2   N1      0.00   0.0  0
 5XG  CONST_41  N18  C17  C15  CL1     0.00   0.0  0
 5XG  CONST_42  O26  C25  N24  C23   180.00   0.0  0
 5XG  CONST_43  H13  C9   C10  C2      0.00   0.0  0
 5XG  CONST_44  H12  N3   N4   C5    180.00   0.0  0
 5XG  CONST_45  H2   C8   C7   C6    180.00   0.0  0
 5XG  CONST_46  H3   C12  C11  C7      0.00   0.0  0
 5XG  CONST_47  H1   C6   C7   C8    180.00   0.0  0
 5XG  CONST_48  H14  C14  N13  C12   180.00   0.0  0
 5XG  CONST_49  H19  N24  C25  C21   180.00   0.0  0
 5XG  Var_01    C19  N18  C17  C11   136.01  30.0  2
 5XG  Var_02    C20  C19  N18  C17  -142.31  30.0  1
 5XG  Var_03    C27  C28  N18  C17   142.03  30.0  1
 5XG  Var_04    C22  C21  C20  C19   -73.06  30.0  1
 5XG  Var_05    N24  C23  C22  C21   -28.12  30.0  1
 5XG  Var_06    N18  C19  C20  C21   -55.31  30.0  1
 5XG  Var_07    N18  C28  C27  C21    53.29  30.0  1
 5XG  Var_08    C20  C21  C22  C23   -87.40  30.0  3
 5XG  Var_09    N24  C25  C21  C27  -138.81  30.0  3
 5XG  Var_10    C28  C27  C21  C20   -52.41  30.0  1
 5XG  Var_11    C25  N24  C23  C22    19.08  30.0  1

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
 5XG  plan-1  C7   0.020
 5XG  plan-1  C11  0.020
 5XG  plan-1  C12  0.020
 5XG  plan-1  N13  0.020
 5XG  plan-1  C15  0.020
 5XG  plan-1  C17  0.020
 5XG  plan-1  C14  0.020
 5XG  plan-1  CL1  0.020
 5XG  plan-1  N18  0.020
 5XG  plan-1  H3   0.020
 5XG  plan-1  H14  0.020
 5XG  plan-2  C2   0.020
 5XG  plan-2  N1   0.020
 5XG  plan-2  H10  0.020
 5XG  plan-2  H11  0.020
 5XG  plan-3  C2   0.020
 5XG  plan-3  C5   0.020
 5XG  plan-3  C6   0.020
 5XG  plan-3  C7   0.020
 5XG  plan-3  C8   0.020
 5XG  plan-3  C11  0.020
 5XG  plan-3  N1   0.020
 5XG  plan-3  N3   0.020
 5XG  plan-3  N4   0.020
 5XG  plan-3  C9   0.020
 5XG  plan-3  C10  0.020
 5XG  plan-3  H1   0.020
 5XG  plan-3  H2   0.020
 5XG  plan-3  H12  0.020
 5XG  plan-3  H13  0.020
 5XG  plan-4  C21  0.020
 5XG  plan-4  C23  0.020
 5XG  plan-4  O26  0.020
 5XG  plan-4  N24  0.020
 5XG  plan-4  C25  0.020
 5XG  plan-4  H19  0.020

