# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 09:58:03 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: (6~{S})-8-(3-pyrimidin-4-yl-1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,8-diazaspiro[5.5]undecane
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC[C@@]2(CCCN(C2)c3ccnc4[nH]cc(c5ccncn5)c34)NC1
#
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
 AQ5  AQ5  (6~{S})-8-(3-pyrimidin-4-yl-1~{H}-pyrrolo[2,3-b]pyridin-4-yl)-1,8-diazaspiro[5.5]undecane  ligand  50  26  .  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_AQ5
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
 AQ5  C4   C  CR6   0   0.172  -2.1064   1.5933   0.1852
 AQ5  C5   C  CR16  0  -0.344  -2.7788   2.6738  -0.3900
 AQ5  C6   C  CR16  0  -0.034  -2.2592   3.9326  -0.1676
 AQ5  N1   N  N     0  -0.401  -1.1548   4.1333   0.5477
 AQ5  N3   N  N     0  -0.397  -0.9969   1.7950   0.8990
 AQ5  CAV  C  CH2   0  -0.434   2.7023   0.7736   0.7730
 AQ5  CAW  C  CH2   0  -0.448   3.1940   0.0427   2.0192
 AQ5  CAX  C  CH2   0  -0.424   4.5919  -0.5211   1.8028
 AQ5  CAY  C  CH2   0  -0.297   4.6097  -1.3909   0.5574
 AQ5  NAZ  N  NH1   0  -0.608   4.1629  -0.6164  -0.5888
 AQ5  CAO  C  CT    0   0.088   2.8151  -0.0632  -0.5079
 AQ5  CAP  C  CH2   0  -0.305   1.7506  -1.1763  -0.5294
 AQ5  CAN  C  CH2   0  -0.431   2.6115   0.8145  -1.7436
 AQ5  CAM  C  CH2   0  -0.458   1.1812   1.3201  -1.8589
 AQ5  CAL  C  CH2   0  -0.311   0.1839   0.1804  -1.7767
 AQ5  NAK  N  NT    0  -0.485   0.4019  -0.6449  -0.5907
 AQ5  CAG  C  CR6   0   0.352  -0.6327  -1.4949  -0.2512
 AQ5  CAF  C  CR56  0  -0.035  -1.9477  -1.0337  -0.0046
 AQ5  CAH  C  CR16  0  -0.445  -0.4589  -2.8805  -0.1540
 AQ5  CAI  C  CR16  0  -0.089  -1.5371  -3.7307   0.0795
 AQ5  NAJ  N  N     0  -0.439  -2.7922  -3.3348   0.2102
 AQ5  CAE  C  CR56  0   0.459  -2.9450  -2.0191   0.1623
 AQ5  NAD  N  NR15  0  -0.660  -4.1464  -1.3864   0.2917
 AQ5  CAC  C  CR15  0  -0.029  -3.9594  -0.0471   0.2457
 AQ5  CAB  C  CR5   0  -0.069  -2.6256   0.2353   0.0797
 AQ5  C2   C  CR16  0   0.033  -0.5825   3.0433   1.0349
 AQ5  H1   H  HCR6  0   0.277  -3.6615   2.5355  -0.9982
 AQ5  H2   H  HCR6  0   0.278  -2.7401   4.8102  -0.5849
 AQ5  H3   H  HCH2  0   0.260   1.6671   1.0864   0.9164
 AQ5  H4   H  HCH2  0   0.214   3.2983   1.6835   0.6425
 AQ5  H5   H  HCH2  0   0.232   3.1823   0.7281   2.8698
 AQ5  H6   H  HCH2  0   0.213   2.5096  -0.7722   2.2796
 AQ5  H7   H  HCH2  0   0.210   5.3070   0.2983   1.6799
 AQ5  H8   H  HCH2  0   0.225   4.9152  -1.1041   2.6681
 AQ5  H9   H  HCH2  0   0.232   5.6241  -1.7393   0.3509
 AQ5  H10  H  HCH2  0   0.188   4.0079  -2.2940   0.7468
 AQ5  H11  H  HNH1  0   0.340   4.2481  -1.1706  -1.4329
 AQ5  H13  H  HCH2  0   0.214   1.9591  -1.8380  -1.3878
 AQ5  H14  H  HCH2  0   0.249   1.8396  -1.7887   0.3680
 AQ5  H15  H  HCH2  0   0.233   3.3148   1.6510  -1.7179
 AQ5  H16  H  HCH2  0   0.217   2.8581   0.2273  -2.6366
 AQ5  H17  H  HCH2  0   0.235   0.9755   2.0511  -1.0760
 AQ5  H18  H  HCH2  0   0.240   1.0412   1.8363  -2.8109
 AQ5  H19  H  HCH2  0   0.258  -0.8313   0.5706  -1.7796
 AQ5  H20  H  HCH2  0   0.221   0.2771  -0.4481  -2.6765
 AQ5  H21  H  HCR6  0   0.274   0.5091  -3.3311  -0.3173
 AQ5  H22  H  HCR6  0   0.255  -1.3601  -4.7997   0.1245
 AQ5  H23  H  HNR5  0   0.416  -5.0272  -1.8484   0.4525
 AQ5  H24  H  HCR5  0   0.302  -4.7839   0.6331   0.3887
 AQ5  H25  H  HCR6  0   0.256   0.3240   3.1891   1.6135

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
 AQ5  C2   N3   aromatic  1.322  0.020  1.322
 AQ5  C2   N1   aromatic  1.324  0.020  1.324
 AQ5  N3   C4   aromatic  1.335  0.020  1.335
 AQ5  N1   C6   aromatic  1.331  0.020  1.331
 AQ5  CAC  CAB  aromatic  1.373  0.020  1.373
 AQ5  CAC  NAD  aromatic  1.353  0.020  1.353
 AQ5  C4   CAB  single    1.458  0.020  1.458
 AQ5  C4   C5   aromatic  1.397  0.020  1.397
 AQ5  C6   C5   aromatic  1.380  0.020  1.380
 AQ5  CAB  CAF  aromatic  1.441  0.020  1.441
 AQ5  NAD  CAE  aromatic  1.364  0.020  1.364
 AQ5  CAF  CAE  aromatic  1.412  0.020  1.412
 AQ5  CAF  CAG  aromatic  1.415  0.020  1.415
 AQ5  CAE  NAJ  aromatic  1.325  0.020  1.325
 AQ5  CAM  CAL  single    1.517  0.020  1.517
 AQ5  CAM  CAN  single    1.521  0.020  1.521
 AQ5  CAL  NAK  single    1.461  0.020  1.461
 AQ5  NAJ  CAI  aromatic  1.323  0.020  1.323
 AQ5  CAG  NAK  single    1.381  0.020  1.381
 AQ5  CAG  CAH  aromatic  1.400  0.020  1.400
 AQ5  NAK  CAP  single    1.451  0.020  1.451
 AQ5  CAN  CAO  single    1.529  0.020  1.529
 AQ5  CAI  CAH  aromatic  1.393  0.020  1.393
 AQ5  CAV  CAO  single    1.534  0.020  1.534
 AQ5  CAV  CAW  single    1.526  0.020  1.526
 AQ5  CAP  CAO  single    1.540  0.020  1.540
 AQ5  CAO  NAZ  single    1.459  0.020  1.459
 AQ5  CAW  CAX  single    1.523  0.020  1.523
 AQ5  NAZ  CAY  single    1.454  0.020  1.454
 AQ5  CAX  CAY  single    1.519  0.020  1.519
 AQ5  C5   H1   single    0.930  0.020  1.080
 AQ5  C6   H2   single    0.930  0.020  1.080
 AQ5  CAV  H3   single    0.970  0.020  1.090
 AQ5  CAV  H4   single    0.970  0.020  1.090
 AQ5  CAW  H5   single    0.970  0.020  1.090
 AQ5  CAW  H6   single    0.970  0.020  1.090
 AQ5  CAX  H7   single    0.970  0.020  1.090
 AQ5  CAX  H8   single    0.970  0.020  1.090
 AQ5  CAY  H9   single    0.970  0.020  1.090
 AQ5  CAY  H10  single    0.970  0.020  1.090
 AQ5  NAZ  H11  single    0.890  0.020  1.040
 AQ5  CAP  H13  single    0.970  0.020  1.090
 AQ5  CAP  H14  single    0.970  0.020  1.090
 AQ5  CAN  H15  single    0.970  0.020  1.090
 AQ5  CAN  H16  single    0.970  0.020  1.090
 AQ5  CAM  H17  single    0.970  0.020  1.090
 AQ5  CAM  H18  single    0.970  0.020  1.090
 AQ5  CAL  H19  single    0.970  0.020  1.090
 AQ5  CAL  H20  single    0.970  0.020  1.090
 AQ5  CAH  H21  single    0.930  0.020  1.080
 AQ5  CAI  H22  single    0.930  0.020  1.080
 AQ5  NAD  H23  single    0.860  0.020  1.020
 AQ5  CAC  H24  single    0.930  0.020  1.080
 AQ5  C2   H25  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
 AQ5  CAB  C4   N3   118.40  3.000
 AQ5  CAB  C4   C5   121.30  3.000
 AQ5  N3   C4   C5   120.24  3.000
 AQ5  H1   C5   C6   120.99  3.000
 AQ5  H1   C5   C4   121.73  3.000
 AQ5  C6   C5   C4   117.27  3.000
 AQ5  H2   C6   N1   116.93  3.000
 AQ5  H2   C6   C5   120.62  3.000
 AQ5  N1   C6   C5   122.45  3.000
 AQ5  C2   N1   C6   115.62  3.000
 AQ5  C2   N3   C4   117.27  3.000
 AQ5  H4   CAV  H3   107.09  3.000
 AQ5  H4   CAV  CAO  108.27  3.000
 AQ5  H3   CAV  CAO  109.62  3.000
 AQ5  H4   CAV  CAW  108.65  3.000
 AQ5  H3   CAV  CAW  109.62  3.000
 AQ5  CAO  CAV  CAW  113.38  3.000
 AQ5  H6   CAW  H5   105.95  3.000
 AQ5  H6   CAW  CAX  109.39  3.000
 AQ5  H5   CAW  CAX  110.66  3.000
 AQ5  H6   CAW  CAV  110.43  3.000
 AQ5  H5   CAW  CAV  109.38  3.000
 AQ5  CAX  CAW  CAV  110.92  3.000
 AQ5  H8   CAX  H7   107.17  3.000
 AQ5  H8   CAX  CAY  109.90  3.000
 AQ5  H7   CAX  CAY  109.20  3.000
 AQ5  H8   CAX  CAW  110.90  3.000
 AQ5  H7   CAX  CAW  109.79  3.000
 AQ5  CAY  CAX  CAW  109.83  3.000
 AQ5  H10  CAY  H9   106.16  3.000
 AQ5  H10  CAY  NAZ  113.85  3.000
 AQ5  H9   CAY  NAZ  107.84  3.000
 AQ5  H10  CAY  CAX  108.78  3.000
 AQ5  H9   CAY  CAX  110.40  3.000
 AQ5  NAZ  CAY  CAX  109.74  3.000
 AQ5  H11  NAZ  CAO  109.34  3.000
 AQ5  H11  NAZ  CAY  109.85  3.000
 AQ5  CAO  NAZ  CAY  116.24  3.000
 AQ5  CAN  CAO  CAP  108.15  3.000
 AQ5  CAP  CAO  NAZ  111.32  3.000
 AQ5  CAN  CAO  NAZ  107.20  3.000
 AQ5  NAZ  CAO  CAV  108.72  3.000
 AQ5  CAP  CAO  CAV  110.79  3.000
 AQ5  CAN  CAO  CAV  110.60  3.000
 AQ5  H14  CAP  H13  106.74  3.000
 AQ5  H14  CAP  NAK  108.44  3.000
 AQ5  H13  CAP  NAK  111.24  3.000
 AQ5  H14  CAP  CAO  109.76  3.000
 AQ5  H13  CAP  CAO  108.27  3.000
 AQ5  NAK  CAP  CAO  112.23  3.000
 AQ5  H16  CAN  H15  106.51  3.000
 AQ5  H16  CAN  CAM  109.12  3.000
 AQ5  H15  CAN  CAM  110.63  3.000
 AQ5  H16  CAN  CAO  108.70  3.000
 AQ5  H15  CAN  CAO  109.54  3.000
 AQ5  CAM  CAN  CAO  112.16  3.000
 AQ5  H18  CAM  H17  106.55  3.000
 AQ5  H18  CAM  CAL  108.55  3.000
 AQ5  H17  CAM  CAL  109.93  3.000
 AQ5  H18  CAM  CAN  110.10  3.000
 AQ5  H17  CAM  CAN  110.22  3.000
 AQ5  CAL  CAM  CAN  111.37  3.000
 AQ5  H20  CAL  H19  106.35  3.000
 AQ5  H20  CAL  NAK  109.15  3.000
 AQ5  H19  CAL  NAK  110.13  3.000
 AQ5  H20  CAL  CAM  109.20  3.000
 AQ5  H19  CAL  CAM  110.12  3.000
 AQ5  NAK  CAL  CAM  111.73  3.000
 AQ5  CAG  NAK  CAL  115.80  3.000
 AQ5  CAG  NAK  CAP  117.42  3.000
 AQ5  CAL  NAK  CAP  112.32  3.000
 AQ5  CAH  CAG  CAF  115.20  3.000
 AQ5  CAH  CAG  NAK  122.22  3.000
 AQ5  CAF  CAG  NAK  122.56  3.000
 AQ5  CAB  CAF  CAE  105.99  3.000
 AQ5  CAE  CAF  CAG  116.71  3.000
 AQ5  CAB  CAF  CAG  137.24  3.000
 AQ5  H21  CAH  CAI  117.68  3.000
 AQ5  H21  CAH  CAG  120.91  3.000
 AQ5  CAI  CAH  CAG  121.32  3.000
 AQ5  H22  CAI  NAJ  116.48  3.000
 AQ5  H22  CAI  CAH  118.83  3.000
 AQ5  NAJ  CAI  CAH  124.65  3.000
 AQ5  CAE  NAJ  CAI  113.76  3.000
 AQ5  NAD  CAE  NAJ  123.95  3.000
 AQ5  NAJ  CAE  CAF  128.01  3.000
 AQ5  NAD  CAE  CAF  108.04  3.000
 AQ5  H23  NAD  CAC  125.46  3.000
 AQ5  H23  NAD  CAE  124.93  3.000
 AQ5  CAC  NAD  CAE  109.52  3.000
 AQ5  H24  CAC  CAB  128.96  3.000
 AQ5  H24  CAC  NAD  120.94  3.000
 AQ5  CAB  CAC  NAD  109.99  3.000
 AQ5  CAC  CAB  CAF  106.43  3.000
 AQ5  CAF  CAB  C4   131.07  3.000
 AQ5  CAC  CAB  C4   121.92  3.000
 AQ5  H25  C2   N3   116.31  3.000
 AQ5  H25  C2   N1   116.53  3.000
 AQ5  N3   C2   N1   127.15  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
 AQ5  CONST_01  N1   C2   N3   C4     0.00   0.0  0
 AQ5  CONST_02  NAD  CAC  CAB  C4   180.00   0.0  0
 AQ5  CONST_03  CAE  CAF  CAB  C4   180.00   0.0  0
 AQ5  CONST_04  CAG  CAF  CAB  C4     0.00   0.0  0
 AQ5  CONST_05  N1   C6   C5   C4     0.00   0.0  0
 AQ5  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 AQ5  CONST_09  C2   N1   C6   C5     0.00   0.0  0
 AQ5  CONST_10  N3   C2   N1   C6     0.00   0.0  0
 AQ5  CONST_11  N3   C4   C5   C6     0.00   0.0  0
 AQ5  CONST_12  CAB  C4   C5   C6   180.00   0.0  0
 AQ5  CONST_15  CAC  CAB  CAF  CAG  180.00   0.0  0
 AQ5  CONST_16  NAD  CAE  CAF  CAG  180.00   0.0  0
 AQ5  CONST_17  NAJ  CAE  CAF  CAG    0.00   0.0  0
 AQ5  CONST_18  NAJ  CAI  CAH  CAG    0.00   0.0  0
 AQ5  CONST_19  NAD  CAC  CAB  CAF    0.00   0.0  0
 AQ5  CONST_20  CAC  NAD  CAE  CAF    0.00   0.0  0
 AQ5  CONST_21  CAI  NAJ  CAE  CAF    0.00   0.0  0
 AQ5  CONST_22  CAI  CAH  CAG  CAF    0.00   0.0  0
 AQ5  CONST_23  CAB  CAF  CAG  CAH  180.00   0.0  0
 AQ5  CONST_24  CAE  CAF  CAG  CAH    0.00   0.0  0
 AQ5  CONST_25  CAE  NAJ  CAI  CAH    0.00   0.0  0
 AQ5  CONST_26  NAD  CAE  NAJ  CAI  180.00   0.0  0
 AQ5  CONST_27  CAC  NAD  CAE  NAJ  180.00   0.0  0
 AQ5  CONST_28  CAB  CAF  CAE  NAJ  180.00   0.0  0
 AQ5  CONST_29  CAB  CAC  NAD  CAE    0.00   0.0  0
 AQ5  CONST_30  CAC  CAB  CAF  CAE    0.00   0.0  0
 AQ5  CONST_31  CAB  CAF  CAE  NAD    0.00   0.0  0
 AQ5  CONST_32  C2   N3   C4   CAB  180.00   0.0  0
 AQ5  CONST_33  CAB  CAF  CAG  NAK    0.00   0.0  0
 AQ5  CONST_34  CAE  CAF  CAG  NAK  180.00   0.0  0
 AQ5  CONST_35  CAI  CAH  CAG  NAK  180.00   0.0  0
 AQ5  CONST_36  H25  C2   N3   C4   180.00   0.0  0
 AQ5  CONST_37  H24  CAC  CAB  C4     0.00   0.0  0
 AQ5  CONST_38  H2   C6   C5   C4   180.00   0.0  0
 AQ5  CONST_39  H1   C5   C6   N1   180.00   0.0  0
 AQ5  CONST_40  H21  CAH  CAG  NAK    0.00   0.0  0
 AQ5  CONST_41  H22  CAI  CAH  CAG  180.00   0.0  0
 AQ5  CONST_42  H23  NAD  CAE  CAF  180.00   0.0  0
 AQ5  Var_01    CAY  CAX  CAW  CAV  -54.32  30.0  1
 AQ5  Var_02    NAZ  CAY  CAX  CAW   57.02  30.0  1
 AQ5  Var_03    CAO  CAV  CAW  CAX   51.84  30.0  1
 AQ5  Var_04    CAO  NAZ  CAY  CAX  -59.95  30.0  1
 AQ5  Var_05    CAL  CAM  CAN  CAO  -52.51  30.0  1
 AQ5  Var_06    CAL  NAK  CAP  CAO   59.28  30.0  1
 AQ5  Var_07    CAM  CAL  NAK  CAP  -56.50  30.0  1
 AQ5  Var_08    CAF  CAG  NAK  CAP  166.66  30.0  1
 AQ5  Var_09    NAK  CAL  CAM  CAN   52.69  30.0  1

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
 AQ5  chir_01  CAO  CAV  CAP  NAZ  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
 AQ5  plan-1  C4   0.020
 AQ5  plan-1  C5   0.020
 AQ5  plan-1  C6   0.020
 AQ5  plan-1  N1   0.020
 AQ5  plan-1  N3   0.020
 AQ5  plan-1  CAB  0.020
 AQ5  plan-1  C2   0.020
 AQ5  plan-1  H1   0.020
 AQ5  plan-1  H2   0.020
 AQ5  plan-1  H25  0.020
 AQ5  plan-2  C4   0.020
 AQ5  plan-2  NAK  0.020
 AQ5  plan-2  CAG  0.020
 AQ5  plan-2  CAF  0.020
 AQ5  plan-2  CAH  0.020
 AQ5  plan-2  CAI  0.020
 AQ5  plan-2  NAJ  0.020
 AQ5  plan-2  CAE  0.020
 AQ5  plan-2  NAD  0.020
 AQ5  plan-2  CAC  0.020
 AQ5  plan-2  CAB  0.020
 AQ5  plan-2  H21  0.020
 AQ5  plan-2  H22  0.020
 AQ5  plan-2  H23  0.020
 AQ5  plan-2  H24  0.020

