# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 11:04:20 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-[4-[(6~{S})-1,8-diazaspiro[5.5]undecan-8-yl]-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-1,3-thiazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1CC[C@@]2(CCCN(C2)c3ccnc4[nH]cc(c5sccn5)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
 AQE  AQE  2-[4-[(6~{S})-1,8-diazaspiro[5.5]undecan-8-yl]-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]-1,3-thiazole  ligand  48  25  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_AQE
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
 AQE  NAN  N  N     0  -0.381  -2.0932   2.9059  -1.1171
 AQE  CAM  C  CR15  0  -0.032  -1.2291   3.9430  -0.9286
 AQE  CAL  C  CR15  0  -0.502  -0.2804   3.7565   0.0250
 AQE  SAK  S  S2    0   0.219  -0.4798   2.2088   0.7304
 AQE  CAJ  C  CR5   0  -0.067  -1.8212   1.9129  -0.3220
 AQE  CAA  C  CR5   0  -0.036  -2.6266   0.7117  -0.2023
 AQE  CAE  C  CR56  0  -0.052  -2.2559  -0.6616   0.0201
 AQE  CAB  C  CR15  0  -0.018  -3.9970   0.7623  -0.1466
 AQE  NAC  N  NR15  0  -0.659  -4.4920  -0.4703   0.1143
 AQE  CAD  C  CR56  0   0.465  -3.4646  -1.3562   0.2461
 AQE  NAI  N  N     0  -0.436  -3.6219  -2.6358   0.5525
 AQE  CAH  C  CR16  0  -0.088  -2.4864  -3.3053   0.6483
 AQE  CAG  C  CR16  0  -0.447  -1.2249  -2.7678   0.3964
 AQE  CAF  C  CR6   0   0.341  -1.0665  -1.4279   0.0304
 AQE  NAO  N  NT    0  -0.493   0.1622  -0.8885  -0.3227
 AQE  CAY  C  CH2   0  -0.310   1.3292  -1.7159  -0.0635
 AQE  CAP  C  CH2   0  -0.326   0.2168  -0.3089  -1.6688
 AQE  CAQ  C  CH2   0  -0.445   1.4706   0.5211  -1.8637
 AQE  CAR  C  CH2   0  -0.432   2.7196  -0.2884  -1.5456
 AQE  CAS  C  CT    0   0.065   2.6429  -0.9326  -0.1564
 AQE  CAX  C  CH2   0  -0.416   2.7221   0.1070   0.9733
 AQE  CAW  C  CH2   0  -0.443   4.1064   0.7368   1.0908
 AQE  CAV  C  CH2   0  -0.437   5.1825  -0.3365   1.2015
 AQE  CAU  C  CH2   0  -0.322   5.0455  -1.3560   0.0752
 AQE  NAT  N  NH1   0  -0.591   3.7109  -1.9300  -0.0361
 AQE  H1   H  HCR5  0   0.269  -1.3252   4.8347  -1.5317
 AQE  H2   H  HCR5  0   0.304   0.5115   4.4246   0.3240
 AQE  H3   H  HCR5  0   0.300  -4.6462   1.6175  -0.2372
 AQE  H4   H  HNR5  0   0.417  -5.4667  -0.6954   0.2331
 AQE  H5   H  HCR6  0   0.256  -2.5642  -4.3545   0.9116
 AQE  H6   H  HCR6  0   0.278  -0.3800  -3.4378   0.4461
 AQE  H7   H  HCH2  0   0.249   1.2510  -2.1336   0.9435
 AQE  H8   H  HCH2  0   0.226   1.3803  -2.5623  -0.7679
 AQE  H9   H  HCH2  0   0.225   0.2029  -1.1230  -2.4102
 AQE  H10  H  HCH2  0   0.269  -0.6667   0.2979  -1.8527
 AQE  H11  H  HCH2  0   0.242   1.5022   0.8607  -2.9009
 AQE  H12  H  HCH2  0   0.228   1.4230   1.4185  -1.2434
 AQE  H13  H  HCH2  0   0.225   2.8272  -1.0924  -2.2820
 AQE  H14  H  HCH2  0   0.237   3.6044   0.3440  -1.6447
 AQE  H15  H  HCH2  0   0.241   1.9608   0.8762   0.8461
 AQE  H16  H  HCH2  0   0.211   2.4818  -0.3953   1.9181
 AQE  H17  H  HCH2  0   0.215   4.3053   1.3762   0.2249
 AQE  H18  H  HCH2  0   0.231   4.1359   1.3963   1.9613
 AQE  H19  H  HCH2  0   0.223   6.1805   0.1098   1.1871
 AQE  H20  H  HCH2  0   0.210   5.0839  -0.8533   2.1629
 AQE  H21  H  HCH2  0   0.219   5.3103  -0.8912  -0.8789
 AQE  H22  H  HCH2  0   0.235   5.7524  -2.1763   0.2167
 AQE  H23  H  HNH1  0   0.334   3.5426  -2.4839   0.7985

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
 AQE  CAM  NAN  aromatic  1.363  0.020  1.363
 AQE  CAM  CAL  aromatic  1.358  0.020  1.358
 AQE  NAN  CAJ  aromatic  1.301  0.020  1.301
 AQE  CAL  SAK  aromatic  1.712  0.020  1.712
 AQE  CAB  CAA  aromatic  1.372  0.020  1.372
 AQE  CAB  NAC  aromatic  1.354  0.020  1.354
 AQE  CAJ  CAA  single    1.451  0.020  1.451
 AQE  CAJ  SAK  aromatic  1.730  0.020  1.730
 AQE  CAA  CAE  aromatic  1.440  0.020  1.440
 AQE  NAC  CAD  aromatic  1.363  0.020  1.363
 AQE  CAE  CAD  aromatic  1.412  0.020  1.412
 AQE  CAE  CAF  aromatic  1.415  0.020  1.415
 AQE  CAQ  CAP  single    1.516  0.020  1.516
 AQE  CAQ  CAR  single    1.522  0.020  1.522
 AQE  CAD  NAI  aromatic  1.325  0.020  1.325
 AQE  CAP  NAO  single    1.467  0.020  1.467
 AQE  NAI  CAH  aromatic  1.322  0.020  1.322
 AQE  CAF  NAO  single    1.388  0.020  1.388
 AQE  CAF  CAG  aromatic  1.398  0.020  1.398
 AQE  NAO  CAY  single    1.454  0.020  1.454
 AQE  CAR  CAS  single    1.533  0.020  1.533
 AQE  CAX  CAS  single    1.537  0.020  1.537
 AQE  CAX  CAW  single    1.525  0.020  1.525
 AQE  CAH  CAG  aromatic  1.394  0.020  1.394
 AQE  CAS  CAY  single    1.532  0.020  1.532
 AQE  CAS  NAT  single    1.466  0.020  1.466
 AQE  CAW  CAV  single    1.524  0.020  1.524
 AQE  NAT  CAU  single    1.457  0.020  1.457
 AQE  CAV  CAU  single    1.525  0.020  1.525
 AQE  CAM  H1   single    0.930  0.020  1.080
 AQE  CAL  H2   single    0.930  0.020  1.080
 AQE  CAB  H3   single    0.930  0.020  1.080
 AQE  NAC  H4   single    0.860  0.020  1.020
 AQE  CAH  H5   single    0.930  0.020  1.080
 AQE  CAG  H6   single    0.930  0.020  1.080
 AQE  CAY  H7   single    0.970  0.020  1.090
 AQE  CAY  H8   single    0.970  0.020  1.090
 AQE  CAP  H9   single    0.970  0.020  1.090
 AQE  CAP  H10  single    0.970  0.020  1.090
 AQE  CAQ  H11  single    0.970  0.020  1.090
 AQE  CAQ  H12  single    0.970  0.020  1.090
 AQE  CAR  H13  single    0.970  0.020  1.090
 AQE  CAR  H14  single    0.970  0.020  1.090
 AQE  CAX  H15  single    0.970  0.020  1.090
 AQE  CAX  H16  single    0.970  0.020  1.090
 AQE  CAW  H17  single    0.970  0.020  1.090
 AQE  CAW  H18  single    0.970  0.020  1.090
 AQE  CAV  H19  single    0.970  0.020  1.090
 AQE  CAV  H20  single    0.970  0.020  1.090
 AQE  CAU  H21  single    0.970  0.020  1.090
 AQE  CAU  H22  single    0.970  0.020  1.090
 AQE  NAT  H23  single    0.890  0.020  1.040

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
 AQE  CAJ  NAN  CAM  111.34  3.000
 AQE  H1   CAM  CAL  124.56  3.000
 AQE  H1   CAM  NAN  119.62  3.000
 AQE  CAL  CAM  NAN  115.81  3.000
 AQE  H2   CAL  SAK  122.09  3.000
 AQE  H2   CAL  CAM  128.50  3.000
 AQE  SAK  CAL  CAM  109.39  3.000
 AQE  CAJ  SAK  CAL   89.67  3.000
 AQE  CAA  CAJ  SAK  121.44  3.000
 AQE  SAK  CAJ  NAN  113.78  3.000
 AQE  CAA  CAJ  NAN  124.49  3.000
 AQE  CAB  CAA  CAE  106.62  3.000
 AQE  CAE  CAA  CAJ  131.25  3.000
 AQE  CAB  CAA  CAJ  121.81  3.000
 AQE  CAF  CAE  CAD  116.87  3.000
 AQE  CAF  CAE  CAA  137.24  3.000
 AQE  CAD  CAE  CAA  105.87  3.000
 AQE  H3   CAB  NAC  121.23  3.000
 AQE  H3   CAB  CAA  128.86  3.000
 AQE  NAC  CAB  CAA  109.84  3.000
 AQE  H4   NAC  CAD  124.93  3.000
 AQE  H4   NAC  CAB  125.45  3.000
 AQE  CAD  NAC  CAB  109.57  3.000
 AQE  NAI  CAD  NAC  124.10  3.000
 AQE  NAI  CAD  CAE  127.84  3.000
 AQE  NAC  CAD  CAE  108.05  3.000
 AQE  CAH  NAI  CAD  113.82  3.000
 AQE  H5   CAH  CAG  118.80  3.000
 AQE  H5   CAH  NAI  116.49  3.000
 AQE  CAG  CAH  NAI  124.68  3.000
 AQE  H6   CAG  CAF  121.22  3.000
 AQE  H6   CAG  CAH  117.42  3.000
 AQE  CAF  CAG  CAH  121.29  3.000
 AQE  NAO  CAF  CAG  122.65  3.000
 AQE  CAG  CAF  CAE  115.20  3.000
 AQE  NAO  CAF  CAE  122.14  3.000
 AQE  CAP  NAO  CAY  111.02  3.000
 AQE  CAY  NAO  CAF  116.37  3.000
 AQE  CAP  NAO  CAF  114.84  3.000
 AQE  H8   CAY  H7   107.37  3.000
 AQE  H8   CAY  CAS  108.30  3.000
 AQE  H7   CAY  CAS  108.21  3.000
 AQE  H8   CAY  NAO  111.12  3.000
 AQE  H7   CAY  NAO  108.93  3.000
 AQE  CAS  CAY  NAO  112.73  3.000
 AQE  H10  CAP  H9   106.76  3.000
 AQE  H10  CAP  CAQ  110.16  3.000
 AQE  H9   CAP  CAQ  109.18  3.000
 AQE  H10  CAP  NAO  110.22  3.000
 AQE  H9   CAP  NAO  108.99  3.000
 AQE  CAQ  CAP  NAO  111.41  3.000
 AQE  H12  CAQ  H11  106.57  3.000
 AQE  H12  CAQ  CAR  110.74  3.000
 AQE  H11  CAQ  CAR  109.89  3.000
 AQE  H12  CAQ  CAP  109.93  3.000
 AQE  H11  CAQ  CAP  108.44  3.000
 AQE  CAR  CAQ  CAP  111.14  3.000
 AQE  H14  CAR  H13  106.52  3.000
 AQE  H14  CAR  CAS  111.47  3.000
 AQE  H13  CAR  CAS  107.79  3.000
 AQE  H14  CAR  CAQ  109.75  3.000
 AQE  H13  CAR  CAQ  109.30  3.000
 AQE  CAS  CAR  CAQ  111.82  3.000
 AQE  NAT  CAS  CAX  111.23  3.000
 AQE  NAT  CAS  CAR  108.89  3.000
 AQE  CAX  CAS  CAR  112.28  3.000
 AQE  NAT  CAS  CAY  105.77  3.000
 AQE  CAX  CAS  CAY  110.20  3.000
 AQE  CAR  CAS  CAY  108.22  3.000
 AQE  H16  CAX  H15  105.71  3.000
 AQE  H16  CAX  CAW  108.76  3.000
 AQE  H15  CAX  CAW  110.58  3.000
 AQE  H16  CAX  CAS  108.19  3.000
 AQE  H15  CAX  CAS  110.83  3.000
 AQE  CAW  CAX  CAS  112.49  3.000
 AQE  H18  CAW  H17  105.83  3.000
 AQE  H18  CAW  CAV  110.37  3.000
 AQE  H17  CAW  CAV  109.91  3.000
 AQE  H18  CAW  CAX  109.58  3.000
 AQE  H17  CAW  CAX  110.19  3.000
 AQE  CAV  CAW  CAX  110.83  3.000
 AQE  H20  CAV  H19  106.63  3.000
 AQE  H20  CAV  CAU  108.94  3.000
 AQE  H19  CAV  CAU  110.19  3.000
 AQE  H20  CAV  CAW  109.41  3.000
 AQE  H19  CAV  CAW  110.86  3.000
 AQE  CAU  CAV  CAW  110.71  3.000
 AQE  H22  CAU  H21  106.00  3.000
 AQE  H22  CAU  NAT  107.87  3.000
 AQE  H21  CAU  NAT  108.82  3.000
 AQE  H22  CAU  CAV  110.37  3.000
 AQE  H21  CAU  CAV  109.77  3.000
 AQE  NAT  CAU  CAV  113.70  3.000
 AQE  H23  NAT  CAU  107.69  3.000
 AQE  H23  NAT  CAS  108.53  3.000
 AQE  CAU  NAT  CAS  113.92  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
 AQE  CONST_01  SAK  CAL  CAM  NAN     0.00   0.0  0
 AQE  CONST_04  CAL  SAK  CAJ  NAN     0.00   0.0  0
 AQE  CONST_05  CAA  CAJ  NAN  CAM   180.00   0.0  0
 AQE  CONST_06  SAK  CAJ  NAN  CAM     0.00   0.0  0
 AQE  CONST_07  CAJ  SAK  CAL  CAM     0.00   0.0  0
 AQE  CONST_08  CAJ  NAN  CAM  CAL     0.00   0.0  0
 AQE  CONST_09  CAA  CAJ  SAK  CAL   180.00   0.0  0
 AQE  CONST_12  NAC  CAB  CAA  CAJ   180.00   0.0  0
 AQE  CONST_13  CAD  CAE  CAA  CAJ   180.00   0.0  0
 AQE  CONST_14  CAF  CAE  CAA  CAJ     0.00   0.0  0
 AQE  CONST_15  CAD  NAC  CAB  CAA     0.00   0.0  0
 AQE  CONST_16  NAC  CAD  CAE  CAA     0.00   0.0  0
 AQE  CONST_17  NAI  CAD  CAE  CAA   180.00   0.0  0
 AQE  CONST_18  CAG  CAF  CAE  CAA   180.00   0.0  0
 AQE  CONST_19  NAC  CAB  CAA  CAE     0.00   0.0  0
 AQE  CONST_20  CAB  NAC  CAD  CAE     0.00   0.0  0
 AQE  CONST_21  CAH  NAI  CAD  CAE     0.00   0.0  0
 AQE  CONST_22  CAH  CAG  CAF  CAE     0.00   0.0  0
 AQE  CONST_23  CAD  CAE  CAA  CAB     0.00   0.0  0
 AQE  CONST_24  CAF  CAE  CAA  CAB   180.00   0.0  0
 AQE  CONST_25  NAI  CAD  NAC  CAB   180.00   0.0  0
 AQE  CONST_26  CAF  CAE  CAD  NAC   180.00   0.0  0
 AQE  CONST_27  CAH  NAI  CAD  NAC   180.00   0.0  0
 AQE  CONST_28  CAG  CAF  CAE  CAD     0.00   0.0  0
 AQE  CONST_29  CAG  CAH  NAI  CAD     0.00   0.0  0
 AQE  CONST_30  CAF  CAE  CAD  NAI     0.00   0.0  0
 AQE  CONST_31  CAF  CAG  CAH  NAI     0.00   0.0  0
 AQE  CONST_32  NAO  CAF  CAE  CAA     0.00   0.0  0
 AQE  CONST_33  NAO  CAF  CAE  CAD   180.00   0.0  0
 AQE  CONST_34  NAO  CAF  CAG  CAH   180.00   0.0  0
 AQE  CONST_35  H2   CAL  CAM  NAN   180.00   0.0  0
 AQE  CONST_36  H1   CAM  CAL  SAK   180.00   0.0  0
 AQE  CONST_37  H3   CAB  CAA  CAJ     0.00   0.0  0
 AQE  CONST_38  H4   NAC  CAB  CAA   180.00   0.0  0
 AQE  CONST_39  H6   CAG  CAF  CAE   180.00   0.0  0
 AQE  CONST_40  H5   CAH  NAI  CAD   180.00   0.0  0
 AQE  Var_01    CAP  NAO  CAF  CAE   -57.49  30.0  2
 AQE  Var_02    CAQ  CAP  NAO  CAF   167.37  30.0  1
 AQE  Var_03    CAS  CAY  NAO  CAF  -165.97  30.0  1
 AQE  Var_04    CAR  CAQ  CAP  NAO    54.59  30.0  1
 AQE  Var_05    CAS  CAR  CAQ  CAP   -52.93  30.0  1
 AQE  Var_06    CAV  CAW  CAX  CAS   -52.76  30.0  1
 AQE  Var_07    CAV  CAU  NAT  CAS    54.03  30.0  1
 AQE  Var_08    CAU  CAV  CAW  CAX    51.84  30.0  1
 AQE  Var_09    NAT  CAU  CAV  CAW   -52.86  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
 AQE  chir_01  CAS  CAX  CAY  NAT  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
 AQE  plan-1  NAN  0.020
 AQE  plan-1  CAM  0.020
 AQE  plan-1  CAL  0.020
 AQE  plan-1  SAK  0.020
 AQE  plan-1  CAJ  0.020
 AQE  plan-1  CAA  0.020
 AQE  plan-1  H1   0.020
 AQE  plan-1  H2   0.020
 AQE  plan-2  CAJ  0.020
 AQE  plan-2  CAA  0.020
 AQE  plan-2  CAE  0.020
 AQE  plan-2  CAB  0.020
 AQE  plan-2  NAC  0.020
 AQE  plan-2  CAD  0.020
 AQE  plan-2  NAI  0.020
 AQE  plan-2  CAH  0.020
 AQE  plan-2  CAG  0.020
 AQE  plan-2  CAF  0.020
 AQE  plan-2  NAO  0.020
 AQE  plan-2  H3   0.020
 AQE  plan-2  H4   0.020
 AQE  plan-2  H5   0.020
 AQE  plan-2  H6   0.020

