# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 15:10:45 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)c1sc(cc1)C(=O)N2CCn3c(C2)ncc3c4ccccc4
#
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
 HA3  HA3  N-hydroxy-5-[(3-phenyl-5,6-dihydroimidazo[1,2-a]pyrazin-7(8H)-yl)carbonyl]thiophene-2-carboxamide  ligand  42  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HA3
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
 HA3  CAA   C  CR16  0  -0.309  17.4335   -5.1938   -9.2009
 HA3  CAB   C  CR16  0  -0.239  16.9795   -5.3665  -10.4994
 HA3  CAC   C  CR16  0  -0.264  16.8649   -6.6425  -11.0362
 HA3  CAD   C  CR16  0  -0.241  17.1996   -7.7436  -10.2593
 HA3  CAE   C  CR16  0  -0.301  17.6404   -7.5744   -8.9550
 HA3  CAF   C  CR6   0   0.053  17.7678   -6.2951   -8.4080
 HA3  CAG   C  CR5   0   0.282  18.1885   -6.0744   -7.0270
 HA3  CAH   C  CR15  0  -0.261  17.7072   -5.1943   -6.0926
 HA3  NAI   N  N     0  -0.461  18.3772   -5.3234   -4.9143
 HA3  CAJ   C  CR5   0   0.457  19.2616   -6.2648   -5.1216
 HA3  CAK   C  CH2   0  -0.393  20.2678   -6.7483   -4.1235
 HA3  NAL   N  NR5   0  -0.501  19.1944   -6.7554   -6.3784
 HA3  CAM   C  CH2   0  -0.290  20.0998   -7.7621   -6.9075
 HA3  CAN   C  CH2   0  -0.366  21.3187   -7.8345   -6.0069
 HA3  NAO   N  NT    0  -0.470  20.9122   -7.9508   -4.6175
 HA3  CAP   C  C     0   0.562  20.8094   -9.1795   -4.0591
 HA3  OAQ   O  O     0  -0.469  20.9902  -10.2108   -4.6891
 HA3  CAR   C  CR5   0  -0.324  20.5166   -9.2673   -2.6104
 HA3  SAS   S  S2    0   0.326  19.6820  -10.6619   -2.0694
 HA3  CAT   C  CR15  0  -0.179  20.9195   -8.4770   -1.5666
 HA3  CAU   C  CR15  0  -0.196  20.5237   -8.9957   -0.3156
 HA3  CAV   C  CR5   0  -0.305  19.8290  -10.1696   -0.4360
 HA3  CAW   C  C     0   0.523  19.2134  -11.0596    0.5691
 HA3  OAY   O  O     0  -0.460  18.7269  -12.1269    0.2396
 HA3  NAX   N  NH1   0  -0.386  19.2717  -10.6101    1.8376
 HA3  OAZ   O  OH1   0  -0.534  18.5692  -11.2714    2.7974
 HA3  HAA   H  HCR6  0   0.253  17.5438   -4.1942   -8.7999
 HA3  HAB   H  HCR6  0   0.259  16.7262   -4.4999  -11.0963
 HA3  HAC   H  HCR6  0   0.259  16.5172   -6.7789  -12.0518
 HA3  HAD   H  HCR6  0   0.260  17.1047   -8.7426  -10.6646
 HA3  HAE   H  HCR6  0   0.254  17.8596   -8.4505   -8.3586
 HA3  HAH   H  HCR5  0   0.259  16.8936   -4.4948   -6.2131
 HA3  HAK1  H  HCH2  0   0.289  21.0161   -5.9699   -3.9460
 HA3  HAK2  H  HCH2  0   0.300  19.7602   -6.9344   -3.1806
 HA3  HAM1  H  HCH2  0   0.270  19.6010   -8.7311   -6.9461
 HA3  HAM2  H  HCH2  0   0.283  20.3955   -7.4889   -7.9200
 HA3  HAN1  H  HCH2  0   0.293  21.9429   -8.6754   -6.2942
 HA3  HAN2  H  HCH2  0   0.284  21.9173   -6.9258   -6.1050
 HA3  HAT   H  HCR5  0   0.295  21.5010   -7.5728   -1.6783
 HA3  HAU   H  HCR5  0   0.282  20.7623   -8.5149    0.6225
 HA3  HAX   H  HNH1  0   0.422  19.4585   -9.6424    2.0576
 HA3  HAZ   H  HOH1  0   0.482  19.2114  -11.8142    3.2733

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
 HA3  CAA  CAB   aromatic  1.386  0.020  1.386
 HA3  CAA  CAF   aromatic  1.398  0.020  1.398
 HA3  CAB  CAC   aromatic  1.389  0.020  1.389
 HA3  CAC  CAD   aromatic  1.389  0.020  1.389
 HA3  CAD  CAE   aromatic  1.387  0.020  1.387
 HA3  CAE  CAF   aromatic  1.397  0.020  1.397
 HA3  CAF  CAG   single    1.460  0.020  1.460
 HA3  CAG  CAH   aromatic  1.371  0.020  1.371
 HA3  CAG  NAL   aromatic  1.377  0.020  1.377
 HA3  CAH  NAI   aromatic  1.362  0.020  1.362
 HA3  NAI  CAJ   aromatic  1.308  0.020  1.308
 HA3  CAJ  CAK   single    1.497  0.020  1.497
 HA3  CAJ  NAL   aromatic  1.351  0.020  1.351
 HA3  CAK  NAO   single    1.451  0.020  1.451
 HA3  NAL  CAM   single    1.454  0.020  1.454
 HA3  CAM  CAN   single    1.517  0.020  1.517
 HA3  CAN  NAO   single    1.452  0.020  1.452
 HA3  NAO  CAP   single    1.354  0.020  1.354
 HA3  CAP  OAQ   double    1.222  0.020  1.222
 HA3  CAP  CAR   single    1.481  0.020  1.481
 HA3  CAR  SAS   aromatic  1.713  0.020  1.713
 HA3  CAR  CAT   aromatic  1.370  0.020  1.370
 HA3  SAS  CAV   aromatic  1.712  0.020  1.712
 HA3  CAT  CAU   aromatic  1.411  0.020  1.411
 HA3  CAU  CAV   aromatic  1.369  0.020  1.369
 HA3  CAV  CAW   single    1.477  0.020  1.477
 HA3  CAW  OAY   double    1.218  0.020  1.218
 HA3  CAW  NAX   single    1.347  0.020  1.347
 HA3  NAX  OAZ   single    1.361  0.020  1.361
 HA3  CAA  HAA   single    0.930  0.020  1.080
 HA3  CAB  HAB   single    0.930  0.020  1.080
 HA3  CAC  HAC   single    0.930  0.020  1.080
 HA3  CAD  HAD   single    0.930  0.020  1.080
 HA3  CAE  HAE   single    0.930  0.020  1.080
 HA3  CAH  HAH   single    0.930  0.020  1.080
 HA3  CAK  HAK1  single    0.970  0.020  1.090
 HA3  CAK  HAK2  single    0.970  0.020  1.090
 HA3  CAM  HAM1  single    0.970  0.020  1.090
 HA3  CAM  HAM2  single    0.970  0.020  1.090
 HA3  CAN  HAN1  single    0.970  0.020  1.090
 HA3  CAN  HAN2  single    0.970  0.020  1.090
 HA3  CAT  HAT   single    0.930  0.020  1.080
 HA3  CAU  HAU   single    0.930  0.020  1.080
 HA3  NAX  HAX   single    0.890  0.020  1.040
 HA3  OAZ  HAZ   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
 HA3  HAA   CAA  CAF   119.54  3.000
 HA3  HAA   CAA  CAB   119.69  3.000
 HA3  CAF   CAA  CAB   120.77  3.000
 HA3  HAB   CAB  CAC   120.20  3.000
 HA3  HAB   CAB  CAA   119.57  3.000
 HA3  CAC   CAB  CAA   120.22  3.000
 HA3  HAC   CAC  CAD   120.17  3.000
 HA3  HAC   CAC  CAB   120.34  3.000
 HA3  CAD   CAC  CAB   119.50  3.000
 HA3  HAD   CAD  CAE   119.51  3.000
 HA3  HAD   CAD  CAC   120.09  3.000
 HA3  CAE   CAD  CAC   120.39  3.000
 HA3  HAE   CAE  CAF   120.47  3.000
 HA3  HAE   CAE  CAD   118.93  3.000
 HA3  CAF   CAE  CAD   120.59  3.000
 HA3  CAG   CAF  CAE   122.34  3.000
 HA3  CAG   CAF  CAA   119.10  3.000
 HA3  CAE   CAF  CAA   118.53  3.000
 HA3  NAL   CAG  CAH   104.65  3.000
 HA3  NAL   CAG  CAF   125.53  3.000
 HA3  CAH   CAG  CAF   129.82  3.000
 HA3  HAH   CAH  NAI   121.93  3.000
 HA3  HAH   CAH  CAG   127.19  3.000
 HA3  NAI   CAH  CAG   110.86  3.000
 HA3  CAJ   NAI  CAH   105.30  3.000
 HA3  NAL   CAJ  CAK   122.43  3.000
 HA3  NAL   CAJ  NAI   112.03  3.000
 HA3  CAK   CAJ  NAI   125.52  3.000
 HA3  HAK2  CAK  HAK1  107.48  3.000
 HA3  HAK2  CAK  NAO   111.15  3.000
 HA3  HAK1  CAK  NAO   109.94  3.000
 HA3  HAK2  CAK  CAJ   108.65  3.000
 HA3  HAK1  CAK  CAJ   109.75  3.000
 HA3  NAO   CAK  CAJ   109.82  3.000
 HA3  CAM   NAL  CAJ   124.00  3.000
 HA3  CAM   NAL  CAG   128.76  3.000
 HA3  CAJ   NAL  CAG   107.15  3.000
 HA3  HAM2  CAM  HAM1  108.30  3.000
 HA3  HAM2  CAM  CAN   110.21  3.000
 HA3  HAM1  CAM  CAN   110.25  3.000
 HA3  HAM2  CAM  NAL   109.49  3.000
 HA3  HAM1  CAM  NAL   110.09  3.000
 HA3  CAN   CAM  NAL   108.50  3.000
 HA3  HAN2  CAN  HAN1  107.78  3.000
 HA3  HAN2  CAN  NAO   107.81  3.000
 HA3  HAN1  CAN  NAO   110.61  3.000
 HA3  HAN2  CAN  CAM   110.31  3.000
 HA3  HAN1  CAN  CAM   109.98  3.000
 HA3  NAO   CAN  CAM   110.29  3.000
 HA3  CAP   NAO  CAN   119.25  3.000
 HA3  CAP   NAO  CAK   125.32  3.000
 HA3  CAN   NAO  CAK   112.56  3.000
 HA3  CAR   CAP  OAQ   118.92  3.000
 HA3  CAR   CAP  NAO   118.20  3.000
 HA3  OAQ   CAP  NAO   122.83  3.000
 HA3  CAT   CAR  SAS   111.86  3.000
 HA3  CAT   CAR  CAP   130.78  3.000
 HA3  SAS   CAR  CAP   116.98  3.000
 HA3  CAV   SAS  CAR    91.46  3.000
 HA3  HAT   CAT  CAU   123.37  3.000
 HA3  HAT   CAT  CAR   124.21  3.000
 HA3  CAU   CAT  CAR   112.39  3.000
 HA3  HAU   CAU  CAV   124.73  3.000
 HA3  HAU   CAU  CAT   122.96  3.000
 HA3  CAV   CAU  CAT   112.31  3.000
 HA3  CAW   CAV  CAU   131.93  3.000
 HA3  CAW   CAV  SAS   116.11  3.000
 HA3  CAU   CAV  SAS   111.95  3.000
 HA3  NAX   CAW  OAY   124.35  3.000
 HA3  NAX   CAW  CAV   114.95  3.000
 HA3  OAY   CAW  CAV   120.68  3.000
 HA3  HAX   NAX  OAZ   114.05  3.000
 HA3  HAX   NAX  CAW   122.20  3.000
 HA3  OAZ   NAX  CAW   118.66  3.000
 HA3  HAZ   OAZ  NAX   106.10  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
 HA3  CONST_01  CAD  CAC  CAB  CAA    0.00   0.0  0
 HA3  CONST_02  CAD  CAE  CAF  CAA    0.00   0.0  0
 HA3  CONST_05  CAE  CAF  CAA  CAB    0.00   0.0  0
 HA3  CONST_06  CAG  CAF  CAA  CAB  180.00   0.0  0
 HA3  CONST_07  CAE  CAD  CAC  CAB    0.00   0.0  0
 HA3  CONST_08  CAF  CAA  CAB  CAC    0.00   0.0  0
 HA3  CONST_09  CAF  CAE  CAD  CAC    0.00   0.0  0
 HA3  CONST_10  CAG  CAF  CAE  CAD  180.00   0.0  0
 HA3  CONST_13  NAI  CAH  CAG  CAF  180.00   0.0  0
 HA3  CONST_14  CAJ  NAL  CAG  CAF  180.00   0.0  0
 HA3  CONST_15  CAJ  NAI  CAH  CAG    0.00   0.0  0
 HA3  CONST_16  NAI  CAJ  NAL  CAG    0.00   0.0  0
 HA3  CONST_17  CAJ  NAL  CAG  CAH    0.00   0.0  0
 HA3  CONST_18  NAL  CAJ  NAI  CAH    0.00   0.0  0
 HA3  CONST_19  NAL  CAG  CAH  NAI    0.00   0.0  0
 HA3  CONST_20  CAU  CAV  SAS  CAR    0.00   0.0  0
 HA3  CONST_21  CAV  CAU  CAT  CAR    0.00   0.0  0
 HA3  CONST_22  CAU  CAT  CAR  SAS    0.00   0.0  0
 HA3  CONST_23  CAT  CAU  CAV  SAS    0.00   0.0  0
 HA3  CONST_24  CAV  SAS  CAR  CAT    0.00   0.0  0
 HA3  CONST_25  CAM  NAL  CAG  CAF    0.00   0.0  0
 HA3  CONST_26  CAV  SAS  CAR  CAP  180.00   0.0  0
 HA3  CONST_27  CAU  CAT  CAR  CAP  180.00   0.0  0
 HA3  CONST_28  CAW  CAV  SAS  CAR  180.00   0.0  0
 HA3  CONST_29  CAW  CAV  CAU  CAT  180.00   0.0  0
 HA3  CONST_31  CAR  CAP  NAO  CAN  180.00   0.0  0
 HA3  CONST_32  HAC  CAC  CAB  CAA  180.00   0.0  0
 HA3  CONST_33  HAE  CAE  CAF  CAA  180.00   0.0  0
 HA3  CONST_34  HAD  CAD  CAC  CAB  180.00   0.0  0
 HA3  CONST_35  HAA  CAA  CAB  CAC  180.00   0.0  0
 HA3  CONST_36  HAB  CAB  CAC  CAD  180.00   0.0  0
 HA3  CONST_37  HAH  CAH  CAG  CAF    0.00   0.0  0
 HA3  CONST_38  HAU  CAU  CAT  CAR  180.00   0.0  0
 HA3  CONST_39  HAT  CAT  CAR  SAS  180.00   0.0  0
 HA3  CONST_41  OAQ  CAP  NAO  CAN    0.00   0.0  0
 HA3  CONST_42  OAZ  NAX  CAW  CAV  180.00   0.0  0
 HA3  CONST_44  OAZ  NAX  CAW  OAY    0.00   0.0  0
 HA3  Var_01    CAN  CAM  NAL  CAG  159.21  30.0  1
 HA3  Var_02    NAO  CAK  CAJ  NAI  169.80  30.0  1
 HA3  Var_03    CAN  NAO  CAK  CAJ   45.81  30.0  1
 HA3  Var_04    CAM  CAN  NAO  CAK  -67.80  30.0  1
 HA3  Var_05    NAO  CAN  CAM  NAL   49.55  30.0  1
 HA3  Var_06    SAS  CAR  CAP  NAO  151.77  30.0  2
 HA3  Var_07    OAY  CAW  CAV  SAS    5.45  30.0  2

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
 HA3  plan-1  CAP  0.020
 HA3  plan-1  CAR  0.020
 HA3  plan-1  SAS  0.020
 HA3  plan-1  CAT  0.020
 HA3  plan-1  CAU  0.020
 HA3  plan-1  CAV  0.020
 HA3  plan-1  CAW  0.020
 HA3  plan-1  HAT  0.020
 HA3  plan-1  HAU  0.020
 HA3  plan-2  CAA  0.020
 HA3  plan-2  CAB  0.020
 HA3  plan-2  CAC  0.020
 HA3  plan-2  CAD  0.020
 HA3  plan-2  CAE  0.020
 HA3  plan-2  CAF  0.020
 HA3  plan-2  CAG  0.020
 HA3  plan-2  HAA  0.020
 HA3  plan-2  HAB  0.020
 HA3  plan-2  HAC  0.020
 HA3  plan-2  HAD  0.020
 HA3  plan-2  HAE  0.020
 HA3  plan-3  CAF  0.020
 HA3  plan-3  CAG  0.020
 HA3  plan-3  CAH  0.020
 HA3  plan-3  NAI  0.020
 HA3  plan-3  CAJ  0.020
 HA3  plan-3  CAK  0.020
 HA3  plan-3  NAL  0.020
 HA3  plan-3  CAM  0.020
 HA3  plan-3  HAH  0.020
 HA3  plan-4  CAK  0.020
 HA3  plan-4  CAN  0.020
 HA3  plan-4  NAO  0.020
 HA3  plan-4  CAP  0.020
 HA3  plan-4  OAQ  0.020
 HA3  plan-4  CAR  0.020
 HA3  plan-5  CAV  0.020
 HA3  plan-5  CAW  0.020
 HA3  plan-5  OAY  0.020
 HA3  plan-5  NAX  0.020
 HA3  plan-5  OAZ  0.020
 HA3  plan-5  HAX  0.020

