# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 13:48:37 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: 4-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}pentan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CCC(=O)N1CCC(CC1)c2onc(n2)c3sccc3
#
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
 LL4  LL4  4-methyl-1-{4-[3-(thiophen-2-yl)-1,2,4-oxadiazol-5-yl]piperidin-1-yl}pentan-1-one  ligand  46  23  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LL4
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
 LL4  CAV   C  CH3   0  -0.658   7.0875  -1.3372  -1.6445
 LL4  CAU   C  CH1   0  -0.236   6.6780  -1.5277  -0.1868
 LL4  CAW   C  CH3   0  -0.651   7.9076  -1.8021   0.6742
 LL4  CAT   C  CH2   0  -0.386   5.9117  -0.3238   0.3662
 LL4  CAS   C  CH2   0  -0.619   4.5805  -0.0834  -0.3292
 LL4  CAQ   C  C     0   0.582   3.7852   1.0555   0.2827
 LL4  OAR   O  O     0  -0.503   4.2147   1.6802   1.2440
 LL4  NAN   N  NT    0  -0.457   2.5955   1.3591  -0.2886
 LL4  CAO   C  CH2   0  -0.323   1.7419   2.3937   0.2672
 LL4  CAP   C  CH2   0  -0.422   0.4557   1.7953   0.8215
 LL4  CAM   C  CH2   0  -0.326   1.9619   0.6190  -1.3620
 LL4  CAL   C  CH2   0  -0.419   0.6832  -0.0512  -0.8762
 LL4  CAK   C  CH1   0  -0.409  -0.2629   0.9972  -0.2704
 LL4  CAH   C  CR5   0   0.570  -1.5151   0.3607   0.2089
 LL4  NAG   N  N     0  -0.461  -2.6836   0.3779  -0.3407
 LL4  OAI   O  O     0  -0.328  -1.4941  -0.3637   1.3197
 LL4  NAJ   N  N     0  -0.157  -2.7531  -0.8653   1.5141
 LL4  CAF   C  CR5   0   0.340  -3.4246  -0.3997   0.5022
 LL4  CAE   C  CR5   0  -0.278  -4.8238  -0.6722   0.2707
 LL4  CAD   C  CR15  0  -0.210  -5.6864  -1.4267   1.0175
 LL4  CAC   C  CR15  0  -0.168  -6.9875  -1.4664   0.4619
 LL4  CAB   C  CR15  0  -0.460  -7.0842  -0.7432  -0.6909
 LL4  SAA   S  S2    0   0.263  -5.6020  -0.0084  -1.1134
 LL4  HAV   H  HCH3  0   0.227   6.2313  -1.1919  -2.3043
 LL4  HAVA  H  HCH3  0   0.212   7.7413  -0.4675  -1.7508
 LL4  HAVB  H  HCH3  0   0.227   7.6339  -2.2066  -2.0138
 LL4  HAU   H  HCH1  0   0.212   6.0202  -2.4037  -0.1268
 LL4  HAW   H  HCH3  0   0.212   8.5998  -0.9575   0.6413
 LL4  HAWA  H  HCH3  0   0.223   7.6358  -1.9678   1.7183
 LL4  HAWB  H  HCH3  0   0.224   8.4471  -2.6850   0.3272
 LL4  HAT   H  HCH2  0   0.224   5.7362  -0.4816   1.4331
 LL4  HATA  H  HCH2  0   0.214   6.5428   0.5673   0.2871
 LL4  HAS   H  HCH2  0   0.269   4.7359   0.1268  -1.3910
 LL4  HASA  H  HCH2  0   0.261   3.9826  -1.0004  -0.2937
 LL4  HAO   H  HCH2  0   0.271   2.2769   2.9288   1.0462
 LL4  HAOA  H  HCH2  0   0.245   1.5091   3.1159  -0.5228
 LL4  HAP   H  HCH2  0   0.246   0.6991   1.1515   1.6705
 LL4  HAPA  H  HCH2  0   0.262  -0.1848   2.5987   1.1903
 LL4  HAM   H  HCH2  0   0.251   1.7247   1.3155  -2.1730
 LL4  HAMA  H  HCH2  0   0.281   2.6332  -0.1254  -1.7787
 LL4  HAL   H  HCH2  0   0.263   0.2008  -0.5557  -1.7153
 LL4  HALA  H  HCH2  0   0.248   0.9302  -0.8124  -0.1315
 LL4  HAK   H  HCH1  0   0.288  -0.5663   1.6828  -1.0669
 LL4  HAD   H  HCR5  0   0.273  -5.4008  -1.9320   1.9291
 LL4  HAC   H  HCR5  0   0.276  -7.8134  -2.0094   0.8970
 LL4  HAB   H  HCR5  0   0.305  -7.9543  -0.6037  -1.3136

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
 LL4  CAU  CAV   single    1.526  0.020  1.526
 LL4  CAV  HAV   single    0.970  0.020  1.090
 LL4  CAV  HAVA  single    0.970  0.020  1.090
 LL4  CAV  HAVB  single    0.970  0.020  1.090
 LL4  CAW  CAU   single    1.526  0.020  1.526
 LL4  CAU  CAT   single    1.531  0.020  1.531
 LL4  CAU  HAU   single    0.970  0.020  1.090
 LL4  CAW  HAW   single    0.970  0.020  1.090
 LL4  CAW  HAWA  single    0.970  0.020  1.090
 LL4  CAW  HAWB  single    0.970  0.020  1.090
 LL4  CAS  CAT   single    1.521  0.020  1.521
 LL4  CAT  HAT   single    0.970  0.020  1.090
 LL4  CAT  HATA  single    0.970  0.020  1.090
 LL4  CAQ  CAS   single    1.518  0.020  1.518
 LL4  CAS  HAS   single    0.970  0.020  1.090
 LL4  CAS  HASA  single    0.970  0.020  1.090
 LL4  OAR  CAQ   double    1.224  0.020  1.224
 LL4  CAQ  NAN   single    1.354  0.020  1.354
 LL4  CAM  NAN   single    1.450  0.020  1.450
 LL4  NAN  CAO   single    1.452  0.020  1.452
 LL4  CAO  CAP   single    1.523  0.020  1.523
 LL4  CAO  HAO   single    0.970  0.020  1.090
 LL4  CAO  HAOA  single    0.970  0.020  1.090
 LL4  CAK  CAP   single    1.532  0.020  1.532
 LL4  CAP  HAP   single    0.970  0.020  1.090
 LL4  CAP  HAPA  single    0.970  0.020  1.090
 LL4  CAM  CAL   single    1.523  0.020  1.523
 LL4  CAM  HAM   single    0.970  0.020  1.090
 LL4  CAM  HAMA  single    0.970  0.020  1.090
 LL4  CAL  CAK   single    1.537  0.020  1.537
 LL4  CAL  HAL   single    0.970  0.020  1.090
 LL4  CAL  HALA  single    0.970  0.020  1.090
 LL4  CAK  CAH   single    1.484  0.020  1.484
 LL4  CAK  HAK   single    0.970  0.020  1.090
 LL4  NAG  CAH   aromatic  1.291  0.020  1.291
 LL4  CAH  OAI   aromatic  1.326  0.020  1.326
 LL4  NAG  CAF   aromatic  1.365  0.020  1.365
 LL4  OAI  NAJ   aromatic  1.369  0.020  1.369
 LL4  CAF  NAJ   aromatic  1.301  0.020  1.301
 LL4  CAE  CAF   single    1.444  0.020  1.444
 LL4  SAA  CAE   aromatic  1.721  0.020  1.721
 LL4  CAE  CAD   aromatic  1.368  0.020  1.368
 LL4  CAC  CAD   aromatic  1.415  0.020  1.415
 LL4  CAD  HAD   single    0.930  0.020  1.080
 LL4  CAB  CAC   aromatic  1.364  0.020  1.364
 LL4  CAC  HAC   single    0.930  0.020  1.080
 LL4  SAA  CAB   aromatic  1.707  0.020  1.707
 LL4  CAB  HAB   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
 LL4  HAVB  CAV  HAVA  107.55  3.000
 LL4  HAVB  CAV  HAV   107.13  3.000
 LL4  HAVA  CAV  HAV   107.74  3.000
 LL4  HAVB  CAV  CAU   110.98  3.000
 LL4  HAVA  CAV  CAU   110.65  3.000
 LL4  HAV   CAV  CAU   112.58  3.000
 LL4  HAU   CAU  CAT   107.94  3.000
 LL4  HAU   CAU  CAW   107.98  3.000
 LL4  CAT   CAU  CAW   109.94  3.000
 LL4  HAU   CAU  CAV   108.23  3.000
 LL4  CAT   CAU  CAV   112.41  3.000
 LL4  CAW   CAU  CAV   110.20  3.000
 LL4  HAWB  CAW  HAWA  107.72  3.000
 LL4  HAWB  CAW  HAW   107.61  3.000
 LL4  HAWA  CAW  HAW   107.69  3.000
 LL4  HAWB  CAW  CAU   111.37  3.000
 LL4  HAWA  CAW  CAU   111.49  3.000
 LL4  HAW   CAW  CAU   110.76  3.000
 LL4  HATA  CAT  HAT   106.30  3.000
 LL4  HATA  CAT  CAS   110.05  3.000
 LL4  HAT   CAT  CAS   109.19  3.000
 LL4  HATA  CAT  CAU   109.00  3.000
 LL4  HAT   CAT  CAU   108.64  3.000
 LL4  CAS   CAT  CAU   113.41  3.000
 LL4  HASA  CAS  HAS   105.67  3.000
 LL4  HASA  CAS  CAQ   109.21  3.000
 LL4  HAS   CAS  CAQ   108.76  3.000
 LL4  HASA  CAS  CAT   109.31  3.000
 LL4  HAS   CAS  CAT   110.48  3.000
 LL4  CAQ   CAS  CAT   113.13  3.000
 LL4  NAN   CAQ  OAR   121.67  3.000
 LL4  NAN   CAQ  CAS   117.29  3.000
 LL4  OAR   CAQ  CAS   121.04  3.000
 LL4  CAM   NAN  CAO   112.97  3.000
 LL4  CAO   NAN  CAQ   120.99  3.000
 LL4  CAM   NAN  CAQ   125.58  3.000
 LL4  HAOA  CAO  HAO   107.28  3.000
 LL4  HAOA  CAO  CAP   110.00  3.000
 LL4  HAO   CAO  CAP   110.40  3.000
 LL4  HAOA  CAO  NAN   108.58  3.000
 LL4  HAO   CAO  NAN   109.64  3.000
 LL4  CAP   CAO  NAN   110.85  3.000
 LL4  HAPA  CAP  HAP   107.56  3.000
 LL4  HAPA  CAP  CAK   110.43  3.000
 LL4  HAP   CAP  CAK   110.57  3.000
 LL4  HAPA  CAP  CAO   109.23  3.000
 LL4  HAP   CAP  CAO   109.03  3.000
 LL4  CAK   CAP  CAO   109.97  3.000
 LL4  HAMA  CAM  HAM   106.61  3.000
 LL4  HAMA  CAM  CAL   109.87  3.000
 LL4  HAM   CAM  CAL   109.52  3.000
 LL4  HAMA  CAM  NAN   111.35  3.000
 LL4  HAM   CAM  NAN   108.56  3.000
 LL4  CAL   CAM  NAN   110.82  3.000
 LL4  HALA  CAL  HAL   107.56  3.000
 LL4  HALA  CAL  CAK   110.22  3.000
 LL4  HAL   CAL  CAK   110.27  3.000
 LL4  HALA  CAL  CAM   109.50  3.000
 LL4  HAL   CAL  CAM   109.22  3.000
 LL4  CAK   CAL  CAM   110.02  3.000
 LL4  HAK   CAK  CAH   105.66  3.000
 LL4  HAK   CAK  CAL   108.14  3.000
 LL4  CAH   CAK  CAL   110.74  3.000
 LL4  HAK   CAK  CAP   108.82  3.000
 LL4  CAH   CAK  CAP   112.90  3.000
 LL4  CAL   CAK  CAP   110.35  3.000
 LL4  OAI   CAH  NAG   112.22  3.000
 LL4  OAI   CAH  CAK   119.43  3.000
 LL4  NAG   CAH  CAK   128.33  3.000
 LL4  CAF   NAG  CAH   102.75  3.000
 LL4  NAJ   OAI  CAH   107.73  3.000
 LL4  CAF   NAJ  OAI   103.48  3.000
 LL4  CAE   CAF  NAJ   123.88  3.000
 LL4  CAE   CAF  NAG   122.30  3.000
 LL4  NAJ   CAF  NAG   113.82  3.000
 LL4  SAA   CAE  CAD   111.51  3.000
 LL4  CAD   CAE  CAF   128.87  3.000
 LL4  SAA   CAE  CAF   119.62  3.000
 LL4  HAD   CAD  CAC   124.12  3.000
 LL4  HAD   CAD  CAE   123.49  3.000
 LL4  CAC   CAD  CAE   112.39  3.000
 LL4  HAC   CAC  CAB   123.56  3.000
 LL4  HAC   CAC  CAD   123.99  3.000
 LL4  CAB   CAC  CAD   112.46  3.000
 LL4  HAB   CAB  SAA   120.10  3.000
 LL4  HAB   CAB  CAC   127.83  3.000
 LL4  SAA   CAB  CAC   112.07  3.000
 LL4  CAB   SAA  CAE    91.58  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
 LL4  CONST_01  NAJ  CAF  NAG  CAH    0.00   0.0  0
 LL4  CONST_02  CAE  CAF  NAG  CAH  180.00   0.0  0
 LL4  CONST_03  CAF  NAJ  OAI  CAH    0.00   0.0  0
 LL4  CONST_04  NAJ  OAI  CAH  NAG    0.00   0.0  0
 LL4  CONST_05  OAI  NAJ  CAF  NAG    0.00   0.0  0
 LL4  CONST_06  SAA  CAE  CAF  NAG    0.00   0.0  0
 LL4  CONST_07  CAD  CAE  CAF  NAG  180.00   0.0  0
 LL4  CONST_08  CAF  NAG  CAH  OAI    0.00   0.0  0
 LL4  CONST_09  CAE  CAF  NAJ  OAI  180.00   0.0  0
 LL4  CONST_10  SAA  CAE  CAF  NAJ  180.00   0.0  0
 LL4  CONST_11  CAD  CAE  CAF  NAJ    0.00   0.0  0
 LL4  CONST_12  CAB  SAA  CAE  CAF  180.00   0.0  0
 LL4  CONST_13  CAC  CAD  CAE  CAF  180.00   0.0  0
 LL4  CONST_14  CAC  CAB  SAA  CAE    0.00   0.0  0
 LL4  CONST_15  CAB  CAC  CAD  CAE    0.00   0.0  0
 LL4  CONST_16  CAB  SAA  CAE  CAD    0.00   0.0  0
 LL4  CONST_17  SAA  CAB  CAC  CAD    0.00   0.0  0
 LL4  CONST_18  SAA  CAE  CAD  CAC    0.00   0.0  0
 LL4  CONST_19  CAF  NAG  CAH  CAK  180.00   0.0  0
 LL4  CONST_20  NAJ  OAI  CAH  CAK  180.00   0.0  0
 LL4  CONST_21  HAD  CAD  CAE  CAF    0.00   0.0  0
 LL4  CONST_22  HAB  CAB  SAA  CAE  180.00   0.0  0
 LL4  CONST_23  HAC  CAC  CAD  CAE  180.00   0.0  0
 LL4  CONST_24  CAM  NAN  CAQ  CAS    0.00   0.0  0
 LL4  CONST_25  CAO  NAN  CAQ  CAS  180.00   0.0  0
 LL4  CONST_26  CAM  NAN  CAQ  OAR  180.00   0.0  0
 LL4  CONST_27  CAO  NAN  CAQ  OAR    0.00   0.0  0
 LL4  Var_01    CAK  CAL  CAM  NAN   55.86  30.0  1
 LL4  Var_02    CAK  CAP  CAO  NAN  -56.10  30.0  1
 LL4  Var_03    CAL  CAM  NAN  CAO  -59.18  30.0  1
 LL4  Var_04    CAM  NAN  CAO  CAP   59.31  30.0  1
 LL4  Var_05    NAN  CAQ  CAS  CAT  178.77  30.0  2
 LL4  Var_06    CAS  CAT  CAU  CAV   63.91  30.0  3
 LL4  Var_07    CAQ  CAS  CAT  CAU  176.27  30.0  1
 LL4  Var_08    HAW  CAW  CAU  CAV   61.58  30.0  3
 LL4  Var_09    HAV  CAV  CAU  CAW  176.90  30.0  3

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
 LL4  chir_01  CAK  CAP  CAL  CAH  negativ

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
 LL4  plan-1  CAK  0.020
 LL4  plan-1  CAH  0.020
 LL4  plan-1  NAG  0.020
 LL4  plan-1  OAI  0.020
 LL4  plan-1  NAJ  0.020
 LL4  plan-1  CAF  0.020
 LL4  plan-1  CAE  0.020
 LL4  plan-2  CAF  0.020
 LL4  plan-2  CAE  0.020
 LL4  plan-2  CAD  0.020
 LL4  plan-2  CAC  0.020
 LL4  plan-2  CAB  0.020
 LL4  plan-2  SAA  0.020
 LL4  plan-2  HAD  0.020
 LL4  plan-2  HAC  0.020
 LL4  plan-2  HAB  0.020
 LL4  plan-3  CAS  0.020
 LL4  plan-3  CAQ  0.020
 LL4  plan-3  OAR  0.020
 LL4  plan-3  NAN  0.020
 LL4  plan-3  CAO  0.020
 LL4  plan-3  CAM  0.020

