# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:11:26 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: 4-({4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-1,4-diazepan-1-yl}carbonyl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)N1CCCN(CC1)C(=O)c2ccc(cc2)C(O)=O)Cc3cc(F)c(F)cc3F
#
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
 AJH  AJH  '4-({4-[(3R)-3-amino-4-(2,4,5-trifluorophenyl)butanoyl]-1,4-diazepan-1-yl}carbonyl)benzoic acid'  ligand  56  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_AJH
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
 AJH  CAP   C  CR16   0  -0.246   5.0291  -0.0207  -0.5847
 AJH  CAX   C  CR16   0  -0.277   5.9676   0.9721  -0.8209
 AJH  CAO   C  CR6    0  -0.099   6.7809   1.4466   0.2044
 AJH  CAJ   C  C      0   0.399   7.8091   2.5414  -0.0590
 AJH  OAW   O  OC    -1  -0.591   8.5189   2.8814   0.9061
 AJH  OBD   O  O      0  -0.591   7.8489   2.9982  -1.2169
 AJH  CAY   C  CR16   0  -0.280   6.6376   0.8901   1.4732
 AJH  CAQ   C  CR16   0  -0.265   5.7119  -0.1132   1.7138
 AJH  CAB   C  CR6    0  -0.074   4.8876  -0.5652   0.6876
 AJH  CAA   C  C      0   0.514   3.9580  -1.7082   0.9464
 AJH  OAN   O  O      0  -0.487   4.4189  -2.7871   1.2962
 AJH  NAD   N  NT     0  -0.446   2.6333  -1.5067   0.7828
 AJH  CAR   C  CH2    0  -0.324   2.0091  -0.2249   0.5009
 AJH  CAS   C  CH2    0  -0.335   1.4391  -0.1272  -0.9129
 AJH  CBE   C  CH2    0  -0.320   1.7240  -2.6350   0.9440
 AJH  CBC   C  CH2    0  -0.445   1.5061  -3.4139  -0.3487
 AJH  CBF   C  CH2    0  -0.313   1.3227  -2.5035  -1.5643
 AJH  NAE   N  NT     0  -0.460   0.6117  -1.2651  -1.2737
 AJH  CAC   C  C      0   0.586  -0.7353  -1.2974  -1.1497
 AJH  OAU   O  O      0  -0.498  -1.3580  -2.3381  -1.3257
 AJH  CAF   C  CH2    0  -0.616  -1.4395  -0.0017  -0.7942
 AJH  CAV   C  CH1    0  -0.074  -2.9596  -0.1442  -0.6680
 AJH  NBG   N  NH2    0  -0.784  -3.6518  -0.4842  -1.8964
 AJH  CAT   C  CH2    0  -0.515  -3.5358   1.1621  -0.1048
 AJH  CAG   C  CR6    0  -0.041  -4.9990   1.0419   0.2014
 AJH  CAM   C  CR16   0  -0.444  -5.4194   0.5170   1.4214
 AJH  CAL   C  CR6    0   0.403  -6.7585   0.3573   1.7055
 AJH  FBB   F  F      0  -0.308  -7.1463  -0.1448   2.8840
 AJH  CAK   C  CR6    0   0.397  -7.7156   0.7211   0.7758
 AJH  FBA   F  F      0  -0.303  -9.0099   0.5621   1.0644
 AJH  CAH   C  CR16   0  -0.558  -7.3388   1.2493  -0.4405
 AJH  CAI   C  CR6    0   0.525  -5.9885   1.3957  -0.7016
 AJH  FAZ   F  F      0  -0.306  -5.6413   1.9229  -1.8838
 AJH  HAP   H  HCR6   0   0.249   4.4200  -0.3835  -1.4034
 AJH  HAX   H  HCR6   0   0.248   6.0706   1.3823  -1.8164
 AJH  HAY   H  HCR6   0   0.248   7.2650   1.2424   2.2811
 AJH  HAQ   H  HCR6   0   0.255   5.6244  -0.5378   2.7063
 AJH  HAR   H  HCH2   0   0.263   1.2086  -0.0763   1.2315
 AJH  HARA  H  HCH2   0   0.281   2.7210   0.5843   0.6527
 AJH  HAS   H  HCH2   0   0.282   0.8777   0.8015  -0.9964
 AJH  HASA  H  HCH2   0   0.262   2.2492  -0.0582  -1.6414
 AJH  HBE   H  HCH2   0   0.267   2.0963  -3.2983   1.7226
 AJH  HBEA  H  HCH2   0   0.249   0.7743  -2.2353   1.3026
 AJH  HBC   H  HCH2   0   0.244   2.3550  -4.0743  -0.5384
 AJH  HBCA  H  HCH2   0   0.244   0.6340  -4.0560  -0.2155
 AJH  HBF   H  HCH2   0   0.247   2.2967  -2.2182  -1.9635
 AJH  HBFA  H  HCH2   0   0.263   0.8110  -3.0424  -2.3611
 AJH  HAF   H  HCH2   0   0.267  -1.0289   0.3785   0.1470
 AJH  HAFA  H  HCH2   0   0.273  -1.2126   0.7599  -1.5490
 AJH  HAV   H  HCH1   0   0.237  -3.1700  -0.9362   0.0578
 AJH  HNBG  H  HNH2   0   0.333  -3.4505   0.2103  -2.6068
 AJH  HNBA  H  HNH2   0   0.350  -3.2965  -1.3640  -2.2464
 AJH  HAT   H  HCH2   0   0.260  -3.0034   1.4213   0.8127
 AJH  HATA  H  HCH2   0   0.254  -3.3501   1.9754  -0.8110
 AJH  HAM   H  HCR6   0   0.291  -4.6858   0.2301   2.1653
 AJH  HAH   H  HCR6   0   0.310  -8.0840   1.5385  -1.1703

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
 AJH  CAP  CAB   aromatic  1.391  0.020  1.391
 AJH  CAP  CAX   aromatic  1.386  0.020  1.386
 AJH  CAP  HAP   single    0.930  0.020  1.080
 AJH  CAX  CAO   aromatic  1.392  0.020  1.392
 AJH  CAX  HAX   single    0.930  0.020  1.080
 AJH  CAO  CAY   aromatic  1.393  0.020  1.393
 AJH  CAO  CAJ   single    1.525  0.020  1.525
 AJH  OBD  CAJ   deloc     1.245  0.020  1.245
 AJH  CAJ  OAW   deloc     1.245  0.020  1.245
 AJH  CAQ  CAY   aromatic  1.386  0.020  1.386
 AJH  CAY  HAY   single    0.930  0.020  1.080
 AJH  CAB  CAQ   aromatic  1.392  0.020  1.392
 AJH  CAQ  HAQ   single    0.930  0.020  1.080
 AJH  CAA  CAB   single    1.496  0.020  1.496
 AJH  NAD  CAA   single    1.350  0.020  1.350
 AJH  CAA  OAN   double    1.224  0.020  1.224
 AJH  CBE  NAD   single    1.458  0.020  1.458
 AJH  NAD  CAR   single    1.453  0.020  1.453
 AJH  CAR  CAS   single    1.528  0.020  1.528
 AJH  CAR  HAR   single    0.970  0.020  1.090
 AJH  CAR  HARA  single    0.970  0.020  1.090
 AJH  CAS  NAE   single    1.452  0.020  1.452
 AJH  CAS  HAS   single    0.970  0.020  1.090
 AJH  CAS  HASA  single    0.970  0.020  1.090
 AJH  CBE  CBC   single    1.525  0.020  1.525
 AJH  CBE  HBE   single    0.970  0.020  1.090
 AJH  CBE  HBEA  single    0.970  0.020  1.090
 AJH  CBC  CBF   single    1.530  0.020  1.530
 AJH  CBC  HBC   single    0.970  0.020  1.090
 AJH  CBC  HBCA  single    0.970  0.020  1.090
 AJH  NAE  CBF   single    1.457  0.020  1.457
 AJH  CBF  HBF   single    0.970  0.020  1.090
 AJH  CBF  HBFA  single    0.970  0.020  1.090
 AJH  NAE  CAC   single    1.353  0.020  1.353
 AJH  OAU  CAC   double    1.225  0.020  1.225
 AJH  CAC  CAF   single    1.517  0.020  1.517
 AJH  CAF  CAV   single    1.532  0.020  1.532
 AJH  CAF  HAF   single    0.970  0.020  1.090
 AJH  CAF  HAFA  single    0.970  0.020  1.090
 AJH  CAT  CAV   single    1.535  0.020  1.535
 AJH  CAV  NBG   single    1.450  0.020  1.450
 AJH  CAV  HAV   single    0.970  0.020  1.090
 AJH  NBG  HNBG  single    0.890  0.020  1.040
 AJH  NBG  HNBA  single    0.890  0.020  1.040
 AJH  CAT  CAG   single    1.500  0.020  1.500
 AJH  CAT  HAT   single    0.970  0.020  1.090
 AJH  CAT  HATA  single    0.970  0.020  1.090
 AJH  CAI  CAG   aromatic  1.386  0.020  1.386
 AJH  CAG  CAM   aromatic  1.393  0.020  1.393
 AJH  CAM  CAL   aromatic  1.378  0.020  1.378
 AJH  CAM  HAM   single    0.930  0.020  1.080
 AJH  CAK  CAL   aromatic  1.383  0.020  1.383
 AJH  CAL  FBB   single    1.338  0.020  1.338
 AJH  CAH  CAK   aromatic  1.379  0.020  1.379
 AJH  FBA  CAK   single    1.336  0.020  1.336
 AJH  CAI  CAH   aromatic  1.383  0.020  1.383
 AJH  CAH  HAH   single    0.930  0.020  1.080
 AJH  FAZ  CAI   single    1.340  0.020  1.340

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
 AJH  HAP   CAP  CAB   120.20  3.000
 AJH  HAP   CAP  CAX   119.47  3.000
 AJH  CAB   CAP  CAX   120.33  3.000
 AJH  HAX   CAX  CAO   119.53  3.000
 AJH  HAX   CAX  CAP   119.52  3.000
 AJH  CAO   CAX  CAP   120.94  3.000
 AJH  CAY   CAO  CAJ   120.90  3.000
 AJH  CAJ   CAO  CAX   120.76  3.000
 AJH  CAY   CAO  CAX   118.33  3.000
 AJH  OBD   CAJ  OAW   127.03  3.000
 AJH  OAW   CAJ  CAO   116.52  3.000
 AJH  OBD   CAJ  CAO   116.45  3.000
 AJH  HAY   CAY  CAQ   119.56  3.000
 AJH  HAY   CAY  CAO   119.37  3.000
 AJH  CAQ   CAY  CAO   121.07  3.000
 AJH  HAQ   CAQ  CAB   120.04  3.000
 AJH  HAQ   CAQ  CAY   119.79  3.000
 AJH  CAB   CAQ  CAY   120.17  3.000
 AJH  CAA   CAB  CAQ   119.25  3.000
 AJH  CAA   CAB  CAP   121.37  3.000
 AJH  CAQ   CAB  CAP   119.15  3.000
 AJH  NAD   CAA  OAN   122.39  3.000
 AJH  OAN   CAA  CAB   119.26  3.000
 AJH  NAD   CAA  CAB   118.35  3.000
 AJH  CBE   NAD  CAR   115.85  3.000
 AJH  CAR   NAD  CAA   125.21  3.000
 AJH  CBE   NAD  CAA   118.89  3.000
 AJH  HARA  CAR  HAR   106.52  3.000
 AJH  HARA  CAR  CAS   109.00  3.000
 AJH  HAR   CAR  CAS   109.65  3.000
 AJH  HARA  CAR  NAD   110.35  3.000
 AJH  HAR   CAR  NAD   107.74  3.000
 AJH  CAS   CAR  NAD   113.34  3.000
 AJH  HASA  CAS  HAS   106.12  3.000
 AJH  HASA  CAS  NAE   107.84  3.000
 AJH  HAS   CAS  NAE   110.83  3.000
 AJH  HASA  CAS  CAR   110.16  3.000
 AJH  HAS   CAS  CAR   108.55  3.000
 AJH  NAE   CAS  CAR   113.11  3.000
 AJH  HBEA  CBE  HBE   106.61  3.000
 AJH  HBEA  CBE  CBC   109.96  3.000
 AJH  HBE   CBE  CBC   110.12  3.000
 AJH  HBEA  CBE  NAD   107.21  3.000
 AJH  HBE   CBE  NAD   109.71  3.000
 AJH  CBC   CBE  NAD   113.00  3.000
 AJH  HBCA  CBC  HBC   106.66  3.000
 AJH  HBCA  CBC  CBF   110.57  3.000
 AJH  HBC   CBC  CBF   108.36  3.000
 AJH  HBCA  CBC  CBE   108.14  3.000
 AJH  HBC   CBC  CBE   110.19  3.000
 AJH  CBF   CBC  CBE   112.75  3.000
 AJH  HBFA  CBF  HBF   106.32  3.000
 AJH  HBFA  CBF  NAE   109.70  3.000
 AJH  HBF   CBF  NAE   106.64  3.000
 AJH  HBFA  CBF  CBC   110.06  3.000
 AJH  HBF   CBF  CBC   109.84  3.000
 AJH  NAE   CBF  CBC   113.95  3.000
 AJH  CAC   NAE  CBF   118.92  3.000
 AJH  CAC   NAE  CAS   124.26  3.000
 AJH  CBF   NAE  CAS   115.94  3.000
 AJH  CAF   CAC  OAU   121.55  3.000
 AJH  CAF   CAC  NAE   117.59  3.000
 AJH  OAU   CAC  NAE   120.86  3.000
 AJH  HAFA  CAF  HAF   105.85  3.000
 AJH  HAFA  CAF  CAV   109.07  3.000
 AJH  HAF   CAF  CAV   109.48  3.000
 AJH  HAFA  CAF  CAC   109.64  3.000
 AJH  HAF   CAF  CAC   108.90  3.000
 AJH  CAV   CAF  CAC   113.61  3.000
 AJH  HAV   CAV  CAT   107.48  3.000
 AJH  HAV   CAV  NBG   107.47  3.000
 AJH  CAT   CAV  NBG   109.34  3.000
 AJH  HAV   CAV  CAF   108.21  3.000
 AJH  NBG   CAV  CAF   115.19  3.000
 AJH  CAT   CAV  CAF   108.88  3.000
 AJH  HNBA  NBG  HNBG  106.48  3.000
 AJH  HNBA  NBG  CAV   109.23  3.000
 AJH  HNBG  NBG  CAV   109.76  3.000
 AJH  HATA  CAT  HAT   106.46  3.000
 AJH  HATA  CAT  CAG   110.93  3.000
 AJH  HAT   CAT  CAG   108.85  3.000
 AJH  HATA  CAT  CAV   109.42  3.000
 AJH  HAT   CAT  CAV   109.11  3.000
 AJH  CAG   CAT  CAV   111.90  3.000
 AJH  CAI   CAG  CAM   116.84  3.000
 AJH  CAM   CAG  CAT   120.23  3.000
 AJH  CAI   CAG  CAT   122.91  3.000
 AJH  HAM   CAM  CAL   119.05  3.000
 AJH  HAM   CAM  CAG   119.79  3.000
 AJH  CAL   CAM  CAG   121.16  3.000
 AJH  CAK   CAL  FBB   119.35  3.000
 AJH  FBB   CAL  CAM   120.43  3.000
 AJH  CAK   CAL  CAM   120.22  3.000
 AJH  CAH   CAK  FBA   120.07  3.000
 AJH  FBA   CAK  CAL   119.61  3.000
 AJH  CAH   CAK  CAL   120.32  3.000
 AJH  HAH   CAH  CAI   121.10  3.000
 AJH  HAH   CAH  CAK   120.61  3.000
 AJH  CAI   CAH  CAK   118.29  3.000
 AJH  FAZ   CAI  CAH   117.46  3.000
 AJH  FAZ   CAI  CAG   119.36  3.000
 AJH  CAH   CAI  CAG   123.18  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
 AJH  CONST_01  CAY  CAQ  CAB  CAP     0.00   0.0  0
 AJH  CONST_02  CAY  CAO  CAX  CAP     0.00   0.0  0
 AJH  CONST_03  CAQ  CAB  CAP  CAX     0.00   0.0  0
 AJH  CONST_04  CAQ  CAY  CAO  CAX     0.00   0.0  0
 AJH  CONST_05  CAB  CAP  CAX  CAO     0.00   0.0  0
 AJH  CONST_06  CAB  CAQ  CAY  CAO     0.00   0.0  0
 AJH  CONST_07  CAK  CAH  CAI  CAG     0.00   0.0  0
 AJH  CONST_08  CAK  CAL  CAM  CAG     0.00   0.0  0
 AJH  CONST_09  CAH  CAI  CAG  CAM     0.00   0.0  0
 AJH  CONST_10  CAH  CAK  CAL  CAM     0.00   0.0  0
 AJH  CONST_11  CAI  CAG  CAM  CAL     0.00   0.0  0
 AJH  CONST_12  CAI  CAH  CAK  CAL     0.00   0.0  0
 AJH  CONST_13  CAJ  CAO  CAX  CAP   180.00   0.0  0
 AJH  CONST_14  CAA  CAB  CAP  CAX   180.00   0.0  0
 AJH  CONST_15  CAQ  CAY  CAO  CAJ   180.00   0.0  0
 AJH  CONST_16  CAA  CAB  CAQ  CAY   180.00   0.0  0
 AJH  CONST_17  CAH  CAI  CAG  CAT   180.00   0.0  0
 AJH  CONST_18  CAL  CAM  CAG  CAT   180.00   0.0  0
 AJH  CONST_19  FBB  CAL  CAM  CAG   180.00   0.0  0
 AJH  CONST_20  FAZ  CAI  CAG  CAM   180.00   0.0  0
 AJH  CONST_21  FBA  CAK  CAL  CAM   180.00   0.0  0
 AJH  CONST_22  CAH  CAK  CAL  FBB   180.00   0.0  0
 AJH  CONST_23  FAZ  CAI  CAH  CAK   180.00   0.0  0
 AJH  CONST_24  CAI  CAH  CAK  FBA   180.00   0.0  0
 AJH  CONST_25  HAQ  CAQ  CAB  CAP   180.00   0.0  0
 AJH  CONST_26  HAY  CAY  CAO  CAX   180.00   0.0  0
 AJH  CONST_27  HAP  CAP  CAX  CAO   180.00   0.0  0
 AJH  CONST_28  HAX  CAX  CAO  CAY   180.00   0.0  0
 AJH  CONST_29  HAH  CAH  CAI  CAG   180.00   0.0  0
 AJH  CONST_30  HAM  CAM  CAL  CAK   180.00   0.0  0
 AJH  Var_01    NAD  CAA  CAB  CAP   -65.08  30.0  2
 AJH  Var_02    OBD  CAJ  CAO  CAX     1.80  30.0  2
 AJH  Var_03    CAI  CAG  CAT  CAV   -93.21  30.0  2
 AJH  Var_04    CAV  CAF  CAC  NAE  -179.61  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
 AJH  chir_01  CAV  CAF  CAT  NBG  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
 AJH  plan-1  CAP  0.020
 AJH  plan-1  CAX  0.020
 AJH  plan-1  CAO  0.020
 AJH  plan-1  CAJ  0.020
 AJH  plan-1  CAY  0.020
 AJH  plan-1  CAQ  0.020
 AJH  plan-1  CAB  0.020
 AJH  plan-1  CAA  0.020
 AJH  plan-1  HAP  0.020
 AJH  plan-1  HAX  0.020
 AJH  plan-1  HAY  0.020
 AJH  plan-1  HAQ  0.020
 AJH  plan-2  CAT  0.020
 AJH  plan-2  CAG  0.020
 AJH  plan-2  CAM  0.020
 AJH  plan-2  CAL  0.020
 AJH  plan-2  FBB  0.020
 AJH  plan-2  CAK  0.020
 AJH  plan-2  FBA  0.020
 AJH  plan-2  CAH  0.020
 AJH  plan-2  CAI  0.020
 AJH  plan-2  FAZ  0.020
 AJH  plan-2  HAM  0.020
 AJH  plan-2  HAH  0.020
 AJH  plan-3  CAB  0.020
 AJH  plan-3  CAA  0.020
 AJH  plan-3  OAN  0.020
 AJH  plan-3  NAD  0.020
 AJH  plan-3  CAR  0.020
 AJH  plan-3  CBE  0.020
 AJH  plan-4  CAS  0.020
 AJH  plan-4  CBF  0.020
 AJH  plan-4  NAE  0.020
 AJH  plan-4  CAC  0.020
 AJH  plan-4  OAU  0.020
 AJH  plan-4  CAF  0.020
 AJH  plan-5  CAO  0.020
 AJH  plan-5  CAJ  0.020
 AJH  plan-5  OAW  0.020
 AJH  plan-5  OBD  0.020

