# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:54:16 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  57  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  -0.244   5.1228  -0.1336  -0.6446
 AJH  CAX   C  CR16  0  -0.242   6.0331   0.8869  -0.8568
 AJH  CAO   C  CR6   0  -0.083   6.7136   1.4564   0.2165
 AJH  CAJ   C  C     0   0.535   7.6719   2.5559  -0.0615
 AJH  OAW   O  OH1   0  -0.592   8.2383   3.0374   1.0350
 AJH  OBD   O  O     0  -0.435   7.9109   2.9715  -1.1695
 AJH  CAY   C  CR16  0  -0.249   6.4803   0.9811   1.5059
 AJH  CAQ   C  CR16  0  -0.254   5.5798  -0.0498   1.7151
 AJH  CAB   C  CR6   0  -0.076   4.8865  -0.6017   0.6435
 AJH  CAA   C  C     0   0.520   3.9816  -1.7735   0.8781
 AJH  OAN   O  O     0  -0.479   4.4762  -2.8567   1.1549
 AJH  NAD   N  NT    0  -0.440   2.6549  -1.5727   0.7782
 AJH  CAR   C  CH2   0  -0.323   2.0304  -0.2887   0.5063
 AJH  CAS   C  CH2   0  -0.334   1.4708  -0.1835  -0.9102
 AJH  CBE   C  CH2   0  -0.321   1.7537  -2.7082   0.9374
 AJH  CBC   C  CH2   0  -0.446   1.5174  -3.4744  -0.3603
 AJH  CBF   C  CH2   0  -0.316   1.3347  -2.5568  -1.5702
 AJH  NAE   N  NT    0  -0.460   0.6346  -1.3140  -1.2730
 AJH  CAC   C  C     0   0.586  -0.7128  -1.3358  -1.1451
 AJH  OAU   O  O     0  -0.497  -1.3438  -2.3714  -1.3192
 AJH  CAF   C  CH2   0  -0.616  -1.4049  -0.0340  -0.7880
 AJH  CAV   C  CH1   0  -0.074  -2.9267  -0.1608  -0.6611
 AJH  NBG   N  NH2   0  -0.784  -3.6222  -0.5039  -1.8864
 AJH  CAT   C  CH2   0  -0.514  -3.4888   1.1560  -0.1088
 AJH  CAG   C  CR6   0  -0.042  -4.9525   1.0560   0.2018
 AJH  CAM   C  CR16  0  -0.444  -5.3766   0.5612   1.4330
 AJH  CAL   C  CR6   0   0.403  -6.7169   0.4229   1.7228
 AJH  FBB   F  F     0  -0.308  -7.1077  -0.0494   2.9128
 AJH  CAK   C  CR6   0   0.397  -7.6717   0.7778   0.7876
 AJH  FBA   F  F     0  -0.303  -8.9669   0.6398   1.0817
 AJH  CAH   C  CR16  0  -0.558  -7.2911   1.2765  -0.4400
 AJH  CAI   C  CR6   0   0.526  -5.9399   1.4025  -0.7064
 AJH  FAZ   F  F     0  -0.306  -5.5894   1.9031  -1.8990
 AJH  HAP   H  HCR6  0   0.269   4.6088  -0.5716  -1.4904
 AJH  HAX   H  HCR6  0   0.272   6.2117   1.2406  -1.8630
 AJH  HOAW  H  HOH1  0   0.489   8.8495   3.7532   0.8063
 AJH  HAY   H  HCR6  0   0.274   6.9995   1.4016   2.3555
 AJH  HAQ   H  HCR6  0   0.273   5.4111  -0.4158   2.7195
 AJH  HAR   H  HCH2  0   0.266   1.2280  -0.1468   1.2353
 AJH  HARA  H  HCH2  0   0.281   2.7400   0.5211   0.6680
 AJH  HAS   H  HCH2  0   0.283   0.9202   0.7511  -0.9985
 AJH  HASA  H  HCH2  0   0.263   2.2881  -0.1237  -1.6322
 AJH  HBE   H  HCH2  0   0.269   2.1431  -3.3785   1.7017
 AJH  HBEA  H  HCH2  0   0.253   0.8097  -2.3166   1.3184
 AJH  HBC   H  HCH2  0   0.245   2.3564  -4.1439  -0.5611
 AJH  HBCA  H  HCH2  0   0.246   0.6391  -4.1069  -0.2237
 AJH  HBF   H  HCH2  0   0.249   2.3086  -2.2779  -1.9744
 AJH  HBFA  H  HCH2  0   0.264   0.8148  -3.0892  -2.3660
 AJH  HAF   H  HCH2  0   0.267  -0.9912   0.3411   0.1539
 AJH  HAFA  H  HCH2  0   0.273  -1.1702   0.7264  -1.5416
 AJH  HAV   H  HCH1  0   0.238  -3.1445  -0.9448   0.0711
 AJH  HNBG  H  HNH2  0   0.333  -3.4118   0.1798  -2.6047
 AJH  HNBA  H  HNH2  0   0.350  -3.2800  -1.3926  -2.2268
 AJH  HAT   H  HCH2  0   0.260  -2.9517   1.4187   0.8048
 AJH  HATA  H  HCH2  0   0.253  -3.2959   1.9611  -0.8225
 AJH  HAM   H  HCR6  0   0.291  -4.6451   0.2816   2.1817
 AJH  HAH   H  HCR6  0   0.309  -8.0343   1.5594  -1.1742

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  1.384  0.020  1.384
 AJH  CAP  HAP   single    0.930  0.020  1.080
 AJH  CAX  CAO   aromatic  1.393  0.020  1.393
 AJH  CAX  HAX   single    0.930  0.020  1.080
 AJH  CAO  CAY   aromatic  1.394  0.020  1.394
 AJH  CAO  CAJ   single    1.485  0.020  1.485
 AJH  OBD  CAJ   double    1.207  0.020  1.207
 AJH  CAJ  OAW   single    1.325  0.020  1.325
 AJH  OAW  HOAW  single    0.850  0.020  0.980
 AJH  CAQ  CAY   aromatic  1.385  0.020  1.385
 AJH  CAY  HAY   single    0.930  0.020  1.080
 AJH  CAB  CAQ   aromatic  1.391  0.020  1.391
 AJH  CAQ  HAQ   single    0.930  0.020  1.080
 AJH  CAA  CAB   single    1.499  0.020  1.499
 AJH  NAD  CAA   single    1.346  0.020  1.346
 AJH  CAA  OAN   double    1.222  0.020  1.222
 AJH  CBE  NAD   single    1.458  0.020  1.458
 AJH  NAD  CAR   single    1.454  0.020  1.454
 AJH  CAR  CAS   single    1.527  0.020  1.527
 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    1.529  0.020  1.529
 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    1.354  0.020  1.354
 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    1.339  0.020  1.339
 AJH  CAH  CAK   aromatic  1.379  0.020  1.379
 AJH  FBA  CAK   single    1.335  0.020  1.335
 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   120.45  3.000
 AJH  HAP   CAP  CAX   119.41  3.000
 AJH  CAB   CAP  CAX   120.14  3.000
 AJH  HAX   CAX  CAO   120.18  3.000
 AJH  HAX   CAX  CAP   119.51  3.000
 AJH  CAO   CAX  CAP   120.32  3.000
 AJH  CAY   CAO  CAJ   122.26  3.000
 AJH  CAJ   CAO  CAX   118.29  3.000
 AJH  CAY   CAO  CAX   119.45  3.000
 AJH  OBD   CAJ  OAW   123.36  3.000
 AJH  OAW   CAJ  CAO   112.96  3.000
 AJH  OBD   CAJ  CAO   123.68  3.000
 AJH  HOAW  OAW  CAJ   110.06  3.000
 AJH  HAY   CAY  CAQ   118.90  3.000
 AJH  HAY   CAY  CAO   120.94  3.000
 AJH  CAQ   CAY  CAO   120.16  3.000
 AJH  HAQ   CAQ  CAB   120.22  3.000
 AJH  HAQ   CAQ  CAY   119.56  3.000
 AJH  CAB   CAQ  CAY   120.22  3.000
 AJH  CAA   CAB  CAQ   119.38  3.000
 AJH  CAA   CAB  CAP   120.71  3.000
 AJH  CAQ   CAB  CAP   119.70  3.000
 AJH  NAD   CAA  OAN   123.22  3.000
 AJH  OAN   CAA  CAB   118.94  3.000
 AJH  NAD   CAA  CAB   117.84  3.000
 AJH  CBE   NAD  CAR   116.28  3.000
 AJH  CAR   NAD  CAA   124.70  3.000
 AJH  CBE   NAD  CAA   119.02  3.000
 AJH  HARA  CAR  HAR   106.43  3.000
 AJH  HARA  CAR  CAS   108.99  3.000
 AJH  HAR   CAR  CAS   109.92  3.000
 AJH  HARA  CAR  NAD   110.44  3.000
 AJH  HAR   CAR  NAD   107.77  3.000
 AJH  CAS   CAR  NAD   113.07  3.000
 AJH  HASA  CAS  HAS   106.14  3.000
 AJH  HASA  CAS  NAE   107.96  3.000
 AJH  HAS   CAS  NAE   110.91  3.000
 AJH  HASA  CAS  CAR   110.05  3.000
 AJH  HAS   CAS  CAR   108.65  3.000
 AJH  NAE   CAS  CAR   112.91  3.000
 AJH  HBEA  CBE  HBE   106.59  3.000
 AJH  HBEA  CBE  CBC   110.09  3.000
 AJH  HBE   CBE  CBC   110.09  3.000
 AJH  HBEA  CBE  NAD   107.06  3.000
 AJH  HBE   CBE  NAD   109.57  3.000
 AJH  CBC   CBE  NAD   113.20  3.000
 AJH  HBCA  CBC  HBC   106.63  3.000
 AJH  HBCA  CBC  CBF   110.53  3.000
 AJH  HBC   CBC  CBF   108.31  3.000
 AJH  HBCA  CBC  CBE   108.02  3.000
 AJH  HBC   CBC  CBE   110.20  3.000
 AJH  CBF   CBC  CBE   112.96  3.000
 AJH  HBFA  CBF  HBF   106.28  3.000
 AJH  HBFA  CBF  NAE   109.67  3.000
 AJH  HBF   CBF  NAE   106.65  3.000
 AJH  HBFA  CBF  CBC   109.97  3.000
 AJH  HBF   CBF  CBC   109.87  3.000
 AJH  NAE   CBF  CBC   114.07  3.000
 AJH  CAC   NAE  CBF   118.93  3.000
 AJH  CAC   NAE  CAS   124.20  3.000
 AJH  CBF   NAE  CAS   116.00  3.000
 AJH  CAF   CAC  OAU   121.59  3.000
 AJH  CAF   CAC  NAE   117.55  3.000
 AJH  OAU   CAC  NAE   120.85  3.000
 AJH  HAFA  CAF  HAF   105.84  3.000
 AJH  HAFA  CAF  CAV   109.09  3.000
 AJH  HAF   CAF  CAV   109.41  3.000
 AJH  HAFA  CAF  CAC   109.62  3.000
 AJH  HAF   CAF  CAC   108.91  3.000
 AJH  CAV   CAF  CAC   113.68  3.000
 AJH  HAV   CAV  CAT   107.51  3.000
 AJH  HAV   CAV  NBG   107.48  3.000
 AJH  CAT   CAV  NBG   109.36  3.000
 AJH  HAV   CAV  CAF   108.19  3.000
 AJH  NBG   CAV  CAF   115.21  3.000
 AJH  CAT   CAV  CAF   108.81  3.000
 AJH  HNBA  NBG  HNBG  106.50  3.000
 AJH  HNBA  NBG  CAV   109.27  3.000
 AJH  HNBG  NBG  CAV   109.85  3.000
 AJH  HATA  CAT  HAT   106.40  3.000
 AJH  HATA  CAT  CAG   110.89  3.000
 AJH  HAT   CAT  CAG   108.83  3.000
 AJH  HATA  CAT  CAV   109.41  3.000
 AJH  HAT   CAT  CAV   109.12  3.000
 AJH  CAG   CAT  CAV   112.01  3.000
 AJH  CAI   CAG  CAM   116.82  3.000
 AJH  CAM   CAG  CAT   120.26  3.000
 AJH  CAI   CAG  CAT   122.89  3.000
 AJH  HAM   CAM  CAL   119.04  3.000
 AJH  HAM   CAM  CAG   119.79  3.000
 AJH  CAL   CAM  CAG   121.17  3.000
 AJH  CAK   CAL  FBB   119.36  3.000
 AJH  FBB   CAL  CAM   120.41  3.000
 AJH  CAK   CAL  CAM   120.23  3.000
 AJH  CAH   CAK  FBA   120.08  3.000
 AJH  FBA   CAK  CAL   119.62  3.000
 AJH  CAH   CAK  CAL   120.29  3.000
 AJH  HAH   CAH  CAI   121.09  3.000
 AJH  HAH   CAH  CAK   120.60  3.000
 AJH  CAI   CAH  CAK   118.31  3.000
 AJH  FAZ   CAI  CAH   117.45  3.000
 AJH  FAZ   CAI  CAG   119.37  3.000
 AJH  CAH   CAI  CAG   123.17  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  CONST_31  HOAW  OAW  CAJ  CAO   180.00   0.0  0
 AJH  Var_01    NAD   CAA  CAB  CAP   -75.53  30.0  2
 AJH  Var_02    OBD   CAJ  CAO  CAX    -1.19  30.0  2
 AJH  Var_03    CAI   CAG  CAT  CAV   -92.66  30.0  2
 AJH  Var_04    CAV   CAF  CAC  NAE  -179.80  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
 AJH  plan-5  HOAW  0.020

