# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:49:24 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: 2-{[(2S)-1-amino-5-{[(1Z)-2-fluoroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@H](CCCNC(=N)CF)NC(=O)c1ccccc1C(O)=O
#
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
 YFF  YFF  '2-{[(2S)-1-amino-5-{[(1Z)-2-fluoroethanimidoyl]amino}-1-oxopentan-2-yl]carbamoyl}benzoic acid'  ligand  42  24  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_YFF
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
 YFF  F     F  F      0  -0.360   7.5726  -2.0889  -0.4766
 YFF  O1    O  OC    -1  -0.587  -4.9053   0.5301  -2.0124
 YFF  O2    O  O      0  -0.567  -3.5324   1.5144  -0.5557
 YFF  NAA   N  NH2    0  -0.798  -1.4638   3.6737   0.9841
 YFF  NAC   N  N      0  -0.674   6.2382  -0.1049  -1.5925
 YFF  OAE   O  O      0  -0.492  -0.6418   3.6799  -1.1209
 YFF  OAF   O  O      0  -0.495  -1.8983   0.6089   1.9270
 YFF  CAH   C  CR16   0  -0.248  -3.6522  -3.2491  -0.7384
 YFF  CAI   C  CR16   0  -0.286  -4.0973  -2.0023  -1.1494
 YFF  CAJ   C  CR16   0  -0.253  -2.5828  -3.3442   0.1425
 YFF  CAK   C  CR6    0  -0.111  -3.4976  -0.8318  -0.6901
 YFF  CAL   C  CR16   0  -0.273  -1.9722  -2.1889   0.6057
 YFF  CAM   C  CH2    0  -0.460   2.2405   0.6483   0.0823
 YFF  CAN   C  CH2    0  -0.263   3.6278   0.6915  -0.5371
 YFF  CAO   C  CH2    0  -0.442   1.4159   1.8608  -0.3295
 YFF  CAP   C  CH2    0  -0.064   6.3016  -1.8995   0.0150
 YFF  NAR   N  NH1    0  -0.646   4.4018  -0.4645  -0.1448
 YFF  NAS   N  NH1    0  -0.596  -0.7311   0.7431  -0.0089
 YFF  CAU   C  C      0   0.559  -0.7207   3.1730  -0.0125
 YFF  CAV   C  C      0   0.340   5.6395  -0.7136  -0.6467
 YFF  CAW   C  C      0   0.512  -1.7114   0.2513   0.7727
 YFF  CAX   C  CR6    0  -0.059  -2.4237  -0.9373   0.1943
 YFF  CAZ   C  CH1    0  -0.231   0.0563   1.9027   0.3523
 YFF  HNAA  H  HNH2   0   0.393  -2.1254   4.4083   0.7888
 YFF  HNAB  H  HNH2   0   0.402  -1.6323   3.1230   1.8098
 YFF  HNAC  H  H      0   0.334   5.6892   0.6726  -1.9468
 YFF  HAH   H  HCR6   0   0.254  -4.1375  -4.1458  -1.1021
 YFF  HAI   H  HCR6   0   0.249  -4.9294  -1.9271  -1.8363
 YFF  HAJ   H  HCR6   0   0.258  -2.2244  -4.3125   0.4667
 YFF  HAL   H  HCR6   0   0.255  -1.1350  -2.2630   1.2894
 YFF  HAM   H  HCH2   0   0.241   1.7398  -0.2737  -0.2220
 YFF  HAMA  H  HCH2   0   0.232   2.3306   0.6172   1.1731
 YFF  HAN   H  HCH2   0   0.234   3.5347   0.7065  -1.6269
 YFF  HANA  H  HCH2   0   0.228   4.1336   1.6217  -0.2485
 YFF  HAO   H  HCH2   0   0.247   1.9554   2.7747  -0.0680
 YFF  HAOA  H  HCH2   0   0.237   1.2860   1.8770  -1.4150
 YFF  HAP   H  HCH2   0   0.238   5.7129  -2.8018  -0.1667
 YFF  HAPA  H  HCH2   0   0.233   6.3609  -1.7440   1.0952
 YFF  HNAS  H  HNH1   0   0.398  -0.7355   0.4797  -0.9827
 YFF  HAZ   H  HCH1   0   0.271   0.2057   1.8721   1.4338
 YFF  HNAR  H  HNH1   0   0.391   4.1720  -0.8736   0.7482
 YFF  C1    C  C      0   0.399  -4.0278   0.5263  -1.1302

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
 YFF  C1   O1    deloc     1.244  0.020  1.244
 YFF  C1   O2    deloc     1.246  0.020  1.246
 YFF  C1   CAK   single    1.523  0.020  1.523
 YFF  NAA  CAU   single    1.340  0.020  1.340
 YFF  NAC  CAV   double    1.274  0.020  1.274
 YFF  OAE  CAU   double    1.221  0.020  1.221
 YFF  OAF  CAW   double    1.223  0.020  1.223
 YFF  CAH  CAI   aromatic  1.386  0.020  1.386
 YFF  CAH  CAJ   aromatic  1.389  0.020  1.389
 YFF  CAI  CAK   aromatic  1.393  0.020  1.393
 YFF  CAJ  CAL   aromatic  1.386  0.020  1.386
 YFF  CAK  CAX   aromatic  1.395  0.020  1.395
 YFF  CAL  CAX   aromatic  1.393  0.020  1.393
 YFF  CAM  CAN   single    1.520  0.020  1.520
 YFF  CAM  CAO   single    1.523  0.020  1.523
 YFF  CAN  NAR   single    1.446  0.020  1.446
 YFF  CAO  CAZ   single    1.522  0.020  1.522
 YFF  CAP  CAV   single    1.511  0.020  1.511
 YFF  NAR  CAV   single    1.359  0.020  1.359
 YFF  NAS  CAW   single    1.347  0.020  1.347
 YFF  NAS  CAZ   single    1.447  0.020  1.447
 YFF  CAU  CAZ   single    1.533  0.020  1.533
 YFF  CAW  CAX   single    1.502  0.020  1.502
 YFF  NAA  HNAA  single    0.890  0.020  1.040
 YFF  NAA  HNAB  single    0.890  0.020  1.040
 YFF  NAC  HNAC  single    0.890  0.020  1.040
 YFF  CAH  HAH   single    0.930  0.020  1.080
 YFF  CAI  HAI   single    0.930  0.020  1.080
 YFF  CAJ  HAJ   single    0.930  0.020  1.080
 YFF  CAL  HAL   single    0.930  0.020  1.080
 YFF  CAM  HAM   single    0.970  0.020  1.090
 YFF  CAM  HAMA  single    0.970  0.020  1.090
 YFF  CAN  HAN   single    0.970  0.020  1.090
 YFF  CAN  HANA  single    0.970  0.020  1.090
 YFF  CAO  HAO   single    0.970  0.020  1.090
 YFF  CAO  HAOA  single    0.970  0.020  1.090
 YFF  CAP  HAP   single    0.970  0.020  1.090
 YFF  CAP  HAPA  single    0.970  0.020  1.090
 YFF  NAS  HNAS  single    0.860  0.020  1.020
 YFF  CAZ  HAZ   single    0.970  0.020  1.090
 YFF  CAP  F     single    1.376  0.020  1.376
 YFF  NAR  HNAR  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
 YFF  HNAB  NAA  HNAA  116.61  3.000
 YFF  HNAB  NAA  CAU   119.89  3.000
 YFF  HNAA  NAA  CAU   119.49  3.000
 YFF  HNAC  NAC  CAV   111.76  3.000
 YFF  HAH   CAH  CAJ   120.11  3.000
 YFF  HAH   CAH  CAI   120.10  3.000
 YFF  CAJ   CAH  CAI   119.80  3.000
 YFF  HAI   CAI  CAK   118.82  3.000
 YFF  HAI   CAI  CAH   119.86  3.000
 YFF  CAK   CAI  CAH   121.32  3.000
 YFF  HAJ   CAJ  CAL   119.98  3.000
 YFF  HAJ   CAJ  CAH   120.41  3.000
 YFF  CAL   CAJ  CAH   119.61  3.000
 YFF  CAX   CAK  CAI   118.48  3.000
 YFF  CAX   CAK  C1    121.24  3.000
 YFF  CAI   CAK  C1    120.28  3.000
 YFF  HAL   CAL  CAX   119.89  3.000
 YFF  HAL   CAL  CAJ   119.62  3.000
 YFF  CAX   CAL  CAJ   120.49  3.000
 YFF  HAMA  CAM  HAM   106.93  3.000
 YFF  HAMA  CAM  CAO   109.66  3.000
 YFF  HAM   CAM  CAO   110.40  3.000
 YFF  HAMA  CAM  CAN   109.37  3.000
 YFF  HAM   CAM  CAN   109.20  3.000
 YFF  CAO   CAM  CAN   111.19  3.000
 YFF  HANA  CAN  HAN   106.84  3.000
 YFF  HANA  CAN  NAR   111.08  3.000
 YFF  HAN   CAN  NAR   109.08  3.000
 YFF  HANA  CAN  CAM   109.73  3.000
 YFF  HAN   CAN  CAM   109.19  3.000
 YFF  NAR   CAN  CAM   110.82  3.000
 YFF  HAOA  CAO  HAO   106.49  3.000
 YFF  HAOA  CAO  CAZ   109.77  3.000
 YFF  HAO   CAO  CAZ   108.11  3.000
 YFF  HAOA  CAO  CAM   110.15  3.000
 YFF  HAO   CAO  CAM   109.50  3.000
 YFF  CAZ   CAO  CAM   112.62  3.000
 YFF  HAPA  CAP  HAP   108.12  3.000
 YFF  HAPA  CAP  CAV   110.18  3.000
 YFF  HAP   CAP  CAV   109.83  3.000
 YFF  HAPA  CAP  F     108.82  3.000
 YFF  HAP   CAP  F     108.94  3.000
 YFF  CAV   CAP  F     110.88  3.000
 YFF  HNAR  NAR  CAV   117.40  3.000
 YFF  HNAR  NAR  CAN   116.27  3.000
 YFF  CAV   NAR  CAN   122.29  3.000
 YFF  HNAS  NAS  CAZ   116.90  3.000
 YFF  HNAS  NAS  CAW   117.50  3.000
 YFF  CAZ   NAS  CAW   122.93  3.000
 YFF  CAZ   CAU  OAE   121.81  3.000
 YFF  CAZ   CAU  NAA   114.43  3.000
 YFF  OAE   CAU  NAA   123.75  3.000
 YFF  NAR   CAV  CAP   112.42  3.000
 YFF  NAR   CAV  NAC   127.93  3.000
 YFF  CAP   CAV  NAC   119.62  3.000
 YFF  CAX   CAW  NAS   114.26  3.000
 YFF  CAX   CAW  OAF   121.50  3.000
 YFF  NAS   CAW  OAF   123.53  3.000
 YFF  CAW   CAX  CAL   116.35  3.000
 YFF  CAW   CAX  CAK   123.33  3.000
 YFF  CAL   CAX  CAK   120.31  3.000
 YFF  HAZ   CAZ  CAU   109.16  3.000
 YFF  HAZ   CAZ  NAS   107.40  3.000
 YFF  CAU   CAZ  NAS   109.19  3.000
 YFF  HAZ   CAZ  CAO   108.70  3.000
 YFF  CAU   CAZ  CAO   111.66  3.000
 YFF  NAS   CAZ  CAO   110.62  3.000
 YFF  CAK   C1   O2    115.83  3.000
 YFF  CAK   C1   O1    116.95  3.000
 YFF  O2    C1   O1    127.23  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
 YFF  CONST_01  CAX   CAK  CAI  CAH     0.00   0.0  0
 YFF  CONST_02  CAX   CAL  CAJ  CAH     0.00   0.0  0
 YFF  CONST_03  CAL   CAJ  CAH  CAI     0.00   0.0  0
 YFF  CONST_04  CAL   CAX  CAK  CAI     0.00   0.0  0
 YFF  CONST_05  CAK   CAI  CAH  CAJ     0.00   0.0  0
 YFF  CONST_06  CAK   CAX  CAL  CAJ     0.00   0.0  0
 YFF  CONST_07  CAH   CAI  CAK  C1    180.00   0.0  0
 YFF  CONST_08  CAL   CAX  CAK  C1    180.00   0.0  0
 YFF  CONST_09  CAW   CAX  CAK  CAI   180.00   0.0  0
 YFF  CONST_10  CAW   CAX  CAL  CAJ   180.00   0.0  0
 YFF  CONST_11  HAL   CAL  CAJ  CAH   180.00   0.0  0
 YFF  CONST_12  HAJ   CAJ  CAH  CAI   180.00   0.0  0
 YFF  CONST_13  HAI   CAI  CAH  CAJ   180.00   0.0  0
 YFF  CONST_14  HAH   CAH  CAI  CAK   180.00   0.0  0
 YFF  CONST_15  CAZ   NAS  CAW  CAX   180.00   0.0  0
 YFF  CONST_17  CAZ   NAS  CAW  OAF     0.00   0.0  0
 YFF  CONST_18  CAN   NAR  CAV  NAC     0.00   0.0  0
 YFF  CONST_19  CAP   CAV  NAR  CAN   180.00   0.0  0
 YFF  CONST_20  HNAA  NAA  CAU  OAE     0.00   0.0  0
 YFF  CONST_21  HNAB  NAA  CAU  OAE   180.00   0.0  0
 YFF  CONST_23  HNAC  NAC  CAV  CAP   180.00   0.0  0
 YFF  Var_01    CAI   CAK  C1   O1     -7.54  30.0  2
 YFF  Var_02    CAK   CAX  CAW  OAF   103.93  30.0  2
 YFF  Var_03    NAC   CAV  CAP  F       4.61  30.0  3
 YFF  Var_04    CAV   NAR  CAN  CAM   174.86  30.0  3
 YFF  Var_05    CAZ   CAO  CAM  CAN  -175.85  30.0  3
 YFF  Var_06    NAR   CAN  CAM  CAO  -179.82  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
 YFF  chir_01  CAZ  CAO  NAS  CAU  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
 YFF  plan-1  CAH   0.020
 YFF  plan-1  CAI   0.020
 YFF  plan-1  CAJ   0.020
 YFF  plan-1  CAK   0.020
 YFF  plan-1  CAL   0.020
 YFF  plan-1  CAW   0.020
 YFF  plan-1  CAX   0.020
 YFF  plan-1  HAH   0.020
 YFF  plan-1  HAI   0.020
 YFF  plan-1  HAJ   0.020
 YFF  plan-1  HAL   0.020
 YFF  plan-1  C1    0.020
 YFF  plan-2  NAA   0.020
 YFF  plan-2  OAE   0.020
 YFF  plan-2  CAU   0.020
 YFF  plan-2  CAZ   0.020
 YFF  plan-2  HNAA  0.020
 YFF  plan-2  HNAB  0.020
 YFF  plan-3  OAF   0.020
 YFF  plan-3  NAS   0.020
 YFF  plan-3  CAW   0.020
 YFF  plan-3  CAX   0.020
 YFF  plan-3  CAZ   0.020
 YFF  plan-3  HNAS  0.020
 YFF  plan-4  NAC   0.020
 YFF  plan-4  CAN   0.020
 YFF  plan-4  CAP   0.020
 YFF  plan-4  NAR   0.020
 YFF  plan-4  CAV   0.020
 YFF  plan-4  HNAC  0.020
 YFF  plan-4  HNAR  0.020
 YFF  plan-5  O1    0.020
 YFF  plan-5  O2    0.020
 YFF  plan-5  CAK   0.020
 YFF  plan-5  C1    0.020

