# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 21:21:50 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: (2R)-5-[(acetyloxy)methyl]-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)OCC1=C(N[C@H](SC1)[C@H](NC(=O)Cc2sccc2)C=O)C(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
 9EP  9EP  '(2R)-5-[(acetyloxy)methyl]-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  44  26  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9EP
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
 9EP  CAA   C  C     0   0.575   6.5035  -1.6807   0.3129
 9EP  OAB   O  O2    0  -0.448   5.2302  -1.3102   0.3269
 9EP  CAC   C  CH2   0  -0.248   4.8500  -0.1947  -0.5011
 9EP  CAD   C  C     0  -0.006   3.3706  -0.0272  -0.3626
 9EP  SAE   S  S2    0   0.016   0.9807  -0.3640  -1.7138
 9EP  CAF   C  C     0   0.269   2.7832   0.9515   0.3560
 9EP  CAG   C  C     0   0.460   3.5372   1.9663   1.1628
 9EP  OAH   O  O     0  -0.423   3.1979   3.1203   1.2321
 9EP  OAI   O  OH1   0  -0.574   4.5536   1.4498   1.8265
 9EP  NAJ   N  NH1   0  -0.669   1.4308   1.2117   0.3865
 9EP  CAK   C  CH1   0  -0.215   0.4718   0.2581  -0.0824
 9EP  CAL   C  CH1   0  -0.219  -0.8994   0.9256  -0.2176
 9EP  NAM   N  NH1   0  -0.641  -1.9132  -0.0606  -0.4412
 9EP  CAN   C  C     0   0.571  -3.2152   0.1825  -0.1806
 9EP  CAO   C  C1    0   0.186  -0.8719   1.9943  -1.3000
 9EP  OAP   O  O     0  -0.354  -1.6755   2.0513  -2.1911
 9EP  CAQ   C  CH3   0  -0.772   6.7737  -2.8358   1.2316
 9EP  CAR   C  CH2   0  -0.609   2.5627  -1.0305  -1.1369
 9EP  OAS   O  O     0  -0.463   7.3473  -1.1320  -0.3535
 9EP  CAT   C  CH2   0  -0.682  -4.1506  -0.9227  -0.6455
 9EP  OAU   O  O     0  -0.467  -3.6006   1.1904   0.3800
 9EP  CAV   C  CR5   0  -0.114  -5.5499  -0.7501  -0.1719
 9EP  CAW   C  CR15  0  -0.239  -6.6505  -0.4357  -0.9105
 9EP  SAX   S  S2    0   0.207  -5.9659  -0.9369   1.4889
 9EP  CAY   C  CR15  0  -0.471  -7.6180  -0.5932   1.1856
 9EP  CAZ   C  CR15  0  -0.184  -7.8389  -0.3453  -0.1335
 9EP  HAC   H  HCH2  0   0.256   5.4232   0.6875  -0.2280
 9EP  HACA  H  HCH2  0   0.255   5.0914  -0.4256  -1.5420
 9EP  HNAJ  H  HNH1  0   0.403   1.1115   1.7768   1.1599
 9EP  HAK   H  HCH1  0   0.315   0.3812  -0.6000   0.5943
 9EP  HAL   H  HCH1  0   0.322  -1.1039   1.4423   0.7290
 9EP  HNAM  H  HNH1  0   0.410  -1.6710  -0.8765  -0.9846
 9EP  HAO   H  H     0   0.219  -0.0638   2.7354  -1.1926
 9EP  HAQ   H  HCH3  0   0.260   5.8658  -3.3104   1.5937
 9EP  HAQA  H  HCH3  0   0.272   7.3889  -3.5744   0.7205
 9EP  HAQB  H  HCH3  0   0.277   7.3446  -2.4796   2.0907
 9EP  HAR   H  HCH2  0   0.298   3.0982  -1.3413  -2.0350
 9EP  HARA  H  HCH2  0   0.304   2.3727  -1.9341  -0.5535
 9EP  HAT   H  HCH2  0   0.310  -4.1469  -0.9263  -1.7391
 9EP  HATA  H  HCH2  0   0.300  -3.7435  -1.8917  -0.3424
 9EP  HAW   H  HCR5  0   0.263  -6.6129  -0.2757  -1.9794
 9EP  HAY   H  HCR5  0   0.294  -8.3328  -0.5915   1.9936
 9EP  HAZ   H  HCR5  0   0.265  -8.8110  -0.1072  -0.5405
 9EP  HOAI  H  HOH1  0   0.493   5.0182   2.1450   2.3186

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
 9EP  CAA  OAB   single    1.326  0.020  1.326
 9EP  CAA  CAQ   single    1.500  0.020  1.500
 9EP  CAA  OAS   double    1.207  0.020  1.207
 9EP  OAB  CAC   single    1.440  0.020  1.440
 9EP  CAC  CAD   single    1.495  0.020  1.495
 9EP  CAD  CAF   double    1.349  0.020  1.349
 9EP  CAD  CAR   single    1.503  0.020  1.503
 9EP  SAE  CAK   single    1.819  0.020  1.819
 9EP  SAE  CAR   single    1.811  0.020  1.811
 9EP  CAF  CAG   single    1.500  0.020  1.500
 9EP  CAF  NAJ   single    1.378  0.020  1.378
 9EP  CAG  OAH   double    1.205  0.020  1.205
 9EP  CAG  OAI   single    1.319  0.020  1.319
 9EP  NAJ  CAK   single    1.431  0.020  1.431
 9EP  CAK  CAL   single    1.531  0.020  1.531
 9EP  CAL  NAM   single    1.432  0.020  1.432
 9EP  CAL  CAO   single    1.521  0.020  1.521
 9EP  NAM  CAN   single    1.350  0.020  1.350
 9EP  CAN  CAT   single    1.521  0.020  1.521
 9EP  CAN  OAU   double    1.216  0.020  1.216
 9EP  CAO  OAP   double    1.201  0.020  1.201
 9EP  CAT  CAV   single    1.487  0.020  1.487
 9EP  CAV  CAW   aromatic  1.362  0.020  1.362
 9EP  CAV  SAX   aromatic  1.722  0.020  1.722
 9EP  CAW  CAZ   aromatic  1.423  0.020  1.423
 9EP  SAX  CAY   aromatic  1.715  0.020  1.715
 9EP  CAY  CAZ   aromatic  1.360  0.020  1.360
 9EP  CAC  HAC   single    0.970  0.020  1.090
 9EP  CAC  HACA  single    0.970  0.020  1.090
 9EP  NAJ  HNAJ  single    0.890  0.020  1.040
 9EP  CAK  HAK   single    0.970  0.020  1.090
 9EP  CAL  HAL   single    0.970  0.020  1.090
 9EP  NAM  HNAM  single    0.860  0.020  1.020
 9EP  CAO  HAO   single    0.930  0.020  1.080
 9EP  CAQ  HAQ   single    0.970  0.020  1.090
 9EP  CAQ  HAQA  single    0.970  0.020  1.090
 9EP  CAQ  HAQB  single    0.970  0.020  1.090
 9EP  CAR  HAR   single    0.970  0.020  1.090
 9EP  CAR  HARA  single    0.970  0.020  1.090
 9EP  CAT  HAT   single    0.970  0.020  1.090
 9EP  CAT  HATA  single    0.970  0.020  1.090
 9EP  CAW  HAW   single    0.930  0.020  1.080
 9EP  CAY  HAY   single    0.930  0.020  1.080
 9EP  CAZ  HAZ   single    0.930  0.020  1.080
 9EP  OAI  HOAI  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
 9EP  OAS   CAA  CAQ   124.20  3.000
 9EP  OAS   CAA  OAB   123.36  3.000
 9EP  CAQ   CAA  OAB   112.43  3.000
 9EP  CAC   OAB  CAA   117.63  3.000
 9EP  HACA  CAC  HAC   107.11  3.000
 9EP  HACA  CAC  CAD   109.29  3.000
 9EP  HAC   CAC  CAD   114.05  3.000
 9EP  HACA  CAC  OAB   109.00  3.000
 9EP  HAC   CAC  OAB   110.18  3.000
 9EP  CAD   CAC  OAB   107.14  3.000
 9EP  CAR   CAD  CAF   121.66  3.000
 9EP  CAR   CAD  CAC   114.16  3.000
 9EP  CAF   CAD  CAC   124.16  3.000
 9EP  CAR   SAE  CAK    94.85  3.000
 9EP  NAJ   CAF  CAG   110.72  3.000
 9EP  NAJ   CAF  CAD   125.20  3.000
 9EP  CAG   CAF  CAD   123.96  3.000
 9EP  OAI   CAG  OAH   124.26  3.000
 9EP  OAI   CAG  CAF   113.15  3.000
 9EP  OAH   CAG  CAF   122.51  3.000
 9EP  HOAI  OAI  CAG   110.10  3.000
 9EP  HNAJ  NAJ  CAK   114.33  3.000
 9EP  HNAJ  NAJ  CAF   115.67  3.000
 9EP  CAK   NAJ  CAF   121.64  3.000
 9EP  HAK   CAK  CAL   108.77  3.000
 9EP  HAK   CAK  NAJ   112.00  3.000
 9EP  CAL   CAK  NAJ   109.79  3.000
 9EP  HAK   CAK  SAE   108.00  3.000
 9EP  CAL   CAK  SAE   108.69  3.000
 9EP  NAJ   CAK  SAE   109.53  3.000
 9EP  HAL   CAL  CAO   106.63  3.000
 9EP  HAL   CAL  NAM   109.08  3.000
 9EP  CAO   CAL  NAM   112.68  3.000
 9EP  HAL   CAL  CAK   107.21  3.000
 9EP  CAO   CAL  CAK   110.67  3.000
 9EP  NAM   CAL  CAK   110.34  3.000
 9EP  HNAM  NAM  CAN   118.73  3.000
 9EP  HNAM  NAM  CAL   118.08  3.000
 9EP  CAN   NAM  CAL   121.92  3.000
 9EP  OAU   CAN  CAT   123.25  3.000
 9EP  OAU   CAN  NAM   122.95  3.000
 9EP  CAT   CAN  NAM   113.79  3.000
 9EP  HAO   CAO  OAP   122.08  3.000
 9EP  HAO   CAO  CAL   114.61  3.000
 9EP  OAP   CAO  CAL   123.30  3.000
 9EP  HAQB  CAQ  HAQA  107.18  3.000
 9EP  HAQB  CAQ  HAQ   108.50  3.000
 9EP  HAQA  CAQ  HAQ   109.41  3.000
 9EP  HAQB  CAQ  CAA   108.96  3.000
 9EP  HAQA  CAQ  CAA   109.67  3.000
 9EP  HAQ   CAQ  CAA   112.94  3.000
 9EP  HARA  CAR  HAR   106.82  3.000
 9EP  HARA  CAR  SAE   108.82  3.000
 9EP  HAR   CAR  SAE   105.75  3.000
 9EP  HARA  CAR  CAD   111.75  3.000
 9EP  HAR   CAR  CAD   110.52  3.000
 9EP  SAE   CAR  CAD   112.83  3.000
 9EP  HATA  CAT  HAT   105.84  3.000
 9EP  HATA  CAT  CAV   111.39  3.000
 9EP  HAT   CAT  CAV   108.78  3.000
 9EP  HATA  CAT  CAN   109.28  3.000
 9EP  HAT   CAT  CAN   107.82  3.000
 9EP  CAV   CAT  CAN   113.39  3.000
 9EP  SAX   CAV  CAW   110.66  3.000
 9EP  SAX   CAV  CAT   121.45  3.000
 9EP  CAW   CAV  CAT   127.90  3.000
 9EP  HAW   CAW  CAZ   124.02  3.000
 9EP  HAW   CAW  CAV   122.82  3.000
 9EP  CAZ   CAW  CAV   113.16  3.000
 9EP  CAY   SAX  CAV    92.31  3.000
 9EP  HAY   CAY  CAZ   128.20  3.000
 9EP  HAY   CAY  SAX   120.42  3.000
 9EP  CAZ   CAY  SAX   111.39  3.000
 9EP  HAZ   CAZ  CAY   123.48  3.000
 9EP  HAZ   CAZ  CAW   124.04  3.000
 9EP  CAY   CAZ  CAW   112.48  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
 9EP  CONST_01  CAY   CAZ  CAW  CAV    0.00   0.0  0
 9EP  CONST_02  CAZ   CAY  SAX  CAV    0.00   0.0  0
 9EP  CONST_03  CAY   SAX  CAV  CAW    0.00   0.0  0
 9EP  CONST_04  SAX   CAY  CAZ  CAW    0.00   0.0  0
 9EP  CONST_05  CAZ   CAW  CAV  SAX    0.00   0.0  0
 9EP  CONST_06  CAZ   CAW  CAV  CAT  180.00   0.0  0
 9EP  CONST_07  CAY   SAX  CAV  CAT  180.00   0.0  0
 9EP  CONST_08  HAZ   CAZ  CAW  CAV  180.00   0.0  0
 9EP  CONST_09  HAY   CAY  SAX  CAV  180.00   0.0  0
 9EP  CONST_10  HAW   CAW  CAV  SAX  180.00   0.0  0
 9EP  CONST_11  HOAI  OAI  CAG  CAF  180.00   0.0  0
 9EP  CONST_12  CAT   CAN  NAM  CAL  180.00   0.0  0
 9EP  CONST_13  OAU   CAN  NAM  CAL    0.00   0.0  0
 9EP  CONST_14  HNAM  NAM  CAN  CAT    0.00   0.0  0
 9EP  Var_01    CAK   NAJ  CAF  CAD   16.04  30.0  1
 9EP  Var_02    CAF   CAD  CAR  SAE   29.72  30.0  1
 9EP  Var_03    CAR   CAD  CAF  NAJ   -5.24  30.0  1
 9EP  Var_04    OAH   CAG  CAF  CAD  141.59  30.0  2
 9EP  Var_05    CAW   CAV  CAT  CAN  110.29  30.0  2
 9EP  Var_06    CAD   CAC  OAB  CAA  177.10  30.0  3
 9EP  Var_07    CAV   CAT  CAN  NAM  171.08  30.0  3
 9EP  Var_08    CAQ   CAA  OAB  CAC  179.06  30.0  1
 9EP  Var_09    HAQ   CAQ  CAA  OAB   12.05  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
 9EP  chir_01  CAK  SAE  NAJ  CAL  negativ
 9EP  chir_02  CAL  NAM  CAK  CAO  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
 9EP  plan-1  CAT   0.020
 9EP  plan-1  CAV   0.020
 9EP  plan-1  CAW   0.020
 9EP  plan-1  SAX   0.020
 9EP  plan-1  CAY   0.020
 9EP  plan-1  CAZ   0.020
 9EP  plan-1  HAW   0.020
 9EP  plan-1  HAY   0.020
 9EP  plan-1  HAZ   0.020
 9EP  plan-2  CAL   0.020
 9EP  plan-2  NAM   0.020
 9EP  plan-2  CAN   0.020
 9EP  plan-2  CAT   0.020
 9EP  plan-2  OAU   0.020
 9EP  plan-2  HNAM  0.020
 9EP  plan-3  CAF   0.020
 9EP  plan-3  NAJ   0.020
 9EP  plan-3  CAK   0.020
 9EP  plan-3  HNAJ  0.020
 9EP  plan-4  CAF   0.020
 9EP  plan-4  CAG   0.020
 9EP  plan-4  OAH   0.020
 9EP  plan-4  OAI   0.020
 9EP  plan-4  HOAI  0.020
 9EP  plan-5  CAA   0.020
 9EP  plan-5  OAB   0.020
 9EP  plan-5  CAQ   0.020
 9EP  plan-5  OAS   0.020
 9EP  plan-6  CAL   0.020
 9EP  plan-6  CAO   0.020
 9EP  plan-6  OAP   0.020
 9EP  plan-6  HAO   0.020

