# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:43:35 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  43  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   0.572   6.5220  -1.7334   0.2245
 9EP  OAB   O  O2     0  -0.453   5.2565  -1.3571   0.2751
 9EP  CAC   C  CH2    0  -0.256   4.8719  -0.1637  -0.4593
 9EP  CAD   C  C      0  -0.049   3.3997  -0.0036  -0.3036
 9EP  SAE   S  S2     0  -0.029   1.0117  -0.4308  -1.6477
 9EP  CAF   C  C      0   0.172   2.8076   1.0047   0.3800
 9EP  CAG   C  C      0   0.398   3.5185   2.1619   1.1163
 9EP  OAH   O  O      0  -0.592   2.7868   3.1422   1.3577
 9EP  OAI   O  OC    -1  -0.563   4.7125   2.0311   1.4223
 9EP  NAJ   N  NH1    0  -0.670   1.4513   1.1422   0.4831
 9EP  CAK   C  CH1    0  -0.179   0.4909   0.2246  -0.0156
 9EP  CAL   C  CH1    0  -0.228  -0.8718   0.9010  -0.1755
 9EP  NAM   N  NH1    0  -0.639  -1.8943  -0.0779  -0.3949
 9EP  CAN   C  C      0   0.571  -3.1996   0.1896  -0.1854
 9EP  CAO   C  C1     0   0.184  -0.8202   1.9402  -1.2850
 9EP  OAP   O  O      0  -0.355  -1.6204   1.9950  -2.1794
 9EP  CAQ   C  CH3    0  -0.771   6.7871  -2.9799   1.0198
 9EP  CAR   C  CH2    0  -0.611   2.5997  -1.0546  -1.0235
 9EP  OAS   O  O      0  -0.473   7.3761  -1.1365  -0.3889
 9EP  CAT   C  CH2    0  -0.684  -4.1374  -0.9011  -0.6783
 9EP  OAU   O  O      0  -0.468  -3.5906   1.2112   0.3472
 9EP  CAV   C  CR5    0  -0.113  -5.5332  -0.7432  -0.1893
 9EP  CAW   C  CR15   0  -0.239  -6.6347  -0.3772  -0.9022
 9EP  SAX   S  S2     0   0.206  -5.9420  -1.0207   1.4608
 9EP  CAY   C  CR15   0  -0.471  -7.5924  -0.6440   1.1876
 9EP  CAZ   C  CR15   0  -0.183  -7.8178  -0.3198  -0.1140
 9EP  HAC   H  HCH2   0   0.264   5.4240   0.6889  -0.0814
 9EP  HACA  H  HCH2   0   0.227   5.1269  -0.3181  -1.5121
 9EP  HNAJ  H  HNH1   0   0.391   1.1629   2.0316   0.8668
 9EP  HAK   H  HCH1   0   0.303   0.3778  -0.6379   0.6507
 9EP  HAL   H  HCH1   0   0.320  -1.0789   1.4393   0.7584
 9EP  HNAM  H  HNH1   0   0.408  -1.6464  -0.9109  -0.9091
 9EP  HAO   H  H      0   0.213   0.0047   2.6662  -1.1988
 9EP  HAQ   H  HCH3   0   0.257   5.8875  -3.4087   1.4524
 9EP  HAQA  H  HCH3   0   0.270   7.2638  -3.7226   0.3804
 9EP  HAQB  H  HCH3   0   0.273   7.4888  -2.7510   1.8223
 9EP  HAR   H  HCH2   0   0.283   3.1419  -1.4071  -1.9032
 9EP  HARA  H  HCH2   0   0.285   2.3989  -1.9343  -0.4073
 9EP  HAT   H  HCH2   0   0.310  -4.1419  -0.8614  -1.7713
 9EP  HATA  H  HCH2   0   0.298  -3.7314  -1.8819  -0.4159
 9EP  HAW   H  HCR5   0   0.263  -6.6014  -0.1571  -1.9606
 9EP  HAY   H  HCR5   0   0.294  -8.3033  -0.6823   1.9981
 9EP  HAZ   H  HCR5   0   0.265  -8.7900  -0.0517  -0.5017

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    1.321  0.020  1.321
 9EP  CAA  CAQ   single    1.502  0.020  1.502
 9EP  CAA  OAS   double    1.209  0.020  1.209
 9EP  OAB  CAC   single    1.453  0.020  1.453
 9EP  CAC  CAD   single    1.489  0.020  1.489
 9EP  CAD  CAF   double    1.354  0.020  1.354
 9EP  CAD  CAR   single    1.504  0.020  1.504
 9EP  SAE  CAK   single    1.834  0.020  1.834
 9EP  SAE  CAR   single    1.817  0.020  1.817
 9EP  CAF  CAG   single    1.545  0.020  1.545
 9EP  CAF  NAJ   single    1.367  0.020  1.367
 9EP  CAG  OAH   deloc     1.247  0.020  1.247
 9EP  CAG  OAI   deloc     1.240  0.020  1.240
 9EP  NAJ  CAK   single    1.419  0.020  1.419
 9EP  CAK  CAL   single    1.530  0.020  1.530
 9EP  CAL  NAM   single    1.432  0.020  1.432
 9EP  CAL  CAO   single    1.521  0.020  1.521
 9EP  NAM  CAN   single    1.349  0.020  1.349
 9EP  CAN  CAT   single    1.521  0.020  1.521
 9EP  CAN  OAU   double    1.217  0.020  1.217
 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  1.723  0.020  1.723
 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    0.860  0.020  1.020
 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

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   123.61  3.000
 9EP  OAS   CAA  OAB   123.74  3.000
 9EP  CAQ   CAA  OAB   112.65  3.000
 9EP  CAC   OAB  CAA   117.91  3.000
 9EP  HACA  CAC  HAC   109.13  3.000
 9EP  HACA  CAC  CAD   110.26  3.000
 9EP  HAC   CAC  CAD   112.49  3.000
 9EP  HACA  CAC  OAB   107.98  3.000
 9EP  HAC   CAC  OAB   109.57  3.000
 9EP  CAD   CAC  OAB   107.29  3.000
 9EP  CAR   CAD  CAF   121.95  3.000
 9EP  CAR   CAD  CAC   113.62  3.000
 9EP  CAF   CAD  CAC   124.40  3.000
 9EP  CAR   SAE  CAK    93.73  3.000
 9EP  NAJ   CAF  CAG   110.20  3.000
 9EP  NAJ   CAF  CAD   123.13  3.000
 9EP  CAG   CAF  CAD   126.66  3.000
 9EP  OAI   CAG  OAH   126.90  3.000
 9EP  OAI   CAG  CAF   118.81  3.000
 9EP  OAH   CAG  CAF   114.28  3.000
 9EP  HNAJ  NAJ  CAK   120.62  3.000
 9EP  HNAJ  NAJ  CAF   113.60  3.000
 9EP  CAK   NAJ  CAF   125.45  3.000
 9EP  HAK   CAK  CAL   108.64  3.000
 9EP  HAK   CAK  NAJ   111.42  3.000
 9EP  CAL   CAK  NAJ   110.72  3.000
 9EP  HAK   CAK  SAE   106.80  3.000
 9EP  CAL   CAK  SAE   108.54  3.000
 9EP  NAJ   CAK  SAE   110.59  3.000
 9EP  HAL   CAL  CAO   106.98  3.000
 9EP  HAL   CAL  NAM   109.32  3.000
 9EP  CAO   CAL  NAM   112.29  3.000
 9EP  HAL   CAL  CAK   107.22  3.000
 9EP  CAO   CAL  CAK   110.37  3.000
 9EP  NAM   CAL  CAK   110.47  3.000
 9EP  HNAM  NAM  CAN   118.71  3.000
 9EP  HNAM  NAM  CAL   117.80  3.000
 9EP  CAN   NAM  CAL   122.10  3.000
 9EP  OAU   CAN  CAT   123.09  3.000
 9EP  OAU   CAN  NAM   123.06  3.000
 9EP  CAT   CAN  NAM   113.84  3.000
 9EP  HAO   CAO  OAP   121.78  3.000
 9EP  HAO   CAO  CAL   114.73  3.000
 9EP  OAP   CAO  CAL   123.48  3.000
 9EP  HAQB  CAQ  HAQA  107.06  3.000
 9EP  HAQB  CAQ  HAQ   108.82  3.000
 9EP  HAQA  CAQ  HAQ   109.07  3.000
 9EP  HAQB  CAQ  CAA   109.22  3.000
 9EP  HAQA  CAQ  CAA   109.40  3.000
 9EP  HAQ   CAQ  CAA   113.09  3.000
 9EP  HARA  CAR  HAR   106.60  3.000
 9EP  HARA  CAR  SAE   108.03  3.000
 9EP  HAR   CAR  SAE   105.55  3.000
 9EP  HARA  CAR  CAD   112.98  3.000
 9EP  HAR   CAR  CAD   110.31  3.000
 9EP  SAE   CAR  CAD   112.92  3.000
 9EP  HATA  CAT  HAT   105.90  3.000
 9EP  HATA  CAT  CAV   111.40  3.000
 9EP  HAT   CAT  CAV   108.71  3.000
 9EP  HATA  CAT  CAN   109.67  3.000
 9EP  HAT   CAT  CAN   107.48  3.000
 9EP  CAV   CAT  CAN   113.33  3.000
 9EP  SAX   CAV  CAW   110.65  3.000
 9EP  SAX   CAV  CAT   121.37  3.000
 9EP  CAW   CAV  CAT   127.98  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   128.19  3.000
 9EP  HAY   CAY  SAX   120.45  3.000
 9EP  CAZ   CAY  SAX   111.37  3.000
 9EP  HAZ   CAZ  CAY   123.48  3.000
 9EP  HAZ   CAZ  CAW   124.02  3.000
 9EP  CAY   CAZ  CAW   112.50  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  CAT   CAN  NAM  CAL   180.00   0.0  0
 9EP  CONST_12  OAU   CAN  NAM  CAL     0.00   0.0  0
 9EP  CONST_13  HNAM  NAM  CAN  CAT     0.00   0.0  0
 9EP  Var_01    CAK   NAJ  CAF  CAD     4.61  30.0  1
 9EP  Var_02    CAF   CAD  CAR  SAE    30.94  30.0  1
 9EP  Var_03    CAR   CAD  CAF  NAJ     0.68  30.0  1
 9EP  Var_04    OAH   CAG  CAF  CAD   161.64  30.0  2
 9EP  Var_05    CAW   CAV  CAT  CAN   108.69  30.0  2
 9EP  Var_06    CAD   CAC  OAB  CAA   176.89  30.0  3
 9EP  Var_07    CAV   CAT  CAN  NAM   167.57  30.0  3
 9EP  Var_08    CAQ   CAA  OAB  CAC  -179.82  30.0  1
 9EP  Var_09    HAQ   CAQ  CAA  OAB     3.88  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-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

