# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 08:53:28 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (2R)-2-[(1S)-1-(benzoylamino)-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@](NC(=O)c1ccccc1)(C=O)[C@H]2SCC(=C)C(=N2)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
 CD8  CD8  '(2R)-2-[(1S)-1-(benzoylamino)-1-methoxy-2-oxoethyl]-5-methylidene-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  39  24  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_CD8
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
 CD8  CAA   C  C2     0  -0.552   4.9386  -1.3130   0.2238
 CD8  OAF   O  O      0  -0.584   2.0292  -3.4941  -0.0843
 CD8  OAG   O  O      0  -0.466  -2.5870   2.1162  -0.3609
 CD8  OAH   O  O      0  -0.361   0.1016   3.8301  -0.4527
 CD8  OAI   O  OC    -1  -0.594   2.5703  -2.6847   1.9338
 CD8  CAJ   C  CR16   0  -0.247  -5.3108  -2.0617  -0.0088
 CD8  CAK   C  CR16   0  -0.241  -5.5354  -0.8617  -0.6719
 CD8  CAL   C  CR16   0  -0.238  -4.0883  -2.2944   0.6062
 CD8  CAM   C  CR16   0  -0.264  -4.5420   0.1032  -0.7176
 CD8  CAN   C  CR16   0  -0.293  -3.0877  -1.3356   0.5502
 CD8  CAO   C  CH2    0  -0.639   3.9047   0.4936  -1.1110
 CD8  NAQ   N  N      0  -0.402   1.3997  -0.5736  -0.0802
 CD8  NAS   N  NH1    0  -0.700  -0.9929   0.5588  -0.0589
 CD8  OAT   O  O2     0  -0.466   0.4942   1.7774   1.3260
 CD8  SAV   S  S2     0   0.010   2.8129   1.7762  -0.4338
 CD8  CAX   C  C      0   0.109   3.8375  -0.7079  -0.2232
 CD8  CAY   C  C      0   0.367   2.3499  -2.6013   0.7147
 CD8  CAZ   C  C      0   0.546  -2.2788   0.9456  -0.1849
 CD8  CBA   C  C1     0   0.159  -0.1523   2.7171  -0.8239
 CD8  CBB   C  C      0   0.162   2.4863  -1.2037   0.1191
 CD8  CBC   C  CR6    0  -0.017  -3.3064  -0.1311  -0.1167
 CD8  CBE   C  CH1    0  -0.247   1.3217   0.7474  -0.6219
 CD8  CBF   C  CT     0   0.328   0.1143   1.4702   0.0280
 CD8  HAA   H  H      0   0.260   5.9214  -0.9474  -0.0451
 CD8  HAAA  H  H      0   0.259   4.9039  -2.1724   0.8785
 CD8  HAC   H  HCH3   0   0.248  -0.0031   2.4277   3.1632
 CD8  HACA  H  HCH3   0   0.223  -0.9871   3.1536   1.8864
 CD8  HACB  H  HCH3   0   0.216  -1.2736   1.4755   2.3958
 CD8  HAJ   H  HCR6   0   0.268  -6.0893  -2.8120   0.0327
 CD8  HAK   H  HCR6   0   0.266  -6.4870  -0.6760  -1.1523
 CD8  HAL   H  HCR6   0   0.268  -3.9121  -3.2211   1.1360
 CD8  HAM   H  HCR6   0   0.264  -4.7240   1.0388  -1.2293
 CD8  HAN   H  HCR6   0   0.256  -2.1528  -1.5356   1.0590
 CD8  HAO   H  HCH2   0   0.293   3.5883   0.2584  -2.1302
 CD8  HAOA  H  HCH2   0   0.301   4.9129   0.9027  -1.1579
 CD8  HNAS  H  HNH1   0   0.411  -0.7383  -0.4164   0.0362
 CD8  HBA   H  H      0   0.214  -0.4705   2.4955  -1.8570
 CD8  HBE   H  HCH1   0   0.309   1.1128   0.6581  -1.6951
 CD8  CAC   C  CH3    0  -0.425  -0.5052   2.2326   2.2176

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
 CD8  CAA  CAX   double    1.334  0.020  1.334
 CD8  CAA  HAA   single    0.930  0.020  1.080
 CD8  CAA  HAAA  single    0.930  0.020  1.080
 CD8  CAC  OAT   single    1.415  0.020  1.415
 CD8  CAC  HAC   single    0.970  0.020  1.090
 CD8  CAC  HACA  single    0.970  0.020  1.090
 CD8  CAC  HACB  single    0.970  0.020  1.090
 CD8  OAF  CAY   deloc     1.240  0.020  1.240
 CD8  OAG  CAZ   double    1.223  0.020  1.223
 CD8  OAH  CBA   double    1.200  0.020  1.200
 CD8  CAY  OAI   deloc     1.242  0.020  1.242
 CD8  CAJ  CAL   aromatic  1.388  0.020  1.388
 CD8  CAJ  CAK   aromatic  1.389  0.020  1.389
 CD8  CAJ  HAJ   single    0.930  0.020  1.080
 CD8  CAK  CAM   aromatic  1.386  0.020  1.386
 CD8  CAK  HAK   single    0.930  0.020  1.080
 CD8  CAL  CAN   aromatic  1.387  0.020  1.387
 CD8  CAL  HAL   single    0.930  0.020  1.080
 CD8  CAM  CBC   aromatic  1.394  0.020  1.394
 CD8  CAM  HAM   single    0.930  0.020  1.080
 CD8  CAN  CBC   aromatic  1.394  0.020  1.394
 CD8  CAN  HAN   single    0.930  0.020  1.080
 CD8  CAX  CAO   single    1.495  0.020  1.495
 CD8  CAO  SAV   single    1.815  0.020  1.815
 CD8  CAO  HAO   single    0.970  0.020  1.090
 CD8  CAO  HAOA  single    0.970  0.020  1.090
 CD8  CBB  NAQ   double    1.272  0.020  1.272
 CD8  NAQ  CBE   single    1.430  0.020  1.430
 CD8  CAZ  NAS   single    1.349  0.020  1.349
 CD8  NAS  CBF   single    1.437  0.020  1.437
 CD8  NAS  HNAS  single    0.860  0.020  1.020
 CD8  CBF  OAT   single    1.387  0.020  1.387
 CD8  CBE  SAV   single    1.821  0.020  1.821
 CD8  CAX  CBB   single    1.479  0.020  1.479
 CD8  CAY  CBB   single    1.525  0.020  1.525
 CD8  CBC  CAZ   single    1.490  0.020  1.490
 CD8  CBA  CBF   single    1.533  0.020  1.533
 CD8  CBA  HBA   single    0.930  0.020  1.080
 CD8  CBF  CBE   single    1.550  0.020  1.550
 CD8  CBE  HBE   single    0.970  0.020  1.090

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
 CD8  HAAA  CAA  HAA   116.62  3.000
 CD8  HAAA  CAA  CAX   122.49  3.000
 CD8  HAA   CAA  CAX   120.87  3.000
 CD8  HAJ   CAJ  CAL   120.03  3.000
 CD8  HAJ   CAJ  CAK   120.06  3.000
 CD8  CAL   CAJ  CAK   119.91  3.000
 CD8  HAK   CAK  CAM   119.76  3.000
 CD8  HAK   CAK  CAJ   120.15  3.000
 CD8  CAM   CAK  CAJ   120.09  3.000
 CD8  HAL   CAL  CAN   119.63  3.000
 CD8  HAL   CAL  CAJ   120.27  3.000
 CD8  CAN   CAL  CAJ   120.10  3.000
 CD8  HAM   CAM  CBC   119.90  3.000
 CD8  HAM   CAM  CAK   119.81  3.000
 CD8  CBC   CAM  CAK   120.28  3.000
 CD8  HAN   CAN  CBC   121.31  3.000
 CD8  HAN   CAN  CAL   118.43  3.000
 CD8  CBC   CAN  CAL   120.23  3.000
 CD8  HAOA  CAO  HAO   107.98  3.000
 CD8  HAOA  CAO  CAX   111.65  3.000
 CD8  HAO   CAO  CAX   111.58  3.000
 CD8  HAOA  CAO  SAV   107.90  3.000
 CD8  HAO   CAO  SAV   109.02  3.000
 CD8  CAX   CAO  SAV   108.61  3.000
 CD8  CBE   NAQ  CBB   124.31  3.000
 CD8  HNAS  NAS  CBF   114.30  3.000
 CD8  HNAS  NAS  CAZ   121.66  3.000
 CD8  CBF   NAS  CAZ   123.95  3.000
 CD8  CBF   OAT  CAC   117.88  3.000
 CD8  CBE   SAV  CAO    93.14  3.000
 CD8  CBB   CAX  CAO   116.59  3.000
 CD8  CBB   CAX  CAA   121.64  3.000
 CD8  CAO   CAX  CAA   121.77  3.000
 CD8  CBB   CAY  OAI   115.40  3.000
 CD8  CBB   CAY  OAF   115.54  3.000
 CD8  OAI   CAY  OAF   129.06  3.000
 CD8  CBC   CAZ  NAS   116.49  3.000
 CD8  CBC   CAZ  OAG   121.63  3.000
 CD8  NAS   CAZ  OAG   121.88  3.000
 CD8  HBA   CBA  CBF   114.01  3.000
 CD8  HBA   CBA  OAH   122.46  3.000
 CD8  CBF   CBA  OAH   123.05  3.000
 CD8  CAY   CBB  CAX   118.62  3.000
 CD8  CAY   CBB  NAQ   116.03  3.000
 CD8  CAX   CBB  NAQ   125.31  3.000
 CD8  CAZ   CBC  CAN   122.55  3.000
 CD8  CAZ   CBC  CAM   118.05  3.000
 CD8  CAN   CBC  CAM   119.38  3.000
 CD8  HBE   CBE  CBF   107.44  3.000
 CD8  HBE   CBE  SAV   107.64  3.000
 CD8  CBF   CBE  SAV   109.33  3.000
 CD8  HBE   CBE  NAQ   107.81  3.000
 CD8  CBF   CBE  NAQ   108.32  3.000
 CD8  SAV   CBE  NAQ   115.98  3.000
 CD8  CBE   CBF  CBA   106.36  3.000
 CD8  CBE   CBF  OAT   106.40  3.000
 CD8  CBA   CBF  OAT   112.79  3.000
 CD8  CBE   CBF  NAS   106.21  3.000
 CD8  CBA   CBF  NAS   110.38  3.000
 CD8  OAT   CBF  NAS   114.10  3.000
 CD8  HACB  CAC  HACA  108.89  3.000
 CD8  HACB  CAC  HAC   107.86  3.000
 CD8  HACA  CAC  HAC   108.44  3.000
 CD8  HACB  CAC  OAT   112.11  3.000
 CD8  HACA  CAC  OAT   113.10  3.000
 CD8  HAC   CAC  OAT   106.23  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
 CD8  CONST_01  CBC   CAN  CAL  CAJ     0.00   0.0  0
 CD8  CONST_02  CBC   CAM  CAK  CAJ     0.00   0.0  0
 CD8  CONST_03  CAN   CAL  CAJ  CAK     0.00   0.0  0
 CD8  CONST_04  CAN   CBC  CAM  CAK     0.00   0.0  0
 CD8  CONST_05  CAM   CAK  CAJ  CAL     0.00   0.0  0
 CD8  CONST_06  CAM   CBC  CAN  CAL     0.00   0.0  0
 CD8  CONST_07  CAZ   CBC  CAM  CAK   180.00   0.0  0
 CD8  CONST_08  CAZ   CBC  CAN  CAL   180.00   0.0  0
 CD8  CONST_09  HAN   CAN  CAL  CAJ   180.00   0.0  0
 CD8  CONST_10  HAM   CAM  CAK  CAJ   180.00   0.0  0
 CD8  CONST_11  HAL   CAL  CAJ  CAK   180.00   0.0  0
 CD8  CONST_12  HAK   CAK  CAJ  CAL   180.00   0.0  0
 CD8  CONST_13  HAJ   CAJ  CAK  CAM   180.00   0.0  0
 CD8  CONST_14  CBF   NAS  CAZ  CBC   180.00   0.0  0
 CD8  CONST_15  HNAS  NAS  CAZ  CBC     0.00   0.0  0
 CD8  CONST_16  CBF   NAS  CAZ  OAG     0.00   0.0  0
 CD8  Var_01    NAQ   CBB  CAX  CAO   -12.83  30.0  1
 CD8  Var_02    CBB   CAX  CAO  SAV    50.27  30.0  1
 CD8  Var_03    CAM   CBC  CAZ  OAG    22.79  30.0  2
 CD8  Var_04    HAA   CAA  CAX  CAO     0.07  30.0  2
 CD8  Var_05    HAC   CAC  OAT  CBF  -179.23  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
 CD8  chir_01  CBE  NAQ  SAV  CBF  positiv
 CD8  chir_02  CBF  NAS  CBE  CBA  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
 CD8  plan-1  CAJ   0.020
 CD8  plan-1  CAK   0.020
 CD8  plan-1  CAL   0.020
 CD8  plan-1  CAM   0.020
 CD8  plan-1  CAN   0.020
 CD8  plan-1  CAZ   0.020
 CD8  plan-1  CBC   0.020
 CD8  plan-1  HAJ   0.020
 CD8  plan-1  HAK   0.020
 CD8  plan-1  HAL   0.020
 CD8  plan-1  HAM   0.020
 CD8  plan-1  HAN   0.020
 CD8  plan-2  OAG   0.020
 CD8  plan-2  NAS   0.020
 CD8  plan-2  CAZ   0.020
 CD8  plan-2  CBC   0.020
 CD8  plan-2  CBF   0.020
 CD8  plan-2  HNAS  0.020
 CD8  plan-3  OAF   0.020
 CD8  plan-3  OAI   0.020
 CD8  plan-3  CAY   0.020
 CD8  plan-3  CBB   0.020
 CD8  plan-4  OAH   0.020
 CD8  plan-4  CBA   0.020
 CD8  plan-4  CBF   0.020
 CD8  plan-4  HBA   0.020

