# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:38:04 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  40  24  .  2021-08-08  2021-08-08  
;
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  -0.536   4.9293  -1.2961   0.2693
 CD8  OAF   O  O     0  -0.416   2.9329  -3.5573   0.0904
 CD8  OAG   O  O     0  -0.463  -2.5707   2.1414  -0.2733
 CD8  OAH   O  O     0  -0.357   0.1325   3.8404  -0.3566
 CD8  OAI   O  OH1   0  -0.568   1.2969  -2.7436   1.3791
 CD8  CAJ   C  CR16  0  -0.247  -5.3126  -2.0352  -0.0268
 CD8  CAK   C  CR16  0  -0.241  -5.5509  -0.7992  -0.6143
 CD8  CAL   C  CR16  0  -0.237  -4.0721  -2.3071   0.5338
 CD8  CAM   C  CR16  0  -0.263  -4.5532   0.1619  -0.6396
 CD8  CAN   C  CR16  0  -0.290  -3.0680  -1.3511   0.4986
 CD8  CAO   C  CH2   0  -0.644   3.9141   0.4809  -1.1228
 CD8  NAQ   N  N     0  -0.353   1.4013  -0.5697  -0.1275
 CD8  NAS   N  NH1   0  -0.706  -0.9821   0.5660  -0.0491
 CD8  OAT   O  O2    0  -0.464   0.5313   1.7336   1.3524
 CD8  SAV   S  S2    0   0.034   2.8326   1.7667  -0.4305
 CD8  CAX   C  C     0   0.127   3.8390  -0.7315  -0.2506
 CD8  CAY   C  C     0   0.499   2.2813  -2.6375   0.5103
 CD8  CAZ   C  C     0   0.551  -2.2690   0.9642  -0.1417
 CD8  CBA   C  C1    0   0.159  -0.1397   2.7433  -0.7593
 CD8  CBB   C  C     0   0.169   2.4778  -1.2122   0.0462
 CD8  CBC   C  CR6   0  -0.017  -3.3002  -0.1101  -0.0932
 CD8  CBE   C  CH1   0  -0.265   1.3297   0.7649  -0.6320
 CD8  CBF   C  CT    0   0.331   0.1301   1.4688   0.0530
 CD8  HAA   H  H     0   0.271   5.9091  -0.8875   0.0594
 CD8  HAAA  H  H     0   0.268   4.8999  -2.1611   0.9155
 CD8  HAC   H  HCH3  0   0.225  -0.9421   3.0949   1.9669
 CD8  HACA  H  HCH3  0   0.218  -1.2169   1.4058   2.4464
 CD8  HACB  H  HCH3  0   0.250   0.0654   2.3450   3.2116
 CD8  HOAI  H  HOH1  0   0.492   1.1654  -3.6740   1.6198
 CD8  HAJ   H  HCR6  0   0.269  -6.0937  -2.7834  -0.0019
 CD8  HAK   H  HCR6  0   0.267  -6.5163  -0.5824  -1.0521
 CD8  HAL   H  HCR6  0   0.269  -3.8840  -3.2627   1.0046
 CD8  HAM   H  HCR6  0   0.265  -4.7461   1.1248  -1.0934
 CD8  HAN   H  HCR6  0   0.249  -2.1188  -1.5883   0.9635
 CD8  HAO   H  HCH2  0   0.302   3.6006   0.2607  -2.1457
 CD8  HAOA  H  HCH2  0   0.310   4.9248   0.8838  -1.1576
 CD8  HNAS  H  HNH1  0   0.417  -0.7422  -0.4141   0.0178
 CD8  HBA   H  H     0   0.219  -0.4777   2.5564  -1.7927
 CD8  HBE   H  HCH1  0   0.332   1.1064   0.6872  -1.7029
 CD8  CAC   C  CH3   0  -0.426  -0.4535   2.1685   2.2716

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    1.333  0.020  1.333
 CD8  CAA  HAA   single    0.930  0.020  1.080
 CD8  CAA  HAAA  single    0.930  0.020  1.080
 CD8  CAC  OAT   single    1.416  0.020  1.416
 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   double    1.203  0.020  1.203
 CD8  OAG  CAZ   double    1.222  0.020  1.222
 CD8  OAH  CBA   double    1.200  0.020  1.200
 CD8  CAY  OAI   single    1.317  0.020  1.317
 CD8  OAI  HOAI  single    0.850  0.020  0.980
 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    1.817  0.020  1.817
 CD8  CAO  HAO   single    0.970  0.020  1.090
 CD8  CAO  HAOA  single    0.970  0.020  1.090
 CD8  CBB  NAQ   double    1.266  0.020  1.266
 CD8  NAQ  CBE   single    1.429  0.020  1.429
 CD8  CAZ  NAS   single    1.350  0.020  1.350
 CD8  NAS  CBF   single    1.436  0.020  1.436
 CD8  NAS  HNAS  single    0.860  0.020  1.020
 CD8  CBF  OAT   single    1.385  0.020  1.385
 CD8  CBE  SAV   single    1.817  0.020  1.817
 CD8  CAX  CBB   single    1.474  0.020  1.474
 CD8  CAY  CBB   single    1.512  0.020  1.512
 CD8  CBC  CAZ   single    1.490  0.020  1.490
 CD8  CBA  CBF   single    1.535  0.020  1.535
 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   116.30  3.000
 CD8  HAAA  CAA  CAX   123.38  3.000
 CD8  HAA   CAA  CAX   120.32  3.000
 CD8  HOAI  OAI  CAY   110.01  3.000
 CD8  HAJ   CAJ  CAL   120.03  3.000
 CD8  HAJ   CAJ  CAK   120.08  3.000
 CD8  CAL   CAJ  CAK   119.89  3.000
 CD8  HAK   CAK  CAM   119.74  3.000
 CD8  HAK   CAK  CAJ   120.17  3.000
 CD8  CAM   CAK  CAJ   120.09  3.000
 CD8  HAL   CAL  CAN   119.61  3.000
 CD8  HAL   CAL  CAJ   120.27  3.000
 CD8  CAN   CAL  CAJ   120.12  3.000
 CD8  HAM   CAM  CBC   119.90  3.000
 CD8  HAM   CAM  CAK   119.78  3.000
 CD8  CBC   CAM  CAK   120.32  3.000
 CD8  HAN   CAN  CBC   121.53  3.000
 CD8  HAN   CAN  CAL   118.21  3.000
 CD8  CBC   CAN  CAL   120.24  3.000
 CD8  HAOA  CAO  HAO   108.13  3.000
 CD8  HAOA  CAO  CAX   111.43  3.000
 CD8  HAO   CAO  CAX   111.61  3.000
 CD8  HAOA  CAO  SAV   107.63  3.000
 CD8  HAO   CAO  SAV   109.18  3.000
 CD8  CAX   CAO  SAV   108.75  3.000
 CD8  CBE   NAQ  CBB   124.43  3.000
 CD8  HNAS  NAS  CBF   114.88  3.000
 CD8  HNAS  NAS  CAZ   121.09  3.000
 CD8  CBF   NAS  CAZ   123.89  3.000
 CD8  CBF   OAT  CAC   117.79  3.000
 CD8  CBE   SAV  CAO    93.43  3.000
 CD8  CBB   CAX  CAO   115.36  3.000
 CD8  CBB   CAX  CAA   122.59  3.000
 CD8  CAO   CAX  CAA   121.98  3.000
 CD8  CBB   CAY  OAI   112.06  3.000
 CD8  CBB   CAY  OAF   122.91  3.000
 CD8  OAI   CAY  OAF   124.99  3.000
 CD8  CBC   CAZ  NAS   116.41  3.000
 CD8  CBC   CAZ  OAG   121.81  3.000
 CD8  NAS   CAZ  OAG   121.78  3.000
 CD8  HBA   CBA  CBF   114.13  3.000
 CD8  HBA   CBA  OAH   122.60  3.000
 CD8  CBF   CBA  OAH   122.79  3.000
 CD8  CAY   CBB  CAX   119.30  3.000
 CD8  CAY   CBB  NAQ   114.22  3.000
 CD8  CAX   CBB  NAQ   126.33  3.000
 CD8  CAZ   CBC  CAN   122.70  3.000
 CD8  CAZ   CBC  CAM   117.95  3.000
 CD8  CAN   CBC  CAM   119.33  3.000
 CD8  HBE   CBE  CBF   107.83  3.000
 CD8  HBE   CBE  SAV   108.40  3.000
 CD8  CBF   CBE  SAV   109.91  3.000
 CD8  HBE   CBE  NAQ   106.79  3.000
 CD8  CBF   CBE  NAQ   107.87  3.000
 CD8  SAV   CBE  NAQ   115.74  3.000
 CD8  CBE   CBF  CBA   106.20  3.000
 CD8  CBE   CBF  OAT   106.09  3.000
 CD8  CBA   CBF  OAT   112.86  3.000
 CD8  CBE   CBF  NAS   106.41  3.000
 CD8  CBA   CBF  NAS   110.38  3.000
 CD8  OAT   CBF  NAS   114.27  3.000
 CD8  HACB  CAC  HACA  107.94  3.000
 CD8  HACB  CAC  HAC   108.49  3.000
 CD8  HACA  CAC  HAC   108.93  3.000
 CD8  HACB  CAC  OAT   106.20  3.000
 CD8  HACA  CAC  OAT   112.04  3.000
 CD8  HAC   CAC  OAT   113.03  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  HOAI  OAI  CAY  CBB  180.00   0.0  0
 CD8  CONST_17  CBF   NAS  CAZ  OAG    0.00   0.0  0
 CD8  Var_01    NAQ   CBB  CAX  CAO  -15.19  30.0  1
 CD8  Var_02    CBB   CAX  CAO  SAV   51.44  30.0  1
 CD8  Var_03    CAM   CBC  CAZ  OAG   21.35  30.0  2
 CD8  Var_04    HAA   CAA  CAX  CAO   -0.61  30.0  2
 CD8  Var_05    HAC   CAC  OAT  CBF  -59.62  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-3  HOAI  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

