# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 03:38:42 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2R)-5-methylidene-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C1=N[C@H](SCC1=C)[C@H](NC(=O)Cc2ccccc2)C=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
 CD6  CD6  '(2R)-5-methylidene-2-{(1R)-2-oxo-1-[(phenylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  39  23  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CD6
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
 CD6  CAA   C  C2    0  -0.533  -5.2860   1.1379   0.8553
 CD6  OAE   O  OH1   0  -0.569  -1.8498   3.0304  -0.0583
 CD6  OAF   O  O     0  -0.480   2.2695  -1.7636   0.1997
 CD6  OAH   O  O     0  -0.416  -3.8837   3.0958  -0.9850
 CD6  CAI   C  CR16  0  -0.268   6.2714   1.1136   0.9370
 CD6  CAJ   C  CR16  0  -0.244   6.2668  -0.0509   0.1799
 CD6  CAK   C  CR16  0  -0.242   5.1465   1.9279   0.9499
 CD6  CAL   C  CR16  0  -0.300   5.1423  -0.4006  -0.5555
 CD6  CAM   C  CR16  0  -0.291   4.0247   1.5762   0.2110
 CD6  CAN   C  CH2   0  -0.636  -4.4570  -1.0573   0.0787
 CD6  CAP   C  CH2   0  -0.678   2.7833   0.0269  -1.3248
 CD6  NAQ   N  N     0  -0.343  -1.9757   0.3939  -0.4250
 CD6  NAS   N  NH1   0  -0.649   0.5470  -0.6082  -0.6400
 CD6  SAU   S  S2    0   0.011  -2.9937  -1.8739   0.7780
 CD6  CAW   C  C     0   0.125  -4.3260   0.4195   0.2719
 CD6  CAX   C  C     0   0.497  -2.9923   2.4988  -0.4409
 CD6  CAY   C  C     0   0.586   1.8602  -0.8555  -0.5088
 CD6  CAZ   C  C1    0   0.155  -0.1617  -2.8407   0.0354
 CD6  CBA   C  C     0   0.162  -3.0495   1.0136  -0.1650
 CD6  CBB   C  CR6   0   0.141   4.0110   0.4099  -0.5490
 CD6  CBD   C  CH1   0  -0.270  -1.8194  -1.0222  -0.3228
 CD6  CBE   C  CH1   0  -0.134  -0.3975  -1.3365   0.1653
 CD6  HAA   H  H     0   0.272  -6.1921   0.6590   1.2023
 CD6  HAAA  H  H     0   0.268  -5.2157   2.2034   1.0188
 CD6  HOAE  H  HOH1  0   0.492  -1.8245   3.9709  -0.2941
 CD6  HAJ   H  HCR6  0   0.255   7.1415  -0.6882   0.1597
 CD6  HAK   H  HCR6  0   0.255   5.1420   2.8397   1.5333
 CD6  HAL   H  HCR6  0   0.249   5.1501  -1.3070  -1.1486
 CD6  HAM   H  HCR6  0   0.251   3.1518   2.2184   0.2216
 CD6  HAN   H  HCH2  0   0.305  -4.5388  -1.3202  -0.9780
 CD6  HANA  H  HCH2  0   0.312  -5.3315  -1.4495   0.5945
 CD6  HAP   H  HCH2  0   0.301   3.0605  -0.5447  -2.2152
 CD6  HAPA  H  HCH2  0   0.280   2.2567   0.9150  -1.6778
 CD6  HNAS  H  HNH1  0   0.410   0.2232   0.2372  -1.0868
 CD6  HAZ   H  H     0   0.222  -0.1075  -3.3944   0.9853
 CD6  HBD   H  HCH1  0   0.321  -1.9307  -1.4275  -1.3357
 CD6  HBE   H  HCH1  0   0.292  -0.3100  -1.0546   1.2208
 CD6  OAG   O  O     0  -0.366  -0.0991  -3.3917  -1.0312
 CD6  HAI   H  HCR6  0   0.255   7.1478   1.3871   1.5105

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
 CD6  CAW  CAA   double    1.333  0.020  1.333
 CD6  CAA  HAA   single    0.930  0.020  1.080
 CD6  CAA  HAAA  single    0.930  0.020  1.080
 CD6  CAX  OAE   single    1.317  0.020  1.317
 CD6  OAE  HOAE  single    0.850  0.020  0.980
 CD6  OAF  CAY   double    1.222  0.020  1.222
 CD6  CAZ  OAG   double    1.202  0.020  1.202
 CD6  OAH  CAX   double    1.203  0.020  1.203
 CD6  CAJ  CAI   aromatic  1.389  0.020  1.389
 CD6  CAI  CAK   aromatic  1.389  0.020  1.389
 CD6  CAI  HAI   single    0.930  0.020  1.080
 CD6  CAJ  CAL   aromatic  1.388  0.020  1.388
 CD6  CAJ  HAJ   single    0.930  0.020  1.080
 CD6  CAK  CAM   aromatic  1.389  0.020  1.389
 CD6  CAK  HAK   single    0.930  0.020  1.080
 CD6  CAL  CBB   aromatic  1.392  0.020  1.392
 CD6  CAL  HAL   single    0.930  0.020  1.080
 CD6  CBB  CAM   aromatic  1.392  0.020  1.392
 CD6  CAM  HAM   single    0.930  0.020  1.080
 CD6  SAU  CAN   single    1.816  0.020  1.816
 CD6  CAN  CAW   single    1.495  0.020  1.495
 CD6  CAN  HAN   single    0.970  0.020  1.090
 CD6  CAN  HANA  single    0.970  0.020  1.090
 CD6  CAY  CAP   single    1.515  0.020  1.515
 CD6  CBB  CAP   single    1.502  0.020  1.502
 CD6  CAP  HAP   single    0.970  0.020  1.090
 CD6  CAP  HAPA  single    0.970  0.020  1.090
 CD6  CBD  NAQ   single    1.428  0.020  1.428
 CD6  NAQ  CBA   double    1.267  0.020  1.267
 CD6  CBE  NAS   single    1.439  0.020  1.439
 CD6  NAS  CAY   single    1.343  0.020  1.343
 CD6  NAS  HNAS  single    0.860  0.020  1.020
 CD6  SAU  CBD   single    1.821  0.020  1.821
 CD6  CBA  CAW   single    1.474  0.020  1.474
 CD6  CBA  CAX   single    1.512  0.020  1.512
 CD6  CBE  CAZ   single    1.528  0.020  1.528
 CD6  CAZ  HAZ   single    0.930  0.020  1.080
 CD6  CBD  CBE   single    1.536  0.020  1.536
 CD6  CBD  HBD   single    0.970  0.020  1.090
 CD6  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
 CD6  HAAA  CAA  HAA  116.27  3.000
 CD6  HAAA  CAA  CAW  123.42  3.000
 CD6  HAA   CAA  CAW  120.31  3.000
 CD6  HOAE  OAE  CAX  110.08  3.000
 CD6  HAI   CAI  CAK  120.18  3.000
 CD6  HAI   CAI  CAJ  120.22  3.000
 CD6  CAK   CAI  CAJ  119.60  3.000
 CD6  HAJ   CAJ  CAL  119.76  3.000
 CD6  HAJ   CAJ  CAI  120.07  3.000
 CD6  CAL   CAJ  CAI  120.17  3.000
 CD6  HAK   CAK  CAM  119.79  3.000
 CD6  HAK   CAK  CAI  120.15  3.000
 CD6  CAM   CAK  CAI  120.06  3.000
 CD6  HAL   CAL  CBB  119.72  3.000
 CD6  HAL   CAL  CAJ  119.66  3.000
 CD6  CBB   CAL  CAJ  120.61  3.000
 CD6  HAM   CAM  CBB  119.60  3.000
 CD6  HAM   CAM  CAK  119.69  3.000
 CD6  CBB   CAM  CAK  120.71  3.000
 CD6  HANA  CAN  HAN  108.15  3.000
 CD6  HANA  CAN  CAW  111.41  3.000
 CD6  HAN   CAN  CAW  111.68  3.000
 CD6  HANA  CAN  SAU  107.64  3.000
 CD6  HAN   CAN  SAU  108.95  3.000
 CD6  CAW   CAN  SAU  108.89  3.000
 CD6  HAPA  CAP  HAP  106.52  3.000
 CD6  HAPA  CAP  CBB  110.73  3.000
 CD6  HAP   CAP  CBB  110.28  3.000
 CD6  HAPA  CAP  CAY  110.74  3.000
 CD6  HAP   CAP  CAY  106.76  3.000
 CD6  CBB   CAP  CAY  111.61  3.000
 CD6  CBD   NAQ  CBA  124.27  3.000
 CD6  HNAS  NAS  CBE  117.45  3.000
 CD6  HNAS  NAS  CAY  120.74  3.000
 CD6  CBE   NAS  CAY  119.61  3.000
 CD6  CBD   SAU  CAN   94.39  3.000
 CD6  CBA   CAW  CAN  115.82  3.000
 CD6  CBA   CAW  CAA  122.41  3.000
 CD6  CAN   CAW  CAA  121.71  3.000
 CD6  CBA   CAX  OAH  122.83  3.000
 CD6  CBA   CAX  OAE  112.11  3.000
 CD6  OAH   CAX  OAE  125.03  3.000
 CD6  NAS   CAY  CAP  115.85  3.000
 CD6  NAS   CAY  OAF  121.39  3.000
 CD6  CAP   CAY  OAF  122.73  3.000
 CD6  HAZ   CAZ  CBE  115.42  3.000
 CD6  HAZ   CAZ  OAG  122.18  3.000
 CD6  CBE   CAZ  OAG  122.32  3.000
 CD6  CAX   CBA  CAW  118.86  3.000
 CD6  CAX   CBA  NAQ  114.28  3.000
 CD6  CAW   CBA  NAQ  126.70  3.000
 CD6  CAP   CBB  CAM  120.24  3.000
 CD6  CAP   CBB  CAL  120.90  3.000
 CD6  CAM   CBB  CAL  118.85  3.000
 CD6  HBD   CBD  CBE  108.17  3.000
 CD6  HBD   CBD  SAU  108.66  3.000
 CD6  CBE   CBD  SAU  108.01  3.000
 CD6  HBD   CBD  NAQ  106.81  3.000
 CD6  CBE   CBD  NAQ  109.08  3.000
 CD6  SAU   CBD  NAQ  115.88  3.000
 CD6  HBE   CBE  CBD  109.11  3.000
 CD6  HBE   CBE  CAZ  108.83  3.000
 CD6  CBD   CBE  CAZ  108.50  3.000
 CD6  HBE   CBE  NAS  110.88  3.000
 CD6  CBD   CBE  NAS  109.04  3.000
 CD6  CAZ   CBE  NAS  110.44  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
 CD6  CONST_01  CBB   CAL  CAJ  CAI    0.00   0.0  0
 CD6  CONST_02  CBB   CAM  CAK  CAI    0.00   0.0  0
 CD6  CONST_03  CAM   CAK  CAI  CAJ    0.00   0.0  0
 CD6  CONST_04  CAM   CBB  CAL  CAJ    0.00   0.0  0
 CD6  CONST_05  CAL   CAJ  CAI  CAK    0.00   0.0  0
 CD6  CONST_06  CAL   CBB  CAM  CAK    0.00   0.0  0
 CD6  CONST_07  CAP   CBB  CAL  CAJ  180.00   0.0  0
 CD6  CONST_08  CAP   CBB  CAM  CAK  180.00   0.0  0
 CD6  CONST_09  HAL   CAL  CAJ  CAI  180.00   0.0  0
 CD6  CONST_10  HAM   CAM  CAK  CAI  180.00   0.0  0
 CD6  CONST_11  HAK   CAK  CAI  CAJ  180.00   0.0  0
 CD6  CONST_12  HAJ   CAJ  CAI  CAK  180.00   0.0  0
 CD6  CONST_13  HAI   CAI  CAJ  CAL  180.00   0.0  0
 CD6  CONST_14  HOAE  OAE  CAX  CBA  180.00   0.0  0
 CD6  CONST_15  CBE   NAS  CAY  OAF    0.00   0.0  0
 CD6  CONST_16  CBE   NAS  CAY  CAP  180.00   0.0  0
 CD6  CONST_17  HNAS  NAS  CAY  OAF  180.00   0.0  0
 CD6  Var_01    NAQ   CBA  CAW  CAN  -15.38  30.0  1
 CD6  Var_02    CBA   CAW  CAN  SAU   50.34  30.0  1
 CD6  Var_03    CAY   CAP  CBB  CAL   87.81  30.0  2
 CD6  Var_04    HAA   CAA  CAW  CAN   -0.17  30.0  2
 CD6  Var_05    CBB   CAP  CAY  OAF  -41.83  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
 CD6  chir_01  CBD  NAQ  SAU  CBE  positiv
 CD6  chir_02  CBE  NAS  CBD  CAZ  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
 CD6  plan-1  CAI   0.020
 CD6  plan-1  CAJ   0.020
 CD6  plan-1  CAK   0.020
 CD6  plan-1  CAL   0.020
 CD6  plan-1  CAM   0.020
 CD6  plan-1  CAP   0.020
 CD6  plan-1  CBB   0.020
 CD6  plan-1  HAJ   0.020
 CD6  plan-1  HAK   0.020
 CD6  plan-1  HAL   0.020
 CD6  plan-1  HAM   0.020
 CD6  plan-1  HAI   0.020
 CD6  plan-2  OAF   0.020
 CD6  plan-2  CAP   0.020
 CD6  plan-2  NAS   0.020
 CD6  plan-2  CAY   0.020
 CD6  plan-2  CBE   0.020
 CD6  plan-2  HNAS  0.020
 CD6  plan-3  OAE   0.020
 CD6  plan-3  OAH   0.020
 CD6  plan-3  CAX   0.020
 CD6  plan-3  CBA   0.020
 CD6  plan-3  HOAE  0.020
 CD6  plan-4  CAZ   0.020
 CD6  plan-4  CBE   0.020
 CD6  plan-4  HAZ   0.020
 CD6  plan-4  OAG   0.020

