# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 10:51:04 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  38  23  .  2021-08-07  2021-08-07  
;
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  -0.571  -5.6176   0.7476   0.1753
 CD6  OAE   O  OC    -1  -0.542  -3.3783   3.1077  -0.1265
 CD6  OAF   O  O      0  -0.383   2.1696  -0.7763   1.2578
 CD6  OAH   O  O      0  -0.462  -3.5019   2.3940  -2.2489
 CD6  CAI   C  CR16   0  -0.271   6.8229   0.2666   0.1047
 CD6  CAJ   C  CR16   0  -0.245   6.1631  -0.1997  -1.0236
 CD6  CAK   C  CR16   0  -0.263   6.1137   0.9592   1.0770
 CD6  CAL   C  CR16   0  -0.231   4.8018   0.0260  -1.1766
 CD6  CAM   C  CR16   0  -0.270   4.7530   1.1811   0.9208
 CD6  CAN   C  CH2    0  -0.557  -4.4234  -1.3990  -0.1082
 CD6  CAP   C  CH2    0  -0.742   2.6115   0.9504  -0.3724
 CD6  NAQ   N  N      0  -0.293  -2.1023   0.3018  -0.5784
 CD6  NAS   N  NH1    0  -0.667   0.5013  -0.1973  -0.1169
 CD6  SAU   S  S2     0  -0.068  -2.9907  -1.8841   0.8940
 CD6  CAW   C  C      0  -0.024  -4.4994   0.0923  -0.1356
 CD6  CAX   C  C      0   0.337  -3.3949   2.2490  -1.0222
 CD6  CAY   C  C      0   0.614   1.7657  -0.0906   0.3335
 CD6  CAZ   C  C1     0   0.192   0.0571  -2.3797   0.8836
 CD6  CBA   C  C      0  -0.015  -3.2700   0.8075  -0.5404
 CD6  CBB   C  CR6    0   0.152   4.0834   0.7193  -0.2084
 CD6  CBD   C  CH1    0  -0.274  -1.7679  -1.0187  -0.1577
 CD6  CBE   C  CH1    0  -0.189  -0.4559  -0.9616   0.6374
 CD6  HAA   H  H      0   0.224  -6.5152   0.2159   0.4621
 CD6  HAAA  H  H      0   0.274  -5.6772   1.8269   0.1771
 CD6  HAK   H  HCR6   0   0.250   6.6208   1.3307   1.9576
 CD6  HAL   H  HCR6   0   0.224   4.2947  -0.3416  -2.0603
 CD6  HAM   H  HCR6   0   0.266   4.2115   1.7287   1.6825
 CD6  HAN   H  HCH2   0   0.308  -4.3158  -1.8175  -1.1110
 CD6  HANA  H  HCH2   0   0.322  -5.3070  -1.8462   0.3437
 CD6  HAP   H  HCH2   0   0.283   2.3394   0.9917  -1.4294
 CD6  HAPA  H  HCH2   0   0.260   2.3268   1.9220   0.0433
 CD6  HNAS  H  HNH1   0   0.391   0.1156   0.4888  -0.7515
 CD6  HAZ   H  H      0   0.232   0.0599  -2.6932   1.9420
 CD6  HBD   H  HCH1   0   0.313  -1.5924  -1.6298  -1.0513
 CD6  HBE   H  HCH1   0   0.315  -0.6538  -0.4889   1.6077
 CD6  HAI   H  HCR6   0   0.261   7.8842   0.0955   0.2250
 CD6  OAG   O  O      0  -0.371   0.3899  -3.1161  -0.0019
 CD6  HAJ   H  HCR6   0   0.221   6.7073  -0.7383  -1.7880

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   deloc     1.241  0.020  1.241
 CD6  OAF  CAY   double    1.220  0.020  1.220
 CD6  CAZ  OAG   double    1.199  0.020  1.199
 CD6  OAH  CAX   deloc     1.240  0.020  1.240
 CD6  CAJ  CAI   aromatic  1.388  0.020  1.388
 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  1.387  0.020  1.387
 CD6  CAK  HAK   single    0.930  0.020  1.080
 CD6  CAL  CBB   aromatic  1.391  0.020  1.391
 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    1.814  0.020  1.814
 CD6  CAN  CAW   single    1.494  0.020  1.494
 CD6  CAN  HAN   single    0.970  0.020  1.090
 CD6  CAN  HANA  single    0.970  0.020  1.090
 CD6  CAY  CAP   single    1.516  0.020  1.516
 CD6  CBB  CAP   single    1.499  0.020  1.499
 CD6  CAP  HAP   single    0.970  0.020  1.090
 CD6  CAP  HAPA  single    0.970  0.020  1.090
 CD6  CBD  NAQ   single    1.426  0.020  1.426
 CD6  NAQ  CBA   double    1.273  0.020  1.273
 CD6  CBE  NAS   single    1.439  0.020  1.439
 CD6  NAS  CAY   single    1.346  0.020  1.346
 CD6  NAS  HNAS  single    0.890  0.020  1.040
 CD6  SAU  CBD   single    1.830  0.020  1.830
 CD6  CBA  CAW   single    1.479  0.020  1.479
 CD6  CBA  CAX   single    1.525  0.020  1.525
 CD6  CBE  CAZ   single    1.528  0.020  1.528
 CD6  CAZ  HAZ   single    0.930  0.020  1.080
 CD6  CBD  CBE   single    1.535  0.020  1.535
 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  116.40  3.000
 CD6  HAAA  CAA  CAW  122.52  3.000
 CD6  HAA   CAA  CAW  121.07  3.000
 CD6  HAI   CAI  CAK  120.14  3.000
 CD6  HAI   CAI  CAJ  120.25  3.000
 CD6  CAK   CAI  CAJ  119.61  3.000
 CD6  HAJ   CAJ  CAL  119.76  3.000
 CD6  HAJ   CAJ  CAI  120.17  3.000
 CD6  CAL   CAJ  CAI  120.07  3.000
 CD6  HAK   CAK  CAM  119.76  3.000
 CD6  HAK   CAK  CAI  120.12  3.000
 CD6  CAM   CAK  CAI  120.12  3.000
 CD6  HAL   CAL  CBB  119.69  3.000
 CD6  HAL   CAL  CAJ  119.59  3.000
 CD6  CBB   CAL  CAJ  120.72  3.000
 CD6  HAM   CAM  CBB  119.86  3.000
 CD6  HAM   CAM  CAK  119.47  3.000
 CD6  CBB   CAM  CAK  120.67  3.000
 CD6  HANA  CAN  HAN  107.68  3.000
 CD6  HANA  CAN  CAW  112.12  3.000
 CD6  HAN   CAN  CAW  111.77  3.000
 CD6  HANA  CAN  SAU  107.57  3.000
 CD6  HAN   CAN  SAU  109.09  3.000
 CD6  CAW   CAN  SAU  108.50  3.000
 CD6  HAPA  CAP  HAP  105.62  3.000
 CD6  HAPA  CAP  CBB  110.53  3.000
 CD6  HAP   CAP  CBB  110.88  3.000
 CD6  HAPA  CAP  CAY  106.71  3.000
 CD6  HAP   CAP  CAY  109.73  3.000
 CD6  CBB   CAP  CAY  113.02  3.000
 CD6  CBD   NAQ  CBA  125.05  3.000
 CD6  HNAS  NAS  CBE  115.84  3.000
 CD6  HNAS  NAS  CAY  120.96  3.000
 CD6  CBE   NAS  CAY  119.44  3.000
 CD6  CBD   SAU  CAN   94.80  3.000
 CD6  CBA   CAW  CAN  116.46  3.000
 CD6  CBA   CAW  CAA  121.57  3.000
 CD6  CAN   CAW  CAA  121.96  3.000
 CD6  CBA   CAX  OAH  115.48  3.000
 CD6  CBA   CAX  OAE  115.14  3.000
 CD6  OAH   CAX  OAE  129.37  3.000
 CD6  NAS   CAY  CAP  115.01  3.000
 CD6  NAS   CAY  OAF  121.33  3.000
 CD6  CAP   CAY  OAF  123.66  3.000
 CD6  HAZ   CAZ  CBE  114.76  3.000
 CD6  HAZ   CAZ  OAG  122.21  3.000
 CD6  CBE   CAZ  OAG  122.98  3.000
 CD6  CAX   CBA  CAW  118.39  3.000
 CD6  CAX   CBA  NAQ  116.18  3.000
 CD6  CAW   CBA  NAQ  125.35  3.000
 CD6  CAP   CBB  CAM  120.67  3.000
 CD6  CAP   CBB  CAL  120.52  3.000
 CD6  CAM   CBB  CAL  118.80  3.000
 CD6  HBD   CBD  CBE  107.81  3.000
 CD6  HBD   CBD  SAU  108.16  3.000
 CD6  CBE   CBD  SAU  106.92  3.000
 CD6  HBD   CBD  NAQ  108.25  3.000
 CD6  CBE   CBD  NAQ  108.59  3.000
 CD6  SAU   CBD  NAQ  116.79  3.000
 CD6  HBE   CBE  CBD  108.65  3.000
 CD6  HBE   CBE  CAZ  108.54  3.000
 CD6  CBD   CBE  CAZ  109.62  3.000
 CD6  HBE   CBE  NAS  110.79  3.000
 CD6  CBD   CBE  NAS  108.47  3.000
 CD6  CAZ   CBE  NAS  110.74  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  CBE   NAS  CAY  OAF    0.00   0.0  0
 CD6  CONST_15  CBE   NAS  CAY  CAP  180.00   0.0  0
 CD6  CONST_16  HNAS  NAS  CAY  OAF  180.00   0.0  0
 CD6  Var_01    NAQ   CBA  CAW  CAN  -16.34  30.0  1
 CD6  Var_02    CBA   CAW  CAN  SAU   52.46  30.0  1
 CD6  Var_03    CAY   CAP  CBB  CAL   95.18  30.0  2
 CD6  Var_04    HAA   CAA  CAW  CAN    0.10  30.0  2
 CD6  Var_05    CBB   CAP  CAY  OAF   21.74  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  HAK   0.020
 CD6  plan-1  HAL   0.020
 CD6  plan-1  HAM   0.020
 CD6  plan-1  HAI   0.020
 CD6  plan-1  HAJ   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-4  CAZ   0.020
 CD6  plan-4  CBE   0.020
 CD6  plan-4  HAZ   0.020
 CD6  plan-4  OAG   0.020

