# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 03:09:56 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: (2S)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)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)Cc2sccc2)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
 63V  63V  '(2S)-5-methylidene-2-{(1R)-2-oxo-1-[(thiophen-2-ylacetyl)amino]ethyl}-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  36  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_63V
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
 63V  OAU  O  O     0  -0.416  -4.6327  -2.3793  -1.2908
 63V  CAK  C  C     0   0.494  -3.7759  -1.9687  -0.5529
 63V  OAV  O  OH1   0  -0.567  -3.0109  -2.7205   0.2106
 63V  CAD  C  C     0   0.160  -3.4283  -0.5020  -0.4419
 63V  NAC  N  N     0  -0.335  -2.1856  -0.2574  -0.4205
 63V  CAE  C  C     0   0.130  -4.5192   0.4883  -0.4688
 63V  CAJ  C  C2    0  -0.535  -5.7694   0.1840  -0.1203
 63V  CAF  C  CH2   0  -0.639  -4.1191   1.8741  -0.8585
 63V  SAA  S  S2    0   0.012  -2.7192   2.4026   0.1702
 63V  CB   C  CH1   0  -0.283  -1.6168   1.0551  -0.3756
 63V  CA   C  CH1   0  -0.197  -0.3804   0.9910   0.5334
 63V  C    C  C1    0   0.193  -0.7573   0.5449   1.9367
 63V  O    O  O     0  -0.354  -0.1767  -0.3231   2.5298
 63V  N    N  NH1   0  -0.632   0.5986   0.1254  -0.0520
 63V  CAM  C  C     0   0.567   1.9208   0.2729   0.1679
 63V  OAO  O  O     0  -0.470   2.3957   1.2266   0.7559
 63V  CAN  C  CH2   0  -0.680   2.7665  -0.8530  -0.4090
 63V  CAP  C  CR5   0  -0.116   4.2269  -0.6517  -0.2106
 63V  SAT  S  S2    0   0.206   5.0946   0.5503  -1.0858
 63V  CAS  C  CR15  0  -0.471   6.5704   0.1500  -0.3105
 63V  CAR  C  CR15  0  -0.185   6.4021  -0.8624   0.5826
 63V  CAQ  C  CR15  0  -0.236   5.0565  -1.3213   0.6380
 63V  H1   H  HOH1  0   0.491  -3.2258  -3.6570   0.0770
 63V  H6   H  H     0   0.272  -6.5397   0.9440  -0.1176
 63V  H7   H  H     0   0.268  -6.0768  -0.8078   0.1782
 63V  H9   H  HCH2  0   0.303  -3.8250   1.9276  -1.9089
 63V  H10  H  HCH2  0   0.311  -4.9286   2.5838  -0.6984
 63V  H11  H  HCH1  0   0.338  -1.2666   1.2939  -1.3849
 63V  H12  H  HCH1  0   0.321   0.0346   2.0019   0.6180
 63V  H13  H  H     0   0.211  -1.5977   1.0947   2.3912
 63V  H14  H  HNH1  0   0.409   0.2588  -0.7429  -0.4403
 63V  H15  H  HCH2  0   0.307   2.4702  -1.7889   0.0719
 63V  H16  H  HCH2  0   0.303   2.5208  -0.9711  -1.4685
 63V  H17  H  HCR5  0   0.293   7.4771   0.6830  -0.5517
 63V  H18  H  HCR5  0   0.265   7.2045  -1.2679   1.1820
 63V  H19  H  HCR5  0   0.262   4.7161  -2.1203   1.2826

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
 63V  CAR  CAQ  aromatic  1.423  0.020  1.423
 63V  CAR  CAS  aromatic  1.360  0.020  1.360
 63V  CAQ  CAP  aromatic  1.363  0.020  1.363
 63V  CAS  SAT  aromatic  1.714  0.020  1.714
 63V  CAP  CAN  single    1.487  0.020  1.487
 63V  CAP  SAT  aromatic  1.722  0.020  1.722
 63V  CAN  CAM  single    1.522  0.020  1.522
 63V  O    C    double    1.201  0.020  1.201
 63V  N    CAM  single    1.348  0.020  1.348
 63V  N    CA   single    1.432  0.020  1.432
 63V  CAM  OAO  double    1.217  0.020  1.217
 63V  OAU  CAK  double    1.203  0.020  1.203
 63V  C    CA   single    1.520  0.020  1.520
 63V  CAE  CAF  single    1.494  0.020  1.494
 63V  CAE  CAJ  double    1.333  0.020  1.333
 63V  CAE  CAD  single    1.474  0.020  1.474
 63V  CAF  SAA  single    1.816  0.020  1.816
 63V  CA   CB   single    1.536  0.020  1.536
 63V  CAK  CAD  single    1.511  0.020  1.511
 63V  CAK  OAV  single    1.317  0.020  1.317
 63V  CB   NAC  single    1.431  0.020  1.431
 63V  CB   SAA  single    1.824  0.020  1.824
 63V  CAD  NAC  double    1.267  0.020  1.267
 63V  OAV  H1   single    0.850  0.020  0.980
 63V  CAJ  H6   single    0.930  0.020  1.080
 63V  CAJ  H7   single    0.930  0.020  1.080
 63V  CAF  H9   single    0.970  0.020  1.090
 63V  CAF  H10  single    0.970  0.020  1.090
 63V  CB   H11  single    0.970  0.020  1.090
 63V  CA   H12  single    0.970  0.020  1.090
 63V  C    H13  single    0.930  0.020  1.080
 63V  N    H14  single    0.860  0.020  1.020
 63V  CAN  H15  single    0.970  0.020  1.090
 63V  CAN  H16  single    0.970  0.020  1.090
 63V  CAS  H17  single    0.930  0.020  1.080
 63V  CAR  H18  single    0.930  0.020  1.080
 63V  CAQ  H19  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
 63V  CAD  CAK  OAV  112.21  3.000
 63V  OAV  CAK  OAU  125.07  3.000
 63V  CAD  CAK  OAU  122.69  3.000
 63V  H1   OAV  CAK  110.04  3.000
 63V  CAE  CAD  NAC  126.64  3.000
 63V  NAC  CAD  CAK  114.47  3.000
 63V  CAE  CAD  CAK  118.72  3.000
 63V  CB   NAC  CAD  124.57  3.000
 63V  CAF  CAE  CAJ  122.09  3.000
 63V  CAJ  CAE  CAD  122.41  3.000
 63V  CAF  CAE  CAD  115.45  3.000
 63V  H7   CAJ  H6   116.20  3.000
 63V  H7   CAJ  CAE  123.28  3.000
 63V  H6   CAJ  CAE  120.52  3.000
 63V  H10  CAF  H9   108.05  3.000
 63V  H10  CAF  SAA  107.47  3.000
 63V  H9   CAF  SAA  108.85  3.000
 63V  H10  CAF  CAE  111.54  3.000
 63V  H9   CAF  CAE  111.62  3.000
 63V  SAA  CAF  CAE  109.19  3.000
 63V  CB   SAA  CAF   94.67  3.000
 63V  H11  CB   CA   107.29  3.000
 63V  H11  CB   SAA  107.94  3.000
 63V  CA   CB   SAA  109.89  3.000
 63V  H11  CB   NAC  107.35  3.000
 63V  SAA  CB   NAC  116.53  3.000
 63V  CA   CB   NAC  107.47  3.000
 63V  H12  CA   N    109.28  3.000
 63V  H12  CA   C    107.06  3.000
 63V  N    CA   C    111.68  3.000
 63V  H12  CA   CB   108.18  3.000
 63V  C    CA   CB   111.04  3.000
 63V  N    CA   CB   109.49  3.000
 63V  H13  C    O    121.70  3.000
 63V  H13  C    CA   115.04  3.000
 63V  O    C    CA   123.25  3.000
 63V  H14  N    CAM  119.11  3.000
 63V  H14  N    CA   116.54  3.000
 63V  CAM  N    CA   122.52  3.000
 63V  CAN  CAM  OAO  123.11  3.000
 63V  OAO  CAM  N    123.17  3.000
 63V  CAN  CAM  N    113.72  3.000
 63V  H16  CAN  H15  105.83  3.000
 63V  H16  CAN  CAP  111.36  3.000
 63V  H15  CAN  CAP  108.86  3.000
 63V  H16  CAN  CAM  108.79  3.000
 63V  H15  CAN  CAM  108.42  3.000
 63V  CAP  CAN  CAM  113.26  3.000
 63V  CAQ  CAP  SAT  110.66  3.000
 63V  SAT  CAP  CAN  121.43  3.000
 63V  CAQ  CAP  CAN  127.90  3.000
 63V  CAS  SAT  CAP   92.35  3.000
 63V  H17  CAS  CAR  128.19  3.000
 63V  H17  CAS  SAT  120.46  3.000
 63V  CAR  CAS  SAT  111.36  3.000
 63V  H18  CAR  CAQ  124.03  3.000
 63V  H18  CAR  CAS  123.48  3.000
 63V  CAQ  CAR  CAS  112.49  3.000
 63V  H19  CAQ  CAR  123.99  3.000
 63V  H19  CAQ  CAP  122.86  3.000
 63V  CAR  CAQ  CAP  113.15  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
 63V  CONST_01  CAS  CAR  CAQ  CAP    0.00   0.0  0
 63V  CONST_02  CAR  CAS  SAT  CAP    0.00   0.0  0
 63V  CONST_03  CAQ  CAR  CAS  SAT    0.00   0.0  0
 63V  CONST_04  CAR  CAQ  CAP  SAT    0.00   0.0  0
 63V  CONST_05  CAQ  CAP  SAT  CAS    0.00   0.0  0
 63V  CONST_06  CAR  CAQ  CAP  CAN  180.00   0.0  0
 63V  CONST_07  CAS  SAT  CAP  CAN  180.00   0.0  0
 63V  CONST_08  H18  CAR  CAQ  CAP  180.00   0.0  0
 63V  CONST_09  H17  CAS  SAT  CAP  180.00   0.0  0
 63V  CONST_10  H19  CAQ  CAP  SAT  180.00   0.0  0
 63V  CONST_11  H1   OAV  CAK  CAD  180.00   0.0  0
 63V  CONST_12  CAN  CAM  N    CA   180.00   0.0  0
 63V  CONST_13  OAO  CAM  N    CA     0.00   0.0  0
 63V  CONST_14  H14  N    CAM  OAO  180.00   0.0  0
 63V  Var_01    SAA  CAF  CAE  CAD  -51.86  30.0  1
 63V  Var_02    CAF  CAE  CAD  NAC   16.70  30.0  1
 63V  Var_03    CAE  CAD  CAK  OAU   39.61  30.0  2
 63V  Var_04    CAQ  CAP  CAN  CAM  107.93  30.0  1
 63V  Var_05    H6   CAJ  CAE  CAD  177.81  30.0  2
 63V  Var_06    CAP  CAN  CAM  N    177.58  30.0  1

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
 63V  chir_01  CB  CA  NAC  SAA  negativ
 63V  chir_02  CA  N   CB   C    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
 63V  plan-1  CAN  0.020
 63V  plan-1  CAP  0.020
 63V  plan-1  SAT  0.020
 63V  plan-1  CAS  0.020
 63V  plan-1  CAR  0.020
 63V  plan-1  CAQ  0.020
 63V  plan-1  H17  0.020
 63V  plan-1  H18  0.020
 63V  plan-1  H19  0.020
 63V  plan-2  CA   0.020
 63V  plan-2  N    0.020
 63V  plan-2  CAM  0.020
 63V  plan-2  OAO  0.020
 63V  plan-2  CAN  0.020
 63V  plan-2  H14  0.020
 63V  plan-3  OAU  0.020
 63V  plan-3  CAK  0.020
 63V  plan-3  OAV  0.020
 63V  plan-3  CAD  0.020
 63V  plan-3  H1   0.020
 63V  plan-4  CA   0.020
 63V  plan-4  C    0.020
 63V  plan-4  O    0.020
 63V  plan-4  H13  0.020

