# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 04:54:15 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CS[C@@H](N=C1C(O)=O)[C@H](NC(=O)[C@H]([NH3+])c2ccccc2)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
 3S3  3S3  (1R)-2-({(R)-carboxy[(2R,5S)-4-carboxy-5-methyl-5,6-dihydro-2H-1,3-thiazin-2-yl]methyl}amino)-2-oxo-1-phenylethanaminium  ligand  43  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3S3
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
 3S3  OAK  O  O      0  -0.480   1.9267  -2.5549   1.0279
 3S3  CAI  C  C      0   0.580   1.7075  -1.7921   0.0996
 3S3  CAG  C  CH1    0  -0.325   2.8817  -1.1661  -0.6620
 3S3  CAF  C  C      0   0.142   3.2669   0.1129   0.0392
 3S3  CAA  C  C1     0  -0.299   2.6373   1.2918  -0.3485
 3S3  CAB  C  C1     0  -0.250   2.9033   2.4764   0.3210
 3S3  CAC  C  C1     0  -0.258   3.8041   2.4946   1.3778
 3S3  CAD  C  C1     0  -0.237   4.4280   1.3187   1.7697
 3S3  CAE  C  C1     0  -0.307   4.1532   0.1275   1.1111
 3S3  NAH  N  NT3    1  -0.787   3.9852  -2.1521  -0.6782
 3S3  N    N  NH1    0  -0.640   0.5218  -1.3580  -0.2991
 3S3  CA   C  CH1    0  -0.139  -0.6896  -1.5482   0.4645
 3S3  C    C  C      0   0.411  -1.0254  -3.0385   0.7281
 3S3  O    O  O     -1  -0.596  -0.7896  -3.8293  -0.1987
 3S3  OXT  O  OC     0  -0.595  -1.5593  -3.2758   1.8259
 3S3  CB   C  CH1    0  -0.251  -1.8335  -0.9169  -0.3544
 3S3  NAQ  N  N      0  -0.351  -1.3712   0.3114  -0.9169
 3S3  SAU  S  S2     0  -0.030  -3.3149  -0.8456   0.7097
 3S3  CAT  C  CH2    0  -0.571  -4.1786   0.4031  -0.2784
 3S3  CAS  C  CH1    0  -0.292  -3.3642   1.6809  -0.4012
 3S3  CAY  C  CH3    0  -0.652  -3.2854   2.4473   0.9194
 3S3  CAR  C  C      0   0.091  -1.9822   1.4174  -0.9449
 3S3  CAV  C  C      0   0.407  -1.2460   2.5994  -1.6216
 3S3  OAW  O  OC    -1  -0.566  -0.0702   2.4102  -1.9678
 3S3  OAX  O  O      0  -0.582  -1.9194   3.6369  -1.7638
 3S3  HAG  H  HCH1   0   0.352   2.6256  -0.9671  -1.7020
 3S3  HAA  H  H      0   0.281   1.9175   1.2983  -1.1578
 3S3  HAB  H  H      0   0.261   2.4006   3.3838   0.0133
 3S3  HAC  H  H      0   0.263   4.0154   3.4202   1.8971
 3S3  HAD  H  H      0   0.266   5.1258   1.3217   2.5962
 3S3  HAE  H  H      0   0.256   4.6453  -0.7750   1.4522
 3S3  HBP  H  HNT3   0   0.489   3.7990  -2.9007  -1.3469
 3S3  HAH  H  HNT3   0   0.483   4.8760  -1.7318  -0.9463
 3S3  HBO  H  HNT3   0   0.466   4.0999  -2.6017   0.2335
 3S3  H    H  HNH1   0   0.411   0.4606  -0.6199  -0.9935
 3S3  HA   H  HCH1   0   0.248  -0.6083  -1.0093   1.4146
 3S3  HB   H  HCH1   0   0.285  -2.0465  -1.5810  -1.1999
 3S3  HBL  H  HCH2   0   0.277  -4.4064  -0.0100  -1.2635
 3S3  HAT  H  HCH2   0   0.284  -5.1293   0.5959   0.2199
 3S3  HAS  H  HCH1   0   0.261  -3.8687   2.3230  -1.1273
 3S3  HBN  H  HCH3   0   0.224  -2.8200   1.8420   1.6976
 3S3  HBM  H  HCH3   0   0.239  -2.7075   3.3629   0.8058
 3S3  HAY  H  HCH3   0   0.230  -4.2852   2.7233   1.2579

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
 3S3  CAY  CAS  single    1.529  0.020  1.529
 3S3  CAS  CAT  single    1.520  0.020  1.520
 3S3  CAS  CAR  single    1.508  0.020  1.508
 3S3  OAX  CAV  deloc     1.245  0.020  1.245
 3S3  CAC  CAB  aromatic  1.389  0.020  1.389
 3S3  CAC  CAD  aromatic  1.388  0.020  1.388
 3S3  CAT  SAU  single    1.811  0.020  1.811
 3S3  CAB  CAA  aromatic  1.386  0.020  1.386
 3S3  CAD  CAE  aromatic  1.389  0.020  1.389
 3S3  SAU  CB   single    1.825  0.020  1.825
 3S3  CAV  CAR  single    1.548  0.020  1.548
 3S3  CAV  OAW  deloc     1.240  0.020  1.240
 3S3  CAR  NAQ  double    1.264  0.020  1.264
 3S3  CAA  CAF  aromatic  1.392  0.020  1.392
 3S3  CAE  CAF  aromatic  1.391  0.020  1.391
 3S3  NAQ  CB   single    1.428  0.020  1.428
 3S3  CAF  CAG  single    1.509  0.020  1.509
 3S3  O    C    deloc     1.241  0.020  1.241
 3S3  CB   CA   single    1.542  0.020  1.542
 3S3  C    OXT  deloc     1.244  0.020  1.244
 3S3  C    CA   single    1.550  0.020  1.550
 3S3  N    CA   single    1.445  0.020  1.445
 3S3  N    CAI  single    1.324  0.020  1.324
 3S3  CAG  CAI  single    1.533  0.020  1.533
 3S3  CAG  NAH  single    1.480  0.020  1.480
 3S3  CAI  OAK  double    1.221  0.020  1.221
 3S3  CAG  HAG  single    0.970  0.020  1.090
 3S3  CAA  HAA  single    0.930  0.020  1.080
 3S3  CAB  HAB  single    0.930  0.020  1.080
 3S3  CAC  HAC  single    0.930  0.020  1.080
 3S3  CAD  HAD  single    0.930  0.020  1.080
 3S3  CAE  HAE  single    0.930  0.020  1.080
 3S3  NAH  HBP  single    0.890  0.020  1.040
 3S3  NAH  HAH  single    0.890  0.020  1.040
 3S3  NAH  HBO  single    0.890  0.020  1.040
 3S3  N    H    single    0.860  0.020  1.020
 3S3  CA   HA   single    0.970  0.020  1.090
 3S3  CB   HB   single    0.970  0.020  1.090
 3S3  CAT  HBL  single    0.970  0.020  1.090
 3S3  CAT  HAT  single    0.970  0.020  1.090
 3S3  CAS  HAS  single    0.970  0.020  1.090
 3S3  CAY  HBN  single    0.970  0.020  1.090
 3S3  CAY  HBM  single    0.970  0.020  1.090
 3S3  CAY  HAY  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
 3S3  N    CAI  CAG  113.73  3.000
 3S3  CAG  CAI  OAK  119.67  3.000
 3S3  N    CAI  OAK  126.47  3.000
 3S3  HAG  CAG  NAH  106.65  3.000
 3S3  HAG  CAG  CAF  110.42  3.000
 3S3  NAH  CAG  CAF  112.31  3.000
 3S3  HAG  CAG  CAI  111.63  3.000
 3S3  NAH  CAG  CAI  107.73  3.000
 3S3  CAF  CAG  CAI  108.11  3.000
 3S3  CAE  CAF  CAA  119.61  3.000
 3S3  CAE  CAF  CAG  121.99  3.000
 3S3  CAA  CAF  CAG  118.24  3.000
 3S3  HAA  CAA  CAB  118.90  3.000
 3S3  HAA  CAA  CAF  120.93  3.000
 3S3  CAB  CAA  CAF  120.16  3.000
 3S3  HAB  CAB  CAC  120.44  3.000
 3S3  HAB  CAB  CAA  119.35  3.000
 3S3  CAC  CAB  CAA  120.21  3.000
 3S3  HAC  CAC  CAD  120.10  3.000
 3S3  HAC  CAC  CAB  120.20  3.000
 3S3  CAD  CAC  CAB  119.70  3.000
 3S3  HAD  CAD  CAE  119.50  3.000
 3S3  HAD  CAD  CAC  120.24  3.000
 3S3  CAE  CAD  CAC  120.27  3.000
 3S3  HAE  CAE  CAD  118.40  3.000
 3S3  HAE  CAE  CAF  121.56  3.000
 3S3  CAD  CAE  CAF  120.04  3.000
 3S3  HBO  NAH  HAH  108.49  3.000
 3S3  HBO  NAH  HBP  106.38  3.000
 3S3  HAH  NAH  HBP  106.80  3.000
 3S3  HBO  NAH  CAG  111.51  3.000
 3S3  HAH  NAH  CAG  112.29  3.000
 3S3  HBP  NAH  CAG  111.08  3.000
 3S3  H    N    CA   113.99  3.000
 3S3  H    N    CAI  119.89  3.000
 3S3  CA   N    CAI  123.27  3.000
 3S3  HA   CA   CB   108.32  3.000
 3S3  HA   CA   C    109.98  3.000
 3S3  CB   CA   C    108.86  3.000
 3S3  HA   CA   N    109.35  3.000
 3S3  C    CA   N    113.46  3.000
 3S3  CB   CA   N    106.71  3.000
 3S3  OXT  C    O    128.27  3.000
 3S3  OXT  C    CA   115.24  3.000
 3S3  O    C    CA   116.39  3.000
 3S3  HB   CB   SAU  108.40  3.000
 3S3  HB   CB   NAQ  106.27  3.000
 3S3  SAU  CB   NAQ  117.31  3.000
 3S3  HB   CB   CA   107.81  3.000
 3S3  NAQ  CB   CA   108.74  3.000
 3S3  SAU  CB   CA   107.97  3.000
 3S3  CAR  NAQ  CB   127.23  3.000
 3S3  CAT  SAU  CB    95.50  3.000
 3S3  HAT  CAT  HBL  107.29  3.000
 3S3  HAT  CAT  CAS  110.81  3.000
 3S3  HBL  CAT  CAS  110.90  3.000
 3S3  HAT  CAT  SAU  106.75  3.000
 3S3  HBL  CAT  SAU  109.31  3.000
 3S3  CAS  CAT  SAU  111.59  3.000
 3S3  HAS  CAS  CAR  106.63  3.000
 3S3  HAS  CAS  CAY  107.65  3.000
 3S3  CAR  CAS  CAY  110.60  3.000
 3S3  HAS  CAS  CAT  107.47  3.000
 3S3  CAR  CAS  CAT  111.91  3.000
 3S3  CAY  CAS  CAT  112.28  3.000
 3S3  HAY  CAY  HBM  107.82  3.000
 3S3  HAY  CAY  HBN  108.07  3.000
 3S3  HBM  CAY  HBN  108.35  3.000
 3S3  HAY  CAY  CAS  110.34  3.000
 3S3  HBM  CAY  CAS  111.02  3.000
 3S3  HBN  CAY  CAS  111.11  3.000
 3S3  CAV  CAR  CAS  117.38  3.000
 3S3  CAV  CAR  NAQ  116.61  3.000
 3S3  CAS  CAR  NAQ  126.01  3.000
 3S3  OAX  CAV  OAW  127.45  3.000
 3S3  OAW  CAV  CAR  117.15  3.000
 3S3  OAX  CAV  CAR  115.39  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
 3S3  CONST_01  CAC  CAB  CAA  CAF    0.00   0.0  0
 3S3  CONST_02  CAC  CAD  CAE  CAF    0.00   0.0  0
 3S3  CONST_03  CAD  CAC  CAB  CAA    0.00   0.0  0
 3S3  CONST_04  CAD  CAE  CAF  CAA    0.00   0.0  0
 3S3  CONST_05  CAE  CAD  CAC  CAB    0.00   0.0  0
 3S3  CONST_06  CAE  CAF  CAA  CAB    0.00   0.0  0
 3S3  CONST_07  CAB  CAA  CAF  CAG  180.00   0.0  0
 3S3  CONST_08  CAD  CAE  CAF  CAG  180.00   0.0  0
 3S3  CONST_09  HAB  CAB  CAA  CAF  180.00   0.0  0
 3S3  CONST_10  HAD  CAD  CAE  CAF  180.00   0.0  0
 3S3  CONST_11  HAC  CAC  CAB  CAA  180.00   0.0  0
 3S3  CONST_12  HAE  CAE  CAF  CAA  180.00   0.0  0
 3S3  CONST_13  HAA  CAA  CAB  CAC  180.00   0.0  0
 3S3  CONST_14  CA   N    CAI  OAK    0.00   0.0  0
 3S3  CONST_16  H    N    CAI  OAK  180.00   0.0  0
 3S3  Var_01    CAS  CAT  SAU  CB   -58.45  30.0  1
 3S3  Var_02    CAS  CAR  NAQ  CB    -1.05  30.0  1
 3S3  Var_03    OAX  CAV  CAR  NAQ  172.71  30.0  2

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
 3S3  chir_01  CAG  CAF  CAI  NAH  positiv
 3S3  chir_02  CA   N    CB   C    negativ
 3S3  chir_03  CB   SAU  NAQ  CA   negativ
 3S3  chir_04  CAS  CAR  CAT  CAY  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
 3S3  plan-1  CAG  0.020
 3S3  plan-1  CAF  0.020
 3S3  plan-1  CAA  0.020
 3S3  plan-1  CAB  0.020
 3S3  plan-1  CAC  0.020
 3S3  plan-1  CAD  0.020
 3S3  plan-1  CAE  0.020
 3S3  plan-1  HAA  0.020
 3S3  plan-1  HAB  0.020
 3S3  plan-1  HAC  0.020
 3S3  plan-1  HAD  0.020
 3S3  plan-1  HAE  0.020
 3S3  plan-2  OAK  0.020
 3S3  plan-2  CAI  0.020
 3S3  plan-2  CAG  0.020
 3S3  plan-2  N    0.020
 3S3  plan-2  CA   0.020
 3S3  plan-2  H    0.020
 3S3  plan-3  CA   0.020
 3S3  plan-3  C    0.020
 3S3  plan-3  O    0.020
 3S3  plan-3  OXT  0.020
 3S3  plan-4  CAR  0.020
 3S3  plan-4  CAV  0.020
 3S3  plan-4  OAW  0.020
 3S3  plan-4  OAX  0.020

