# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:11:53 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  45  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  -0.462   1.6647  -3.0161   0.6997
 3S3  CAI  C  C     0   0.592   1.6878  -2.0042   0.0221
 3S3  CAG  C  CH1   0  -0.330   2.9938  -1.4529  -0.5518
 3S3  CAF  C  CR6   0   0.096   3.2059   0.0067  -0.2525
 3S3  CAA  C  CR16  0  -0.280   3.4846   0.8940  -1.2845
 3S3  CAB  C  CR16  0  -0.236   3.6758   2.2420  -1.0106
 3S3  CAC  C  CR16  0  -0.253   3.5946   2.7031   0.2948
 3S3  CAD  C  CR16  0  -0.231   3.3168   1.8176   1.3294
 3S3  CAE  C  CR16  0  -0.281   3.1188   0.4740   1.0573
 3S3  NAH  N  NT3   1  -0.766   4.1127  -2.2707  -0.0166
 3S3  N    N  NH1   0  -0.650   0.6058  -1.2997  -0.3125
 3S3  CA   C  CH1   0  -0.138  -0.6905  -1.6156   0.2280
 3S3  C    C  C     0   0.533  -1.0501  -3.0686  -0.0583
 3S3  O    O  O     0  -0.423  -0.8554  -3.5995  -1.1185
 3S3  OXT  O  OH1   0  -0.574  -1.6532  -3.6315   0.9717
 3S3  CB   C  CH1   0  -0.268  -1.7254  -0.7068  -0.4677
 3S3  NAQ  N  N     0  -0.337  -1.1985   0.6190  -0.4646
 3S3  SAU  S  S2    0   0.010  -3.3466  -0.9323   0.3251
 3S3  CAT  C  CH2   0  -0.577  -4.0848   0.5387  -0.4337
 3S3  CAS  C  CH1   0  -0.313  -3.3444   1.8004  -0.0187
 3S3  CAY  C  CH3   0  -0.652  -3.6163   2.1775   1.4394
 3S3  CAR  C  C     0   0.162  -1.8672   1.6704  -0.2733
 3S3  CAV  C  C     0   0.536  -1.0819   2.9623  -0.3421
 3S3  OAW  O  OH1   0  -0.561   0.2192   2.7650  -0.3416
 3S3  OAX  O  O     0  -0.419  -1.6156   4.0411  -0.3975
 3S3  HAG  H  HCH1  0   0.368   2.9902  -1.6173  -1.6311
 3S3  HAA  H  HCR6  0   0.272   3.5524   0.5334  -2.3036
 3S3  HAB  H  HCR6  0   0.268   3.8897   2.9285  -1.8189
 3S3  HAC  H  HCR6  0   0.270   3.7468   3.7530   0.5084
 3S3  HAD  H  HCR6  0   0.269   3.2495   2.1747   2.3484
 3S3  HAE  H  HCR6  0   0.268   2.8928  -0.2036   1.8737
 3S3  HBP  H  HNT3  0   0.482   3.9961  -3.2638  -0.2265
 3S3  HAH  H  HNT3  0   0.486   4.9998  -1.9797  -0.4286
 3S3  HBO  H  HNT3  0   0.474   4.2129  -2.1930   0.9965
 3S3  H    H  HNH1  0   0.425   0.6974  -0.3740  -0.7151
 3S3  HA   H  HCH1  0   0.312  -0.7182  -1.4255   1.3056
 3S3  H1   H  HOH1  0   0.490  -1.9423  -4.5293   0.7453
 3S3  HB   H  HCH1  0   0.325  -1.7976  -1.0087  -1.5192
 3S3  HBL  H  HCH2  0   0.299  -4.0847   0.4174  -1.5182
 3S3  HAT  H  HCH2  0   0.306  -5.1232   0.5771  -0.1063
 3S3  HAS  H  HCH1  0   0.292  -3.7085   2.6141  -0.6531
 3S3  HBN  H  HCH3  0   0.236  -3.3111   1.3770   2.1129
 3S3  HBM  H  HCH3  0   0.247  -3.0900   3.0851   1.7300
 3S3  HAY  H  HCH3  0   0.247  -4.6827   2.3544   1.5794
 3S3  H2   H  HOH1  0   0.486   0.6872   3.6112  -0.4002

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    1.530  0.020  1.530
 3S3  CAS  CAT  single    1.521  0.020  1.521
 3S3  CAS  CAR  single    1.505  0.020  1.505
 3S3  OAX  CAV  double    1.205  0.020  1.205
 3S3  CAC  CAB  aromatic  1.387  0.020  1.387
 3S3  CAC  CAD  aromatic  1.390  0.020  1.390
 3S3  CAT  SAU  single    1.812  0.020  1.812
 3S3  CAB  CAA  aromatic  1.389  0.020  1.389
 3S3  CAD  CAE  aromatic  1.385  0.020  1.385
 3S3  SAU  CB   single    1.819  0.020  1.819
 3S3  CAV  CAR  single    1.514  0.020  1.514
 3S3  CAV  OAW  single    1.316  0.020  1.316
 3S3  CAR  NAQ  double    1.261  0.020  1.261
 3S3  CAA  CAF  aromatic  1.389  0.020  1.389
 3S3  CAE  CAF  aromatic  1.393  0.020  1.393
 3S3  NAQ  CB   single    1.427  0.020  1.427
 3S3  CAF  CAG  single    1.505  0.020  1.505
 3S3  O    C    double    1.202  0.020  1.202
 3S3  CB   CA   single    1.543  0.020  1.543
 3S3  C    OXT  single    1.320  0.020  1.320
 3S3  C    CA   single    1.524  0.020  1.524
 3S3  N    CA   single    1.440  0.020  1.440
 3S3  N    CAI  single    1.334  0.020  1.334
 3S3  CAG  CAI  single    1.529  0.020  1.529
 3S3  CAG  NAH  single    1.486  0.020  1.486
 3S3  CAI  OAK  double    1.218  0.020  1.218
 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  OXT  H1   single    0.850  0.020  0.980
 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
 3S3  OAW  H2   single    0.850  0.020  0.980

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  114.09  3.000
 3S3  CAG  CAI  OAK  121.63  3.000
 3S3  N    CAI  OAK  124.27  3.000
 3S3  HAG  CAG  NAH  106.00  3.000
 3S3  HAG  CAG  CAF  110.07  3.000
 3S3  NAH  CAG  CAF  110.86  3.000
 3S3  HAG  CAG  CAI  108.30  3.000
 3S3  NAH  CAG  CAI  108.03  3.000
 3S3  CAF  CAG  CAI  113.29  3.000
 3S3  CAE  CAF  CAA  119.78  3.000
 3S3  CAE  CAF  CAG  120.23  3.000
 3S3  CAA  CAF  CAG  120.00  3.000
 3S3  HAA  CAA  CAB  120.01  3.000
 3S3  HAA  CAA  CAF  119.93  3.000
 3S3  CAB  CAA  CAF  120.07  3.000
 3S3  HAB  CAB  CAC  120.26  3.000
 3S3  HAB  CAB  CAA  119.72  3.000
 3S3  CAC  CAB  CAA  120.02  3.000
 3S3  HAC  CAC  CAD  119.95  3.000
 3S3  HAC  CAC  CAB  120.01  3.000
 3S3  CAD  CAC  CAB  120.04  3.000
 3S3  HAD  CAD  CAE  119.76  3.000
 3S3  HAD  CAD  CAC  120.21  3.000
 3S3  CAE  CAD  CAC  120.02  3.000
 3S3  HAE  CAE  CAD  119.20  3.000
 3S3  HAE  CAE  CAF  120.73  3.000
 3S3  CAD  CAE  CAF  120.07  3.000
 3S3  HBO  NAH  HAH  107.07  3.000
 3S3  HBO  NAH  HBP  106.80  3.000
 3S3  HAH  NAH  HBP  107.07  3.000
 3S3  HBO  NAH  CAG  112.92  3.000
 3S3  HAH  NAH  CAG  110.63  3.000
 3S3  HBP  NAH  CAG  112.03  3.000
 3S3  H    N    CA   115.53  3.000
 3S3  H    N    CAI  120.58  3.000
 3S3  CA   N    CAI  121.35  3.000
 3S3  HA   CA   CB   108.94  3.000
 3S3  HA   CA   C    110.16  3.000
 3S3  CB   CA   C    108.58  3.000
 3S3  HA   CA   N    110.75  3.000
 3S3  C    CA   N    110.56  3.000
 3S3  CB   CA   N    107.78  3.000
 3S3  OXT  C    O    125.04  3.000
 3S3  OXT  C    CA   111.59  3.000
 3S3  O    C    CA   123.28  3.000
 3S3  H1   OXT  C    110.42  3.000
 3S3  HB   CB   SAU  108.98  3.000
 3S3  HB   CB   NAQ  106.40  3.000
 3S3  SAU  CB   NAQ  116.32  3.000
 3S3  HB   CB   CA   108.32  3.000
 3S3  NAQ  CB   CA   107.38  3.000
 3S3  SAU  CB   CA   109.17  3.000
 3S3  CAR  NAQ  CB   125.41  3.000
 3S3  CAT  SAU  CB    94.58  3.000
 3S3  HAT  CAT  HBL  107.61  3.000
 3S3  HAT  CAT  CAS  110.66  3.000
 3S3  HBL  CAT  CAS  111.31  3.000
 3S3  HAT  CAT  SAU  106.92  3.000
 3S3  HBL  CAT  SAU  109.02  3.000
 3S3  CAS  CAT  SAU  111.15  3.000
 3S3  HAS  CAS  CAR  107.03  3.000
 3S3  HAS  CAS  CAY  108.07  3.000
 3S3  CAR  CAS  CAY  110.92  3.000
 3S3  HAS  CAS  CAT  107.26  3.000
 3S3  CAR  CAS  CAT  111.11  3.000
 3S3  CAY  CAS  CAT  112.21  3.000
 3S3  HAY  CAY  HBM  107.66  3.000
 3S3  HAY  CAY  HBN  108.29  3.000
 3S3  HBM  CAY  HBN  108.18  3.000
 3S3  HAY  CAY  CAS  109.65  3.000
 3S3  HBM  CAY  CAS  111.95  3.000
 3S3  HBN  CAY  CAS  110.98  3.000
 3S3  CAV  CAR  CAS  116.32  3.000
 3S3  CAV  CAR  NAQ  115.45  3.000
 3S3  CAS  CAR  NAQ  128.21  3.000
 3S3  OAX  CAV  OAW  124.91  3.000
 3S3  OAW  CAV  CAR  112.64  3.000
 3S3  OAX  CAV  CAR  122.45  3.000
 3S3  H2   OAW  CAV  110.28  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  H2   OAW  CAV  CAR  180.00   0.0  0
 3S3  CONST_15  CA   N    CAI  OAK    0.00   0.0  0
 3S3  CONST_16  CA   N    CAI  CAG  180.00   0.0  0
 3S3  CONST_17  H    N    CAI  OAK  180.00   0.0  0
 3S3  CONST_18  H1   OXT  C    CA   180.00   0.0  0
 3S3  Var_01    CAS  CAT  SAU  CB   -61.28  30.0  1
 3S3  Var_02    CAS  CAR  NAQ  CB    -0.54  30.0  1
 3S3  Var_03    OAX  CAV  CAR  NAQ  167.59  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-3  H1   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
 3S3  plan-4  H2   0.020

