# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 06:49:44 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: (2R)-2-[(1R)-1-({(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetyl}amino)-2-oxoethyl]-5-ethenyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1scc(n1)/C(=N/OCC(O)=O)C(=O)N[C@H](C=O)[C@@H]2NC(=C(CS2)C=C)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
 NZM  NZM  '(2R)-2-[(1R)-1-({(2Z)-2-(2-amino-1,3-thiazol-4-yl)-2-[(carboxymethoxy)imino]acetyl}amino)-2-oxoethyl]-5-ethenyl-3,6-dihydro-2H-1,3-thiazine-4-carboxylic acid'  ligand  47  30  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NZM
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
 NZM  OAL  O  OH1   0  -0.592   6.7803   2.9745  -1.9020
 NZM  CAK  C  C     0   0.493   5.6424   2.7854  -1.2508
 NZM  OAM  O  O     0  -0.423   4.9395   3.6634  -0.8305
 NZM  CAJ  C  CH2   0  -0.237   5.3634   1.3107  -1.1169
 NZM  OAI  O  O2    0  -0.375   4.1389   1.1673  -0.4330
 NZM  NAH  N  N     0  -0.077   3.8870  -0.1457  -0.2556
 NZM  CAG  C  C     0   0.033   2.7507  -0.4180   0.2506
 NZM  CAD  C  CR5   0   0.363   2.4852  -1.8474   0.4823
 NZM  CAE  C  CR15  0  -0.537   3.3854  -2.7389   0.9613
 NZM  SAF  S  S2    0   0.194   2.6489  -4.2970   1.0702
 NZM  CAB  C  CR5   0   0.294   1.1647  -3.6146   0.4622
 NZM  NAA  N  NH2   0  -0.814   0.0713  -4.3681   0.2366
 NZM  NAC  N  N     0  -0.494   1.2402  -2.3455   0.2023
 NZM  CAN  C  C     0   0.519   1.7175   0.6091   0.6696
 NZM  OAO  O  O     0  -0.456   2.0293   1.6341   1.2437
 NZM  N    N  NH1   0  -0.659   0.4563   0.2764   0.3448
 NZM  CA   C  CH1   0  -0.226  -0.6587   1.0328   0.8293
 NZM  C    C  C1    0   0.183  -0.8846   0.8509   2.3240
 NZM  O    O  O     0  -0.351  -0.1866   0.1658   3.0207
 NZM  CB   C  CH1   0  -0.220  -1.9174   0.6433   0.0510
 NZM  NAU  N  NH1   0  -0.667  -2.9895   1.5289   0.3745
 NZM  SBB  S  S2    0   0.029  -2.4137  -1.0501   0.5100
 NZM  CBA  C  CH2   0  -0.643  -3.8207  -1.1141  -0.6172
 NZM  CAZ  C  C     0   0.038  -4.7083   0.1011  -0.5760
 NZM  CBC  C  C1    0  -0.203  -6.0142  -0.0638  -1.2069
 NZM  CBD  C  C2    0  -0.561  -6.5194  -1.2133  -1.6669
 NZM  CAV  C  C     0   0.228  -4.2668   1.2851  -0.0776
 NZM  CAW  C  C     0   0.481  -5.1061   2.5177   0.0783
 NZM  OAX  O  OH1   0  -0.575  -6.3603   2.2793   0.4028
 NZM  OAY  O  O     0  -0.432  -4.6348   3.6243  -0.0237
 NZM  H1   H  HOH1  0   0.489   6.9690   3.9216  -1.9822
 NZM  H2   H  HCH2  0   0.274   5.3218   0.8579  -2.1132
 NZM  H3   H  HCH2  0   0.276   6.1853   0.8346  -0.5720
 NZM  H4   H  HCR5  0   0.309   4.4031  -2.5723   1.2740
 NZM  H5   H  HNH2  0   0.411  -0.0296  -5.2458   0.7180
 NZM  H6   H  HNH2  0   0.398  -0.7891  -3.8598   0.1000
 NZM  H7   H  HNH1  0   0.433   0.2972  -0.6891   0.0531
 NZM  H8   H  HCH1  0   0.324  -0.4902   2.1036   0.6604
 NZM  H9   H  H     0   0.224  -1.7426   1.4121   2.7278
 NZM  H10  H  HCH1  0   0.315  -1.6882   0.6453  -1.0218
 NZM  H11  H  HCH2  0   0.301  -3.4718  -1.3127  -1.6331
 NZM  H12  H  HCH2  0   0.299  -4.3838  -1.9941  -0.3011
 NZM  H14  H  H     0   0.250  -6.6074   0.8242  -1.3701
 NZM  H15  H  H     0   0.248  -7.4797  -1.2188  -2.1639
 NZM  H16  H  H     0   0.241  -6.0263  -2.1719  -1.5780
 NZM  H17  H  HOH1  0   0.494  -6.8494   3.1136   0.4818
 NZM  H18  H  HNH1  0   0.404  -2.7434   2.5079   0.4272

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
 NZM  OAY  CAW  double    1.207  0.020  1.207
 NZM  CBD  CBC  double    1.337  0.020  1.337
 NZM  CBC  CAZ  single    1.460  0.020  1.460
 NZM  CAW  OAX  single    1.317  0.020  1.317
 NZM  CAW  CAV  single    1.499  0.020  1.499
 NZM  CAZ  CAV  double    1.358  0.020  1.358
 NZM  CAZ  CBA  single    1.505  0.020  1.505
 NZM  CAV  NAU  single    1.377  0.020  1.377
 NZM  CBA  SBB  single    1.804  0.020  1.804
 NZM  NAU  CB   single    1.428  0.020  1.428
 NZM  OAM  CAK  double    1.201  0.020  1.201
 NZM  O    C    double    1.201  0.020  1.201
 NZM  CAJ  CAK  single    1.507  0.020  1.507
 NZM  CAJ  OAI  single    1.410  0.020  1.410
 NZM  CAK  OAL  single    1.325  0.020  1.325
 NZM  C    CA   single    1.523  0.020  1.523
 NZM  CB   SBB  single    1.823  0.020  1.823
 NZM  CB   CA   single    1.530  0.020  1.530
 NZM  OAI  NAH  single    1.349  0.020  1.349
 NZM  N    CA   single    1.432  0.020  1.432
 NZM  N    CAN  single    1.344  0.020  1.344
 NZM  NAH  CAG  double    1.273  0.020  1.273
 NZM  CAG  CAN  single    1.516  0.020  1.516
 NZM  CAG  CAD  single    1.472  0.020  1.472
 NZM  CAN  OAO  double    1.216  0.020  1.216
 NZM  NAC  CAD  aromatic  1.370  0.020  1.370
 NZM  NAC  CAB  aromatic  1.298  0.020  1.298
 NZM  CAD  CAE  aromatic  1.354  0.020  1.354
 NZM  NAA  CAB  single    1.347  0.020  1.347
 NZM  CAB  SAF  aromatic  1.743  0.020  1.743
 NZM  CAE  SAF  aromatic  1.727  0.020  1.727
 NZM  OAL  H1   single    0.850  0.020  0.980
 NZM  CAJ  H2   single    0.970  0.020  1.090
 NZM  CAJ  H3   single    0.970  0.020  1.090
 NZM  CAE  H4   single    0.930  0.020  1.080
 NZM  NAA  H5   single    0.890  0.020  1.040
 NZM  NAA  H6   single    0.890  0.020  1.040
 NZM  N    H7   single    0.890  0.020  1.040
 NZM  CA   H8   single    0.970  0.020  1.090
 NZM  C    H9   single    0.930  0.020  1.080
 NZM  CB   H10  single    0.970  0.020  1.090
 NZM  CBA  H11  single    0.970  0.020  1.090
 NZM  CBA  H12  single    0.970  0.020  1.090
 NZM  CBC  H14  single    0.930  0.020  1.080
 NZM  CBD  H15  single    0.930  0.020  1.080
 NZM  CBD  H16  single    0.930  0.020  1.080
 NZM  OAX  H17  single    0.850  0.020  0.980
 NZM  NAU  H18  single    0.890  0.020  1.040

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
 NZM  H1   OAL  CAK  110.33  3.000
 NZM  CAJ  CAK  OAM  125.18  3.000
 NZM  CAJ  CAK  OAL  110.03  3.000
 NZM  OAM  CAK  OAL  124.79  3.000
 NZM  H3   CAJ  H2   107.54  3.000
 NZM  H3   CAJ  OAI  111.48  3.000
 NZM  H2   CAJ  OAI  111.49  3.000
 NZM  H3   CAJ  CAK  109.31  3.000
 NZM  H2   CAJ  CAK  109.32  3.000
 NZM  OAI  CAJ  CAK  107.67  3.000
 NZM  NAH  OAI  CAJ  108.97  3.000
 NZM  CAG  NAH  OAI  115.29  3.000
 NZM  CAN  CAG  CAD  119.44  3.000
 NZM  CAD  CAG  NAH  115.54  3.000
 NZM  CAN  CAG  NAH  124.97  3.000
 NZM  NAC  CAD  CAE  115.91  3.000
 NZM  CAE  CAD  CAG  125.09  3.000
 NZM  NAC  CAD  CAG  119.00  3.000
 NZM  H4   CAE  SAF  121.60  3.000
 NZM  H4   CAE  CAD  128.94  3.000
 NZM  SAF  CAE  CAD  109.43  3.000
 NZM  CAB  SAF  CAE   89.31  3.000
 NZM  NAC  CAB  NAA  124.11  3.000
 NZM  NAA  CAB  SAF  122.05  3.000
 NZM  NAC  CAB  SAF  113.78  3.000
 NZM  H6   NAA  H5   114.77  3.000
 NZM  H6   NAA  CAB  115.67  3.000
 NZM  H5   NAA  CAB  119.29  3.000
 NZM  CAB  NAC  CAD  111.57  3.000
 NZM  N    CAN  OAO  124.30  3.000
 NZM  OAO  CAN  CAG  121.81  3.000
 NZM  N    CAN  CAG  113.89  3.000
 NZM  H7   N    CA   118.35  3.000
 NZM  H7   N    CAN  116.70  3.000
 NZM  CA   N    CAN  121.20  3.000
 NZM  H8   CA   CB   107.24  3.000
 NZM  H8   CA   C    106.89  3.000
 NZM  CB   CA   C    110.29  3.000
 NZM  H8   CA   N    110.12  3.000
 NZM  CB   CA   N    109.51  3.000
 NZM  C    CA   N    112.62  3.000
 NZM  H9   C    O    122.04  3.000
 NZM  H9   C    CA   114.49  3.000
 NZM  O    C    CA   123.47  3.000
 NZM  H10  CB   SBB  107.74  3.000
 NZM  H10  CB   NAU  112.17  3.000
 NZM  SBB  CB   NAU  108.34  3.000
 NZM  H10  CB   CA   108.97  3.000
 NZM  SBB  CB   CA   109.40  3.000
 NZM  NAU  CB   CA   110.16  3.000
 NZM  H18  NAU  CAV  114.49  3.000
 NZM  H18  NAU  CB   115.45  3.000
 NZM  CAV  NAU  CB   120.83  3.000
 NZM  CBA  SBB  CB    95.05  3.000
 NZM  H12  CBA  H11  106.71  3.000
 NZM  H12  CBA  CAZ  109.80  3.000
 NZM  H11  CBA  CAZ  111.13  3.000
 NZM  H12  CBA  SBB  104.48  3.000
 NZM  H11  CBA  SBB  109.78  3.000
 NZM  CAZ  CBA  SBB  114.46  3.000
 NZM  CAV  CAZ  CBC  123.22  3.000
 NZM  CAV  CAZ  CBA  121.47  3.000
 NZM  CBC  CAZ  CBA  115.12  3.000
 NZM  H14  CBC  CBD  116.57  3.000
 NZM  H14  CBC  CAZ  117.62  3.000
 NZM  CBD  CBC  CAZ  125.72  3.000
 NZM  H16  CBD  H15  115.98  3.000
 NZM  H16  CBD  CBC  124.15  3.000
 NZM  H15  CBD  CBC  119.87  3.000
 NZM  CAW  CAV  CAZ  124.95  3.000
 NZM  CAZ  CAV  NAU  125.20  3.000
 NZM  CAW  CAV  NAU  109.85  3.000
 NZM  OAY  CAW  OAX  123.95  3.000
 NZM  OAX  CAW  CAV  114.19  3.000
 NZM  OAY  CAW  CAV  121.76  3.000
 NZM  H17  OAX  CAW  110.15  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
 NZM  CONST_01  SAF  CAB  NAC  CAD     0.00   0.0  0
 NZM  CONST_02  CAB  SAF  CAE  CAD     0.00   0.0  0
 NZM  CONST_03  CAB  NAC  CAD  CAE     0.00   0.0  0
 NZM  CONST_04  NAC  CAB  SAF  CAE     0.00   0.0  0
 NZM  CONST_05  NAC  CAD  CAE  SAF     0.00   0.0  0
 NZM  CONST_06  CAB  NAC  CAD  CAG   180.00   0.0  0
 NZM  CONST_07  SAF  CAE  CAD  CAG   180.00   0.0  0
 NZM  CONST_08  NAA  CAB  NAC  CAD   180.00   0.0  0
 NZM  CONST_09  NAA  CAB  SAF  CAE   180.00   0.0  0
 NZM  CONST_10  H4   CAE  SAF  CAB   180.00   0.0  0
 NZM  CONST_12  H6   NAA  CAB  SAF   180.00   0.0  0
 NZM  CONST_13  H17  OAX  CAW  CAV   180.00   0.0  0
 NZM  CONST_14  CA   N    CAN  CAG   180.00   0.0  0
 NZM  CONST_15  CA   N    CAN  OAO     0.00   0.0  0
 NZM  CONST_16  H7   N    CAN  CAG     0.00   0.0  0
 NZM  CONST_17  H1   OAL  CAK  OAM     0.00   0.0  0
 NZM  Var_01    CAZ  CAV  NAU  CB     15.82  30.0  1
 NZM  Var_02    CAZ  CBA  SBB  CB    -46.96  30.0  1
 NZM  Var_03    CBA  CAZ  CAV  NAU     3.10  30.0  1
 NZM  Var_04    CAV  CAZ  CBA  SBB    19.92  30.0  1
 NZM  Var_05    NAC  CAD  CAG  NAH  -139.32  30.0  2
 NZM  Var_06    OAY  CAW  CAV  NAU    32.36  30.0  1
 NZM  Var_07    CBD  CBC  CAZ  CBA     7.77  30.0  2
 NZM  Var_08    CAD  CAG  NAH  OAI  -178.32   0.0  2
 NZM  Var_09    N    CAN  CAG  CAD   -44.23  30.0  2
 NZM  Var_10    H15  CBD  CBC  CAZ  -176.93   0.0  2
 NZM  Var_11    OAI  CAJ  CAK  OAL  -179.34  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
 NZM  chir_01  CA  C    CB   N   positiv
 NZM  chir_02  CB  SBB  NAU  CA  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
 NZM  plan-1  CAG  0.020
 NZM  plan-1  CAD  0.020
 NZM  plan-1  CAE  0.020
 NZM  plan-1  SAF  0.020
 NZM  plan-1  CAB  0.020
 NZM  plan-1  NAA  0.020
 NZM  plan-1  NAC  0.020
 NZM  plan-1  H4   0.020
 NZM  plan-2  CAZ  0.020
 NZM  plan-2  CBC  0.020
 NZM  plan-2  CBD  0.020
 NZM  plan-2  H14  0.020
 NZM  plan-2  H15  0.020
 NZM  plan-2  H16  0.020
 NZM  plan-3  CA   0.020
 NZM  plan-3  C    0.020
 NZM  plan-3  O    0.020
 NZM  plan-3  H9   0.020
 NZM  plan-4  OAI  0.020
 NZM  plan-4  NAH  0.020
 NZM  plan-4  CAG  0.020
 NZM  plan-4  CAD  0.020
 NZM  plan-4  CAN  0.020
 NZM  plan-5  CAG  0.020
 NZM  plan-5  CAN  0.020
 NZM  plan-5  OAO  0.020
 NZM  plan-5  N    0.020
 NZM  plan-5  CA   0.020
 NZM  plan-5  H7   0.020
 NZM  plan-6  CAB  0.020
 NZM  plan-6  NAA  0.020
 NZM  plan-6  H5   0.020
 NZM  plan-6  H6   0.020
 NZM  plan-7  CB   0.020
 NZM  plan-7  NAU  0.020
 NZM  plan-7  CAV  0.020
 NZM  plan-7  H18  0.020
 NZM  plan-8  OAL  0.020
 NZM  plan-8  CAK  0.020
 NZM  plan-8  OAM  0.020
 NZM  plan-8  CAJ  0.020
 NZM  plan-8  H1   0.020
 NZM  plan-9  CAV  0.020
 NZM  plan-9  CAW  0.020
 NZM  plan-9  OAX  0.020
 NZM  plan-9  OAY  0.020
 NZM  plan-9  H17  0.020

