# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:26:34 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  45  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  OC    -1  -0.624   6.7695   2.9477  -2.0960
 NZM  CAK  C  C      0   0.366   5.7441   2.7601  -1.4126
 NZM  OAM  O  O      0  -0.591   5.0457   3.6036  -0.8326
 NZM  CAJ  C  CH2    0  -0.281   5.3474   1.2809  -1.2991
 NZM  OAI  O  O2     0  -0.371   4.1370   1.1379  -0.5613
 NZM  NAH  N  N      0  -0.076   3.8754  -0.1611  -0.3645
 NZM  CAG  C  C      0   0.015   2.7433  -0.4314   0.1577
 NZM  CAD  C  CR5    0   0.365   2.4873  -1.8603   0.4080
 NZM  CAE  C  CR15   0  -0.542   3.4019  -2.7459   0.8713
 NZM  SAF  S  S2     0   0.188   2.6749  -4.3074   1.0099
 NZM  CAB  C  CR5    0   0.290   1.1735  -3.6350   0.4362
 NZM  NAA  N  NH2    0  -0.814   0.0749  -4.3930   0.2440
 NZM  NAC  N  N      0  -0.494   1.2382  -2.3686   0.1633
 NZM  CAN  C  C      0   0.515   1.7114   0.5961   0.5731
 NZM  OAO  O  O      0  -0.462   2.0233   1.6437   1.1072
 NZM  N    N  NH1    0  -0.661   0.4446   0.2451   0.2891
 NZM  CA   C  CH1    0  -0.219  -0.6672   1.0116   0.7651
 NZM  C    C  C1     0   0.183  -0.8690   0.8836   2.2671
 NZM  O    O  O      0  -0.356  -0.1528   0.2362   2.9823
 NZM  CB   C  CH1    0  -0.216  -1.9390   0.5910   0.0241
 NZM  NAU  N  NH1    0  -0.652  -3.0073   1.4820   0.3331
 NZM  SBB  S  S2     0   0.008  -2.4149  -1.0896   0.5515
 NZM  CBA  C  CH2    0  -0.639  -3.8685  -1.1944  -0.5155
 NZM  CAZ  C  C      0  -0.007  -4.7472   0.0300  -0.4950
 NZM  CBC  C  C1     0  -0.203  -6.0814  -0.1625  -1.0443
 NZM  CBD  C  C2     0  -0.589  -6.5840  -1.3109  -1.5180
 NZM  CAV  C  C      0   0.146  -4.2957   1.2442  -0.0777
 NZM  CAW  C  C      0   0.391  -5.1311   2.5372   0.0263
 NZM  OAX  O  OC    -1  -0.569  -6.3487   2.4436   0.2364
 NZM  OAY  O  O      0  -0.591  -4.4648   3.5856  -0.0865
 NZM  H2   H  HCH2   0   0.225   5.2259   0.8569  -2.3016
 NZM  H3   H  HCH2   0   0.228   6.1535   0.7257  -0.8075
 NZM  H4   H  HCR5   0   0.305   4.4262  -2.5742   1.1582
 NZM  H5   H  HNH2   0   0.409  -0.0140  -5.2598   0.7475
 NZM  H6   H  HNH2   0   0.397  -0.7881  -3.8821   0.1334
 NZM  H7   H  HNH1   0   0.431   0.2845  -0.7274   0.0236
 NZM  H8   H  HCH1   0   0.317  -0.5072   2.0769   0.5550
 NZM  H9   H  H      0   0.220  -1.7294   1.4488   2.6602
 NZM  H10  H  HCH1   0   0.302  -1.7246   0.5529  -1.0516
 NZM  H11  H  HCH2   0   0.283  -3.5549  -1.4486  -1.5312
 NZM  H12  H  HCH2   0   0.282  -4.4212  -2.0574  -0.1371
 NZM  H14  H  H      0   0.246  -6.7079   0.7156  -1.0926
 NZM  H15  H  H      0   0.231  -7.5816  -1.3345  -1.9364
 NZM  H16  H  H      0   0.226  -6.0488  -2.2521  -1.5184
 NZM  H18  H  HNH1   0   0.388  -2.7908   2.4722   0.3141

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  deloc     1.247  0.020  1.247
 NZM  CBD  CBC  double    1.340  0.020  1.340
 NZM  CBC  CAZ  single    1.456  0.020  1.456
 NZM  CAW  OAX  deloc     1.239  0.020  1.239
 NZM  CAW  CAV  single    1.543  0.020  1.543
 NZM  CAZ  CAV  double    1.361  0.020  1.361
 NZM  CAZ  CBA  single    1.507  0.020  1.507
 NZM  CAV  NAU  single    1.373  0.020  1.373
 NZM  CBA  SBB  single    1.806  0.020  1.806
 NZM  NAU  CB   single    1.425  0.020  1.425
 NZM  OAM  CAK  deloc     1.239  0.020  1.239
 NZM  O    C    double    1.201  0.020  1.201
 NZM  CAJ  CAK  single    1.536  0.020  1.536
 NZM  CAJ  OAI  single    1.425  0.020  1.425
 NZM  CAK  OAL  deloc     1.246  0.020  1.246
 NZM  C    CA   single    1.521  0.020  1.521
 NZM  CB   SBB  single    1.825  0.020  1.825
 NZM  CB   CA   single    1.531  0.020  1.531
 NZM  OAI  NAH  single    1.340  0.020  1.340
 NZM  N    CA   single    1.432  0.020  1.432
 NZM  N    CAN  single    1.345  0.020  1.345
 NZM  NAH  CAG  double    1.276  0.020  1.276
 NZM  CAG  CAN  single    1.514  0.020  1.514
 NZM  CAG  CAD  single    1.473  0.020  1.473
 NZM  CAN  OAO  double    1.217  0.020  1.217
 NZM  NAC  CAD  aromatic  1.371  0.020  1.371
 NZM  NAC  CAB  aromatic  1.297  0.020  1.297
 NZM  CAD  CAE  aromatic  1.355  0.020  1.355
 NZM  NAA  CAB  single    1.349  0.020  1.349
 NZM  CAB  SAF  aromatic  1.742  0.020  1.742
 NZM  CAE  SAF  aromatic  1.728  0.020  1.728
 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  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  CAJ  CAK  OAM  118.39  3.000
 NZM  CAJ  CAK  OAL  113.45  3.000
 NZM  OAM  CAK  OAL  128.16  3.000
 NZM  H3   CAJ  H2   107.23  3.000
 NZM  H3   CAJ  OAI  109.99  3.000
 NZM  H2   CAJ  OAI  109.93  3.000
 NZM  H3   CAJ  CAK  109.35  3.000
 NZM  H2   CAJ  CAK  109.51  3.000
 NZM  OAI  CAJ  CAK  110.76  3.000
 NZM  NAH  OAI  CAJ  109.83  3.000
 NZM  CAG  NAH  OAI  116.03  3.000
 NZM  CAN  CAG  CAD  119.55  3.000
 NZM  CAD  CAG  NAH  115.42  3.000
 NZM  CAN  CAG  NAH  124.98  3.000
 NZM  NAC  CAD  CAE  115.71  3.000
 NZM  CAE  CAD  CAG  125.09  3.000
 NZM  NAC  CAD  CAG  119.20  3.000
 NZM  H4   CAE  SAF  121.51  3.000
 NZM  H4   CAE  CAD  128.95  3.000
 NZM  SAF  CAE  CAD  109.52  3.000
 NZM  CAB  SAF  CAE   89.28  3.000
 NZM  NAC  CAB  NAA  124.02  3.000
 NZM  NAA  CAB  SAF  122.14  3.000
 NZM  NAC  CAB  SAF  113.77  3.000
 NZM  H6   NAA  H5   114.54  3.000
 NZM  H6   NAA  CAB  115.33  3.000
 NZM  H5   NAA  CAB  119.01  3.000
 NZM  CAB  NAC  CAD  111.72  3.000
 NZM  N    CAN  OAO  123.98  3.000
 NZM  OAO  CAN  CAG  122.01  3.000
 NZM  N    CAN  CAG  114.01  3.000
 NZM  H7   N    CA   118.34  3.000
 NZM  H7   N    CAN  116.83  3.000
 NZM  CA   N    CAN  121.44  3.000
 NZM  H8   CA   CB   107.17  3.000
 NZM  H8   CA   C    106.86  3.000
 NZM  CB   CA   C    110.16  3.000
 NZM  H8   CA   N    110.04  3.000
 NZM  CB   CA   N    109.71  3.000
 NZM  C    CA   N    112.72  3.000
 NZM  H9   C    O    121.97  3.000
 NZM  H9   C    CA   114.38  3.000
 NZM  O    C    CA   123.65  3.000
 NZM  H10  CB   SBB  107.59  3.000
 NZM  H10  CB   NAU  112.37  3.000
 NZM  SBB  CB   NAU  108.52  3.000
 NZM  H10  CB   CA   108.76  3.000
 NZM  SBB  CB   CA   109.26  3.000
 NZM  NAU  CB   CA   110.25  3.000
 NZM  H18  NAU  CAV  111.34  3.000
 NZM  H18  NAU  CB   116.52  3.000
 NZM  CAV  NAU  CB   122.03  3.000
 NZM  CBA  SBB  CB    95.31  3.000
 NZM  H12  CBA  H11  106.46  3.000
 NZM  H12  CBA  CAZ  110.01  3.000
 NZM  H11  CBA  CAZ  111.64  3.000
 NZM  H12  CBA  SBB  104.38  3.000
 NZM  H11  CBA  SBB  109.36  3.000
 NZM  CAZ  CBA  SBB  114.46  3.000
 NZM  CAV  CAZ  CBC  122.53  3.000
 NZM  CAV  CAZ  CBA  122.38  3.000
 NZM  CBC  CAZ  CBA  114.95  3.000
 NZM  H14  CBC  CBD  117.61  3.000
 NZM  H14  CBC  CAZ  116.18  3.000
 NZM  CBD  CBC  CAZ  126.19  3.000
 NZM  H16  CBD  H15  115.89  3.000
 NZM  H16  CBD  CBC  124.03  3.000
 NZM  H15  CBD  CBC  120.07  3.000
 NZM  CAW  CAV  CAZ  126.06  3.000
 NZM  CAZ  CAV  NAU  123.89  3.000
 NZM  CAW  CAV  NAU  110.05  3.000
 NZM  OAY  CAW  OAX  127.13  3.000
 NZM  OAX  CAW  CAV  118.70  3.000
 NZM  OAY  CAW  CAV  114.14  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  CA   N    CAN  CAG   180.00   0.0  0
 NZM  CONST_14  CA   N    CAN  OAO     0.00   0.0  0
 NZM  CONST_15  H7   N    CAN  CAG     0.00   0.0  0
 NZM  Var_01    CAZ  CAV  NAU  CB     17.49  30.0  1
 NZM  Var_02    CAZ  CBA  SBB  CB    -45.91  30.0  1
 NZM  Var_03    CBA  CAZ  CAV  NAU     1.46  30.0  1
 NZM  Var_04    CAV  CAZ  CBA  SBB    20.17  30.0  1
 NZM  Var_05    NAC  CAD  CAG  NAH  -140.10  30.0  2
 NZM  Var_06    OAY  CAW  CAV  NAU    27.56  30.0  2
 NZM  Var_07    CBD  CBC  CAZ  CBA     1.80  30.0  2
 NZM  Var_08    CAD  CAG  NAH  OAI  -178.12   0.0  2
 NZM  Var_09    N    CAN  CAG  CAD   -42.95  30.0  2
 NZM  Var_10    H15  CBD  CBC  CAZ  -177.90   0.0  2
 NZM  Var_11    OAI  CAJ  CAK  OAL  -177.27  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
 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-9  CAV  0.020
 NZM  plan-9  CAW  0.020
 NZM  plan-9  OAX  0.020
 NZM  plan-9  OAY  0.020

