# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 00:37:50 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2R,3aR,6R,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6,7-dihydroxyhexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C[C@@]1(C[C@H]2OC[C@@H](O)[C@@H](O)[C@H]2O1)C(O)=O)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
 NDZ  NDZ  '(2R,3aR,6R,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-6,7-dihydroxyhexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid (non-preferred name)'  ligand  37  20  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NDZ
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
 NDZ  O     O  O     0  -0.435   4.6281  -1.4659   0.3511
 NDZ  C     C  C     0   0.549   4.0838  -0.4116   0.1458
 NDZ  OXT   O  OH1   0  -0.593   4.6530   0.7641   0.3828
 NDZ  CA    C  CH1   0  -0.234   2.6666  -0.2618  -0.3775
 NDZ  N     N  NH2   0  -0.782   2.2790  -1.4934  -1.0285
 NDZ  CB    C  CH2   0  -0.465   1.7860   0.2065   0.8006
 NDZ  CAJ   C  CT    0   0.147   0.3067   0.4906   0.4943
 NDZ  CAD   C  C     0   0.545   0.2408   1.5191  -0.6341
 NDZ  OAA   O  O     0  -0.447   0.4241   2.6992  -0.4571
 NDZ  OAE   O  OH1   0  -0.567   0.0612   0.9802  -1.8235
 NDZ  CAR   C  CH2   0  -0.515  -0.4006   1.0200   1.7513
 NDZ  OAI   O  O2    0  -0.492  -0.3848  -0.6873   0.1314
 NDZ  CAH   C  CH1   0   0.039  -1.4870  -0.8992   0.9970
 NDZ  CAQ   C  CH1   0  -0.025  -1.7982   0.4732   1.5844
 NDZ  OAP   O  O2    0  -0.477  -2.4793   1.2935   0.6647
 NDZ  CAO   C  CH2   0  -0.231  -3.6853   0.7276   0.2089
 NDZ  CAF   C  CH1   0  -0.017  -3.4507  -0.5525  -0.5826
 NDZ  OAB   O  OH1   0  -0.646  -2.7356  -0.3383  -1.7681
 NDZ  CAG   C  CH1   0   0.034  -2.6871  -1.5263   0.3104
 NDZ  OAC   O  OH1   0  -0.664  -2.2740  -2.6947  -0.3459
 NDZ  HOXT  H  HOH1  0   0.483   5.5363   0.6366   0.7602
 NDZ  HA    H  HCH1  0   0.278   2.6976   0.5255  -1.1376
 NDZ  HN    H  HNH2  0   0.342   2.1873  -2.2334  -0.3429
 NDZ  HNA   H  HNH2  0   0.359   1.3590  -1.3799  -1.4315
 NDZ  HB    H  HCH2  0   0.261   1.8103  -0.5533   1.5883
 NDZ  HBA   H  HCH2  0   0.263   2.2075   1.1167   1.2344
 NDZ  HOAE  H  HOH1  0   0.478   0.0890   1.6727  -2.5010
 NDZ  HAR   H  HCH2  0   0.270   0.0529   0.5855   2.6449
 NDZ  HARA  H  HCH2  0   0.277  -0.3584   2.1025   1.8520
 NDZ  HAH   H  HCH1  0   0.232  -1.1850  -1.5639   1.8197
 NDZ  HAQ   H  HCH1  0   0.250  -2.3519   0.3929   2.5296
 NDZ  HAO   H  HCH2  0   0.210  -4.3633   0.5150   1.0482
 NDZ  HAOA  H  HCH2  0   0.251  -4.1765   1.4786  -0.4146
 NDZ  HAF   H  HCH1  0   0.214  -4.4428  -0.9876  -0.7899
 NDZ  HOAB  H  HOH1  0   0.445  -3.2124   0.3106  -2.2943
 NDZ  HAG   H  HCH1  0   0.214  -3.3770  -1.7626   1.1364
 NDZ  HOAC  H  HOH1  0   0.451  -3.0572  -3.1552  -0.6635

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
 NDZ  O    C     double  1.204  0.020  1.204
 NDZ  C    OXT   single  1.328  0.020  1.328
 NDZ  C    CA    single  1.518  0.020  1.518
 NDZ  CA   N     single  1.446  0.020  1.446
 NDZ  CA   CB    single  1.544  0.020  1.544
 NDZ  CB   CAJ   single  1.537  0.020  1.537
 NDZ  CAJ  CAD   single  1.528  0.020  1.528
 NDZ  CAJ  CAR   single  1.536  0.020  1.536
 NDZ  CAJ  OAI   single  1.413  0.020  1.413
 NDZ  CAD  OAA   double  1.207  0.020  1.207
 NDZ  CAD  OAE   single  1.318  0.020  1.318
 NDZ  CAR  CAQ   single  1.510  0.020  1.510
 NDZ  OAI  CAH   single  1.417  0.020  1.417
 NDZ  CAH  CAQ   single  1.525  0.020  1.525
 NDZ  CAH  CAG   single  1.518  0.020  1.518
 NDZ  CAQ  OAP   single  1.408  0.020  1.408
 NDZ  OAP  CAO   single  1.408  0.020  1.408
 NDZ  CAO  CAF   single  1.523  0.020  1.523
 NDZ  CAF  OAB   single  1.401  0.020  1.401
 NDZ  CAF  CAG   single  1.526  0.020  1.526
 NDZ  CAG  OAC   single  1.402  0.020  1.402
 NDZ  OXT  HOXT  single  0.850  0.020  0.980
 NDZ  CA   HA    single  0.970  0.020  1.090
 NDZ  N    HN    single  0.890  0.020  1.040
 NDZ  N    HNA   single  0.890  0.020  1.040
 NDZ  CB   HB    single  0.970  0.020  1.090
 NDZ  CB   HBA   single  0.970  0.020  1.090
 NDZ  OAE  HOAE  single  0.850  0.020  0.980
 NDZ  CAR  HAR   single  0.970  0.020  1.090
 NDZ  CAR  HARA  single  0.970  0.020  1.090
 NDZ  CAH  HAH   single  0.970  0.020  1.090
 NDZ  CAQ  HAQ   single  0.970  0.020  1.090
 NDZ  CAO  HAO   single  0.970  0.020  1.090
 NDZ  CAO  HAOA  single  0.970  0.020  1.090
 NDZ  CAF  HAF   single  0.970  0.020  1.090
 NDZ  OAB  HOAB  single  0.850  0.020  0.980
 NDZ  CAG  HAG   single  0.970  0.020  1.090
 NDZ  OAC  HOAC  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
 NDZ  CA    C    OXT  111.99  3.000
 NDZ  CA    C    O    124.55  3.000
 NDZ  OXT   C    O    123.44  3.000
 NDZ  HOXT  OXT  C    110.11  3.000
 NDZ  HA    CA   CB   109.14  3.000
 NDZ  HA    CA   N    107.91  3.000
 NDZ  CB    CA   N    116.69  3.000
 NDZ  HA    CA   C    106.49  3.000
 NDZ  CB    CA   C    107.43  3.000
 NDZ  N     CA   C    108.74  3.000
 NDZ  HNA   N    HN   105.63  3.000
 NDZ  HNA   N    CA   109.14  3.000
 NDZ  HN    N    CA   109.99  3.000
 NDZ  HBA   CB   HB   106.49  3.000
 NDZ  HBA   CB   CAJ  107.24  3.000
 NDZ  HB    CB   CAJ  107.04  3.000
 NDZ  HBA   CB   CA   109.61  3.000
 NDZ  HB    CB   CA   109.02  3.000
 NDZ  CAJ   CB   CA   116.94  3.000
 NDZ  OAI   CAJ  CAR  105.78  3.000
 NDZ  OAI   CAJ  CAD  110.50  3.000
 NDZ  CAR   CAJ  CAD  110.63  3.000
 NDZ  OAI   CAJ  CB   111.59  3.000
 NDZ  CAR   CAJ  CB   110.10  3.000
 NDZ  CAD   CAJ  CB   108.24  3.000
 NDZ  OAE   CAD  OAA  123.54  3.000
 NDZ  OAE   CAD  CAJ  113.39  3.000
 NDZ  OAA   CAD  CAJ  122.89  3.000
 NDZ  HOAE  OAE  CAD  109.56  3.000
 NDZ  HARA  CAR  HAR  107.70  3.000
 NDZ  HARA  CAR  CAQ  113.98  3.000
 NDZ  HAR   CAR  CAQ  109.31  3.000
 NDZ  HARA  CAR  CAJ  113.62  3.000
 NDZ  HAR   CAR  CAJ  109.95  3.000
 NDZ  CAQ   CAR  CAJ  102.18  3.000
 NDZ  CAH   OAI  CAJ  110.38  3.000
 NDZ  HAH   CAH  CAG  107.79  3.000
 NDZ  HAH   CAH  CAQ  108.16  3.000
 NDZ  CAG   CAH  CAQ  112.62  3.000
 NDZ  HAH   CAH  OAI  109.49  3.000
 NDZ  CAG   CAH  OAI  113.60  3.000
 NDZ  CAQ   CAH  OAI  105.04  3.000
 NDZ  HAQ   CAQ  OAP  111.16  3.000
 NDZ  HAQ   CAQ  CAH  111.63  3.000
 NDZ  OAP   CAQ  CAH  111.80  3.000
 NDZ  HAQ   CAQ  CAR  113.45  3.000
 NDZ  OAP   CAQ  CAR  107.99  3.000
 NDZ  CAH   CAQ  CAR  100.34  3.000
 NDZ  CAO   OAP  CAQ  113.05  3.000
 NDZ  HAOA  CAO  HAO  106.94  3.000
 NDZ  HAOA  CAO  CAF  110.50  3.000
 NDZ  HAO   CAO  CAF  109.21  3.000
 NDZ  HAOA  CAO  OAP  107.07  3.000
 NDZ  HAO   CAO  OAP  111.02  3.000
 NDZ  CAF   CAO  OAP  111.96  3.000
 NDZ  HAF   CAF  CAG  107.96  3.000
 NDZ  HAF   CAF  OAB  111.13  3.000
 NDZ  CAG   CAF  OAB  109.71  3.000
 NDZ  HAF   CAF  CAO  106.89  3.000
 NDZ  CAG   CAF  CAO  108.01  3.000
 NDZ  OAB   CAF  CAO  112.94  3.000
 NDZ  HOAB  OAB  CAF  108.24  3.000
 NDZ  HAG   CAG  OAC  110.89  3.000
 NDZ  HAG   CAG  CAF  105.20  3.000
 NDZ  OAC   CAG  CAF  113.90  3.000
 NDZ  HAG   CAG  CAH  104.16  3.000
 NDZ  OAC   CAG  CAH  108.84  3.000
 NDZ  CAF   CAG  CAH  113.37  3.000
 NDZ  HOAC  OAC  CAG  108.26  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
 NDZ  CONST_01  HOAE  OAE  CAD  CAJ  180.00   0.0  0
 NDZ  CONST_02  HOXT  OXT  C    O      0.00   0.0  0
 NDZ  Var_01    CAF   CAO  OAP  CAQ  -64.22  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
 NDZ  chir_01  CA   C    N    CB   negativ
 NDZ  chir_02  CAJ  CAR  OAI  CB   positiv
 NDZ  chir_03  CAH  OAI  CAQ  CAG  negativ
 NDZ  chir_04  CAQ  OAP  CAR  CAH  positiv
 NDZ  chir_05  CAF  OAB  CAG  CAO  negativ
 NDZ  chir_06  CAG  OAC  CAF  CAH  positiv

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
 NDZ  plan-1  O     0.020
 NDZ  plan-1  C     0.020
 NDZ  plan-1  OXT   0.020
 NDZ  plan-1  CA    0.020
 NDZ  plan-1  HOXT  0.020
 NDZ  plan-2  CAJ   0.020
 NDZ  plan-2  CAD   0.020
 NDZ  plan-2  OAA   0.020
 NDZ  plan-2  OAE   0.020
 NDZ  plan-2  HOAE  0.020

