# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:54:36 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  35  20  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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  -0.611   4.3541  -1.6663   0.6195
 NDZ  C     C  C      0   0.398   4.0332  -0.5085   0.2803
 NDZ  OXT   O  OC    -1  -0.622   4.7204   0.5218   0.4340
 NDZ  CA    C  CH1    0  -0.205   2.6319  -0.3129  -0.3404
 NDZ  N     N  NH2    0  -0.820   2.1660  -1.5476  -0.9575
 NDZ  CB    C  CH2    0  -0.451   1.7137   0.2473   0.7588
 NDZ  CAJ   C  CR5    0   0.157   0.3213   0.7330   0.3254
 NDZ  CAD   C  C      0   0.392   0.4827   1.8167  -0.7635
 NDZ  OAA   O  O      0  -0.623   0.9514   2.9020  -0.3555
 NDZ  OAE   O  OC    -1  -0.590   0.1837   1.5270  -1.9315
 NDZ  CAR   C  CH2    0  -0.515  -0.4546   1.2471   1.5635
 NDZ  OAI   O  O      0  -0.497  -0.4594  -0.3507  -0.1793
 NDZ  CAH   C  CR15   0   0.034  -1.3453  -0.7809   0.8164
 NDZ  CAQ   C  CR15   0   0.011  -1.7758   0.5094   1.5090
 NDZ  OAP   O  O2     0  -0.481  -2.6800   1.2473   0.7179
 NDZ  CAO   C  CH2    0  -0.223  -3.8355   0.5184   0.3904
 NDZ  CAF   C  CH1    0  -0.018  -3.5227  -0.6908  -0.4844
 NDZ  OAB   O  OH1    0  -0.652  -3.0154  -0.3360  -1.7433
 NDZ  CAG   C  CH1    0   0.030  -2.5173  -1.5671   0.2598
 NDZ  OAC   O  OH1    0  -0.665  -2.0251  -2.6388  -0.5018
 NDZ  HA    H  HCH1   0   0.201   2.7288   0.4507  -1.1201
 NDZ  HN    H  HNH2   0   0.316   2.3708  -2.3015  -0.3126
 NDZ  HNA   H  HNH2   0   0.338   1.1584  -1.5112  -1.0422
 NDZ  HB    H  HCH2   0   0.208   1.5947  -0.5174   1.5380
 NDZ  HBA   H  HCH2   0   0.218   2.2126   1.0951   1.2345
 NDZ  HAR   H  HCH2   0   0.238   0.0630   0.9776   2.4875
 NDZ  HARA  H  HCH2   0   0.249  -0.5781   2.3287   1.5690
 NDZ  HAH   H  HCR5   0   0.208  -0.8332  -1.4147   1.5614
 NDZ  HAQ   H  HCR5   0   0.222  -2.2059   0.3138   2.5017
 NDZ  HAO   H  HCH2   0   0.199  -4.3613   0.1788   1.2963
 NDZ  HAOA  H  HCH2   0   0.242  -4.5112   1.1998  -0.1333
 NDZ  HAF   H  HCH1   0   0.210  -4.4595  -1.2632  -0.5857
 NDZ  HOAB  H  HOH1   0   0.445  -3.7155   0.1148  -2.2250
 NDZ  HAG   H  HCH1   0   0.208  -3.0587  -1.9324   1.1468
 NDZ  HOAC  H  HOH1   0   0.448  -2.7700  -3.1875  -0.7672

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     deloc   1.248  0.020  1.248
 NDZ  C    OXT   deloc   1.248  0.020  1.248
 NDZ  C    CA    single  1.545  0.020  1.545
 NDZ  CA   N     single  1.457  0.020  1.457
 NDZ  CA   CB    single  1.538  0.020  1.538
 NDZ  CB   CAJ   single  1.537  0.020  1.537
 NDZ  CAJ  CAD   single  1.545  0.020  1.545
 NDZ  CAJ  CAR   single  1.549  0.020  1.549
 NDZ  CAJ  OAI   single  1.428  0.020  1.428
 NDZ  CAD  OAA   deloc   1.251  0.020  1.251
 NDZ  CAD  OAE   deloc   1.240  0.020  1.240
 NDZ  CAR  CAQ   single  1.514  0.020  1.514
 NDZ  OAI  CAH   single  1.400  0.020  1.400
 NDZ  CAH  CAQ   single  1.526  0.020  1.526
 NDZ  CAH  CAG   single  1.517  0.020  1.517
 NDZ  CAQ  OAP   single  1.410  0.020  1.410
 NDZ  OAP  CAO   single  1.405  0.020  1.405
 NDZ  CAO  CAF   single  1.525  0.020  1.525
 NDZ  CAF  OAB   single  1.403  0.020  1.403
 NDZ  CAF  CAG   single  1.527  0.020  1.527
 NDZ  CAG  OAC   single  1.404  0.020  1.404
 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  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  116.38  3.000
 NDZ  CA    C    O    117.37  3.000
 NDZ  OXT   C    O    126.20  3.000
 NDZ  HA    CA   CB   107.92  3.000
 NDZ  HA    CA   N    108.51  3.000
 NDZ  CB    CA   N    114.87  3.000
 NDZ  HA    CA   C    107.09  3.000
 NDZ  CB    CA   C    107.49  3.000
 NDZ  N     CA   C    110.66  3.000
 NDZ  HNA   N    HN   106.35  3.000
 NDZ  HNA   N    CA   108.87  3.000
 NDZ  HN    N    CA   107.24  3.000
 NDZ  HBA   CB   HB   106.31  3.000
 NDZ  HBA   CB   CAJ  106.93  3.000
 NDZ  HB    CB   CAJ  108.78  3.000
 NDZ  HBA   CB   CA   108.73  3.000
 NDZ  HB    CB   CA   108.55  3.000
 NDZ  CAJ   CB   CA   117.03  3.000
 NDZ  OAI   CAJ  CAR  105.10  3.000
 NDZ  OAI   CAJ  CAD  109.90  3.000
 NDZ  CAR   CAJ  CAD  112.52  3.000
 NDZ  OAI   CAJ  CB   110.80  3.000
 NDZ  CAR   CAJ  CB   109.47  3.000
 NDZ  CAD   CAJ  CB   109.01  3.000
 NDZ  OAE   CAD  OAA  126.90  3.000
 NDZ  OAE   CAD  CAJ  118.35  3.000
 NDZ  OAA   CAD  CAJ  114.71  3.000
 NDZ  HARA  CAR  HAR  107.12  3.000
 NDZ  HARA  CAR  CAQ  112.66  3.000
 NDZ  HAR   CAR  CAQ  108.88  3.000
 NDZ  HARA  CAR  CAJ  112.99  3.000
 NDZ  HAR   CAR  CAJ  110.90  3.000
 NDZ  CAQ   CAR  CAJ  104.28  3.000
 NDZ  CAH   OAI  CAJ  109.13  3.000
 NDZ  HAH   CAH  CAG  107.96  3.000
 NDZ  HAH   CAH  CAQ  108.06  3.000
 NDZ  CAG   CAH  CAQ  112.75  3.000
 NDZ  HAH   CAH  OAI  111.26  3.000
 NDZ  CAG   CAH  OAI  112.77  3.000
 NDZ  CAQ   CAH  OAI  103.97  3.000
 NDZ  HAQ   CAQ  OAP  110.42  3.000
 NDZ  HAQ   CAQ  CAH  111.70  3.000
 NDZ  OAP   CAQ  CAH  111.64  3.000
 NDZ  HAQ   CAQ  CAR  113.29  3.000
 NDZ  OAP   CAQ  CAR  108.95  3.000
 NDZ  CAH   CAQ  CAR  100.49  3.000
 NDZ  CAO   OAP  CAQ  112.75  3.000
 NDZ  HAOA  CAO  HAO  106.93  3.000
 NDZ  HAOA  CAO  CAF  110.26  3.000
 NDZ  HAO   CAO  CAF  108.99  3.000
 NDZ  HAOA  CAO  OAP  107.26  3.000
 NDZ  HAO   CAO  OAP  111.16  3.000
 NDZ  CAF   CAO  OAP  112.11  3.000
 NDZ  HAF   CAF  CAG  107.83  3.000
 NDZ  HAF   CAF  OAB  110.86  3.000
 NDZ  CAG   CAF  OAB  110.14  3.000
 NDZ  HAF   CAF  CAO  106.86  3.000
 NDZ  CAG   CAF  CAO  108.09  3.000
 NDZ  OAB   CAF  CAO  112.85  3.000
 NDZ  HOAB  OAB  CAF  107.74  3.000
 NDZ  HAG   CAG  OAC  110.85  3.000
 NDZ  HAG   CAG  CAF  105.02  3.000
 NDZ  OAC   CAG  CAF  113.86  3.000
 NDZ  HAG   CAG  CAH  104.84  3.000
 NDZ  OAC   CAG  CAH  108.90  3.000
 NDZ  CAF   CAG  CAH  112.96  3.000
 NDZ  HOAC  OAC  CAG  108.27  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  Var_01  CAF  CAO  OAP  CAQ  -64.31  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-2  CAJ  0.020
 NDZ  plan-2  CAD  0.020
 NDZ  plan-2  OAA  0.020
 NDZ  plan-2  OAE  0.020

