# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 12:22:13 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: (2R,3aR,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-7-hydroxyhexahydro-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]2OCC[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
 9DX  9DX  '(2R,3aR,7R,7aR)-2-[(2S)-2-amino-2-carboxyethyl]-7-hydroxyhexahydro-2H-furo[3,2-b]pyran-2-carboxylic acid (non-preferred name)'  ligand  34  19  .  2022-07-24  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_9DX
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
 9DX  OAC   O  OC    -1  -0.598   0.2546   0.9294   1.9247
 9DX  CAN   C  C      0   0.419  -0.0510   1.4234   0.8248
 9DX  OAE   O  O      0  -0.620  -0.3813   2.6082   0.6074
 9DX  CAS   C  CR5    0   0.143  -0.1120   0.4872  -0.4076
 9DX  CB    C  CH2    0  -0.434  -1.5799   0.2493  -0.7797
 9DX  CA    C  CH1    0  -0.218  -2.5381  -0.1513   0.3562
 9DX  N     N  NH2    0  -0.803  -2.1479  -1.3169   1.1333
 9DX  C     C  C      0   0.400  -3.9337  -0.3472  -0.2723
 9DX  O     O  O     -1  -0.611  -4.3080  -1.5172  -0.4876
 9DX  OXT   O  OC     0  -0.627  -4.5618   0.6941  -0.5592
 9DX  OAL   O  O      0  -0.510   0.5332  -0.7586  -0.1321
 9DX  CAR   C  CR15   0   0.046   1.6736  -0.9226  -0.9400
 9DX  CAP   C  CH1    0   0.044   2.7977  -1.6094  -0.1905
 9DX  OAF   O  OH1    0  -0.673   2.3219  -2.8348   0.3159
 9DX  CAH   C  CH2    0  -0.505   3.3587  -0.6822   0.8749
 9DX  CAG   C  CH2    0  -0.190   3.7829   0.6131   0.2054
 9DX  OAK   O  O2     0  -0.480   2.6926   1.2515  -0.4183
 9DX  CAQ   C  CR15   0  -0.022   2.0455   0.4838  -1.4104
 9DX  CAJ   C  CH2    0  -0.501   0.6611   1.0611  -1.6047
 9DX  HB    H  HCH2   0   0.216  -1.9605   1.1679  -1.2329
 9DX  HBA   H  HCH2   0   0.206  -1.6086  -0.5174  -1.5646
 9DX  HA    H  HCH1   0   0.203  -2.6079   0.6973   1.0456
 9DX  HN    H  HNH2   0   0.315  -2.1313  -2.1226   0.5205
 9DX  HNA   H  HNH2   0   0.337  -1.1971  -1.1874   1.4554
 9DX  HAR   H  HCR5   0   0.210   1.4294  -1.5179  -1.8351
 9DX  HAP   H  HCH1   0   0.193   3.5934  -1.7817  -0.9339
 9DX  HOAF  H  HOH1   0   0.447   3.0647  -3.2942   0.7198
 9DX  HAH   H  HCH2   0   0.243   2.6001  -0.4790   1.6337
 9DX  HAHA  H  HCH2   0   0.231   4.2243  -1.1390   1.3640
 9DX  HAG   H  HCH2   0   0.236   4.1837   1.3180   0.9354
 9DX  HAGA  H  HCH2   0   0.193   4.5819   0.4094  -0.5238
 9DX  HAQ   H  HCR5   0   0.225   2.6482   0.4489  -2.3291
 9DX  HAJ   H  HCH2   0   0.234   0.2472   0.6870  -2.5467
 9DX  HAJA  H  HCH2   0   0.250   0.6391   2.1484  -1.6403

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
 9DX  OAC  CAN   deloc   1.244  0.020  1.244
 9DX  CAN  OAE   deloc   1.249  0.020  1.249
 9DX  CAN  CAS   single  1.549  0.020  1.549
 9DX  CAS  CB    single  1.533  0.020  1.533
 9DX  CAS  OAL   single  1.430  0.020  1.430
 9DX  CAS  CAJ   single  1.536  0.020  1.536
 9DX  CB   CA    single  1.539  0.020  1.539
 9DX  CA   N     single  1.454  0.020  1.454
 9DX  CA   C     single  1.543  0.020  1.543
 9DX  C    O     deloc   1.247  0.020  1.247
 9DX  C    OXT   deloc   1.249  0.020  1.249
 9DX  OAL  CAR   single  1.407  0.020  1.407
 9DX  CAR  CAP   single  1.516  0.020  1.516
 9DX  CAR  CAQ   single  1.529  0.020  1.529
 9DX  CAP  OAF   single  1.409  0.020  1.409
 9DX  CAP  CAH   single  1.520  0.020  1.520
 9DX  CAH  CAG   single  1.519  0.020  1.519
 9DX  CAG  OAK   single  1.409  0.020  1.409
 9DX  OAK  CAQ   single  1.411  0.020  1.411
 9DX  CAQ  CAJ   single  1.513  0.020  1.513
 9DX  CB   HB    single  0.970  0.020  1.090
 9DX  CB   HBA   single  0.970  0.020  1.090
 9DX  CA   HA    single  0.970  0.020  1.090
 9DX  N    HN    single  0.890  0.020  1.040
 9DX  N    HNA   single  0.890  0.020  1.040
 9DX  CAR  HAR   single  0.970  0.020  1.090
 9DX  CAP  HAP   single  0.970  0.020  1.090
 9DX  OAF  HOAF  single  0.850  0.020  0.980
 9DX  CAH  HAH   single  0.970  0.020  1.090
 9DX  CAH  HAHA  single  0.970  0.020  1.090
 9DX  CAG  HAG   single  0.970  0.020  1.090
 9DX  CAG  HAGA  single  0.970  0.020  1.090
 9DX  CAQ  HAQ   single  0.970  0.020  1.090
 9DX  CAJ  HAJ   single  0.970  0.020  1.090
 9DX  CAJ  HAJA  single  0.970  0.020  1.090

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
 9DX  CAS   CAN  OAE  115.11  3.000
 9DX  CAS   CAN  OAC  118.24  3.000
 9DX  OAE   CAN  OAC  126.56  3.000
 9DX  CAJ   CAS  OAL  104.39  3.000
 9DX  CAJ   CAS  CB   110.53  3.000
 9DX  OAL   CAS  CB   110.10  3.000
 9DX  CAJ   CAS  CAN  111.99  3.000
 9DX  OAL   CAS  CAN  110.83  3.000
 9DX  CB    CAS  CAN  108.95  3.000
 9DX  HBA   CB   HB   106.36  3.000
 9DX  HBA   CB   CA   109.25  3.000
 9DX  HB    CB   CA   107.94  3.000
 9DX  HBA   CB   CAS  107.88  3.000
 9DX  HB    CB   CAS  107.68  3.000
 9DX  CA    CB   CAS  117.22  3.000
 9DX  HA    CA   C    107.28  3.000
 9DX  HA    CA   N    107.56  3.000
 9DX  C     CA   N    111.01  3.000
 9DX  HA    CA   CB   107.60  3.000
 9DX  C     CA   CB   107.19  3.000
 9DX  N     CA   CB   115.85  3.000
 9DX  HNA   N    HN   106.20  3.000
 9DX  HNA   N    CA   108.64  3.000
 9DX  HN    N    CA   108.59  3.000
 9DX  OXT   C    O    126.25  3.000
 9DX  OXT   C    CA   116.26  3.000
 9DX  O     C    CA   117.44  3.000
 9DX  CAR   OAL  CAS  110.89  3.000
 9DX  HAR   CAR  CAQ  107.51  3.000
 9DX  HAR   CAR  CAP  108.73  3.000
 9DX  CAQ   CAR  CAP  112.86  3.000
 9DX  HAR   CAR  OAL  110.46  3.000
 9DX  CAQ   CAR  OAL  105.46  3.000
 9DX  CAP   CAR  OAL  111.71  3.000
 9DX  HAP   CAP  CAH  107.56  3.000
 9DX  HAP   CAP  OAF  110.50  3.000
 9DX  CAH   CAP  OAF  113.79  3.000
 9DX  HAP   CAP  CAR  105.83  3.000
 9DX  CAH   CAP  CAR  110.12  3.000
 9DX  OAF   CAP  CAR  108.75  3.000
 9DX  HOAF  OAF  CAP  107.79  3.000
 9DX  HAHA  CAH  HAH  108.46  3.000
 9DX  HAHA  CAH  CAG  109.40  3.000
 9DX  HAH   CAH  CAG  109.98  3.000
 9DX  HAHA  CAH  CAP  110.53  3.000
 9DX  HAH   CAH  CAP  110.14  3.000
 9DX  CAG   CAH  CAP  108.33  3.000
 9DX  HAGA  CAG  HAG  107.23  3.000
 9DX  HAGA  CAG  OAK  110.63  3.000
 9DX  HAG   CAG  OAK  106.72  3.000
 9DX  HAGA  CAG  CAH  109.69  3.000
 9DX  HAG   CAG  CAH  111.02  3.000
 9DX  OAK   CAG  CAH  111.43  3.000
 9DX  CAQ   OAK  CAG  114.80  3.000
 9DX  HAQ   CAQ  CAJ  113.99  3.000
 9DX  HAQ   CAQ  OAK  110.69  3.000
 9DX  CAJ   CAQ  OAK  107.60  3.000
 9DX  HAQ   CAQ  CAR  111.18  3.000
 9DX  CAJ   CAQ  CAR   99.67  3.000
 9DX  OAK   CAQ  CAR  113.30  3.000
 9DX  HAJA  CAJ  HAJ  107.80  3.000
 9DX  HAJA  CAJ  CAQ  113.83  3.000
 9DX  HAJ   CAJ  CAQ  109.04  3.000
 9DX  HAJA  CAJ  CAS  112.86  3.000
 9DX  HAJ   CAJ  CAS  110.65  3.000
 9DX  CAQ   CAJ  CAS  102.59  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
 9DX  Var_01  OAK  CAG  CAH  CAP  60.55  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
 9DX  chir_01  CAS  CB   OAL  CAJ  negativ
 9DX  chir_02  CA   N    C    CB   positiv
 9DX  chir_03  CAR  OAL  CAP  CAQ  positiv
 9DX  chir_04  CAP  OAF  CAR  CAH  negativ
 9DX  chir_05  CAQ  OAK  CAR  CAJ  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
 9DX  plan-1  OAC  0.020
 9DX  plan-1  CAN  0.020
 9DX  plan-1  OAE  0.020
 9DX  plan-1  CAS  0.020
 9DX  plan-2  CA   0.020
 9DX  plan-2  C    0.020
 9DX  plan-2  O    0.020
 9DX  plan-2  OXT  0.020

