# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 13:10:07 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (2S,3R,4S,5R)-2-benzylpiperidine-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CN[C@@H](Cc2ccccc2)[C@@H](O)[C@H]1O
#
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
 ZXB  ZXB  (2S,3R,4S,5R)-2-benzylpiperidine-3,4,5-triol  ligand  33  16  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZXB
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
 ZXB  CAG   C  CR16  0  -0.313  -2.8499   0.2429  -1.1449
 ZXB  CAE   C  CR16  0  -0.244  -4.0613   0.8736  -0.8947
 ZXB  CAD   C  CR16  0  -0.276  -4.6910   0.7129   0.3329
 ZXB  CAF   C  CR16  0  -0.241  -4.1009  -0.0858   1.3041
 ZXB  CAH   C  CR16  0  -0.312  -2.8914  -0.7173   1.0457
 ZXB  CAL   C  CR6   0   0.167  -2.2479  -0.5612  -0.1806
 ZXB  CAJ   C  CH2   0  -0.534  -0.9239  -1.2228  -0.4370
 ZXB  CAP   C  CH1   0  -0.107   0.2461  -0.4253   0.1439
 ZXB  NAK   N  NH1   0  -0.570   0.3209   0.8844  -0.4774
 ZXB  CAI   C  CH2   0  -0.349   1.4051   1.6852   0.0561
 ZXB  CAM   C  CH1   0   0.018   2.7668   0.9931  -0.0267
 ZXB  OAA   O  OH1   0  -0.679   3.7816   1.7323   0.6252
 ZXB  CAN   C  CH1   0   0.012   2.6910  -0.3650   0.6558
 ZXB  OAB   O  OH1   0  -0.680   3.8891  -1.0968   0.5176
 ZXB  CAO   C  CH1   0   0.021   1.5611  -1.2064   0.0653
 ZXB  OAC   O  OH1   0  -0.677   1.8118  -1.5327  -1.2825
 ZXB  HAG   H  HCR6  0   0.240  -2.3688   0.3729  -2.1072
 ZXB  HAE   H  HCR6  0   0.251  -4.5138   1.4930  -1.6587
 ZXB  HAD   H  HCR6  0   0.251  -5.6364   1.2020   0.5297
 ZXB  HAF   H  HCR6  0   0.251  -4.5840  -0.2201   2.2637
 ZXB  HAH   H  HCR6  0   0.243  -2.4402  -1.3428   1.8080
 ZXB  HAJ   H  HCH2  0   0.249  -0.9162  -2.2222   0.0051
 ZXB  HAJA  H  HCH2  0   0.248  -0.7771  -1.3557  -1.5117
 ZXB  HAP   H  HCH1  0   0.241   0.0485  -0.2673   1.2124
 ZXB  HNAK  H  HNH1  0   0.340   0.4293   0.7804  -1.4799
 ZXB  HAI   H  HCH2  0   0.242   1.4400   2.6382  -0.4778
 ZXB  HAIA  H  HCH2  0   0.221   1.1865   1.9159   1.1050
 ZXB  HAM   H  HCH1  0   0.208   3.0216   0.8411  -1.0845
 ZXB  HOAA  H  HOH1  0   0.456   4.0385   2.4656   0.0585
 ZXB  HAN   H  HCH1  0   0.204   2.4593  -0.1985   1.7211
 ZXB  HOAB  H  HOH1  0   0.451   4.6251  -0.5010   0.6953
 ZXB  HAO   H  HCH1  0   0.218   1.4603  -2.1184   0.6751
 ZXB  HOAC  H  HOH1  0   0.449   2.7081  -1.8809  -1.3415

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
 ZXB  CAG  CAE   aromatic  1.389  0.020  1.389
 ZXB  CAG  CAL   aromatic  1.392  0.020  1.392
 ZXB  CAE  CAD   aromatic  1.389  0.020  1.389
 ZXB  CAD  CAF   aromatic  1.389  0.020  1.389
 ZXB  CAF  CAH   aromatic  1.389  0.020  1.389
 ZXB  CAH  CAL   aromatic  1.394  0.020  1.394
 ZXB  CAL  CAJ   single    1.502  0.020  1.502
 ZXB  CAJ  CAP   single    1.530  0.020  1.530
 ZXB  CAP  NAK   single    1.452  0.020  1.452
 ZXB  CAP  CAO   single    1.532  0.020  1.532
 ZXB  NAK  CAI   single    1.450  0.020  1.450
 ZXB  CAI  CAM   single    1.530  0.020  1.530
 ZXB  CAM  OAA   single    1.415  0.020  1.415
 ZXB  CAM  CAN   single    1.522  0.020  1.522
 ZXB  CAN  OAB   single    1.411  0.020  1.411
 ZXB  CAN  CAO   single    1.527  0.020  1.527
 ZXB  CAO  OAC   single    1.409  0.020  1.409
 ZXB  CAG  HAG   single    0.930  0.020  1.080
 ZXB  CAE  HAE   single    0.930  0.020  1.080
 ZXB  CAD  HAD   single    0.930  0.020  1.080
 ZXB  CAF  HAF   single    0.930  0.020  1.080
 ZXB  CAH  HAH   single    0.930  0.020  1.080
 ZXB  CAJ  HAJ   single    0.970  0.020  1.090
 ZXB  CAJ  HAJA  single    0.970  0.020  1.090
 ZXB  CAP  HAP   single    0.970  0.020  1.090
 ZXB  NAK  HNAK  single    0.890  0.020  1.040
 ZXB  CAI  HAI   single    0.970  0.020  1.090
 ZXB  CAI  HAIA  single    0.970  0.020  1.090
 ZXB  CAM  HAM   single    0.970  0.020  1.090
 ZXB  OAA  HOAA  single    0.850  0.020  0.980
 ZXB  CAN  HAN   single    0.970  0.020  1.090
 ZXB  OAB  HOAB  single    0.850  0.020  0.980
 ZXB  CAO  HAO   single    0.970  0.020  1.090
 ZXB  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
 ZXB  HAG   CAG  CAL  119.50  3.000
 ZXB  HAG   CAG  CAE  119.53  3.000
 ZXB  CAL   CAG  CAE  120.97  3.000
 ZXB  HAE   CAE  CAD  120.03  3.000
 ZXB  HAE   CAE  CAG  119.82  3.000
 ZXB  CAD   CAE  CAG  120.15  3.000
 ZXB  HAD   CAD  CAF  120.25  3.000
 ZXB  HAD   CAD  CAE  120.29  3.000
 ZXB  CAF   CAD  CAE  119.46  3.000
 ZXB  HAF   CAF  CAH  119.81  3.000
 ZXB  HAF   CAF  CAD  120.09  3.000
 ZXB  CAH   CAF  CAD  120.09  3.000
 ZXB  HAH   CAH  CAL  119.40  3.000
 ZXB  HAH   CAH  CAF  119.60  3.000
 ZXB  CAL   CAH  CAF  121.00  3.000
 ZXB  CAJ   CAL  CAH  120.52  3.000
 ZXB  CAJ   CAL  CAG  121.14  3.000
 ZXB  CAH   CAL  CAG  118.32  3.000
 ZXB  HAJA  CAJ  HAJ  106.59  3.000
 ZXB  HAJA  CAJ  CAP  109.51  3.000
 ZXB  HAJ   CAJ  CAP  108.52  3.000
 ZXB  HAJA  CAJ  CAL  109.87  3.000
 ZXB  HAJ   CAJ  CAL  109.87  3.000
 ZXB  CAP   CAJ  CAL  112.30  3.000
 ZXB  HAP   CAP  CAO  106.13  3.000
 ZXB  HAP   CAP  NAK  107.22  3.000
 ZXB  CAO   CAP  NAK  113.20  3.000
 ZXB  HAP   CAP  CAJ  107.87  3.000
 ZXB  CAO   CAP  CAJ  111.79  3.000
 ZXB  NAK   CAP  CAJ  110.31  3.000
 ZXB  HNAK  NAK  CAI  109.92  3.000
 ZXB  HNAK  NAK  CAP  109.64  3.000
 ZXB  CAI   NAK  CAP  112.30  3.000
 ZXB  HAIA  CAI  HAI  106.87  3.000
 ZXB  HAIA  CAI  CAM  108.94  3.000
 ZXB  HAI   CAI  CAM  109.86  3.000
 ZXB  HAIA  CAI  NAK  108.62  3.000
 ZXB  HAI   CAI  NAK  109.02  3.000
 ZXB  CAM   CAI  NAK  113.33  3.000
 ZXB  HAM   CAM  CAN  108.66  3.000
 ZXB  HAM   CAM  OAA  110.46  3.000
 ZXB  CAN   CAM  OAA  107.18  3.000
 ZXB  HAM   CAM  CAI  108.73  3.000
 ZXB  CAN   CAM  CAI  109.58  3.000
 ZXB  OAA   CAM  CAI  112.16  3.000
 ZXB  HOAA  OAA  CAM  108.57  3.000
 ZXB  HAN   CAN  CAO  107.53  3.000
 ZXB  HAN   CAN  OAB  110.57  3.000
 ZXB  CAO   CAN  OAB  107.73  3.000
 ZXB  HAN   CAN  CAM  108.00  3.000
 ZXB  CAO   CAN  CAM  110.80  3.000
 ZXB  OAB   CAN  CAM  112.13  3.000
 ZXB  HOAB  OAB  CAN  108.06  3.000
 ZXB  HAO   CAO  OAC  110.73  3.000
 ZXB  HAO   CAO  CAN  108.04  3.000
 ZXB  OAC   CAO  CAN  111.45  3.000
 ZXB  HAO   CAO  CAP  108.38  3.000
 ZXB  OAC   CAO  CAP  108.65  3.000
 ZXB  CAN   CAO  CAP  109.53  3.000
 ZXB  HOAC  OAC  CAO  107.92  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
 ZXB  CONST_01  CAF  CAD  CAE  CAG    0.00   0.0  0
 ZXB  CONST_02  CAF  CAH  CAL  CAG    0.00   0.0  0
 ZXB  CONST_03  CAH  CAL  CAG  CAE    0.00   0.0  0
 ZXB  CONST_04  CAH  CAF  CAD  CAE    0.00   0.0  0
 ZXB  CONST_05  CAL  CAG  CAE  CAD    0.00   0.0  0
 ZXB  CONST_06  CAL  CAH  CAF  CAD    0.00   0.0  0
 ZXB  CONST_07  CAJ  CAL  CAG  CAE  180.00   0.0  0
 ZXB  CONST_08  CAJ  CAL  CAH  CAF  180.00   0.0  0
 ZXB  CONST_09  HAD  CAD  CAE  CAG  180.00   0.0  0
 ZXB  CONST_10  HAH  CAH  CAL  CAG  180.00   0.0  0
 ZXB  CONST_11  HAF  CAF  CAD  CAE  180.00   0.0  0
 ZXB  CONST_12  HAG  CAG  CAE  CAD  180.00   0.0  0
 ZXB  CONST_13  HAE  CAE  CAD  CAF  180.00   0.0  0
 ZXB  Var_01    CAM  CAI  NAK  CAP   54.82  30.0  1
 ZXB  Var_02    CAP  CAJ  CAL  CAG   96.98  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
 ZXB  chir_01  CAP  CAJ  NAK  CAO  positiv
 ZXB  chir_02  CAM  OAA  CAI  CAN  positiv
 ZXB  chir_03  CAN  OAB  CAM  CAO  negativ
 ZXB  chir_04  CAO  OAC  CAN  CAP  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
 ZXB  plan-1  CAG  0.020
 ZXB  plan-1  CAE  0.020
 ZXB  plan-1  CAD  0.020
 ZXB  plan-1  CAF  0.020
 ZXB  plan-1  CAH  0.020
 ZXB  plan-1  CAL  0.020
 ZXB  plan-1  CAJ  0.020
 ZXB  plan-1  HAG  0.020
 ZXB  plan-1  HAE  0.020
 ZXB  plan-1  HAD  0.020
 ZXB  plan-1  HAF  0.020
 ZXB  plan-1  HAH  0.020

