# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:42:20 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 2-amino-4-O-(4-chlorobenzyl)-2-deoxy-alpha-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](OCc2ccc(Cl)cc2)[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
 WUN  WUN  2-amino-4-O-(4-chlorobenzyl)-2-deoxy-alpha-D-glucopyranose  D-saccharide  38  20  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_WUN
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
 WUN  C1    C   CH1   0   0.249  -4.3647  -0.2038  -0.2906
 WUN  O1    O   OH1   0  -0.663  -4.3279  -0.1846  -1.6801
 WUN  C2    C   CH1   0  -0.137  -3.8881   1.1435   0.2450
 WUN  N2    N   NH2   0  -0.811  -4.6594   2.2324  -0.3280
 WUN  C3    C   CH1   0   0.033  -2.4012   1.3279  -0.0578
 WUN  O3    O   OH1   0  -0.671  -1.9067   2.5126   0.5314
 WUN  C4    C   CH1   0   0.030  -1.6127   0.1485   0.4978
 WUN  O4    O   O2    0  -0.504  -0.2614   0.2076   0.0993
 WUN  C5    C   CH1   0  -0.000  -2.1997  -1.1706  -0.0185
 WUN  O5    O   O2    0  -0.502  -3.5878  -1.2368   0.2560
 WUN  C6    C   CH2   0  -0.170  -1.5546  -2.3658   0.6527
 WUN  O6    O   OH1   0  -0.670  -2.0728  -3.5442   0.0832
 WUN  CAN   C   CR16  0  -0.195   4.2357   1.2506  -0.0233
 WUN  CAO   C   CR16  0  -0.196   3.7705  -1.1183  -0.0143
 WUN  CAP   C   CR16  0  -0.317   2.9305   1.4940   0.3846
 WUN  CAQ   C   CR16  0  -0.298   2.4742  -0.8546   0.3959
 WUN  CAU   C   CH2   0  -0.212   0.6347   0.7285   1.0590
 WUN  CBD   C   CR6   0  -0.054   4.6421  -0.0578  -0.2201
 WUN  CBE   C   CR6   0   0.083   2.0383   0.4523   0.6049
 WUN  H1    H   HCH1  0   0.232  -5.3804  -0.4059   0.0727
 WUN  H2    H   HCH1  0   0.222  -3.9957   1.0788   1.3399
 WUN  HN2   H   HNH2  0   0.349  -5.6465   2.0735  -0.1628
 WUN  HN2A  H   HNH2  0   0.346  -4.4447   3.0847   0.1746
 WUN  H3    H   HCH1  0   0.218  -2.2604   1.3580  -1.1461
 WUN  HO3   H   HOH1  0   0.457  -2.0287   3.2380  -0.0875
 WUN  H4    H   HCH1  0   0.218  -1.6921   0.1587   1.5967
 WUN  H5    H   HCH1  0   0.222  -2.0162  -1.2359  -1.1002
 WUN  H6    H   HCH2  0   0.216  -0.4715  -2.2954   0.5102
 WUN  H6A   H   HCH2  0   0.193  -1.7413  -2.3167   1.7351
 WUN  HO6   H   HOH1  0   0.456  -1.5467  -4.2829   0.4010
 WUN  HAN   H   HCR6  0   0.280   4.9192   2.0723  -0.1886
 WUN  HAO   H   HCR6  0   0.280   4.0986  -2.1371  -0.1689
 WUN  HAP   H   HCR6  0   0.266   2.6093   2.5177   0.5330
 WUN  HAQ   H   HCR6  0   0.269   1.8014  -1.6868   0.5636
 WUN  HAU   H   HCH2  0   0.231   0.4945   1.8044   1.1975
 WUN  HAUA  H   HCH2  0   0.223   0.4621   0.2548   2.0348
 WUN  H7    H   HOH1  0   0.460  -4.7634  -0.9762  -2.0145
 WUN  CLA   CL  CL    0  -0.130   6.2680  -0.3805  -0.7292

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
 WUN  C1   O1    single    1.390  0.020  1.390
 WUN  C1   C2    single    1.526  0.020  1.526
 WUN  C1   O5    single    1.403  0.020  1.403
 WUN  C2   N2    single    1.452  0.020  1.452
 WUN  C2   C3    single    1.529  0.020  1.529
 WUN  C3   O3    single    1.412  0.020  1.412
 WUN  C3   C4    single    1.524  0.020  1.524
 WUN  C4   O4    single    1.410  0.020  1.410
 WUN  C4   C5    single    1.533  0.020  1.533
 WUN  O4   CAU   single    1.412  0.020  1.412
 WUN  C5   O5    single    1.416  0.020  1.416
 WUN  C5   C6    single    1.515  0.020  1.515
 WUN  C6   O6    single    1.408  0.020  1.408
 WUN  CAN  CAP   aromatic  1.389  0.020  1.389
 WUN  CAN  CBD   aromatic  1.384  0.020  1.384
 WUN  CAO  CAQ   aromatic  1.385  0.020  1.385
 WUN  CAO  CBD   aromatic  1.388  0.020  1.388
 WUN  CAP  CBE   aromatic  1.389  0.020  1.389
 WUN  CAQ  CBE   aromatic  1.393  0.020  1.393
 WUN  CAU  CBE   single    1.501  0.020  1.501
 WUN  CBD  CLA   single    1.734  0.020  1.734
 WUN  C1   H1    single    0.970  0.020  1.090
 WUN  C2   H2    single    0.970  0.020  1.090
 WUN  N2   HN2   single    0.890  0.020  1.040
 WUN  N2   HN2A  single    0.890  0.020  1.040
 WUN  C3   H3    single    0.970  0.020  1.090
 WUN  O3   HO3   single    0.850  0.020  0.980
 WUN  C4   H4    single    0.970  0.020  1.090
 WUN  C5   H5    single    0.970  0.020  1.090
 WUN  C6   H6    single    0.970  0.020  1.090
 WUN  C6   H6A   single    0.970  0.020  1.090
 WUN  O6   HO6   single    0.850  0.020  0.980
 WUN  CAN  HAN   single    0.930  0.020  1.080
 WUN  CAO  HAO   single    0.930  0.020  1.080
 WUN  CAP  HAP   single    0.930  0.020  1.080
 WUN  CAQ  HAQ   single    0.930  0.020  1.080
 WUN  CAU  HAU   single    0.970  0.020  1.090
 WUN  CAU  HAUA  single    0.970  0.020  1.090
 WUN  O1   H7    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
 WUN  H1    C1   O5   104.35  3.000
 WUN  H1    C1   C2   109.59  3.000
 WUN  O5    C1   C2   109.89  3.000
 WUN  H1    C1   O1   110.97  3.000
 WUN  O5    C1   O1   112.63  3.000
 WUN  C2    C1   O1   109.29  3.000
 WUN  H7    O1   C1   108.88  3.000
 WUN  H2    C2   C3   107.39  3.000
 WUN  H2    C2   N2   112.59  3.000
 WUN  C3    C2   N2   110.36  3.000
 WUN  H2    C2   C1   105.45  3.000
 WUN  C3    C2   C1   109.92  3.000
 WUN  N2    C2   C1   110.96  3.000
 WUN  HN2A  N2   HN2  104.93  3.000
 WUN  HN2A  N2   C2   108.83  3.000
 WUN  HN2   N2   C2   109.60  3.000
 WUN  H3    C3   C4   108.44  3.000
 WUN  H3    C3   O3   110.22  3.000
 WUN  C4    C3   O3   108.42  3.000
 WUN  H3    C3   C2   108.93  3.000
 WUN  C4    C3   C2   109.74  3.000
 WUN  O3    C3   C2   111.05  3.000
 WUN  HO3   O3   C3   108.66  3.000
 WUN  H4    C4   C5   108.43  3.000
 WUN  H4    C4   O4   110.51  3.000
 WUN  C5    C4   O4   107.92  3.000
 WUN  H4    C4   C3   108.62  3.000
 WUN  C5    C4   C3   110.19  3.000
 WUN  O4    C4   C3   111.13  3.000
 WUN  CAU   O4   C4   115.56  3.000
 WUN  H5    C5   C6   108.54  3.000
 WUN  H5    C5   O5   110.58  3.000
 WUN  C6    C5   O5   107.14  3.000
 WUN  H5    C5   C4   108.57  3.000
 WUN  C6    C5   C4   111.50  3.000
 WUN  O5    C5   C4   110.49  3.000
 WUN  C5    O5   C1   115.64  3.000
 WUN  H6A   C6   H6   107.05  3.000
 WUN  H6A   C6   O6   111.91  3.000
 WUN  H6    C6   O6   111.44  3.000
 WUN  H6A   C6   C5   109.18  3.000
 WUN  H6    C6   C5   108.24  3.000
 WUN  O6    C6   C5   108.93  3.000
 WUN  HO6   O6   C6   107.95  3.000
 WUN  HAN   CAN  CBD  120.72  3.000
 WUN  HAN   CAN  CAP  120.38  3.000
 WUN  CBD   CAN  CAP  118.90  3.000
 WUN  HAO   CAO  CBD  120.53  3.000
 WUN  HAO   CAO  CAQ  120.38  3.000
 WUN  CBD   CAO  CAQ  119.09  3.000
 WUN  HAP   CAP  CBE  119.77  3.000
 WUN  HAP   CAP  CAN  118.99  3.000
 WUN  CBE   CAP  CAN  121.24  3.000
 WUN  HAQ   CAQ  CBE  120.20  3.000
 WUN  HAQ   CAQ  CAO  118.75  3.000
 WUN  CBE   CAQ  CAO  121.05  3.000
 WUN  HAUA  CAU  HAU  106.95  3.000
 WUN  HAUA  CAU  CBE  109.65  3.000
 WUN  HAU   CAU  CBE  109.83  3.000
 WUN  HAUA  CAU  O4   110.18  3.000
 WUN  HAU   CAU  O4   111.56  3.000
 WUN  CBE   CAU  O4   108.66  3.000
 WUN  CLA   CBD  CAO  119.35  3.000
 WUN  CLA   CBD  CAN  119.53  3.000
 WUN  CAO   CBD  CAN  121.12  3.000
 WUN  CAU   CBE  CAQ  120.70  3.000
 WUN  CAU   CBE  CAP  120.71  3.000
 WUN  CAQ   CBE  CAP  118.60  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
 WUN  CONST_01  CAQ  CBE  CAP  CAN    0.00   0.0  0
 WUN  CONST_02  CAQ  CAO  CBD  CAN    0.00   0.0  0
 WUN  CONST_03  CAP  CBE  CAQ  CAO    0.00   0.0  0
 WUN  CONST_04  CAP  CAN  CBD  CAO    0.00   0.0  0
 WUN  CONST_05  CBE  CAP  CAN  CBD    0.00   0.0  0
 WUN  CONST_06  CBE  CAQ  CAO  CBD    0.00   0.0  0
 WUN  CONST_07  CAU  CBE  CAP  CAN  180.00   0.0  0
 WUN  CONST_08  CAU  CBE  CAQ  CAO  180.00   0.0  0
 WUN  CONST_09  CLA  CBD  CAN  CAP  180.00   0.0  0
 WUN  CONST_10  CLA  CBD  CAO  CAQ  180.00   0.0  0
 WUN  CONST_11  HAO  CAO  CBD  CAN  180.00   0.0  0
 WUN  CONST_12  HAN  CAN  CBD  CAO  180.00   0.0  0
 WUN  CONST_13  HAQ  CAQ  CBE  CAP  180.00   0.0  0
 WUN  CONST_14  HAP  CAP  CBE  CAQ  180.00   0.0  0
 WUN  Var_01    CBE  CAU  O4   C4   167.98  30.0  3
 WUN  Var_02    CAP  CBE  CAU  O4   120.45  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
 WUN  chir_01  C1  O1  C2  O5  positiv
 WUN  chir_02  C2  N2  C1  C3  negativ
 WUN  chir_03  C3  O3  C2  C4  positiv
 WUN  chir_04  C4  O4  C5  C3  positiv
 WUN  chir_05  C5  O5  C4  C6  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
 WUN  plan-1  CAN  0.020
 WUN  plan-1  CAO  0.020
 WUN  plan-1  CAP  0.020
 WUN  plan-1  CAQ  0.020
 WUN  plan-1  CAU  0.020
 WUN  plan-1  CBD  0.020
 WUN  plan-1  CBE  0.020
 WUN  plan-1  HAN  0.020
 WUN  plan-1  HAO  0.020
 WUN  plan-1  HAP  0.020
 WUN  plan-1  HAQ  0.020
 WUN  plan-1  CLA  0.020

