# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sun Jul  5 07:11:01 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N-[(1E)-2-phenylethanimidoyl]-6-O-beta-D-xylopyranosyl-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](OC[C@H]2O[C@@H](NC(=N)Cc3ccccc3)[C@H](O)[C@@H](O)[C@@H]2O)[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
 VPA  VPA  N-[(1E)-2-phenylethanimidoyl]-6-O-beta-D-xylopyranosyl-beta-D-glucopyranosylamine  ligand  58  30  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_VPA
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
 VPA  C1   C  C     0   0.438  -2.3762  -0.1177   0.0215
 VPA  C2   C  CH2   0  -0.627  -2.7990  -1.2069   0.9878
 VPA  N2   N  N     0  -0.655  -2.2073  -0.2359  -1.2329
 VPA  C3   C  CR6   0   0.074  -3.0962  -2.5290   0.3442
 VPA  C4   C  CR16  0  -0.300  -2.0609  -3.3903  -0.0188
 VPA  C5   C  CR16  0  -0.246  -2.3373  -4.6151  -0.6107
 VPA  C6   C  CR16  0  -0.265  -3.6518  -4.9954  -0.8501
 VPA  C8   C  CR16  0  -0.293  -4.4100  -2.9173   0.0963
 VPA  C7   C  CR16  0  -0.243  -4.6884  -4.1426  -0.4957
 VPA  N1   N  NH1   0  -0.684  -2.1839   1.0931   0.6447
 VPA  C1'  C  CH1   0   0.204  -1.4736   2.1462   0.0099
 VPA  O5'  O  O2    0  -0.492  -0.0869   1.8892   0.1077
 VPA  C2'  C  CH1   0  -0.017  -1.7849   3.4910   0.6668
 VPA  O2'  O  OH1   0  -0.665  -3.1368   3.8416   0.5174
 VPA  C3'  C  CH1   0  -0.008  -0.9516   4.5759  -0.0057
 VPA  O3'  O  OH1   0  -0.672  -1.0692   5.8164   0.6487
 VPA  C4'  C  CH1   0   0.037   0.5281   4.2022  -0.0076
 VPA  O4'  O  OH1   0  -0.673   1.2903   5.1029  -0.7706
 VPA  C5'  C  CH1   0  -0.006   0.7039   2.8081  -0.6067
 VPA  C6'  C  CH2   0  -0.182   2.1412   2.3269  -0.5203
 VPA  O6'  O  O2    0  -0.502   2.2293   1.0123  -1.0364
 VPA  C1A  C  CH1   0   0.285   2.6390   0.0261  -0.1642
 VPA  O5A  O  O2    0  -0.488   4.0410  -0.0448  -0.2296
 VPA  C5A  C  CH2   0  -0.228   4.5654  -1.0297   0.6331
 VPA  C4A  C  CH1   0  -0.003   4.0727  -2.4146   0.2232
 VPA  O4A  O  OH1   0  -0.671   4.5264  -3.4046   1.1178
 VPA  C3A  C  CH1   0   0.012   2.5496  -2.4352   0.2506
 VPA  O3A  O  OH1   0  -0.664   2.0239  -3.6428  -0.2383
 VPA  C2A  C  CH1   0  -0.005   1.9945  -1.2965  -0.5919
 VPA  O2A  O  OH1   0  -0.657   0.6087  -1.2669  -0.3992
 VPA  H1   H  HCH2  0   0.287  -1.9953  -1.3198   1.7214
 VPA  H2   H  HCH2  0   0.287  -3.6702  -0.8526   1.5449
 VPA  H3   H  H     0   0.340  -2.4286  -1.1779  -1.5342
 VPA  H4   H  HCR6  0   0.278  -1.0326  -3.0963   0.1533
 VPA  H5   H  HCR6  0   0.253  -1.5236  -5.2746  -0.8851
 VPA  H6   H  HCR6  0   0.256  -3.8681  -5.9511  -1.3098
 VPA  H7   H  HCR6  0   0.250  -5.2247  -2.2586   0.3742
 VPA  H8   H  HCR6  0   0.256  -5.7155  -4.4323  -0.6761
 VPA  H9   H  HNH1  0   0.394  -2.1166   1.0635   1.6523
 VPA  H10  H  HCH1  0   0.228  -1.7752   2.1801  -1.0445
 VPA  H11  H  HCH1  0   0.219  -1.4992   3.4317   1.7294
 VPA  H12  H  HOH1  0   0.454  -3.6736   3.1971   0.9903
 VPA  H13  H  HCH1  0   0.216  -1.2813   4.6549  -1.0545
 VPA  H14  H  HOH1  0   0.457  -1.9593   6.1546   0.5104
 VPA  H15  H  HCH1  0   0.215   0.8764   4.1713   1.0373
 VPA  H16  H  HOH1  0   0.455   1.1889   5.9825  -0.3924
 VPA  H17  H  HCH1  0   0.226   0.3925   2.8355  -1.6640
 VPA  H18  H  HCH2  0   0.247   2.7876   2.9851  -1.1030
 VPA  H19  H  HCH2  0   0.223   2.4805   2.3671   0.5215
 VPA  H20  H  HCH1  0   0.190   2.3289   0.2542   0.8715
 VPA  H21  H  HCH2  0   0.251   5.6531  -0.9692   0.5679
 VPA  H22  H  HCH2  0   0.212   4.2810  -0.8346   1.6777
 VPA  H23  H  HCH1  0   0.220   4.4097  -2.6225  -0.8022
 VPA  H24  H  HOH1  0   0.460   5.4433  -3.6101   0.9123
 VPA  H25  H  HCH1  0   0.206   2.2336  -2.2670   1.2946
 VPA  H26  H  HOH1  0   0.449   2.3410  -4.3527   0.3292
 VPA  H27  H  HCH1  0   0.213   2.2593  -1.4750  -1.6470
 VPA  H28  H  HOH1  0   0.452   0.2213  -0.5219  -0.8734

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
 VPA  O4'  C4'  single    1.405  0.020  1.405
 VPA  O3'  C3'  single    1.407  0.020  1.407
 VPA  C3'  C4'  single    1.526  0.020  1.526
 VPA  C3'  C2'  single    1.524  0.020  1.524
 VPA  C4'  C5'  single    1.528  0.020  1.528
 VPA  C5'  C6'  single    1.518  0.020  1.518
 VPA  C5'  O5'  single    1.407  0.020  1.407
 VPA  C6'  O6'  single    1.415  0.020  1.415
 VPA  O2A  C2A  single    1.400  0.020  1.400
 VPA  O2'  C2'  single    1.405  0.020  1.405
 VPA  C2'  C1'  single    1.529  0.020  1.529
 VPA  O6'  C1A  single    1.379  0.020  1.379
 VPA  O5'  C1'  single    1.414  0.020  1.414
 VPA  C1A  C2A  single    1.532  0.020  1.532
 VPA  C1A  O5A  single    1.405  0.020  1.405
 VPA  C1'  N1   single    1.420  0.020  1.420
 VPA  C2A  C3A  single    1.521  0.020  1.521
 VPA  C3A  O3A  single    1.405  0.020  1.405
 VPA  C3A  C4A  single    1.523  0.020  1.523
 VPA  O5A  C5A  single    1.410  0.020  1.410
 VPA  C5A  C4A  single    1.526  0.020  1.526
 VPA  N1   C1   single    1.375  0.020  1.375
 VPA  N2   C1   double    1.271  0.020  1.271
 VPA  C4A  O4A  single    1.409  0.020  1.409
 VPA  C1   C2   single    1.516  0.020  1.516
 VPA  C8   C7   aromatic  1.389  0.020  1.389
 VPA  C8   C3   aromatic  1.392  0.020  1.392
 VPA  C2   C3   single    1.500  0.020  1.500
 VPA  C7   C6   aromatic  1.388  0.020  1.388
 VPA  C3   C4   aromatic  1.395  0.020  1.395
 VPA  C6   C5   aromatic  1.389  0.020  1.389
 VPA  C4   C5   aromatic  1.388  0.020  1.388
 VPA  C2   H1   single    0.970  0.020  1.090
 VPA  C2   H2   single    0.970  0.020  1.090
 VPA  N2   H3   single    0.890  0.020  1.040
 VPA  C4   H4   single    0.930  0.020  1.080
 VPA  C5   H5   single    0.930  0.020  1.080
 VPA  C6   H6   single    0.930  0.020  1.080
 VPA  C8   H7   single    0.930  0.020  1.080
 VPA  C7   H8   single    0.930  0.020  1.080
 VPA  N1   H9   single    0.890  0.020  1.040
 VPA  C1'  H10  single    0.970  0.020  1.090
 VPA  C2'  H11  single    0.970  0.020  1.090
 VPA  O2'  H12  single    0.850  0.020  0.980
 VPA  C3'  H13  single    0.970  0.020  1.090
 VPA  O3'  H14  single    0.850  0.020  0.980
 VPA  C4'  H15  single    0.970  0.020  1.090
 VPA  O4'  H16  single    0.850  0.020  0.980
 VPA  C5'  H17  single    0.970  0.020  1.090
 VPA  C6'  H18  single    0.970  0.020  1.090
 VPA  C6'  H19  single    0.970  0.020  1.090
 VPA  C1A  H20  single    0.970  0.020  1.090
 VPA  C5A  H21  single    0.970  0.020  1.090
 VPA  C5A  H22  single    0.970  0.020  1.090
 VPA  C4A  H23  single    0.970  0.020  1.090
 VPA  O4A  H24  single    0.850  0.020  0.980
 VPA  C3A  H25  single    0.970  0.020  1.090
 VPA  O3A  H26  single    0.850  0.020  0.980
 VPA  C2A  H27  single    0.970  0.020  1.090
 VPA  O2A  H28  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
 VPA  N1   C1   N2   120.69  3.000
 VPA  N2   C1   C2   126.81  3.000
 VPA  N1   C1   C2   112.50  3.000
 VPA  H2   C2   H1   106.10  3.000
 VPA  H2   C2   C3   110.26  3.000
 VPA  H1   C2   C3   110.01  3.000
 VPA  H2   C2   C1   108.31  3.000
 VPA  H1   C2   C1   107.26  3.000
 VPA  C3   C2   C1   114.52  3.000
 VPA  H3   N2   C1   110.53  3.000
 VPA  C8   C3   C4   118.81  3.000
 VPA  C4   C3   C2   120.58  3.000
 VPA  C8   C3   C2   120.61  3.000
 VPA  H4   C4   C5   119.75  3.000
 VPA  H4   C4   C3   119.71  3.000
 VPA  C5   C4   C3   120.53  3.000
 VPA  H5   C5   C6   120.04  3.000
 VPA  H5   C5   C4   119.73  3.000
 VPA  C6   C5   C4   120.23  3.000
 VPA  H6   C6   C7   120.11  3.000
 VPA  H6   C6   C5   120.27  3.000
 VPA  C7   C6   C5   119.63  3.000
 VPA  H7   C8   C7   119.65  3.000
 VPA  H7   C8   C3   119.61  3.000
 VPA  C7   C8   C3   120.74  3.000
 VPA  H8   C7   C8   119.83  3.000
 VPA  H8   C7   C6   120.10  3.000
 VPA  C8   C7   C6   120.07  3.000
 VPA  H9   N1   C1'  115.74  3.000
 VPA  H9   N1   C1   115.82  3.000
 VPA  C1'  N1   C1   121.35  3.000
 VPA  H10  C1'  C2'  109.26  3.000
 VPA  H10  C1'  O5'  109.98  3.000
 VPA  C2'  C1'  O5'  109.26  3.000
 VPA  H10  C1'  N1   108.36  3.000
 VPA  O5'  C1'  N1   108.96  3.000
 VPA  C2'  C1'  N1   111.01  3.000
 VPA  C5'  O5'  C1'  113.41  3.000
 VPA  H11  C2'  C3'  108.78  3.000
 VPA  H11  C2'  O2'  111.44  3.000
 VPA  C3'  C2'  O2'  107.55  3.000
 VPA  H11  C2'  C1'  108.32  3.000
 VPA  O2'  C2'  C1'  111.70  3.000
 VPA  C3'  C2'  C1'  108.98  3.000
 VPA  H12  O2'  C2'  108.50  3.000
 VPA  H13  C3'  C4'  107.84  3.000
 VPA  H13  C3'  O3'  110.75  3.000
 VPA  C4'  C3'  O3'  107.30  3.000
 VPA  H13  C3'  C2'  107.90  3.000
 VPA  C4'  C3'  C2'  110.87  3.000
 VPA  O3'  C3'  C2'  112.12  3.000
 VPA  H14  O3'  C3'  108.67  3.000
 VPA  H15  C4'  C5'  108.05  3.000
 VPA  H15  C4'  O4'  111.19  3.000
 VPA  C5'  C4'  O4'  108.03  3.000
 VPA  H15  C4'  C3'  108.19  3.000
 VPA  C5'  C4'  C3'  109.61  3.000
 VPA  O4'  C4'  C3'  111.70  3.000
 VPA  H16  O4'  C4'  108.37  3.000
 VPA  H17  C5'  C6'  109.26  3.000
 VPA  H17  C5'  C4'  108.72  3.000
 VPA  C6'  C5'  C4'  112.08  3.000
 VPA  H17  C5'  O5'  110.14  3.000
 VPA  C6'  C5'  O5'  107.22  3.000
 VPA  C4'  C5'  O5'  109.40  3.000
 VPA  H19  C6'  H18  107.57  3.000
 VPA  H19  C6'  O6'  111.18  3.000
 VPA  H18  C6'  O6'  109.19  3.000
 VPA  H19  C6'  C5'  109.60  3.000
 VPA  H18  C6'  C5'  109.83  3.000
 VPA  O6'  C6'  C5'  109.43  3.000
 VPA  C1A  O6'  C6'  116.89  3.000
 VPA  H20  C1A  C2A  108.77  3.000
 VPA  H20  C1A  O5A  109.52  3.000
 VPA  C2A  C1A  O5A  111.29  3.000
 VPA  H20  C1A  O6'  111.21  3.000
 VPA  O5A  C1A  O6'  107.64  3.000
 VPA  C2A  C1A  O6'  108.41  3.000
 VPA  C5A  O5A  C1A  112.19  3.000
 VPA  H22  C5A  H21  107.73  3.000
 VPA  H22  C5A  C4A  109.43  3.000
 VPA  H21  C5A  C4A  110.86  3.000
 VPA  H22  C5A  O5A  111.16  3.000
 VPA  H21  C5A  O5A  107.18  3.000
 VPA  C4A  C5A  O5A  110.45  3.000
 VPA  H23  C4A  C3A  108.71  3.000
 VPA  H23  C4A  O4A  111.14  3.000
 VPA  C3A  C4A  O4A  107.51  3.000
 VPA  H23  C4A  C5A  108.86  3.000
 VPA  O4A  C4A  C5A  111.28  3.000
 VPA  C3A  C4A  C5A  109.28  3.000
 VPA  H24  O4A  C4A  108.75  3.000
 VPA  H25  C3A  C2A  107.78  3.000
 VPA  H25  C3A  O3A  110.67  3.000
 VPA  C2A  C3A  O3A  108.31  3.000
 VPA  H25  C3A  C4A  107.53  3.000
 VPA  O3A  C3A  C4A  112.30  3.000
 VPA  C2A  C3A  C4A  110.16  3.000
 VPA  H26  O3A  C3A  107.78  3.000
 VPA  H27  C2A  O2A  111.90  3.000
 VPA  H27  C2A  C3A  108.73  3.000
 VPA  O2A  C2A  C3A  107.51  3.000
 VPA  H27  C2A  C1A  107.82  3.000
 VPA  C3A  C2A  C1A  109.76  3.000
 VPA  O2A  C2A  C1A  111.09  3.000
 VPA  H28  O2A  C2A  110.27  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
 VPA  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 VPA  CONST_02  C6   C5   C4   C3      0.00   0.0  0
 VPA  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 VPA  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 VPA  CONST_05  C8   C7   C6   C5      0.00   0.0  0
 VPA  CONST_06  C8   C3   C4   C5      0.00   0.0  0
 VPA  CONST_07  C7   C8   C3   C2    180.00   0.0  0
 VPA  CONST_08  C5   C4   C3   C2    180.00   0.0  0
 VPA  CONST_09  H8   C7   C8   C3    180.00   0.0  0
 VPA  CONST_10  H5   C5   C4   C3    180.00   0.0  0
 VPA  CONST_11  H7   C8   C3   C4    180.00   0.0  0
 VPA  CONST_12  H6   C6   C5   C4    180.00   0.0  0
 VPA  CONST_13  H4   C4   C5   C6    180.00   0.0  0
 VPA  CONST_16  H9   N1   C1   C2      0.00   0.0  0
 VPA  CONST_17  H3   N2   C1   C2      0.00   0.0  0
 VPA  Var_01    C4A  C5A  O5A  C1A    62.86  30.0  1
 VPA  Var_02    C8   C3   C2   C1   -100.20  30.0  2
 VPA  Var_03    C3   C2   C1   N2     -2.86  30.0  3
 VPA  Var_04    H18  C6'  O6'  C1A   121.85  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
 VPA  chir_01  C1'  C2'  O5'  N1   negativ
 VPA  chir_02  C2'  O2'  C1'  C3'  negativ
 VPA  chir_03  C3'  O3'  C2'  C4'  positiv
 VPA  chir_04  C4'  O4'  C3'  C5'  negativ
 VPA  chir_05  C5'  O5'  C4'  C6'  negativ
 VPA  chir_06  C1A  O6'  O5A  C2A  positiv
 VPA  chir_07  C4A  O4A  C3A  C5A  negativ
 VPA  chir_08  C3A  O3A  C4A  C2A  negativ
 VPA  chir_09  C2A  O2A  C3A  C1A  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
 VPA  plan-1  C2   0.020
 VPA  plan-1  C3   0.020
 VPA  plan-1  C4   0.020
 VPA  plan-1  C5   0.020
 VPA  plan-1  C6   0.020
 VPA  plan-1  C8   0.020
 VPA  plan-1  C7   0.020
 VPA  plan-1  H4   0.020
 VPA  plan-1  H5   0.020
 VPA  plan-1  H6   0.020
 VPA  plan-1  H7   0.020
 VPA  plan-1  H8   0.020
 VPA  plan-2  C1   0.020
 VPA  plan-2  C2   0.020
 VPA  plan-2  N2   0.020
 VPA  plan-2  N1   0.020
 VPA  plan-2  C1'  0.020
 VPA  plan-2  H3   0.020
 VPA  plan-2  H9   0.020

