# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 11:13:45 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (3S)-3-hydroxybutyl beta-D-xylopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)CCO[C@@H]1OC[C@@H](O)[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
 07E  07E  '(3S)-3-hydroxybutyl beta-D-xylopyranoside'  D-saccharide  33  15  .  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_07E
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
 07E  C1   C  CH1   0   0.299   0.4412  -0.0756  -0.1545
 07E  C2   C  CH1   0  -0.013   1.4866   0.9678   0.2499
 07E  C3   C  CH1   0   0.011   2.8551   0.5236  -0.2378
 07E  C4   C  CH1   0  -0.006   3.1381  -0.8936   0.2477
 07E  C5   C  CH2   0  -0.225   1.9928  -1.8176  -0.1562
 07E  O1   O  O2    0  -0.505  -0.7701   0.3159   0.3684
 07E  O2   O  OH1   0  -0.664   1.1935   2.2149  -0.3239
 07E  O3   O  OH1   0  -0.668   3.8134   1.4402   0.2253
 07E  O4   O  OH1   0  -0.671   4.3554  -1.3059  -0.3303
 07E  O5   O  O2    0  -0.491   0.7692  -1.3420   0.3586
 07E  C1'  C  CH2   0  -0.137  -1.9156  -0.2622  -0.2409
 07E  C2'  C  CH2   0  -0.491  -3.1427   0.4716   0.2608
 07E  C3'  C  CH1   0   0.021  -4.4345  -0.0329  -0.3767
 07E  C4'  C  CH3   0  -0.681  -5.6318   0.7884   0.0781
 07E  O'   O  OH1   0  -0.667  -4.6321  -1.4166  -0.1462
 07E  H1   H  HCH1  0   0.184   0.3943  -0.1280  -1.2597
 07E  H2   H  HCH1  0   0.218   1.5021   1.0247   1.3499
 07E  H3   H  HCH1  0   0.208   2.8332   0.5018  -1.3413
 07E  H4   H  HCH1  0   0.221   3.2087  -0.8785   1.3444
 07E  H5   H  HCH2  0   0.214   1.9562  -1.9019  -1.2523
 07E  H6   H  HCH2  0   0.251   2.1464  -2.8198   0.2477
 07E  H7   H  HOH1  0   0.450   0.3485   2.5130   0.0285
 07E  H8   H  HOH1  0   0.450   4.6771   1.1413  -0.0784
 07E  H9   H  HOH1  0   0.461   4.7088  -2.0372   0.1850
 07E  H10  H  HCH2  0   0.206  -1.8413  -0.1694  -1.3325
 07E  H11  H  HCH2  0   0.214  -1.9808  -1.3284  -0.0072
 07E  H12  H  HCH2  0   0.229  -3.2136   0.3804   1.3507
 07E  H13  H  HCH2  0   0.233  -3.0394   1.5377   0.0404
 07E  H14  H  HCH1  0   0.222  -4.3417   0.0623  -1.4636
 07E  H15  H  HCH3  0   0.228  -5.5054   1.8395  -0.1833
 07E  H16  H  HCH3  0   0.236  -6.5498   0.4338  -0.3916
 07E  H17  H  HCH3  0   0.221  -5.7593   0.7299   1.1622
 07E  H18  H  HOH1  0   0.441  -4.7346  -1.5485   0.8029

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
 07E  C4'  C3'  single  1.521  0.020  1.521
 07E  C3'  C2'  single  1.526  0.020  1.526
 07E  C3'  O'   single  1.417  0.020  1.417
 07E  C2'  C1'  single  1.515  0.020  1.515
 07E  C1'  O1   single  1.420  0.020  1.420
 07E  O1   C1   single  1.376  0.020  1.376
 07E  C1   O5   single  1.405  0.020  1.405
 07E  C1   C2   single  1.531  0.020  1.531
 07E  O2   C2   single  1.404  0.020  1.404
 07E  O5   C5   single  1.410  0.020  1.410
 07E  C2   C3   single  1.519  0.020  1.519
 07E  C5   C4   single  1.526  0.020  1.526
 07E  C3   C4   single  1.525  0.020  1.525
 07E  C3   O3   single  1.405  0.020  1.405
 07E  C4   O4   single  1.409  0.020  1.409
 07E  C1   H1   single  0.970  0.020  1.090
 07E  C2   H2   single  0.970  0.020  1.090
 07E  C3   H3   single  0.970  0.020  1.090
 07E  C4   H4   single  0.970  0.020  1.090
 07E  C5   H5   single  0.970  0.020  1.090
 07E  C5   H6   single  0.970  0.020  1.090
 07E  O2   H7   single  0.850  0.020  0.980
 07E  O3   H8   single  0.850  0.020  0.980
 07E  O4   H9   single  0.850  0.020  0.980
 07E  C1'  H10  single  0.970  0.020  1.090
 07E  C1'  H11  single  0.970  0.020  1.090
 07E  C2'  H12  single  0.970  0.020  1.090
 07E  C2'  H13  single  0.970  0.020  1.090
 07E  C3'  H14  single  0.970  0.020  1.090
 07E  C4'  H15  single  0.970  0.020  1.090
 07E  C4'  H16  single  0.970  0.020  1.090
 07E  C4'  H17  single  0.970  0.020  1.090
 07E  O'   H18  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
 07E  H1   C1   O5   109.37  3.000
 07E  H1   C1   O1   110.82  3.000
 07E  O5   C1   O1   108.85  3.000
 07E  H1   C1   C2   108.95  3.000
 07E  O5   C1   C2   111.00  3.000
 07E  O1   C1   C2   107.86  3.000
 07E  H2   C2   O2   111.42  3.000
 07E  H2   C2   C3   108.84  3.000
 07E  O2   C2   C3   108.46  3.000
 07E  H2   C2   C1   107.97  3.000
 07E  C3   C2   C1   109.33  3.000
 07E  O2   C2   C1   110.79  3.000
 07E  H3   C3   O3   110.86  3.000
 07E  H3   C3   C4   107.68  3.000
 07E  O3   C3   C4   112.02  3.000
 07E  H3   C3   C2   107.99  3.000
 07E  O3   C3   C2   108.54  3.000
 07E  C4   C3   C2   109.68  3.000
 07E  H4   C4   O4   110.97  3.000
 07E  H4   C4   C5   108.70  3.000
 07E  O4   C4   C5   111.26  3.000
 07E  H4   C4   C3   108.48  3.000
 07E  O4   C4   C3   107.56  3.000
 07E  C5   C4   C3   109.83  3.000
 07E  H6   C5   H5   107.64  3.000
 07E  H6   C5   O5   107.26  3.000
 07E  H5   C5   O5   111.15  3.000
 07E  H6   C5   C4   110.64  3.000
 07E  H5   C5   C4   109.58  3.000
 07E  O5   C5   C4   110.51  3.000
 07E  C1'  O1   C1   115.53  3.000
 07E  H7   O2   C2   107.98  3.000
 07E  H8   O3   C3   107.78  3.000
 07E  H9   O4   C4   108.66  3.000
 07E  C5   O5   C1   111.91  3.000
 07E  H11  C1'  H10  107.39  3.000
 07E  H11  C1'  C2'  110.68  3.000
 07E  H10  C1'  C2'  110.06  3.000
 07E  H11  C1'  O1   110.69  3.000
 07E  H10  C1'  O1   109.72  3.000
 07E  C2'  C1'  O1   108.30  3.000
 07E  H13  C2'  H12  106.72  3.000
 07E  H13  C2'  C3'  108.55  3.000
 07E  H12  C2'  C3'  109.46  3.000
 07E  H13  C2'  C1'  109.20  3.000
 07E  H12  C2'  C1'  109.95  3.000
 07E  C3'  C2'  C1'  112.77  3.000
 07E  H14  C3'  O'   104.97  3.000
 07E  H14  C3'  C4'  108.45  3.000
 07E  O'   C3'  C4'  111.64  3.000
 07E  H14  C3'  C2'  108.30  3.000
 07E  O'   C3'  C2'  111.90  3.000
 07E  C4'  C3'  C2'  111.27  3.000
 07E  H17  C4'  H16  108.16  3.000
 07E  H17  C4'  H15  107.63  3.000
 07E  H16  C4'  H15  107.92  3.000
 07E  H17  C4'  C3'  111.06  3.000
 07E  H16  C4'  C3'  110.99  3.000
 07E  H15  C4'  C3'  110.94  3.000
 07E  H18  O'   C3'  107.98  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
 07E  Var_01  C4   C5   O5   C1    62.25  30.0  1
 07E  Var_02  C2'  C1'  O1   C1  -169.02  30.0  1
 07E  Var_03  C3'  C2'  C1'  O1   177.65  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
 07E  chir_01  C1   O1  O5   C2   positiv
 07E  chir_02  C2   O2  C1   C3   negativ
 07E  chir_03  C3   O3  C2   C4   positiv
 07E  chir_04  C4   O4  C3   C5   negativ
 07E  chir_05  C3'  O'  C4'  C2'  negativ

