# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:25:02 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-[(2R)-oxiran-2-yl]propyl beta-D-xylopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](OCCC[C@@H]2CO2)[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
 C5X  C5X  '3-[(2R)-oxiran-2-yl]propyl beta-D-xylopyranoside'  D-saccharide  34  16  .  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_C5X
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
 C5X  C1    C  CH1   0   0.329  82.3867  22.7994  10.4866
 C5X  C2    C  CH1   0  -0.005  81.9728  23.9323  11.4215
 C5X  C3    C  CH1   0  -0.015  83.0885  24.1810  12.4322
 C5X  C4    C  CH1   0   0.003  83.4682  22.8908  13.1442
 C5X  C5    C  CH2   0  -0.226  83.7742  21.8193  12.0998
 C5X  O1    O  O2    0  -0.492  81.3450  22.5217   9.6346
 C5X  O2    O  OH1   0  -0.666  81.7201  25.0721  10.6421
 C5X  O3    O  OH1   0  -0.668  82.6321  25.1730  13.3208
 C5X  O4    O  OH1   0  -0.665  84.5919  23.1644  13.9477
 C5X  O5    O  O2    0  -0.490  82.6738  21.6443  11.2369
 C5X  C1'   C  CH2   0  -0.162  81.6815  21.7282   8.5065
 C5X  C2'   C  CH2   0  -0.466  80.4764  21.5869   7.6010
 C5X  C3'   C  CH2   0  -0.479  79.3323  20.7319   8.1466
 C5X  C4'   C  CH1   0   0.016  78.5646  21.3374   9.2898
 C5X  C5'   C  CH2   0  -0.249  77.1075  21.2763   9.3421
 C5X  O'    O  O2    0  -0.488  77.7737  22.4792   8.9896
 C5X  H1    H  HCH1  0   0.182  83.2898  23.1047   9.9217
 C5X  H2    H  HCH1  0   0.212  81.0712  23.6082  11.9666
 C5X  H3    H  HCH1  0   0.212  83.9742  24.5314  11.8765
 C5X  H4    H  HCH1  0   0.216  82.6135  22.5598  13.7511
 C5X  H51   H  HCH2  0   0.211  84.6788  22.1017  11.5413
 C5X  H52   H  HCH2  0   0.248  83.9668  20.8567  12.5771
 C5X  HO2   H  HOH1  0   0.450  81.5680  25.8123  11.2391
 C5X  HO3   H  HOH1  0   0.454  83.3757  25.4695  13.8547
 C5X  HO4   H  HOH1  0   0.457  84.7118  22.4408  14.5703
 C5X  H1'1  H  HCH2  0   0.217  82.5027  22.2040   7.9548
 C5X  H1'2  H  HCH2  0   0.209  82.0291  20.7356   8.8142
 C5X  H2'1  H  HCH2  0   0.231  80.1078  22.5762   7.3165
 C5X  H2'2  H  HCH2  0   0.244  80.8333  21.1208   6.6792
 C5X  H3'1  H  HCH2  0   0.240  78.6384  20.5217   7.3280
 C5X  H3'2  H  HCH2  0   0.231  79.7242  19.7628   8.4704
 C5X  H4'   H  HCH1  0   0.246  79.0936  21.4029  10.2375
 C5X  H5'1  H  HCH2  0   0.231  76.5644  20.7822   8.5397
 C5X  H5'2  H  HCH2  0   0.232  76.5972  21.2783  10.3018

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
 C5X  C1   C2    single  1.526  0.020  1.526
 C5X  C1   O1    single  1.374  0.020  1.374
 C5X  C1   O5    single  1.407  0.020  1.407
 C5X  C1   H1    single  0.970  0.020  1.090
 C5X  C2   C3    single  1.526  0.020  1.526
 C5X  C2   O2    single  1.404  0.020  1.404
 C5X  C2   H2    single  0.970  0.020  1.090
 C5X  C3   C4    single  1.522  0.020  1.522
 C5X  C3   O3    single  1.408  0.020  1.408
 C5X  C3   H3    single  0.970  0.020  1.090
 C5X  C4   C5    single  1.527  0.020  1.527
 C5X  C4   O4    single  1.408  0.020  1.408
 C5X  C4   H4    single  0.970  0.020  1.090
 C5X  C5   O5    single  1.409  0.020  1.409
 C5X  C5   H51   single  0.970  0.020  1.090
 C5X  C5   H52   single  0.970  0.020  1.090
 C5X  O1   C1'   single  1.420  0.020  1.420
 C5X  O2   HO2   single  0.850  0.020  0.980
 C5X  O3   HO3   single  0.850  0.020  0.980
 C5X  O4   HO4   single  0.850  0.020  0.980
 C5X  C1'  C2'   single  1.514  0.020  1.514
 C5X  C1'  H1'1  single  0.970  0.020  1.090
 C5X  C1'  H1'2  single  0.970  0.020  1.090
 C5X  C2'  C3'   single  1.529  0.020  1.529
 C5X  C2'  H2'1  single  0.970  0.020  1.090
 C5X  C2'  H2'2  single  0.970  0.020  1.090
 C5X  C3'  C4'   single  1.504  0.020  1.504
 C5X  C3'  H3'1  single  0.970  0.020  1.090
 C5X  C3'  H3'2  single  0.970  0.020  1.090
 C5X  C4'  C5'   single  1.459  0.020  1.459
 C5X  C4'  O'    single  1.421  0.020  1.421
 C5X  C4'  H4'   single  0.970  0.020  1.090
 C5X  C5'  O'    single  1.419  0.020  1.419
 C5X  C5'  H5'1  single  0.970  0.020  1.090
 C5X  C5'  H5'2  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
 C5X  H1    C1   O5    109.38  3.000
 C5X  H1    C1   O1    110.94  3.000
 C5X  O5    C1   O1    108.63  3.000
 C5X  H1    C1   C2    109.20  3.000
 C5X  O5    C1   C2    109.76  3.000
 C5X  O1    C1   C2    108.92  3.000
 C5X  H2    C2   O2    111.48  3.000
 C5X  H2    C2   C3    108.57  3.000
 C5X  O2    C2   C3    111.53  3.000
 C5X  H2    C2   C1    107.85  3.000
 C5X  O2    C2   C1    108.14  3.000
 C5X  C3    C2   C1    109.18  3.000
 C5X  H3    C3   O3    110.76  3.000
 C5X  H3    C3   C4    107.74  3.000
 C5X  O3    C3   C4    112.52  3.000
 C5X  H3    C3   C2    107.77  3.000
 C5X  O3    C3   C2    107.21  3.000
 C5X  C4    C3   C2    110.74  3.000
 C5X  H4    C4   O4    111.34  3.000
 C5X  H4    C4   C5    108.79  3.000
 C5X  O4    C4   C5    111.50  3.000
 C5X  H4    C4   C3    108.64  3.000
 C5X  O4    C4   C3    107.54  3.000
 C5X  C5    C4   C3    108.96  3.000
 C5X  H52   C5   H51   107.65  3.000
 C5X  H52   C5   O5    107.21  3.000
 C5X  H51   C5   O5    111.29  3.000
 C5X  H52   C5   C4    110.80  3.000
 C5X  H51   C5   C4    109.39  3.000
 C5X  O5    C5   C4    110.45  3.000
 C5X  C1'   O1   C1    115.21  3.000
 C5X  HO2   O2   C2    107.96  3.000
 C5X  HO3   O3   C3    108.47  3.000
 C5X  HO4   O4   C4    108.82  3.000
 C5X  C5    O5   C1    112.57  3.000
 C5X  H1'2  C1'  H1'1  107.24  3.000
 C5X  H1'2  C1'  C2'   109.63  3.000
 C5X  H1'1  C1'  C2'   109.59  3.000
 C5X  H1'2  C1'  O1    111.00  3.000
 C5X  H1'1  C1'  O1    109.54  3.000
 C5X  C2'   C1'  O1    109.80  3.000
 C5X  H2'2  C2'  H2'1  106.05  3.000
 C5X  H2'2  C2'  C3'   107.87  3.000
 C5X  H2'1  C2'  C3'   110.27  3.000
 C5X  H2'2  C2'  C1'   106.52  3.000
 C5X  H2'1  C2'  C1'   109.85  3.000
 C5X  C3'   C2'  C1'   115.75  3.000
 C5X  H3'2  C3'  H3'1  106.18  3.000
 C5X  H3'2  C3'  C4'   108.33  3.000
 C5X  H3'1  C3'  C4'   108.81  3.000
 C5X  H3'2  C3'  C2'   109.44  3.000
 C5X  H3'1  C3'  C2'   108.38  3.000
 C5X  C4'   C3'  C2'   115.34  3.000
 C5X  H4'   C4'  O'    113.99  3.000
 C5X  H4'   C4'  C5'   117.20  3.000
 C5X  O'    C4'  C5'    59.04  3.000
 C5X  H4'   C4'  C3'   115.99  3.000
 C5X  O'    C4'  C3'   116.55  3.000
 C5X  C5'   C4'  C3'   121.33  3.000
 C5X  H5'2  C5'  H5'1  114.69  3.000
 C5X  H5'2  C5'  O'    115.98  3.000
 C5X  H5'1  C5'  O'    115.86  3.000
 C5X  H5'2  C5'  C4'   120.02  3.000
 C5X  H5'1  C5'  C4'   119.42  3.000
 C5X  O'    C5'  C4'    59.13  3.000
 C5X  C5'   O'   C4'    61.83  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
 C5X  Var_01  C4    C5   O5   C1     63.48  30.0  1
 C5X  Var_02  O'    C5'  C4'  C3'  -104.18  30.0  1
 C5X  Var_03  H5'1  C5'  O'   C4'  -110.25  30.0  1
 C5X  Var_04  H4'   C4'  O'   C5'  -108.45  30.0  1
 C5X  Var_05  C5'   C4'  C3'  C2'   136.59  30.0  3
 C5X  Var_06  C2'   C1'  O1   C1   -175.68  30.0  3
 C5X  Var_07  C4'   C3'  C2'  C1'    70.50  30.0  3
 C5X  Var_08  C3'   C2'  C1'  O1    -69.59  30.0  3

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
 C5X  chir_01  C1   C2   O1   O5  positiv
 C5X  chir_02  C2   O2   C1   C3  negativ
 C5X  chir_03  C3   O3   C2   C4  positiv
 C5X  chir_04  C4   O4   C3   C5  negativ
 C5X  chir_05  C4'  C3'  C5'  O'  both

