# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 16:27:55 2022
#   Inital geometry file: a 69 line input string
#   Ligand name: 2-[(2R)-oxiran-2-yl]ethyl beta-D-xylopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[C@@H](OCC[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
 C4X  C4X  '2-[(2R)-oxiran-2-yl]ethyl beta-D-xylopyranoside'  D-saccharide  31  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_C4X
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
 C4X  C1    C  CH1   0   0.321  81.6822  22.6024  10.4545
 C4X  C2    C  CH1   0  -0.003  81.2674  23.7058  11.4246
 C4X  C3    C  CH1   0  -0.015  82.4979  24.2062  12.1743
 C4X  C4    C  CH1   0   0.003  83.2279  23.0442  12.8313
 C4X  C5    C  CH2   0  -0.226  83.5275  21.9908  11.7675
 C4X  O1    O  O2    0  -0.487  80.5565  22.0859   9.8607
 C4X  O2    O  OH1   0  -0.665  80.6611  24.7339  10.6859
 C4X  O3    O  OH1   0  -0.668  82.0561  25.1656  13.1047
 C4X  O4    O  OH1   0  -0.665  84.4093  23.5499  13.4056
 C4X  O5    O  O2    0  -0.491  82.3351  21.5667  11.1474
 C4X  C1'   C  CH2   0  -0.173  80.7910  21.2650   8.7304
 C4X  C2'   C  CH2   0  -0.499  79.5026  21.0630   7.9603
 C4X  C3'   C  CH1   0   0.015  78.8964  22.2592   7.2713
 C4X  C4'   C  CH2   0  -0.254  79.5525  23.5533   7.1075
 C4X  O'    O  O2    0  -0.482  78.5016  23.3806   8.0433
 C4X  H1    H  HCH1  0   0.182  82.3709  23.0273   9.6971
 C4X  H2    H  HCH1  0   0.212  80.5689  23.2684  12.1562
 C4X  H3    H  HCH1  0   0.212  83.1832  24.6622  11.4400
 C4X  H4    H  HCH1  0   0.216  82.5701  22.6021  13.5934
 C4X  H51   H  HCH2  0   0.211  84.2324  22.4053  11.0318
 C4X  H52   H  HCH2  0   0.249  83.9907  21.1090  12.2122
 C4X  HO2   H  HOH1  0   0.451  80.5010  25.4723  11.2831
 C4X  HO3   H  HOH1  0   0.454  82.8257  25.6173  13.4650
 C4X  HO4   H  HOH1  0   0.457  84.7626  22.8938  14.0142
 C4X  H1'1  H  HCH2  0   0.208  81.5540  21.7169   8.0837
 C4X  H1'2  H  HCH2  0   0.231  81.1710  20.2846   9.0359
 C4X  H2'1  H  HCH2  0   0.245  79.7115  20.3212   7.1850
 C4X  H2'2  H  HCH2  0   0.248  78.7486  20.6052   8.6084
 C4X  H3'   H  HCH1  0   0.246  78.1664  21.9826   6.5104
 C4X  H4'1  H  HCH2  0   0.234  80.5384  23.7341   7.5278
 C4X  H4'2  H  HCH2  0   0.236  79.3218  24.1600   6.2352

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
 C4X  C1   C2    single  1.527  0.020  1.527
 C4X  C1   O1    single  1.373  0.020  1.373
 C4X  C1   O5    single  1.407  0.020  1.407
 C4X  C1   H1    single  0.970  0.020  1.090
 C4X  C2   C3    single  1.525  0.020  1.525
 C4X  C2   O2    single  1.404  0.020  1.404
 C4X  C2   H2    single  0.970  0.020  1.090
 C4X  C3   C4    single  1.521  0.020  1.521
 C4X  C3   O3    single  1.408  0.020  1.408
 C4X  C3   H3    single  0.970  0.020  1.090
 C4X  C4   C5    single  1.527  0.020  1.527
 C4X  C4   O4    single  1.408  0.020  1.408
 C4X  C4   H4    single  0.970  0.020  1.090
 C4X  C5   O5    single  1.409  0.020  1.409
 C4X  C5   H51   single  0.970  0.020  1.090
 C4X  C5   H52   single  0.970  0.020  1.090
 C4X  O1   C1'   single  1.416  0.020  1.416
 C4X  O2   HO2   single  0.850  0.020  0.980
 C4X  O3   HO3   single  0.850  0.020  0.980
 C4X  O4   HO4   single  0.850  0.020  0.980
 C4X  C1'  C2'   single  1.514  0.020  1.514
 C4X  C1'  H1'1  single  0.970  0.020  1.090
 C4X  C1'  H1'2  single  0.970  0.020  1.090
 C4X  C2'  C3'   single  1.508  0.020  1.508
 C4X  C2'  H2'1  single  0.970  0.020  1.090
 C4X  C2'  H2'2  single  0.970  0.020  1.090
 C4X  C3'  C4'   single  1.460  0.020  1.460
 C4X  C3'  O'    single  1.417  0.020  1.417
 C4X  C3'  H3'   single  0.970  0.020  1.090
 C4X  C4'  O'    single  1.418  0.020  1.418
 C4X  C4'  H4'1  single  0.970  0.020  1.090
 C4X  C4'  H4'2  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
 C4X  H1    C1   O5    109.29  3.000
 C4X  H1    C1   O1    110.98  3.000
 C4X  O5    C1   O1    108.45  3.000
 C4X  H1    C1   C2    109.02  3.000
 C4X  O5    C1   C2    110.19  3.000
 C4X  O1    C1   C2    108.89  3.000
 C4X  H2    C2   O2    111.49  3.000
 C4X  H2    C2   C3    108.38  3.000
 C4X  O2    C2   C3    111.52  3.000
 C4X  H2    C2   C1    107.89  3.000
 C4X  O2    C2   C1    108.20  3.000
 C4X  C3    C2   C1    109.28  3.000
 C4X  H3    C3   O3    110.69  3.000
 C4X  H3    C3   C4    107.77  3.000
 C4X  O3    C3   C4    112.69  3.000
 C4X  H3    C3   C2    108.04  3.000
 C4X  O3    C3   C2    107.17  3.000
 C4X  C4    C3   C2    110.41  3.000
 C4X  H4    C4   O4    111.34  3.000
 C4X  H4    C4   C5    108.84  3.000
 C4X  O4    C4   C5    111.56  3.000
 C4X  H4    C4   C3    108.63  3.000
 C4X  O4    C4   C3    107.72  3.000
 C4X  C5    C4   C3    108.67  3.000
 C4X  H52   C5   H51   107.77  3.000
 C4X  H52   C5   O5    107.18  3.000
 C4X  H51   C5   O5    111.19  3.000
 C4X  H52   C5   C4    110.91  3.000
 C4X  H51   C5   C4    109.38  3.000
 C4X  O5    C5   C4    110.37  3.000
 C4X  C1'   O1   C1    115.29  3.000
 C4X  HO2   O2   C2    107.88  3.000
 C4X  HO3   O3   C3    108.44  3.000
 C4X  HO4   O4   C4    108.74  3.000
 C4X  C5    O5   C1    112.82  3.000
 C4X  H1'2  C1'  H1'1  106.96  3.000
 C4X  H1'2  C1'  C2'   108.52  3.000
 C4X  H1'1  C1'  C2'   110.28  3.000
 C4X  H1'2  C1'  O1    110.72  3.000
 C4X  H1'1  C1'  O1    110.28  3.000
 C4X  C2'   C1'  O1    110.01  3.000
 C4X  H2'2  C2'  H2'1  105.53  3.000
 C4X  H2'2  C2'  C3'   108.99  3.000
 C4X  H2'1  C2'  C3'   106.92  3.000
 C4X  H2'2  C2'  C1'   109.92  3.000
 C4X  H2'1  C2'  C1'   106.78  3.000
 C4X  C3'   C2'  C1'   117.94  3.000
 C4X  H3'   C3'  O'    113.23  3.000
 C4X  H3'   C3'  C4'   116.58  3.000
 C4X  O'    C3'  C4'    59.01  3.000
 C4X  H3'   C3'  C2'   112.76  3.000
 C4X  O'    C3'  C2'   119.39  3.000
 C4X  C4'   C3'  C2'   125.01  3.000
 C4X  H4'2  C4'  H4'1  114.20  3.000
 C4X  H4'2  C4'  O'    116.11  3.000
 C4X  H4'1  C4'  O'    115.94  3.000
 C4X  H4'2  C4'  C3'   119.29  3.000
 C4X  H4'1  C4'  C3'   120.78  3.000
 C4X  O'    C4'  C3'    59.00  3.000
 C4X  C4'   O'   C3'    61.99  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
 C4X  Var_01  C4    C5   O5   C1     63.11  30.0  1
 C4X  Var_02  O'    C4'  C3'  C2'  -106.15  30.0  1
 C4X  Var_03  H4'1  C4'  O'   C3'  -111.81  30.0  1
 C4X  Var_04  H3'   C3'  O'   C4'  -108.07  30.0  1
 C4X  Var_05  C4'   C3'  C2'  C1'    10.12  30.0  3
 C4X  Var_06  C2'   C1'  O1   C1   -165.10  30.0  3
 C4X  Var_07  C3'   C2'  C1'  O1     67.17  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
 C4X  chir_01  C1   C2   O1   O5  positiv
 C4X  chir_02  C2   O2   C1   C3  negativ
 C4X  chir_03  C3   O3   C2   C4  positiv
 C4X  chir_04  C4   O4   C3   C5  negativ
 C4X  chir_05  C3'  C2'  C4'  O'  both

