# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 03:46:27 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: beta-L-xylopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CO[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
 LXC  LXC  'beta-L-xylopyranose      '  L-saccharide  20  10  .  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_LXC
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
 LXC  C5    C  CH2   0  -0.226   1.7643  -0.2111   0.6047
 LXC  O5    O  O2    0  -0.489   1.6739   0.2683  -0.7178
 LXC  C1    C  CH1   0   0.265   0.5422  -0.2367  -1.3846
 LXC  O1    O  OH1   0  -0.662   0.5364   0.2542  -2.6742
 LXC  C2    C  CH1   0  -0.012  -0.7425   0.2318  -0.6960
 LXC  O2    O  OH1   0  -0.665  -1.8742  -0.3291  -1.3092
 LXC  C3    C  CH1   0   0.011  -0.7280  -0.1997   0.7613
 LXC  O3    O  OH1   0  -0.668  -1.8605   0.3376   1.3969
 LXC  C4    C  CH1   0  -0.006   0.5661   0.2566   1.4249
 LXC  O4    O  OH1   0  -0.671   0.5862  -0.2885   2.7242
 LXC  H5C1  H  HCH2  0   0.250   2.6932   0.1769   1.0257
 LXC  H5C2  H  HCH2  0   0.212   1.8234  -1.3094   0.6278
 LXC  H1    H  HCH1  0   0.190   0.5742  -1.3407  -1.3704
 LXC  HA    H  HOH1  0   0.467   1.1323  -0.2663  -3.2230
 LXC  H2    H  HCH1  0   0.217  -0.7652   1.3328  -0.7381
 LXC  HB    H  HOH1  0   0.451  -1.8993  -0.0281  -2.2233
 LXC  H3    H  HCH1  0   0.207  -0.7497  -1.3026   0.7918
 LXC  HC    H  HOH1  0   0.449  -1.8232   0.0857   2.3256
 LXC  H4    H  HCH1  0   0.220   0.5704   1.3555   1.4564
 LXC  HD    H  HOH1  0   0.461   1.2354   0.1873   3.2507

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
 LXC  C5  O5    single  1.410  0.020  1.410
 LXC  C5  C4    single  1.525  0.020  1.525
 LXC  C5  H5C1  single  0.970  0.020  1.090
 LXC  C5  H5C2  single  0.970  0.020  1.090
 LXC  O5  C1    single  1.407  0.020  1.407
 LXC  C1  O1    single  1.380  0.020  1.380
 LXC  C1  C2    single  1.531  0.020  1.531
 LXC  C1  H1    single  0.970  0.020  1.090
 LXC  O1  HA    single  0.850  0.020  0.980
 LXC  C2  O2    single  1.404  0.020  1.404
 LXC  C2  C3    single  1.520  0.020  1.520
 LXC  C2  H2    single  0.970  0.020  1.090
 LXC  O2  HB    single  0.850  0.020  0.980
 LXC  C3  O3    single  1.405  0.020  1.405
 LXC  C3  C4    single  1.524  0.020  1.524
 LXC  C3  H3    single  0.970  0.020  1.090
 LXC  O3  HC    single  0.850  0.020  0.980
 LXC  C4  O4    single  1.409  0.020  1.409
 LXC  C4  H4    single  0.970  0.020  1.090
 LXC  O4  HD    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
 LXC  H5C2  C5  H5C1  107.53  3.000
 LXC  H5C2  C5  C4    109.69  3.000
 LXC  H5C1  C5  C4    110.62  3.000
 LXC  H5C2  C5  O5    111.27  3.000
 LXC  H5C1  C5  O5    107.19  3.000
 LXC  C4    C5  O5    110.48  3.000
 LXC  C1    O5  C5    111.96  3.000
 LXC  H1    C1  C2    108.92  3.000
 LXC  H1    C1  O1    111.57  3.000
 LXC  C2    C1  O1    107.94  3.000
 LXC  H1    C1  O5    109.22  3.000
 LXC  C2    C1  O5    110.60  3.000
 LXC  O1    C1  O5    108.57  3.000
 LXC  HA    O1  C1    109.74  3.000
 LXC  H2    C2  C3    108.69  3.000
 LXC  H2    C2  O2    111.45  3.000
 LXC  C3    C2  O2    108.24  3.000
 LXC  H2    C2  C1    107.80  3.000
 LXC  C3    C2  C1    109.66  3.000
 LXC  O2    C2  C1    110.96  3.000
 LXC  HB    O2  C2    108.11  3.000
 LXC  H3    C3  C4    107.69  3.000
 LXC  H3    C3  O3    110.72  3.000
 LXC  C4    C3  O3    111.89  3.000
 LXC  H3    C3  C2    108.06  3.000
 LXC  C4    C3  C2    109.91  3.000
 LXC  O3    C3  C2    108.51  3.000
 LXC  HC    O3  C3    107.76  3.000
 LXC  H4    C4  O4    111.11  3.000
 LXC  H4    C4  C3    108.36  3.000
 LXC  O4    C4  C3    107.32  3.000
 LXC  H4    C4  C5    108.59  3.000
 LXC  O4    C4  C5    111.47  3.000
 LXC  C3    C4  C5    109.94  3.000
 LXC  HD    O4  C4    108.85  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
 LXC  Var_01  C4  C5  O5  C1  -62.76  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
 LXC  chir_01  C1  O5  O1  C2  positiv
 LXC  chir_02  C2  O2  C1  C3  positiv
 LXC  chir_03  C3  O3  C2  C4  negativ
 LXC  chir_04  C4  O4  C3  C5  positiv

