# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 15:03:31 2022
#   Inital geometry file: a 49 line input string
#   Ligand name: 3,6-anhydro-beta-L-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1O[C@H]2CO[C@@H]([C@@H]1O)[C@@H]2O
#
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
 3DY  3DY  3,6-anhydro-beta-L-galactopyranose  L-saccharide  21  11  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3DY
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
 3DY  C1   C  CH1   0   0.249  23.5504  78.0297  -29.2889
 3DY  C2   C  CH1   0  -0.039  22.2321  77.2193  -29.3669
 3DY  C3   C  CH1   0  -0.060  21.9903  76.7099  -30.7886
 3DY  C4   C  CH1   0   0.019  22.0173  77.8976  -31.7476
 3DY  C5   C  CH1   0  -0.081  23.5240  78.1313  -31.6979
 3DY  C6   C  CH2   0  -0.180  24.0355  76.7064  -31.8586
 3DY  O1   O  OH1   0  -0.657  24.6612  77.2244  -29.0021
 3DY  O2   O  OH1   0  -0.665  21.1195  78.0124  -29.0299
 3DY  O3   O  O2    0  -0.495  23.0701  75.8898  -31.1993
 3DY  O4   O  OH1   0  -0.666  21.6528  77.5565  -33.0585
 3DY  O5   O  O2    0  -0.488  23.8447  78.7373  -30.4547
 3DY  H1   H  HCH1  0   0.239  22.3137  76.3581  -28.6886
 3DY  H2   H  HCH1  0   0.261  21.0637  76.1285  -30.8307
 3DY  H3   H  HCH1  0   0.245  21.4560  78.7618  -31.3790
 3DY  H4   H  HCH1  0   0.268  23.8977  78.8036  -32.4712
 3DY  H5   H  HCH2  0   0.227  24.0857  76.4464  -32.9203
 3DY  H6   H  HCH2  0   0.239  25.0257  76.5563  -31.4282
 3DY  H7   H  HOH1  0   0.457  21.1608  78.2245  -28.0922
 3DY  H8   H  HOH1  0   0.454  20.7295  77.2844  -33.0573
 3DY  H9   H  HCH1  0   0.222  23.4290  78.7949  -28.5080
 3DY  H10  H  HOH1  0   0.452  24.4782  76.7058  -28.2114

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
 3DY  O4  C4   single  1.403  0.020  1.403
 3DY  C6  C5   single  1.522  0.020  1.522
 3DY  C6  O3   single  1.426  0.020  1.426
 3DY  C5  C4   single  1.526  0.020  1.526
 3DY  C5  O5   single  1.420  0.020  1.420
 3DY  C4  C3   single  1.527  0.020  1.527
 3DY  O3  C3   single  1.417  0.020  1.417
 3DY  C3  C2   single  1.529  0.020  1.529
 3DY  O5  C1   single  1.395  0.020  1.395
 3DY  C2  C1   single  1.549  0.020  1.549
 3DY  C2  O2   single  1.407  0.020  1.407
 3DY  C1  O1   single  1.402  0.020  1.402
 3DY  C2  H1   single  0.970  0.020  1.090
 3DY  C3  H2   single  0.970  0.020  1.090
 3DY  C4  H3   single  0.970  0.020  1.090
 3DY  C5  H4   single  0.970  0.020  1.090
 3DY  C6  H5   single  0.970  0.020  1.090
 3DY  C6  H6   single  0.970  0.020  1.090
 3DY  O2  H7   single  0.850  0.020  0.980
 3DY  O4  H8   single  0.850  0.020  0.980
 3DY  C1  H9   single  0.970  0.020  1.090
 3DY  O1  H10  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
 3DY  H9   C1  O5  105.28  3.000
 3DY  H9   C1  O1  109.99  3.000
 3DY  O5   C1  O1  107.17  3.000
 3DY  H9   C1  C2  107.80  3.000
 3DY  O1   C1  C2  112.59  3.000
 3DY  O5   C1  C2  113.75  3.000
 3DY  H1   C2  O2  110.64  3.000
 3DY  H1   C2  C3  108.93  3.000
 3DY  O2   C2  C3  106.58  3.000
 3DY  H1   C2  C1  108.39  3.000
 3DY  O2   C2  C1  111.46  3.000
 3DY  C3   C2  C1  110.82  3.000
 3DY  H2   C3  O3  109.06  3.000
 3DY  H2   C3  C4  113.82  3.000
 3DY  O3   C3  C4  104.76  3.000
 3DY  H2   C3  C2  110.27  3.000
 3DY  O3   C3  C2  109.99  3.000
 3DY  C4   C3  C2  108.79  3.000
 3DY  H3   C4  O4  111.94  3.000
 3DY  H3   C4  C5  112.00  3.000
 3DY  O4   C4  C5  108.92  3.000
 3DY  H3   C4  C3  113.18  3.000
 3DY  C5   C4  C3   96.67  3.000
 3DY  O4   C4  C3  113.16  3.000
 3DY  H4   C5  O5  106.28  3.000
 3DY  H4   C5  C6  112.76  3.000
 3DY  O5   C5  C6  114.59  3.000
 3DY  H4   C5  C4  114.19  3.000
 3DY  O5   C5  C4  108.48  3.000
 3DY  C6   C5  C4  100.66  3.000
 3DY  H6   C6  H5  107.98  3.000
 3DY  H6   C6  O3  110.70  3.000
 3DY  H5   C6  O3  110.09  3.000
 3DY  H6   C6  C5  113.11  3.000
 3DY  H5   C6  C5  109.89  3.000
 3DY  O3   C6  C5  105.05  3.000
 3DY  H10  O1  C1  109.07  3.000
 3DY  H7   O2  C2  108.88  3.000
 3DY  C6   O3  C3  108.57  3.000
 3DY  H8   O4  C4  108.47  3.000
 3DY  C5   O5  C1  117.87  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
 3DY  Var_01  C5  C6  O3  C3  5.50  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
 3DY  chir_01  C1  O5  C2  O1  negativ
 3DY  chir_02  C2  O2  C1  C3  positiv
 3DY  chir_03  C3  O3  C4  C2  positiv
 3DY  chir_04  C4  O4  C3  C5  negativ
 3DY  chir_05  C5  O5  C4  C6  positiv

