# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 13:51:44 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: alpha-D-altropyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O)[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
 SHD  SHD  'alpha-D-altropyranose    '  D-saccharide  24  12  .  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_SHD
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
 SHD  C1    C  CH1   0   0.229  -0.8052   1.4833   0.0668
 SHD  C2    C  CH1   0  -0.031  -1.7799   0.3881  -0.3775
 SHD  C3    C  CH1   0  -0.025  -1.2841  -1.0077   0.0159
 SHD  C4    C  CH1   0   0.040   0.1679  -1.1855  -0.4312
 SHD  C5    C  CH1   0  -0.006   1.0330  -0.0497   0.1143
 SHD  C6    C  CH2   0  -0.157   2.4568  -0.1324  -0.3960
 SHD  O1    O  OH1   0  -0.672  -1.9056   0.3827  -1.7802
 SHD  O2    O  OH1   0  -0.661  -1.3385  -1.2220   1.4021
 SHD  O3    O  OH1   0  -0.673   0.7070  -2.4057   0.0146
 SHD  O4    O  O2    0  -0.504   0.5069   1.1930  -0.3246
 SHD  O5    O  OH1   0  -0.672   3.2049   0.9163   0.1751
 SHD  H11   H  HCH1  0   0.227  -1.0478   2.4112  -0.4699
 SHD  O6    O  OH1   0  -0.663  -0.9350   1.6649   1.4398
 SHD  H2    H  HCH1  0   0.231  -2.7530   0.5782   0.0997
 SHD  H4    H  HCH1  0   0.218   0.1884  -1.1254  -1.5279
 SHD  H5    H  HCH1  0   0.222   1.0483  -0.0966   1.2108
 SHD  H16   H  HCH2  0   0.210   2.8651  -1.1115  -0.1261
 SHD  H26   H  HCH2  0   0.190   2.4506  -0.0755  -1.4942
 SHD  HO3   H  HOH1  0   0.450  -2.2199  -0.9975   1.7150
 SHD  HO4   H  HOH1  0   0.454   0.2782  -3.1206  -0.4659
 SHD  HO6   H  HOH1  0   0.455   4.1220   0.8023  -0.0884
 SHD  H111  H  HCH1  0   0.227  -1.9090  -1.7422  -0.5165
 SHD  H12   H  HOH1  0   0.456  -2.2630   1.2296  -2.0649
 SHD  H121  H  HOH1  0   0.458  -0.4772   2.4752   1.6874

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
 SHD  C1  C2    single  1.532  0.020  1.532
 SHD  C1  O4    single  1.400  0.020  1.400
 SHD  C1  H11   single  0.970  0.020  1.090
 SHD  C1  O6    single  1.391  0.020  1.391
 SHD  C2  C3    single  1.533  0.020  1.533
 SHD  C2  O1    single  1.408  0.020  1.408
 SHD  C2  H2    single  0.970  0.020  1.090
 SHD  C3  C4    single  1.530  0.020  1.530
 SHD  C3  O2    single  1.404  0.020  1.404
 SHD  C3  H111  single  0.970  0.020  1.090
 SHD  C4  C5    single  1.528  0.020  1.528
 SHD  C4  O3    single  1.406  0.020  1.406
 SHD  C4  H4    single  0.970  0.020  1.090
 SHD  C5  C6    single  1.515  0.020  1.515
 SHD  C5  O4    single  1.419  0.020  1.419
 SHD  C5  H5    single  0.970  0.020  1.090
 SHD  C6  O5    single  1.409  0.020  1.409
 SHD  C6  H16   single  0.970  0.020  1.090
 SHD  C6  H26   single  0.970  0.020  1.090
 SHD  O1  H12   single  0.850  0.020  0.980
 SHD  O2  HO3   single  0.850  0.020  0.980
 SHD  O3  HO4   single  0.850  0.020  0.980
 SHD  O5  HO6   single  0.850  0.020  0.980
 SHD  O6  H121  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
 SHD  O6    C1  H11  110.56  3.000
 SHD  O6    C1  O4   112.99  3.000
 SHD  H11   C1  O4   104.22  3.000
 SHD  O6    C1  C2   108.67  3.000
 SHD  H11   C1  C2   108.75  3.000
 SHD  O4    C1  C2   111.53  3.000
 SHD  H2    C2  O1   110.72  3.000
 SHD  H2    C2  C3   109.40  3.000
 SHD  O1    C2  C3   106.32  3.000
 SHD  H2    C2  C1   108.27  3.000
 SHD  O1    C2  C1   110.39  3.000
 SHD  C3    C2  C1   111.76  3.000
 SHD  H111  C3  O2   110.70  3.000
 SHD  H111  C3  C4   108.65  3.000
 SHD  O2    C3  C4   107.92  3.000
 SHD  H111  C3  C2   107.43  3.000
 SHD  O2    C3  C2   112.33  3.000
 SHD  C4    C3  C2   109.75  3.000
 SHD  H4    C4  O3   110.90  3.000
 SHD  H4    C4  C5   107.76  3.000
 SHD  O3    C4  C5   108.34  3.000
 SHD  H4    C4  C3   107.65  3.000
 SHD  O3    C4  C3   111.84  3.000
 SHD  C5    C4  C3   110.28  3.000
 SHD  H5    C5  O4   110.58  3.000
 SHD  H5    C5  C6   108.73  3.000
 SHD  O4    C5  C6   106.98  3.000
 SHD  H5    C5  C4   109.43  3.000
 SHD  O4    C5  C4   109.30  3.000
 SHD  C6    C5  C4   111.79  3.000
 SHD  H26   C6  H16  107.14  3.000
 SHD  H26   C6  O5   111.67  3.000
 SHD  H16   C6  O5   111.57  3.000
 SHD  H26   C6  C5   109.16  3.000
 SHD  H16   C6  C5   108.44  3.000
 SHD  O5    C6  C5   108.77  3.000
 SHD  H12   O1  C2   108.93  3.000
 SHD  HO3   O2  C3   108.74  3.000
 SHD  HO4   O3  C4   108.39  3.000
 SHD  C5    O4  C1   116.28  3.000
 SHD  HO6   O5  C6   107.89  3.000
 SHD  H121  O6  C1   108.61  3.000

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
 SHD  chir_01  C1  C2  O4  O6  positiv
 SHD  chir_02  C2  O1  C1  C3  positiv
 SHD  chir_03  C3  O2  C2  C4  negativ
 SHD  chir_04  C4  O3  C3  C5  negativ
 SHD  chir_05  C5  O4  C4  C6  negativ

