# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 06:53:20 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 1,5-anhydro-2-deoxy-D-arabino-hex-1-enitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1OC=C[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
 DGO  DGO  1,5-anhydro-2-deoxy-D-arabino-hex-1-enitol  D-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 OK (reasonable std)
;

data_comp_DGO
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
 DGO  C1   C  CR16  0   0.045  -0.3896  -1.9719   0.0848
 DGO  C2   C  CR16  0  -0.013   0.8299   0.0170  -0.2276
 DGO  C3   C  CR16  0   0.004  -0.4182   0.7632   0.2394
 DGO  C5   C  CH2   0  -0.160   2.1071   0.6256   0.3105
 DGO  C4   C  CR16  0   0.018  -1.6535   0.1067  -0.3640
 DGO  O3   O  OH1   0  -0.670   3.1984  -0.1027  -0.2001
 DGO  O    O  O     0  -0.465   0.7934  -1.3376   0.2114
 DGO  O2   O  OH1   0  -0.671  -0.2932   2.1079  -0.1469
 DGO  O1   O  OH1   0  -0.674  -2.7797   0.6434   0.3029
 DGO  C    C  CR16  0  -0.410  -1.5455  -1.3809  -0.2004
 DGO  H1   H  HCR6  0   0.271  -0.2965  -3.0399   0.2420
 DGO  H2   H  HCR6  0   0.237   0.8578   0.0252  -1.3275
 DGO  H3   H  HCR6  0   0.218  -0.4853   0.6677   1.3352
 DGO  H4   H  HCH2  0   0.217   2.1463   1.6765   0.0088
 DGO  H5   H  HCH2  0   0.198   2.0781   0.6042   1.4089
 DGO  H6   H  HCR6  0   0.225  -1.6929   0.3671  -1.4316
 DGO  H7   H  HOH1  0   0.458   4.0051   0.3435   0.0718
 DGO  H8   H  HOH1  0   0.455  -1.0838   2.5743   0.1443
 DGO  H9   H  HOH1  0   0.458  -3.5616   0.4609  -0.2267
 DGO  H10  H  HCR6  0   0.260  -2.4296  -1.9959  -0.3100

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
 DGO  O2  C3   single  1.405  0.020  1.405
 DGO  O3  C5   single  1.408  0.020  1.408
 DGO  C5  C2   single  1.514  0.020  1.514
 DGO  C3  C2   single  1.527  0.020  1.527
 DGO  C3  C4   single  1.524  0.020  1.524
 DGO  O1  C4   single  1.415  0.020  1.415
 DGO  C2  O    single  1.424  0.020  1.424
 DGO  C4  C    single  1.501  0.020  1.501
 DGO  O   C1   single  1.348  0.020  1.348
 DGO  C   C1   double  1.329  0.020  1.329
 DGO  C1  H1   single  0.930  0.020  1.080
 DGO  C2  H2   single  0.970  0.020  1.090
 DGO  C3  H3   single  0.970  0.020  1.090
 DGO  C5  H4   single  0.970  0.020  1.090
 DGO  C5  H5   single  0.970  0.020  1.090
 DGO  C4  H6   single  0.970  0.020  1.090
 DGO  O3  H7   single  0.850  0.020  0.980
 DGO  O2  H8   single  0.850  0.020  0.980
 DGO  O1  H9   single  0.850  0.020  0.980
 DGO  C   H10  single  0.930  0.020  1.080

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
 DGO  H1   C1  C   122.96  3.000
 DGO  H1   C1  O   112.01  3.000
 DGO  C    C1  O   125.03  3.000
 DGO  H2   C2  O   108.42  3.000
 DGO  H2   C2  C5  109.33  3.000
 DGO  O    C2  C5  107.12  3.000
 DGO  H2   C2  C3  108.83  3.000
 DGO  O    C2  C3  110.45  3.000
 DGO  C5   C2  C3  112.60  3.000
 DGO  H3   C3  O2  111.21  3.000
 DGO  H3   C3  C4  107.89  3.000
 DGO  O2   C3  C4  112.07  3.000
 DGO  H3   C3  C2  108.15  3.000
 DGO  C4   C3  C2  109.33  3.000
 DGO  O2   C3  C2  108.11  3.000
 DGO  H5   C5  H4  107.17  3.000
 DGO  H5   C5  O3  111.89  3.000
 DGO  H4   C5  O3  111.66  3.000
 DGO  H5   C5  C2  108.98  3.000
 DGO  H4   C5  C2  108.57  3.000
 DGO  O3   C5  C2  108.49  3.000
 DGO  H6   C4  C   110.07  3.000
 DGO  H6   C4  O1  109.84  3.000
 DGO  C    C4  O1  112.46  3.000
 DGO  H6   C4  C3  108.15  3.000
 DGO  C    C4  C3  109.00  3.000
 DGO  O1   C4  C3  107.18  3.000
 DGO  H7   O3  C5  107.93  3.000
 DGO  C2   O   C1  116.16  3.000
 DGO  H8   O2  C3  107.90  3.000
 DGO  H9   O1  C4  108.40  3.000
 DGO  H10  C   C4  119.56  3.000
 DGO  H10  C   C1  118.65  3.000
 DGO  C4   C   C1  121.79  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
 DGO  Var_01  C  C1  O  C2  -11.67  30.0  1
 DGO  Var_02  O  C1  C  C4   -2.37  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
 DGO  chir_01  C2  C5  C3  O   positiv
 DGO  chir_02  C3  O2  C2  C4  positiv
 DGO  chir_03  C4  O1  C3  C   negativ

