# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:33:24 2020
#   Inital geometry file: a 58 line input string
#   Ligand name: D-mannose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)C=O
#
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
 DNO  DNO  'D-mannose                '  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_DNO
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
 DNO  C1   C  C1    0   0.157   3.1661   0.4804  -0.2083
 DNO  C2   C  CH1   0  -0.093   1.9786  -0.4459  -0.0926
 DNO  C3   C  CH1   0  -0.021   0.6746   0.3820  -0.1873
 DNO  C4   C  CH1   0  -0.023  -0.5633  -0.5080  -0.0296
 DNO  C5   C  CH1   0  -0.026  -1.8662   0.3119  -0.0332
 DNO  C6   C  CH2   0  -0.156  -3.0675  -0.5812   0.2371
 DNO  O1   O  O     0  -0.374   3.9699   0.6263   0.6781
 DNO  O2   O  OH1   0  -0.651   2.0371  -1.2315   1.0587
 DNO  O3   O  OH1   0  -0.663   0.6481   1.1289  -1.3819
 DNO  O4   O  OH1   0  -0.666  -0.5891  -1.5248  -1.0095
 DNO  O5   O  OH1   0  -0.659  -1.7998   1.3832   0.8785
 DNO  O6   O  OH1   0  -0.670  -4.2407   0.1877   0.1139
 DNO  H1   H  H     0   0.208   3.2548   1.0270  -1.1597
 DNO  H2   H  HCH1  0   0.269   2.0179  -1.1246  -0.9550
 DNO  H3   H  HCH1  0   0.257   0.6757   1.1138   0.6253
 DNO  H4   H  HCH1  0   0.240  -0.4870  -1.0210   0.9348
 DNO  H5   H  HCH1  0   0.230  -1.9873   0.7715  -1.0212
 DNO  H6   H  HCH2  0   0.205  -3.0627  -1.4209  -0.4660
 DNO  H6A  H  HCH2  0   0.191  -2.9688  -1.0125   1.2456
 DNO  HO2  H  HOH1  0   0.449   2.2456  -0.6675   1.8122
 DNO  HO3  H  HOH1  0   0.446   0.7468   0.5352  -2.1345
 DNO  HO4  H  HOH1  0   0.447  -0.9071  -1.1613  -1.8431
 DNO  HO5  H  HOH1  0   0.446  -1.7657   1.0257   1.7730
 DNO  HO6  H  HOH1  0   0.455  -4.9922  -0.3966   0.2470

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
 DNO  C1  C2   single  1.510  0.020  1.510
 DNO  C1  O1   double  1.205  0.020  1.205
 DNO  C2  C3   single  1.547  0.020  1.547
 DNO  C2  O2   single  1.395  0.020  1.395
 DNO  C3  C4   single  1.533  0.020  1.533
 DNO  C3  O3   single  1.409  0.020  1.409
 DNO  C4  C5   single  1.539  0.020  1.539
 DNO  C4  O4   single  1.412  0.020  1.412
 DNO  C5  C6   single  1.521  0.020  1.521
 DNO  C5  O5   single  1.408  0.020  1.408
 DNO  C6  O6   single  1.408  0.020  1.408
 DNO  C1  H1   single  0.930  0.020  1.080
 DNO  C2  H2   single  0.970  0.020  1.090
 DNO  C3  H3   single  0.970  0.020  1.090
 DNO  C4  H4   single  0.970  0.020  1.090
 DNO  C5  H5   single  0.970  0.020  1.090
 DNO  C6  H6   single  0.970  0.020  1.090
 DNO  C6  H6A  single  0.970  0.020  1.090
 DNO  O2  HO2  single  0.850  0.020  0.980
 DNO  O3  HO3  single  0.850  0.020  0.980
 DNO  O4  HO4  single  0.850  0.020  0.980
 DNO  O5  HO5  single  0.850  0.020  0.980
 DNO  O6  HO6  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
 DNO  H1   C1  O1  121.45  3.000
 DNO  H1   C1  C2  115.73  3.000
 DNO  O1   C1  C2  122.83  3.000
 DNO  H2   C2  O2  107.37  3.000
 DNO  H2   C2  C3  108.22  3.000
 DNO  O2   C2  C3  112.77  3.000
 DNO  H2   C2  C1  106.90  3.000
 DNO  O2   C2  C1  112.06  3.000
 DNO  C3   C2  C1  109.25  3.000
 DNO  H3   C3  O3  105.97  3.000
 DNO  H3   C3  C4  108.24  3.000
 DNO  O3   C3  C4  112.32  3.000
 DNO  H3   C3  C2  108.16  3.000
 DNO  O3   C3  C2  110.57  3.000
 DNO  C4   C3  C2  111.33  3.000
 DNO  H4   C4  O4  105.96  3.000
 DNO  H4   C4  C5  108.09  3.000
 DNO  O4   C4  C5  111.50  3.000
 DNO  H4   C4  C3  107.84  3.000
 DNO  O4   C4  C3  111.18  3.000
 DNO  C5   C4  C3  111.97  3.000
 DNO  H5   C5  O5  105.64  3.000
 DNO  H5   C5  C6  108.60  3.000
 DNO  O5   C5  C6  111.64  3.000
 DNO  H5   C5  C4  108.60  3.000
 DNO  O5   C5  C4  111.33  3.000
 DNO  C6   C5  C4  110.81  3.000
 DNO  H6A  C6  H6  106.69  3.000
 DNO  H6A  C6  O6  111.63  3.000
 DNO  H6   C6  O6  111.48  3.000
 DNO  H6A  C6  C5  108.78  3.000
 DNO  H6   C6  C5  109.43  3.000
 DNO  O6   C6  C5  108.78  3.000
 DNO  HO2  O2  C2  108.95  3.000
 DNO  HO3  O3  C3  109.49  3.000
 DNO  HO4  O4  C4  109.55  3.000
 DNO  HO5  O5  C5  108.68  3.000
 DNO  HO6  O6  C6  107.90  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
 DNO  chir_01  C2  C1  C3  O2  positiv
 DNO  chir_02  C3  O3  C2  C4  positiv
 DNO  chir_03  C4  O4  C3  C5  negativ
 DNO  chir_04  C5  O5  C4  C6  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DNO  plan-1  C1  0.020
 DNO  plan-1  C2  0.020
 DNO  plan-1  O1  0.020
 DNO  plan-1  H1  0.020

