# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 15:55:38 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: 2,6-diamino-2,6-dideoxy-beta-L-idopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@@H]1O[C@H](O)[C@H](N)[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
 IDG  IDG  2,6-diamino-2,6-dideoxy-beta-L-idopyranose  L-saccharide  26  12  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_IDG
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
 IDG  C5    C  CH1   0  -0.044   8.5644  -6.1759  -5.9571
 IDG  O5    O  O2    0  -0.507   8.9668  -6.1648  -4.5989
 IDG  C1    C  CH1   0   0.291   8.3185  -5.1518  -3.8467
 IDG  O1    O  OH1   0  -0.661   8.8265  -5.1687  -2.5720
 IDG  C2    C  CH1   0  -0.197   6.7980  -5.3895  -3.8115
 IDG  N2    N  NH2   0  -0.819   6.5222  -6.4170  -2.8175
 IDG  C3    C  CH1   0   0.005   6.2355  -5.6432  -5.2173
 IDG  O3    O  OH1   0  -0.666   6.1912  -4.3816  -5.8504
 IDG  C4    C  CH1   0   0.008   7.1082  -6.6181  -6.0302
 IDG  O4    O  OH1   0  -0.671   6.9298  -7.9503  -5.5928
 IDG  C6    C  CH2   0  -0.296   9.5271  -7.0665  -6.7355
 IDG  N6    N  NH2   0  -0.785  10.9042  -6.6104  -6.7659
 IDG  H5    H  HCH1  0   0.220   8.6310  -5.1612  -6.3795
 IDG  H1    H  HCH1  0   0.200   8.5396  -4.1779  -4.3060
 IDG  HO1   H  HOH1  0   0.441   8.2281  -5.7640  -2.0783
 IDG  H2    H  HCH1  0   0.264   6.3405  -4.4667  -3.4434
 IDG  HN21  H  HNH2  0   0.353   6.5339  -7.3481  -3.2090
 IDG  HN22  H  HNH2  0   0.370   5.6049  -6.2833  -2.4158
 IDG  H3    H  HCH1  0   0.227   5.2275  -6.0712  -5.1185
 IDG  HO3   H  HOH1  0   0.452   5.8531  -4.4928  -6.7452
 IDG  H4    H  HCH1  0   0.238   6.7794  -6.5821  -7.0768
 IDG  HO4   H  HOH1  0   0.448   7.6275  -8.1737  -4.9671
 IDG  H61   H  HCH2  0   0.221   9.5125  -8.0819  -6.3313
 IDG  H62   H  HCH2  0   0.229   9.1588  -7.1406  -7.7621
 IDG  HN61  H  HNH2  0   0.339  10.9468  -5.6800  -7.1641
 IDG  HN62  H  HNH2  0   0.341  11.2535  -6.5233  -5.8199

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
 IDG  C5  O5    single  1.417  0.020  1.417
 IDG  C5  C4    single  1.524  0.020  1.524
 IDG  C5  C6    single  1.525  0.020  1.525
 IDG  C5  H5    single  0.970  0.020  1.090
 IDG  O5  C1    single  1.419  0.020  1.419
 IDG  C1  O1    single  1.372  0.020  1.372
 IDG  C1  C2    single  1.539  0.020  1.539
 IDG  C1  H1    single  0.970  0.020  1.090
 IDG  O1  HO1   single  0.850  0.020  0.980
 IDG  C2  N2    single  1.456  0.020  1.456
 IDG  C2  C3    single  1.535  0.020  1.535
 IDG  C2  H2    single  0.970  0.020  1.090
 IDG  N2  HN21  single  0.890  0.020  1.040
 IDG  N2  HN22  single  0.890  0.020  1.040
 IDG  C3  O3    single  1.412  0.020  1.412
 IDG  C3  C4    single  1.540  0.020  1.540
 IDG  C3  H3    single  0.970  0.020  1.090
 IDG  O3  HO3   single  0.850  0.020  0.980
 IDG  C4  O4    single  1.413  0.020  1.413
 IDG  C4  H4    single  0.970  0.020  1.090
 IDG  O4  HO4   single  0.850  0.020  0.980
 IDG  C6  N6    single  1.451  0.020  1.451
 IDG  C6  H61   single  0.970  0.020  1.090
 IDG  C6  H62   single  0.970  0.020  1.090
 IDG  N6  HN61  single  0.890  0.020  1.040
 IDG  N6  HN62  single  0.890  0.020  1.040

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
 IDG  H5    C5  C6    107.71  3.000
 IDG  H5    C5  C4    107.87  3.000
 IDG  C6    C5  C4    114.16  3.000
 IDG  H5    C5  O5    110.08  3.000
 IDG  C6    C5  O5    108.34  3.000
 IDG  C4    C5  O5    108.65  3.000
 IDG  C1    O5  C5    112.59  3.000
 IDG  H1    C1  C2    110.19  3.000
 IDG  H1    C1  O1    108.94  3.000
 IDG  C2    C1  O1    110.03  3.000
 IDG  H1    C1  O5    108.61  3.000
 IDG  C2    C1  O5    110.69  3.000
 IDG  O1    C1  O5    108.33  3.000
 IDG  HO1   O1  C1    104.47  3.000
 IDG  H2    C2  C3    107.12  3.000
 IDG  H2    C2  N2    106.64  3.000
 IDG  C3    C2  N2    116.05  3.000
 IDG  H2    C2  C1    106.89  3.000
 IDG  C3    C2  C1    111.50  3.000
 IDG  N2    C2  C1    108.16  3.000
 IDG  HN22  N2  HN21  106.66  3.000
 IDG  HN22  N2  C2    110.49  3.000
 IDG  HN21  N2  C2    112.57  3.000
 IDG  H3    C3  C4    108.69  3.000
 IDG  H3    C3  O3    111.06  3.000
 IDG  C4    C3  O3    110.28  3.000
 IDG  H3    C3  C2    108.54  3.000
 IDG  C4    C3  C2    112.35  3.000
 IDG  O3    C3  C2    105.92  3.000
 IDG  HO3   O3  C3    108.93  3.000
 IDG  H4    C4  O4    106.75  3.000
 IDG  H4    C4  C3    108.22  3.000
 IDG  O4    C4  C3    111.21  3.000
 IDG  H4    C4  C5    108.81  3.000
 IDG  O4    C4  C5    112.29  3.000
 IDG  C3    C4  C5    109.42  3.000
 IDG  HO4   O4  C4    109.15  3.000
 IDG  H62   C6  H61   106.25  3.000
 IDG  H62   C6  N6    108.75  3.000
 IDG  H61   C6  N6    108.20  3.000
 IDG  H62   C6  C5    107.84  3.000
 IDG  H61   C6  C5    110.20  3.000
 IDG  N6    C6  C5    115.23  3.000
 IDG  HN62  N6  HN61  105.90  3.000
 IDG  HN62  N6  C6    109.57  3.000
 IDG  HN61  N6  C6    109.69  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
 IDG  Var_01  HN61  N6  C6  C5  -57.89  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
 IDG  chir_01  C5  O5  C4  C6  positiv
 IDG  chir_02  C1  O5  O1  C2  positiv
 IDG  chir_03  C2  N2  C3  C1  positiv
 IDG  chir_04  C3  O3  C2  C4  positiv
 IDG  chir_05  C4  O4  C3  C5  negativ

