# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 04:22:21 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: 2,4-bis(acetylamino)-2,4-dideoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](NC(C)=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
 DT6  DT6  2,4-bis(acetylamino)-2,4-dideoxy-beta-D-glucopyranose  D-saccharide  36  18  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DT6
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
 DT6  O1    O  OH1   0  -0.646   4.8666  47.0172  6.3772
 DT6  C1    C  CH1   0   0.310   3.6793  46.3444  6.5447
 DT6  C2    C  CH1   0  -0.155   3.0704  46.0713  5.1681
 DT6  N2    N  NH1   0  -0.631   2.7682  47.3032  4.4883
 DT6  C3    C  CH1   0   0.059   1.8151  45.2217  5.3288
 DT6  N3    N  NH1   0  -0.637   0.8692  43.2633  6.3871
 DT6  O3    O  OH1   0  -0.654   1.3561  44.8772  4.0508
 DT6  C4    C  CH1   0  -0.133   2.1028  43.9804  6.1802
 DT6  C5    C  CH1   0   0.035   2.7797  44.3797  7.4974
 DT6  O5    O  O2    0  -0.498   3.9403  45.1273  7.2005
 DT6  C6    C  CH2   0  -0.177   3.2473  43.2060  8.3482
 DT6  O6    O  OH1   0  -0.661   2.1339  42.5889  8.9479
 DT6  C7    C  C     0   0.518   3.4459  47.7726  3.4230
 DT6  O7    O  O     0  -0.494   4.3711  47.1731  2.8954
 DT6  C8    C  CH3   0  -0.779   2.9816  49.1134  2.9093
 DT6  O8    O  O     0  -0.488   1.6187  41.1971  5.8391
 DT6  C9    C  C     0   0.527   0.7430  41.9210  6.2843
 DT6  C10   C  CH3   0  -0.783  -0.5764  41.3802  6.7741
 DT6  HO1   H  HOH1  0   0.463   5.1130  47.4467  7.2033
 DT6  H1    H  HCH1  0   0.186   2.9602  46.9282  7.1476
 DT6  H2    H  HCH1  0   0.272   3.8021  45.5195  4.5718
 DT6  HN2   H  HNH1  0   0.400   2.0199  47.8646  4.8646
 DT6  H3    H  HCH1  0   0.208   1.0630  45.8280  5.8651
 DT6  HN3   H  HNH1  0   0.399   0.1332  43.7634  6.8638
 DT6  HO3   H  HOH1  0   0.450   0.5518  44.3567  4.1536
 DT6  H4    H  HCH1  0   0.263   2.7833  43.3281  5.6270
 DT6  H5    H  HCH1  0   0.221   2.0785  44.9888  8.0924
 DT6  H61   H  HCH2  0   0.203   3.8146  42.5077  7.7198
 DT6  H62   H  HCH2  0   0.214   3.9404  43.5987  9.1035
 DT6  HO6   H  HOH1  0   0.457   2.4456  41.8155  9.4261
 DT6  H81   H  HCH3  0   0.263   2.7263  49.0276  1.8534
 DT6  H82   H  HCH3  0   0.247   2.1229  49.5179  3.4414
 DT6  H83   H  HCH3  0   0.265   3.8010  49.8283  2.9861
 DT6  H10   H  HCH3  0   0.259  -0.8548  40.4941  6.2081
 DT6  H10A  H  HCH3  0   0.267  -0.4684  41.0891  7.8207
 DT6  H10B  H  HCH3  0   0.250  -1.3842  42.1081  6.7141

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
 DT6  O1   C1    single  1.375  0.020  1.375
 DT6  O1   HO1   single  0.850  0.020  0.980
 DT6  C2   C1    single  1.530  0.020  1.530
 DT6  C1   O5    single  1.407  0.020  1.407
 DT6  C1   H1    single  0.970  0.020  1.090
 DT6  N2   C2    single  1.439  0.020  1.439
 DT6  C2   C3    single  1.524  0.020  1.524
 DT6  C2   H2    single  0.970  0.020  1.090
 DT6  C7   N2    single  1.347  0.020  1.347
 DT6  N2   HN2   single  0.860  0.020  1.020
 DT6  O3   C3    single  1.401  0.020  1.401
 DT6  C3   C4    single  1.532  0.020  1.532
 DT6  C3   H3    single  0.970  0.020  1.090
 DT6  C9   N3    single  1.352  0.020  1.352
 DT6  C4   N3    single  1.442  0.020  1.442
 DT6  N3   HN3   single  0.860  0.020  1.020
 DT6  O3   HO3   single  0.850  0.020  0.980
 DT6  C4   C5    single  1.534  0.020  1.534
 DT6  C4   H4    single  0.970  0.020  1.090
 DT6  O5   C5    single  1.412  0.020  1.412
 DT6  C5   C6    single  1.523  0.020  1.523
 DT6  C5   H5    single  0.970  0.020  1.090
 DT6  C6   O6    single  1.407  0.020  1.407
 DT6  C6   H61   single  0.970  0.020  1.090
 DT6  C6   H62   single  0.970  0.020  1.090
 DT6  O6   HO6   single  0.850  0.020  0.980
 DT6  O7   C7    double  1.222  0.020  1.222
 DT6  C8   C7    single  1.509  0.020  1.509
 DT6  C8   H81   single  0.970  0.020  1.090
 DT6  C8   H82   single  0.970  0.020  1.090
 DT6  C8   H83   single  0.970  0.020  1.090
 DT6  O8   C9    double  1.220  0.020  1.220
 DT6  C9   C10   single  1.508  0.020  1.508
 DT6  C10  H10   single  0.970  0.020  1.090
 DT6  C10  H10A  single  0.970  0.020  1.090
 DT6  C10  H10B  single  0.970  0.020  1.090

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
 DT6  HO1   O1   C1    109.55  3.000
 DT6  H1    C1   O5    108.87  3.000
 DT6  H1    C1   C2    109.04  3.000
 DT6  O5    C1   C2    109.81  3.000
 DT6  H1    C1   O1    111.70  3.000
 DT6  O5    C1   O1    108.66  3.000
 DT6  C2    C1   O1    108.75  3.000
 DT6  H2    C2   C3    109.10  3.000
 DT6  H2    C2   N2    108.36  3.000
 DT6  C3    C2   N2    110.73  3.000
 DT6  H2    C2   C1    108.33  3.000
 DT6  C3    C2   C1    109.41  3.000
 DT6  N2    C2   C1    110.85  3.000
 DT6  HN2   N2   C7    118.33  3.000
 DT6  HN2   N2   C2    117.14  3.000
 DT6  C7    N2   C2    124.49  3.000
 DT6  H3    C3   C4    107.62  3.000
 DT6  H3    C3   O3    110.78  3.000
 DT6  C4    C3   O3    111.66  3.000
 DT6  H3    C3   C2    107.81  3.000
 DT6  C4    C3   C2    110.82  3.000
 DT6  O3    C3   C2    108.10  3.000
 DT6  HN3   N3   C9    117.37  3.000
 DT6  HN3   N3   C4    116.44  3.000
 DT6  C9    N3   C4    124.24  3.000
 DT6  HO3   O3   C3    108.00  3.000
 DT6  H4    C4   C5    108.37  3.000
 DT6  H4    C4   N3    107.97  3.000
 DT6  C5    C4   N3    112.57  3.000
 DT6  H4    C4   C3    108.61  3.000
 DT6  C5    C4   C3    110.43  3.000
 DT6  N3    C4   C3    108.78  3.000
 DT6  H5    C5   C6    108.62  3.000
 DT6  H5    C5   O5    110.09  3.000
 DT6  C6    C5   O5    105.85  3.000
 DT6  H5    C5   C4    109.05  3.000
 DT6  C6    C5   C4    114.49  3.000
 DT6  O5    C5   C4    108.66  3.000
 DT6  C5    O5   C1    113.80  3.000
 DT6  H62   C6   H61   107.17  3.000
 DT6  H62   C6   O6    111.30  3.000
 DT6  H61   C6   O6    111.96  3.000
 DT6  H62   C6   C5    107.61  3.000
 DT6  H61   C6   C5    109.22  3.000
 DT6  O6    C6   C5    109.46  3.000
 DT6  HO6   O6   C6    107.95  3.000
 DT6  C8    C7   O7    121.45  3.000
 DT6  C8    C7   N2    115.09  3.000
 DT6  O7    C7   N2    123.46  3.000
 DT6  H83   C8   H82   108.35  3.000
 DT6  H83   C8   H81   107.22  3.000
 DT6  H82   C8   H81   108.56  3.000
 DT6  H83   C8   C7    109.11  3.000
 DT6  H82   C8   C7    114.00  3.000
 DT6  H81   C8   C7    109.39  3.000
 DT6  C10   C9   O8    122.26  3.000
 DT6  C10   C9   N3    114.40  3.000
 DT6  O8    C9   N3    123.35  3.000
 DT6  H10B  C10  H10A  107.72  3.000
 DT6  H10B  C10  H10   109.03  3.000
 DT6  H10A  C10  H10   107.88  3.000
 DT6  H10B  C10  C9    113.04  3.000
 DT6  H10A  C10  C9    108.69  3.000
 DT6  H10   C10  C9    110.31  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
 DT6  CONST_01  O7   C7   N2  C2     0.00   0.0  0
 DT6  CONST_02  C8   C7   N2  C2   180.00   0.0  0
 DT6  CONST_03  O8   C9   N3  C4     0.00   0.0  0
 DT6  CONST_04  C10  C9   N3  C4   180.00   0.0  0
 DT6  CONST_05  HN2  N2   C7  O7   180.00   0.0  0
 DT6  CONST_06  HN3  N3   C9  O8   180.00   0.0  0
 DT6  Var_01    H81  C8   C7  N2  -124.20  30.0  3
 DT6  Var_02    H10  C10  C9  N3   148.58  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
 DT6  chir_01  C1  O1  C2  O5  negativ
 DT6  chir_02  C2  N2  C3  C1  positiv
 DT6  chir_03  C3  O3  C2  C4  positiv
 DT6  chir_04  C4  N3  C5  C3  positiv
 DT6  chir_05  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
 DT6  plan-1  C2   0.020
 DT6  plan-1  N2   0.020
 DT6  plan-1  C7   0.020
 DT6  plan-1  O7   0.020
 DT6  plan-1  C8   0.020
 DT6  plan-1  HN2  0.020
 DT6  plan-2  N3   0.020
 DT6  plan-2  C4   0.020
 DT6  plan-2  O8   0.020
 DT6  plan-2  C9   0.020
 DT6  plan-2  C10  0.020
 DT6  plan-2  HN3  0.020

