# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 17:04:19 2022
#   Inital geometry file: a 83 line input string
#   Ligand name: 2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](O)[C@H](NC(C)=O)[C@@H](O)[C@@H]1NC(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
 B6D  B6D  2,4-bis(acetylamino)-2,4,6-trideoxy-beta-D-glucopyranose  D-saccharide  35  17  .  2019-10-31  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_B6D
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
 B6D  C1   C  CH1   0   0.308  -19.7526  4.0202  12.7848
 B6D  N2   N  NH1   0  -0.630  -18.8567  2.1351  14.0656
 B6D  C3   C  CH1   0   0.047  -19.0253  1.9223  11.6387
 B6D  C4   C  CH1   0  -0.100  -19.8032  2.4302  10.4174
 B6D  C5   C  CH1   0   0.030  -19.8974  3.9639  10.4310
 B6D  C6   C  CH3   0  -0.682  -20.7326  4.5113   9.2940
 B6D  C7   C  C     0   0.517  -19.3648  1.5766  15.1807
 B6D  C8   C  CH3   0  -0.779  -18.3600  1.3012  16.2729
 B6D  C9   C  CH3   0  -0.770  -17.8168  1.4519   7.3146
 B6D  C2   C  CH1   0  -0.150  -19.6377  2.4987  12.9129
 B6D  O7   O  O     0  -0.495  -20.5473  1.2968  15.3152
 B6D  N4   N  NH1   0  -0.660  -19.2912  1.8791   9.1774
 B6D  C10  C  C     0   0.522  -18.0909  2.1481   8.6254
 B6D  O10  O  O     0  -0.490  -17.2674  2.8940   9.1359
 B6D  O5   O  O2    0  -0.492  -20.5119  4.3473  11.6484
 B6D  O3   O  OH1   0  -0.659  -19.0642  0.5229  11.7382
 B6D  H2   H  HCH1  0   0.268  -20.6438  2.0906  13.0432
 B6D  H1   H  HCH1  0   0.183  -18.7392  4.4480  12.6776
 B6D  H3   H  HCH1  0   0.218  -17.9888  2.2828  11.5632
 B6D  HN2  H  HNH1  0   0.399  -17.8698  2.3401  14.0389
 B6D  H5   H  HCH1  0   0.222  -18.8885  4.3927  10.3791
 B6D  H81  H  HCH3  0   0.247  -17.3479  1.6207  16.0322
 B6D  H83  H  HCH3  0   0.264  -18.3423  0.2321  16.4851
 B6D  H82  H  HCH3  0   0.263  -18.6730  1.8061  17.1865
 B6D  H4   H  HCH1  0   0.264  -20.8270  2.0512  10.4995
 B6D  HN4  H  HNH1  0   0.406  -19.9133  1.2750   8.6669
 B6D  H9   H  HCH3  0   0.266  -16.9438  0.8088   7.4256
 B6D  H9A  H  HCH3  0   0.265  -17.5760  2.1968   6.5566
 B6D  H9B  H  HCH3  0   0.250  -18.6460  0.8473   6.9532
 B6D  H62  H  HCH3  0   0.242  -20.8185  5.5954   9.3695
 B6D  H6A  H  HCH3  0   0.237  -20.2720  4.2847   8.3339
 B6D  H61  H  HCH3  0   0.228  -21.7365  4.0835   9.2981
 B6D  O1   O  OH1   0  -0.648  -20.3951  4.5095  13.8994
 B6D  HO3  H  HOH1  0   0.451  -18.5676  0.1517  11.0020
 B6D  HO1  H  HOH1  0   0.462  -20.2207  5.4531  13.9816

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
 B6D  C1   C2   single  1.531  0.020  1.531
 B6D  C1   O1   single  1.376  0.020  1.376
 B6D  N2   C7   single  1.347  0.020  1.347
 B6D  C3   O3   single  1.404  0.020  1.404
 B6D  C3   C2   single  1.527  0.020  1.527
 B6D  C4   C3   single  1.534  0.020  1.534
 B6D  C4   H4   single  0.970  0.020  1.090
 B6D  C5   C4   single  1.537  0.020  1.537
 B6D  C5   O5   single  1.417  0.020  1.417
 B6D  C6   C5   single  1.513  0.020  1.513
 B6D  C6   H61  single  0.970  0.020  1.090
 B6D  C7   O7   double  1.223  0.020  1.223
 B6D  C7   C8   single  1.509  0.020  1.509
 B6D  C8   H81  single  0.970  0.020  1.090
 B6D  C8   H82  single  0.970  0.020  1.090
 B6D  C9   H9A  single  0.970  0.020  1.090
 B6D  C9   C10  single  1.509  0.020  1.509
 B6D  C2   N2   single  1.439  0.020  1.439
 B6D  C2   H2   single  0.970  0.020  1.090
 B6D  N4   C4   single  1.450  0.020  1.450
 B6D  C10  N4   single  1.348  0.020  1.348
 B6D  C10  O10  double  1.223  0.020  1.223
 B6D  O5   C1   single  1.405  0.020  1.405
 B6D  O3   HO3  single  0.850  0.020  0.980
 B6D  H1   C1   single  0.970  0.020  1.090
 B6D  H3   C3   single  0.970  0.020  1.090
 B6D  HN2  N2   single  0.860  0.020  1.020
 B6D  H5   C5   single  0.970  0.020  1.090
 B6D  H83  C8   single  0.970  0.020  1.090
 B6D  HN4  N4   single  0.860  0.020  1.020
 B6D  H9   C9   single  0.970  0.020  1.090
 B6D  H9B  C9   single  0.970  0.020  1.090
 B6D  H62  C6   single  0.970  0.020  1.090
 B6D  H6A  C6   single  0.970  0.020  1.090
 B6D  O1   HO1  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
 B6D  O1   C1   H1   111.65  3.000
 B6D  H1   C1   O5   109.08  3.000
 B6D  O1   C1   O5   108.66  3.000
 B6D  H1   C1   C2   108.90  3.000
 B6D  O5   C1   C2   109.84  3.000
 B6D  O1   C1   C2   108.69  3.000
 B6D  HN2  N2   C2   117.30  3.000
 B6D  HN2  N2   C7   118.39  3.000
 B6D  C2   N2   C7   124.28  3.000
 B6D  H3   C3   O3   110.96  3.000
 B6D  H3   C3   C2   108.15  3.000
 B6D  O3   C3   C2   107.83  3.000
 B6D  H3   C3   C4   108.34  3.000
 B6D  C2   C3   C4   109.63  3.000
 B6D  O3   C3   C4   111.86  3.000
 B6D  H4   C4   N4   105.23  3.000
 B6D  N4   C4   C5   114.11  3.000
 B6D  H4   C4   C5   106.71  3.000
 B6D  N4   C4   C3   112.07  3.000
 B6D  C5   C4   C3   110.75  3.000
 B6D  H4   C4   C3   107.45  3.000
 B6D  H5   C5   O5   109.49  3.000
 B6D  H5   C5   C6   109.30  3.000
 B6D  O5   C5   C6   107.97  3.000
 B6D  H5   C5   C4   109.46  3.000
 B6D  C6   C5   C4   112.84  3.000
 B6D  O5   C5   C4   107.72  3.000
 B6D  H61  C6   H6A  108.11  3.000
 B6D  H6A  C6   H62  107.54  3.000
 B6D  H61  C6   H62  108.49  3.000
 B6D  H6A  C6   C5   110.72  3.000
 B6D  H62  C6   C5   110.56  3.000
 B6D  H61  C6   C5   111.29  3.000
 B6D  O7   C7   C8   121.50  3.000
 B6D  C8   C7   N2   115.06  3.000
 B6D  O7   C7   N2   123.43  3.000
 B6D  H82  C8   H83  107.21  3.000
 B6D  H83  C8   H81  108.41  3.000
 B6D  H82  C8   H81  108.46  3.000
 B6D  H83  C8   C7   109.30  3.000
 B6D  H82  C8   C7   109.32  3.000
 B6D  H81  C8   C7   113.92  3.000
 B6D  H9B  C9   H9A  108.49  3.000
 B6D  H9B  C9   H9   108.44  3.000
 B6D  H9A  C9   H9   107.29  3.000
 B6D  H9B  C9   C10  113.98  3.000
 B6D  H9   C9   C10  109.22  3.000
 B6D  H9A  C9   C10  109.20  3.000
 B6D  H2   C2   C3   109.12  3.000
 B6D  H2   C2   N2   108.04  3.000
 B6D  C3   C2   N2   110.82  3.000
 B6D  H2   C2   C1   108.17  3.000
 B6D  N2   C2   C1   111.02  3.000
 B6D  C3   C2   C1   109.60  3.000
 B6D  HN4  N4   C10  117.54  3.000
 B6D  HN4  N4   C4   116.34  3.000
 B6D  C10  N4   C4   126.05  3.000
 B6D  O10  C10  N4   123.39  3.000
 B6D  O10  C10  C9   121.44  3.000
 B6D  N4   C10  C9   115.16  3.000
 B6D  C5   O5   C1   113.43  3.000
 B6D  HO3  O3   C3   108.42  3.000
 B6D  HO1  O1   C1   109.44  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
 B6D  CONST_01  C9   C10  N4   C4  180.00   0.0  0
 B6D  CONST_02  O10  C10  N4   C4    0.00   0.0  0
 B6D  CONST_03  C2   N2   C7   C8  180.00   0.0  0
 B6D  CONST_04  O7   C7   N2   C2    0.00   0.0  0
 B6D  CONST_05  HN2  N2   C7   C8    0.00   0.0  0
 B6D  CONST_06  HN4  N4   C10  C9    0.00   0.0  0
 B6D  Var_01    H81  C8   C7   N2    1.87  30.0  3
 B6D  Var_02    H9A  C9   C10  N4  124.00  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
 B6D  chir_01  C1  C2  O1  O5  positiv
 B6D  chir_02  C3  O3  C4  C2  negativ
 B6D  chir_03  C4  N4  C5  C3  positiv
 B6D  chir_04  C5  O5  C4  C6  negativ
 B6D  chir_05  C2  N2  C3  C1  positiv

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
 B6D  plan-1  N2   0.020
 B6D  plan-1  C7   0.020
 B6D  plan-1  C8   0.020
 B6D  plan-1  C2   0.020
 B6D  plan-1  O7   0.020
 B6D  plan-1  HN2  0.020
 B6D  plan-2  C4   0.020
 B6D  plan-2  C9   0.020
 B6D  plan-2  N4   0.020
 B6D  plan-2  C10  0.020
 B6D  plan-2  O10  0.020
 B6D  plan-2  HN4  0.020

