# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 18:09:13 2022
#   Inital geometry file: a 70 line input string
#   Ligand name: 2-(acetylamino)-2-deoxy-beta-D-gulopyranose
#   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](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
 LXB  LXB  2-(acetylamino)-2-deoxy-beta-D-gulopyranose  D-saccharide  30  15  .  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_LXB
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
 LXB  O1   O  OH1   0  -0.646  43.3179  -58.6110  -29.6368
 LXB  C1   C  CH1   0   0.303  42.3508  -59.5144  -30.0118
 LXB  C2   C  CH1   0  -0.137  41.3489  -59.6711  -28.8639
 LXB  C3   C  CH1   0  -0.046  40.1567  -60.5434  -29.2895
 LXB  C4   C  CH1   0   0.019  39.5628  -60.0176  -30.6086
 LXB  C5   C  CH1   0  -0.034  40.6745  -59.8680  -31.6414
 LXB  C6   C  CH2   0  -0.181  40.2560  -59.3646  -33.0172
 LXB  C8   C  CH3   0  -0.778  43.0004  -60.2730  -25.5075
 LXB  N2   N  NH1   0  -0.632  41.9786  -60.2144  -27.6908
 LXB  O3   O  OH1   0  -0.657  40.4741  -61.9155  -29.3443
 LXB  O4   O  OH1   0  -0.657  38.9474  -58.7714  -30.4023
 LXB  O5   O  O2    0  -0.500  41.6921  -59.0179  -31.1554
 LXB  O6   O  OH1   0  -0.650  39.8238  -58.0320  -33.0710
 LXB  O7   O  O     0  -0.494  42.0918  -58.2964  -26.4916
 LXB  HO1  H  HOH1  0   0.462  44.0924  -58.7172  -30.1996
 LXB  H1   H  HCH1  0   0.182  42.7970  -60.4962  -30.2557
 LXB  H2   H  HCH1  0   0.270  40.9677  -58.6777  -28.6192
 LXB  H3   H  HCH1  0   0.259  39.3925  -60.4655  -28.5090
 LXB  H4   H  HCH1  0   0.232  38.8485  -60.7647  -30.9840
 LXB  H5   H  HCH1  0   0.219  41.0769  -60.8782  -31.8284
 LXB  H61  H  HCH2  0   0.209  41.0991  -59.5386  -33.6997
 LXB  H62  H  HCH2  0   0.226  39.4326  -59.9895  -33.3702
 LXB  H81  H  HCH3  0   0.247  43.1342  -61.3283  -25.7369
 LXB  H82  H  HCH3  0   0.263  43.9802  -59.8370  -25.3125
 LXB  H83  H  HCH3  0   0.263  42.4213  -60.1891  -24.5881
 LXB  HN2  H  HNH1  0   0.395  42.1836  -61.2013  -27.6941
 LXB  HO3  H  HOH1  0   0.450  41.0992  -62.1017  -30.0527
 LXB  HO4  H  HOH1  0   0.451  38.2482  -58.8874  -29.7508
 LXB  HO6  H  HOH1  0   0.443  40.5200  -57.4764  -32.7077
 LXB  C7   C  C     0   0.518  42.3181  -59.4920  -26.6045

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
 LXB  C1  O1   single  1.376  0.020  1.376
 LXB  O1  HO1  single  0.850  0.020  0.980
 LXB  O5  C1   single  1.410  0.020  1.410
 LXB  C1  C2   single  1.532  0.020  1.532
 LXB  C1  H1   single  0.970  0.020  1.090
 LXB  C3  C2   single  1.537  0.020  1.537
 LXB  C2  N2   single  1.438  0.020  1.438
 LXB  C2  H2   single  0.970  0.020  1.090
 LXB  C4  C3   single  1.539  0.020  1.539
 LXB  C3  O3   single  1.409  0.020  1.409
 LXB  C3  H3   single  0.970  0.020  1.090
 LXB  C5  C4   single  1.525  0.020  1.525
 LXB  O4  C4   single  1.405  0.020  1.405
 LXB  C4  H4   single  0.970  0.020  1.090
 LXB  C6  C5   single  1.524  0.020  1.524
 LXB  C5  O5   single  1.412  0.020  1.412
 LXB  C5  H5   single  0.970  0.020  1.090
 LXB  C6  O6   single  1.402  0.020  1.402
 LXB  C6  H61  single  0.970  0.020  1.090
 LXB  C6  H62  single  0.970  0.020  1.090
 LXB  N2  C7   single  1.348  0.020  1.348
 LXB  C7  O7   double  1.222  0.020  1.222
 LXB  C7  C8   single  1.510  0.020  1.510
 LXB  C8  H81  single  0.970  0.020  1.090
 LXB  C8  H82  single  0.970  0.020  1.090
 LXB  C8  H83  single  0.970  0.020  1.090
 LXB  N2  HN2  single  0.860  0.020  1.020
 LXB  O3  HO3  single  0.850  0.020  0.980
 LXB  O4  HO4  single  0.850  0.020  0.980
 LXB  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
 LXB  HO1  O1  C1   109.49  3.000
 LXB  H1   C1  O5   108.80  3.000
 LXB  H1   C1  C2   109.78  3.000
 LXB  O5   C1  C2   109.77  3.000
 LXB  H1   C1  O1   111.08  3.000
 LXB  C2   C1  O1   108.83  3.000
 LXB  O5   C1  O1   108.56  3.000
 LXB  H2   C2  N2   108.29  3.000
 LXB  H2   C2  C3   107.92  3.000
 LXB  N2   C2  C3   110.55  3.000
 LXB  H2   C2  C1   107.66  3.000
 LXB  N2   C2  C1   111.32  3.000
 LXB  C3   C2  C1   110.97  3.000
 LXB  H3   C3  O3   104.72  3.000
 LXB  H3   C3  C4   108.50  3.000
 LXB  O3   C3  C4   112.71  3.000
 LXB  H3   C3  C2   107.67  3.000
 LXB  O3   C3  C2   112.86  3.000
 LXB  C4   C3  C2   110.04  3.000
 LXB  H4   C4  O4   111.60  3.000
 LXB  H4   C4  C5   108.00  3.000
 LXB  O4   C4  C5   109.38  3.000
 LXB  H4   C4  C3   108.12  3.000
 LXB  O4   C4  C3   110.25  3.000
 LXB  C5   C4  C3   109.43  3.000
 LXB  H5   C5  O5   110.29  3.000
 LXB  H5   C5  C6   104.45  3.000
 LXB  O5   C5  C6   108.05  3.000
 LXB  H5   C5  C4   106.91  3.000
 LXB  O5   C5  C4   110.57  3.000
 LXB  C6   C5  C4   116.34  3.000
 LXB  H62  C6  H61  106.69  3.000
 LXB  H62  C6  O6   107.39  3.000
 LXB  H61  C6  O6   111.30  3.000
 LXB  H62  C6  C5   108.05  3.000
 LXB  H61  C6  C5   107.33  3.000
 LXB  O6   C6  C5   115.68  3.000
 LXB  H83  C8  H82  107.21  3.000
 LXB  H83  C8  H81  108.53  3.000
 LXB  H82  C8  H81  108.36  3.000
 LXB  H83  C8  C7   109.46  3.000
 LXB  H82  C8  C7   109.23  3.000
 LXB  H81  C8  C7   113.83  3.000
 LXB  HN2  N2  C7   118.43  3.000
 LXB  HN2  N2  C2   117.15  3.000
 LXB  C7   N2  C2   124.42  3.000
 LXB  HO3  O3  C3   111.28  3.000
 LXB  HO4  O4  C4   108.10  3.000
 LXB  C5   O5  C1   113.81  3.000
 LXB  HO6  O6  C6   108.14  3.000
 LXB  O7   C7  N2   123.51  3.000
 LXB  O7   C7  C8   121.51  3.000
 LXB  N2   C7  C8   114.97  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
 LXB  CONST_01  O7   C7  N2  C2    0.00   0.0  0
 LXB  CONST_02  C8   C7  N2  C2  180.00   0.0  0
 LXB  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 LXB  Var_01    H81  C8  C7  N2    0.14  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
 LXB  chir_01  C1  O1  O5  C2  positiv
 LXB  chir_02  C2  N2  C3  C1  positiv
 LXB  chir_03  C3  O3  C2  C4  negativ
 LXB  chir_04  C4  O4  C5  C3  negativ
 LXB  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
 LXB  plan-1  C2   0.020
 LXB  plan-1  C8   0.020
 LXB  plan-1  N2   0.020
 LXB  plan-1  O7   0.020
 LXB  plan-1  HN2  0.020
 LXB  plan-1  C7   0.020

