# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 06:17:00 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-(acetylamino)-1,5-anhydro-2-deoxy-D-glucitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@H]1CO[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
 5AX  5AX  2-(acetylamino)-1,5-anhydro-2-deoxy-D-glucitol  ligand  29  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5AX
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
 5AX  C4   C  CH1   0  -0.008   1.3743   0.9393   0.3083
 5AX  C5   C  CH1   0  -0.009   2.0230  -0.3369  -0.2422
 5AX  C6   C  CH2   0  -0.162   3.4243  -0.5374   0.2917
 5AX  C7   C  C     0   0.523  -3.2951  -0.1221   0.2335
 5AX  C8   C  CH3   0  -0.781  -4.5467  -0.0053  -0.6001
 5AX  C1   C  CH2   0  -0.171  -0.0517  -1.4345  -0.3914
 5AX  C2   C  CH1   0  -0.138  -0.8319  -0.2230   0.1165
 5AX  C3   C  CH1   0   0.054  -0.0611   1.0531  -0.1971
 5AX  N2   N  NH1   0  -0.629  -2.1488  -0.1994  -0.4693
 5AX  O3   O  OH1   0  -0.664  -0.7372   2.1363   0.3841
 5AX  O4   O  OH1   0  -0.674   2.0550   2.1009  -0.1163
 5AX  O5   O  O2    0  -0.484   1.2514  -1.4584   0.1323
 5AX  O6   O  OH1   0  -0.670   3.9963  -1.6622  -0.3319
 5AX  O7   O  O     0  -0.503  -3.3370  -0.1370   1.4556
 5AX  H4   H  HCH1  0   0.225   1.3523   0.8745   1.4058
 5AX  H5   H  HCH1  0   0.215   2.0679  -0.2577  -1.3418
 5AX  H61  H  HCH2  0   0.204   4.0054   0.3697   0.0907
 5AX  H62  H  HCH2  0   0.198   3.3777  -0.6558   1.3835
 5AX  H81  H  HCH3  0   0.264  -5.2999  -0.6998  -0.2309
 5AX  H82  H  HCH3  0   0.269  -4.9523   1.0018  -0.4933
 5AX  H83  H  HCH3  0   0.249  -4.3854  -0.1943  -1.6597
 5AX  H11  H  HCH2  0   0.254  -0.5475  -2.3524  -0.0730
 5AX  H12  H  HCH2  0   0.205  -0.0329  -1.4311  -1.4917
 5AX  H2   H  HCH1  0   0.266  -0.9525  -0.3096   1.1982
 5AX  H3   H  HCH1  0   0.202  -0.0159   1.1641  -1.2947
 5AX  HN2  H  HNH1  0   0.398  -2.2055  -0.1435  -1.4743
 5AX  HO3  H  HOH1  0   0.449  -0.2308   2.9337   0.1955
 5AX  HO4  H  HOH1  0   0.463   2.7205   2.3328   0.5369
 5AX  HO6  H  HOH1  0   0.456   4.9107  -1.7289  -0.0431

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
 5AX  C4  C3   single  1.526  0.020  1.526
 5AX  C4  O4   single  1.412  0.020  1.412
 5AX  C4  C5   single  1.534  0.020  1.534
 5AX  C4  H4   single  0.970  0.020  1.090
 5AX  C5  O5   single  1.412  0.020  1.412
 5AX  C5  C6   single  1.513  0.020  1.513
 5AX  C5  H5   single  0.970  0.020  1.090
 5AX  C6  O6   single  1.408  0.020  1.408
 5AX  C6  H61  single  0.970  0.020  1.090
 5AX  C6  H62  single  0.970  0.020  1.090
 5AX  C7  C8   single  1.508  0.020  1.508
 5AX  C7  O7   double  1.223  0.020  1.223
 5AX  C7  N2   single  1.347  0.020  1.347
 5AX  C8  H81  single  0.970  0.020  1.090
 5AX  C8  H82  single  0.970  0.020  1.090
 5AX  C8  H83  single  0.970  0.020  1.090
 5AX  C1  C2   single  1.528  0.020  1.528
 5AX  C1  O5   single  1.405  0.020  1.405
 5AX  C1  H11  single  0.970  0.020  1.090
 5AX  C1  H12  single  0.970  0.020  1.090
 5AX  C2  C3   single  1.523  0.020  1.523
 5AX  C2  N2   single  1.441  0.020  1.441
 5AX  C2  H2   single  0.970  0.020  1.090
 5AX  C3  O3   single  1.403  0.020  1.403
 5AX  C3  H3   single  0.970  0.020  1.090
 5AX  N2  HN2  single  0.860  0.020  1.020
 5AX  O3  HO3  single  0.850  0.020  0.980
 5AX  O4  HO4  single  0.850  0.020  0.980
 5AX  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
 5AX  H4   C4  O4   110.99  3.000
 5AX  H4   C4  C3   108.43  3.000
 5AX  O4   C4  C3   107.01  3.000
 5AX  H4   C4  C5   108.52  3.000
 5AX  O4   C4  C5   111.89  3.000
 5AX  C3   C4  C5   109.94  3.000
 5AX  H5   C5  O5   110.10  3.000
 5AX  H5   C5  C6   108.88  3.000
 5AX  O5   C5  C6   107.90  3.000
 5AX  H5   C5  C4   108.37  3.000
 5AX  C6   C5  C4   112.04  3.000
 5AX  O5   C5  C4   109.54  3.000
 5AX  H62  C6  H61  107.08  3.000
 5AX  H62  C6  O6   111.79  3.000
 5AX  H61  C6  O6   111.39  3.000
 5AX  H62  C6  C5   109.00  3.000
 5AX  H61  C6  C5   108.47  3.000
 5AX  O6   C6  C5   109.02  3.000
 5AX  O7   C7  N2   123.36  3.000
 5AX  N2   C7  C8   114.98  3.000
 5AX  O7   C7  C8   121.66  3.000
 5AX  H83  C8  H82  108.10  3.000
 5AX  H83  C8  H81  108.77  3.000
 5AX  H82  C8  H81  107.36  3.000
 5AX  H83  C8  C7   113.68  3.000
 5AX  H82  C8  C7   109.02  3.000
 5AX  H81  C8  C7   109.70  3.000
 5AX  H12  C1  H11  107.59  3.000
 5AX  H12  C1  O5   110.91  3.000
 5AX  H11  C1  O5   107.37  3.000
 5AX  H12  C1  C2   109.79  3.000
 5AX  H11  C1  C2   109.77  3.000
 5AX  O5   C1  C2   111.30  3.000
 5AX  H2   C2  N2   107.64  3.000
 5AX  H2   C2  C3   109.04  3.000
 5AX  N2   C2  C3   111.40  3.000
 5AX  H2   C2  C1   108.83  3.000
 5AX  N2   C2  C1   110.15  3.000
 5AX  C3   C2  C1   109.72  3.000
 5AX  H3   C3  O3   110.73  3.000
 5AX  H3   C3  C2   108.03  3.000
 5AX  O3   C3  C2   108.52  3.000
 5AX  H3   C3  C4   107.35  3.000
 5AX  O3   C3  C4   111.94  3.000
 5AX  C2   C3  C4   110.20  3.000
 5AX  HN2  N2  C2   117.22  3.000
 5AX  HN2  N2  C7   117.98  3.000
 5AX  C2   N2  C7   124.50  3.000
 5AX  HO3  O3  C3   107.74  3.000
 5AX  HO4  O4  C4   109.15  3.000
 5AX  C1   O5  C5   113.24  3.000
 5AX  HO6  O6  C6   107.99  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
 5AX  CONST_01  C2   N2  C7  C8  180.00   0.0  0
 5AX  CONST_02  O7   C7  N2  C2    0.00   0.0  0
 5AX  CONST_03  HN2  N2  C7  C8    0.00   0.0  0
 5AX  Var_01    C2   C1  O5  C5  -61.70  30.0  1
 5AX  Var_02    H81  C8  C7  N2  133.43  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
 5AX  chir_01  C4  C3  O4  C5  positiv
 5AX  chir_02  C5  O5  C4  C6  negativ
 5AX  chir_03  C2  N2  C3  C1  positiv
 5AX  chir_04  C3  O3  C2  C4  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
 5AX  plan-1  C7   0.020
 5AX  plan-1  C8   0.020
 5AX  plan-1  C2   0.020
 5AX  plan-1  N2   0.020
 5AX  plan-1  O7   0.020
 5AX  plan-1  HN2  0.020

