# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 15:39:01 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: N-(carboxycarbonyl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@H](NC(=O)C(O)=O)[C@H](O)[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
 4GP  4GP  N-(carboxycarbonyl)-beta-D-glucopyranosylamine  D-saccharide  29  17  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4GP
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
 4GP  C1   C  CH1    0   0.219  -0.1022  -0.2282   0.2179
 4GP  C2   C  CH1    0  -0.029   0.6468  -1.5085  -0.1596
 4GP  O2   O  OH1    0  -0.664   0.0976  -2.6332   0.4788
 4GP  C3   C  CH1    0  -0.005   2.0991  -1.3920   0.2792
 4GP  O3   O  OH1    0  -0.672   2.8792  -2.4698  -0.1808
 4GP  C4   C  CH1    0   0.036   2.7249  -0.1106  -0.2603
 4GP  O4   O  OH1    0  -0.672   4.0112   0.0909   0.2705
 4GP  C5   C  CH1    0  -0.014   1.8537   1.0856   0.1248
 4GP  O5   O  O2     0  -0.490   0.5412   0.8888  -0.3558
 4GP  C6   C  CH2    0  -0.156   2.3741   2.3814  -0.4607
 4GP  O6   O  OH1    0  -0.670   1.5781   3.4413   0.0126
 4GP  N1   N  NH1    0  -0.673  -1.4411  -0.2767  -0.2540
 4GP  C7   C  C      0   0.365  -2.5038   0.2423   0.4001
 4GP  C8   C  C      0   0.340  -3.8393   0.1076  -0.3957
 4GP  O7   O  O      0  -0.478  -2.4412   0.7545   1.5025
 4GP  O8   O  OC    -1  -0.571  -4.8445   0.5245   0.1875
 4GP  O9   O  O      0  -0.586  -3.7415  -0.4006  -1.5274
 4GP  H1   H  HCH1   0   0.223  -0.1213  -0.1314   1.3118
 4GP  H2   H  HCH1   0   0.224   0.6172  -1.6153  -1.2556
 4GP  HO2  H  HOH1   0   0.455  -0.7544  -2.8340   0.0789
 4GP  H3   H  HCH1   0   0.216   2.1205  -1.3376   1.3797
 4GP  HO3  H  HOH1   0   0.457   2.6174  -3.2636   0.2959
 4GP  H4   H  HCH1   0   0.212   2.7548  -0.1748  -1.3600
 4GP  HO4  H  HOH1   0   0.455   4.5633  -0.6537   0.0100
 4GP  H5   H  HCH1   0   0.221   1.8439   1.1714   1.2244
 4GP  H61  H  HCH2   0   0.196   2.3517   2.3118  -1.5571
 4GP  H62  H  HCH2   0   0.212   3.4221   2.4984  -0.1666
 4GP  HO6  H  HOH1   0   0.456   1.9465   4.2627  -0.3242
 4GP  HN1  H  HNH1   0   0.395  -1.6305  -0.6139  -1.1880

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
 4GP  C1  C2   single  1.531  0.020  1.531
 4GP  C1  O5   single  1.411  0.020  1.411
 4GP  C1  N1   single  1.420  0.020  1.420
 4GP  C1  H1   single  0.970  0.020  1.090
 4GP  C2  O2   single  1.405  0.020  1.405
 4GP  C2  C3   single  1.522  0.020  1.522
 4GP  C2  H2   single  0.970  0.020  1.090
 4GP  O2  HO2  single  0.850  0.020  0.980
 4GP  C3  O3   single  1.408  0.020  1.408
 4GP  C3  C4   single  1.525  0.020  1.525
 4GP  C3  H3   single  0.970  0.020  1.090
 4GP  O3  HO3  single  0.850  0.020  0.980
 4GP  C4  O4   single  1.406  0.020  1.406
 4GP  C4  C5   single  1.529  0.020  1.529
 4GP  C4  H4   single  0.970  0.020  1.090
 4GP  O4  HO4  single  0.850  0.020  0.980
 4GP  C5  O5   single  1.412  0.020  1.412
 4GP  C5  C6   single  1.514  0.020  1.514
 4GP  C5  H5   single  0.970  0.020  1.090
 4GP  C6  O6   single  1.408  0.020  1.408
 4GP  C6  H61  single  0.970  0.020  1.090
 4GP  C6  H62  single  0.970  0.020  1.090
 4GP  O6  HO6  single  0.850  0.020  0.980
 4GP  N1  C7   single  1.351  0.020  1.351
 4GP  N1  HN1  single  0.860  0.020  1.020
 4GP  C7  C8   single  1.560  0.020  1.560
 4GP  C7  O7   double  1.217  0.020  1.217
 4GP  C8  O8   deloc   1.235  0.020  1.235
 4GP  C8  O9   deloc   1.244  0.020  1.244

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
 4GP  H1   C1  N1   108.51  3.000
 4GP  H1   C1  O5   110.07  3.000
 4GP  N1   C1  O5   108.77  3.000
 4GP  H1   C1  C2   109.14  3.000
 4GP  N1   C1  C2   110.53  3.000
 4GP  O5   C1  C2   109.80  3.000
 4GP  H2   C2  C3   108.66  3.000
 4GP  H2   C2  O2   111.34  3.000
 4GP  C3   C2  O2   107.66  3.000
 4GP  H2   C2  C1   108.26  3.000
 4GP  C3   C2  C1   109.38  3.000
 4GP  O2   C2  C1   111.48  3.000
 4GP  HO2  O2  C2   108.93  3.000
 4GP  H3   C3  C4   107.70  3.000
 4GP  H3   C3  O3   110.69  3.000
 4GP  C4   C3  O3   107.48  3.000
 4GP  H3   C3  C2   108.08  3.000
 4GP  C4   C3  C2   110.73  3.000
 4GP  O3   C3  C2   112.09  3.000
 4GP  HO3  O3  C3   108.59  3.000
 4GP  H4   C4  C5   108.20  3.000
 4GP  H4   C4  O4   111.11  3.000
 4GP  C5   C4  O4   108.30  3.000
 4GP  H4   C4  C3   108.38  3.000
 4GP  C5   C4  C3   109.54  3.000
 4GP  O4   C4  C3   111.24  3.000
 4GP  HO4  O4  C4   108.16  3.000
 4GP  H5   C5  C6   108.79  3.000
 4GP  H5   C5  O5   110.00  3.000
 4GP  C6   C5  O5   107.89  3.000
 4GP  H5   C5  C4   108.48  3.000
 4GP  C6   C5  C4   112.10  3.000
 4GP  O5   C5  C4   109.56  3.000
 4GP  C5   O5  C1   113.33  3.000
 4GP  H62  C6  H61  107.11  3.000
 4GP  H62  C6  O6   111.75  3.000
 4GP  H61  C6  O6   111.82  3.000
 4GP  H62  C6  C5   108.46  3.000
 4GP  H61  C6  C5   108.95  3.000
 4GP  O6   C6  C5   108.67  3.000
 4GP  HO6  O6  C6   108.00  3.000
 4GP  HN1  N1  C7   115.34  3.000
 4GP  HN1  N1  C1   119.66  3.000
 4GP  C7   N1  C1   124.56  3.000
 4GP  O7   C7  C8   122.84  3.000
 4GP  O7   C7  N1   124.02  3.000
 4GP  C8   C7  N1   113.14  3.000
 4GP  O9   C8  O8   129.16  3.000
 4GP  O9   C8  C7   115.58  3.000
 4GP  O8   C8  C7   115.26  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
 4GP  CONST_01  C8   C7  N1  C1  180.00   0.0  0
 4GP  CONST_02  O7   C7  N1  C1    0.00   0.0  0
 4GP  CONST_03  HN1  N1  C7  C8    0.00   0.0  0
 4GP  Var_01    O8   C8  C7  N1  177.41  30.0  2

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
 4GP  chir_01  C1  C2  O5  N1  negativ
 4GP  chir_02  C2  O2  C1  C3  negativ
 4GP  chir_03  C3  O3  C2  C4  positiv
 4GP  chir_04  C4  O4  C5  C3  positiv
 4GP  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
 4GP  plan-1  C1   0.020
 4GP  plan-1  N1   0.020
 4GP  plan-1  C7   0.020
 4GP  plan-1  C8   0.020
 4GP  plan-1  O7   0.020
 4GP  plan-1  HN1  0.020
 4GP  plan-2  C7   0.020
 4GP  plan-2  C8   0.020
 4GP  plan-2  O8   0.020
 4GP  plan-2  O9   0.020

