# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 22:39:11 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: N-[ethoxy(oxo)acetyl]-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)C(=O)N[C@@H]1O[C@H](CO)[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
 7GP  7GP  N-[ethoxy(oxo)acetyl]-beta-D-glucopyranosylamine  D-saccharide  36  19  .  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_7GP
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
 7GP  C1    C  CH1   0   0.211  -0.5814  -0.2466  -0.2270
 7GP  C2    C  CH1   0  -0.030  -1.3813  -1.5129   0.0864
 7GP  O2    O  OH1   0  -0.663  -0.8549  -2.6277  -0.5860
 7GP  C3    C  CH1   0  -0.004  -2.8171  -1.3171  -0.3806
 7GP  O3    O  OH1   0  -0.671  -3.6463  -2.3844   0.0086
 7GP  C4    C  CH1   0   0.035  -3.4047  -0.0396   0.2079
 7GP  O4    O  OH1   0  -0.671  -4.6688   0.2406  -0.3392
 7GP  C5    C  CH1   0  -0.017  -2.4826   1.1413  -0.1015
 7GP  O5    O  O2    0  -0.487  -1.1817   0.8699   0.3803
 7GP  C6    C  CH2   0  -0.156  -2.9585   2.4208   0.5535
 7GP  O6    O  OH1   0  -0.670  -2.1139   3.4729   0.1531
 7GP  N1    N  NH1   0  -0.675   0.7507  -0.3572   0.2763
 7GP  C7    C  C     0   0.451   1.8372   0.0532  -0.3958
 7GP  O7    O  O     0  -0.436   1.8565   0.5159  -1.5151
 7GP  C8    C  C     0   0.505   3.1274  -0.1342   0.4194
 7GP  O8    O  O     0  -0.425   3.1279  -0.5279   1.5574
 7GP  C9    C  CH2   0  -0.190   5.4699   0.1010   0.3461
 7GP  O9    O  O2    0  -0.430   4.1753   0.1939  -0.2854
 7GP  C10   C  CH3   0  -0.689   6.5063   0.5214  -0.6648
 7GP  H1    H  HCH1  0   0.239  -0.5279  -0.1139  -1.3151
 7GP  H2    H  HCH1  0   0.233  -1.3812  -1.6628   1.1767
 7GP  HO2   H  HOH1  0   0.460  -0.0859  -2.9498  -0.1061
 7GP  H3    H  HCH1  0   0.218  -2.8090  -1.2082  -1.4774
 7GP  HO3   H  HOH1  0   0.457  -3.3909  -3.1679  -0.4886
 7GP  H4    H  HCH1  0   0.215  -3.4630  -0.1549   1.3021
 7GP  HO4   H  HOH1  0   0.456  -5.2623  -0.4836  -0.1154
 7GP  H5    H  HCH1  0   0.226  -2.4546   1.2855  -1.1941
 7GP  H61   H  HCH2  0   0.213  -3.9969   2.5958   0.2543
 7GP  H62   H  HCH2  0   0.198  -2.9534   2.2855   1.6440
 7GP  HO6   H  HOH1  0   0.457  -2.4298   4.2811   0.5667
 7GP  HN1   H  HNH1  0   0.417   0.8771  -0.6760   1.2276
 7GP  H91   H  HCH2  0   0.248   5.6355  -0.9254   0.6783
 7GP  H92   H  HCH2  0   0.248   5.4851   0.7514   1.2223
 7GP  H101  H  HCH3  0   0.241   6.3447   1.5436  -1.0058
 7GP  H102  H  HCH3  0   0.244   7.4901   0.4763  -0.1986
 7GP  H103  H  HCH3  0   0.240   6.5161  -0.1405  -1.5305

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
 7GP  C1   C2    single  1.530  0.020  1.530
 7GP  C1   O5    single  1.406  0.020  1.406
 7GP  C1   N1    single  1.428  0.020  1.428
 7GP  C1   H1    single  0.970  0.020  1.090
 7GP  C2   O2    single  1.404  0.020  1.404
 7GP  C2   C3    single  1.522  0.020  1.522
 7GP  C2   H2    single  0.970  0.020  1.090
 7GP  O2   HO2   single  0.850  0.020  0.980
 7GP  C3   O3    single  1.406  0.020  1.406
 7GP  C3   C4    single  1.524  0.020  1.524
 7GP  C3   H3    single  0.970  0.020  1.090
 7GP  O3   HO3   single  0.850  0.020  0.980
 7GP  C4   O4    single  1.406  0.020  1.406
 7GP  C4   C5    single  1.530  0.020  1.530
 7GP  C4   H4    single  0.970  0.020  1.090
 7GP  O4   HO4   single  0.850  0.020  0.980
 7GP  C5   O5    single  1.414  0.020  1.414
 7GP  C5   C6    single  1.514  0.020  1.514
 7GP  C5   H5    single  0.970  0.020  1.090
 7GP  C6   O6    single  1.407  0.020  1.407
 7GP  C6   H61   single  0.970  0.020  1.090
 7GP  C6   H62   single  0.970  0.020  1.090
 7GP  O6   HO6   single  0.850  0.020  0.980
 7GP  N1   C7    single  1.342  0.020  1.342
 7GP  N1   HN1   single  0.860  0.020  1.020
 7GP  C7   O7    double  1.211  0.020  1.211
 7GP  C7   C8    single  1.538  0.020  1.538
 7GP  C8   O8    double  1.204  0.020  1.204
 7GP  C8   O9    single  1.305  0.020  1.305
 7GP  C9   O9    single  1.443  0.020  1.443
 7GP  C9   C10   single  1.508  0.020  1.508
 7GP  C9   H91   single  0.970  0.020  1.090
 7GP  C9   H92   single  0.970  0.020  1.090
 7GP  C10  H101  single  0.970  0.020  1.090
 7GP  C10  H102  single  0.970  0.020  1.090
 7GP  C10  H103  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
 7GP  H1    C1   N1    108.26  3.000
 7GP  H1    C1   O5    110.68  3.000
 7GP  N1    C1   O5    107.91  3.000
 7GP  H1    C1   C2    109.18  3.000
 7GP  N1    C1   C2    110.56  3.000
 7GP  O5    C1   C2    110.22  3.000
 7GP  H2    C2   C3    108.76  3.000
 7GP  H2    C2   O2    111.48  3.000
 7GP  C3    C2   O2    107.98  3.000
 7GP  H2    C2   C1    108.40  3.000
 7GP  C3    C2   C1    108.88  3.000
 7GP  O2    C2   C1    111.28  3.000
 7GP  HO2   O2   C2    109.06  3.000
 7GP  H3    C3   C4    107.71  3.000
 7GP  H3    C3   O3    110.77  3.000
 7GP  C4    C3   O3    107.57  3.000
 7GP  H3    C3   C2    108.12  3.000
 7GP  C4    C3   C2    110.67  3.000
 7GP  O3    C3   C2    111.93  3.000
 7GP  HO3   O3   C3    108.56  3.000
 7GP  H4    C4   C5    108.27  3.000
 7GP  H4    C4   O4    111.09  3.000
 7GP  C5    C4   O4    108.02  3.000
 7GP  H4    C4   C3    108.43  3.000
 7GP  C5    C4   C3    109.66  3.000
 7GP  O4    C4   C3    111.32  3.000
 7GP  HO4   O4   C4    108.30  3.000
 7GP  H5    C5   C6    109.04  3.000
 7GP  H5    C5   O5    109.85  3.000
 7GP  C6    C5   O5    107.70  3.000
 7GP  H5    C5   C4    108.46  3.000
 7GP  C6    C5   C4    112.04  3.000
 7GP  O5    C5   C4    109.73  3.000
 7GP  C5    O5   C1    113.47  3.000
 7GP  H62   C6   H61   107.18  3.000
 7GP  H62   C6   O6    111.81  3.000
 7GP  H61   C6   O6    111.83  3.000
 7GP  H62   C6   C5    108.90  3.000
 7GP  H61   C6   C5    108.36  3.000
 7GP  O6    C6   C5    108.66  3.000
 7GP  HO6   O6   C6    108.00  3.000
 7GP  HN1   N1   C7    117.80  3.000
 7GP  HN1   N1   C1    118.20  3.000
 7GP  C7    N1   C1    123.71  3.000
 7GP  C8    C7   O7    121.54  3.000
 7GP  C8    C7   N1    112.12  3.000
 7GP  O7    C7   N1    126.34  3.000
 7GP  O9    C8   O8    126.32  3.000
 7GP  O9    C8   C7    110.91  3.000
 7GP  O8    C8   C7    122.77  3.000
 7GP  H92   C9   H91   108.29  3.000
 7GP  H92   C9   C10   111.27  3.000
 7GP  H91   C9   C10   111.22  3.000
 7GP  H92   C9   O9    108.99  3.000
 7GP  H91   C9   O9    109.25  3.000
 7GP  C10   C9   O9    107.78  3.000
 7GP  C9    O9   C8    117.89  3.000
 7GP  H103  C10  H102  107.86  3.000
 7GP  H103  C10  H101  108.81  3.000
 7GP  H102  C10  H101  107.86  3.000
 7GP  H103  C10  C9    111.68  3.000
 7GP  H102  C10  C9    108.80  3.000
 7GP  H101  C10  C9    111.68  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
 7GP  CONST_01  O7    C7   N1  C1    0.00   0.0  0
 7GP  CONST_02  C8    C7   N1  C1  180.00   0.0  0
 7GP  CONST_03  HN1   N1   C7  O7  180.00   0.0  0
 7GP  Var_01    O8    C8   C7  N1   -4.28  30.0  2
 7GP  Var_02    C10   C9   O9  C8  179.69  30.0  1
 7GP  Var_03    H101  C10  C9  O9   59.95  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
 7GP  chir_01  C1  C2  O5  N1  negativ
 7GP  chir_02  C2  O2  C1  C3  negativ
 7GP  chir_03  C3  O3  C2  C4  positiv
 7GP  chir_04  C4  O4  C5  C3  positiv
 7GP  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
 7GP  plan-1  C1   0.020
 7GP  plan-1  N1   0.020
 7GP  plan-1  C7   0.020
 7GP  plan-1  O7   0.020
 7GP  plan-1  C8   0.020
 7GP  plan-1  HN1  0.020
 7GP  plan-2  C7   0.020
 7GP  plan-2  C8   0.020
 7GP  plan-2  O8   0.020
 7GP  plan-2  O9   0.020

