# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 05:59:56 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: N-(dimethoxyphosphoryl)-beta-D-glucopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](=O)(N[C@@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O)OC
#
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
 GL6  GL6  N-(dimethoxyphosphoryl)-beta-D-glucopyranosylamine  D-saccharide  36  18  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GL6
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
 GL6  P     P  P     0   1.465  -2.4578  -0.4081  -0.0990
 GL6  O11   O  O     0  -0.716  -3.6158  -1.0826  -0.7293
 GL6  O13   O  O2    0  -0.584  -2.7828   0.9428   0.6927
 GL6  O12   O  O2    0  -0.583  -1.7737  -1.1515   1.1374
 GL6  O2    O  OH1   0  -0.665  -0.2967   2.5593  -0.6154
 GL6  O3    O  OH1   0  -0.676   2.1383   2.6087   0.9962
 GL6  O4    O  OH1   0  -0.673   3.9172   0.4673   0.4776
 GL6  O5    O  O2    0  -0.482   0.7454  -0.8967  -0.5866
 GL6  N1    N  NH1   0  -0.827  -1.3057  -0.0657  -1.2473
 GL6  C1    C  CH1   0   0.212   0.0734   0.2523  -1.0527
 GL6  C15   C  CH3   0  -0.416  -1.4561  -2.5419   1.0407
 GL6  C16   C  CH3   0  -0.422  -3.4756   1.9862   0.0064
 GL6  C2    C  CH1   0  -0.015   0.3223   1.4131  -0.0891
 GL6  C3    C  CH1   0  -0.017   1.8311   1.6166   0.0408
 GL6  C4    C  CH1   0   0.035   2.5185   0.3274   0.4715
 GL6  C5    C  CH1   0  -0.011   2.1477  -0.7842  -0.5082
 GL6  C6    C  CH2   0  -0.151   2.6855  -2.1289  -0.0656
 GL6  HO3   H  HOH1  0   0.460   2.1330   3.4692   0.5675
 GL6  HO4   H  HOH1  0   0.452   4.1355   1.2137   1.0461
 GL6  HO6   H  HOH1  0   0.456   2.7477  -3.9284  -0.7682
 GL6  HN1   H  HNH1  0   0.411  -1.5255  -0.4290  -2.1629
 GL6  H1    H  HCH1  0   0.238   0.4672   0.5374  -2.0394
 GL6  H151  H  HCH3  0   0.247  -0.9814  -2.8198   1.9784
 GL6  H152  H  HCH3  0   0.233  -2.3568  -3.1414   0.9095
 GL6  H153  H  HCH3  0   0.239  -0.7610  -2.7390   0.2260
 GL6  H161  H  HCH3  0   0.234  -2.9828   2.2446  -0.9300
 GL6  H162  H  HCH3  0   0.236  -4.5092   1.7024  -0.1920
 GL6  H163  H  HCH3  0   0.248  -3.4664   2.8556   0.6586
 GL6  H2    H  HCH1  0   0.228  -0.0790   1.1566   0.9007
 GL6  H3    H  HCH1  0   0.221   2.2254   1.8963  -0.9485
 GL6  H4    H  HCH1  0   0.209   2.1448   0.0461   1.4700
 GL6  H5    H  HCH1  0   0.218   2.5667  -0.5331  -1.4975
 GL6  H61   H  HCH2  0   0.212   3.7704  -2.0448   0.0578
 GL6  H62   H  HCH2  0   0.195   2.2632  -2.3682   0.9201
 GL6  HO2   H  HOH1  0   0.459  -0.4455   3.1864   0.0977
 GL6  O6    O  OH1   0  -0.670   2.3436  -3.0962  -1.0289

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
 GL6  P    O11   double  1.481  0.020  1.481
 GL6  P    O13   single  1.599  0.020  1.599
 GL6  P    O12   single  1.597  0.020  1.597
 GL6  P    N1    single  1.662  0.020  1.662
 GL6  O13  C16   single  1.428  0.020  1.428
 GL6  O12  C15   single  1.430  0.020  1.430
 GL6  O2   C2    single  1.405  0.020  1.405
 GL6  O2   HO2   single  0.850  0.020  0.980
 GL6  O3   C3    single  1.411  0.020  1.411
 GL6  O3   HO3   single  0.850  0.020  0.980
 GL6  O4   C4    single  1.406  0.020  1.406
 GL6  O4   HO4   single  0.850  0.020  0.980
 GL6  O5   C1    single  1.410  0.020  1.410
 GL6  O5   C5    single  1.409  0.020  1.409
 GL6  O6   C6    single  1.407  0.020  1.407
 GL6  O6   HO6   single  0.850  0.020  0.980
 GL6  N1   C1    single  1.429  0.020  1.429
 GL6  N1   HN1   single  0.890  0.020  1.040
 GL6  C1   C2    single  1.529  0.020  1.529
 GL6  C1   H1    single  0.970  0.020  1.090
 GL6  C15  H151  single  0.970  0.020  1.090
 GL6  C15  H152  single  0.970  0.020  1.090
 GL6  C15  H153  single  0.970  0.020  1.090
 GL6  C16  H161  single  0.970  0.020  1.090
 GL6  C16  H162  single  0.970  0.020  1.090
 GL6  C16  H163  single  0.970  0.020  1.090
 GL6  C2   C3    single  1.528  0.020  1.528
 GL6  C2   H2    single  0.970  0.020  1.090
 GL6  C3   C4    single  1.523  0.020  1.523
 GL6  C3   H3    single  0.970  0.020  1.090
 GL6  C4   C5    single  1.527  0.020  1.527
 GL6  C4   H4    single  0.970  0.020  1.090
 GL6  C5   C6    single  1.514  0.020  1.514
 GL6  C5   H5    single  0.970  0.020  1.090
 GL6  C6   H61   single  0.970  0.020  1.090
 GL6  C6   H62   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
 GL6  N1    P    O12   109.50  3.000
 GL6  N1    P    O13   107.99  3.000
 GL6  O12   P    O13    95.57  3.000
 GL6  N1    P    O11   109.98  3.000
 GL6  O12   P    O11   116.90  3.000
 GL6  O13   P    O11   115.88  3.000
 GL6  C16   O13  P     118.55  3.000
 GL6  C15   O12  P     119.72  3.000
 GL6  HO2   O2   C2    108.82  3.000
 GL6  HO3   O3   C3    109.04  3.000
 GL6  HO4   O4   C4    107.77  3.000
 GL6  C5    O5   C1    115.31  3.000
 GL6  HN1   N1   C1    114.45  3.000
 GL6  HN1   N1   P     113.68  3.000
 GL6  C1    N1   P     128.38  3.000
 GL6  H1    C1   C2    108.08  3.000
 GL6  H1    C1   N1    106.33  3.000
 GL6  C2    C1   N1    114.33  3.000
 GL6  H1    C1   O5    109.70  3.000
 GL6  C2    C1   O5    109.43  3.000
 GL6  N1    C1   O5    108.88  3.000
 GL6  H153  C15  H152  109.74  3.000
 GL6  H153  C15  H151  108.69  3.000
 GL6  H152  C15  H151  108.92  3.000
 GL6  H153  C15  O12   111.62  3.000
 GL6  H152  C15  O12   111.07  3.000
 GL6  H151  C15  O12   106.70  3.000
 GL6  H163  C16  H162  109.00  3.000
 GL6  H163  C16  H161  108.80  3.000
 GL6  H162  C16  H161  109.52  3.000
 GL6  H163  C16  O13   106.98  3.000
 GL6  H162  C16  O13   110.93  3.000
 GL6  H161  C16  O13   111.53  3.000
 GL6  H2    C2   C3    108.38  3.000
 GL6  H2    C2   C1    109.34  3.000
 GL6  C3    C2   C1    108.39  3.000
 GL6  H2    C2   O2    111.53  3.000
 GL6  C3    C2   O2    110.99  3.000
 GL6  C1    C2   O2    108.15  3.000
 GL6  H3    C3   C4    107.91  3.000
 GL6  H3    C3   C2    108.12  3.000
 GL6  C4    C3   C2    110.91  3.000
 GL6  H3    C3   O3    110.59  3.000
 GL6  C4    C3   O3    107.78  3.000
 GL6  C2    C3   O3    111.48  3.000
 GL6  H4    C4   C5    108.24  3.000
 GL6  H4    C4   C3    108.60  3.000
 GL6  C5    C4   C3    108.97  3.000
 GL6  H4    C4   O4    111.02  3.000
 GL6  C5    C4   O4    108.47  3.000
 GL6  C3    C4   O4    111.47  3.000
 GL6  H5    C5   C6    109.22  3.000
 GL6  H5    C5   C4    108.50  3.000
 GL6  C6    C5   C4    111.87  3.000
 GL6  H5    C5   O5    110.26  3.000
 GL6  C6    C5   O5    107.39  3.000
 GL6  C4    C5   O5    109.60  3.000
 GL6  H62   C6   H61   107.24  3.000
 GL6  H62   C6   C5    108.60  3.000
 GL6  H61   C6   C5    108.46  3.000
 GL6  H62   C6   O6    111.78  3.000
 GL6  H61   C6   O6    111.76  3.000
 GL6  C5    C6   O6    108.90  3.000
 GL6  HO6   O6   C6    107.90  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
 GL6  Var_01  C1    N1   P    O11  -162.33  30.0  3
 GL6  Var_02  H161  C16  O13  P     -52.93  30.0  3
 GL6  Var_03  H151  C15  O12  P     178.55  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
 GL6  chir_01  C1  O5  N1  C2  negativ
 GL6  chir_02  C2  O2  C1  C3  negativ
 GL6  chir_03  C3  O3  C2  C4  positiv
 GL6  chir_04  C4  O4  C5  C3  positiv
 GL6  chir_05  C5  O5  C4  C6  negativ

