# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 00:17:34 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]-methyl-phosphonamidic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[P](O)(=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
 MQG  MQG  '~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-2,4,5-tris(oxidanyl)oxan-3-yl]-methyl-phosphonamidic acid'  D-saccharide  31  16  .  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_MQG
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
 MQG  C2   C  CH1    0  -0.114   0.3591  -0.2569   0.1408
 MQG  C3   C  CH1    0   0.036  -0.3838   1.0063   0.5804
 MQG  C4   C  CH1    0  -0.002  -1.7565   1.1164  -0.0761
 MQG  C5   C  CH1    0  -0.019  -2.5409  -0.1781   0.1454
 MQG  C6   C  CH2    0  -0.160  -3.8850  -0.1584  -0.5492
 MQG  C8   C  CH3    0  -0.940   3.7062   1.3067   0.3551
 MQG  O1   O  OH1    0  -0.649   0.0268  -2.5750  -0.2417
 MQG  C1   C  CH1    0   0.302  -0.5732  -1.4627   0.3049
 MQG  O3   O  OH1    0  -0.657   0.4119   2.1246   0.2815
 MQG  O71  O  O      0  -0.828   4.0300  -1.2758   1.0676
 MQG  O72  O  OP    -1  -0.822   3.0021  -0.7453  -1.2834
 MQG  N2   N  NH1    0  -0.785   1.5799  -0.4604   0.8682
 MQG  O4   O  OH1    0  -0.676  -2.3999   2.2353   0.4993
 MQG  O5   O  O2     0  -0.501  -1.7930  -1.2531  -0.3741
 MQG  O6   O  OH1    0  -0.669  -4.5796  -1.3433  -0.2426
 MQG  H1   H  HCH1   0   0.237   0.5985  -0.1727  -0.9241
 MQG  H2   H  HCH1   0   0.191  -0.5519   0.9333   1.6705
 MQG  H3   H  HCH1   0   0.219  -1.6155   1.2575  -1.1578
 MQG  H4   H  HCH1   0   0.214  -2.7015  -0.3107   1.2291
 MQG  H5   H  HCH2   0   0.201  -4.4359   0.7269  -0.2108
 MQG  H6   H  HCH2   0   0.197  -3.7253  -0.0453  -1.6308
 MQG  H7   H  HCH3   0   0.221   4.7223   1.4117  -0.0308
 MQG  H8   H  HCH3   0   0.233   3.0595   1.9902  -0.1922
 MQG  H9   H  HCH3   0   0.221   3.7161   1.6202   1.4003
 MQG  H10  H  HOH1   0   0.457  -0.4215  -3.3634   0.0809
 MQG  H11  H  HCH1   0   0.167  -0.7889  -1.6047   1.3801
 MQG  H12  H  HOH1   0   0.444  -0.0725   2.9082   0.5620
 MQG  H14  H  HNH1   0   0.352   1.5146  -0.2641   1.8571
 MQG  H15  H  HOH1   0   0.461  -3.0186   2.6059  -0.1361
 MQG  H16  H  HOH1   0   0.456  -5.4405  -1.3002  -0.6681
 MQG  P7   P  P      0   1.214   3.1402  -0.4269   0.1872

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
 MQG  O6   C6   single  1.407  0.020  1.407
 MQG  C6   C5   single  1.513  0.020  1.513
 MQG  O4   C4   single  1.413  0.020  1.413
 MQG  C4   C5   single  1.530  0.020  1.530
 MQG  C4   C3   single  1.526  0.020  1.526
 MQG  C5   O5   single  1.409  0.020  1.409
 MQG  O3   C3   single  1.405  0.020  1.405
 MQG  O5   C1   single  1.412  0.020  1.412
 MQG  C3   C2   single  1.530  0.020  1.530
 MQG  C2   C1   single  1.533  0.020  1.533
 MQG  C2   N2   single  1.436  0.020  1.436
 MQG  C1   O1   single  1.377  0.020  1.377
 MQG  O71  P7   deloc   1.512  0.020  1.512
 MQG  O72  P7   deloc   1.511  0.020  1.511
 MQG  N2   P7   single  1.703  0.020  1.703
 MQG  P7   C8   single  1.831  0.020  1.831
 MQG  C2   H1   single  0.970  0.020  1.090
 MQG  C3   H2   single  0.970  0.020  1.090
 MQG  C4   H3   single  0.970  0.020  1.090
 MQG  C5   H4   single  0.970  0.020  1.090
 MQG  C6   H5   single  0.970  0.020  1.090
 MQG  C6   H6   single  0.970  0.020  1.090
 MQG  C8   H7   single  0.970  0.020  1.090
 MQG  C8   H8   single  0.970  0.020  1.090
 MQG  C8   H9   single  0.970  0.020  1.090
 MQG  O1   H10  single  0.850  0.020  0.980
 MQG  C1   H11  single  0.970  0.020  1.090
 MQG  O3   H12  single  0.850  0.020  0.980
 MQG  N2   H14  single  0.890  0.020  1.040
 MQG  O4   H15  single  0.850  0.020  0.980
 MQG  O6   H16  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
 MQG  H1   C2  N2   108.53  3.000
 MQG  H1   C2  C1   107.31  3.000
 MQG  N2   C2  C1   110.58  3.000
 MQG  H1   C2  C3   108.79  3.000
 MQG  N2   C2  C3   112.61  3.000
 MQG  C1   C2  C3   108.86  3.000
 MQG  H2   C3  O3   110.40  3.000
 MQG  H2   C3  C4   106.99  3.000
 MQG  O3   C3  C4   111.14  3.000
 MQG  H2   C3  C2   107.62  3.000
 MQG  O3   C3  C2   108.73  3.000
 MQG  C4   C3  C2   111.90  3.000
 MQG  H3   C4  O4   110.93  3.000
 MQG  H3   C4  C5   108.46  3.000
 MQG  O4   C4  C5   112.19  3.000
 MQG  H3   C4  C3   108.49  3.000
 MQG  C5   C4  C3   109.76  3.000
 MQG  O4   C4  C3   106.95  3.000
 MQG  H4   C5  O5   110.34  3.000
 MQG  H4   C5  C6   108.85  3.000
 MQG  O5   C5  C6   108.20  3.000
 MQG  H4   C5  C4   108.57  3.000
 MQG  O5   C5  C4   108.67  3.000
 MQG  C6   C5  C4   112.21  3.000
 MQG  H6   C6  H5   107.08  3.000
 MQG  H6   C6  O6   111.88  3.000
 MQG  H5   C6  O6   111.38  3.000
 MQG  H6   C6  C5   108.90  3.000
 MQG  H5   C6  C5   108.38  3.000
 MQG  O6   C6  C5   109.12  3.000
 MQG  H9   C8  H8   107.85  3.000
 MQG  H9   C8  H7   107.60  3.000
 MQG  H8   C8  H7   108.34  3.000
 MQG  H9   C8  P7   111.26  3.000
 MQG  H8   C8  P7   111.39  3.000
 MQG  H7   C8  P7   110.26  3.000
 MQG  H10  O1  C1   109.00  3.000
 MQG  H11  C1  O5   108.56  3.000
 MQG  H11  C1  O1   111.54  3.000
 MQG  O5   C1  O1   107.79  3.000
 MQG  H11  C1  C2   108.89  3.000
 MQG  O1   C1  C2   109.14  3.000
 MQG  O5   C1  C2   110.93  3.000
 MQG  H12  O3  C3   107.52  3.000
 MQG  H14  N2  P7   116.54  3.000
 MQG  H14  N2  C2   114.42  3.000
 MQG  P7   N2  C2   125.02  3.000
 MQG  H15  O4  C4   109.22  3.000
 MQG  C1   O5  C5   113.24  3.000
 MQG  H16  O6  C6   107.93  3.000
 MQG  N2   P7  O72  107.54  3.000
 MQG  N2   P7  O71  107.17  3.000
 MQG  O72  P7  O71  120.14  3.000
 MQG  N2   P7  C8   105.38  3.000
 MQG  O72  P7  C8   108.48  3.000
 MQG  O71  P7  C8   107.22  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
 MQG  Var_01  O71  P7  N2  C2   -154.36  30.0  3
 MQG  Var_02  H7   C8  P7  O71    64.19  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
 MQG  chir_01  C2  C3  C1  N2  positiv
 MQG  chir_02  C3  O3  C2  C4  positiv
 MQG  chir_03  C4  O4  C5  C3  positiv
 MQG  chir_04  C5  O5  C4  C6  negativ
 MQG  chir_05  C1  O1  O5  C2  positiv

