# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 23:58:42 2021
#   Inital geometry file: a 116 line input string
#   Ligand name: {[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](CO)N(C[P](O)(O)=O)[C@@H]2CO)[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
 9KJ  9KJ  '{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid'  D-saccharide  53  27  .  2023-02-15  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9KJ
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
 9KJ  C20  C  CH2   0  -0.115  140.7858  146.4506  -342.9169
 9KJ  C2   C  CH1   0  -0.026  137.8243  148.1780  -346.9283
 9KJ  C3   C  CH1   0   0.014  136.3868  147.7718  -346.6149
 9KJ  C4   C  CH1   0   0.032  136.3434  146.2773  -346.3392
 9KJ  O4   O  OH1   0  -0.671  135.0327  145.9304  -345.9632
 9KJ  C5   C  CH1   0  -0.028  137.3390  145.9453  -345.2202
 9KJ  O5   O  O2    0  -0.502  138.6474  146.3645  -345.5874
 9KJ  C1   C  CH1   0   0.244  138.7821  147.7382  -345.8190
 9KJ  O1   O  O2    0  -0.496  138.5351  148.5026  -344.6849
 9KJ  C07  C  CH1   0   0.047  139.5473  148.5046  -343.7071
 9KJ  C08  C  CH1   0   0.027  139.3839  149.7100  -342.7944
 9KJ  O09  O  OH1   0  -0.665  140.0160  150.8349  -343.3430
 9KJ  C10  C  CH1   0  -0.153  139.9832  149.1967  -341.4810
 9KJ  C11  C  CH2   0  -0.179  139.7171  150.1032  -340.3031
 9KJ  O12  O  OH1   0  -0.665  140.3178  149.5584  -339.1523
 9KJ  N13  N  NT    0  -0.432  139.4733  147.8279  -341.3692
 9KJ  C14  C  CH2   0  -0.595  138.2036  147.6771  -340.6841
 9KJ  P15  P  P     0   1.354  137.7673  145.9220  -340.4420
 9KJ  O16  O  OH1   0  -0.744  136.9484  145.9681  -339.0592
 9KJ  O17  O  OH1   0  -0.784  139.1238  145.2066  -340.0065
 9KJ  O18  O  O     0  -0.710  137.0337  145.2858  -341.5698
 9KJ  C19  C  CH1   0  -0.214  139.5361  147.2950  -342.7375
 9KJ  O21  O  OH1   0  -0.681  140.6669  145.2691  -342.1396
 9KJ  O3   O  OH1   0  -0.670  135.5378  148.0514  -347.7001
 9KJ  H1A  H  HCH2  0   0.219  140.9014  146.1913  -343.9733
 9KJ  H2A  H  HCH2  0   0.218  141.6680  147.0276  -342.6165
 9KJ  H2   H  HCH1  0   0.232  138.1311  147.6386  -347.8354
 9KJ  H3   H  HCH1  0   0.211  136.0534  148.3070  -345.7115
 9KJ  H4   H  HCH1  0   0.222  136.6454  145.7520  -347.2554
 9KJ  HO4  H  HOH1  0   0.456  134.9075  144.9900  -346.1194
 9KJ  HO6  H  HOH1  0   0.459  137.6571  142.7900  -345.7882
 9KJ  H5   H  HCH1  0   0.229  137.0098  146.4594  -344.3072
 9KJ  H1   H  HCH1  0   0.234  139.8224  147.8714  -346.1489
 9KJ  H12  H  HCH1  0   0.233  140.5318  148.5735  -344.1979
 9KJ  H13  H  HCH1  0   0.222  138.3095  149.8917  -342.6456
 9KJ  H14  H  HOH1  0   0.457  139.6481  151.6275  -342.9428
 9KJ  H15  H  HCH1  0   0.248  141.0732  149.1344  -341.6125
 9KJ  H16  H  HCH2  0   0.219  140.1334  151.0899  -340.5453
 9KJ  H17  H  HCH2  0   0.207  138.6366  150.2455  -340.1716
 9KJ  H18  H  HOH1  0   0.458  140.1251  150.1399  -338.4111
 9KJ  H20  H  HCH2  0   0.290  138.2981  148.0989  -339.6822
 9KJ  H21  H  HCH2  0   0.250  137.3428  148.1661  -341.1628
 9KJ  H22  H  HOH1  0   0.492  136.2029  145.3540  -339.0375
 9KJ  H23  H  HOH1  0   0.492  139.8015  145.2399  -340.7348
 9KJ  H24  H  HCH1  0   0.290  138.6653  146.6692  -342.9370
 9KJ  H25  H  HOH1  0   0.479  141.5243  144.8349  -342.0834
 9KJ  HO3  H  HOH1  0   0.448  135.6340  148.9851  -347.9163
 9KJ  O2   O  OH1   0  -0.666  137.8483  149.5667  -347.1375
 9KJ  C6   C  CH2   0  -0.199  137.4066  144.4761  -344.8700
 9KJ  H61  H  HCH2  0   0.205  136.4517  144.1912  -344.4132
 9KJ  O6   O  OH1   0  -0.673  137.6856  143.7208  -346.0255
 9KJ  H62  H  HCH2  0   0.221  138.1704  144.3411  -344.0937
 9KJ  HO2  H  HOH1  0   0.460  138.6151  149.7871  -347.6743

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
 9KJ  O3   C3   single  1.406  0.020  1.406
 9KJ  O4   C4   single  1.407  0.020  1.407
 9KJ  O6   C6   single  1.408  0.020  1.408
 9KJ  C4   C3   single  1.520  0.020  1.520
 9KJ  C4   C5   single  1.534  0.020  1.534
 9KJ  C6   C5   single  1.512  0.020  1.512
 9KJ  C3   C2   single  1.526  0.020  1.526
 9KJ  C2   C1   single  1.530  0.020  1.530
 9KJ  C2   O2   single  1.405  0.020  1.405
 9KJ  C5   O5   single  1.422  0.020  1.422
 9KJ  O5   C1   single  1.400  0.020  1.400
 9KJ  C1   O1   single  1.390  0.020  1.390
 9KJ  O1   C07  single  1.407  0.020  1.407
 9KJ  C07  C08  single  1.521  0.020  1.521
 9KJ  C07  C19  single  1.550  0.020  1.550
 9KJ  O09  C08  single  1.402  0.020  1.402
 9KJ  C20  C19  single  1.519  0.020  1.519
 9KJ  C20  O21  single  1.419  0.020  1.419
 9KJ  C08  C10  single  1.532  0.020  1.532
 9KJ  C19  N13  single  1.470  0.020  1.470
 9KJ  C10  N13  single  1.465  0.020  1.465
 9KJ  C10  C11  single  1.510  0.020  1.510
 9KJ  N13  C14  single  1.451  0.020  1.451
 9KJ  C14  P15  single  1.825  0.020  1.825
 9KJ  C11  O12  single  1.408  0.020  1.408
 9KJ  P15  O18  double  1.488  0.020  1.488
 9KJ  P15  O16  single  1.608  0.020  1.608
 9KJ  P15  O17  single  1.594  0.020  1.594
 9KJ  C20  H1A  single  0.970  0.020  1.090
 9KJ  C20  H2A  single  0.970  0.020  1.090
 9KJ  C2   H2   single  0.970  0.020  1.090
 9KJ  C3   H3   single  0.970  0.020  1.090
 9KJ  C4   H4   single  0.970  0.020  1.090
 9KJ  O4   HO4  single  0.850  0.020  0.980
 9KJ  O6   HO6  single  0.850  0.020  0.980
 9KJ  C6   H61  single  0.970  0.020  1.090
 9KJ  C6   H62  single  0.970  0.020  1.090
 9KJ  C5   H5   single  0.970  0.020  1.090
 9KJ  C1   H1   single  0.970  0.020  1.090
 9KJ  C07  H12  single  0.970  0.020  1.090
 9KJ  C08  H13  single  0.970  0.020  1.090
 9KJ  O09  H14  single  0.850  0.020  0.980
 9KJ  C10  H15  single  0.970  0.020  1.090
 9KJ  C11  H16  single  0.970  0.020  1.090
 9KJ  C11  H17  single  0.970  0.020  1.090
 9KJ  O12  H18  single  0.850  0.020  0.980
 9KJ  C14  H20  single  0.970  0.020  1.090
 9KJ  C14  H21  single  0.970  0.020  1.090
 9KJ  O16  H22  single  0.850  0.020  0.980
 9KJ  O17  H23  single  0.850  0.020  0.980
 9KJ  C19  H24  single  0.970  0.020  1.090
 9KJ  O21  H25  single  0.850  0.020  0.980
 9KJ  O2   HO2  single  0.850  0.020  0.980
 9KJ  O3   HO3  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
 9KJ  H2A  C20  H1A  107.72  3.000
 9KJ  H2A  C20  O21  110.83  3.000
 9KJ  H1A  C20  O21  109.90  3.000
 9KJ  H2A  C20  C19  109.71  3.000
 9KJ  H1A  C20  C19  109.44  3.000
 9KJ  O21  C20  C19  109.22  3.000
 9KJ  H2   C2   O2   110.95  3.000
 9KJ  H2   C2   C1   106.41  3.000
 9KJ  O2   C2   C1   112.42  3.000
 9KJ  H2   C2   C3   107.57  3.000
 9KJ  O2   C2   C3   108.04  3.000
 9KJ  C1   C2   C3   111.36  3.000
 9KJ  H3   C3   O3   110.71  3.000
 9KJ  H3   C3   C4   108.67  3.000
 9KJ  O3   C3   C4   108.56  3.000
 9KJ  H3   C3   C2   108.92  3.000
 9KJ  C4   C3   C2   109.00  3.000
 9KJ  O3   C3   C2   110.94  3.000
 9KJ  H4   C4   C5   109.05  3.000
 9KJ  H4   C4   O4   111.16  3.000
 9KJ  C5   C4   O4   110.87  3.000
 9KJ  H4   C4   C3   108.12  3.000
 9KJ  C5   C4   C3   109.06  3.000
 9KJ  O4   C4   C3   108.51  3.000
 9KJ  HO4  O4   C4   108.61  3.000
 9KJ  H5   C5   O5   110.63  3.000
 9KJ  H5   C5   C6   106.01  3.000
 9KJ  O5   C5   C6   107.76  3.000
 9KJ  H5   C5   C4   108.09  3.000
 9KJ  O5   C5   C4   110.18  3.000
 9KJ  C6   C5   C4   114.10  3.000
 9KJ  C1   O5   C5   114.87  3.000
 9KJ  H1   C1   O1   110.26  3.000
 9KJ  H1   C1   O5   105.05  3.000
 9KJ  O1   C1   O5   112.81  3.000
 9KJ  H1   C1   C2   109.87  3.000
 9KJ  O1   C1   C2   108.80  3.000
 9KJ  O5   C1   C2   109.99  3.000
 9KJ  C07  O1   C1   116.10  3.000
 9KJ  H12  C07  C19  109.49  3.000
 9KJ  H12  C07  C08  108.28  3.000
 9KJ  C19  C07  C08  104.03  3.000
 9KJ  H12  C07  O1   109.45  3.000
 9KJ  C19  C07  O1   115.36  3.000
 9KJ  C08  C07  O1   109.93  3.000
 9KJ  H13  C08  C10  108.75  3.000
 9KJ  H13  C08  O09  111.15  3.000
 9KJ  C10  C08  O09  115.33  3.000
 9KJ  H13  C08  C07  108.49  3.000
 9KJ  C10  C08  C07  101.94  3.000
 9KJ  O09  C08  C07  110.65  3.000
 9KJ  H14  O09  C08  109.03  3.000
 9KJ  H15  C10  N13  107.53  3.000
 9KJ  H15  C10  C11  107.57  3.000
 9KJ  N13  C10  C11  116.11  3.000
 9KJ  H15  C10  C08  107.71  3.000
 9KJ  C11  C10  C08  113.50  3.000
 9KJ  N13  C10  C08  104.03  3.000
 9KJ  H17  C11  H16  106.45  3.000
 9KJ  H17  C11  O12  111.85  3.000
 9KJ  H16  C11  O12  111.49  3.000
 9KJ  H17  C11  C10  110.16  3.000
 9KJ  H16  C11  C10  107.50  3.000
 9KJ  O12  C11  C10  109.28  3.000
 9KJ  H18  O12  C11  108.09  3.000
 9KJ  C19  N13  C14  116.07  3.000
 9KJ  C14  N13  C10  115.97  3.000
 9KJ  C19  N13  C10  104.64  3.000
 9KJ  H21  C14  H20  107.20  3.000
 9KJ  H21  C14  P15  107.36  3.000
 9KJ  H20  C14  P15  105.70  3.000
 9KJ  H21  C14  N13  115.68  3.000
 9KJ  H20  C14  N13  108.52  3.000
 9KJ  P15  C14  N13  111.83  3.000
 9KJ  O18  P15  O17  115.76  3.000
 9KJ  O17  P15  O16  102.20  3.000
 9KJ  O18  P15  O16  114.39  3.000
 9KJ  O17  P15  C14  105.34  3.000
 9KJ  O16  P15  C14  102.03  3.000
 9KJ  O18  P15  C14  115.37  3.000
 9KJ  H22  O16  P15  113.21  3.000
 9KJ  H23  O17  P15  111.37  3.000
 9KJ  H24  C19  N13  110.13  3.000
 9KJ  H24  C19  C07  109.82  3.000
 9KJ  N13  C19  C07  107.44  3.000
 9KJ  H24  C19  C20  108.44  3.000
 9KJ  N13  C19  C20  110.28  3.000
 9KJ  C07  C19  C20  110.73  3.000
 9KJ  H25  O21  C20  109.44  3.000
 9KJ  HO3  O3   C3   107.80  3.000
 9KJ  HO2  O2   C2   108.86  3.000
 9KJ  H62  C6   H61  106.23  3.000
 9KJ  H62  C6   C5   108.33  3.000
 9KJ  H61  C6   C5   108.07  3.000
 9KJ  H62  C6   O6   112.12  3.000
 9KJ  H61  C6   O6   112.03  3.000
 9KJ  C5   C6   O6   109.87  3.000
 9KJ  HO6  O6   C6   108.11  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
 9KJ  Var_01  P15  C14  N13  C10  -173.54  30.0  3
 9KJ  Var_02  O18  P15  C14  N13   -87.17  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
 9KJ  chir_01  C2   C3   C1   O2   positiv
 9KJ  chir_02  C3   O3   C2   C4   positiv
 9KJ  chir_03  C4   O4   C5   C3   positiv
 9KJ  chir_04  C5   O5   C4   C6   negativ
 9KJ  chir_05  C1   O5   O1   C2   positiv
 9KJ  chir_06  C07  O1   C19  C08  positiv
 9KJ  chir_07  C08  O09  C07  C10  negativ
 9KJ  chir_08  C10  N13  C08  C11  negativ
 9KJ  chir_09  C19  N13  C07  C20  negativ

