# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 16 14:12:26 2020
#   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  51  27  .  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_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  -0.168   0.8842   1.8670   0.0769
 9KJ  C22  C  CH1    0   0.022  -3.3931  -1.3358   0.6874
 9KJ  C24  C  CH1    0  -0.015  -4.1676  -0.8892  -0.5446
 9KJ  C26  C  CH1    0   0.034  -4.7450   0.5041  -0.3207
 9KJ  O27  O  OH1    0  -0.674  -5.3611   0.9979  -1.4847
 9KJ  C03  C  CH1    0  -0.013  -3.6248   1.4648   0.0731
 9KJ  O04  O  O2     0  -0.495  -2.9580   0.9687   1.2228
 9KJ  C05  C  CH1    0   0.209  -2.3524  -0.2781   1.0711
 9KJ  O06  O  O2     0  -0.503  -1.3417  -0.2330   0.1137
 9KJ  C07  C  CH1    0   0.019  -0.0234  -0.4083   0.5691
 9KJ  C08  C  CH1    0   0.012   0.4780  -1.8310   0.4342
 9KJ  O09  O  OH1    0  -0.677   0.0113  -2.6186   1.5139
 9KJ  C10  C  CH1    0  -0.070   2.0071  -1.6776   0.3439
 9KJ  C11  C  CH2    0  -0.207   2.5994  -2.5570  -0.7470
 9KJ  O12  O  OH1    0  -0.672   2.0419  -2.2231  -2.0020
 9KJ  N13  N  NT     0  -0.448   2.2147  -0.2429   0.1907
 9KJ  C14  C  CH2    0  -0.574   3.4859   0.2227  -0.3190
 9KJ  P15  P  P      0   1.157   4.9460  -0.0271   0.8165
 9KJ  O16  O  OP    -1  -0.895   5.1253  -1.5430   1.0121
 9KJ  O17  O  OP    -1  -0.918   6.0978   0.6176   0.0255
 9KJ  O18  O  O      0  -0.910   4.5976   0.7168   2.1112
 9KJ  C19  C  CH1    0  -0.065   0.9873   0.3854  -0.2480
 9KJ  O21  O  OH1    0  -0.673   1.4495   2.6475  -0.9576
 9KJ  O25  O  OH1    0  -0.677  -5.2504  -1.7489  -0.8278
 9KJ  H1   H  HCH2   0   0.210  -0.1763   2.1241   0.2070
 9KJ  H2   H  HCH2   0   0.194   1.3838   2.0402   1.0395
 9KJ  H4   H  HCH1   0   0.219  -3.4789  -0.8431  -1.4009
 9KJ  H5   H  HCH1   0   0.208  -5.4644   0.4502   0.5133
 9KJ  H6   H  HOH1   0   0.453  -6.0219   0.3551  -1.7640
 9KJ  H7   H  HOH1   0   0.455  -3.3813   4.5801   0.7918
 9KJ  H10  H  HCH1   0   0.226  -2.9221   1.5570  -0.7671
 9KJ  H11  H  HCH1   0   0.244  -1.9388  -0.5182   2.0586
 9KJ  H12  H  HCH1   0   0.222   0.0690  -0.0907   1.6185
 9KJ  H13  H  HCH1   0   0.216   0.0913  -2.2298  -0.5121
 9KJ  H14  H  HOH1   0   0.457   0.2673  -3.5337   1.3593
 9KJ  H15  H  HCH1   0   0.216   2.4710  -2.0183   1.2763
 9KJ  H16  H  HCH2   0   0.222   3.6858  -2.4366  -0.7342
 9KJ  H17  H  HCH2   0   0.185   2.3894  -3.6054  -0.4830
 9KJ  H18  H  HOH1   0   0.451   2.4763  -2.7582  -2.6715
 9KJ  H20  H  HCH2   0   0.163   3.7115  -0.1939  -1.3155
 9KJ  H21  H  HCH2   0   0.213   3.4020   1.2992  -0.4736
 9KJ  H24  H  HCH1   0   0.189   0.7702   0.2520  -1.3248
 9KJ  H25  H  HOH1   0   0.451   1.4105   3.5691  -0.6867
 9KJ  H27  H  HOH1   0   0.457  -4.9084  -2.5581  -1.2197
 9KJ  O23  O  OH1    0  -0.683  -2.8210  -2.5903   0.4238
 9KJ  C02  C  CH2    0  -0.162  -4.1444   2.8442   0.4165
 9KJ  H8   H  HCH2   0   0.193  -4.8217   2.7693   1.2790
 9KJ  O01  O  OH1    0  -0.666  -3.0470   3.6856   0.6828
 9KJ  H9   H  HCH2   0   0.212  -4.7367   3.2102  -0.4285
 9KJ  H26  H  HOH1   0   0.449  -2.0836  -2.7495   1.0289
 9KJ  H3   H  HCH1   0   0.207  -4.0999  -1.3966   1.5301

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  O25  C24  single  1.411  0.020  1.411
 9KJ  O27  C26  single  1.407  0.020  1.407
 9KJ  O01  C02  single  1.408  0.020  1.408
 9KJ  C26  C24  single  1.525  0.020  1.525
 9KJ  C26  C03  single  1.527  0.020  1.527
 9KJ  C02  C03  single  1.514  0.020  1.514
 9KJ  C24  C22  single  1.522  0.020  1.522
 9KJ  C22  C05  single  1.533  0.020  1.533
 9KJ  C22  O23  single  1.404  0.020  1.404
 9KJ  C03  O04  single  1.419  0.020  1.419
 9KJ  O04  C05  single  1.394  0.020  1.394
 9KJ  C05  O06  single  1.393  0.020  1.393
 9KJ  O06  C07  single  1.406  0.020  1.406
 9KJ  C07  C08  single  1.514  0.020  1.514
 9KJ  C07  C19  single  1.523  0.020  1.523
 9KJ  O09  C08  single  1.416  0.020  1.416
 9KJ  C20  C19  single  1.520  0.020  1.520
 9KJ  C20  O21  single  1.414  0.020  1.414
 9KJ  C08  C10  single  1.539  0.020  1.539
 9KJ  C19  N13  single  1.447  0.020  1.447
 9KJ  C10  N13  single  1.458  0.020  1.458
 9KJ  C10  C11  single  1.521  0.020  1.521
 9KJ  N13  C14  single  1.447  0.020  1.447
 9KJ  C14  P15  single  1.866  0.020  1.866
 9KJ  C11  O12  single  1.413  0.020  1.413
 9KJ  P15  O18  deloc   1.533  0.020  1.533
 9KJ  P15  O16  deloc   1.539  0.020  1.539
 9KJ  P15  O17  deloc   1.539  0.020  1.539
 9KJ  C20  H1   single  0.970  0.020  1.090
 9KJ  C20  H2   single  0.970  0.020  1.090
 9KJ  C22  H3   single  0.970  0.020  1.090
 9KJ  C24  H4   single  0.970  0.020  1.090
 9KJ  C26  H5   single  0.970  0.020  1.090
 9KJ  O27  H6   single  0.850  0.020  0.980
 9KJ  O01  H7   single  0.850  0.020  0.980
 9KJ  C02  H8   single  0.970  0.020  1.090
 9KJ  C02  H9   single  0.970  0.020  1.090
 9KJ  C03  H10  single  0.970  0.020  1.090
 9KJ  C05  H11  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  C19  H24  single  0.970  0.020  1.090
 9KJ  O21  H25  single  0.850  0.020  0.980
 9KJ  O23  H26  single  0.850  0.020  0.980
 9KJ  O25  H27  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  H2   C20  H1   107.36  3.000
 9KJ  H2   C20  O21  111.86  3.000
 9KJ  H1   C20  O21  110.07  3.000
 9KJ  H2   C20  C19  108.07  3.000
 9KJ  H1   C20  C19  108.59  3.000
 9KJ  O21  C20  C19  110.77  3.000
 9KJ  H3   C22  O23  110.85  3.000
 9KJ  H3   C22  C05  106.40  3.000
 9KJ  O23  C22  C05  112.77  3.000
 9KJ  H3   C22  C24  107.99  3.000
 9KJ  O23  C22  C24  108.52  3.000
 9KJ  C05  C22  C24  110.22  3.000
 9KJ  H4   C24  O25  110.48  3.000
 9KJ  H4   C24  C26  108.25  3.000
 9KJ  O25  C24  C26  107.19  3.000
 9KJ  H4   C24  C22  108.90  3.000
 9KJ  C26  C24  C22  109.99  3.000
 9KJ  O25  C24  C22  111.96  3.000
 9KJ  H5   C26  C03  108.31  3.000
 9KJ  H5   C26  O27  110.93  3.000
 9KJ  C03  C26  O27  108.29  3.000
 9KJ  H5   C26  C24  108.27  3.000
 9KJ  C03  C26  C24  109.56  3.000
 9KJ  O27  C26  C24  111.42  3.000
 9KJ  H6   O27  C26  107.83  3.000
 9KJ  H10  C03  O04  110.39  3.000
 9KJ  H10  C03  C02  108.45  3.000
 9KJ  O04  C03  C02  107.23  3.000
 9KJ  H10  C03  C26  108.94  3.000
 9KJ  O04  C03  C26  109.50  3.000
 9KJ  C02  C03  C26  112.33  3.000
 9KJ  C05  O04  C03  115.38  3.000
 9KJ  H11  C05  O06  110.62  3.000
 9KJ  H11  C05  O04  105.15  3.000
 9KJ  O06  C05  O04  111.16  3.000
 9KJ  H11  C05  C22  109.29  3.000
 9KJ  O06  C05  C22  110.06  3.000
 9KJ  O04  C05  C22  110.45  3.000
 9KJ  C07  O06  C05  116.98  3.000
 9KJ  H12  C07  C19  107.79  3.000
 9KJ  H12  C07  C08  109.17  3.000
 9KJ  C19  C07  C08  102.83  3.000
 9KJ  H12  C07  O06  110.59  3.000
 9KJ  C19  C07  O06  112.56  3.000
 9KJ  C08  C07  O06  113.50  3.000
 9KJ  H13  C08  C10  109.61  3.000
 9KJ  H13  C08  O09  109.84  3.000
 9KJ  C10  C08  O09  115.31  3.000
 9KJ  H13  C08  C07  107.55  3.000
 9KJ  C10  C08  C07  103.92  3.000
 9KJ  O09  C08  C07  110.22  3.000
 9KJ  H14  O09  C08  108.59  3.000
 9KJ  H15  C10  N13  109.58  3.000
 9KJ  H15  C10  C11  105.41  3.000
 9KJ  N13  C10  C11  115.98  3.000
 9KJ  H15  C10  C08  109.86  3.000
 9KJ  C11  C10  C08  111.79  3.000
 9KJ  N13  C10  C08  104.22  3.000
 9KJ  H17  C11  H16  106.95  3.000
 9KJ  H17  C11  O12  111.26  3.000
 9KJ  H16  C11  O12  112.11  3.000
 9KJ  H17  C11  C10  107.70  3.000
 9KJ  H16  C11  C10  108.35  3.000
 9KJ  O12  C11  C10  110.28  3.000
 9KJ  H18  O12  C11  107.99  3.000
 9KJ  C19  N13  C14  119.93  3.000
 9KJ  C14  N13  C10  118.62  3.000
 9KJ  C19  N13  C10  109.78  3.000
 9KJ  H21  C14  H20  105.09  3.000
 9KJ  H21  C14  P15  106.17  3.000
 9KJ  H20  C14  P15  109.81  3.000
 9KJ  H21  C14  N13  107.46  3.000
 9KJ  H20  C14  N13  112.10  3.000
 9KJ  P15  C14  N13  115.47  3.000
 9KJ  O18  P15  O17  113.63  3.000
 9KJ  O17  P15  O16  113.01  3.000
 9KJ  O18  P15  O16  113.39  3.000
 9KJ  O17  P15  C14  102.52  3.000
 9KJ  O16  P15  C14  107.48  3.000
 9KJ  O18  P15  C14  105.72  3.000
 9KJ  H24  C19  N13  114.15  3.000
 9KJ  H24  C19  C07  109.21  3.000
 9KJ  N13  C19  C07  100.02  3.000
 9KJ  H24  C19  C20  108.18  3.000
 9KJ  N13  C19  C20  114.58  3.000
 9KJ  C07  C19  C20  110.38  3.000
 9KJ  H25  O21  C20  107.87  3.000
 9KJ  H27  O25  C24  108.75  3.000
 9KJ  H26  O23  C22  109.90  3.000
 9KJ  H9   C02  H8   107.16  3.000
 9KJ  H9   C02  C03  108.37  3.000
 9KJ  H8   C02  C03  109.11  3.000
 9KJ  H9   C02  O01  111.58  3.000
 9KJ  H8   C02  O01  111.87  3.000
 9KJ  C03  C02  O01  108.66  3.000
 9KJ  H7   O01  C02  107.85  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  -68.51  30.0  3
 9KJ  Var_02  O18  P15  C14  N13  -58.23  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  C22  C24  C05  O23  positiv
 9KJ  chir_02  C24  O25  C22  C26  positiv
 9KJ  chir_03  C26  O27  C03  C24  positiv
 9KJ  chir_04  C03  O04  C26  C02  negativ
 9KJ  chir_05  C05  O04  O06  C22  positiv
 9KJ  chir_06  C07  O06  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

