# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 01:50:24 2021
#   Inital geometry file: a 122 line input string
#   Ligand name: {2-[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]ethyl}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(CC[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
 9HV  9HV  '{2-[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]ethyl}phosphonic acid'  ligand  56  28  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9HV
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
 9HV  C10  C  CH1   0  -0.124  24.2399  -30.1318  282.9119
 9HV  C11  C  CH2   0  -0.189  23.0584  -29.8398  283.8208
 9HV  C14  C  CH2   0  -0.307  24.7064  -32.0915  284.3777
 9HV  C15  C  CH2   0  -0.751  25.8670  -32.7913  285.0816
 9HV  O18  O  OH1   0  -0.745  26.7088  -34.4980  286.9106
 9HV  C20  C  CH1   0  -0.126  25.8882  -31.6958  282.2794
 9HV  C21  C  CH2   0  -0.151  27.3816  -31.4204  282.2796
 9HV  O24  O  OH1   0  -0.666  23.3814  -33.5524  278.3931
 9HV  C02  C  CH2   0  -0.180  28.5295  -31.4502  277.7496
 9HV  C03  C  CH1   0  -0.005  27.3289  -32.2458  278.2447
 9HV  C05  C  CH1   0   0.237  25.0326  -31.7865  278.7297
 9HV  C07  C  CH1   0   0.017  25.1837  -31.1601  281.0207
 9HV  C08  C  CH1   0   0.056  23.8400  -30.6787  281.5386
 9HV  C23  C  CH1   0  -0.018  24.5613  -32.9787  277.8934
 9HV  C25  C  CH1   0  -0.017  25.6404  -34.0506  277.8604
 9HV  C27  C  CH1   0   0.048  26.9582  -33.4496  277.3790
 9HV  N13  N  NT    0  -0.443  25.2018  -31.1039  283.4349
 9HV  O01  O  OH1   0  -0.664  29.7155  -32.1627  277.9969
 9HV  O04  O  O2    0  -0.507  26.2574  -31.3140  278.2423
 9HV  O06  O  O2    0  -0.506  25.1166  -32.1901  280.0581
 9HV  O09  O  OH1   0  -0.677  23.2576  -29.7447  280.6677
 9HV  O12  O  OH1   0  -0.673  22.3141  -28.8052  283.2063
 9HV  O17  O  OH1   0  -0.751  24.7294  -32.9505  287.4715
 9HV  O19  O  O     0  -0.721  24.3500  -34.9970  285.9176
 9HV  O22  O  OH1   0  -0.664  27.6003  -30.0306  282.2848
 9HV  O26  O  OH1   0  -0.676  25.3120  -35.0946  276.9706
 9HV  O28  O  OH1   0  -0.665  27.9964  -34.3932  277.4382
 9HV  P16  P  P     0   1.368  25.3082  -33.9441  286.3429
 9HV  H1   H  HCH1  0   0.239  24.7701  -29.1813  282.7555
 9HV  H2   H  HCH2  0   0.214  22.4429  -30.7384  283.9461
 9HV  H3   H  HCH2  0   0.222  23.4105  -29.5367  284.8151
 9HV  H4   H  HCH2  0   0.255  24.1077  -31.5875  285.1356
 9HV  H5   H  HCH2  0   0.220  24.0624  -32.8489  283.9065
 9HV  H6   H  HCH2  0   0.287  26.4634  -33.3706  284.3734
 9HV  H7   H  HCH2  0   0.289  26.5302  -32.0509  285.5342
 9HV  H8   H  HOH1  0   0.492  26.6276  -35.3096  287.4296
 9HV  H9   H  HCH1  0   0.249  25.7619  -32.7866  282.2874
 9HV  H10  H  HCH2  0   0.202  27.8208  -31.9001  281.3940
 9HV  H11  H  HCH2  0   0.204  27.8375  -31.8998  283.1551
 9HV  H12  H  HOH1  0   0.457  22.6428  -32.9718  278.1866
 9HV  H13  H  HCH2  0   0.211  28.5235  -30.4898  278.2810
 9HV  H14  H  HCH2  0   0.194  28.3998  -31.2259  276.6814
 9HV  H15  H  HCH1  0   0.228  27.5423  -32.5933  279.2649
 9HV  H16  H  HCH1  0   0.243  24.3386  -30.9465  278.6119
 9HV  H17  H  HCH1  0   0.231  25.7312  -30.2943  280.6276
 9HV  H18  H  HCH1  0   0.196  23.1820  -31.5520  281.6864
 9HV  H19  H  HCH1  0   0.226  24.4158  -32.6074  276.8687
 9HV  H20  H  HCH1  0   0.220  25.7901  -34.4447  278.8765
 9HV  H21  H  HCH1  0   0.202  26.8113  -33.0898  276.3464
 9HV  H23  H  HOH1  0   0.456  30.4514  -31.5811  277.7872
 9HV  H24  H  HOH1  0   0.447  22.5527  -29.3022  281.1564
 9HV  H25  H  HOH1  0   0.466  21.4626  -28.7411  283.6481
 9HV  H26  H  HOH1  0   0.491  24.1234  -33.3759  288.0929
 9HV  H27  H  HOH1  0   0.457  28.5396  -29.8731  282.1571
 9HV  H28  H  HOH1  0   0.456  24.5894  -35.6033  277.3505
 9HV  H29  H  HOH1  0   0.448  27.7069  -35.1731  276.9526

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
 9HV  O28  C27  single  1.404  0.020  1.404
 9HV  C02  O01  single  1.406  0.020  1.406
 9HV  C02  C03  single  1.523  0.020  1.523
 9HV  C27  C03  single  1.528  0.020  1.528
 9HV  C27  C25  single  1.526  0.020  1.526
 9HV  O26  C25  single  1.410  0.020  1.410
 9HV  C03  O04  single  1.420  0.020  1.420
 9HV  C25  C23  single  1.521  0.020  1.521
 9HV  O04  C05  single  1.400  0.020  1.400
 9HV  C23  C05  single  1.531  0.020  1.531
 9HV  C23  O24  single  1.404  0.020  1.404
 9HV  C05  O06  single  1.391  0.020  1.391
 9HV  O06  C07  single  1.411  0.020  1.411
 9HV  O09  C08  single  1.404  0.020  1.404
 9HV  C07  C08  single  1.518  0.020  1.518
 9HV  C07  C20  single  1.539  0.020  1.539
 9HV  C08  C10  single  1.531  0.020  1.531
 9HV  O22  C21  single  1.407  0.020  1.407
 9HV  C21  C20  single  1.519  0.020  1.519
 9HV  C20  N13  single  1.469  0.020  1.469
 9HV  C10  N13  single  1.464  0.020  1.464
 9HV  C10  C11  single  1.519  0.020  1.519
 9HV  O19  P16  double  1.486  0.020  1.486
 9HV  N13  C14  single  1.452  0.020  1.452
 9HV  O12  C11  single  1.415  0.020  1.415
 9HV  C15  C14  single  1.527  0.020  1.527
 9HV  C15  P16  single  1.798  0.020  1.798
 9HV  P16  O17  single  1.611  0.020  1.611
 9HV  P16  O18  single  1.610  0.020  1.610
 9HV  C10  H1   single  0.970  0.020  1.090
 9HV  C11  H2   single  0.970  0.020  1.090
 9HV  C11  H3   single  0.970  0.020  1.090
 9HV  C14  H4   single  0.970  0.020  1.090
 9HV  C14  H5   single  0.970  0.020  1.090
 9HV  C15  H6   single  0.970  0.020  1.090
 9HV  C15  H7   single  0.970  0.020  1.090
 9HV  O18  H8   single  0.850  0.020  0.980
 9HV  C20  H9   single  0.970  0.020  1.090
 9HV  C21  H10  single  0.970  0.020  1.090
 9HV  C21  H11  single  0.970  0.020  1.090
 9HV  O24  H12  single  0.850  0.020  0.980
 9HV  C02  H13  single  0.970  0.020  1.090
 9HV  C02  H14  single  0.970  0.020  1.090
 9HV  C03  H15  single  0.970  0.020  1.090
 9HV  C05  H16  single  0.970  0.020  1.090
 9HV  C07  H17  single  0.970  0.020  1.090
 9HV  C08  H18  single  0.970  0.020  1.090
 9HV  C23  H19  single  0.970  0.020  1.090
 9HV  C25  H20  single  0.970  0.020  1.090
 9HV  C27  H21  single  0.970  0.020  1.090
 9HV  O01  H23  single  0.850  0.020  0.980
 9HV  O09  H24  single  0.850  0.020  0.980
 9HV  O12  H25  single  0.850  0.020  0.980
 9HV  O17  H26  single  0.850  0.020  0.980
 9HV  O22  H27  single  0.850  0.020  0.980
 9HV  O26  H28  single  0.850  0.020  0.980
 9HV  O28  H29  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
 9HV  H1   C10  N13  107.94  3.000
 9HV  H1   C10  C08  107.88  3.000
 9HV  N13  C10  C08  104.76  3.000
 9HV  H1   C10  C11  107.10  3.000
 9HV  N13  C10  C11  115.14  3.000
 9HV  C08  C10  C11  113.71  3.000
 9HV  H3   C11  H2   107.64  3.000
 9HV  H3   C11  O12  111.12  3.000
 9HV  H2   C11  O12  110.70  3.000
 9HV  H3   C11  C10  110.22  3.000
 9HV  H2   C11  C10  110.34  3.000
 9HV  O12  C11  C10  106.85  3.000
 9HV  H5   C14  H4   107.14  3.000
 9HV  H5   C14  N13  112.94  3.000
 9HV  H4   C14  N13  108.93  3.000
 9HV  H5   C14  C15  109.07  3.000
 9HV  H4   C14  C15  108.00  3.000
 9HV  N13  C14  C15  110.58  3.000
 9HV  H7   C15  H6   107.26  3.000
 9HV  H7   C15  P16  109.43  3.000
 9HV  H6   C15  P16  106.53  3.000
 9HV  H7   C15  C14  109.99  3.000
 9HV  H6   C15  C14  111.05  3.000
 9HV  P16  C15  C14  112.39  3.000
 9HV  H8   O18  P16  113.90  3.000
 9HV  H9   C20  N13  109.93  3.000
 9HV  H9   C20  C07  107.40  3.000
 9HV  N13  C20  C07  106.82  3.000
 9HV  H9   C20  C21  107.05  3.000
 9HV  N13  C20  C21  112.73  3.000
 9HV  C07  C20  C21  112.78  3.000
 9HV  H11  C21  H10  106.63  3.000
 9HV  H11  C21  O22  111.35  3.000
 9HV  H10  C21  O22  111.85  3.000
 9HV  H11  C21  C20  109.24  3.000
 9HV  H10  C21  C20  108.29  3.000
 9HV  O22  C21  C20  109.39  3.000
 9HV  H12  O24  C23  108.80  3.000
 9HV  H14  C02  H13  106.94  3.000
 9HV  H14  C02  O01  111.96  3.000
 9HV  H13  C02  O01  111.28  3.000
 9HV  H14  C02  C03  109.24  3.000
 9HV  H13  C02  C03  107.18  3.000
 9HV  O01  C02  C03  110.07  3.000
 9HV  H15  C03  O04  110.83  3.000
 9HV  H15  C03  C27  108.90  3.000
 9HV  O04  C03  C27  109.45  3.000
 9HV  H15  C03  C02  108.30  3.000
 9HV  O04  C03  C02  104.57  3.000
 9HV  C27  C03  C02  114.74  3.000
 9HV  H16  C05  O06  111.31  3.000
 9HV  H16  C05  O04  104.94  3.000
 9HV  O06  C05  O04  112.18  3.000
 9HV  H16  C05  C23  110.07  3.000
 9HV  O06  C05  C23  108.33  3.000
 9HV  O04  C05  C23  110.00  3.000
 9HV  H17  C07  O06  110.80  3.000
 9HV  H17  C07  C08  108.28  3.000
 9HV  O06  C07  C08  114.96  3.000
 9HV  H17  C07  C20  109.84  3.000
 9HV  C08  C07  C20  103.68  3.000
 9HV  O06  C07  C20  109.00  3.000
 9HV  H18  C08  O09  111.24  3.000
 9HV  H18  C08  C07  108.82  3.000
 9HV  O09  C08  C07  111.50  3.000
 9HV  H18  C08  C10  108.56  3.000
 9HV  C07  C08  C10  100.84  3.000
 9HV  O09  C08  C10  115.29  3.000
 9HV  H19  C23  C25  108.15  3.000
 9HV  H19  C23  C05  106.67  3.000
 9HV  C25  C23  C05  110.01  3.000
 9HV  H19  C23  O24  111.01  3.000
 9HV  C05  C23  O24  112.50  3.000
 9HV  C25  C23  O24  108.41  3.000
 9HV  H20  C25  O26  110.44  3.000
 9HV  H20  C25  C27  108.35  3.000
 9HV  O26  C25  C27  107.07  3.000
 9HV  H20  C25  C23  109.20  3.000
 9HV  O26  C25  C23  111.72  3.000
 9HV  C27  C25  C23  109.99  3.000
 9HV  H21  C27  O28  110.92  3.000
 9HV  H21  C27  C25  107.98  3.000
 9HV  O28  C27  C25  111.13  3.000
 9HV  H21  C27  C03  107.78  3.000
 9HV  C25  C27  C03  109.93  3.000
 9HV  O28  C27  C03  109.03  3.000
 9HV  C20  N13  C14  113.34  3.000
 9HV  C14  N13  C10  117.34  3.000
 9HV  C20  N13  C10  107.07  3.000
 9HV  H23  O01  C02  107.52  3.000
 9HV  C05  O04  C03  115.97  3.000
 9HV  C07  O06  C05  116.26  3.000
 9HV  H24  O09  C08  107.10  3.000
 9HV  H25  O12  C11  108.37  3.000
 9HV  H26  O17  P16  113.84  3.000
 9HV  H27  O22  C21  108.26  3.000
 9HV  H28  O26  C25  108.49  3.000
 9HV  H29  O28  C27  107.49  3.000
 9HV  O19  P16  O17  113.95  3.000
 9HV  O17  P16  O18  106.13  3.000
 9HV  O19  P16  O18  114.72  3.000
 9HV  O18  P16  C15  101.40  3.000
 9HV  O17  P16  C15  101.99  3.000
 9HV  O19  P16  C15  117.00  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
 9HV  Var_01  C15  C14  N13  C10  -165.94  30.0  3
 9HV  Var_02  P16  C15  C14  N13   176.02  30.0  1
 9HV  Var_03  O19  P16  C15  C14    55.19  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
 9HV  chir_01  C10  C08  N13  C11  positiv
 9HV  chir_02  C20  N13  C21  C07  positiv
 9HV  chir_03  C03  C02  C27  O04  positiv
 9HV  chir_04  C05  O06  O04  C23  negativ
 9HV  chir_05  C07  O06  C20  C08  positiv
 9HV  chir_06  C08  O09  C07  C10  negativ
 9HV  chir_07  C23  O24  C25  C05  positiv
 9HV  chir_08  C25  O26  C23  C27  positiv
 9HV  chir_09  C27  O28  C25  C03  negativ

