# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 00:36:09 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1N[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[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
 RZM  RZM  '(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside'  D-saccharide  45  22  .  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_RZM
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
 RZM  O6'  O  OH1   0  -0.674  -2.3417   3.3431   0.6194
 RZM  C6'  C  CH2   0  -0.141  -1.6112   2.4163  -0.1538
 RZM  C5'  C  CH1   0  -0.126  -2.0316   1.0205   0.2475
 RZM  C2'  C  CH1   0  -0.114  -3.5903  -0.7202  -0.2011
 RZM  C1'  C  CH2   0  -0.159  -4.3533  -1.3076   0.9717
 RZM  O1'  O  OH1   0  -0.672  -5.6631  -0.7868   0.9640
 RZM  C3'  C  CH1   0   0.013  -2.1606  -1.2889  -0.2692
 RZM  O3'  O  OH1   0  -0.668  -1.9390  -2.2609  -1.2625
 RZM  C4'  C  CH1   0   0.038  -1.2988  -0.0641  -0.5261
 RZM  O4'  O  O2    0  -0.500   0.0242  -0.2422  -0.0991
 RZM  C1   C  CH1   0   0.202   0.9940  -0.4611  -1.0749
 RZM  C2   C  CH1   0   0.023   1.8488  -1.6697  -0.6807
 RZM  O2   O  OH1   0  -0.678   1.0769  -2.8056  -0.3869
 RZM  C3   C  CH1   0  -0.013   2.6990  -1.3356   0.5369
 RZM  O3   O  OH1   0  -0.677   3.6304  -2.3550   0.8270
 RZM  C4   C  CH1   0   0.034   3.4899  -0.0565   0.2890
 RZM  O4   O  OH1   0  -0.674   4.1816   0.3491   1.4445
 RZM  C5   C  CH1   0  -0.015   2.5350   1.0654  -0.1160
 RZM  C6   C  CH2   0  -0.162   3.2667   2.3411  -0.4718
 RZM  O6   O  OH1   0  -0.665   2.3182   3.3382  -0.7698
 RZM  O5   O  O2    0  -0.492   1.7931   0.6662  -1.2577
 RZM  N5'  N  NH1   0  -0.625  -3.4077   0.7309  -0.1217
 RZM  H1   H  HOH1  0   0.455  -2.0725   4.2291   0.3615
 RZM  H2   H  HCH2  0   0.185  -1.8047   2.5409  -1.2278
 RZM  H3   H  HCH2  0   0.205  -0.5298   2.5269  -0.0009
 RZM  H4   H  HCH1  0   0.217  -1.8291   0.8866   1.3236
 RZM  H5   H  HCH1  0   0.231  -4.1241  -0.9802  -1.1237
 RZM  H6   H  HCH2  0   0.200  -4.3523  -2.4038   0.8863
 RZM  H7   H  HCH2  0   0.197  -3.8258  -1.0571   1.9030
 RZM  H8   H  HOH1  0   0.457  -6.1160  -1.0951   1.7539
 RZM  H9   H  HCH1  0   0.221  -1.8789  -1.6825   0.7185
 RZM  H10  H  HOH1  0   0.461  -2.3362  -3.0908  -0.9802
 RZM  H11  H  HCH1  0   0.231  -1.3377   0.1858  -1.5964
 RZM  H12  H  HCH1  0   0.249   0.5273  -0.6494  -2.0504
 RZM  H13  H  HCH1  0   0.211   2.5240  -1.8610  -1.5293
 RZM  H14  H  HOH1  0   0.446   0.3036  -2.8379  -0.9634
 RZM  H15  H  HCH1  0   0.220   2.0329  -1.1655   1.3949
 RZM  H16  H  HOH1  0   0.458   3.1681  -3.0845   1.2502
 RZM  H17  H  HCH1  0   0.209   4.1879  -0.2348  -0.5456
 RZM  H18  H  HOH1  0   0.453   4.7460  -0.3805   1.7215
 RZM  H19  H  HCH1  0   0.227   1.8588   1.2767   0.7241
 RZM  H20  H  HCH2  0   0.213   3.8951   2.6224   0.3795
 RZM  H21  H  HCH2  0   0.192   3.9392   2.1487  -1.3199
 RZM  H22  H  HOH1  0   0.455   2.7845   4.1751  -0.8470
 RZM  H23  H  HNH1  0   0.353  -4.0807   1.1763   0.4861

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
 RZM  O6   C6   single  1.408  0.020  1.408
 RZM  O4   C4   single  1.406  0.020  1.406
 RZM  C4   C5   single  1.528  0.020  1.528
 RZM  C4   C3   single  1.524  0.020  1.524
 RZM  C6   C5   single  1.513  0.020  1.513
 RZM  O3   C3   single  1.411  0.020  1.411
 RZM  C5   O5   single  1.419  0.020  1.419
 RZM  O5   C1   single  1.394  0.020  1.394
 RZM  C3   C2   single  1.522  0.020  1.522
 RZM  C2   C1   single  1.532  0.020  1.532
 RZM  C2   O2   single  1.404  0.020  1.404
 RZM  C1   O4'  single  1.393  0.020  1.393
 RZM  O4'  C4'  single  1.402  0.020  1.402
 RZM  O3'  C3'  single  1.407  0.020  1.407
 RZM  C4'  C3'  single  1.520  0.020  1.520
 RZM  C4'  C5'  single  1.520  0.020  1.520
 RZM  O6'  C6'  single  1.411  0.020  1.411
 RZM  C3'  C2'  single  1.540  0.020  1.540
 RZM  C6'  C5'  single  1.512  0.020  1.512
 RZM  C5'  N5'  single  1.454  0.020  1.454
 RZM  C2'  N5'  single  1.465  0.020  1.465
 RZM  C2'  C1'  single  1.517  0.020  1.517
 RZM  C1'  O1'  single  1.410  0.020  1.410
 RZM  O6'  H1   single  0.850  0.020  0.980
 RZM  C6'  H2   single  0.970  0.020  1.090
 RZM  C6'  H3   single  0.970  0.020  1.090
 RZM  C5'  H4   single  0.970  0.020  1.090
 RZM  C2'  H5   single  0.970  0.020  1.090
 RZM  C1'  H6   single  0.970  0.020  1.090
 RZM  C1'  H7   single  0.970  0.020  1.090
 RZM  O1'  H8   single  0.850  0.020  0.980
 RZM  C3'  H9   single  0.970  0.020  1.090
 RZM  O3'  H10  single  0.850  0.020  0.980
 RZM  C4'  H11  single  0.970  0.020  1.090
 RZM  C1   H12  single  0.970  0.020  1.090
 RZM  C2   H13  single  0.970  0.020  1.090
 RZM  O2   H14  single  0.850  0.020  0.980
 RZM  C3   H15  single  0.970  0.020  1.090
 RZM  O3   H16  single  0.850  0.020  0.980
 RZM  C4   H17  single  0.970  0.020  1.090
 RZM  O4   H18  single  0.850  0.020  0.980
 RZM  C5   H19  single  0.970  0.020  1.090
 RZM  C6   H20  single  0.970  0.020  1.090
 RZM  C6   H21  single  0.970  0.020  1.090
 RZM  O6   H22  single  0.850  0.020  0.980
 RZM  N5'  H23  single  0.890  0.020  1.040

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
 RZM  H1   O6'  C6'  108.27  3.000
 RZM  H3   C6'  H2   107.36  3.000
 RZM  H3   C6'  C5'  109.26  3.000
 RZM  H2   C6'  C5'  108.37  3.000
 RZM  H3   C6'  O6'  111.57  3.000
 RZM  H2   C6'  O6'  111.72  3.000
 RZM  C5'  C6'  O6'  108.48  3.000
 RZM  H4   C5'  N5'  113.41  3.000
 RZM  H4   C5'  C4'  108.74  3.000
 RZM  N5'  C5'  C4'  100.66  3.000
 RZM  H4   C5'  C6'  108.66  3.000
 RZM  N5'  C5'  C6'  112.32  3.000
 RZM  C4'  C5'  C6'  112.92  3.000
 RZM  H5   C2'  N5'  109.94  3.000
 RZM  H5   C2'  C3'  109.08  3.000
 RZM  N5'  C2'  C3'  104.63  3.000
 RZM  H5   C2'  C1'  108.27  3.000
 RZM  N5'  C2'  C1'  113.85  3.000
 RZM  C3'  C2'  C1'  110.98  3.000
 RZM  H7   C1'  H6   107.02  3.000
 RZM  H7   C1'  O1'  111.49  3.000
 RZM  H6   C1'  O1'  111.65  3.000
 RZM  H7   C1'  C2'  108.98  3.000
 RZM  H6   C1'  C2'  108.99  3.000
 RZM  O1'  C1'  C2'  108.66  3.000
 RZM  H8   O1'  C1'  108.35  3.000
 RZM  H9   C3'  C4'  107.15  3.000
 RZM  H9   C3'  O3'  110.27  3.000
 RZM  C4'  C3'  O3'  110.37  3.000
 RZM  H9   C3'  C2'  109.28  3.000
 RZM  C4'  C3'  C2'  103.67  3.000
 RZM  O3'  C3'  C2'  115.62  3.000
 RZM  H10  O3'  C3'  108.87  3.000
 RZM  H11  C4'  O4'  111.02  3.000
 RZM  H11  C4'  C3'  109.12  3.000
 RZM  O4'  C4'  C3'  112.42  3.000
 RZM  H11  C4'  C5'  108.42  3.000
 RZM  C3'  C4'  C5'  102.45  3.000
 RZM  O4'  C4'  C5'  113.00  3.000
 RZM  C1   O4'  C4'  117.63  3.000
 RZM  H12  C1   O5   105.42  3.000
 RZM  H12  C1   C2   109.31  3.000
 RZM  O5   C1   C2   110.60  3.000
 RZM  H12  C1   O4'  110.70  3.000
 RZM  C2   C1   O4'  109.40  3.000
 RZM  O5   C1   O4'  111.34  3.000
 RZM  H13  C2   C3   108.19  3.000
 RZM  H13  C2   O2   110.96  3.000
 RZM  C3   C2   O2   108.49  3.000
 RZM  H13  C2   C1   106.31  3.000
 RZM  O2   C2   C1   112.66  3.000
 RZM  C3   C2   C1   110.14  3.000
 RZM  H14  O2   C2   110.03  3.000
 RZM  H15  C3   C4   108.14  3.000
 RZM  H15  C3   O3   110.57  3.000
 RZM  C4   C3   O3   107.29  3.000
 RZM  H15  C3   C2   108.65  3.000
 RZM  O3   C3   C2   112.00  3.000
 RZM  C4   C3   C2   110.11  3.000
 RZM  H16  O3   C3   108.73  3.000
 RZM  H17  C4   C5   108.28  3.000
 RZM  H17  C4   O4   110.93  3.000
 RZM  C5   C4   O4   108.26  3.000
 RZM  H17  C4   C3   108.42  3.000
 RZM  C5   C4   C3   109.58  3.000
 RZM  O4   C4   C3   111.32  3.000
 RZM  H18  O4   C4   107.82  3.000
 RZM  H19  C5   O5   110.33  3.000
 RZM  H19  C5   C6   108.37  3.000
 RZM  O5   C5   C6   107.51  3.000
 RZM  H19  C5   C4   108.85  3.000
 RZM  O5   C5   C4   109.48  3.000
 RZM  C6   C5   C4   112.28  3.000
 RZM  H21  C6   H20  107.08  3.000
 RZM  H21  C6   O6   111.88  3.000
 RZM  H20  C6   O6   111.67  3.000
 RZM  H21  C6   C5   109.25  3.000
 RZM  H20  C6   C5   108.14  3.000
 RZM  O6   C6   C5   108.72  3.000
 RZM  H22  O6   C6   107.86  3.000
 RZM  C5   O5   C1   114.95  3.000
 RZM  H23  N5'  C2'  112.73  3.000
 RZM  H23  N5'  C5'  112.95  3.000
 RZM  C2'  N5'  C5'  109.22  3.000

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
 RZM  chir_01  C5'  C4'  C6'  N5'  negativ
 RZM  chir_02  C2'  N5'  C1'  C3'  positiv
 RZM  chir_03  C3'  O3'  C4'  C2'  negativ
 RZM  chir_04  C4'  O4'  C3'  C5'  negativ
 RZM  chir_05  C1   O4'  O5   C2   negativ
 RZM  chir_06  C2   O2   C1   C3   negativ
 RZM  chir_07  C3   O3   C2   C4   positiv
 RZM  chir_08  C4   O4   C5   C3   positiv
 RZM  chir_09  C5   O5   C4   C6   negativ

