# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 20:19:41 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3O)[C@H](N)[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
 RIO  RIO  '(1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-(beta-D-ribofuranosyloxy)cyclohexyl 2,6-diamino-2,6-dideoxy-alpha-D-glucopyranoside'  ligand  65  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_RIO
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
 RIO  O1    O  OH1   0  -0.709  -1.4862   3.9942   0.8112
 RIO  C1    C  CH2   0  -0.174  -2.6752   3.2577   0.8518
 RIO  C2    C  CR15  0  -0.039  -2.9337   2.4746  -0.4312
 RIO  O2    O  O     0  -0.499  -1.9069   1.5094  -0.6694
 RIO  C3    C  CR15  0   0.302  -2.3690   0.2083  -0.4279
 RIO  O3    O  O2    0  -0.515  -1.5134  -0.4487   0.4559
 RIO  C4    C  CH1   0   0.001  -0.7705  -1.5429  -0.0347
 RIO  C5    C  CH1   0   0.097  -1.4864  -2.8443   0.2842
 RIO  O4    O  OH1   0  -0.694  -2.7657  -2.8400  -0.3115
 RIO  C6    C  CH1   0  -0.139  -0.6789  -4.0339  -0.2215
 RIO  N1    N  NH2   0  -0.807  -1.4669  -5.2344   0.0073
 RIO  C7    C  CH2   0  -0.473   0.7056  -4.0112   0.4129
 RIO  C8    C  CH1   0  -0.094   1.4546  -2.7123   0.1183
 RIO  N2    N  NH2   0  -0.830   2.7446  -2.7493   0.7889
 RIO  C9    C  CH1   0   0.064   0.6217  -1.5190   0.6011
 RIO  O5    O  O2    0  -0.514   1.1779  -0.2745   0.2390
 RIO  C10   C  CH1   0   0.257   2.0776   0.3717   1.0865
 RIO  O6    O  O2    0  -0.496   3.3883   0.2368   0.6291
 RIO  C11   C  CH1   0   0.006   3.6060   0.7377  -0.6797
 RIO  C12   C  CH2   0  -0.304   5.0347   0.3931  -1.0567
 RIO  N3    N  NH2   0  -0.789   5.2109  -1.0501  -1.1095
 RIO  C13   C  CH1   0   0.013   3.3030   2.2376  -0.7041
 RIO  O7    O  OH1   0  -0.676   3.3759   2.7615  -2.0138
 RIO  C14   C  CH1   0   0.044   1.8901   2.5153  -0.1883
 RIO  O8    O  OH1   0  -0.667   1.6755   3.8984  -0.0454
 RIO  C15   C  CH1   0  -0.135   1.6863   1.8542   1.1705
 RIO  N4    N  NH2   0  -0.837   0.3323   2.0449   1.6633
 RIO  C16   C  CR15  0  -0.056  -3.7582   0.3632   0.1964
 RIO  O9    O  OH1   0  -0.692  -4.6355  -0.6895  -0.0815
 RIO  C17   C  CR15  0  -0.018  -4.2360   1.6801  -0.4007
 RIO  O10   O  OH1   0  -0.675  -4.6965   1.5041  -1.7180
 RIO  HO1   H  HOH1  0   0.474  -0.7389   3.3958   1.0467
 RIO  H1    H  HCH2  0   0.187  -2.7075   2.5802   1.7183
 RIO  H1A   H  HCH2  0   0.213  -3.5061   3.9598   0.9794
 RIO  H2    H  HCR5  0   0.241  -2.9358   3.1793  -1.2700
 RIO  H3    H  HCR5  0   0.215  -2.4207  -0.3430  -1.3775
 RIO  H4    H  HCH1  0   0.234  -0.6521  -1.4623  -1.1254
 RIO  H5    H  HCH1  0   0.205  -1.5794  -2.9309   1.3802
 RIO  HO4   H  HOH1  0   0.455  -3.0261  -3.7745  -0.3547
 RIO  H6    H  HCH1  0   0.240  -0.5687  -3.9271  -1.3070
 RIO  HN1   H  HNH2  0   0.363  -1.1020  -6.0059  -0.5358
 RIO  HN1A  H  HNH2  0   0.350  -1.4071  -5.5136   0.9803
 RIO  H7    H  HCH2  0   0.228   0.6179  -4.1435   1.4978
 RIO  H7A   H  HCH2  0   0.249   1.2918  -4.8551   0.0383
 RIO  H8    H  HCH1  0   0.205   1.5510  -2.6195  -0.9766
 RIO  HN2   H  HNH2  0   0.342   3.1838  -3.6399   0.5891
 RIO  HN2A  H  HNH2  0   0.364   3.3721  -2.0496   0.4068
 RIO  H9    H  HCH1  0   0.220   0.5263  -1.5878   1.6953
 RIO  H10   H  HCH1  0   0.238   2.0586  -0.0733   2.0886
 RIO  H11   H  HCH1  0   0.217   2.9369   0.2413  -1.3976
 RIO  H12   H  HCH2  0   0.201   5.2748   0.8939  -2.0035
 RIO  H12A  H  HCH2  0   0.225   5.7143   0.8035  -0.3043
 RIO  HN3   H  HNH2  0   0.342   4.6953  -1.4220  -1.8977
 RIO  HN3A  H  HNH2  0   0.354   6.1831  -1.2632  -1.2920
 RIO  H13   H  HCH1  0   0.213   4.0127   2.7484  -0.0360
 RIO  HO7   H  HOH1  0   0.458   4.2842   3.0110  -2.2034
 RIO  H14   H  HCH1  0   0.210   1.1680   2.0837  -0.8979
 RIO  HO8   H  HOH1  0   0.447   1.7137   4.2924  -0.9222
 RIO  H15   H  HCH1  0   0.249   2.3724   2.3267   1.8813
 RIO  HN4   H  HNH2  0   0.380  -0.2712   1.3309   1.2713
 RIO  HN4A  H  HNH2  0   0.363   0.3092   1.9229   2.6681
 RIO  H16   H  HCR5  0   0.221  -3.6281   0.5002   1.2800
 RIO  HO9   H  HOH1  0   0.461  -4.1271  -1.5189  -0.0864
 RIO  H17   H  HCR5  0   0.237  -4.9937   2.1682   0.2270
 RIO  HO10  H  HOH1  0   0.447  -5.2364   0.7050  -1.7336

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
 RIO  O1   C1    single  1.399  0.020  1.399
 RIO  C1   C2    single  1.525  0.020  1.525
 RIO  C2   O2    single  1.429  0.020  1.429
 RIO  C2   C17   single  1.526  0.020  1.526
 RIO  O2   C3    single  1.402  0.020  1.402
 RIO  C3   O3    single  1.395  0.020  1.395
 RIO  C3   C16   single  1.531  0.020  1.531
 RIO  O3   C4    single  1.411  0.020  1.411
 RIO  C4   C5    single  1.519  0.020  1.519
 RIO  C4   C9    single  1.531  0.020  1.531
 RIO  C5   O4    single  1.411  0.020  1.411
 RIO  C5   C6    single  1.524  0.020  1.524
 RIO  C6   N1    single  1.454  0.020  1.454
 RIO  C6   C7    single  1.523  0.020  1.523
 RIO  C7   C8    single  1.528  0.020  1.528
 RIO  C8   N2    single  1.454  0.020  1.454
 RIO  C8   C9    single  1.533  0.020  1.533
 RIO  C9   O5    single  1.410  0.020  1.410
 RIO  O5   C10   single  1.395  0.020  1.395
 RIO  C10  O6    single  1.395  0.020  1.395
 RIO  C10  C15   single  1.536  0.020  1.536
 RIO  O6   C11   single  1.418  0.020  1.418
 RIO  C11  C12   single  1.517  0.020  1.517
 RIO  C11  C13   single  1.530  0.020  1.530
 RIO  C12  N3    single  1.455  0.020  1.455
 RIO  C13  O7    single  1.413  0.020  1.413
 RIO  C13  C14   single  1.530  0.020  1.530
 RIO  C14  O8    single  1.407  0.020  1.407
 RIO  C14  C15   single  1.525  0.020  1.525
 RIO  C15  N4    single  1.453  0.020  1.453
 RIO  C16  O9    single  1.398  0.020  1.398
 RIO  C16  C17   single  1.523  0.020  1.523
 RIO  C17  O10   single  1.407  0.020  1.407
 RIO  O1   HO1   single  0.850  0.020  0.980
 RIO  C1   H1    single  0.970  0.020  1.090
 RIO  C1   H1A   single  0.970  0.020  1.090
 RIO  C2   H2    single  0.970  0.020  1.090
 RIO  C3   H3    single  0.970  0.020  1.090
 RIO  C4   H4    single  0.970  0.020  1.090
 RIO  C5   H5    single  0.970  0.020  1.090
 RIO  O4   HO4   single  0.850  0.020  0.980
 RIO  C6   H6    single  0.970  0.020  1.090
 RIO  N1   HN1   single  0.890  0.020  1.040
 RIO  N1   HN1A  single  0.890  0.020  1.040
 RIO  C7   H7    single  0.970  0.020  1.090
 RIO  C7   H7A   single  0.970  0.020  1.090
 RIO  C8   H8    single  0.970  0.020  1.090
 RIO  N2   HN2   single  0.890  0.020  1.040
 RIO  N2   HN2A  single  0.890  0.020  1.040
 RIO  C9   H9    single  0.970  0.020  1.090
 RIO  C10  H10   single  0.970  0.020  1.090
 RIO  C11  H11   single  0.970  0.020  1.090
 RIO  C12  H12   single  0.970  0.020  1.090
 RIO  C12  H12A  single  0.970  0.020  1.090
 RIO  N3   HN3   single  0.890  0.020  1.040
 RIO  N3   HN3A  single  0.890  0.020  1.040
 RIO  C13  H13   single  0.970  0.020  1.090
 RIO  O7   HO7   single  0.850  0.020  0.980
 RIO  C14  H14   single  0.970  0.020  1.090
 RIO  O8   HO8   single  0.850  0.020  0.980
 RIO  C15  H15   single  0.970  0.020  1.090
 RIO  N4   HN4   single  0.890  0.020  1.040
 RIO  N4   HN4A  single  0.890  0.020  1.040
 RIO  C16  H16   single  0.970  0.020  1.090
 RIO  O9   HO9   single  0.850  0.020  0.980
 RIO  C17  H17   single  0.970  0.020  1.090
 RIO  O10  HO10  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
 RIO  HO1   O1   C1   108.52  3.000
 RIO  H1A   C1   H1   106.30  3.000
 RIO  H1A   C1   C2   107.37  3.000
 RIO  H1    C1   C2   109.96  3.000
 RIO  H1A   C1   O1   108.09  3.000
 RIO  H1    C1   O1   111.83  3.000
 RIO  C2    C1   O1   112.95  3.000
 RIO  H2    C2   C17  110.41  3.000
 RIO  H2    C2   O2   107.95  3.000
 RIO  C17   C2   O2   105.36  3.000
 RIO  H2    C2   C1   108.31  3.000
 RIO  C17   C2   C1   113.28  3.000
 RIO  O2    C2   C1   111.42  3.000
 RIO  C3    O2   C2   111.18  3.000
 RIO  H3    C3   C16  111.12  3.000
 RIO  H3    C3   O3   109.88  3.000
 RIO  C16   C3   O3   110.24  3.000
 RIO  H3    C3   O2   109.40  3.000
 RIO  C16   C3   O2   105.99  3.000
 RIO  O3    C3   O2   110.13  3.000
 RIO  C4    O3   C3   117.91  3.000
 RIO  H4    C4   C9   108.22  3.000
 RIO  H4    C4   C5   108.76  3.000
 RIO  C9    C4   C5   110.78  3.000
 RIO  H4    C4   O3   110.16  3.000
 RIO  C9    C4   O3   108.81  3.000
 RIO  C5    C4   O3   110.08  3.000
 RIO  H5    C5   C6   108.24  3.000
 RIO  H5    C5   O4   110.07  3.000
 RIO  C6    C5   O4   110.04  3.000
 RIO  H5    C5   C4   108.38  3.000
 RIO  C6    C5   C4   110.44  3.000
 RIO  O4    C5   C4   109.63  3.000
 RIO  HO4   O4   C5   105.01  3.000
 RIO  H6    C6   C7   108.64  3.000
 RIO  H6    C6   N1   106.90  3.000
 RIO  C7    C6   N1   116.06  3.000
 RIO  H6    C6   C5   107.80  3.000
 RIO  C7    C6   C5   109.38  3.000
 RIO  N1    C6   C5   107.76  3.000
 RIO  HN1A  N1   HN1  106.50  3.000
 RIO  HN1A  N1   C6   110.26  3.000
 RIO  HN1   N1   C6   110.47  3.000
 RIO  H7A   C7   H7   106.78  3.000
 RIO  H7A   C7   C8   109.09  3.000
 RIO  H7    C7   C8   109.42  3.000
 RIO  H7A   C7   C6   109.46  3.000
 RIO  H7    C7   C6   109.74  3.000
 RIO  C8    C7   C6   112.20  3.000
 RIO  H8    C8   C9   107.13  3.000
 RIO  H8    C8   N2   112.47  3.000
 RIO  C9    C8   N2   110.89  3.000
 RIO  H8    C8   C7   107.80  3.000
 RIO  C9    C8   C7   109.55  3.000
 RIO  N2    C8   C7   108.92  3.000
 RIO  HN2A  N2   HN2  105.31  3.000
 RIO  HN2A  N2   C8   110.94  3.000
 RIO  HN2   N2   C8   108.43  3.000
 RIO  H9    C9   O5   110.15  3.000
 RIO  H9    C9   C8   108.15  3.000
 RIO  O5    C9   C8   113.06  3.000
 RIO  H9    C9   C4   109.46  3.000
 RIO  O5    C9   C4   105.41  3.000
 RIO  C8    C9   C4   110.56  3.000
 RIO  C10   O5   C9   120.48  3.000
 RIO  H10   C10  C15  109.72  3.000
 RIO  H10   C10  O6   106.06  3.000
 RIO  C15   C10  O6   110.53  3.000
 RIO  H10   C10  O5   110.86  3.000
 RIO  C15   C10  O5   108.43  3.000
 RIO  O6    C10  O5   111.23  3.000
 RIO  C11   O6   C10  114.38  3.000
 RIO  H11   C11  C13  108.15  3.000
 RIO  H11   C11  C12  107.95  3.000
 RIO  C13   C11  C12  113.90  3.000
 RIO  H11   C11  O6   110.46  3.000
 RIO  C13   C11  O6   109.30  3.000
 RIO  C12   C11  O6   107.07  3.000
 RIO  H12A  C12  H12  106.63  3.000
 RIO  H12A  C12  N3   108.78  3.000
 RIO  H12   C12  N3   113.25  3.000
 RIO  H12A  C12  C11  109.20  3.000
 RIO  H12   C12  C11  108.46  3.000
 RIO  N3    C12  C11  110.39  3.000
 RIO  HN3A  N3   HN3  105.75  3.000
 RIO  HN3A  N3   C12  109.38  3.000
 RIO  HN3   N3   C12  109.32  3.000
 RIO  H13   C13  C14  107.86  3.000
 RIO  H13   C13  O7   110.95  3.000
 RIO  C14   C13  O7   107.04  3.000
 RIO  H13   C13  C11  108.52  3.000
 RIO  C14   C13  C11  110.82  3.000
 RIO  O7    C13  C11  111.60  3.000
 RIO  HO7   O7   C13  109.15  3.000
 RIO  H14   C14  C15  108.47  3.000
 RIO  H14   C14  O8   110.54  3.000
 RIO  C15   C14  O8   108.38  3.000
 RIO  H14   C14  C13  108.51  3.000
 RIO  C15   C14  C13  110.20  3.000
 RIO  O8    C14  C13  110.71  3.000
 RIO  HO8   O8   C14  107.70  3.000
 RIO  H15   C15  N4   107.87  3.000
 RIO  H15   C15  C14  107.91  3.000
 RIO  N4    C15  C14  111.71  3.000
 RIO  H15   C15  C10  107.00  3.000
 RIO  N4    C15  C10  112.49  3.000
 RIO  C14   C15  C10  109.62  3.000
 RIO  HN4A  N4   HN4  106.58  3.000
 RIO  HN4A  N4   C15  110.00  3.000
 RIO  HN4   N4   C15  109.33  3.000
 RIO  H16   C16  C17  108.40  3.000
 RIO  H16   C16  O9   111.34  3.000
 RIO  C17   C16  O9   112.11  3.000
 RIO  H16   C16  C3   107.87  3.000
 RIO  C17   C16  C3   102.26  3.000
 RIO  O9    C16  C3   114.34  3.000
 RIO  HO9   O9   C16  108.36  3.000
 RIO  H17   C17  O10  111.40  3.000
 RIO  H17   C17  C16  112.13  3.000
 RIO  O10   C17  C16  111.21  3.000
 RIO  H17   C17  C2   111.64  3.000
 RIO  O10   C17  C2   109.02  3.000
 RIO  C16   C17  C2   100.98  3.000
 RIO  HO10  O10  C17  107.59  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
 RIO  Var_01  HN3  N3  C12  C11  68.94  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
 RIO  chir_01  C2   C1   O2   C17  negativ
 RIO  chir_02  C3   O2   O3   C16  negativ
 RIO  chir_03  C4   O3   C9   C5   negativ
 RIO  chir_04  C5   O4   C4   C6   positiv
 RIO  chir_05  C6   N1   C7   C5   positiv
 RIO  chir_06  C8   N2   C9   C7   positiv
 RIO  chir_07  C9   O5   C4   C8   negativ
 RIO  chir_08  C10  O5   O6   C15  negativ
 RIO  chir_09  C11  O6   C12  C13  positiv
 RIO  chir_10  C13  O7   C11  C14  positiv
 RIO  chir_11  C14  O8   C13  C15  negativ
 RIO  chir_12  C15  N4   C14  C10  positiv
 RIO  chir_13  C16  C3   O9   C17  positiv
 RIO  chir_14  C17  O10  C2   C16  positiv

