# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 12 07:49:37 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-phenyl-1~{H}-imidazol-4-yl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1O)c2c[nH]c(n2)c3ccccc3
#
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
 KUQ  KUQ  (2~{R},3~{S},4~{R},5~{R},6~{S})-2-(hydroxymethyl)-6-(2-phenyl-1~{H}-imidazol-4-yl)oxane-3,4,5-triol  ligand  40  22  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_KUQ
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
 KUQ  C11  C  CR16  0  -0.309  -4.7592   0.2346   0.6196
 KUQ  N3   N  NR15  0  -0.642  -2.1595   0.1209   2.0576
 KUQ  C10  C  CR16  0  -0.237  -5.9362   0.2896  -0.1125
 KUQ  C8   C  CR16  0  -0.238  -4.6809   0.1023  -2.1486
 KUQ  C7   C  CR16  0  -0.297  -3.5039   0.0475  -1.4209
 KUQ  C4   C  CR5   0   0.461  -2.2672   0.0516   0.7095
 KUQ  C9   C  CR16  0  -0.263  -5.9034   0.2237  -1.4987
 KUQ  O5'  O  O2    0  -0.498   1.6987   0.9141   0.2105
 KUQ  C5'  C  CH1   0  -0.010   3.0901   0.9733  -0.0109
 KUQ  C4'  C  CH1   0   0.040   3.5322  -0.2278  -0.8475
 KUQ  C3'  C  CH1   0  -0.023   3.1072  -1.5117  -0.1471
 KUQ  C2'  C  CH1   0   0.020   1.6153  -1.4894   0.1624
 KUQ  C1'  C  CH1   0  -0.060   1.2780  -0.2182   0.9436
 KUQ  C1   C  CR5   0   0.158  -0.1837  -0.0879   1.1857
 KUQ  N5   N  N     0  -0.465  -1.0811  -0.0773   0.1615
 KUQ  C2   C  CR15  0  -0.126  -0.8392   0.0353   2.3785
 KUQ  C6   C  CR6   0   0.040  -3.5279   0.1133  -0.0259
 KUQ  O2'  O  OH1   0  -0.674   1.2346  -2.5913   0.9518
 KUQ  O3'  O  OH1   0  -0.678   3.4558  -2.5945  -0.9856
 KUQ  O4'  O  OH1   0  -0.675   4.9284  -0.1689  -1.0076
 KUQ  H1   H  HCR6  0   0.244  -4.8219   0.2856   1.6996
 KUQ  H2   H  HNR5  0   0.423  -2.9081   0.2212   2.7240
 KUQ  H3   H  HCR6  0   0.262  -6.8815   0.3851   0.4054
 KUQ  H4   H  HCR6  0   0.260  -4.6437   0.0512  -3.2289
 KUQ  H5   H  HCR6  0   0.253  -2.5557  -0.0483  -1.9329
 KUQ  H6   H  HCR6  0   0.260  -6.8219   0.2671  -2.0691
 KUQ  H7   H  HCH1  0   0.214   3.6312   0.9460   0.9501
 KUQ  H8   H  HCH1  0   0.207   3.0218  -0.1739  -1.8230
 KUQ  H9   H  HCH1  0   0.216   3.6543  -1.5723   0.8063
 KUQ  H10  H  HCH1  0   0.218   1.0516  -1.4656  -0.7804
 KUQ  H11  H  HCH1  0   0.227   1.7978  -0.2569   1.9145
 KUQ  H13  H  HCR5  0   0.292  -0.4900   0.0666   3.3968
 KUQ  H14  H  HOH1  0   0.456   1.1106  -3.3521   0.3777
 KUQ  H15  H  HOH1  0   0.459   3.6197  -3.3690  -0.4406
 KUQ  H16  H  HOH1  0   0.452   5.2082  -0.9749  -1.4549
 KUQ  H19  H  HOH1  0   0.456   3.2949   4.1678  -0.2621
 KUQ  C6'  C  CH2   0  -0.156   3.3897   2.2867  -0.7027
 KUQ  O6'  O  OH1   0  -0.671   3.0442   3.3427   0.1622
 KUQ  H17  H  HCH2  0   0.211   4.4529   2.3087  -0.9631
 KUQ  H18  H  HCH2  0   0.195   2.8241   2.3285  -1.6441

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
 KUQ  O3'  C3'  single    1.413  0.020  1.413
 KUQ  O4'  C4'  single    1.407  0.020  1.407
 KUQ  C3'  C4'  single    1.523  0.020  1.523
 KUQ  C3'  C2'  single    1.524  0.020  1.524
 KUQ  C4'  C5'  single    1.529  0.020  1.529
 KUQ  O2'  C2'  single    1.408  0.020  1.408
 KUQ  C2'  C1'  single    1.530  0.020  1.530
 KUQ  O6'  C6'  single    1.408  0.020  1.408
 KUQ  C5'  C6'  single    1.514  0.020  1.514
 KUQ  C5'  O5'  single    1.410  0.020  1.410
 KUQ  C1'  O5'  single    1.413  0.020  1.413
 KUQ  C1'  C1   single    1.487  0.020  1.487
 KUQ  C2   C1   aromatic  1.367  0.020  1.367
 KUQ  C2   N3   aromatic  1.361  0.020  1.361
 KUQ  C1   N5   aromatic  1.362  0.020  1.362
 KUQ  N3   C4   aromatic  1.354  0.020  1.354
 KUQ  N5   C4   aromatic  1.313  0.020  1.313
 KUQ  C4   C6   single    1.461  0.020  1.461
 KUQ  C6   C7   aromatic  1.397  0.020  1.397
 KUQ  C6   C11  aromatic  1.396  0.020  1.396
 KUQ  C7   C8   aromatic  1.385  0.020  1.385
 KUQ  C11  C10  aromatic  1.387  0.020  1.387
 KUQ  C8   C9   aromatic  1.390  0.020  1.390
 KUQ  C10  C9   aromatic  1.388  0.020  1.388
 KUQ  C11  H1   single    0.930  0.020  1.080
 KUQ  N3   H2   single    0.860  0.020  1.020
 KUQ  C10  H3   single    0.930  0.020  1.080
 KUQ  C8   H4   single    0.930  0.020  1.080
 KUQ  C7   H5   single    0.930  0.020  1.080
 KUQ  C9   H6   single    0.930  0.020  1.080
 KUQ  C5'  H7   single    0.970  0.020  1.090
 KUQ  C4'  H8   single    0.970  0.020  1.090
 KUQ  C3'  H9   single    0.970  0.020  1.090
 KUQ  C2'  H10  single    0.970  0.020  1.090
 KUQ  C1'  H11  single    0.970  0.020  1.090
 KUQ  C2   H13  single    0.930  0.020  1.080
 KUQ  O2'  H14  single    0.850  0.020  0.980
 KUQ  O3'  H15  single    0.850  0.020  0.980
 KUQ  O4'  H16  single    0.850  0.020  0.980
 KUQ  C6'  H17  single    0.970  0.020  1.090
 KUQ  C6'  H18  single    0.970  0.020  1.090
 KUQ  O6'  H19  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
 KUQ  H1   C11  C6   121.09  3.000
 KUQ  H1   C11  C10  118.38  3.000
 KUQ  C6   C11  C10  120.53  3.000
 KUQ  H2   N3   C2   124.83  3.000
 KUQ  H2   N3   C4   127.20  3.000
 KUQ  C2   N3   C4   107.97  3.000
 KUQ  H3   C10  C9   120.18  3.000
 KUQ  H3   C10  C11  119.48  3.000
 KUQ  C9   C10  C11  120.34  3.000
 KUQ  H4   C8   C9   120.08  3.000
 KUQ  H4   C8   C7   119.57  3.000
 KUQ  C9   C8   C7   120.35  3.000
 KUQ  H5   C7   C6   119.46  3.000
 KUQ  H5   C7   C8   119.98  3.000
 KUQ  C6   C7   C8   120.55  3.000
 KUQ  C6   C4   N5   125.01  3.000
 KUQ  C6   C4   N3   124.58  3.000
 KUQ  N5   C4   N3   110.41  3.000
 KUQ  H6   C9   C8   120.24  3.000
 KUQ  H6   C9   C10  120.29  3.000
 KUQ  C8   C9   C10  119.47  3.000
 KUQ  C1'  O5'  C5'  114.13  3.000
 KUQ  H7   C5'  C6'  108.81  3.000
 KUQ  H7   C5'  C4'  108.39  3.000
 KUQ  C6'  C5'  C4'  111.97  3.000
 KUQ  H7   C5'  O5'  110.25  3.000
 KUQ  C6'  C5'  O5'  107.66  3.000
 KUQ  C4'  C5'  O5'  109.77  3.000
 KUQ  H8   C4'  O4'  110.91  3.000
 KUQ  H8   C4'  C3'  108.60  3.000
 KUQ  O4'  C4'  C3'  111.38  3.000
 KUQ  H8   C4'  C5'  108.18  3.000
 KUQ  C3'  C4'  C5'  109.26  3.000
 KUQ  O4'  C4'  C5'  108.44  3.000
 KUQ  H9   C3'  O3'  110.44  3.000
 KUQ  H9   C3'  C2'  108.14  3.000
 KUQ  O3'  C3'  C2'  111.91  3.000
 KUQ  H9   C3'  C4'  107.82  3.000
 KUQ  C2'  C3'  C4'  110.74  3.000
 KUQ  O3'  C3'  C4'  107.71  3.000
 KUQ  H10  C2'  O2'  111.05  3.000
 KUQ  H10  C2'  C1'  107.89  3.000
 KUQ  O2'  C2'  C1'  107.72  3.000
 KUQ  H10  C2'  C3'  109.17  3.000
 KUQ  C1'  C2'  C3'  109.38  3.000
 KUQ  O2'  C2'  C3'  111.54  3.000
 KUQ  H11  C1'  C1   108.86  3.000
 KUQ  H11  C1'  C2'  108.47  3.000
 KUQ  C1   C1'  C2'  111.88  3.000
 KUQ  H11  C1'  O5'  110.17  3.000
 KUQ  C1   C1'  O5'  107.87  3.000
 KUQ  C2'  C1'  O5'  109.59  3.000
 KUQ  C2   C1   N5   109.86  3.000
 KUQ  N5   C1   C1'  121.73  3.000
 KUQ  C2   C1   C1'  128.42  3.000
 KUQ  C1   N5   C4   106.39  3.000
 KUQ  H13  C2   C1   132.25  3.000
 KUQ  H13  C2   N3   122.38  3.000
 KUQ  C1   C2   N3   105.38  3.000
 KUQ  C4   C6   C7   119.07  3.000
 KUQ  C7   C6   C11  118.76  3.000
 KUQ  C4   C6   C11  122.16  3.000
 KUQ  H14  O2'  C2'  108.64  3.000
 KUQ  H15  O3'  C3'  108.85  3.000
 KUQ  H16  O4'  C4'  107.82  3.000
 KUQ  H18  C6'  H17  107.18  3.000
 KUQ  H18  C6'  O6'  111.79  3.000
 KUQ  H17  C6'  O6'  111.67  3.000
 KUQ  H18  C6'  C5'  108.82  3.000
 KUQ  H17  C6'  C5'  108.55  3.000
 KUQ  O6'  C6'  C5'  108.74  3.000
 KUQ  H19  O6'  C6'  107.98  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
 KUQ  CONST_01  N3   C4   C6   C11    0.00  0.0  0
 KUQ  CONST_02  N5   C4   C6   C11  180.00  0.0  0
 KUQ  CONST_03  C8   C7   C6   C11    0.00  0.0  0
 KUQ  CONST_04  C8   C9   C10  C11    0.00  0.0  0
 KUQ  CONST_05  N5   C1   C2   N3     0.00  0.0  0
 KUQ  CONST_06  C1   N5   C4   N3     0.00  0.0  0
 KUQ  CONST_07  C7   C6   C4   N3   180.00  0.0  0
 KUQ  CONST_08  C4   C6   C11  C10  180.00  0.0  0
 KUQ  CONST_09  C7   C6   C11  C10    0.00  0.0  0
 KUQ  CONST_10  C7   C8   C9   C10    0.00  0.0  0
 KUQ  CONST_11  C4   C6   C7   C8   180.00  0.0  0
 KUQ  CONST_12  N5   C4   C6   C7     0.00  0.0  0
 KUQ  CONST_13  C1   C2   N3   C4     0.00  0.0  0
 KUQ  CONST_14  C2   C1   N5   C4     0.00  0.0  0
 KUQ  CONST_15  C6   C7   C8   C9     0.00  0.0  0
 KUQ  CONST_16  C6   C11  C10  C9     0.00  0.0  0
 KUQ  CONST_17  C6   C4   N5   C1   180.00  0.0  0
 KUQ  CONST_18  C2   N3   C4   N5     0.00  0.0  0
 KUQ  CONST_19  C6   C4   N3   C2   180.00  0.0  0
 KUQ  CONST_20  C1'  C1   C2   N3   180.00  0.0  0
 KUQ  CONST_21  C1'  C1   N5   C4   180.00  0.0  0
 KUQ  CONST_22  H5   C7   C6   C11  180.00  0.0  0
 KUQ  CONST_23  H6   C9   C10  C11  180.00  0.0  0
 KUQ  CONST_24  H4   C8   C9   C10  180.00  0.0  0
 KUQ  CONST_25  H3   C10  C9   C8   180.00  0.0  0
 KUQ  CONST_26  H1   C11  C6   C7   180.00  0.0  0
 KUQ  CONST_27  H13  C2   N3   C4   180.00  0.0  0
 KUQ  CONST_28  H2   N3   C2   C1   180.00  0.0  0

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
 KUQ  chir_01  C5'  C4'  C6'  O5'  negativ
 KUQ  chir_02  C4'  O4'  C5'  C3'  positiv
 KUQ  chir_03  C3'  O3'  C4'  C2'  negativ
 KUQ  chir_04  C2'  O2'  C3'  C1'  positiv
 KUQ  chir_05  C1'  O5'  C1   C2'  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 KUQ  plan-1  N3   0.020
 KUQ  plan-1  C4   0.020
 KUQ  plan-1  C1'  0.020
 KUQ  plan-1  C1   0.020
 KUQ  plan-1  N5   0.020
 KUQ  plan-1  C2   0.020
 KUQ  plan-1  C6   0.020
 KUQ  plan-1  H2   0.020
 KUQ  plan-1  H13  0.020
 KUQ  plan-2  C11  0.020
 KUQ  plan-2  C10  0.020
 KUQ  plan-2  C8   0.020
 KUQ  plan-2  C7   0.020
 KUQ  plan-2  C4   0.020
 KUQ  plan-2  C9   0.020
 KUQ  plan-2  C6   0.020
 KUQ  plan-2  H1   0.020
 KUQ  plan-2  H3   0.020
 KUQ  plan-2  H4   0.020
 KUQ  plan-2  H5   0.020
 KUQ  plan-2  H6   0.020

