# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 14:55:38 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2~{R},3'~{S},4'~{S},4~{a}~{R},5'~{R},6~{R},7~{R},7~{a}~{S})-4~{a},5',6-tris(hydroxymethyl)spiro[3,6,7,7~{a}-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane]-3',4',7-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@@]2(CO[C@]3(CO)O[C@H](CO)[C@@H](O)[C@@H]3O2)[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
 9F3  9F3  (2~{R},3'~{S},4'~{S},4~{a}~{R},5'~{R},6~{R},7~{R},7~{a}~{S})-4~{a},5',6-tris(hydroxymethyl)spiro[3,6,7,7~{a}-tetrahydrofuro[2,3-b][1,4]dioxine-2,2'-oxolane]-3',4',7-triol  ligand  42  22  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9F3
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
 9F3  C1   C  CH1   0  -0.037   1.0084   0.3758   1.0390
 9F3  C2   C  CT    0   0.483   1.7200   0.9084  -0.2188
 9F3  C3   C  CH1   0  -0.018   2.0488  -0.5486   1.6598
 9F3  C4   C  CH1   0  -0.013  -1.7970   1.2197   0.1958
 9F3  C5   C  CH2   0  -0.228  -0.1332   0.2601  -1.5440
 9F3  C6   C  CH1   0  -0.021   2.8293  -1.0501   0.4300
 9F3  O1   O  O2    0  -0.503   0.8582   1.2252  -1.2616
 9F3  C9   C  CH2   0  -0.171   2.5024   2.1826   0.0824
 9F3  O7   O  OH1   0  -0.668   3.1889   2.5756  -1.0774
 9F3  O2   O  O2    0  -0.516   2.5740  -0.1348  -0.6251
 9F3  C10  C  CH2   0  -0.156   2.4285  -2.4511   0.0205
 9F3  O8   O  OH1   0  -0.672   3.1927  -2.8248  -1.1006
 9F3  O4   O  OH1   0  -0.668   2.8357   0.2008   2.5514
 9F3  O    O  O2    0  -0.505  -0.1040  -0.4303   0.7257
 9F3  C    C  CT    0   0.467  -0.9637   0.0268  -0.2989
 9F3  O3   O  O2    0  -0.511  -1.8713  -0.9886  -0.5337
 9F3  C8   C  CH1   0  -0.013  -3.0609  -0.8151   0.2406
 9F3  C11  C  CH2   0  -0.162  -4.2682  -0.8173  -0.6710
 9F3  O9   O  OH1   0  -0.670  -4.3393  -2.0578  -1.3316
 9F3  C7   C  CH1   0  -0.043  -2.8981   0.5156   0.9942
 9F3  O6   O  OH1   0  -0.666  -2.4677   0.3602   2.3215
 9F3  O5   O  OH1   0  -0.663  -2.3182   1.8778  -0.9277
 9F3  H1   H  HCH1  0   0.254   0.7285   1.1883   1.7217
 9F3  H2   H  HCH1  0   0.252   1.5545  -1.3773   2.1819
 9F3  H3   H  HCH1  0   0.251  -1.2268   1.9038   0.8351
 9F3  H4   H  HCH2  0   0.254  -0.7312   0.6531  -2.3635
 9F3  H5   H  HCH2  0   0.241   0.3070  -0.6902  -1.8687
 9F3  H6   H  HCH1  0   0.241   3.9050  -1.0470   0.6495
 9F3  H7   H  HCH2  0   0.198   1.7951   2.9523   0.4228
 9F3  H8   H  HCH2  0   0.220   3.1850   1.9881   0.9145
 9F3  H9   H  HOH1  0   0.459   3.8950   3.1718  -0.8153
 9F3  H10  H  HCH2  0   0.202   2.6095  -3.1139   0.8774
 9F3  H11  H  HCH2  0   0.202   1.3522  -2.4829  -0.1882
 9F3  H12  H  HOH1  0   0.457   2.9092  -3.7005  -1.3775
 9F3  H13  H  HOH1  0   0.459   3.5496  -0.3577   2.8759
 9F3  H14  H  HCH1  0   0.245  -3.1456  -1.6471   0.9498
 9F3  H15  H  HCH2  0   0.201  -5.1542  -0.6386  -0.0474
 9F3  H16  H  HCH2  0   0.202  -4.1927   0.0212  -1.3739
 9F3  H17  H  HOH1  0   0.457  -5.1024  -2.0405  -1.9158
 9F3  H18  H  HCH1  0   0.243  -3.8257   1.1033   0.9541
 9F3  H19  H  HOH1  0   0.455  -3.1800  -0.0468   2.8243
 9F3  H20  H  HOH1  0   0.462  -2.8718   2.6041  -0.6237

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
 9F3  O8   C10  single  1.407  0.020  1.407
 9F3  C10  C6   single  1.514  0.020  1.514
 9F3  C6   O2   single  1.420  0.020  1.420
 9F3  C6   C3   single  1.541  0.020  1.541
 9F3  O2   C2   single  1.408  0.020  1.408
 9F3  C3   O4   single  1.406  0.020  1.406
 9F3  C3   C1   single  1.524  0.020  1.524
 9F3  C2   O1   single  1.389  0.020  1.389
 9F3  C2   C9   single  1.525  0.020  1.525
 9F3  C2   C1   single  1.540  0.020  1.540
 9F3  O1   C5   single  1.412  0.020  1.412
 9F3  O9   C11  single  1.407  0.020  1.407
 9F3  C11  C8   single  1.513  0.020  1.513
 9F3  O7   C9   single  1.404  0.020  1.404
 9F3  C1   O    single  1.409  0.020  1.409
 9F3  O3   C8   single  1.430  0.020  1.430
 9F3  O3   C    single  1.382  0.020  1.382
 9F3  C8   C7   single  1.538  0.020  1.538
 9F3  C5   C    single  1.515  0.020  1.515
 9F3  C    O    single  1.413  0.020  1.413
 9F3  C    C4   single  1.537  0.020  1.537
 9F3  C7   C4   single  1.531  0.020  1.531
 9F3  C7   O6   single  1.404  0.020  1.404
 9F3  C4   O5   single  1.402  0.020  1.402
 9F3  C1   H1   single  0.970  0.020  1.090
 9F3  C3   H2   single  0.970  0.020  1.090
 9F3  C4   H3   single  0.970  0.020  1.090
 9F3  C5   H4   single  0.970  0.020  1.090
 9F3  C5   H5   single  0.970  0.020  1.090
 9F3  C6   H6   single  0.970  0.020  1.090
 9F3  C9   H7   single  0.970  0.020  1.090
 9F3  C9   H8   single  0.970  0.020  1.090
 9F3  O7   H9   single  0.850  0.020  0.980
 9F3  C10  H10  single  0.970  0.020  1.090
 9F3  C10  H11  single  0.970  0.020  1.090
 9F3  O8   H12  single  0.850  0.020  0.980
 9F3  O4   H13  single  0.850  0.020  0.980
 9F3  C8   H14  single  0.970  0.020  1.090
 9F3  C11  H15  single  0.970  0.020  1.090
 9F3  C11  H16  single  0.970  0.020  1.090
 9F3  O9   H17  single  0.850  0.020  0.980
 9F3  C7   H18  single  0.970  0.020  1.090
 9F3  O6   H19  single  0.850  0.020  0.980
 9F3  O5   H20  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
 9F3  H1   C1   O    111.13  3.000
 9F3  H1   C1   C3   111.70  3.000
 9F3  O    C1   C3   106.41  3.000
 9F3  H1   C1   C2   111.70  3.000
 9F3  O    C1   C2   112.39  3.000
 9F3  C3   C1   C2   103.12  3.000
 9F3  O2   C2   C9   111.39  3.000
 9F3  C9   C2   O1   106.02  3.000
 9F3  O2   C2   O1   109.18  3.000
 9F3  C9   C2   C1   111.38  3.000
 9F3  O1   C2   C1   113.91  3.000
 9F3  O2   C2   C1   105.05  3.000
 9F3  H2   C3   O4   110.67  3.000
 9F3  H2   C3   C6   111.24  3.000
 9F3  O4   C3   C6   113.35  3.000
 9F3  H2   C3   C1   110.15  3.000
 9F3  O4   C3   C1   108.50  3.000
 9F3  C6   C3   C1   102.60  3.000
 9F3  H3   C4   O5   111.57  3.000
 9F3  H3   C4   C7   110.90  3.000
 9F3  O5   C4   C7   111.48  3.000
 9F3  H3   C4   C    112.96  3.000
 9F3  O5   C4   C    107.93  3.000
 9F3  C7   C4   C    101.58  3.000
 9F3  H5   C5   H4   108.10  3.000
 9F3  H5   C5   C    109.27  3.000
 9F3  H4   C5   C    111.92  3.000
 9F3  H5   C5   O1   111.70  3.000
 9F3  H4   C5   O1   106.84  3.000
 9F3  C    C5   O1   109.02  3.000
 9F3  H6   C6   C10  108.43  3.000
 9F3  H6   C6   O2   108.84  3.000
 9F3  C10  C6   O2   110.36  3.000
 9F3  H6   C6   C3   109.63  3.000
 9F3  O2   C6   C3   106.99  3.000
 9F3  C10  C6   C3   112.53  3.000
 9F3  C5   O1   C2   115.45  3.000
 9F3  H8   C9   H7   106.89  3.000
 9F3  H8   C9   O7   111.91  3.000
 9F3  H7   C9   O7   111.99  3.000
 9F3  H8   C9   C2   108.77  3.000
 9F3  H7   C9   C2   108.42  3.000
 9F3  O7   C9   C2   108.76  3.000
 9F3  H9   O7   C9   107.93  3.000
 9F3  C6   O2   C2   111.85  3.000
 9F3  H11  C10  H10  107.02  3.000
 9F3  H11  C10  O8   111.94  3.000
 9F3  H10  C10  O8   111.82  3.000
 9F3  H11  C10  C6   109.77  3.000
 9F3  H10  C10  C6   107.69  3.000
 9F3  O8   C10  C6   108.51  3.000
 9F3  H12  O8   C10  108.13  3.000
 9F3  H13  O4   C3   108.65  3.000
 9F3  C    O    C1   117.16  3.000
 9F3  O3   C    O    106.56  3.000
 9F3  O    C    C5   108.19  3.000
 9F3  O3   C    C5   109.49  3.000
 9F3  O    C    C4   110.33  3.000
 9F3  C5   C    C4   116.25  3.000
 9F3  O3   C    C4   105.60  3.000
 9F3  C8   O3   C    111.42  3.000
 9F3  H14  C8   C7   110.36  3.000
 9F3  H14  C8   C11  109.08  3.000
 9F3  C7   C8   C11  112.40  3.000
 9F3  H14  C8   O3   108.81  3.000
 9F3  C7   C8   O3   106.39  3.000
 9F3  C11  C8   O3   109.72  3.000
 9F3  H16  C11  H15  107.15  3.000
 9F3  H16  C11  O9   112.13  3.000
 9F3  H15  C11  O9   111.67  3.000
 9F3  H16  C11  C8   109.28  3.000
 9F3  H15  C11  C8   107.55  3.000
 9F3  O9   C11  C8   108.94  3.000
 9F3  H17  O9   C11  108.04  3.000
 9F3  H18  C7   O6   110.64  3.000
 9F3  H18  C7   C8   110.82  3.000
 9F3  O6   C7   C8   113.57  3.000
 9F3  H18  C7   C4   110.00  3.000
 9F3  O6   C7   C4   108.87  3.000
 9F3  C8   C7   C4   102.62  3.000
 9F3  H19  O6   C7   108.30  3.000
 9F3  H20  O5   C4   108.35  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
 9F3  Var_01  C  C5  O1  C2  58.03  30.0  1

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
 9F3  chir_01  C1  C3  C2   O    negativ
 9F3  chir_02  C2  O1  O2   C1   positiv
 9F3  chir_03  C3  O4  C6   C1   positiv
 9F3  chir_04  C4  O5  C    C7   positiv
 9F3  chir_05  C6  O2  C3   C10  negativ
 9F3  chir_06  C   O   C5   C4   positiv
 9F3  chir_07  C8  O3  C11  C7   positiv
 9F3  chir_08  C7  O6  C8   C4   positiv

