# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 18:57:31 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: (2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{R},4~{R},5~{S},6~{S})-4-fluoranyl-2-(hydroxymethyl)-5,6-bis(oxidanyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[C@H]2[C@H](F)[C@@H](O)[C@@H](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
 D0N  D0N  (2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{R},3~{R},4~{R},5~{S},6~{S})-4-fluoranyl-2-(hydroxymethyl)-5,6-bis(oxidanyl)oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol  saccharide  44  23  .  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_D0N
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
 D0N  F3'  F  F     0  -0.374  -1.7702  -2.2912  -0.8896
 D0N  C3'  C  CH1   0   0.183  -2.1500  -1.2452  -0.0466
 D0N  C2'  C  CH1   0  -0.034  -3.5993  -0.9023  -0.3187
 D0N  O2'  O  OH1   0  -0.663  -4.3881  -2.0129   0.0063
 D0N  C1'  C  CH1   0   0.210  -3.9801   0.3488   0.4802
 D0N  O1'  O  OH1   0  -0.661  -3.9598   0.0321   1.8308
 D0N  O5'  O  O2    0  -0.499  -3.1121   1.3993   0.1491
 D0N  C5'  C  CH1   0  -0.011  -1.7445   1.1811   0.4452
 D0N  C6'  C  CH2   0  -0.172  -0.9944   2.4276   0.0258
 D0N  O6'  O  OH1   0  -0.670  -1.4487   3.5094   0.8037
 D0N  C4'  C  CH1   0  -0.038  -1.2398  -0.0557  -0.3069
 D0N  O1   O  O2    0  -0.506   0.0662  -0.3620   0.1277
 D0N  C1   C  CH1   0   0.228   0.9875  -0.7432  -0.8481
 D0N  C2   C  CH1   0  -0.008   1.9023  -1.8351  -0.2814
 D0N  O2   O  OH1   0  -0.663   1.1851  -2.8808   0.3184
 D0N  O5   O  O2    0  -0.495   1.7406   0.3390  -1.3076
 D0N  C5   C  CH1   0  -0.022   2.6020   0.9471  -0.3586
 D0N  C6   C  CH2   0  -0.160   3.2821   2.1085  -1.0520
 D0N  O6   O  OH1   0  -0.663   2.3048   3.0539  -1.4164
 D0N  C4   C  CH1   0   0.042   3.6059  -0.0768   0.1677
 D0N  O4   O  OH1   0  -0.673   4.4089   0.5558   1.1328
 D0N  C3   C  CH1   0  -0.010   2.8548  -1.2631   0.7577
 D0N  O3   O  OH1   0  -0.675   3.8160  -2.2113   1.1610
 D0N  H1   H  HCH1  0   0.228  -2.0176  -1.5959   0.9811
 D0N  H2   H  HCH1  0   0.239  -3.6977  -0.6385  -1.3813
 D0N  H3   H  HOH1  0   0.458  -5.2672  -1.8835  -0.3629
 D0N  H4   H  HCH1  0   0.242  -4.9709   0.6995   0.1667
 D0N  H5   H  HOH1  0   0.465  -4.3718   0.7469   2.3282
 D0N  H6   H  HCH1  0   0.232  -1.5998   1.0240   1.5225
 D0N  H7   H  HCH2  0   0.228   0.0756   2.2576   0.1646
 D0N  H8   H  HCH2  0   0.194  -1.1571   2.5970  -1.0479
 D0N  H9   H  HOH1  0   0.456  -0.8934   4.2685   0.6059
 D0N  H10  H  HCH1  0   0.243  -1.2548   0.1655  -1.3840
 D0N  H11  H  HCH1  0   0.244   0.4738  -1.1241  -1.7376
 D0N  H12  H  HCH1  0   0.224   2.5059  -2.2008  -1.1252
 D0N  H13  H  HOH1  0   0.452   0.6652  -3.3324  -0.3534
 D0N  H14  H  HCH1  0   0.227   2.0258   1.3344   0.4935
 D0N  H15  H  HCH2  0   0.211   4.0220   2.5361  -0.3677
 D0N  H16  H  HCH2  0   0.194   3.8303   1.7291  -1.9260
 D0N  H17  H  HOH1  0   0.455   2.7526   3.8020  -1.8211
 D0N  H18  H  HCH1  0   0.211   4.2116  -0.4368  -0.6797
 D0N  H19  H  HOH1  0   0.454   5.0217  -0.0968   1.4874
 D0N  H20  H  HCH1  0   0.219   2.2763  -0.9060   1.6233
 D0N  H21  H  HOH1  0   0.457   3.3757  -2.8958   1.6741

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
 D0N  O1'  C1'  single  1.387  0.020  1.387
 D0N  O2   C2   single  1.403  0.020  1.403
 D0N  C1'  O5'  single  1.402  0.020  1.402
 D0N  C1'  C2'  single  1.533  0.020  1.533
 D0N  O3   C3   single  1.409  0.020  1.409
 D0N  O2'  C2'  single  1.400  0.020  1.400
 D0N  C5'  O5'  single  1.416  0.020  1.416
 D0N  C5'  C6'  single  1.514  0.020  1.514
 D0N  C5'  C4'  single  1.533  0.020  1.533
 D0N  C3'  C2'  single  1.514  0.020  1.514
 D0N  C3'  C4'  single  1.520  0.020  1.520
 D0N  C3'  F3'  single  1.396  0.020  1.396
 D0N  O1   C4'  single  1.410  0.020  1.410
 D0N  O1   C1   single  1.395  0.020  1.395
 D0N  C3   C2   single  1.521  0.020  1.521
 D0N  C3   C4   single  1.523  0.020  1.523
 D0N  C6'  O6'  single  1.408  0.020  1.408
 D0N  C2   C1   single  1.533  0.020  1.533
 D0N  C1   O5   single  1.396  0.020  1.396
 D0N  O4   C4   single  1.406  0.020  1.406
 D0N  C4   C5   single  1.527  0.020  1.527
 D0N  C5   O5   single  1.419  0.020  1.419
 D0N  C5   C6   single  1.514  0.020  1.514
 D0N  C6   O6   single  1.408  0.020  1.408
 D0N  C3'  H1   single  0.970  0.020  1.090
 D0N  C2'  H2   single  0.970  0.020  1.090
 D0N  O2'  H3   single  0.850  0.020  0.980
 D0N  C1'  H4   single  0.970  0.020  1.090
 D0N  O1'  H5   single  0.850  0.020  0.980
 D0N  C5'  H6   single  0.970  0.020  1.090
 D0N  C6'  H7   single  0.970  0.020  1.090
 D0N  C6'  H8   single  0.970  0.020  1.090
 D0N  O6'  H9   single  0.850  0.020  0.980
 D0N  C4'  H10  single  0.970  0.020  1.090
 D0N  C1   H11  single  0.970  0.020  1.090
 D0N  C2   H12  single  0.970  0.020  1.090
 D0N  O2   H13  single  0.850  0.020  0.980
 D0N  C5   H14  single  0.970  0.020  1.090
 D0N  C6   H15  single  0.970  0.020  1.090
 D0N  C6   H16  single  0.970  0.020  1.090
 D0N  O6   H17  single  0.850  0.020  0.980
 D0N  C4   H18  single  0.970  0.020  1.090
 D0N  O4   H19  single  0.850  0.020  0.980
 D0N  C3   H20  single  0.970  0.020  1.090
 D0N  O3   H21  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
 D0N  H1   C3'  C4'  109.83  3.000
 D0N  H1   C3'  C2'  110.93  3.000
 D0N  C4'  C3'  C2'  111.42  3.000
 D0N  H1   C3'  F3'  107.11  3.000
 D0N  C4'  C3'  F3'  108.66  3.000
 D0N  C2'  C3'  F3'  108.76  3.000
 D0N  H2   C2'  C1'  106.60  3.000
 D0N  H2   C2'  O2'  111.36  3.000
 D0N  C1'  C2'  O2'  112.74  3.000
 D0N  H2   C2'  C3'  108.29  3.000
 D0N  O2'  C2'  C3'  108.54  3.000
 D0N  C1'  C2'  C3'  109.21  3.000
 D0N  H3   O2'  C2'  108.60  3.000
 D0N  H4   C1'  O5'  104.61  3.000
 D0N  H4   C1'  O1'  111.38  3.000
 D0N  O5'  C1'  O1'  113.07  3.000
 D0N  H4   C1'  C2'  109.66  3.000
 D0N  O5'  C1'  C2'  109.55  3.000
 D0N  O1'  C1'  C2'  108.51  3.000
 D0N  H5   O1'  C1'  109.08  3.000
 D0N  C5'  O5'  C1'  115.65  3.000
 D0N  H6   C5'  C4'  108.81  3.000
 D0N  H6   C5'  C6'  108.92  3.000
 D0N  C4'  C5'  C6'  111.42  3.000
 D0N  H6   C5'  O5'  110.76  3.000
 D0N  C4'  C5'  O5'  109.86  3.000
 D0N  C6'  C5'  O5'  107.08  3.000
 D0N  H8   C6'  H7   107.05  3.000
 D0N  H8   C6'  O6'  111.94  3.000
 D0N  H7   C6'  O6'  111.44  3.000
 D0N  H8   C6'  C5'  108.92  3.000
 D0N  H7   C6'  C5'  108.78  3.000
 D0N  O6'  C6'  C5'  108.64  3.000
 D0N  H9   O6'  C6'  107.86  3.000
 D0N  H10  C4'  O1   110.99  3.000
 D0N  H10  C4'  C5'  108.29  3.000
 D0N  O1   C4'  C5'  109.21  3.000
 D0N  H10  C4'  C3'  108.48  3.000
 D0N  O1   C4'  C3'  109.37  3.000
 D0N  C5'  C4'  C3'  110.49  3.000
 D0N  C1   O1   C4'  117.09  3.000
 D0N  H11  C1   O5   104.78  3.000
 D0N  H11  C1   C2   109.41  3.000
 D0N  O5   C1   C2   110.60  3.000
 D0N  H11  C1   O1   110.68  3.000
 D0N  O5   C1   O1   112.00  3.000
 D0N  C2   C1   O1   109.28  3.000
 D0N  H12  C2   C3   107.79  3.000
 D0N  H12  C2   O2   111.14  3.000
 D0N  C3   C2   O2   107.96  3.000
 D0N  H12  C2   C1   106.30  3.000
 D0N  C3   C2   C1   111.00  3.000
 D0N  O2   C2   C1   112.57  3.000
 D0N  H13  O2   C2   109.13  3.000
 D0N  C5   O5   C1   116.08  3.000
 D0N  H14  C5   C4   108.28  3.000
 D0N  H14  C5   C6   108.67  3.000
 D0N  C4   C5   C6   112.14  3.000
 D0N  H14  C5   O5   110.57  3.000
 D0N  C6   C5   O5   107.17  3.000
 D0N  C4   C5   O5   110.01  3.000
 D0N  H16  C6   H15  107.14  3.000
 D0N  H16  C6   O6   111.85  3.000
 D0N  H15  C6   O6   111.63  3.000
 D0N  H16  C6   C5   108.87  3.000
 D0N  H15  C6   C5   108.48  3.000
 D0N  O6   C6   C5   108.78  3.000
 D0N  H17  O6   C6   107.96  3.000
 D0N  H18  C4   C3   108.33  3.000
 D0N  H18  C4   O4   111.16  3.000
 D0N  C3   C4   O4   111.48  3.000
 D0N  H18  C4   C5   108.38  3.000
 D0N  O4   C4   C5   108.08  3.000
 D0N  C3   C4   C5   109.36  3.000
 D0N  H19  O4   C4   108.15  3.000
 D0N  H20  C3   O3   110.60  3.000
 D0N  H20  C3   C4   108.13  3.000
 D0N  O3   C3   C4   107.37  3.000
 D0N  H20  C3   C2   109.28  3.000
 D0N  C4   C3   C2   109.69  3.000
 D0N  O3   C3   C2   111.69  3.000
 D0N  H21  O3   C3   108.61  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
 D0N  chir_01  C3'  C2'  C4'  F3'  positiv
 D0N  chir_02  C2'  O2'  C1'  C3'  negativ
 D0N  chir_03  C1'  O5'  O1'  C2'  positiv
 D0N  chir_04  C5'  O5'  C6'  C4'  positiv
 D0N  chir_05  C4'  O1   C3'  C5'  negativ
 D0N  chir_06  C1   O5   O1   C2   positiv
 D0N  chir_07  C2   O2   C1   C3   negativ
 D0N  chir_08  C5   O5   C4   C6   negativ
 D0N  chir_09  C4   O4   C5   C3   positiv
 D0N  chir_10  C3   O3   C2   C4   positiv

