# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:30:44 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](F)[C@@H]1O)N2C=CC(=O)NC2=O
#
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
 DKX  DKX  1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidine-2,4-dione  D-saccharide  32  19  .  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_DKX
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
 DKX  C1   C  CH1   0   0.167  -0.1443   0.1302   0.3800
 DKX  N1   N  NR6   0  -0.564   1.2613  -0.0410   0.0763
 DKX  C2   C  CH1   0  -0.036  -0.6814   1.4391  -0.2016
 DKX  N2   N  NR16  0  -0.734   3.4897  -0.1026   0.6915
 DKX  O2   O  OH1   0  -0.658   0.0297   2.4831   0.3998
 DKX  C3   C  CH1   0   0.158  -2.1699   1.4917   0.0948
 DKX  F3   F  F     0  -0.373  -2.7150   2.6178  -0.5219
 DKX  C4   C  CH1   0  -0.018  -2.8899   0.2527  -0.4126
 DKX  O4   O  OH1   0  -0.666  -4.2317   0.2303  -0.0018
 DKX  C5   C  CH1   0  -0.028  -2.2019  -0.9904   0.1594
 DKX  O5   O  O2    0  -0.487  -0.8214  -0.9634  -0.1600
 DKX  C6   C  CH2   0  -0.156  -2.7781  -2.2671  -0.4129
 DKX  O6   O  OH1   0  -0.668  -2.1592  -3.3621   0.2160
 DKX  C7   C  CR16  0   0.100   1.6477  -0.2545  -1.2185
 DKX  C8   C  CR16  0  -0.509   2.9290  -0.3955  -1.5886
 DKX  C9   C  CR6   0   0.570   3.9694  -0.3191  -0.5915
 DKX  O9   O  O     0  -0.460   5.1635  -0.4263  -0.7955
 DKX  C10  C  CR6   0   0.736   2.1902   0.0435   1.0967
 DKX  O10  O  O     0  -0.473   1.8926   0.2284   2.2569
 DKX  H1   H  HCH1  0   0.284  -0.2376   0.1567   1.4711
 DKX  H2   H  HCH1  0   0.248  -0.5443   1.4318  -1.2929
 DKX  HO2  H  HOH1  0   0.467  -0.0694   3.2779  -0.1328
 DKX  H3   H  HCH1  0   0.227  -2.3318   1.6025   1.1730
 DKX  H4   H  HCH1  0   0.236  -2.8034   0.2212  -1.5093
 DKX  HO4  H  HOH1  0   0.463  -4.7212   0.8925  -0.4993
 DKX  H5   H  HCH1  0   0.240  -2.3292  -0.9962   1.2535
 DKX  H6   H  HCH2  0   0.221  -3.8594  -2.2585  -0.2463
 DKX  H6A  H  HCH2  0   0.201  -2.6183  -2.2732  -1.5003
 DKX  HO6  H  HOH1  0   0.459  -2.6209  -4.1600  -0.0563
 DKX  H7   H  HCR6  0   0.328   0.8510  -0.3170  -1.9453
 DKX  H8   H  HCR6  0   0.296   3.1881  -0.5671  -2.6216
 DKX  HN2  H  HNR6  0   0.428   4.1790  -0.0419   1.4312

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
 DKX  C2   C1   single  1.530  0.020  1.530
 DKX  C1   O5   single  1.395  0.020  1.395
 DKX  C1   N1   single  1.448  0.020  1.448
 DKX  C1   H1   single  0.970  0.020  1.090
 DKX  C7   N1   single  1.368  0.020  1.368
 DKX  N1   C10  single  1.382  0.020  1.382
 DKX  C3   C2   single  1.519  0.020  1.519
 DKX  O2   C2   single  1.399  0.020  1.399
 DKX  C2   H2   single  0.970  0.020  1.090
 DKX  C10  N2   single  1.369  0.020  1.369
 DKX  C9   N2   single  1.387  0.020  1.387
 DKX  O2   HO2  single  0.850  0.020  0.980
 DKX  F3   C3   single  1.395  0.020  1.395
 DKX  C3   C4   single  1.520  0.020  1.520
 DKX  C3   H3   single  0.970  0.020  1.090
 DKX  O4   C4   single  1.403  0.020  1.403
 DKX  C4   C5   single  1.532  0.020  1.532
 DKX  C4   H4   single  0.970  0.020  1.090
 DKX  O4   HO4  single  0.850  0.020  0.980
 DKX  C5   C6   single  1.513  0.020  1.513
 DKX  C5   O5   single  1.417  0.020  1.417
 DKX  C5   H5   single  0.970  0.020  1.090
 DKX  O6   C6   single  1.406  0.020  1.406
 DKX  C6   H6   single  0.970  0.020  1.090
 DKX  C6   H6A  single  0.970  0.020  1.090
 DKX  O6   HO6  single  0.850  0.020  0.980
 DKX  C7   C8   double  1.341  0.020  1.341
 DKX  C7   H7   single  0.930  0.020  1.080
 DKX  C8   C9   single  1.443  0.020  1.443
 DKX  C8   H8   single  0.930  0.020  1.080
 DKX  C9   O9   double  1.216  0.020  1.216
 DKX  C10  O10  double  1.212  0.020  1.212
 DKX  N2   HN2  single  0.860  0.020  1.020

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
 DKX  H1   C1   O5   111.29  3.000
 DKX  H1   C1   C2   109.16  3.000
 DKX  O5   C1   C2   110.68  3.000
 DKX  H1   C1   N1   107.13  3.000
 DKX  O5   C1   N1   107.29  3.000
 DKX  C2   C1   N1   111.23  3.000
 DKX  C10  N1   C7   121.23  3.000
 DKX  C10  N1   C1   119.35  3.000
 DKX  C7   N1   C1   119.41  3.000
 DKX  H2   C2   C3   108.43  3.000
 DKX  H2   C2   O2   111.60  3.000
 DKX  C3   C2   O2   112.86  3.000
 DKX  H2   C2   C1   109.13  3.000
 DKX  O2   C2   C1   107.25  3.000
 DKX  C3   C2   C1   107.43  3.000
 DKX  HN2  N2   C10  115.05  3.000
 DKX  HN2  N2   C9   116.72  3.000
 DKX  C10  N2   C9   128.23  3.000
 DKX  HO2  O2   C2   109.04  3.000
 DKX  H3   C3   C4   109.93  3.000
 DKX  H3   C3   F3   107.20  3.000
 DKX  C4   C3   F3   108.98  3.000
 DKX  H3   C3   C2   109.90  3.000
 DKX  C4   C3   C2   111.77  3.000
 DKX  F3   C3   C2   108.95  3.000
 DKX  H4   C4   C5   108.28  3.000
 DKX  H4   C4   O4   111.49  3.000
 DKX  C5   C4   O4   107.89  3.000
 DKX  H4   C4   C3   108.59  3.000
 DKX  C5   C4   C3   108.91  3.000
 DKX  O4   C4   C3   111.60  3.000
 DKX  HO4  O4   C4   108.91  3.000
 DKX  H5   C5   C6   109.10  3.000
 DKX  H5   C5   O5   109.67  3.000
 DKX  C6   C5   O5   107.56  3.000
 DKX  H5   C5   C4   108.87  3.000
 DKX  O5   C5   C4   109.75  3.000
 DKX  C6   C5   C4   111.87  3.000
 DKX  C5   O5   C1   113.61  3.000
 DKX  H6A  C6   H6   107.12  3.000
 DKX  H6A  C6   O6   111.97  3.000
 DKX  H6   C6   O6   111.89  3.000
 DKX  H6A  C6   C5   108.88  3.000
 DKX  H6   C6   C5   108.19  3.000
 DKX  O6   C6   C5   108.68  3.000
 DKX  HO6  O6   C6   107.96  3.000
 DKX  H7   C7   C8   120.85  3.000
 DKX  H7   C7   N1   115.95  3.000
 DKX  C8   C7   N1   123.19  3.000
 DKX  H8   C8   C9   119.79  3.000
 DKX  H8   C8   C7   120.70  3.000
 DKX  C9   C8   C7   119.51  3.000
 DKX  O9   C9   C8   125.97  3.000
 DKX  O9   C9   N2   120.57  3.000
 DKX  C8   C9   N2   113.46  3.000
 DKX  O10  C10  N2   122.19  3.000
 DKX  O10  C10  N1   123.43  3.000
 DKX  N2   C10  N1   114.38  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
 DKX  CONST_01  N2   C10  N1   C1  180.00  0.0  0
 DKX  CONST_02  C9   N2   C10  N1    0.00  0.0  0
 DKX  CONST_03  C7   N1   C10  N2    0.00  0.0  0
 DKX  CONST_04  C10  N2   C9   C8    0.00  0.0  0
 DKX  CONST_05  O10  C10  N1   C1    0.00  0.0  0
 DKX  CONST_06  O10  C10  N1   C7  180.00  0.0  0
 DKX  CONST_07  O10  C10  N2   C9  180.00  0.0  0
 DKX  CONST_08  C10  N2   C9   O9  180.00  0.0  0
 DKX  CONST_09  HN2  N2   C10  N1  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
 DKX  chir_01  C1  C2  O5  N1  negativ
 DKX  chir_02  C2  O2  C1  C3  negativ
 DKX  chir_03  C3  F3  C4  C2  negativ
 DKX  chir_04  C4  O4  C5  C3  positiv
 DKX  chir_05  C5  O5  C6  C4  positiv

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
 DKX  plan-1  C1   0.020
 DKX  plan-1  N1   0.020
 DKX  plan-1  N2   0.020
 DKX  plan-1  C7   0.020
 DKX  plan-1  C8   0.020
 DKX  plan-1  C9   0.020
 DKX  plan-1  O9   0.020
 DKX  plan-1  C10  0.020
 DKX  plan-1  O10  0.020
 DKX  plan-1  H7   0.020
 DKX  plan-1  H8   0.020
 DKX  plan-1  HN2  0.020

