# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 17:07:20 2020
#   Inital geometry file: a 81 line input string
#   Ligand name: 5-fluoro-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=C(F)C(=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
 DK4  DK4  5-fluoro-1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]pyrimidine-2,4-dione  D-saccharide  32  20  .  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_DK4
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
 DK4  C1   C  CH1   0   0.168  -0.3811   0.1910   0.5501
 DK4  N1   N  NR6   0  -0.560   1.0482   0.0399   0.3704
 DK4  C2   C  CH1   0  -0.038  -0.9004   1.4297  -0.1824
 DK4  N2   N  NR16  0  -0.740   3.2270   0.0901   1.1457
 DK4  O2   O  OH1   0  -0.658  -0.2760   2.5411   0.3938
 DK4  C3   C  CH1   0   0.160  -2.4110   1.4536  -0.0281
 DK4  F3   F  F     0  -0.373  -2.9254   2.5111  -0.7769
 DK4  C4   C  CH1   0  -0.020  -3.0440   0.1537  -0.4982
 DK4  O4   O  OH1   0  -0.665  -4.4196   0.1208  -0.2224
 DK4  C5   C  CH1   0  -0.030  -2.3842  -1.0109   0.2464
 DK4  O5   O  O2    0  -0.486  -0.9804  -0.9666   0.0559
 DK4  C6   C  CH2   0  -0.154  -2.8702  -2.3523  -0.2580
 DK4  O6   O  OH1   0  -0.668  -2.2819  -3.3643   0.5209
 DK4  C7   C  CR16  0  -0.079   1.5271  -0.2661  -0.8787
 DK4  C8   C  CR6   0   0.291   2.8338  -0.3915  -1.1161
 DK4  F8   F  F     0  -0.292   3.2974  -0.6975  -2.3290
 DK4  C9   C  CR6   0   0.473   3.8134  -0.2109  -0.0669
 DK4  O9   O  O     0  -0.441   5.0138  -0.3069  -0.2025
 DK4  C10  C  CR6   0   0.745   1.8929   0.2298   1.4432
 DK4  O10  O  O     0  -0.469   1.5112   0.4962   2.5613
 DK4  H1   H  HCH1  0   0.288  -0.5583   0.3082   1.6247
 DK4  H2   H  HCH1  0   0.251  -0.6618   1.3415  -1.2526
 DK4  HN2  H  HNR6  0   0.437   3.8576   0.2299   1.9265
 DK4  HO2  H  HOH1  0   0.467  -0.3401   3.2862  -0.2110
 DK4  H3   H  HCH1  0   0.227  -2.6776   1.6378   1.0188
 DK4  H4   H  HCH1  0   0.237  -2.8471   0.0320  -1.5738
 DK4  HO4  H  HOH1  0   0.463  -4.8772   0.6853  -0.8528
 DK4  H5   H  HCH1  0   0.241  -2.6152  -0.9232   1.3198
 DK4  H6   H  HCH2  0   0.219  -3.9623  -2.3679  -0.1888
 DK4  H6A  H  HCH2  0   0.202  -2.6106  -2.4473  -1.3215
 DK4  HO6  H  HOH1  0   0.459  -2.6567  -4.2059   0.2464
 DK4  H7   H  HCR6  0   0.344   0.7991  -0.4145  -1.6640

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
 DK4  C2   C1   single  1.530  0.020  1.530
 DK4  C1   O5   single  1.394  0.020  1.394
 DK4  C1   N1   single  1.448  0.020  1.448
 DK4  C1   H1   single  0.970  0.020  1.090
 DK4  C7   N1   single  1.372  0.020  1.372
 DK4  N1   C10  single  1.379  0.020  1.379
 DK4  C3   C2   single  1.519  0.020  1.519
 DK4  O2   C2   single  1.399  0.020  1.399
 DK4  C2   H2   single  0.970  0.020  1.090
 DK4  C10  N2   single  1.374  0.020  1.374
 DK4  C9   N2   single  1.380  0.020  1.380
 DK4  N2   HN2  single  0.860  0.020  1.020
 DK4  O2   HO2  single  0.850  0.020  0.980
 DK4  F3   C3   single  1.394  0.020  1.394
 DK4  C3   C4   single  1.520  0.020  1.520
 DK4  C3   H3   single  0.970  0.020  1.090
 DK4  O4   C4   single  1.403  0.020  1.403
 DK4  C4   C5   single  1.532  0.020  1.532
 DK4  C4   H4   single  0.970  0.020  1.090
 DK4  O4   HO4  single  0.850  0.020  0.980
 DK4  C5   C6   single  1.513  0.020  1.513
 DK4  C5   O5   single  1.417  0.020  1.417
 DK4  C5   H5   single  0.970  0.020  1.090
 DK4  O6   C6   single  1.406  0.020  1.406
 DK4  C6   H6   single  0.970  0.020  1.090
 DK4  C6   H6A  single  0.970  0.020  1.090
 DK4  O6   HO6  single  0.850  0.020  0.980
 DK4  C7   C8   double  1.334  0.020  1.334
 DK4  C7   H7   single  0.930  0.020  1.080
 DK4  F8   C8   single  1.334  0.020  1.334
 DK4  C8   C9   single  1.447  0.020  1.447
 DK4  C9   O9   double  1.212  0.020  1.212
 DK4  C10  O10  double  1.211  0.020  1.211

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
 DK4  H1   C1   O5   111.53  3.000
 DK4  H1   C1   C2   109.15  3.000
 DK4  O5   C1   C2   110.90  3.000
 DK4  H1   C1   N1   107.01  3.000
 DK4  O5   C1   N1   107.08  3.000
 DK4  C2   C1   N1   111.10  3.000
 DK4  C10  N1   C7   121.69  3.000
 DK4  C10  N1   C1   119.58  3.000
 DK4  C7   N1   C1   118.72  3.000
 DK4  H2   C2   C3   108.41  3.000
 DK4  H2   C2   O2   111.57  3.000
 DK4  C3   C2   O2   112.94  3.000
 DK4  H2   C2   C1   109.09  3.000
 DK4  O2   C2   C1   107.13  3.000
 DK4  C3   C2   C1   107.56  3.000
 DK4  HN2  N2   C10  115.04  3.000
 DK4  HN2  N2   C9   116.28  3.000
 DK4  C10  N2   C9   128.68  3.000
 DK4  HO2  O2   C2   109.07  3.000
 DK4  H3   C3   C4   109.74  3.000
 DK4  H3   C3   F3   107.20  3.000
 DK4  C4   C3   F3   109.20  3.000
 DK4  H3   C3   C2   109.98  3.000
 DK4  C4   C3   C2   111.68  3.000
 DK4  F3   C3   C2   108.93  3.000
 DK4  H4   C4   C5   108.30  3.000
 DK4  H4   C4   O4   111.41  3.000
 DK4  C5   C4   O4   107.99  3.000
 DK4  H4   C4   C3   108.80  3.000
 DK4  C5   C4   C3   108.69  3.000
 DK4  O4   C4   C3   111.56  3.000
 DK4  HO4  O4   C4   108.88  3.000
 DK4  H5   C5   C6   109.16  3.000
 DK4  H5   C5   O5   109.64  3.000
 DK4  C6   C5   O5   107.52  3.000
 DK4  H5   C5   C4   108.84  3.000
 DK4  O5   C5   C4   109.72  3.000
 DK4  C6   C5   C4   111.94  3.000
 DK4  C5   O5   C1   113.84  3.000
 DK4  H6A  C6   H6   107.20  3.000
 DK4  H6A  C6   O6   112.03  3.000
 DK4  H6   C6   O6   111.86  3.000
 DK4  H6A  C6   C5   108.87  3.000
 DK4  H6   C6   C5   108.18  3.000
 DK4  O6   C6   C5   108.60  3.000
 DK4  HO6  O6   C6   107.99  3.000
 DK4  H7   C7   C8   121.16  3.000
 DK4  H7   C7   N1   117.18  3.000
 DK4  C8   C7   N1   121.65  3.000
 DK4  C9   C8   F8   116.92  3.000
 DK4  C9   C8   C7   121.49  3.000
 DK4  F8   C8   C7   121.59  3.000
 DK4  O9   C9   C8   125.43  3.000
 DK4  O9   C9   N2   122.44  3.000
 DK4  C8   C9   N2   112.13  3.000
 DK4  O10  C10  N2   121.89  3.000
 DK4  O10  C10  N1   123.75  3.000
 DK4  N2   C10  N1   114.35  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
 DK4  CONST_01  N2   C10  N1   C1  180.00  0.0  0
 DK4  CONST_02  C9   N2   C10  N1    0.00  0.0  0
 DK4  CONST_03  C7   N1   C10  N2    0.00  0.0  0
 DK4  CONST_04  C10  N2   C9   C8    0.00  0.0  0
 DK4  CONST_05  O10  C10  N1   C1    0.00  0.0  0
 DK4  CONST_06  O10  C10  N1   C7  180.00  0.0  0
 DK4  CONST_07  O10  C10  N2   C9  180.00  0.0  0
 DK4  CONST_08  C10  N2   C9   O9  180.00  0.0  0
 DK4  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
 DK4  chir_01  C1  C2  O5  N1  negativ
 DK4  chir_02  C2  O2  C1  C3  negativ
 DK4  chir_03  C3  F3  C4  C2  negativ
 DK4  chir_04  C4  O4  C5  C3  positiv
 DK4  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
 DK4  plan-1  C1   0.020
 DK4  plan-1  N1   0.020
 DK4  plan-1  N2   0.020
 DK4  plan-1  C7   0.020
 DK4  plan-1  C8   0.020
 DK4  plan-1  F8   0.020
 DK4  plan-1  C9   0.020
 DK4  plan-1  O9   0.020
 DK4  plan-1  C10  0.020
 DK4  plan-1  O10  0.020
 DK4  plan-1  HN2  0.020
 DK4  plan-1  H7   0.020

