# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 18:35:19 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: N-[1-[(2R,4R,5R,6R)-4-fluoro-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]-2-oxo-pyrimidin-4-yl]benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](C[C@@H](F)[C@@H]1O)N2C=CC(=NC2=O)NC(=O)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
 DK5  DK5  N-[1-[(2R,4R,5R,6R)-4-fluoro-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]-2-oxo-pyrimidin-4-yl]benzamide  ligand  44  26  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DK5
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
 DK5  C1   C  CH1   0   0.213  -2.5008   0.3339   0.6638
 DK5  N1   N  NR6   0  -0.570  -1.0560   0.2068   0.5599
 DK5  C2   C  CH2   0  -0.551  -3.0606   1.6266   0.0856
 DK5  N2   N  N     0  -0.498   0.9453   0.1160  -0.7013
 DK5  C3   C  CH1   0   0.181  -4.5589   1.6056   0.3031
 DK5  F3   F  F     0  -0.374  -5.1317   2.7232  -0.3069
 DK5  C4   C  CH1   0  -0.005  -5.1818   0.3503  -0.2838
 DK5  O4   O  OH1   0  -0.669  -6.5457   0.2425   0.0332
 DK5  C5   C  CH1   0  -0.025  -4.4723  -0.8776   0.3008
 DK5  O5   O  O2    0  -0.476  -3.0788  -0.7933   0.0773
 DK5  C6   C  CH2   0  -0.157  -4.9603  -2.1634  -0.3319
 DK5  O6   O  OH1   0  -0.669  -4.3218  -3.2466   0.2993
 DK5  C7   C  CR16  0   0.117  -0.3433   0.0341   1.6977
 DK5  C8   C  CR16  0  -0.502   0.9996  -0.0885   1.6822
 DK5  C9   C  CR6   0   0.574   1.6164  -0.0258   0.4028
 DK5  C10  C  CR6   0   0.615  -0.4108   0.2151  -0.6895
 DK5  O10  O  O     0  -0.484  -1.0574   0.3150  -1.7152
 DK5  C11  C  C     0   0.541   3.8407  -0.1578  -0.6975
 DK5  O11  O  O     0  -0.409   3.4707  -0.2780  -1.8416
 DK5  C12  C  CR6   0  -0.056   5.2871  -0.0760  -0.3415
 DK5  C13  C  CR16  0  -0.290   5.7495   0.5971   0.7884
 DK5  C14  C  CR16  0  -0.239   7.1102   0.6711   1.0481
 DK5  C15  C  CR16  0  -0.246   8.0170   0.0667   0.1885
 DK5  C16  C  CR16  0  -0.240   7.5616  -0.6010  -0.9417
 DK5  C17  C  CR16  0  -0.259   6.2044  -0.6638  -1.2114
 DK5  H1   H  HCH1  0   0.251  -2.7109   0.3382   1.7424
 DK5  H2   H  HCH2  0   0.272  -2.6109   2.4790   0.5987
 DK5  H2A  H  HCH2  0   0.278  -2.8435   1.7062  -0.9782
 DK5  H3   H  HCH1  0   0.218  -4.7988   1.6676   1.3703
 DK5  HN3  H  HNH1  0   0.435   3.4148  -0.1859   1.2955
 DK5  H4   H  HCH1  0   0.228  -5.0198   0.3596  -1.3728
 DK5  HO4  H  HOH1  0   0.460  -7.0236   0.9513  -0.4088
 DK5  H5   H  HCH1  0   0.230  -4.6743  -0.9143   1.3842
 DK5  H6   H  HCH2  0   0.219  -6.0477  -2.2107  -0.2193
 DK5  H6A  H  HCH2  0   0.199  -4.7470  -2.1332  -1.4096
 DK5  HO6  H  HOH1  0   0.458  -4.7408  -4.0563  -0.0052
 DK5  H7   H  HCR6  0   0.332  -0.9056   0.0015   2.6205
 DK5  H8   H  HCR6  0   0.302   1.5581  -0.2253   2.5955
 DK5  H13  H  HCR6  0   0.266   5.0655   1.1002   1.4612
 DK5  H14  H  HCR6  0   0.269   7.4604   1.2041   1.9215
 DK5  H15  H  HCR6  0   0.269   9.0775   0.1200   0.3968
 DK5  H16  H  HCR6  0   0.267   8.2652  -1.0716  -1.6154
 DK5  H17  H  HCR6  0   0.267   5.8556  -1.1793  -2.0962
 DK5  N3   N  NH1   0  -0.740   2.9874  -0.1070   0.3853

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
 DK5  C2   C1   single    1.523  0.020  1.523
 DK5  C1   O5   single    1.396  0.020  1.396
 DK5  C1   N1   single    1.454  0.020  1.454
 DK5  C1   H1   single    0.970  0.020  1.090
 DK5  C7   N1   single    1.354  0.020  1.354
 DK5  N1   C10  single    1.406  0.020  1.406
 DK5  C3   C2   single    1.514  0.020  1.514
 DK5  C2   H2   single    0.970  0.020  1.090
 DK5  C2   H2A  single    0.970  0.020  1.090
 DK5  C10  N2   single    1.360  0.020  1.360
 DK5  C9   N2   double    1.300  0.020  1.300
 DK5  F3   C3   single    1.396  0.020  1.396
 DK5  C3   C4   single    1.519  0.020  1.519
 DK5  C3   H3   single    0.970  0.020  1.090
 DK5  C9   N3   single    1.373  0.020  1.373
 DK5  C11  N3   single    1.380  0.020  1.380
 DK5  N3   HN3  single    0.860  0.020  1.020
 DK5  O4   C4   single    1.404  0.020  1.404
 DK5  C4   C5   single    1.534  0.020  1.534
 DK5  C4   H4   single    0.970  0.020  1.090
 DK5  O4   HO4  single    0.850  0.020  0.980
 DK5  C5   C6   single    1.514  0.020  1.514
 DK5  C5   O5   single    1.414  0.020  1.414
 DK5  C5   H5   single    0.970  0.020  1.090
 DK5  O6   C6   single    1.407  0.020  1.407
 DK5  C6   H6   single    0.970  0.020  1.090
 DK5  C6   H6A  single    0.970  0.020  1.090
 DK5  O6   HO6  single    0.850  0.020  0.980
 DK5  C7   C8   double    1.349  0.020  1.349
 DK5  C7   H7   single    0.930  0.020  1.080
 DK5  C8   C9   single    1.422  0.020  1.422
 DK5  C8   H8   single    0.930  0.020  1.080
 DK5  C10  O10  double    1.217  0.020  1.217
 DK5  O11  C11  double    1.208  0.020  1.208
 DK5  C11  C12  single    1.492  0.020  1.492
 DK5  C13  C12  aromatic  1.394  0.020  1.394
 DK5  C12  C17  aromatic  1.394  0.020  1.394
 DK5  C13  C14  aromatic  1.387  0.020  1.387
 DK5  C13  H13  single    0.930  0.020  1.080
 DK5  C14  C15  aromatic  1.388  0.020  1.388
 DK5  C14  H14  single    0.930  0.020  1.080
 DK5  C15  C16  aromatic  1.389  0.020  1.389
 DK5  C15  H15  single    0.930  0.020  1.080
 DK5  C17  C16  aromatic  1.385  0.020  1.385
 DK5  C16  H16  single    0.930  0.020  1.080
 DK5  C17  H17  single    0.930  0.020  1.080

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
 DK5  H1   C1   O5   109.66  3.000
 DK5  H1   C1   C2   107.41  3.000
 DK5  O5   C1   C2   111.94  3.000
 DK5  H1   C1   N1   105.10  3.000
 DK5  O5   C1   N1   108.11  3.000
 DK5  C2   C1   N1   114.35  3.000
 DK5  C10  N1   C7   120.40  3.000
 DK5  C10  N1   C1   121.26  3.000
 DK5  C7   N1   C1   118.31  3.000
 DK5  H2A  C2   H2   108.66  3.000
 DK5  H2A  C2   C3   109.80  3.000
 DK5  H2   C2   C3   110.54  3.000
 DK5  H2A  C2   C1   111.09  3.000
 DK5  H2   C2   C1   109.45  3.000
 DK5  C3   C2   C1   107.30  3.000
 DK5  C10  N2   C9   121.03  3.000
 DK5  H3   C3   C4   109.47  3.000
 DK5  H3   C3   F3   106.88  3.000
 DK5  C4   C3   F3   108.93  3.000
 DK5  H3   C3   C2   110.85  3.000
 DK5  C4   C3   C2   111.20  3.000
 DK5  F3   C3   C2   109.40  3.000
 DK5  H4   C4   C5   108.40  3.000
 DK5  H4   C4   O4   111.52  3.000
 DK5  C5   C4   O4   107.56  3.000
 DK5  H4   C4   C3   108.35  3.000
 DK5  C5   C4   C3   108.94  3.000
 DK5  O4   C4   C3   111.99  3.000
 DK5  HO4  O4   C4   108.79  3.000
 DK5  H5   C5   C6   108.86  3.000
 DK5  H5   C5   O5   109.75  3.000
 DK5  C6   C5   O5   107.60  3.000
 DK5  H5   C5   C4   108.44  3.000
 DK5  O5   C5   C4   110.35  3.000
 DK5  C6   C5   C4   111.81  3.000
 DK5  C5   O5   C1   112.95  3.000
 DK5  H6A  C6   H6   107.16  3.000
 DK5  H6A  C6   O6   111.90  3.000
 DK5  H6   C6   O6   111.81  3.000
 DK5  H6A  C6   C5   108.90  3.000
 DK5  H6   C6   C5   108.31  3.000
 DK5  O6   C6   C5   108.67  3.000
 DK5  HO6  O6   C6   107.97  3.000
 DK5  H7   C7   C8   121.66  3.000
 DK5  H7   C7   N1   116.59  3.000
 DK5  C8   C7   N1   121.75  3.000
 DK5  H8   C8   C9   122.86  3.000
 DK5  H8   C8   C7   121.14  3.000
 DK5  C9   C8   C7   116.00  3.000
 DK5  C8   C9   N3   116.23  3.000
 DK5  C8   C9   N2   123.04  3.000
 DK5  N3   C9   N2   120.73  3.000
 DK5  O10  C10  N2   121.92  3.000
 DK5  O10  C10  N1   120.38  3.000
 DK5  N2   C10  N1   117.70  3.000
 DK5  C12  C11  O11  121.89  3.000
 DK5  C12  C11  N3   114.23  3.000
 DK5  O11  C11  N3   123.88  3.000
 DK5  C17  C12  C13  119.41  3.000
 DK5  C17  C12  C11  117.77  3.000
 DK5  C13  C12  C11  122.79  3.000
 DK5  H13  C13  C14  118.58  3.000
 DK5  H13  C13  C12  121.20  3.000
 DK5  C14  C13  C12  120.18  3.000
 DK5  H14  C14  C15  120.21  3.000
 DK5  H14  C14  C13  119.67  3.000
 DK5  C15  C14  C13  120.11  3.000
 DK5  H15  C15  C16  120.10  3.000
 DK5  H15  C15  C14  119.98  3.000
 DK5  C16  C15  C14  119.93  3.000
 DK5  H16  C16  C17  119.76  3.000
 DK5  H16  C16  C15  120.16  3.000
 DK5  C17  C16  C15  120.08  3.000
 DK5  H17  C17  C16  119.78  3.000
 DK5  H17  C17  C12  119.94  3.000
 DK5  C16  C17  C12  120.27  3.000
 DK5  HN3  N3   C11  116.31  3.000
 DK5  HN3  N3   C9   114.59  3.000
 DK5  C11  N3   C9   129.02  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
 DK5  CONST_01  C15  C14  C13  C12    0.00   0.0  0
 DK5  CONST_02  C15  C16  C17  C12    0.00   0.0  0
 DK5  CONST_03  C16  C17  C12  C13    0.00   0.0  0
 DK5  CONST_04  C16  C15  C14  C13    0.00   0.0  0
 DK5  CONST_05  C17  C12  C13  C14    0.00   0.0  0
 DK5  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 DK5  CONST_07  N2   C10  N1   C1   180.00   0.0  0
 DK5  CONST_08  C9   N2   C10  N1     0.00   0.0  0
 DK5  CONST_09  C7   N1   C10  N2     0.00   0.0  0
 DK5  CONST_10  C10  N2   C9   C8     0.00   0.0  0
 DK5  CONST_11  C14  C13  C12  C11  180.00   0.0  0
 DK5  CONST_12  C16  C17  C12  C11  180.00   0.0  0
 DK5  CONST_13  O10  C10  N1   C1     0.00   0.0  0
 DK5  CONST_14  C10  N2   C9   N3   180.00   0.0  0
 DK5  CONST_15  O10  C10  N1   C7   180.00   0.0  0
 DK5  CONST_16  O10  C10  N2   C9   180.00   0.0  0
 DK5  CONST_17  H14  C14  C13  C12  180.00   0.0  0
 DK5  CONST_18  H16  C16  C17  C12  180.00   0.0  0
 DK5  CONST_19  H17  C17  C12  C13  180.00   0.0  0
 DK5  CONST_20  H15  C15  C14  C13  180.00   0.0  0
 DK5  CONST_21  H13  C13  C14  C15  180.00   0.0  0
 DK5  CONST_22  C12  C11  N3   C9   180.00   0.0  0
 DK5  CONST_23  C11  N3   C9   N2     0.00   0.0  0
 DK5  CONST_24  C11  N3   C9   C8   180.00   0.0  0
 DK5  CONST_25  HN3  N3   C9   N2   180.00   0.0  0
 DK5  CONST_26  O11  C11  N3   C9     0.00   0.0  0
 DK5  Var_01    C13  C12  C11  N3   -28.93  30.0  2

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
 DK5  chir_01  C1  C2  O5  N1  negativ
 DK5  chir_02  C3  F3  C2  C4  positiv
 DK5  chir_03  C4  O4  C5  C3  positiv
 DK5  chir_04  C5  O5  C4  C6  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
 DK5  plan-1  C11  0.020
 DK5  plan-1  C12  0.020
 DK5  plan-1  C13  0.020
 DK5  plan-1  C14  0.020
 DK5  plan-1  C15  0.020
 DK5  plan-1  C16  0.020
 DK5  plan-1  C17  0.020
 DK5  plan-1  H13  0.020
 DK5  plan-1  H14  0.020
 DK5  plan-1  H15  0.020
 DK5  plan-1  H16  0.020
 DK5  plan-1  H17  0.020
 DK5  plan-2  C1   0.020
 DK5  plan-2  N1   0.020
 DK5  plan-2  N2   0.020
 DK5  plan-2  C7   0.020
 DK5  plan-2  C8   0.020
 DK5  plan-2  C9   0.020
 DK5  plan-2  C10  0.020
 DK5  plan-2  O10  0.020
 DK5  plan-2  C11  0.020
 DK5  plan-2  O11  0.020
 DK5  plan-2  C12  0.020
 DK5  plan-2  HN3  0.020
 DK5  plan-2  H7   0.020
 DK5  plan-2  H8   0.020
 DK5  plan-2  N3   0.020

