# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 20:36:04 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N-[1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-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@H](O)[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
 DKY  DKY  N-[1-[(2R,3S,4S,5R,6R)-4-fluoro-3,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]-2-oxo-pyrimidin-4-yl]benzamide  ligand  45  27  .  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_DKY
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
 DKY  C1   C  CH1   0   0.203  -2.4074   0.2260   0.5662
 DKY  N1   N  NR6   0  -0.565  -0.9616   0.1414   0.4816
 DKY  C2   C  CH1   0  -0.050  -2.9865   1.4576  -0.1343
 DKY  N2   N  N     0  -0.498   1.0445  -0.0372  -0.7619
 DKY  O2   O  OH1   0  -0.664  -2.3980   2.5812   0.4626
 DKY  C3   C  CH1   0   0.157  -4.4912   1.4080   0.0707
 DKY  F3   F  F     0  -0.374  -5.0785   2.4512  -0.6462
 DKY  C4   C  CH1   0  -0.015  -5.0810   0.0867  -0.3973
 DKY  O4   O  OH1   0  -0.667  -6.4457  -0.0097  -0.0807
 DKY  C5   C  CH1   0  -0.030  -4.3490  -1.0568   0.3128
 DKY  O5   O  O2    0  -0.476  -2.9577  -0.9531   0.0742
 DKY  C6   C  CH2   0  -0.157  -4.8008  -2.4129  -0.1831
 DKY  O6   O  OH1   0  -0.668  -4.1451  -3.4060   0.5664
 DKY  C7   C  CR16  0   0.115  -0.2457   0.1899   1.6286
 DKY  C8   C  CR16  0  -0.502   1.1015   0.1258   1.6249
 DKY  C9   C  CR6   0   0.575   1.7177   0.0054   0.3495
 DKY  C10  C  CR6   0   0.615  -0.3133   0.0256  -0.7599
 DKY  O10  O  O     0  -0.485  -0.9619  -0.0170  -1.7886
 DKY  C11  C  C     0   0.542   3.9467  -0.2502  -0.7196
 DKY  O11  O  O     0  -0.410   3.5798  -0.5110  -1.8412
 DKY  C12  C  CR6   0  -0.055   5.3934  -0.1415  -0.3701
 DKY  C13  C  CR16  0  -0.258   6.3056  -0.8298  -1.1691
 DKY  C14  C  CR16  0  -0.241   7.6627  -0.7569  -0.9018
 DKY  C15  C  CR16  0  -0.246   8.1240   0.0197   0.1540
 DKY  C16  C  CR16  0  -0.239   7.2230   0.7233   0.9411
 DKY  C17  C  CR16  0  -0.292   5.8624   0.6420   0.6836
 DKY  H1   H  HCH1  0   0.257  -2.6316   0.3293   1.6382
 DKY  H2   H  HCH1  0   0.263  -2.7777   1.4080  -1.2067
 DKY  HO2  H  HOH1  0   0.466  -2.5091   3.3372  -0.1213
 DKY  H3   H  HCH1  0   0.222  -4.7340   1.5677   1.1277
 DKY  HN3  H  HNH1  0   0.435   3.5139   0.0047   1.2568
 DKY  H4   H  HCH1  0   0.236  -4.9124  -0.0138  -1.4799
 DKY  HO4  H  HOH1  0   0.462  -6.9419   0.5741  -0.6626
 DKY  H5   H  HCH1  0   0.235  -4.5481  -0.9848   1.3947
 DKY  H6   H  HCH2  0   0.218  -5.8882  -2.4719  -0.0744
 DKY  H6A  H  HCH2  0   0.201  -4.5770  -2.4919  -1.2560
 DKY  HO6  H  HOH1  0   0.459  -4.4971  -4.2599   0.3001
 DKY  H7   H  HCR6  0   0.332  -0.8072   0.2787   2.5478
 DKY  H8   H  HCR6  0   0.302   1.6643   0.1643   2.5450
 DKY  H13  H  HCR6  0   0.266   5.9520  -1.4311  -1.9960
 DKY  H14  H  HCR6  0   0.267   8.3612  -1.3065  -1.5184
 DKY  H15  H  HCR6  0   0.269   9.1845   0.0793   0.3608
 DKY  H16  H  HCR6  0   0.269   7.5780   1.3401   1.7558
 DKY  H17  H  HCR6  0   0.265   5.1846   1.2228   1.2968
 DKY  N3   N  NH1   0  -0.741   3.0898  -0.0540   0.3436

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
 DKY  C2   C1   single    1.531  0.020  1.531
 DKY  C1   O5   single    1.391  0.020  1.391
 DKY  C1   N1   single    1.451  0.020  1.451
 DKY  C1   H1   single    0.970  0.020  1.090
 DKY  C7   N1   single    1.353  0.020  1.353
 DKY  N1   C10  single    1.405  0.020  1.405
 DKY  C3   C2   single    1.519  0.020  1.519
 DKY  O2   C2   single    1.402  0.020  1.402
 DKY  C2   H2   single    0.970  0.020  1.090
 DKY  C10  N2   single    1.359  0.020  1.359
 DKY  C9   N2   double    1.300  0.020  1.300
 DKY  O2   HO2  single    0.850  0.020  0.980
 DKY  F3   C3   single    1.395  0.020  1.395
 DKY  C3   C4   single    1.521  0.020  1.521
 DKY  C3   H3   single    0.970  0.020  1.090
 DKY  C9   N3   single    1.373  0.020  1.373
 DKY  C11  N3   single    1.380  0.020  1.380
 DKY  N3   HN3  single    0.860  0.020  1.020
 DKY  O4   C4   single    1.404  0.020  1.404
 DKY  C4   C5   single    1.532  0.020  1.532
 DKY  C4   H4   single    0.970  0.020  1.090
 DKY  O4   HO4  single    0.850  0.020  0.980
 DKY  C5   C6   single    1.513  0.020  1.513
 DKY  C5   O5   single    1.415  0.020  1.415
 DKY  C5   H5   single    0.970  0.020  1.090
 DKY  O6   C6   single    1.406  0.020  1.406
 DKY  C6   H6   single    0.970  0.020  1.090
 DKY  C6   H6A  single    0.970  0.020  1.090
 DKY  O6   HO6  single    0.850  0.020  0.980
 DKY  C7   C8   double    1.349  0.020  1.349
 DKY  C7   H7   single    0.930  0.020  1.080
 DKY  C8   C9   single    1.422  0.020  1.422
 DKY  C8   H8   single    0.930  0.020  1.080
 DKY  C10  O10  double    1.217  0.020  1.217
 DKY  O11  C11  double    1.209  0.020  1.209
 DKY  C11  C12  single    1.492  0.020  1.492
 DKY  C12  C13  aromatic  1.394  0.020  1.394
 DKY  C12  C17  aromatic  1.394  0.020  1.394
 DKY  C13  C14  aromatic  1.385  0.020  1.385
 DKY  C13  H13  single    0.930  0.020  1.080
 DKY  C14  C15  aromatic  1.389  0.020  1.389
 DKY  C14  H14  single    0.930  0.020  1.080
 DKY  C16  C15  aromatic  1.388  0.020  1.388
 DKY  C15  H15  single    0.930  0.020  1.080
 DKY  C17  C16  aromatic  1.387  0.020  1.387
 DKY  C16  H16  single    0.930  0.020  1.080
 DKY  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
 DKY  H1   C1   O5   110.09  3.000
 DKY  H1   C1   C2   107.06  3.000
 DKY  O5   C1   C2   111.74  3.000
 DKY  H1   C1   N1   105.39  3.000
 DKY  O5   C1   N1   108.92  3.000
 DKY  C2   C1   N1   113.41  3.000
 DKY  C10  N1   C7   120.51  3.000
 DKY  C10  N1   C1   121.07  3.000
 DKY  C7   N1   C1   118.42  3.000
 DKY  H2   C2   C3   108.66  3.000
 DKY  H2   C2   O2   111.94  3.000
 DKY  C3   C2   O2   112.61  3.000
 DKY  H2   C2   C1   109.88  3.000
 DKY  O2   C2   C1   106.93  3.000
 DKY  C3   C2   C1   106.66  3.000
 DKY  C10  N2   C9   120.96  3.000
 DKY  HO2  O2   C2   108.85  3.000
 DKY  H3   C3   C4   109.71  3.000
 DKY  H3   C3   F3   107.06  3.000
 DKY  C4   C3   F3   109.16  3.000
 DKY  H3   C3   C2   110.16  3.000
 DKY  C4   C3   C2   111.77  3.000
 DKY  F3   C3   C2   108.85  3.000
 DKY  H4   C4   C5   108.34  3.000
 DKY  H4   C4   O4   111.38  3.000
 DKY  C5   C4   O4   107.97  3.000
 DKY  H4   C4   C3   108.83  3.000
 DKY  C5   C4   C3   108.69  3.000
 DKY  O4   C4   C3   111.55  3.000
 DKY  HO4  O4   C4   108.86  3.000
 DKY  H5   C5   C6   109.04  3.000
 DKY  H5   C5   O5   109.76  3.000
 DKY  C6   C5   O5   107.69  3.000
 DKY  H5   C5   C4   108.65  3.000
 DKY  O5   C5   C4   109.68  3.000
 DKY  C6   C5   C4   111.99  3.000
 DKY  C5   O5   C1   113.04  3.000
 DKY  H6A  C6   H6   107.19  3.000
 DKY  H6A  C6   O6   112.00  3.000
 DKY  H6   C6   O6   111.86  3.000
 DKY  H6A  C6   C5   108.88  3.000
 DKY  H6   C6   C5   108.20  3.000
 DKY  O6   C6   C5   108.60  3.000
 DKY  HO6  O6   C6   107.99  3.000
 DKY  H7   C7   C8   121.68  3.000
 DKY  H7   C7   N1   116.68  3.000
 DKY  C8   C7   N1   121.64  3.000
 DKY  H8   C8   C9   122.81  3.000
 DKY  H8   C8   C7   121.12  3.000
 DKY  C9   C8   C7   116.07  3.000
 DKY  C8   C9   N3   116.14  3.000
 DKY  C8   C9   N2   123.04  3.000
 DKY  N3   C9   N2   120.81  3.000
 DKY  O10  C10  N2   121.98  3.000
 DKY  O10  C10  N1   120.25  3.000
 DKY  N2   C10  N1   117.77  3.000
 DKY  C12  C11  O11  121.83  3.000
 DKY  C12  C11  N3   114.29  3.000
 DKY  O11  C11  N3   123.87  3.000
 DKY  C17  C12  C13  119.37  3.000
 DKY  C17  C12  C11  122.96  3.000
 DKY  C13  C12  C11  117.65  3.000
 DKY  H13  C13  C14  119.80  3.000
 DKY  H13  C13  C12  119.90  3.000
 DKY  C14  C13  C12  120.29  3.000
 DKY  H14  C14  C15  120.17  3.000
 DKY  H14  C14  C13  119.73  3.000
 DKY  C15  C14  C13  120.09  3.000
 DKY  H15  C15  C16  119.99  3.000
 DKY  H15  C15  C14  120.09  3.000
 DKY  C16  C15  C14  119.91  3.000
 DKY  H16  C16  C17  119.67  3.000
 DKY  H16  C16  C15  120.21  3.000
 DKY  C17  C16  C15  120.12  3.000
 DKY  H17  C17  C16  118.51  3.000
 DKY  H17  C17  C12  121.25  3.000
 DKY  C16  C17  C12  120.21  3.000
 DKY  HN3  N3   C11  116.41  3.000
 DKY  HN3  N3   C9   114.43  3.000
 DKY  C11  N3   C9   129.06  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
 DKY  CONST_01  C15  C14  C13  C12    0.00   0.0  0
 DKY  CONST_02  C15  C16  C17  C12    0.00   0.0  0
 DKY  CONST_03  C16  C17  C12  C13    0.00   0.0  0
 DKY  CONST_04  C16  C15  C14  C13    0.00   0.0  0
 DKY  CONST_05  C17  C12  C13  C14    0.00   0.0  0
 DKY  CONST_06  C17  C16  C15  C14    0.00   0.0  0
 DKY  CONST_07  N2   C10  N1   C1   180.00   0.0  0
 DKY  CONST_08  C9   N2   C10  N1     0.00   0.0  0
 DKY  CONST_09  C7   N1   C10  N2     0.00   0.0  0
 DKY  CONST_10  C10  N2   C9   C8     0.00   0.0  0
 DKY  CONST_11  C14  C13  C12  C11  180.00   0.0  0
 DKY  CONST_12  C16  C17  C12  C11  180.00   0.0  0
 DKY  CONST_13  O10  C10  N1   C1     0.00   0.0  0
 DKY  CONST_14  C10  N2   C9   N3   180.00   0.0  0
 DKY  CONST_15  O10  C10  N1   C7   180.00   0.0  0
 DKY  CONST_16  O10  C10  N2   C9   180.00   0.0  0
 DKY  CONST_17  H14  C14  C13  C12  180.00   0.0  0
 DKY  CONST_18  H16  C16  C17  C12  180.00   0.0  0
 DKY  CONST_19  H17  C17  C12  C13  180.00   0.0  0
 DKY  CONST_20  H15  C15  C14  C13  180.00   0.0  0
 DKY  CONST_21  H13  C13  C14  C15  180.00   0.0  0
 DKY  CONST_22  C12  C11  N3   C9   180.00   0.0  0
 DKY  CONST_23  C11  N3   C9   N2     0.00   0.0  0
 DKY  CONST_24  C11  N3   C9   C8   180.00   0.0  0
 DKY  CONST_25  HN3  N3   C9   N2   180.00   0.0  0
 DKY  CONST_26  O11  C11  N3   C9     0.00   0.0  0
 DKY  Var_01    C13  C12  C11  N3   154.26  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
 DKY  chir_01  C1  C2  O5  N1  negativ
 DKY  chir_02  C2  O2  C1  C3  negativ
 DKY  chir_03  C3  F3  C4  C2  negativ
 DKY  chir_04  C4  O4  C5  C3  positiv
 DKY  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
 DKY  plan-1  C11  0.020
 DKY  plan-1  C12  0.020
 DKY  plan-1  C13  0.020
 DKY  plan-1  C14  0.020
 DKY  plan-1  C15  0.020
 DKY  plan-1  C16  0.020
 DKY  plan-1  C17  0.020
 DKY  plan-1  H13  0.020
 DKY  plan-1  H14  0.020
 DKY  plan-1  H15  0.020
 DKY  plan-1  H16  0.020
 DKY  plan-1  H17  0.020
 DKY  plan-2  C1   0.020
 DKY  plan-2  N1   0.020
 DKY  plan-2  N2   0.020
 DKY  plan-2  C7   0.020
 DKY  plan-2  C8   0.020
 DKY  plan-2  C9   0.020
 DKY  plan-2  C10  0.020
 DKY  plan-2  O10  0.020
 DKY  plan-2  C11  0.020
 DKY  plan-2  O11  0.020
 DKY  plan-2  C12  0.020
 DKY  plan-2  HN3  0.020
 DKY  plan-2  H7   0.020
 DKY  plan-2  H8   0.020
 DKY  plan-2  N3   0.020

