# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 21:17:11 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[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
 GPK  GPK  5-fluoro-1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione  D-saccharide  33  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_GPK
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
 GPK  C1    C  CR16  0  -0.081  -1.9596  -0.0000  -1.1207
 GPK  F1    F  F     0  -0.293  -4.1491  -0.1551  -1.9008
 GPK  C2    C  CR6   0   0.288  -3.2671  -0.1517  -0.8989
 GPK  C3    C  CR6   0   0.472  -3.7910  -0.3224   0.4369
 GPK  O3    O  O     0  -0.445  -4.9602  -0.4692   0.7223
 GPK  N4    N  NR16  0  -0.741  -2.7924  -0.3039   1.3889
 GPK  C5    C  CR6   0   0.753  -1.4369  -0.1433   1.2141
 GPK  O5    O  O     0  -0.463  -0.6721  -0.1367   2.1515
 GPK  C1'   C  CH1   0   0.216   0.3617   0.1927  -0.4302
 GPK  N1'   N  NR6   0  -0.573  -1.0429   0.0046  -0.1009
 GPK  C2'   C  CH1   0  -0.004   0.9366   1.4914   0.1318
 GPK  O2'   O  OH1   0  -0.665   0.1700   2.5313  -0.4145
 GPK  C3'   C  CH1   0   0.000   2.4033   1.5675  -0.2719
 GPK  O3'   O  OH1   0  -0.670   2.9408   2.7219   0.3210
 GPK  C4'   C  CH1   0  -0.001   3.1386   0.3036   0.1624
 GPK  O4'   O  OH1   0  -0.671   4.4594   0.4013  -0.3186
 GPK  C5'   C  CH1   0  -0.026   2.4239  -0.9275  -0.4083
 GPK  O5'   O  O2    0  -0.479   1.0656  -0.9260  -0.0003
 GPK  C6'   C  CH2   0  -0.162   3.0397  -2.2199   0.0774
 GPK  O6'   O  OH1   0  -0.668   2.4086  -3.2988  -0.5671
 GPK  H1    H  HCR6  0   0.344  -1.5704   0.1219  -2.1217
 GPK  HN4   H  HNR6  0   0.435  -3.0871  -0.4192   2.3517
 GPK  H1'   H  HCH1  0   0.259   0.3966   0.2679  -1.5265
 GPK  H2'   H  HCH1  0   0.247   0.8818   1.4813   1.2261
 GPK  HO2'  H  HOH1  0   0.460   0.4705   3.3640  -0.0368
 GPK  H3'   H  HCH1  0   0.215   2.4573   1.6332  -1.3715
 GPK  HO3'  H  HOH1  0   0.456   3.8433   2.8331   0.0045
 GPK  H4'   H  HCH1  0   0.232   3.1170   0.2442   1.2600
 GPK  HO4'  H  HOH1  0   0.464   5.0522  -0.0485   0.2895
 GPK  H5'   H  HCH1  0   0.230   2.4857  -0.8909  -1.5084
 GPK  H6'   H  HCH2  0   0.207   4.1131  -2.1913  -0.1418
 GPK  H6'A  H  HCH2  0   0.203   2.9351  -2.2748   1.1699
 GPK  HO6'  H  HOH1  0   0.458   2.8478  -4.1080  -0.2907

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
 GPK  C1   C2    double  1.335  0.020  1.335
 GPK  C1   N1'   single  1.371  0.020  1.371
 GPK  F1   C2    single  1.335  0.020  1.335
 GPK  C2   C3    single  1.445  0.020  1.445
 GPK  C3   O3    double  1.212  0.020  1.212
 GPK  C3   N4    single  1.380  0.020  1.380
 GPK  N4   C5    single  1.376  0.020  1.376
 GPK  C5   O5    double  1.210  0.020  1.210
 GPK  C5   N1'   single  1.381  0.020  1.381
 GPK  C1'  N1'   single  1.455  0.020  1.455
 GPK  C1'  C2'   single  1.527  0.020  1.527
 GPK  C1'  O5'   single  1.390  0.020  1.390
 GPK  C2'  O2'   single  1.403  0.020  1.403
 GPK  C2'  C3'   single  1.523  0.020  1.523
 GPK  C3'  O3'   single  1.405  0.020  1.405
 GPK  C3'  C4'   single  1.525  0.020  1.525
 GPK  C4'  O4'   single  1.409  0.020  1.409
 GPK  C4'  C5'   single  1.534  0.020  1.534
 GPK  C5'  O5'   single  1.418  0.020  1.418
 GPK  C5'  C6'   single  1.512  0.020  1.512
 GPK  C6'  O6'   single  1.406  0.020  1.406
 GPK  C1   H1    single  0.930  0.020  1.080
 GPK  N4   HN4   single  0.860  0.020  1.020
 GPK  C1'  H1'   single  0.970  0.020  1.090
 GPK  C2'  H2'   single  0.970  0.020  1.090
 GPK  O2'  HO2'  single  0.850  0.020  0.980
 GPK  C3'  H3'   single  0.970  0.020  1.090
 GPK  O3'  HO3'  single  0.850  0.020  0.980
 GPK  C4'  H4'   single  0.970  0.020  1.090
 GPK  O4'  HO4'  single  0.850  0.020  0.980
 GPK  C5'  H5'   single  0.970  0.020  1.090
 GPK  C6'  H6'   single  0.970  0.020  1.090
 GPK  C6'  H6'A  single  0.970  0.020  1.090
 GPK  O6'  HO6'  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
 GPK  H1    C1   N1'  116.60  3.000
 GPK  H1    C1   C2   121.29  3.000
 GPK  N1'   C1   C2   122.11  3.000
 GPK  C3    C2   F1   117.00  3.000
 GPK  C3    C2   C1   121.48  3.000
 GPK  F1    C2   C1   121.52  3.000
 GPK  N4    C3   O3   122.49  3.000
 GPK  N4    C3   C2   111.95  3.000
 GPK  O3    C3   C2   125.56  3.000
 GPK  HN4   N4   C5   114.86  3.000
 GPK  HN4   N4   C3   116.33  3.000
 GPK  C5    N4   C3   128.81  3.000
 GPK  N1'   C5   O5   123.85  3.000
 GPK  N1'   C5   N4   114.50  3.000
 GPK  O5    C5   N4   121.66  3.000
 GPK  H1'   C1'  O5'  110.33  3.000
 GPK  H1'   C1'  C2'  107.27  3.000
 GPK  O5'   C1'  C2'  112.33  3.000
 GPK  H1'   C1'  N1'  105.38  3.000
 GPK  O5'   C1'  N1'  108.35  3.000
 GPK  C2'   C1'  N1'  112.96  3.000
 GPK  C1'   N1'  C5   120.33  3.000
 GPK  C1'   N1'  C1   118.52  3.000
 GPK  C5    N1'  C1   121.14  3.000
 GPK  H2'   C2'  C3'  108.26  3.000
 GPK  H2'   C2'  O2'  111.62  3.000
 GPK  C3'   C2'  O2'  112.71  3.000
 GPK  H2'   C2'  C1'  109.92  3.000
 GPK  C3'   C2'  C1'  107.90  3.000
 GPK  O2'   C2'  C1'  106.34  3.000
 GPK  HO2'  O2'  C2'  108.53  3.000
 GPK  H3'   C3'  C4'  108.04  3.000
 GPK  H3'   C3'  O3'  110.68  3.000
 GPK  C4'   C3'  O3'  112.11  3.000
 GPK  H3'   C3'  C2'  108.32  3.000
 GPK  C4'   C3'  C2'  110.33  3.000
 GPK  O3'   C3'  C2'  107.31  3.000
 GPK  HO3'  O3'  C3'  108.35  3.000
 GPK  H4'   C4'  C5'  108.60  3.000
 GPK  H4'   C4'  O4'  111.28  3.000
 GPK  C5'   C4'  O4'  111.44  3.000
 GPK  H4'   C4'  C3'  108.64  3.000
 GPK  C5'   C4'  C3'  109.54  3.000
 GPK  O4'   C4'  C3'  107.29  3.000
 GPK  HO4'  O4'  C4'  109.26  3.000
 GPK  H5'   C5'  C6'  109.03  3.000
 GPK  H5'   C5'  O5'  109.92  3.000
 GPK  C6'   C5'  O5'  107.38  3.000
 GPK  H5'   C5'  C4'  108.57  3.000
 GPK  C6'   C5'  C4'  112.14  3.000
 GPK  O5'   C5'  C4'  109.78  3.000
 GPK  C5'   O5'  C1'  113.38  3.000
 GPK  H6'A  C6'  H6'  107.06  3.000
 GPK  H6'A  C6'  O6'  112.00  3.000
 GPK  H6'   C6'  O6'  111.59  3.000
 GPK  H6'A  C6'  C5'  108.86  3.000
 GPK  H6'   C6'  C5'  108.20  3.000
 GPK  O6'   C6'  C5'  109.02  3.000
 GPK  HO6'  O6'  C6'  108.00  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
 GPK  CONST_01  N4   C5   N1'  C1    0.00  0.0  0
 GPK  CONST_02  C5   N4   C3   C2    0.00  0.0  0
 GPK  CONST_03  N1'  C5   N4   C3    0.00  0.0  0
 GPK  CONST_04  C1'  N1'  C5   N4  180.00  0.0  0
 GPK  CONST_05  O5   C5   N1'  C1  180.00  0.0  0
 GPK  CONST_06  O5   C5   N4   C3  180.00  0.0  0
 GPK  CONST_07  C5   N4   C3   O3  180.00  0.0  0
 GPK  CONST_08  C1'  N1'  C5   O5    0.00  0.0  0
 GPK  CONST_09  HN4  N4   C3   C2  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
 GPK  chir_01  C1'  N1'  C2'  O5'  negativ
 GPK  chir_02  C2'  O2'  C1'  C3'  negativ
 GPK  chir_03  C3'  O3'  C2'  C4'  positiv
 GPK  chir_04  C4'  O4'  C5'  C3'  positiv
 GPK  chir_05  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
 GPK  plan-1  C1   0.020
 GPK  plan-1  F1   0.020
 GPK  plan-1  C2   0.020
 GPK  plan-1  C3   0.020
 GPK  plan-1  O3   0.020
 GPK  plan-1  N4   0.020
 GPK  plan-1  C5   0.020
 GPK  plan-1  O5   0.020
 GPK  plan-1  C1'  0.020
 GPK  plan-1  N1'  0.020
 GPK  plan-1  H1   0.020
 GPK  plan-1  HN4  0.020

