# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 15:21:04 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: 5-fluoro-1-[3-C-(hydroxymethyl)-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@](O)(CO)[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
 GP0  GP0  5-fluoro-1-[3-C-(hydroxymethyl)-beta-D-glucopyranosyl]pyrimidine-2,4(1H,3H)-dione  D-saccharide  37  22  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GP0
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
 GP0  C1    C  CR16  0  -0.083   2.1756  -0.1916  -1.1279
 GP0  F1    F  F     0  -0.293   4.2794  -0.4286  -2.0976
 GP0  N1    N  NR6   0  -0.575   1.3675   0.0908  -0.0561
 GP0  C2    C  CR6   0   0.289   3.5072  -0.1525  -1.0445
 GP0  C3    C  CR6   0   0.471   4.1755   0.1950   0.1885
 GP0  O3    O  O     0  -0.444   5.3757   0.2551   0.3481
 GP0  N4    N  NR16  0  -0.741   3.2787   0.4630   1.2021
 GP0  C5    C  CR6   0   0.756   1.9032   0.4325   1.1692
 GP0  O5    O  O     0  -0.464   1.2397   0.6899   2.1474
 GP0  C1'   C  CH1   0   0.220  -0.0735   0.0137  -0.2394
 GP0  C2'   C  CH1   0  -0.005  -0.7441  -1.0305   0.6496
 GP0  O2'   O  OH1   0  -0.661  -0.0715  -2.2419   0.4534
 GP0  C3'   C  CT    0   0.146  -2.2422  -1.0903   0.3014
 GP0  O3'   O  OH1   0  -0.684  -2.8201  -1.9552   1.2478
 GP0  C4'   C  CH1   0   0.015  -2.8039   0.3328   0.4673
 GP0  O4'   O  OH1   0  -0.661  -4.1519   0.3323   0.0710
 GP0  C5'   C  CH1   0  -0.034  -1.9940   1.3607  -0.3417
 GP0  O5'   O  O2    0  -0.478  -0.6140   1.2756  -0.0235
 GP0  C6'   C  CH2   0  -0.159  -2.4289   2.7773  -0.0329
 GP0  O6'   O  OH1   0  -0.668  -1.7083   3.6654  -0.8505
 GP0  C7'   C  CH2   0  -0.197  -2.4807  -1.6709  -1.1113
 GP0  H1    H  HCR6  0   0.345   1.6809  -0.4505  -2.0537
 GP0  HN4   H  HNR6  0   0.435   3.6772   0.7184   2.0981
 GP0  H1'   H  HCH1  0   0.260  -0.2028  -0.2879  -1.2877
 GP0  H2'   H  HCH1  0   0.258  -0.6762  -0.7063   1.6946
 GP0  HO2'  H  HOH1  0   0.459  -0.4972  -2.9126   0.9989
 GP0  HO3'  H  HOH1  0   0.447  -3.6118  -2.3242   0.8316
 GP0  H4'   H  HCH1  0   0.236  -2.7083   0.5935   1.5323
 GP0  HO4'  H  HOH1  0   0.459  -4.6287   0.9930   0.5803
 GP0  H5'   H  HCH1  0   0.233  -2.1393   1.1716  -1.4170
 GP0  H6'   H  HCH2  0   0.204  -3.5076   2.8549  -0.2115
 GP0  H6'A  H  HCH2  0   0.204  -2.2620   2.9732   1.0354
 GP0  HO6'  H  HOH1  0   0.458  -2.0043   4.5583  -0.6518
 GP0  H7'   H  HCH2  0   0.240  -1.7260  -2.4374  -1.3031
 GP0  O7'   O  OH1   0  -0.667  -3.7793  -2.2236  -1.1870
 GP0  H14   H  HCH2  0   0.213  -2.3544  -0.9023  -1.8796
 GP0  H15   H  HOH1  0   0.464  -3.7078  -3.1122  -1.5440

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
 GP0  C1   N1    single  1.372  0.020  1.372
 GP0  C1   C2    double  1.335  0.020  1.335
 GP0  C1   H1    single  0.930  0.020  1.080
 GP0  F1   C2    single  1.335  0.020  1.335
 GP0  N1   C5    single  1.380  0.020  1.380
 GP0  N1   C1'   single  1.455  0.020  1.455
 GP0  C2   C3    single  1.445  0.020  1.445
 GP0  C3   O3    double  1.212  0.020  1.212
 GP0  C3   N4    single  1.380  0.020  1.380
 GP0  N4   C5    single  1.376  0.020  1.376
 GP0  N4   HN4   single  0.860  0.020  1.020
 GP0  C5   O5    double  1.210  0.020  1.210
 GP0  C1'  C2'   single  1.526  0.020  1.526
 GP0  C1'  O5'   single  1.390  0.020  1.390
 GP0  C1'  H1'   single  0.970  0.020  1.090
 GP0  C2'  O2'   single  1.399  0.020  1.399
 GP0  C2'  C3'   single  1.539  0.020  1.539
 GP0  C2'  H2'   single  0.970  0.020  1.090
 GP0  O2'  HO2'  single  0.850  0.020  0.980
 GP0  C3'  O3'   single  1.406  0.020  1.406
 GP0  C3'  C4'   single  1.539  0.020  1.539
 GP0  C3'  C7'   single  1.546  0.020  1.546
 GP0  O3'  HO3'  single  0.850  0.020  0.980
 GP0  C4'  O4'   single  1.405  0.020  1.405
 GP0  C4'  C5'   single  1.539  0.020  1.539
 GP0  C4'  H4'   single  0.970  0.020  1.090
 GP0  O4'  HO4'  single  0.850  0.020  0.980
 GP0  C5'  O5'   single  1.419  0.020  1.419
 GP0  C5'  C6'   single  1.514  0.020  1.514
 GP0  C5'  H5'   single  0.970  0.020  1.090
 GP0  C6'  O6'   single  1.406  0.020  1.406
 GP0  C6'  H6'   single  0.970  0.020  1.090
 GP0  C6'  H6'A  single  0.970  0.020  1.090
 GP0  O6'  HO6'  single  0.850  0.020  0.980
 GP0  C7'  H7'   single  0.970  0.020  1.090
 GP0  C7'  O7'   single  1.413  0.020  1.413
 GP0  C7'  H14   single  0.970  0.020  1.090
 GP0  O7'  H15   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
 GP0  H1    C1   C2   121.13  3.000
 GP0  H1    C1   N1   116.67  3.000
 GP0  C2    C1   N1   122.20  3.000
 GP0  C1'   N1   C5   120.63  3.000
 GP0  C1'   N1   C1   118.31  3.000
 GP0  C5    N1   C1   121.06  3.000
 GP0  C3    C2   F1   117.10  3.000
 GP0  C3    C2   C1   121.45  3.000
 GP0  F1    C2   C1   121.45  3.000
 GP0  N4    C3   O3   122.49  3.000
 GP0  N4    C3   C2   111.90  3.000
 GP0  O3    C3   C2   125.60  3.000
 GP0  HN4   N4   C5   114.82  3.000
 GP0  HN4   N4   C3   116.29  3.000
 GP0  C5    N4   C3   128.89  3.000
 GP0  O5    C5   N4   121.61  3.000
 GP0  O5    C5   N1   123.89  3.000
 GP0  N4    C5   N1   114.50  3.000
 GP0  H1'   C1'  O5'  110.60  3.000
 GP0  H1'   C1'  C2'  108.44  3.000
 GP0  O5'   C1'  C2'  111.09  3.000
 GP0  H1'   C1'  N1   104.56  3.000
 GP0  O5'   C1'  N1   108.52  3.000
 GP0  C2'   C1'  N1   113.46  3.000
 GP0  H2'   C2'  C3'  106.70  3.000
 GP0  H2'   C2'  O2'  111.10  3.000
 GP0  C3'   C2'  O2'  113.73  3.000
 GP0  H2'   C2'  C1'  109.01  3.000
 GP0  C3'   C2'  C1'  108.81  3.000
 GP0  O2'   C2'  C1'  107.42  3.000
 GP0  HO2'  O2'  C2'  108.11  3.000
 GP0  C7'   C3'  C4'  112.93  3.000
 GP0  C7'   C3'  O3'  108.70  3.000
 GP0  C4'   C3'  O3'  110.25  3.000
 GP0  C7'   C3'  C2'  111.81  3.000
 GP0  C4'   C3'  C2'  107.15  3.000
 GP0  O3'   C3'  C2'  105.76  3.000
 GP0  HO3'  O3'  C3'  106.34  3.000
 GP0  H4'   C4'  C5'  107.74  3.000
 GP0  H4'   C4'  O4'  110.88  3.000
 GP0  C5'   C4'  O4'  110.91  3.000
 GP0  H4'   C4'  C3'  106.96  3.000
 GP0  C5'   C4'  C3'  111.65  3.000
 GP0  O4'   C4'  C3'  108.63  3.000
 GP0  HO4'  O4'  C4'  109.05  3.000
 GP0  H5'   C5'  C6'  108.78  3.000
 GP0  H5'   C5'  O5'  109.69  3.000
 GP0  C6'   C5'  O5'  106.85  3.000
 GP0  H5'   C5'  C4'  109.22  3.000
 GP0  C6'   C5'  C4'  111.52  3.000
 GP0  O5'   C5'  C4'  110.73  3.000
 GP0  C5'   O5'  C1'  113.45  3.000
 GP0  H6'A  C6'  H6'  107.18  3.000
 GP0  H6'A  C6'  O6'  112.02  3.000
 GP0  H6'   C6'  O6'  111.40  3.000
 GP0  H6'A  C6'  C5'  108.75  3.000
 GP0  H6'   C6'  C5'  108.40  3.000
 GP0  O6'   C6'  C5'  108.98  3.000
 GP0  HO6'  O6'  C6'  107.98  3.000
 GP0  H14   C7'  O7'  110.07  3.000
 GP0  H14   C7'  H7'  106.84  3.000
 GP0  O7'   C7'  H7'  110.54  3.000
 GP0  H14   C7'  C3'  111.11  3.000
 GP0  O7'   C7'  C3'  109.73  3.000
 GP0  H7'   C7'  C3'  108.50  3.000
 GP0  H15   O7'  C7'  108.26  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
 GP0  CONST_01  N4   C5  N1  C1    0.00  0.0  0
 GP0  CONST_02  C3   N4  C5  N1    0.00  0.0  0
 GP0  CONST_03  C5   N4  C3  C2    0.00  0.0  0
 GP0  CONST_04  C1'  N1  C5  N4  180.00  0.0  0
 GP0  CONST_05  O5   C5  N1  C1  180.00  0.0  0
 GP0  CONST_06  O5   C5  N4  C3  180.00  0.0  0
 GP0  CONST_07  C5   N4  C3  O3  180.00  0.0  0
 GP0  CONST_08  C1'  N1  C5  O5    0.00  0.0  0
 GP0  CONST_09  HN4  N4  C5  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
 GP0  chir_01  C1'  N1   C2'  O5'  negativ
 GP0  chir_02  C2'  O2'  C3'  C1'  positiv
 GP0  chir_03  C3'  C7'  C4'  C2'  positiv
 GP0  chir_04  C4'  O4'  C5'  C3'  positiv
 GP0  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
 GP0  plan-1  C1   0.020
 GP0  plan-1  F1   0.020
 GP0  plan-1  N1   0.020
 GP0  plan-1  C2   0.020
 GP0  plan-1  C3   0.020
 GP0  plan-1  O3   0.020
 GP0  plan-1  N4   0.020
 GP0  plan-1  C5   0.020
 GP0  plan-1  O5   0.020
 GP0  plan-1  C1'  0.020
 GP0  plan-1  H1   0.020
 GP0  plan-1  HN4  0.020

