# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:46:22 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-(beta-D-glucopyranosyl)-5-(trifluoromethyl)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(C(=O)NC2=O)C(F)(F)F
#
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
 GPW  GPW  1-(beta-D-glucopyranosyl)-5-(trifluoromethyl)pyrimidine-2,4(1H,3H)-dione  D-saccharide  36  23  .  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_GPW
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
 GPW  F1    F  F     0  -0.309   4.4372   1.2472  -1.0897
 GPW  N1    N  NR6   0  -0.585   0.2938  -0.0068   0.3481
 GPW  C2    C  CR6   0   0.756   0.4849   0.1969   1.7103
 GPW  F2    F  F     0  -0.302   3.3234  -0.1018  -2.3419
 GPW  O2    O  O     0  -0.448  -0.4189   0.2356   2.5085
 GPW  F3    F  F     0  -0.309   4.6284  -0.8738  -0.8155
 GPW  N3    N  NR16  0  -0.739   1.7952   0.3509   2.0804
 GPW  C4    C  CR6   0   0.590   2.9221   0.3299   1.2830
 GPW  O4    O  O     0  -0.433   4.0296   0.4761   1.7565
 GPW  C5    C  CR6   0  -0.504   2.6237   0.1238  -0.1196
 GPW  C6    C  CR16  0   0.111   1.3440  -0.0325  -0.5086
 GPW  C7    C  CT    0   1.073   3.7498   0.0981  -1.0900
 GPW  C1'   C  CH1   0   0.213  -1.0494  -0.2060  -0.1817
 GPW  C2'   C  CH1   0   0.000  -1.7319  -1.4620   0.3543
 GPW  O2'   O  OH1   0  -0.665  -0.8983  -2.5423   0.0341
 GPW  C3'   C  CH1   0  -0.029  -3.0968  -1.5497  -0.3179
 GPW  O3'   O  OH1   0  -0.673  -3.7698  -2.6664   0.2197
 GPW  C4'   C  CH1   0   0.024  -3.8811  -0.2579  -0.0869
 GPW  O4'   O  OH1   0  -0.670  -5.0965  -0.2654  -0.7947
 GPW  C5'   C  CH1   0  -0.025  -3.0584   0.9349  -0.5777
 GPW  O5'   O  O2    0  -0.478  -1.7937   0.9397   0.0662
 GPW  C6'   C  CH2   0  -0.156  -3.7275   2.2576  -0.2761
 GPW  O6'   O  OH1   0  -0.670  -2.9532   3.2933  -0.8306
 GPW  H6    H  HCR6  0   0.344   1.0818  -0.1863  -1.5455
 GPW  H1'   H  HCH1  0   0.260  -0.9127  -0.3487  -1.2632
 GPW  H2'   H  HCH1  0   0.246  -1.8857  -1.3763   1.4361
 GPW  HO2'  H  HOH1  0   0.458  -1.3485  -3.3543   0.2904
 GPW  H3'   H  HCH1  0   0.230  -2.9452  -1.6736  -1.4006
 GPW  HO3'  H  HOH1  0   0.463  -4.3071  -3.0704  -0.4672
 GPW  H4'   H  HCH1  0   0.223  -4.0516  -0.1394   0.9941
 GPW  HO4'  H  HOH1  0   0.457  -5.7014  -0.8716  -0.3565
 GPW  H5'   H  HCH1  0   0.232  -2.9170   0.8418  -1.6671
 GPW  H6'   H  HCH2  0   0.217  -4.7366   2.2317  -0.6985
 GPW  H6'A  H  HCH2  0   0.200  -3.8340   2.3629   0.8125
 GPW  HO6'  H  HOH1  0   0.458  -3.4302   4.1185  -0.7070
 GPW  HN3   H  HNR6  0   0.437   1.9462   0.4926   3.0726

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
 GPW  F1   C7    single  1.339  0.020  1.339
 GPW  N1   C2    single  1.391  0.020  1.391
 GPW  N1   C6    single  1.356  0.020  1.356
 GPW  N1   C1'   single  1.458  0.020  1.458
 GPW  C2   O2    double  1.206  0.020  1.206
 GPW  C2   N3    single  1.370  0.020  1.370
 GPW  F2   C7    single  1.338  0.020  1.338
 GPW  F3   C7    single  1.339  0.020  1.339
 GPW  N3   C4    single  1.381  0.020  1.381
 GPW  C4   O4    double  1.213  0.020  1.213
 GPW  C4   C5    single  1.449  0.020  1.449
 GPW  C5   C6    double  1.347  0.020  1.347
 GPW  C5   C7    single  1.487  0.020  1.487
 GPW  C1'  C2'   single  1.527  0.020  1.527
 GPW  C1'  O5'   single  1.389  0.020  1.389
 GPW  C2'  O2'   single  1.402  0.020  1.402
 GPW  C2'  C3'   single  1.524  0.020  1.524
 GPW  C3'  O3'   single  1.410  0.020  1.410
 GPW  C3'  C4'   single  1.529  0.020  1.529
 GPW  C4'  O4'   single  1.406  0.020  1.406
 GPW  C4'  C5'   single  1.530  0.020  1.530
 GPW  C5'  O5'   single  1.419  0.020  1.419
 GPW  C5'  C6'   single  1.513  0.020  1.513
 GPW  C6'  O6'   single  1.407  0.020  1.407
 GPW  N3   HN3   single  0.860  0.020  1.020
 GPW  C6   H6    single  0.930  0.020  1.080
 GPW  C1'  H1'   single  0.970  0.020  1.090
 GPW  C2'  H2'   single  0.970  0.020  1.090
 GPW  O2'  HO2'  single  0.850  0.020  0.980
 GPW  C3'  H3'   single  0.970  0.020  1.090
 GPW  O3'  HO3'  single  0.850  0.020  0.980
 GPW  C4'  H4'   single  0.970  0.020  1.090
 GPW  O4'  HO4'  single  0.850  0.020  0.980
 GPW  C5'  H5'   single  0.970  0.020  1.090
 GPW  C6'  H6'   single  0.970  0.020  1.090
 GPW  C6'  H6'A  single  0.970  0.020  1.090
 GPW  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
 GPW  C1'   N1   C6   118.79  3.000
 GPW  C1'   N1   C2   120.18  3.000
 GPW  C6    N1   C2   121.03  3.000
 GPW  N3    C2   O2   122.28  3.000
 GPW  N3    C2   N1   114.36  3.000
 GPW  O2    C2   N1   123.36  3.000
 GPW  HN3   N3   C4   116.48  3.000
 GPW  HN3   N3   C2   115.00  3.000
 GPW  C4    N3   C2   128.52  3.000
 GPW  C5    C4   O4   125.66  3.000
 GPW  C5    C4   N3   113.16  3.000
 GPW  O4    C4   N3   121.18  3.000
 GPW  C7    C5   C6   121.95  3.000
 GPW  C7    C5   C4   118.58  3.000
 GPW  C6    C5   C4   119.46  3.000
 GPW  H6    C6   C5   121.62  3.000
 GPW  H6    C6   N1   114.91  3.000
 GPW  C5    C6   N1   123.47  3.000
 GPW  C5    C7   F3   112.08  3.000
 GPW  C5    C7   F2   111.84  3.000
 GPW  F3    C7   F2   107.01  3.000
 GPW  C5    C7   F1   111.95  3.000
 GPW  F3    C7   F1   106.62  3.000
 GPW  F2    C7   F1   106.99  3.000
 GPW  H1'   C1'  O5'  110.45  3.000
 GPW  H1'   C1'  C2'  107.11  3.000
 GPW  O5'   C1'  C2'  112.12  3.000
 GPW  H1'   C1'  N1   105.11  3.000
 GPW  O5'   C1'  N1   108.44  3.000
 GPW  C2'   C1'  N1   113.38  3.000
 GPW  H2'   C2'  C3'  108.31  3.000
 GPW  H2'   C2'  O2'  111.66  3.000
 GPW  C3'   C2'  O2'  112.81  3.000
 GPW  H2'   C2'  C1'  110.18  3.000
 GPW  C3'   C2'  C1'  107.03  3.000
 GPW  O2'   C2'  C1'  106.74  3.000
 GPW  HO2'  O2'  C2'  108.12  3.000
 GPW  H3'   C3'  C4'  108.34  3.000
 GPW  H3'   C3'  O3'  110.59  3.000
 GPW  C4'   C3'  O3'  111.51  3.000
 GPW  H3'   C3'  C2'  108.48  3.000
 GPW  C4'   C3'  C2'  110.13  3.000
 GPW  O3'   C3'  C2'  107.74  3.000
 GPW  HO3'  O3'  C3'  109.10  3.000
 GPW  H4'   C4'  C5'  108.33  3.000
 GPW  H4'   C4'  O4'  111.16  3.000
 GPW  C5'   C4'  O4'  107.91  3.000
 GPW  H4'   C4'  C3'  108.59  3.000
 GPW  C5'   C4'  C3'  109.54  3.000
 GPW  O4'   C4'  C3'  111.27  3.000
 GPW  HO4'  O4'  C4'  108.52  3.000
 GPW  H5'   C5'  C6'  109.12  3.000
 GPW  H5'   C5'  O5'  109.54  3.000
 GPW  C6'   C5'  O5'  107.50  3.000
 GPW  H5'   C5'  C4'  108.67  3.000
 GPW  C6'   C5'  C4'  112.33  3.000
 GPW  O5'   C5'  C4'  109.65  3.000
 GPW  C5'   O5'  C1'  113.20  3.000
 GPW  H6'A  C6'  H6'  107.17  3.000
 GPW  H6'A  C6'  O6'  111.91  3.000
 GPW  H6'   C6'  O6'  111.89  3.000
 GPW  H6'A  C6'  C5'  108.92  3.000
 GPW  H6'   C6'  C5'  108.08  3.000
 GPW  O6'   C6'  C5'  108.76  3.000
 GPW  HO6'  O6'  C6'  107.95  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
 GPW  CONST_01  C4   N3  C2  N1    0.00   0.0  0
 GPW  CONST_02  C5   C4  N3  C2    0.00   0.0  0
 GPW  CONST_03  C6   N1  C2  N3    0.00   0.0  0
 GPW  CONST_04  C1'  N1  C2  N3  180.00   0.0  0
 GPW  CONST_05  O4   C4  N3  C2  180.00   0.0  0
 GPW  CONST_06  C6   N1  C2  O2  180.00   0.0  0
 GPW  CONST_07  C1'  N1  C2  O2    0.00   0.0  0
 GPW  CONST_08  C4   N3  C2  O2  180.00   0.0  0
 GPW  CONST_09  HN3  N3  C2  N1  180.00   0.0  0
 GPW  Var_01    C4   C5  C7  F1  -60.03  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
 GPW  chir_01  C1'  N1   C2'  O5'  negativ
 GPW  chir_02  C2'  O2'  C1'  C3'  negativ
 GPW  chir_03  C3'  O3'  C2'  C4'  positiv
 GPW  chir_04  C4'  O4'  C5'  C3'  positiv
 GPW  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
 GPW  plan-1  N1   0.020
 GPW  plan-1  C2   0.020
 GPW  plan-1  O2   0.020
 GPW  plan-1  N3   0.020
 GPW  plan-1  C4   0.020
 GPW  plan-1  O4   0.020
 GPW  plan-1  C5   0.020
 GPW  plan-1  C6   0.020
 GPW  plan-1  C7   0.020
 GPW  plan-1  C1'  0.020
 GPW  plan-1  H6   0.020
 GPW  plan-1  HN3  0.020

