# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 09:21:13 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-bromo-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(Br)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
 GPU  GPU  5-bromo-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_GPU
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
 GPU  N1    N   NR6   0  -0.565   0.1473  -0.7821  -0.5647
 GPU  BR1   BR  BR    0   0.010   3.3418   1.4915   0.6534
 GPU  C2    C   CR6   0   0.745   0.6869  -1.8582  -1.2443
 GPU  O2    O   O     0  -0.464   0.0208  -2.7339  -1.7479
 GPU  N3    N   NR16  0  -0.736   2.0561  -1.8554  -1.3062
 GPU  C4    C   CR6   0   0.599   2.9427  -0.9320  -0.7856
 GPU  O4    O   O     0  -0.428   4.1401  -1.0622  -0.9149
 GPU  C5    C   CR6   0  -0.377   2.2763   0.1576  -0.0972
 GPU  C6    C   CR16  0   0.134   0.9361   0.1856  -0.0146
 GPU  C1'   C   CH1   0   0.174  -1.2919  -0.7049  -0.3755
 GPU  C2'   C   CH1   0   0.016  -1.6663  -0.9287   1.0858
 GPU  O2'   O   OH1   0  -0.661  -1.2158  -2.2042   1.4414
 GPU  C3'   C   CH1   0  -0.021  -3.1768  -0.7763   1.2081
 GPU  O3'   O   OH1   0  -0.672  -3.5198  -0.9276   2.5662
 GPU  C4'   C   CH1   0   0.018  -3.6138   0.5842   0.6645
 GPU  O4'   O   OH1   0  -0.671  -5.0157   0.6948   0.6373
 GPU  C5'   C   CH1   0  -0.021  -3.0997   0.7548  -0.7667
 GPU  O5'   O   O2    0  -0.489  -1.6937   0.5595  -0.8007
 GPU  C6'   C   CH2   0  -0.156  -3.3745   2.1378  -1.3154
 GPU  O6'   O   OH1   0  -0.669  -2.9368   2.1882  -2.6517
 GPU  HN3   H   HNR6  0   0.437   2.4650  -2.6429  -1.7956
 GPU  H6    H   HCR6  0   0.341   0.4148   0.9883   0.4884
 GPU  H1'   H   HCH1  0   0.282  -1.7377  -1.4944  -0.9899
 GPU  H2'   H   HCH1  0   0.229  -1.1882  -0.1480   1.7004
 GPU  HO2'  H   HOH1  0   0.459  -1.4677  -2.3677   2.3567
 GPU  H3'   H   HCH1  0   0.230  -3.6491  -1.5602   0.5973
 GPU  HO3'  H   HOH1  0   0.464  -4.3823  -1.3475   2.6252
 GPU  H4'   H   HCH1  0   0.224  -3.1660   1.3715   1.2895
 GPU  HO4'  H   HOH1  0   0.460  -5.3249   0.9223   1.5188
 GPU  H5'   H   HCH1  0   0.234  -3.5899   0.0071  -1.4107
 GPU  H6'   H   HCH2  0   0.217  -4.4484   2.3311  -1.2306
 GPU  H6'A  H   HCH2  0   0.200  -2.8606   2.8799  -0.6887
 GPU  HO6'  H   HOH1  0   0.458  -3.1912   3.0415  -3.0140

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
 GPU  N1   C2    single  1.382  0.020  1.382
 GPU  N1   C6    single  1.364  0.020  1.364
 GPU  N1   C1'   single  1.454  0.020  1.454
 GPU  BR1  C5    single  1.865  0.020  1.865
 GPU  C2   O2    double  1.210  0.020  1.210
 GPU  C2   N3    single  1.371  0.020  1.371
 GPU  N3   C4    single  1.382  0.020  1.382
 GPU  C4   O4    double  1.211  0.020  1.211
 GPU  C4   C5    single  1.451  0.020  1.451
 GPU  C5   C6    double  1.343  0.020  1.343
 GPU  C1'  C2'   single  1.525  0.020  1.525
 GPU  C1'  O5'   single  1.393  0.020  1.393
 GPU  C2'  O2'   single  1.399  0.020  1.399
 GPU  C2'  C3'   single  1.523  0.020  1.523
 GPU  C3'  O3'   single  1.409  0.020  1.409
 GPU  C3'  C4'   single  1.529  0.020  1.529
 GPU  C4'  O4'   single  1.407  0.020  1.407
 GPU  C4'  C5'   single  1.530  0.020  1.530
 GPU  C5'  O5'   single  1.420  0.020  1.420
 GPU  C5'  C6'   single  1.513  0.020  1.513
 GPU  C6'  O6'   single  1.407  0.020  1.407
 GPU  N3   HN3   single  0.860  0.020  1.020
 GPU  C6   H6    single  0.930  0.020  1.080
 GPU  C1'  H1'   single  0.970  0.020  1.090
 GPU  C2'  H2'   single  0.970  0.020  1.090
 GPU  O2'  HO2'  single  0.850  0.020  0.980
 GPU  C3'  H3'   single  0.970  0.020  1.090
 GPU  O3'  HO3'  single  0.850  0.020  0.980
 GPU  C4'  H4'   single  0.970  0.020  1.090
 GPU  O4'  HO4'  single  0.850  0.020  0.980
 GPU  C5'  H5'   single  0.970  0.020  1.090
 GPU  C6'  H6'   single  0.970  0.020  1.090
 GPU  C6'  H6'A  single  0.970  0.020  1.090
 GPU  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
 GPU  C1'   N1   C6   118.83  3.000
 GPU  C1'   N1   C2   119.46  3.000
 GPU  C6    N1   C2   121.65  3.000
 GPU  N3    C2   O2   122.18  3.000
 GPU  N3    C2   N1   114.24  3.000
 GPU  O2    C2   N1   123.58  3.000
 GPU  HN3   N3   C4   116.25  3.000
 GPU  HN3   N3   C2   115.05  3.000
 GPU  C4    N3   C2   128.70  3.000
 GPU  C5    C4   O4   125.83  3.000
 GPU  C5    C4   N3   112.69  3.000
 GPU  O4    C4   N3   121.48  3.000
 GPU  C6    C5   C4   120.21  3.000
 GPU  C6    C5   BR1  122.03  3.000
 GPU  C4    C5   BR1  117.75  3.000
 GPU  H6    C6   C5   121.69  3.000
 GPU  H6    C6   N1   115.81  3.000
 GPU  C5    C6   N1   122.50  3.000
 GPU  H1'   C1'  O5'  111.45  3.000
 GPU  H1'   C1'  C2'  109.37  3.000
 GPU  O5'   C1'  C2'  110.78  3.000
 GPU  H1'   C1'  N1   106.96  3.000
 GPU  O5'   C1'  N1   107.10  3.000
 GPU  C2'   C1'  N1   111.10  3.000
 GPU  H2'   C2'  C3'  108.33  3.000
 GPU  H2'   C2'  O2'  111.37  3.000
 GPU  C3'   C2'  O2'  112.97  3.000
 GPU  H2'   C2'  C1'  108.89  3.000
 GPU  C3'   C2'  C1'  107.81  3.000
 GPU  O2'   C2'  C1'  107.36  3.000
 GPU  HO2'  O2'  C2'  108.18  3.000
 GPU  H3'   C3'  C4'  108.29  3.000
 GPU  H3'   C3'  O3'  110.75  3.000
 GPU  C4'   C3'  O3'  111.64  3.000
 GPU  H3'   C3'  C2'  108.05  3.000
 GPU  C4'   C3'  C2'  110.11  3.000
 GPU  O3'   C3'  C2'  107.94  3.000
 GPU  HO3'  O3'  C3'  108.94  3.000
 GPU  H4'   C4'  C5'  108.35  3.000
 GPU  H4'   C4'  O4'  111.12  3.000
 GPU  C5'   C4'  O4'  107.94  3.000
 GPU  H4'   C4'  C3'  108.56  3.000
 GPU  C5'   C4'  C3'  109.62  3.000
 GPU  O4'   C4'  C3'  111.21  3.000
 GPU  HO4'  O4'  C4'  108.75  3.000
 GPU  H5'   C5'  C6'  109.12  3.000
 GPU  H5'   C5'  O5'  109.47  3.000
 GPU  C6'   C5'  O5'  107.27  3.000
 GPU  H5'   C5'  C4'  108.75  3.000
 GPU  C6'   C5'  C4'  112.33  3.000
 GPU  O5'   C5'  C4'  109.86  3.000
 GPU  C5'   O5'  C1'  113.77  3.000
 GPU  H6'A  C6'  H6'  107.18  3.000
 GPU  H6'A  C6'  O6'  111.84  3.000
 GPU  H6'   C6'  O6'  111.87  3.000
 GPU  H6'A  C6'  C5'  109.00  3.000
 GPU  H6'   C6'  C5'  108.16  3.000
 GPU  O6'   C6'  C5'  108.70  3.000
 GPU  HO6'  O6'  C6'  107.91  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
 GPU  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 GPU  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 GPU  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 GPU  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 GPU  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 GPU  CONST_06  C6   N1  C2  O2  180.00  0.0  0
 GPU  CONST_07  C1'  N1  C2  O2    0.00  0.0  0
 GPU  CONST_08  C4   N3  C2  O2  180.00  0.0  0
 GPU  CONST_09  HN3  N3  C2  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
 GPU  chir_01  C1'  N1   C2'  O5'  negativ
 GPU  chir_02  C2'  O2'  C1'  C3'  negativ
 GPU  chir_03  C3'  O3'  C2'  C4'  positiv
 GPU  chir_04  C4'  O4'  C5'  C3'  positiv
 GPU  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
 GPU  plan-1  N1   0.020
 GPU  plan-1  BR1  0.020
 GPU  plan-1  C2   0.020
 GPU  plan-1  O2   0.020
 GPU  plan-1  N3   0.020
 GPU  plan-1  C4   0.020
 GPU  plan-1  O4   0.020
 GPU  plan-1  C5   0.020
 GPU  plan-1  C6   0.020
 GPU  plan-1  C1'  0.020
 GPU  plan-1  HN3  0.020
 GPU  plan-1  H6   0.020

