# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:52:02 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 5-chloro-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(Cl)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
 GPQ  GPQ  5-chloro-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 GRAND
;

data_comp_GPQ
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
 GPQ  N1    N   NR6   0  -0.570   0.7712   0.2228   0.5682
 GPQ  CL1   CL  CL    0  -0.080   3.4244  -1.1421  -2.0352
 GPQ  C2    C   CR6   0   0.741   1.5150   0.6686   1.6435
 GPQ  O2    O   O     0  -0.465   1.0277   1.1496   2.6418
 GPQ  N3    N   NR16  0  -0.739   2.8699   0.5206   1.4925
 GPQ  C4    C   CR6   0   0.608   3.5663  -0.0112   0.4245
 GPQ  O4    O   O     0  -0.429   4.7752  -0.0831   0.4236
 GPQ  C5    C   CR6   0  -0.304   2.6940  -0.4512  -0.6470
 GPQ  C6    C   CR16  0   0.155   1.3639  -0.3196  -0.5358
 GPQ  C1'   C   CH1   0   0.175  -0.6757   0.3579   0.5897
 GPQ  C2'   C   CH1   0   0.014  -1.1494   1.3788  -0.4402
 GPQ  O2'   O   OH1   0  -0.661  -0.5759   2.6085  -0.1001
 GPQ  C3'   C   CH1   0  -0.021  -2.6715   1.4046  -0.4089
 GPQ  O3'   O   OH1   0  -0.672  -3.1049   2.3091  -1.3984
 GPQ  C4'   C   CH1   0   0.015  -3.2257  -0.0007  -0.6424
 GPQ  O4'   O   OH1   0  -0.670  -4.6235  -0.0279  -0.4850
 GPQ  C5'   C   CH1   0  -0.021  -2.6184  -0.9693   0.3749
 GPQ  O5'   O   O2    0  -0.489  -1.2014  -0.9042   0.3185
 GPQ  C6'   C   CH2   0  -0.154  -3.0119  -2.4044   0.0999
 GPQ  O6'   O   OH1   0  -0.669  -2.4961  -3.2208   1.1230
 GPQ  HN3   H   HNR6  0   0.436   3.4262   0.8474   2.2738
 GPQ  H6    H   HCR6  0   0.345   0.7030  -0.6521  -1.3240
 GPQ  H1'   H   HCH1  0   0.281  -0.9501   0.7029   1.5921
 GPQ  H2'   H   HCH1  0   0.229  -0.8288   1.0509  -1.4427
 GPQ  HO2'  H   HOH1  0   0.459  -0.9093   3.2739  -0.7118
 GPQ  H3'   H   HCH1  0   0.229  -2.9894   1.7397   0.5903
 GPQ  HO3'  H   HOH1  0   0.463  -3.9330   2.7088  -1.1179
 GPQ  H4'   H   HCH1  0   0.224  -2.9356  -0.3306  -1.6515
 GPQ  HO4'  H   HOH1  0   0.460  -5.0301   0.3095  -1.2885
 GPQ  H5'   H   HCH1  0   0.234  -2.9614  -0.6848   1.3826
 GPQ  H6'   H   HCH2  0   0.216  -4.1041  -2.4554   0.0497
 GPQ  H6'A  H   HCH2  0   0.201  -2.6275  -2.6935  -0.8880
 GPQ  HO6'  H   HOH1  0   0.458  -2.7840  -4.1225   0.9562

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
 GPQ  N1   C2    single  1.381  0.020  1.381
 GPQ  N1   C6    single  1.365  0.020  1.365
 GPQ  N1   C1'   single  1.453  0.020  1.453
 GPQ  CL1  C5    single  1.714  0.020  1.714
 GPQ  C2   O2    double  1.210  0.020  1.210
 GPQ  C2   N3    single  1.371  0.020  1.371
 GPQ  N3   C4    single  1.381  0.020  1.381
 GPQ  C4   O4    double  1.211  0.020  1.211
 GPQ  C4   C5    single  1.450  0.020  1.450
 GPQ  C5   C6    double  1.341  0.020  1.341
 GPQ  C1'  C2'   single  1.526  0.020  1.526
 GPQ  C1'  O5'   single  1.394  0.020  1.394
 GPQ  C2'  O2'   single  1.399  0.020  1.399
 GPQ  C2'  C3'   single  1.523  0.020  1.523
 GPQ  C3'  O3'   single  1.409  0.020  1.409
 GPQ  C3'  C4'   single  1.529  0.020  1.529
 GPQ  C4'  O4'   single  1.407  0.020  1.407
 GPQ  C4'  C5'   single  1.530  0.020  1.530
 GPQ  C5'  O5'   single  1.420  0.020  1.420
 GPQ  C5'  C6'   single  1.513  0.020  1.513
 GPQ  C6'  O6'   single  1.407  0.020  1.407
 GPQ  N3   HN3   single  0.860  0.020  1.020
 GPQ  C6   H6    single  0.930  0.020  1.080
 GPQ  C1'  H1'   single  0.970  0.020  1.090
 GPQ  C2'  H2'   single  0.970  0.020  1.090
 GPQ  O2'  HO2'  single  0.850  0.020  0.980
 GPQ  C3'  H3'   single  0.970  0.020  1.090
 GPQ  O3'  HO3'  single  0.850  0.020  0.980
 GPQ  C4'  H4'   single  0.970  0.020  1.090
 GPQ  O4'  HO4'  single  0.850  0.020  0.980
 GPQ  C5'  H5'   single  0.970  0.020  1.090
 GPQ  C6'  H6'   single  0.970  0.020  1.090
 GPQ  C6'  H6'A  single  0.970  0.020  1.090
 GPQ  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
 GPQ  C1'   N1   C6   118.75  3.000
 GPQ  C1'   N1   C2   119.64  3.000
 GPQ  C6    N1   C2   121.59  3.000
 GPQ  N3    C2   O2   122.10  3.000
 GPQ  N3    C2   N1   114.30  3.000
 GPQ  O2    C2   N1   123.60  3.000
 GPQ  HN3   N3   C4   116.32  3.000
 GPQ  HN3   N3   C2   115.01  3.000
 GPQ  C4    N3   C2   128.66  3.000
 GPQ  C5    C4   O4   125.59  3.000
 GPQ  C5    C4   N3   112.63  3.000
 GPQ  O4    C4   N3   121.78  3.000
 GPQ  C6    C5   C4   120.37  3.000
 GPQ  C6    C5   CL1  121.96  3.000
 GPQ  C4    C5   CL1  117.67  3.000
 GPQ  H6    C6   C5   121.04  3.000
 GPQ  H6    C6   N1   116.51  3.000
 GPQ  C5    C6   N1   122.44  3.000
 GPQ  H1'   C1'  O5'  111.64  3.000
 GPQ  H1'   C1'  C2'  109.23  3.000
 GPQ  O5'   C1'  C2'  110.94  3.000
 GPQ  H1'   C1'  N1   107.00  3.000
 GPQ  O5'   C1'  N1   106.76  3.000
 GPQ  C2'   C1'  N1   111.19  3.000
 GPQ  H2'   C2'  C3'  108.33  3.000
 GPQ  H2'   C2'  O2'  111.31  3.000
 GPQ  C3'   C2'  O2'  112.95  3.000
 GPQ  H2'   C2'  C1'  108.94  3.000
 GPQ  C3'   C2'  C1'  107.93  3.000
 GPQ  O2'   C2'  C1'  107.27  3.000
 GPQ  HO2'  O2'  C2'  108.11  3.000
 GPQ  H3'   C3'  C4'  108.29  3.000
 GPQ  H3'   C3'  O3'  110.68  3.000
 GPQ  C4'   C3'  O3'  111.80  3.000
 GPQ  H3'   C3'  C2'  108.21  3.000
 GPQ  C4'   C3'  C2'  110.10  3.000
 GPQ  O3'   C3'  C2'  107.69  3.000
 GPQ  HO3'  O3'  C3'  109.08  3.000
 GPQ  H4'   C4'  C5'  108.37  3.000
 GPQ  H4'   C4'  O4'  111.02  3.000
 GPQ  C5'   C4'  O4'  107.92  3.000
 GPQ  H4'   C4'  C3'  108.67  3.000
 GPQ  C5'   C4'  C3'  109.66  3.000
 GPQ  O4'   C4'  C3'  111.16  3.000
 GPQ  HO4'  O4'  C4'  108.65  3.000
 GPQ  H5'   C5'  C6'  109.27  3.000
 GPQ  H5'   C5'  O5'  109.59  3.000
 GPQ  C6'   C5'  O5'  107.21  3.000
 GPQ  H5'   C5'  C4'  108.72  3.000
 GPQ  C6'   C5'  C4'  112.10  3.000
 GPQ  O5'   C5'  C4'  109.92  3.000
 GPQ  C5'   O5'  C1'  114.22  3.000
 GPQ  H6'A  C6'  H6'  107.19  3.000
 GPQ  H6'A  C6'  O6'  111.90  3.000
 GPQ  H6'   C6'  O6'  111.85  3.000
 GPQ  H6'A  C6'  C5'  108.78  3.000
 GPQ  H6'   C6'  C5'  108.18  3.000
 GPQ  O6'   C6'  C5'  108.83  3.000
 GPQ  HO6'  O6'  C6'  107.96  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
 GPQ  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 GPQ  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 GPQ  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 GPQ  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 GPQ  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 GPQ  CONST_06  C6   N1  C2  O2  180.00  0.0  0
 GPQ  CONST_07  C1'  N1  C2  O2    0.00  0.0  0
 GPQ  CONST_08  C4   N3  C2  O2  180.00  0.0  0
 GPQ  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
 GPQ  chir_01  C1'  N1   C2'  O5'  negativ
 GPQ  chir_02  C2'  O2'  C1'  C3'  negativ
 GPQ  chir_03  C3'  O3'  C2'  C4'  positiv
 GPQ  chir_04  C4'  O4'  C5'  C3'  positiv
 GPQ  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
 GPQ  plan-1  N1   0.020
 GPQ  plan-1  CL1  0.020
 GPQ  plan-1  C2   0.020
 GPQ  plan-1  O2   0.020
 GPQ  plan-1  N3   0.020
 GPQ  plan-1  C4   0.020
 GPQ  plan-1  O4   0.020
 GPQ  plan-1  C5   0.020
 GPQ  plan-1  C6   0.020
 GPQ  plan-1  C1'  0.020
 GPQ  plan-1  HN3  0.020
 GPQ  plan-1  H6   0.020

