# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:08:13 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 1-(beta-D-glucopyranosyl)-5-iodopyrimidine-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(I)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
 GPV  GPV  1-(beta-D-glucopyranosyl)-5-iodopyrimidine-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_GPV
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
 GPV  I     I  I     0   0.118   3.1514   1.2271   0.2762
 GPV  N1    N  NR6   0  -0.562  -0.4252  -1.0985  -0.3624
 GPV  C2    C  CR6   0   0.745  -0.0143  -2.3419  -0.8072
 GPV  O2    O  O     0  -0.464  -0.7783  -3.2357  -1.0927
 GPV  N3    N  NR16  0  -0.735   1.3449  -2.4842  -0.9030
 GPV  C4    C  CR6   0   0.608   2.3325  -1.5588  -0.6193
 GPV  O4    O  O     0  -0.432   3.5055  -1.8326  -0.7501
 GPV  C5    C  CR6   0  -0.484   1.8003  -0.2866  -0.1718
 GPV  C6    C  CR16  0   0.132   0.4721  -0.1147  -0.0653
 GPV  C1'   C  CH1   0   0.172  -1.8434  -0.8329  -0.1850
 GPV  C2'   C  CH1   0   0.015  -2.1914  -0.6552   1.2906
 GPV  O2'   O  OH1   0  -0.661  -1.8790  -1.8569   1.9354
 GPV  C3'   C  CH1   0  -0.018  -3.6673  -0.2935   1.3884
 GPV  O3'   O  OH1   0  -0.672  -3.9597  -0.0634   2.7470
 GPV  C4'   C  CH1   0   0.014  -3.9704   0.9307   0.5248
 GPV  O4'   O  OH1   0  -0.671  -5.3518   1.1994   0.5021
 GPV  C5'   C  CH1   0  -0.023  -3.5084   0.6698  -0.9101
 GPV  O5'   O  O2    0  -0.488  -2.1317   0.3219  -0.9100
 GPV  C6'   C  CH2   0  -0.155  -3.6694   1.8857  -1.7954
 GPV  O6'   O  OH1   0  -0.669  -3.2820   1.5469  -3.1047
 GPV  H6    H  HCR6  0   0.339   0.0478   0.8264   0.2549
 GPV  H1'   H  HCH1  0   0.282  -2.3831  -1.6996  -0.5811
 GPV  H2'   H  HCH1  0   0.229  -1.6038   0.1835   1.6993
 GPV  HO2'  H  HOH1  0   0.459  -2.1330  -1.7761   2.8610
 GPV  H3'   H  HCH1  0   0.228  -4.2559  -1.1401   1.0024
 GPV  HO3'  H  HOH1  0   0.462  -4.8886  -0.2568   2.9029
 GPV  H4'   H  HCH1  0   0.227  -3.4067   1.7893   0.9183
 GPV  HO4'  H  HOH1  0   0.462  -5.5729   1.7426   1.2637
 GPV  H5'   H  HCH1  0   0.234  -4.0974  -0.1622  -1.3283
 GPV  H6'   H  HCH2  0   0.218  -4.7159   2.2019  -1.7477
 GPV  H6'A  H  HCH2  0   0.199  -3.0642   2.7078  -1.3879
 GPV  HO6'  H  HOH1  0   0.458  -3.5034   2.2839  -3.6807
 GPV  HN3   H  HNR6  0   0.435   1.6599  -3.3906  -1.2289

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
 GPV  I    C5    single  2.078  0.020  2.078
 GPV  N1   C2    single  1.383  0.020  1.383
 GPV  N1   C6    single  1.364  0.020  1.364
 GPV  N1   C1'   single  1.454  0.020  1.454
 GPV  C2   O2    double  1.210  0.020  1.210
 GPV  C2   N3    single  1.370  0.020  1.370
 GPV  N3   C4    single  1.383  0.020  1.383
 GPV  C4   O4    double  1.212  0.020  1.212
 GPV  C4   C5    single  1.450  0.020  1.450
 GPV  C5   C6    double  1.344  0.020  1.344
 GPV  C1'  C2'   single  1.527  0.020  1.527
 GPV  C1'  O5'   single  1.394  0.020  1.394
 GPV  C2'  O2'   single  1.399  0.020  1.399
 GPV  C2'  C3'   single  1.523  0.020  1.523
 GPV  C3'  O3'   single  1.409  0.020  1.409
 GPV  C3'  C4'   single  1.529  0.020  1.529
 GPV  C4'  O4'   single  1.408  0.020  1.408
 GPV  C4'  C5'   single  1.530  0.020  1.530
 GPV  C5'  O5'   single  1.420  0.020  1.420
 GPV  C5'  C6'   single  1.513  0.020  1.513
 GPV  C6'  O6'   single  1.407  0.020  1.407
 GPV  N3   HN3   single  0.860  0.020  1.020
 GPV  C6   H6    single  0.930  0.020  1.080
 GPV  C1'  H1'   single  0.970  0.020  1.090
 GPV  C2'  H2'   single  0.970  0.020  1.090
 GPV  O2'  HO2'  single  0.850  0.020  0.980
 GPV  C3'  H3'   single  0.970  0.020  1.090
 GPV  O3'  HO3'  single  0.850  0.020  0.980
 GPV  C4'  H4'   single  0.970  0.020  1.090
 GPV  O4'  HO4'  single  0.850  0.020  0.980
 GPV  C5'  H5'   single  0.970  0.020  1.090
 GPV  C6'  H6'   single  0.970  0.020  1.090
 GPV  C6'  H6'A  single  0.970  0.020  1.090
 GPV  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
 GPV  C1'   N1   C6   118.90  3.000
 GPV  C1'   N1   C2   119.56  3.000
 GPV  C6    N1   C2   121.53  3.000
 GPV  N3    C2   O2   122.22  3.000
 GPV  N3    C2   N1   114.25  3.000
 GPV  O2    C2   N1   123.53  3.000
 GPV  HN3   N3   C4   116.26  3.000
 GPV  HN3   N3   C2   115.08  3.000
 GPV  C4    N3   C2   128.66  3.000
 GPV  C5    C4   O4   125.95  3.000
 GPV  C5    C4   N3   112.86  3.000
 GPV  O4    C4   N3   121.20  3.000
 GPV  C6    C5   C4   119.98  3.000
 GPV  C6    C5   I    122.18  3.000
 GPV  C4    C5   I    117.85  3.000
 GPV  H6    C6   C5   121.53  3.000
 GPV  H6    C6   N1   115.74  3.000
 GPV  C5    C6   N1   122.73  3.000
 GPV  H1'   C1'  O5'  111.45  3.000
 GPV  H1'   C1'  C2'  109.24  3.000
 GPV  O5'   C1'  C2'  111.05  3.000
 GPV  H1'   C1'  N1   106.98  3.000
 GPV  O5'   C1'  N1   106.84  3.000
 GPV  C2'   C1'  N1   111.20  3.000
 GPV  H2'   C2'  C3'  108.19  3.000
 GPV  H2'   C2'  O2'  111.32  3.000
 GPV  C3'   C2'  O2'  113.01  3.000
 GPV  H2'   C2'  C1'  108.99  3.000
 GPV  C3'   C2'  C1'  108.10  3.000
 GPV  O2'   C2'  C1'  107.13  3.000
 GPV  HO2'  O2'  C2'  108.17  3.000
 GPV  H3'   C3'  C4'  108.17  3.000
 GPV  H3'   C3'  O3'  110.66  3.000
 GPV  C4'   C3'  O3'  111.90  3.000
 GPV  H3'   C3'  C2'  108.24  3.000
 GPV  C4'   C3'  C2'  110.25  3.000
 GPV  O3'   C3'  C2'  107.57  3.000
 GPV  HO3'  O3'  C3'  108.91  3.000
 GPV  H4'   C4'  C5'  108.30  3.000
 GPV  H4'   C4'  O4'  111.09  3.000
 GPV  C5'   C4'  O4'  108.29  3.000
 GPV  H4'   C4'  C3'  108.75  3.000
 GPV  C5'   C4'  C3'  109.48  3.000
 GPV  O4'   C4'  C3'  110.89  3.000
 GPV  HO4'  O4'  C4'  108.71  3.000
 GPV  H5'   C5'  C6'  109.14  3.000
 GPV  H5'   C5'  O5'  109.47  3.000
 GPV  C6'   C5'  O5'  107.47  3.000
 GPV  H5'   C5'  C4'  108.87  3.000
 GPV  C6'   C5'  C4'  112.32  3.000
 GPV  O5'   C5'  C4'  109.54  3.000
 GPV  C5'   O5'  C1'  113.81  3.000
 GPV  H6'A  C6'  H6'  107.12  3.000
 GPV  H6'A  C6'  O6'  111.93  3.000
 GPV  H6'   C6'  O6'  111.93  3.000
 GPV  H6'A  C6'  C5'  109.00  3.000
 GPV  H6'   C6'  C5'  107.97  3.000
 GPV  O6'   C6'  C5'  108.77  3.000
 GPV  HO6'  O6'  C6'  108.03  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
 GPV  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 GPV  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 GPV  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 GPV  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 GPV  CONST_05  O4   C4  N3  C2  180.00  0.0  0
 GPV  CONST_06  C6   N1  C2  O2  180.00  0.0  0
 GPV  CONST_07  C1'  N1  C2  O2    0.00  0.0  0
 GPV  CONST_08  C4   N3  C2  O2  180.00  0.0  0
 GPV  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
 GPV  chir_01  C1'  N1   C2'  O5'  negativ
 GPV  chir_02  C2'  O2'  C1'  C3'  negativ
 GPV  chir_03  C3'  O3'  C2'  C4'  positiv
 GPV  chir_04  C4'  O4'  C5'  C3'  positiv
 GPV  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
 GPV  plan-1  I    0.020
 GPV  plan-1  N1   0.020
 GPV  plan-1  C2   0.020
 GPV  plan-1  O2   0.020
 GPV  plan-1  N3   0.020
 GPV  plan-1  C4   0.020
 GPV  plan-1  O4   0.020
 GPV  plan-1  C5   0.020
 GPV  plan-1  C6   0.020
 GPV  plan-1  C1'  0.020
 GPV  plan-1  H6   0.020
 GPV  plan-1  HN3  0.020

