# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 12:00:27 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: 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=CC(=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
 CJB  CJB  1-(beta-D-glucopyranosyl)pyrimidine-2,4(1H,3H)-dione  D-saccharide  33  19  .  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_CJB
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
 CJB  N1    N  NR6   0  -0.566   1.2382  -0.0321   0.0932
 CJB  O2    O  O     0  -0.473   1.8585   0.2772   2.2721
 CJB  C2    C  CR6   0   0.735   2.1608   0.0653   1.1176
 CJB  N3    N  NR16  0  -0.734   3.4623  -0.0997   0.7242
 CJB  C4    C  CR6   0   0.569   3.9482  -0.3499  -0.5500
 CJB  O4    O  O     0  -0.461   5.1430  -0.4718  -0.7438
 CJB  C5    C  CR16  0  -0.511   2.9136  -0.4417  -1.5513
 CJB  C6    C  CR16  0   0.102   1.6310  -0.2819  -1.1925
 CJB  C1'   C  CH1   0   0.176  -0.1710   0.1502   0.3827
 CJB  O5'   O  O2    0  -0.489  -0.8370  -0.9767  -0.1022
 CJB  C5'   C  CH1   0  -0.021  -2.2230  -0.9977   0.2000
 CJB  C6'   C  CH2   0  -0.156  -2.7805  -2.3030  -0.3237
 CJB  O6'   O  OH1   0  -0.669  -2.1594  -3.3667   0.3557
 CJB  C4'   C  CH1   0   0.028  -2.9055   0.2171  -0.4306
 CJB  O4'   O  OH1   0  -0.670  -4.2583   0.2018  -0.0513
 CJB  C3'   C  CH1   0  -0.031  -2.2095   1.4938   0.0380
 CJB  O3'   O  OH1   0  -0.674  -2.7463   2.6243  -0.6148
 CJB  C2'   C  CH1   0   0.014  -0.7176   1.4203  -0.2633
 CJB  O2'   O  OH1   0  -0.661  -0.0033   2.4991   0.2694
 CJB  HN3   H  HNR6  0   0.427   4.1469  -0.0296   1.4674
 CJB  H5    H  HCR6  0   0.295   3.1779  -0.6414  -2.5779
 CJB  H6    H  HCR6  0   0.328   0.8380  -0.3563  -1.9223
 CJB  H1'   H  HCH1  0   0.277  -0.2677   0.2322   1.4706
 CJB  H5'   H  HCH1  0   0.233  -2.3637  -0.9575   1.2920
 CJB  H6'   H  HCH2  0   0.217  -3.8640  -2.2986  -0.1690
 CJB  H6'A  H  HCH2  0   0.200  -2.6094  -2.3529  -1.4082
 CJB  HO6'  H  HOH1  0   0.458  -2.5823  -4.1837   0.0771
 CJB  H4'   H  HCH1  0   0.217  -2.7997   0.1430  -1.5247
 CJB  HO4'  H  HOH1  0   0.456  -4.7130   0.9056  -0.5253
 CJB  H3'   H  HCH1  0   0.234  -2.3375   1.5786   1.1266
 CJB  HO3'  H  HOH1  0   0.466  -3.3119   3.1041  -0.0042
 CJB  H2'   H  HCH1  0   0.227  -0.5884   1.3543  -1.3557
 CJB  HO2'  H  HOH1  0   0.458  -0.3535   3.3097  -0.1155

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
 CJB  N1   C2    single  1.382  0.020  1.382
 CJB  N1   C6    single  1.367  0.020  1.367
 CJB  N1   C1'   single  1.450  0.020  1.450
 CJB  O2   C2    double  1.212  0.020  1.212
 CJB  C2   N3    single  1.370  0.020  1.370
 CJB  N3   C4    single  1.387  0.020  1.387
 CJB  C4   O4    double  1.216  0.020  1.216
 CJB  C4   C5    single  1.443  0.020  1.443
 CJB  C5   C6    double  1.341  0.020  1.341
 CJB  C1'  O5'   single  1.396  0.020  1.396
 CJB  C1'  C2'   single  1.526  0.020  1.526
 CJB  O5'  C5'   single  1.419  0.020  1.419
 CJB  C5'  C6'   single  1.513  0.020  1.513
 CJB  C5'  C4'   single  1.529  0.020  1.529
 CJB  C6'  O6'   single  1.407  0.020  1.407
 CJB  C4'  O4'   single  1.405  0.020  1.405
 CJB  C4'  C3'   single  1.528  0.020  1.528
 CJB  C3'  O3'   single  1.411  0.020  1.411
 CJB  C3'  C2'   single  1.524  0.020  1.524
 CJB  C2'  O2'   single  1.399  0.020  1.399
 CJB  N3   HN3   single  0.860  0.020  1.020
 CJB  C5   H5    single  0.930  0.020  1.080
 CJB  C6   H6    single  0.930  0.020  1.080
 CJB  C1'  H1'   single  0.970  0.020  1.090
 CJB  C5'  H5'   single  0.970  0.020  1.090
 CJB  C6'  H6'   single  0.970  0.020  1.090
 CJB  C6'  H6'A  single  0.970  0.020  1.090
 CJB  O6'  HO6'  single  0.850  0.020  0.980
 CJB  C4'  H4'   single  0.970  0.020  1.090
 CJB  O4'  HO4'  single  0.850  0.020  0.980
 CJB  C3'  H3'   single  0.970  0.020  1.090
 CJB  O3'  HO3'  single  0.850  0.020  0.980
 CJB  C2'  H2'   single  0.970  0.020  1.090
 CJB  O2'  HO2'  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
 CJB  C1'   N1   C6   119.33  3.000
 CJB  C1'   N1   C2   119.46  3.000
 CJB  C6    N1   C2   121.20  3.000
 CJB  N3    C2   O2   122.12  3.000
 CJB  N3    C2   N1   114.39  3.000
 CJB  O2    C2   N1   123.49  3.000
 CJB  HN3   N3   C4   116.74  3.000
 CJB  HN3   N3   C2   115.04  3.000
 CJB  C4    N3   C2   128.23  3.000
 CJB  C5    C4   O4   125.97  3.000
 CJB  C5    C4   N3   113.45  3.000
 CJB  O4    C4   N3   120.58  3.000
 CJB  H5    C5   C6   120.72  3.000
 CJB  H5    C5   C4   119.77  3.000
 CJB  C6    C5   C4   119.50  3.000
 CJB  H6    C6   C5   120.86  3.000
 CJB  H6    C6   N1   115.91  3.000
 CJB  C5    C6   N1   123.22  3.000
 CJB  H1'   C1'  C2'  109.05  3.000
 CJB  H1'   C1'  O5'  111.31  3.000
 CJB  C2'   C1'  O5'  110.72  3.000
 CJB  H1'   C1'  N1   107.07  3.000
 CJB  C2'   C1'  N1   111.60  3.000
 CJB  O5'   C1'  N1   107.03  3.000
 CJB  C5'   O5'  C1'  113.83  3.000
 CJB  H5'   C5'  C4'  108.83  3.000
 CJB  H5'   C5'  C6'  109.12  3.000
 CJB  C4'   C5'  C6'  112.22  3.000
 CJB  H5'   C5'  O5'  109.59  3.000
 CJB  C4'   C5'  O5'  109.65  3.000
 CJB  C6'   C5'  O5'  107.39  3.000
 CJB  H6'A  C6'  H6'  107.08  3.000
 CJB  H6'A  C6'  O6'  111.94  3.000
 CJB  H6'   C6'  O6'  111.83  3.000
 CJB  H6'A  C6'  C5'  108.87  3.000
 CJB  H6'   C6'  C5'  108.20  3.000
 CJB  O6'   C6'  C5'  108.82  3.000
 CJB  HO6'  O6'  C6'  107.96  3.000
 CJB  H4'   C4'  C3'  108.49  3.000
 CJB  H4'   C4'  O4'  111.09  3.000
 CJB  C3'   C4'  O4'  111.40  3.000
 CJB  H4'   C4'  C5'  108.25  3.000
 CJB  C3'   C4'  C5'  109.51  3.000
 CJB  O4'   C4'  C5'  108.04  3.000
 CJB  HO4'  O4'  C4'  108.29  3.000
 CJB  H3'   C3'  C2'  108.27  3.000
 CJB  H3'   C3'  O3'  110.60  3.000
 CJB  C2'   C3'  O3'  108.64  3.000
 CJB  H3'   C3'  C4'  108.37  3.000
 CJB  C2'   C3'  C4'  110.18  3.000
 CJB  O3'   C3'  C4'  110.75  3.000
 CJB  HO3'  O3'  C3'  109.27  3.000
 CJB  H2'   C2'  O2'  111.32  3.000
 CJB  H2'   C2'  C3'  108.29  3.000
 CJB  O2'   C2'  C3'  112.79  3.000
 CJB  H2'   C2'  C1'  109.13  3.000
 CJB  O2'   C2'  C1'  107.32  3.000
 CJB  C3'   C2'  C1'  107.89  3.000
 CJB  HO2'  O2'  C2'  108.13  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
 CJB  CONST_01  C4   N3  C2  N1    0.00  0.0  0
 CJB  CONST_02  C5   C4  N3  C2    0.00  0.0  0
 CJB  CONST_03  C6   N1  C2  N3    0.00  0.0  0
 CJB  CONST_04  C1'  N1  C2  N3  180.00  0.0  0
 CJB  CONST_05  C6   N1  C2  O2  180.00  0.0  0
 CJB  CONST_06  C1'  N1  C2  O2    0.00  0.0  0
 CJB  CONST_07  C4   N3  C2  O2  180.00  0.0  0
 CJB  CONST_08  O4   C4  N3  C2  180.00  0.0  0
 CJB  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
 CJB  chir_01  C1'  N1   O5'  C2'  positiv
 CJB  chir_02  C5'  O5'  C6'  C4'  positiv
 CJB  chir_03  C4'  O4'  C5'  C3'  positiv
 CJB  chir_04  C3'  O3'  C4'  C2'  negativ
 CJB  chir_05  C2'  O2'  C3'  C1'  positiv

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
 CJB  plan-1  N1   0.020
 CJB  plan-1  O2   0.020
 CJB  plan-1  C2   0.020
 CJB  plan-1  N3   0.020
 CJB  plan-1  C4   0.020
 CJB  plan-1  O4   0.020
 CJB  plan-1  C5   0.020
 CJB  plan-1  C6   0.020
 CJB  plan-1  C1'  0.020
 CJB  plan-1  HN3  0.020
 CJB  plan-1  H5   0.020
 CJB  plan-1  H6   0.020

