# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 15:39:53 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)C(=O)NC1=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
 CKB  CKB  1-beta-D-glucopyranosyl-5-methylpyrimidine-2,4(1H,3H)-dione  D-saccharide  36  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_CKB
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
 CKB  C2    C  CR6   0   0.739   1.4950  -0.0866  -1.2396
 CKB  C4    C  CR6   0   0.560   3.8322  -0.2325  -0.4270
 CKB  C5    C  CR6   0  -0.181   3.3334  -0.0882   0.9260
 CKB  C6    C  CR16  0   0.053   2.0076   0.0419   1.0956
 CKB  C7    C  CH3   0  -0.706   4.3081  -0.0893   2.0575
 CKB  N1    N  NR6   0  -0.579   1.0919   0.0473   0.0727
 CKB  N3    N  NR16  0  -0.735   2.8506  -0.2164  -1.4009
 CKB  C1'   C  CH1   0   0.214  -0.3160   0.2025   0.3938
 CKB  C2'   C  CH1   0  -0.001  -0.9349   1.4729  -0.1841
 CKB  C3'   C  CH1   0  -0.030  -2.3970   1.5054   0.2417
 CKB  C4'   C  CH1   0   0.025  -3.1013   0.2167  -0.1803
 CKB  C5'   C  CH1   0  -0.021  -2.3468  -0.9862   0.3889
 CKB  C6'   C  CH2   0  -0.157  -2.9202  -2.3013  -0.0916
 CKB  O6'   O  OH1   0  -0.670  -2.2409  -3.3537   0.5497
 CKB  O2'   O  OH1   0  -0.666  -0.2014   2.5521   0.3305
 CKB  O3'   O  OH1   0  -0.674  -2.9982   2.6360  -0.3526
 CKB  O4'   O  OH1   0  -0.671  -4.4200   0.1726   0.3072
 CKB  O5'   O  O2    0  -0.480  -0.9920  -0.9406  -0.0242
 CKB  O2    O  O     0  -0.473   0.7349  -0.0917  -2.1835
 CKB  O4    O  O     0  -0.453   5.0041  -0.3609  -0.7299
 CKB  H6    H  HCR6  0   0.317   1.5833   0.1504   2.0842
 CKB  H7    H  HCH3  0   0.248   4.8876  -1.0131   2.0798
 CKB  H7A   H  HCH3  0   0.248   5.0164   0.7354   1.9706
 CKB  H7B   H  HCH3  0   0.248   3.7964   0.0077   3.0135
 CKB  HN3   H  HNR6  0   0.425   3.1590  -0.3217  -2.3600
 CKB  H1'   H  HCH1  0   0.254  -0.3576   0.2902   1.4892
 CKB  H2'   H  HCH1  0   0.243  -0.8930   1.4431  -1.2787
 CKB  H3'   H  HCH1  0   0.228  -2.4404   1.5782   1.3385
 CKB  H4'   H  HCH1  0   0.220  -3.0820   0.1492  -1.2791
 CKB  H5'   H  HCH1  0   0.229  -2.4036  -0.9493   1.4895
 CKB  H6'   H  HCH2  0   0.215  -3.9913  -2.3124   0.1333
 CKB  H6'A  H  HCH2  0   0.199  -2.8187  -2.3532  -1.1845
 CKB  HO6'  H  HOH1  0   0.458  -2.6586  -4.1790   0.2882
 CKB  HO2'  H  HOH1  0   0.456  -0.6087   3.3659   0.0153
 CKB  HO3'  H  HOH1  0   0.463  -3.6246   3.0228   0.2650
 CKB  HO4'  H  HOH1  0   0.455  -4.9425   0.8253  -0.1690

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
 CKB  C2   N1    single  1.379  0.020  1.379
 CKB  C2   N3    single  1.371  0.020  1.371
 CKB  C2   O2    double  1.212  0.020  1.212
 CKB  C4   C5    single  1.449  0.020  1.449
 CKB  C4   N3    single  1.383  0.020  1.383
 CKB  C4   O4    double  1.217  0.020  1.217
 CKB  C5   C6    double  1.343  0.020  1.343
 CKB  C5   C7    single  1.493  0.020  1.493
 CKB  C6   N1    single  1.373  0.020  1.373
 CKB  N1   C1'   single  1.452  0.020  1.452
 CKB  C1'  C2'   single  1.527  0.020  1.527
 CKB  C1'  O5'   single  1.392  0.020  1.392
 CKB  C2'  C3'   single  1.523  0.020  1.523
 CKB  C2'  O2'   single  1.403  0.020  1.403
 CKB  C3'  C4'   single  1.528  0.020  1.528
 CKB  C3'  O3'   single  1.412  0.020  1.412
 CKB  C4'  C5'   single  1.530  0.020  1.530
 CKB  C4'  O4'   single  1.407  0.020  1.407
 CKB  C5'  C6'   single  1.513  0.020  1.513
 CKB  C5'  O5'   single  1.417  0.020  1.417
 CKB  C6'  O6'   single  1.407  0.020  1.407
 CKB  C6   H6    single  0.930  0.020  1.080
 CKB  C7   H7    single  0.970  0.020  1.090
 CKB  C7   H7A   single  0.970  0.020  1.090
 CKB  C7   H7B   single  0.970  0.020  1.090
 CKB  N3   HN3   single  0.860  0.020  1.020
 CKB  C1'  H1'   single  0.970  0.020  1.090
 CKB  C2'  H2'   single  0.970  0.020  1.090
 CKB  C3'  H3'   single  0.970  0.020  1.090
 CKB  C4'  H4'   single  0.970  0.020  1.090
 CKB  C5'  H5'   single  0.970  0.020  1.090
 CKB  C6'  H6'   single  0.970  0.020  1.090
 CKB  C6'  H6'A  single  0.970  0.020  1.090
 CKB  O6'  HO6'  single  0.850  0.020  0.980
 CKB  O2'  HO2'  single  0.850  0.020  0.980
 CKB  O3'  HO3'  single  0.850  0.020  0.980
 CKB  O4'  HO4'  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
 CKB  O2    C2   N3   121.87  3.000
 CKB  O2    C2   N1   123.92  3.000
 CKB  N3    C2   N1   114.21  3.000
 CKB  O4    C4   N3   120.63  3.000
 CKB  O4    C4   C5   125.04  3.000
 CKB  N3    C4   C5   114.33  3.000
 CKB  C7    C5   C6   123.28  3.000
 CKB  C7    C5   C4   118.86  3.000
 CKB  C6    C5   C4   117.87  3.000
 CKB  H6    C6   N1   114.78  3.000
 CKB  H6    C6   C5   120.84  3.000
 CKB  N1    C6   C5   124.38  3.000
 CKB  H7B   C7   H7A  107.93  3.000
 CKB  H7B   C7   H7   107.90  3.000
 CKB  H7A   C7   H7   107.28  3.000
 CKB  H7B   C7   C5   111.00  3.000
 CKB  H7A   C7   C5   111.28  3.000
 CKB  H7    C7   C5   111.28  3.000
 CKB  C1'   N1   C6   118.83  3.000
 CKB  C1'   N1   C2   120.27  3.000
 CKB  C6    N1   C2   120.90  3.000
 CKB  HN3   N3   C4   116.71  3.000
 CKB  HN3   N3   C2   114.97  3.000
 CKB  C4    N3   C2   128.32  3.000
 CKB  H1'   C1'  O5'  110.26  3.000
 CKB  H1'   C1'  C2'  107.18  3.000
 CKB  O5'   C1'  C2'  111.88  3.000
 CKB  H1'   C1'  N1   105.39  3.000
 CKB  O5'   C1'  N1   108.46  3.000
 CKB  C2'   C1'  N1   113.47  3.000
 CKB  H2'   C2'  O2'  111.56  3.000
 CKB  H2'   C2'  C3'  108.45  3.000
 CKB  O2'   C2'  C3'  112.52  3.000
 CKB  H2'   C2'  C1'  109.87  3.000
 CKB  O2'   C2'  C1'  106.82  3.000
 CKB  C3'   C2'  C1'  107.52  3.000
 CKB  H3'   C3'  O3'  110.48  3.000
 CKB  H3'   C3'  C4'  108.24  3.000
 CKB  O3'   C3'  C4'  111.28  3.000
 CKB  H3'   C3'  C2'  108.54  3.000
 CKB  O3'   C3'  C2'  107.95  3.000
 CKB  C4'   C3'  C2'  110.32  3.000
 CKB  H4'   C4'  O4'  111.12  3.000
 CKB  H4'   C4'  C5'  108.33  3.000
 CKB  O4'   C4'  C5'  107.99  3.000
 CKB  H4'   C4'  C3'  108.62  3.000
 CKB  O4'   C4'  C3'  111.27  3.000
 CKB  C5'   C4'  C3'  109.46  3.000
 CKB  H5'   C5'  O5'  109.82  3.000
 CKB  H5'   C5'  C6'  109.05  3.000
 CKB  O5'   C5'  C6'  107.32  3.000
 CKB  H5'   C5'  C4'  108.64  3.000
 CKB  O5'   C5'  C4'  109.74  3.000
 CKB  C6'   C5'  C4'  112.24  3.000
 CKB  H6'A  C6'  H6'  107.11  3.000
 CKB  H6'A  C6'  O6'  111.92  3.000
 CKB  H6'   C6'  O6'  111.79  3.000
 CKB  H6'A  C6'  C5'  108.78  3.000
 CKB  H6'   C6'  C5'  108.33  3.000
 CKB  O6'   C6'  C5'  108.81  3.000
 CKB  HO6'  O6'  C6'  107.96  3.000
 CKB  HO2'  O2'  C2'  107.99  3.000
 CKB  HO3'  O3'  C3'  109.23  3.000
 CKB  HO4'  O4'  C4'  108.44  3.000
 CKB  C5'   O5'  C1'  113.77  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
 CKB  CONST_01  C5   C4  N3  C2     0.00   0.0  0
 CKB  CONST_02  N1   C2  N3  C4     0.00   0.0  0
 CKB  CONST_03  N3   C2  N1  C6     0.00   0.0  0
 CKB  CONST_04  C1'  N1  C2  N3   180.00   0.0  0
 CKB  CONST_05  O4   C4  N3  C2   180.00   0.0  0
 CKB  CONST_06  O2   C2  N3  C4   180.00   0.0  0
 CKB  CONST_07  O2   C2  N1  C6   180.00   0.0  0
 CKB  CONST_08  O2   C2  N1  C1'    0.00   0.0  0
 CKB  CONST_09  HN3  N3  C4  C5   180.00   0.0  0
 CKB  Var_01    H7   C7  C5  C4   -58.76  30.0  3

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
 CKB  chir_01  C1'  N1   C2'  O5'  negativ
 CKB  chir_02  C2'  O2'  C1'  C3'  negativ
 CKB  chir_03  C3'  O3'  C2'  C4'  positiv
 CKB  chir_04  C4'  O4'  C5'  C3'  positiv
 CKB  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
 CKB  plan-1  C2   0.020
 CKB  plan-1  C4   0.020
 CKB  plan-1  C5   0.020
 CKB  plan-1  C6   0.020
 CKB  plan-1  C7   0.020
 CKB  plan-1  N1   0.020
 CKB  plan-1  N3   0.020
 CKB  plan-1  C1'  0.020
 CKB  plan-1  O2   0.020
 CKB  plan-1  O4   0.020
 CKB  plan-1  H6   0.020
 CKB  plan-1  HN3  0.020

