# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Wed May 20 12:03:01 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](O)[C@H]1O
#
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
 1JB  1JB  '[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methyltetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  saccharide  59  35  .  2023-02-15  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1JB
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
 1JB  N1   N  NR6    0  -0.567  -5.1313   0.5976   0.9034
 1JB  N3   N  NR16   0  -0.734  -5.8496   1.7577  -0.9602
 1JB  C4   C  CR6    0   0.558  -6.1130   2.9354  -0.2847
 1JB  C5   C  CR6    0  -0.185  -5.8216   2.8869   1.1336
 1JB  C6   C  CR16   0   0.059  -5.3476   1.7348   1.6379
 1JB  O1B  O  O      0  -0.785   3.1510  -0.9719  -2.1775
 1JB  PB   P  P      0   1.352   2.9479  -1.1623  -0.7087
 1JB  O2B  O  OP    -1  -0.792   3.5736  -2.3070   0.0213
 1JB  O3B  O  O2     0  -0.630   3.2984   0.2457   0.0852
 1JB  C1Q  C  CH1    0   0.253   4.5431   0.4023   0.6958
 1JB  O5Q  O  O2     0  -0.504   5.5967   0.3244  -0.2166
 1JB  C5Q  C  CH1    0   0.019   5.6142   1.3391  -1.2137
 1JB  C6Q  C  CH3    0  -0.711   6.7717   1.0326  -2.1410
 1JB  C4Q  C  CH1    0  -0.004   5.7059   2.7268  -0.5762
 1JB  O4Q  O  OH1    0  -0.675   6.9120   2.9256   0.1234
 1JB  C3Q  C  CH1    0   0.022   4.5503   2.8927   0.4008
 1JB  O3Q  O  OH1    0  -0.674   4.6486   4.1511   1.0199
 1JB  C2Q  C  CH1    0  -0.021   4.5567   1.7557   1.4159
 1JB  O2Q  O  OH1    0  -0.672   3.4400   1.9226   2.2553
 1JB  O3A  O  O2     0  -0.736   1.3423  -1.0838  -0.3625
 1JB  PA   P  P      0   1.344   0.1802  -1.7394  -1.3184
 1JB  O1A  O  OP    -1  -0.794  -0.3171  -0.7275  -2.3014
 1JB  O2A  O  O      0  -0.803   0.5867  -3.1054  -1.7746
 1JB  O5X  O  O2     0  -0.621  -0.8991  -1.8693  -0.0793
 1JB  C5X  C  CH2    0  -0.155  -2.1882  -2.3470  -0.3991
 1JB  C4X  C  CH1    0   0.013  -3.0917  -2.1954   0.7990
 1JB  O4X  O  O2     0  -0.489  -3.2884  -0.8215   1.0864
 1JB  C3X  C  CH1    0   0.023  -4.4793  -2.7984   0.5764
 1JB  O3X  O  OH1    0  -0.669  -4.4627  -4.1399   0.9968
 1JB  C2X  C  CH2    0  -0.560  -5.3791  -1.8807   1.4046
 1JB  C1X  C  CH1    0   0.218  -4.5801  -0.5843   1.5660
 1JB  C2   C  CR6    0   0.743  -5.3669   0.5794  -0.4517
 1JB  O2   O  O      0  -0.472  -5.1750  -0.3908  -1.1538
 1JB  C5M  C  CH3    0  -0.707  -6.0561   4.1064   1.9630
 1JB  O4   O  O      0  -0.456  -6.5499   3.9056  -0.8768
 1JB  H1   H  HNR6   0   0.425  -6.0302   1.7541  -1.9566
 1JB  H2   H  HCR6   0   0.316  -5.1104   1.6466   2.6896
 1JB  H4   H  HCH1   0   0.229   4.7227  -0.4055   1.4144
 1JB  H5   H  HCH1   0   0.222   4.6889   1.3060  -1.8011
 1JB  H6   H  HCH3   0   0.248   6.6219   0.0729  -2.6355
 1JB  H7   H  HCH3   0   0.234   6.8485   1.7950  -2.9172
 1JB  H8   H  HCH3   0   0.226   7.7234   0.9888  -1.6093
 1JB  H9   H  HCH1   0   0.230   5.5906   3.4681  -1.3807
 1JB  H10  H  HOH1   0   0.456   7.6236   3.0324  -0.5143
 1JB  H11  H  HCH1   0   0.217   3.6242   2.8243  -0.1889
 1JB  H12  H  HOH1   0   0.448   3.9035   4.2389   1.6230
 1JB  H13  H  HCH1   0   0.226   5.4891   1.8024   1.9939
 1JB  H14  H  HOH1   0   0.457   3.5661   1.3945   3.0494
 1JB  H16  H  HCH2   0   0.213  -2.6211  -1.8005  -1.2446
 1JB  H17  H  HCH2   0   0.212  -2.1590  -3.4094  -0.6700
 1JB  H18  H  HCH1   0   0.227  -2.6355  -2.6928   1.6677
 1JB  H19  H  HCH1   0   0.233  -4.7499  -2.7303  -0.4810
 1JB  H20  H  HOH1   0   0.457  -5.2353  -4.5801   0.6315
 1JB  H21  H  HCH2   0   0.275  -6.3651  -1.7249   0.9699
 1JB  H22  H  HCH2   0   0.267  -5.5237  -2.3226   2.3921
 1JB  H23  H  HCH1   0   0.253  -4.5433  -0.3047   2.6216
 1JB  H24  H  HCH3   0   0.247  -7.1038   4.4090   1.9375
 1JB  H25  H  HCH3   0   0.247  -5.7851   3.9273   3.0021
 1JB  H26  H  HCH3   0   0.247  -5.4678   4.9519   1.6038

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
 1JB  C6Q  C5Q  single  1.514  0.020  1.514
 1JB  C4Q  O4Q  single  1.408  0.020  1.408
 1JB  C4Q  C5Q  single  1.530  0.020  1.530
 1JB  C4Q  C3Q  single  1.522  0.020  1.522
 1JB  C5Q  O5Q  single  1.423  0.020  1.423
 1JB  O3Q  C3Q  single  1.406  0.020  1.406
 1JB  C3Q  C2Q  single  1.524  0.020  1.524
 1JB  O5Q  C1Q  single  1.396  0.020  1.396
 1JB  O1B  PB   deloc   1.495  0.020  1.495
 1JB  O3B  C1Q  single  1.395  0.020  1.395
 1JB  O3B  PB   single  1.654  0.020  1.654
 1JB  C2Q  C1Q  single  1.533  0.020  1.533
 1JB  C2Q  O2Q  single  1.407  0.020  1.407
 1JB  PB   O2B  deloc   1.495  0.020  1.495
 1JB  PB   O3A  single  1.644  0.020  1.644
 1JB  O2A  PA   deloc   1.496  0.020  1.496
 1JB  O3A  PA   single  1.641  0.020  1.641
 1JB  O3X  C3X  single  1.406  0.020  1.406
 1JB  PA   O5X  single  1.648  0.020  1.648
 1JB  PA   O1A  deloc   1.496  0.020  1.496
 1JB  C5X  O5X  single  1.411  0.020  1.411
 1JB  C5X  C4X  single  1.508  0.020  1.508
 1JB  C3X  C4X  single  1.529  0.020  1.529
 1JB  C3X  C2X  single  1.529  0.020  1.529
 1JB  C4X  O4X  single  1.417  0.020  1.417
 1JB  C2X  C1X  single  1.531  0.020  1.531
 1JB  O4X  C1X  single  1.398  0.020  1.398
 1JB  C1X  N1   single  1.463  0.020  1.463
 1JB  C6   N1   single  1.371  0.020  1.371
 1JB  C6   C5   double  1.344  0.020  1.344
 1JB  N1   C2   single  1.376  0.020  1.376
 1JB  C5M  C5   single  1.493  0.020  1.493
 1JB  C5   C4   single  1.449  0.020  1.449
 1JB  C2   O2   double  1.213  0.020  1.213
 1JB  C2   N3   single  1.371  0.020  1.371
 1JB  C4   N3   single  1.383  0.020  1.383
 1JB  C4   O4   double  1.218  0.020  1.218
 1JB  N3   H1   single  0.860  0.020  1.020
 1JB  C6   H2   single  0.930  0.020  1.080
 1JB  C1Q  H4   single  0.970  0.020  1.090
 1JB  C5Q  H5   single  0.970  0.020  1.090
 1JB  C6Q  H6   single  0.970  0.020  1.090
 1JB  C6Q  H7   single  0.970  0.020  1.090
 1JB  C6Q  H8   single  0.970  0.020  1.090
 1JB  C4Q  H9   single  0.970  0.020  1.090
 1JB  O4Q  H10  single  0.850  0.020  0.980
 1JB  C3Q  H11  single  0.970  0.020  1.090
 1JB  O3Q  H12  single  0.850  0.020  0.980
 1JB  C2Q  H13  single  0.970  0.020  1.090
 1JB  O2Q  H14  single  0.850  0.020  0.980
 1JB  C5X  H16  single  0.970  0.020  1.090
 1JB  C5X  H17  single  0.970  0.020  1.090
 1JB  C4X  H18  single  0.970  0.020  1.090
 1JB  C3X  H19  single  0.970  0.020  1.090
 1JB  O3X  H20  single  0.850  0.020  0.980
 1JB  C2X  H21  single  0.970  0.020  1.090
 1JB  C2X  H22  single  0.970  0.020  1.090
 1JB  C1X  H23  single  0.970  0.020  1.090
 1JB  C5M  H24  single  0.970  0.020  1.090
 1JB  C5M  H25  single  0.970  0.020  1.090
 1JB  C5M  H26  single  0.970  0.020  1.090

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
 1JB  C2   N1   C1X  120.01  3.000
 1JB  C2   N1   C6   120.78  3.000
 1JB  C1X  N1   C6   119.14  3.000
 1JB  H1   N3   C2   115.12  3.000
 1JB  H1   N3   C4   116.73  3.000
 1JB  C2   N3   C4   128.15  3.000
 1JB  O4   C4   C5   125.09  3.000
 1JB  O4   C4   N3   120.62  3.000
 1JB  C5   C4   N3   114.29  3.000
 1JB  C5M  C5   C6   123.16  3.000
 1JB  C5M  C5   C4   119.00  3.000
 1JB  C6   C5   C4   117.84  3.000
 1JB  H2   C6   C5   120.80  3.000
 1JB  H2   C6   N1   114.75  3.000
 1JB  C5   C6   N1   124.45  3.000
 1JB  O3A  PB   O3B   93.74  3.000
 1JB  O3A  PB   O2B  110.02  3.000
 1JB  O3B  PB   O2B  109.19  3.000
 1JB  O3A  PB   O1B  109.47  3.000
 1JB  O2B  PB   O1B  121.36  3.000
 1JB  O3B  PB   O1B  109.54  3.000
 1JB  C1Q  O3B  PB   119.65  3.000
 1JB  H4   C1Q  C2Q  109.95  3.000
 1JB  H4   C1Q  O5Q  105.29  3.000
 1JB  C2Q  C1Q  O5Q  110.46  3.000
 1JB  H4   C1Q  O3B  110.51  3.000
 1JB  C2Q  C1Q  O3B  108.22  3.000
 1JB  O5Q  C1Q  O3B  112.40  3.000
 1JB  C5Q  O5Q  C1Q  115.31  3.000
 1JB  H5   C5Q  C4Q  107.52  3.000
 1JB  H5   C5Q  C6Q  108.11  3.000
 1JB  C4Q  C5Q  C6Q  113.14  3.000
 1JB  H5   C5Q  O5Q  110.09  3.000
 1JB  C4Q  C5Q  O5Q  110.83  3.000
 1JB  C6Q  C5Q  O5Q  107.11  3.000
 1JB  H8   C6Q  H7   108.27  3.000
 1JB  H8   C6Q  H6   107.80  3.000
 1JB  H7   C6Q  H6   107.59  3.000
 1JB  H8   C6Q  C5Q  112.11  3.000
 1JB  H7   C6Q  C5Q  110.37  3.000
 1JB  H6   C6Q  C5Q  110.55  3.000
 1JB  H9   C4Q  C3Q  108.45  3.000
 1JB  H9   C4Q  O4Q  110.97  3.000
 1JB  C3Q  C4Q  O4Q  108.41  3.000
 1JB  H9   C4Q  C5Q  107.48  3.000
 1JB  C3Q  C4Q  C5Q  108.71  3.000
 1JB  O4Q  C4Q  C5Q  112.73  3.000
 1JB  H10  O4Q  C4Q  108.66  3.000
 1JB  H11  C3Q  C2Q  108.31  3.000
 1JB  H11  C3Q  O3Q  110.52  3.000
 1JB  C2Q  C3Q  O3Q  111.97  3.000
 1JB  H11  C3Q  C4Q  106.75  3.000
 1JB  C2Q  C3Q  C4Q  110.06  3.000
 1JB  O3Q  C3Q  C4Q  109.09  3.000
 1JB  H12  O3Q  C3Q  107.67  3.000
 1JB  H13  C2Q  O2Q  110.79  3.000
 1JB  H13  C2Q  C3Q  108.81  3.000
 1JB  O2Q  C2Q  C3Q  107.79  3.000
 1JB  H13  C2Q  C1Q  107.00  3.000
 1JB  O2Q  C2Q  C1Q  112.20  3.000
 1JB  C3Q  C2Q  C1Q  110.22  3.000
 1JB  H14  O2Q  C2Q  108.87  3.000
 1JB  PA   O3A  PB   123.34  3.000
 1JB  O5X  PA   O2A  109.58  3.000
 1JB  O5X  PA   O1A  109.24  3.000
 1JB  O2A  PA   O1A  120.50  3.000
 1JB  O1A  PA   O3A  110.36  3.000
 1JB  O5X  PA   O3A   93.28  3.000
 1JB  O2A  PA   O3A  110.48  3.000
 1JB  C5X  O5X  PA   117.02  3.000
 1JB  H17  C5X  H16  107.64  3.000
 1JB  H17  C5X  C4X  108.03  3.000
 1JB  H16  C5X  C4X  109.03  3.000
 1JB  H17  C5X  O5X  111.07  3.000
 1JB  H16  C5X  O5X  111.52  3.000
 1JB  C4X  C5X  O5X  109.46  3.000
 1JB  H18  C4X  C3X  108.24  3.000
 1JB  H18  C4X  O4X  109.62  3.000
 1JB  C3X  C4X  O4X  106.61  3.000
 1JB  H18  C4X  C5X  109.48  3.000
 1JB  O4X  C4X  C5X  109.98  3.000
 1JB  C3X  C4X  C5X  112.85  3.000
 1JB  C1X  O4X  C4X  111.23  3.000
 1JB  H19  C3X  C2X  109.92  3.000
 1JB  H19  C3X  O3X  110.58  3.000
 1JB  C2X  C3X  O3X  114.69  3.000
 1JB  H19  C3X  C4X  109.92  3.000
 1JB  C2X  C3X  C4X  102.62  3.000
 1JB  O3X  C3X  C4X  108.78  3.000
 1JB  H20  O3X  C3X  108.29  3.000
 1JB  H22  C2X  H21  107.41  3.000
 1JB  H22  C2X  C1X  108.45  3.000
 1JB  H21  C2X  C1X  113.17  3.000
 1JB  H22  C2X  C3X  108.97  3.000
 1JB  H21  C2X  C3X  113.74  3.000
 1JB  C1X  C2X  C3X  104.96  3.000
 1JB  H23  C1X  C2X  109.63  3.000
 1JB  H23  C1X  O4X  110.10  3.000
 1JB  C2X  C1X  O4X  107.59  3.000
 1JB  H23  C1X  N1   104.10  3.000
 1JB  O4X  C1X  N1   109.26  3.000
 1JB  C2X  C1X  N1   116.08  3.000
 1JB  O2   C2   N3   121.90  3.000
 1JB  N3   C2   N1   114.47  3.000
 1JB  O2   C2   N1   123.63  3.000
 1JB  H26  C5M  H25  107.91  3.000
 1JB  H26  C5M  H24  107.17  3.000
 1JB  H25  C5M  H24  107.89  3.000
 1JB  H26  C5M  C5   111.43  3.000
 1JB  H25  C5M  C5   110.90  3.000
 1JB  H24  C5M  C5   111.37  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
 1JB  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 1JB  CONST_02  C1X  N1   C2   N3    180.00   0.0  0
 1JB  CONST_03  C6   N1   C2   N3      0.00   0.0  0
 1JB  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 1JB  CONST_05  O2   C2   N3   C4    180.00   0.0  0
 1JB  CONST_06  O2   C2   N1   C6    180.00   0.0  0
 1JB  CONST_07  O2   C2   N1   C1X     0.00   0.0  0
 1JB  CONST_08  O4   C4   N3   C2    180.00   0.0  0
 1JB  CONST_09  H1   N3   C2   N1    180.00   0.0  0
 1JB  Var_01    H24  C5M  C5   C4     60.42  30.0  3
 1JB  Var_02    O3A  PB   O3B  C1Q   148.74  30.0  3
 1JB  Var_03    C4X  C5X  O5X  PA   -171.22  30.0  1
 1JB  Var_04    O2A  PA   O3A  PB     43.76  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
 1JB  chir_02  C1Q  O5Q  O3B  C2Q  positiv
 1JB  chir_03  C5Q  O5Q  C6Q  C4Q  positiv
 1JB  chir_04  C4Q  O4Q  C5Q  C3Q  negativ
 1JB  chir_05  C3Q  O3Q  C4Q  C2Q  negativ
 1JB  chir_06  C2Q  O2Q  C3Q  C1Q  positiv
 1JB  chir_08  C4X  C5X  C3X  O4X  positiv
 1JB  chir_09  C3X  O3X  C2X  C4X  negativ
 1JB  chir_10  C1X  O4X  N1   C2X  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
 1JB  plan-1  N1   0.020
 1JB  plan-1  N3   0.020
 1JB  plan-1  C4   0.020
 1JB  plan-1  C5   0.020
 1JB  plan-1  C6   0.020
 1JB  plan-1  C1X  0.020
 1JB  plan-1  C2   0.020
 1JB  plan-1  O2   0.020
 1JB  plan-1  C5M  0.020
 1JB  plan-1  O4   0.020
 1JB  plan-1  H1   0.020
 1JB  plan-1  H2   0.020

