# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat Jul  4 05:00:45 2020
#   Inital geometry file: a 150 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl hydrogen (S)-phosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H]([C@H](O)[C@@H]1O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)N4C=CC(=O)NC4=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
 UPU  UPU  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl hydrogen (S)-phosphate (non-preferred name)'  ligand  59  37  .  2021-08-24  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_UPU
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
 UPU  O2A   O  O      0  -0.469   2.2331   1.9715  -2.4510
 UPU  C2A   C  CR6    0   0.725   2.1723   1.9454  -1.2406
 UPU  N3A   N  NR16   0  -0.744   1.9796   3.0852  -0.5006
 UPU  C4A   C  CR6    0   0.553   1.9333   3.2139   0.8831
 UPU  O4A   O  O      0  -0.457   1.8039   4.3097   1.3952
 UPU  C5A   C  CR16   0  -0.511   2.0369   1.9543   1.5723
 UPU  C6A   C  CR16   0   0.103   2.2069   0.8210   0.8720
 UPU  N1A   N  NR6    0  -0.569   2.2762   0.7882  -0.4929
 UPU  C1'A  C  CR15   0   0.214   2.4738  -0.4786  -1.1845
 UPU  O4'A  O  O      0  -0.480   1.5981  -1.4303  -0.6609
 UPU  C2'A  C  CR15   0  -0.039   3.8678  -1.0750  -1.0158
 UPU  O2'A  O  OH1    0  -0.652   4.7641  -0.4613  -1.8913
 UPU  C3'A  C  CR15   0  -0.039   3.5756  -2.5503  -1.3088
 UPU  O3'A  O  OH1    0  -0.668   3.4272  -2.7682  -2.6881
 UPU  C4'A  C  CR15   0  -0.024   2.2194  -2.7196  -0.6293
 UPU  C5'A  C  CH2    0  -0.175   2.3752  -3.2191   0.7955
 UPU  O5'A  O  O2     0  -0.618   1.1373  -3.3075   1.4635
 UPU  P     P  P      0   1.383   0.7280  -2.3132   2.7101
 UPU  O1    O  OP    -1  -0.785  -0.1377  -3.1387   3.6066
 UPU  O2    O  O      0  -0.780   1.9476  -1.5940   3.1993
 UPU  O3'B  O  O2     0  -0.607  -0.1828  -1.1591   1.9883
 UPU  C3'B  C  CR15   0  -0.058  -1.5347  -1.3515   1.6633
 UPU  C4'B  C  CR15   0  -0.018  -1.7170  -1.7811   0.2041
 UPU  C5'B  C  CH2    0  -0.146  -2.9731  -2.6009  -0.0031
 UPU  O5'B  O  OH1    0  -0.672  -3.0856  -2.9083  -1.3717
 UPU  O4'B  O  O      0  -0.486  -1.7629  -0.5707  -0.5619
 UPU  C2'B  C  CR15   0  -0.021  -2.2120   0.0157   1.6619
 UPU  O2'B  O  OH1    0  -0.650  -1.8022   0.8269   2.7180
 UPU  C1'B  C  CR15   0   0.224  -1.7581   0.5283   0.2911
 UPU  N1B   N  NR6    0  -0.582  -2.5271   1.6235  -0.2876
 UPU  C2B   C  CR6    0   0.748  -3.8784   1.4795  -0.5554
 UPU  O2B   O  O      0  -0.462  -4.5111   0.4809  -0.2949
 UPU  C6B   C  CR16   0   0.116  -1.8777   2.7785  -0.6259
 UPU  C5B   C  CR16   0  -0.507  -2.4710   3.8358  -1.1982
 UPU  C4B   C  CR6    0   0.569  -3.8794   3.7756  -1.5019
 UPU  N3B   N  NR16   0  -0.735  -4.4640   2.5715  -1.1436
 UPU  O4B   O  O      0  -0.461  -4.5382   4.6559  -2.0218
 UPU  HN3A  H  HNR6   0   0.428   1.9374   3.9410  -1.0411
 UPU  H5A   H  HCR6   0   0.286   1.9820   1.9243   2.6490
 UPU  H6A   H  HCR6   0   0.325   2.2806  -0.1250   1.3889
 UPU  H1'A  H  HCR5   0   0.269   2.2757  -0.2865  -2.2412
 UPU  H2AC  H  HCR5   0   0.247   4.1912  -0.9760   0.0298
 UPU  H2AO  H  HOH1   0   0.469   5.6618  -0.6538  -1.6019
 UPU  H3AC  H  HCR5   0   0.252   4.3366  -3.2126  -0.8746
 UPU  H3AO  H  HOH1   0   0.449   4.1716  -2.3503  -3.1368
 UPU  H4'A  H  HCR5   0   0.256   1.5896  -3.4168  -1.1910
 UPU  H'A1  H  HCH2   0   0.234   2.8083  -4.2231   0.7437
 UPU  H'A2  H  HCH2   0   0.217   3.0815  -2.5933   1.3491
 UPU  H3BC  H  HCR5   0   0.259  -2.0157  -2.0468   2.3582
 UPU  H4'B  H  HCR5   0   0.264  -0.8560  -2.3614  -0.1324
 UPU  H'B1  H  HCH2   0   0.197  -2.8769  -3.5081   0.6091
 UPU  H'B2  H  HCH2   0   0.205  -3.8505  -2.0566   0.3640
 UPU  H5'B  H  HOH1   0   0.456  -3.9002  -3.4022  -1.4985
 UPU  H2BC  H  HCR5   0   0.263  -3.2929  -0.1440   1.6691
 UPU  H2BO  H  HOH1   0   0.459  -2.4975   1.4659   2.8969
 UPU  H1'B  H  HCR5   0   0.234  -0.7444   0.9318   0.4125
 UPU  H6B   H  HCR6   0   0.288  -0.8221   2.7960  -0.3958
 UPU  H5B   H  HCR6   0   0.296  -1.9050   4.7217  -1.4406
 UPU  HN3B  H  HNR6   0   0.427  -5.4531   2.4700  -1.3373

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
 UPU  O2A   C2A   double  1.212  0.020  1.212
 UPU  C2A   N3A   single  1.373  0.020  1.373
 UPU  C2A   N1A   single  1.382  0.020  1.382
 UPU  N3A   C4A   single  1.390  0.020  1.390
 UPU  N3A   HN3A  single  0.860  0.020  1.020
 UPU  C4A   O4A   double  1.216  0.020  1.216
 UPU  C4A   C5A   single  1.440  0.020  1.440
 UPU  C5A   C6A   double  1.343  0.020  1.343
 UPU  C5A   H5A   single  0.930  0.020  1.080
 UPU  C6A   N1A   single  1.367  0.020  1.367
 UPU  C6A   H6A   single  0.930  0.020  1.080
 UPU  N1A   C1'A  single  1.457  0.020  1.457
 UPU  C1'A  O4'A  single  1.395  0.020  1.395
 UPU  C1'A  C2'A  single  1.526  0.020  1.526
 UPU  C1'A  H1'A  single  0.970  0.020  1.090
 UPU  O4'A  C4'A  single  1.432  0.020  1.432
 UPU  C2'A  O2'A  single  1.395  0.020  1.395
 UPU  C2'A  C3'A  single  1.532  0.020  1.532
 UPU  C2'A  H2AC  single  0.970  0.020  1.090
 UPU  O2'A  H2AO  single  0.850  0.020  0.980
 UPU  C3'A  C4'A  single  1.526  0.020  1.526
 UPU  C3'A  O3'A  single  1.404  0.020  1.404
 UPU  C3'A  H3AC  single  0.970  0.020  1.090
 UPU  O3'A  H3AO  single  0.850  0.020  0.980
 UPU  C4'A  C5'A  single  1.518  0.020  1.518
 UPU  C4'A  H4'A  single  0.970  0.020  1.090
 UPU  C5'A  O5'A  single  1.409  0.020  1.409
 UPU  C5'A  H'A1  single  0.970  0.020  1.090
 UPU  C5'A  H'A2  single  0.970  0.020  1.090
 UPU  O5'A  P     single  1.646  0.020  1.646
 UPU  P     O3'B  single  1.638  0.020  1.638
 UPU  P     O2    deloc   1.498  0.020  1.498
 UPU  P     O1    deloc   1.495  0.020  1.495
 UPU  O3'B  C3'B  single  1.404  0.020  1.404
 UPU  C3'B  C4'B  single  1.532  0.020  1.532
 UPU  C3'B  C2'B  single  1.526  0.020  1.526
 UPU  C3'B  H3BC  single  0.970  0.020  1.090
 UPU  C4'B  O4'B  single  1.433  0.020  1.433
 UPU  C4'B  C5'B  single  1.514  0.020  1.514
 UPU  C4'B  H4'B  single  0.970  0.020  1.090
 UPU  C5'B  O5'B  single  1.407  0.020  1.407
 UPU  C5'B  H'B1  single  0.970  0.020  1.090
 UPU  C5'B  H'B2  single  0.970  0.020  1.090
 UPU  O5'B  H5'B  single  0.850  0.020  0.980
 UPU  O4'B  C1'B  single  1.391  0.020  1.391
 UPU  C2'B  C1'B  single  1.532  0.020  1.532
 UPU  C2'B  O2'B  single  1.393  0.020  1.393
 UPU  C2'B  H2BC  single  0.970  0.020  1.090
 UPU  O2'B  H2BO  single  0.850  0.020  0.980
 UPU  C1'B  N1B   single  1.458  0.020  1.458
 UPU  C1'B  H1'B  single  0.970  0.020  1.090
 UPU  N1B   C6B   single  1.368  0.020  1.368
 UPU  N1B   C2B   single  1.385  0.020  1.385
 UPU  C2B   O2B   double  1.210  0.020  1.210
 UPU  C2B   N3B   single  1.372  0.020  1.372
 UPU  C6B   C5B   double  1.341  0.020  1.341
 UPU  C6B   H6B   single  0.930  0.020  1.080
 UPU  C5B   C4B   single  1.442  0.020  1.442
 UPU  C5B   H5B   single  0.930  0.020  1.080
 UPU  C4B   N3B   single  1.386  0.020  1.386
 UPU  C4B   O4B   double  1.216  0.020  1.216
 UPU  N3B   HN3B  single  0.860  0.020  1.020

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
 UPU  N1A   C2A   N3A   114.47  3.000
 UPU  N1A   C2A   O2A   123.69  3.000
 UPU  N3A   C2A   O2A   121.84  3.000
 UPU  HN3A  N3A   C4A   116.83  3.000
 UPU  HN3A  N3A   C2A   114.82  3.000
 UPU  C4A   N3A   C2A   128.18  3.000
 UPU  C5A   C4A   O4A   126.47  3.000
 UPU  C5A   C4A   N3A   113.14  3.000
 UPU  O4A   C4A   N3A   120.39  3.000
 UPU  H5A   C5A   C6A   120.23  3.000
 UPU  H5A   C5A   C4A   119.90  3.000
 UPU  C6A   C5A   C4A   119.86  3.000
 UPU  H6A   C6A   N1A   116.94  3.000
 UPU  H6A   C6A   C5A   119.87  3.000
 UPU  N1A   C6A   C5A   123.18  3.000
 UPU  C1'A  N1A   C6A   120.12  3.000
 UPU  C1'A  N1A   C2A   118.79  3.000
 UPU  C6A   N1A   C2A   121.09  3.000
 UPU  H1'A  C1'A  C2'A  109.97  3.000
 UPU  H1'A  C1'A  O4'A  111.67  3.000
 UPU  C2'A  C1'A  O4'A  105.38  3.000
 UPU  H1'A  C1'A  N1A   106.37  3.000
 UPU  C2'A  C1'A  N1A   114.29  3.000
 UPU  O4'A  C1'A  N1A   109.26  3.000
 UPU  C4'A  O4'A  C1'A  110.50  3.000
 UPU  H2AC  C2'A  C3'A  108.96  3.000
 UPU  H2AC  C2'A  O2'A  111.61  3.000
 UPU  C3'A  C2'A  O2'A  115.22  3.000
 UPU  H2AC  C2'A  C1'A  109.81  3.000
 UPU  C3'A  C2'A  C1'A  100.43  3.000
 UPU  O2'A  C2'A  C1'A  110.22  3.000
 UPU  H2AO  O2'A  C2'A  108.81  3.000
 UPU  H3AC  C3'A  C4'A  111.89  3.000
 UPU  H3AC  C3'A  O3'A  111.59  3.000
 UPU  C4'A  C3'A  O3'A  109.04  3.000
 UPU  H3AC  C3'A  C2'A  111.89  3.000
 UPU  O3'A  C3'A  C2'A  110.94  3.000
 UPU  C4'A  C3'A  C2'A  101.02  3.000
 UPU  H3AO  O3'A  C3'A  107.95  3.000
 UPU  H4'A  C4'A  C5'A  109.34  3.000
 UPU  H4'A  C4'A  C3'A  110.70  3.000
 UPU  C5'A  C4'A  C3'A  111.30  3.000
 UPU  H4'A  C4'A  O4'A  108.21  3.000
 UPU  C5'A  C4'A  O4'A  111.20  3.000
 UPU  C3'A  C4'A  O4'A  106.02  3.000
 UPU  H'A2  C5'A  H'A1  107.05  3.000
 UPU  H'A2  C5'A  O5'A  111.29  3.000
 UPU  H'A1  C5'A  O5'A  108.20  3.000
 UPU  H'A2  C5'A  C4'A  110.67  3.000
 UPU  H'A1  C5'A  C4'A  107.33  3.000
 UPU  O5'A  C5'A  C4'A  112.05  3.000
 UPU  P     O5'A  C5'A  122.64  3.000
 UPU  O3'B  P     O2    104.97  3.000
 UPU  O2    P     O1    122.74  3.000
 UPU  O3'B  P     O1    109.35  3.000
 UPU  O1    P     O5'A  105.34  3.000
 UPU  O2    P     O5'A  109.56  3.000
 UPU  O3'B  P     O5'A  103.31  3.000
 UPU  C3'B  O3'B  P     122.75  3.000
 UPU  H3BC  C3'B  C2'B  112.01  3.000
 UPU  H3BC  C3'B  C4'B  111.98  3.000
 UPU  C2'B  C3'B  C4'B  101.40  3.000
 UPU  H3BC  C3'B  O3'B  111.31  3.000
 UPU  C2'B  C3'B  O3'B  107.75  3.000
 UPU  C4'B  C3'B  O3'B  111.94  3.000
 UPU  H4'B  C4'B  O4'B  108.03  3.000
 UPU  H4'B  C4'B  C5'B  108.92  3.000
 UPU  O4'B  C4'B  C5'B  110.95  3.000
 UPU  H4'B  C4'B  C3'B  110.42  3.000
 UPU  C5'B  C4'B  C3'B  112.39  3.000
 UPU  O4'B  C4'B  C3'B  106.03  3.000
 UPU  H'B2  C5'B  H'B1  107.06  3.000
 UPU  H'B2  C5'B  O5'B  111.74  3.000
 UPU  H'B1  C5'B  O5'B  111.63  3.000
 UPU  H'B2  C5'B  C4'B  110.46  3.000
 UPU  H'B1  C5'B  C4'B  107.35  3.000
 UPU  O5'B  C5'B  C4'B  108.53  3.000
 UPU  H5'B  O5'B  C5'B  107.97  3.000
 UPU  C1'B  O4'B  C4'B  109.84  3.000
 UPU  H2BC  C2'B  C1'B  110.35  3.000
 UPU  H2BC  C2'B  O2'B  111.78  3.000
 UPU  C1'B  C2'B  O2'B  113.34  3.000
 UPU  H2BC  C2'B  C3'B  107.94  3.000
 UPU  O2'B  C2'B  C3'B  112.99  3.000
 UPU  C1'B  C2'B  C3'B   99.73  3.000
 UPU  H2BO  O2'B  C2'B  108.38  3.000
 UPU  H1'B  C1'B  N1B   104.77  3.000
 UPU  H1'B  C1'B  C2'B  107.31  3.000
 UPU  N1B   C1'B  C2'B  116.75  3.000
 UPU  H1'B  C1'B  O4'B  111.18  3.000
 UPU  N1B   C1'B  O4'B  110.38  3.000
 UPU  C2'B  C1'B  O4'B  106.45  3.000
 UPU  C6B   N1B   C2B   120.22  3.000
 UPU  C2B   N1B   C1'B  120.88  3.000
 UPU  C6B   N1B   C1'B  118.82  3.000
 UPU  N3B   C2B   O2B   121.73  3.000
 UPU  N3B   C2B   N1B   114.62  3.000
 UPU  O2B   C2B   N1B   123.65  3.000
 UPU  H6B   C6B   C5B   120.70  3.000
 UPU  H6B   C6B   N1B   115.14  3.000
 UPU  C5B   C6B   N1B   124.16  3.000
 UPU  H5B   C5B   C4B   119.96  3.000
 UPU  H5B   C5B   C6B   120.76  3.000
 UPU  C4B   C5B   C6B   119.29  3.000
 UPU  O4B   C4B   N3B   120.73  3.000
 UPU  O4B   C4B   C5B   126.07  3.000
 UPU  N3B   C4B   C5B   113.20  3.000
 UPU  HN3B  N3B   C4B   116.71  3.000
 UPU  HN3B  N3B   C2B   114.78  3.000
 UPU  C4B   N3B   C2B   128.51  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
 UPU  CONST_01  C6A   N1A   C2A   N3A     0.00   0.0  0
 UPU  CONST_02  C1'A  N1A   C2A   N3A   180.00   0.0  0
 UPU  CONST_03  N1A   C2A   N3A   C4A     0.00   0.0  0
 UPU  CONST_04  N3B   C2B   N1B   C1'B  180.00   0.0  0
 UPU  CONST_05  C4B   N3B   C2B   N1B     0.00   0.0  0
 UPU  CONST_06  C5B   C4B   N3B   C2B     0.00   0.0  0
 UPU  CONST_07  N3B   C2B   N1B   C6B     0.00   0.0  0
 UPU  CONST_08  C4A   N3A   C2A   O2A   180.00   0.0  0
 UPU  CONST_09  C6A   N1A   C2A   O2A   180.00   0.0  0
 UPU  CONST_10  C1'A  N1A   C2A   O2A     0.00   0.0  0
 UPU  CONST_11  O2B   C2B   N1B   C1'B    0.00   0.0  0
 UPU  CONST_12  O4B   C4B   N3B   C2B   180.00   0.0  0
 UPU  CONST_13  C6B   N1B   C2B   O2B   180.00   0.0  0
 UPU  CONST_14  C4B   N3B   C2B   O2B   180.00   0.0  0
 UPU  CONST_15  HN3A  N3A   C2A   N1A   180.00   0.0  0
 UPU  CONST_16  HN3B  N3B   C2B   N1B   180.00   0.0  0
 UPU  Var_01    O3'B  P     O5'A  C5'A   97.80  30.0  3
 UPU  Var_02    H'A1  C5'A  O5'A  P     130.52  30.0  2

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
 UPU  chir_01  C1'A  N1A   O4'A  C2'A  positiv
 UPU  chir_02  C2'A  O2'A  C1'A  C3'A  negativ
 UPU  chir_03  C3'A  O3'A  C4'A  C2'A  positiv
 UPU  chir_04  C4'A  O4'A  C3'A  C5'A  negativ
 UPU  chir_06  C3'B  O3'B  C4'B  C2'B  positiv
 UPU  chir_07  C4'B  O4'B  C3'B  C5'B  negativ
 UPU  chir_08  C2'B  O2'B  C3'B  C1'B  positiv
 UPU  chir_09  C1'B  O4'B  N1B   C2'B  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
 UPU  plan-1  O2A   0.020
 UPU  plan-1  C2A   0.020
 UPU  plan-1  N3A   0.020
 UPU  plan-1  C4A   0.020
 UPU  plan-1  O4A   0.020
 UPU  plan-1  C5A   0.020
 UPU  plan-1  C6A   0.020
 UPU  plan-1  N1A   0.020
 UPU  plan-1  C1'A  0.020
 UPU  plan-1  HN3A  0.020
 UPU  plan-1  H5A   0.020
 UPU  plan-1  H6A   0.020
 UPU  plan-2  C1'B  0.020
 UPU  plan-2  N1B   0.020
 UPU  plan-2  C2B   0.020
 UPU  plan-2  O2B   0.020
 UPU  plan-2  C6B   0.020
 UPU  plan-2  C5B   0.020
 UPU  plan-2  C4B   0.020
 UPU  plan-2  N3B   0.020
 UPU  plan-2  O4B   0.020
 UPU  plan-2  H6B   0.020
 UPU  plan-2  H5B   0.020
 UPU  plan-2  HN3B  0.020

