# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Fri Jul  3 23:32:35 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: [(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@H]2O)N3C=CC(=O)NC3=O)[C@@H](F)[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
 UP1  UP1  '[(2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4R,5R,6R)-3-fluoro-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  57  36  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UP1
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
 UP1  N1    N  NR6    0  -0.556   1.7126  -1.4130   2.1416
 UP1  C2    C  CR6    0   0.735   1.4126  -1.1312   3.4601
 UP1  N3    N  NR16   0  -0.734   0.0723  -1.1168   3.7464
 UP1  C4    C  CR6    0   0.570  -0.9907  -1.3404   2.8852
 UP1  C5    C  CR16   0  -0.515  -0.5823  -1.6182   1.5295
 UP1  C6    C  CR16   0   0.106   0.7243  -1.6383   1.2258
 UP1  O2    O  O      0  -0.472   2.2542  -0.9154   4.3057
 UP1  O4    O  O      0  -0.463  -2.1369  -1.2933   3.2910
 UP1  C1'   C  CH1    0   0.151   3.1044  -1.4371   1.7098
 UP1  C2'   C  CH1    0  -0.061   3.5761  -2.8247   1.2580
 UP1  O2'   O  OH1    0  -0.665   4.0571  -3.6279   2.2912
 UP1  C3'   C  CH1    0  -0.013   4.5724  -2.4819   0.1538
 UP1  C4'   C  CH1    0  -0.018   3.9974  -1.1950  -0.4362
 UP1  O4'   O  O2     0  -0.488   3.2533  -0.5805   0.6137
 UP1  O3'   O  OH1    0  -0.658   4.7151  -3.4525  -0.8422
 UP1  C5'   C  CH2    0  -0.146   5.0971  -0.2764  -0.9218
 UP1  O5'   O  O2     0  -0.619   4.5677   0.9750  -1.2931
 UP1  PA    P  P      0   1.358   5.6201   2.2162  -1.5333
 UP1  O1A   O  O      0  -0.787   4.7853   3.3775  -1.9644
 UP1  O2A   O  OP    -1  -0.793   6.7823   1.7373  -2.3385
 UP1  O3A   O  O2     0  -0.752   6.0599   2.4362   0.0405
 UP1  PB    P  P      0   1.345   7.3026   3.2733   0.7021
 UP1  O1B   O  OP    -1  -0.779   8.5404   3.1134  -0.1113
 UP1  O2B   O  O      0  -0.778   6.8134   4.6089   1.1536
 UP1  O3B   O  O2     0  -0.632   7.4425   2.3953   2.1100
 UP1  C1    C  CH1    0   0.282   7.8228   1.0706   2.0774
 UP1  C23   C  CH1    0   0.138   6.8299   0.2359   2.8772
 UP1  C3    C  CH1    0  -0.047   7.2522  -1.2221   2.8686
 UP1  C45   C  CH1    0  -0.002   8.6531  -1.2995   3.4719
 UP1  C56   C  CH1    0  -0.078   9.6179  -0.3412   2.7407
 UP1  C67   C  CH2    0  -0.154  10.0603  -0.8495   1.3735
 UP1  F2    F  F      0  -0.352   5.5723   0.3638   2.3138
 UP1  O3    O  OH1    0  -0.666   6.3273  -2.0611   3.5152
 UP1  O45   O  OH1    0  -0.655   9.0819  -2.6325   3.4226
 UP1  O5    O  O2     0  -0.487   9.0750   0.9671   2.6992
 UP1  O6    O  OH1    0  -0.663  10.9588   0.0906   0.8402
 UP1  H6    H  HCR6   0   0.328   1.0542  -1.8366   0.2157
 UP1  H1'   H  HCH1   0   0.272   3.6918  -1.0901   2.5597
 UP1  H3    H  HNR6   0   0.427  -0.1579  -0.9133   4.7116
 UP1  H5    H  HCR6   0   0.294  -1.3281  -1.8015   0.7718
 UP1  H2'   H  HCH1   0   0.268   2.7417  -3.3719   0.8030
 UP1  HA    H  HOH1   0   0.449   4.8122  -3.1867   2.7108
 UP1  H3'   H  HCH1   0   0.219   5.5437  -2.2532   0.6209
 UP1  H4'   H  HCH1   0   0.244   3.3137  -1.4360  -1.2611
 UP1  HB    H  HOH1   0   0.461   5.2062  -4.1953  -0.4772
 UP1  H5'1  H  HCH2   0   0.218   5.5950  -0.7669  -1.7654
 UP1  H5'2  H  HCH2   0   0.202   5.8405  -0.1693  -0.1280
 UP1  H1    H  HCH1   0   0.194   7.8719   0.6945   1.0437
 UP1  H2    H  HCH1   0   0.237   6.7718   0.6157   3.9042
 UP1  H33   H  HCH1   0   0.246   7.2828  -1.5773   1.8319
 UP1  H4    H  HCH1   0   0.242   8.5815  -0.9514   4.5143
 UP1  HC    H  HOH1   0   0.461   6.2303  -1.7977   4.4381
 UP1  H56   H  HCH1   0   0.262  10.5191  -0.2459   3.3544
 UP1  HD    H  HOH1   0   0.461   9.8682  -2.7207   3.9707
 UP1  H61   H  HCH2   0   0.192   9.2089  -1.0165   0.7002
 UP1  H62   H  HCH2   0   0.217  10.5311  -1.8283   1.5155
 UP1  H66   H  HOH1   0   0.455  11.2255  -0.2153  -0.0310

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
 UP1  N1   C2    single  1.381  0.020  1.381
 UP1  N1   C6    single  1.366  0.020  1.366
 UP1  N1   C1'   single  1.457  0.020  1.457
 UP1  C2   N3    single  1.371  0.020  1.371
 UP1  C2   O2    double  1.212  0.020  1.212
 UP1  N3   C4    single  1.386  0.020  1.386
 UP1  N3   H3    single  0.860  0.020  1.020
 UP1  C4   C5    single  1.443  0.020  1.443
 UP1  C4   O4    double  1.217  0.020  1.217
 UP1  C5   C6    double  1.342  0.020  1.342
 UP1  C5   H5    single  0.930  0.020  1.080
 UP1  C6   H6    single  0.930  0.020  1.080
 UP1  C1'  C2'   single  1.534  0.020  1.534
 UP1  C1'  O4'   single  1.399  0.020  1.399
 UP1  C1'  H1'   single  0.970  0.020  1.090
 UP1  C2'  O2'   single  1.394  0.020  1.394
 UP1  C2'  C3'   single  1.526  0.020  1.526
 UP1  C2'  H2'   single  0.970  0.020  1.090
 UP1  O2'  HA    single  0.850  0.020  0.980
 UP1  C3'  C4'   single  1.528  0.020  1.528
 UP1  C3'  O3'   single  1.398  0.020  1.398
 UP1  C3'  H3'   single  0.970  0.020  1.090
 UP1  C4'  O4'   single  1.426  0.020  1.426
 UP1  C4'  C5'   single  1.513  0.020  1.513
 UP1  C4'  H4'   single  0.970  0.020  1.090
 UP1  O3'  HB    single  0.850  0.020  0.980
 UP1  C5'  O5'   single  1.409  0.020  1.409
 UP1  C5'  H5'1  single  0.970  0.020  1.090
 UP1  C5'  H5'2  single  0.970  0.020  1.090
 UP1  O5'  PA    single  1.645  0.020  1.645
 UP1  PA   O1A   deloc   1.494  0.020  1.494
 UP1  PA   O2A   deloc   1.493  0.020  1.493
 UP1  PA   O3A   single  1.649  0.020  1.649
 UP1  O3A  PB    single  1.638  0.020  1.638
 UP1  PB   O1B   deloc   1.490  0.020  1.490
 UP1  PB   O2B   deloc   1.492  0.020  1.492
 UP1  PB   O3B   single  1.665  0.020  1.665
 UP1  O3B  C1    single  1.379  0.020  1.379
 UP1  C1   C23   single  1.524  0.020  1.524
 UP1  C1   O5    single  1.402  0.020  1.402
 UP1  C1   H1    single  0.970  0.020  1.090
 UP1  C23  C3    single  1.518  0.020  1.518
 UP1  C23  F2    single  1.384  0.020  1.384
 UP1  C23  H2    single  0.970  0.020  1.090
 UP1  C3   C45   single  1.527  0.020  1.527
 UP1  C3   O3    single  1.406  0.020  1.406
 UP1  C3   H33   single  0.970  0.020  1.090
 UP1  C45  C56   single  1.544  0.020  1.544
 UP1  C45  O45   single  1.401  0.020  1.401
 UP1  C45  H4    single  0.970  0.020  1.090
 UP1  C56  C67   single  1.524  0.020  1.524
 UP1  C56  O5    single  1.417  0.020  1.417
 UP1  C56  H56   single  0.970  0.020  1.090
 UP1  C67  O6    single  1.406  0.020  1.406
 UP1  C67  H61   single  0.970  0.020  1.090
 UP1  C67  H62   single  0.970  0.020  1.090
 UP1  O3   HC    single  0.850  0.020  0.980
 UP1  O45  HD    single  0.850  0.020  0.980
 UP1  O6   H66   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
 UP1  C1'   N1   C6    119.31  3.000
 UP1  C1'   N1   C2    119.57  3.000
 UP1  C6    N1   C2    121.10  3.000
 UP1  O2    C2   N3    122.09  3.000
 UP1  O2    C2   N1    123.46  3.000
 UP1  N3    C2   N1    114.45  3.000
 UP1  H3    N3   C4    116.75  3.000
 UP1  H3    N3   C2    115.05  3.000
 UP1  C4    N3   C2    128.20  3.000
 UP1  O4    C4   C5    125.97  3.000
 UP1  O4    C4   N3    120.59  3.000
 UP1  C5    C4   N3    113.44  3.000
 UP1  H5    C5   C6    120.78  3.000
 UP1  H5    C5   C4    119.80  3.000
 UP1  C6    C5   C4    119.42  3.000
 UP1  H6    C6   C5    120.76  3.000
 UP1  H6    C6   N1    115.85  3.000
 UP1  C5    C6   N1    123.39  3.000
 UP1  H1'   C1'  O4'   111.02  3.000
 UP1  H1'   C1'  C2'   110.61  3.000
 UP1  O4'   C1'  C2'   106.88  3.000
 UP1  H1'   C1'  N1    106.16  3.000
 UP1  O4'   C1'  N1    108.88  3.000
 UP1  C2'   C1'  N1    113.32  3.000
 UP1  H2'   C2'  C3'   107.97  3.000
 UP1  H2'   C2'  O2'   106.41  3.000
 UP1  C3'   C2'  O2'   116.12  3.000
 UP1  H2'   C2'  C1'   109.86  3.000
 UP1  C3'   C2'  C1'   102.16  3.000
 UP1  O2'   C2'  C1'   114.14  3.000
 UP1  HA    O2'  C2'   109.09  3.000
 UP1  H3'   C3'  O3'   110.87  3.000
 UP1  H3'   C3'  C4'   108.70  3.000
 UP1  O3'   C3'  C4'   110.36  3.000
 UP1  H3'   C3'  C2'   108.39  3.000
 UP1  O3'   C3'  C2'   115.22  3.000
 UP1  C4'   C3'  C2'   102.87  3.000
 UP1  H4'   C4'  C5'   110.16  3.000
 UP1  H4'   C4'  O4'   108.83  3.000
 UP1  C5'   C4'  O4'   110.73  3.000
 UP1  H4'   C4'  C3'   109.85  3.000
 UP1  C5'   C4'  C3'   111.21  3.000
 UP1  O4'   C4'  C3'   105.96  3.000
 UP1  C4'   O4'  C1'   111.62  3.000
 UP1  HB    O3'  C3'   108.52  3.000
 UP1  H5'2  C5'  H5'1  107.10  3.000
 UP1  H5'2  C5'  O5'   111.10  3.000
 UP1  H5'1  C5'  O5'   111.45  3.000
 UP1  H5'2  C5'  C4'   108.71  3.000
 UP1  H5'1  C5'  C4'   107.80  3.000
 UP1  O5'   C5'  C4'   110.54  3.000
 UP1  PA    O5'  C5'   117.93  3.000
 UP1  O3A   PA   O2A   110.49  3.000
 UP1  O3A   PA   O1A   108.71  3.000
 UP1  O2A   PA   O1A   121.93  3.000
 UP1  O3A   PA   O5'    97.58  3.000
 UP1  O2A   PA   O5'   109.57  3.000
 UP1  O1A   PA   O5'   105.73  3.000
 UP1  PB    O3A  PA    131.00  3.000
 UP1  O3B   PB   O2B   104.10  3.000
 UP1  O3B   PB   O1B   109.59  3.000
 UP1  O2B   PB   O1B   122.25  3.000
 UP1  O3B   PB   O3A    97.81  3.000
 UP1  O2B   PB   O3A   109.32  3.000
 UP1  O1B   PB   O3A   110.79  3.000
 UP1  C1    O3B  PB    120.65  3.000
 UP1  H1    C1   O5    110.57  3.000
 UP1  H1    C1   C23   109.55  3.000
 UP1  O5    C1   C23   107.99  3.000
 UP1  H1    C1   O3B   111.27  3.000
 UP1  O5    C1   O3B   107.87  3.000
 UP1  C23   C1   O3B   109.52  3.000
 UP1  H2    C23  F2    107.53  3.000
 UP1  H2    C23  C3    110.66  3.000
 UP1  F2    C23  C3    109.83  3.000
 UP1  H2    C23  C1    109.65  3.000
 UP1  F2    C23  C1    109.14  3.000
 UP1  C3    C23  C1    109.99  3.000
 UP1  H33   C3   O3    105.06  3.000
 UP1  H33   C3   C45   109.36  3.000
 UP1  O3    C3   C45   113.04  3.000
 UP1  H33   C3   C23   108.93  3.000
 UP1  O3    C3   C23   112.80  3.000
 UP1  C45   C3   C23   107.56  3.000
 UP1  H4    C45  O45   110.73  3.000
 UP1  H4    C45  C56   107.02  3.000
 UP1  O45   C45  C56   112.50  3.000
 UP1  H4    C45  C3    107.35  3.000
 UP1  O45   C45  C3    108.36  3.000
 UP1  C56   C45  C3    110.77  3.000
 UP1  H56   C56  O5    104.57  3.000
 UP1  H56   C56  C67   107.04  3.000
 UP1  O5    C56  C67   113.12  3.000
 UP1  H56   C56  C45   107.64  3.000
 UP1  O5    C56  C45   110.34  3.000
 UP1  C67   C56  C45   113.53  3.000
 UP1  H62   C67  H61   106.07  3.000
 UP1  H62   C67  O6    111.85  3.000
 UP1  H61   C67  O6    111.39  3.000
 UP1  H62   C67  C56   107.84  3.000
 UP1  H61   C67  C56   112.06  3.000
 UP1  O6    C67  C56   107.63  3.000
 UP1  HC    O3   C3    110.07  3.000
 UP1  HD    O45  C45   108.49  3.000
 UP1  C56   O5   C1    115.05  3.000
 UP1  H66   O6   C67   107.96  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
 UP1  CONST_01  C4    N3   C2   N1     0.00   0.0  0
 UP1  CONST_02  C5    C4   N3   C2     0.00   0.0  0
 UP1  CONST_03  C6    N1   C2   N3     0.00   0.0  0
 UP1  CONST_04  C1'   N1   C2   N3   180.00   0.0  0
 UP1  CONST_05  O4    C4   N3   C2   180.00   0.0  0
 UP1  CONST_06  O2    C2   N3   C4   180.00   0.0  0
 UP1  CONST_07  O2    C2   N1   C6   180.00   0.0  0
 UP1  CONST_08  C1'   N1   C2   O2     0.00   0.0  0
 UP1  CONST_09  H3    N3   C2   N1   180.00   0.0  0
 UP1  Var_01    O1A   PA   O5'  C5'  177.75  30.0  3
 UP1  Var_02    O1B   PB   O3A  PA   -39.19  30.0  3
 UP1  Var_03    H5'1  C5'  O5'  PA   -73.27  30.0  1

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
 UP1  chir_01  C1'  N1   C2'  O4'  negativ
 UP1  chir_02  C2'  O2'  C3'  C1'  positiv
 UP1  chir_03  C3'  O3'  C2'  C4'  positiv
 UP1  chir_04  C4'  O4'  C3'  C5'  positiv
 UP1  chir_07  C1   O3B  C23  O5   positiv
 UP1  chir_08  C23  F2   C3   C1   negativ
 UP1  chir_09  C3   O3   C23  C45  negativ
 UP1  chir_10  C45  O45  C56  C3   negativ
 UP1  chir_11  C56  O5   C45  C67  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
 UP1  plan-1  N1   0.020
 UP1  plan-1  C2   0.020
 UP1  plan-1  N3   0.020
 UP1  plan-1  C4   0.020
 UP1  plan-1  C5   0.020
 UP1  plan-1  C6   0.020
 UP1  plan-1  O2   0.020
 UP1  plan-1  O4   0.020
 UP1  plan-1  C1'  0.020
 UP1  plan-1  H6   0.020
 UP1  plan-1  H3   0.020
 UP1  plan-1  H5   0.020

