# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:30:27 2022
#   Inital geometry file: a 135 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,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1CO[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](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
 UDX  UDX  '[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R)-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)'  ligand  54  34  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UDX
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
 UDX  C1'   C  CH1    0   0.242  -0.1748  -0.4192   4.9508
 UDX  C2'   C  CH1    0   0.000   0.1771   0.9868   5.4571
 UDX  O2'   O  OH1    0  -0.663  -0.6760   1.9640   4.9250
 UDX  C3'   C  CH1    0   0.010   1.6115   1.3389   5.0977
 UDX  O3'   O  OH1    0  -0.671   1.9199   2.5845   5.6763
 UDX  C4'   C  CH1    0  -0.009   2.5311   0.2397   5.6156
 UDX  O4'   O  OH1    0  -0.673   3.8404   0.5348   5.1808
 UDX  C5'   C  CH2    0  -0.224   2.0762  -1.1224   5.1052
 UDX  O5'   O  O2     0  -0.496   0.7241  -1.3665   5.4511
 UDX  O1B   O  O      0  -0.799  -1.7288  -2.4540   3.4629
 UDX  O2B   O  OP    -1  -0.777   0.5667  -2.4405   2.2220
 UDX  O3B   O  O2     0  -0.626  -0.1913  -0.3884   3.5585
 UDX  O3A   O  O2     0  -0.735  -1.3085  -0.8594   1.4802
 UDX  PA    P  P      0   1.337  -2.3922  -1.4656   0.4081
 UDX  O1A   O  O      0  -0.791  -3.7683  -1.0079   0.7785
 UDX  O2A   O  OP    -1  -0.800  -2.1270  -2.9132   0.1388
 UDX  O5D   O  O2     0  -0.617  -1.8346  -0.5505  -0.8403
 UDX  C5D   C  CH2    0  -0.145  -2.4007  -0.7794  -2.1108
 UDX  C4D   C  CH1    0  -0.026  -2.3668   0.5124  -2.9012
 UDX  O4D   O  O2     0  -0.485  -1.0407   1.0459  -2.9690
 UDX  C3D   C  CH1    0  -0.038  -2.8221   0.3259  -4.3444
 UDX  O3D   O  OH1    0  -0.670  -3.4314   1.5124  -4.7855
 UDX  C2D   C  CH1    0  -0.060  -1.4884   0.0952  -5.0659
 UDX  O2D   O  OH1    0  -0.658  -1.4912   0.4608  -6.4168
 UDX  C1D   C  CH1    0   0.239  -0.5837   1.0480  -4.2853
 UDX  N1    N  NR6    0  -0.578   0.8446   0.7681  -4.3289
 UDX  C6    C  CR16   0   0.098   1.6920   1.7369  -4.7920
 UDX  C2    C  CR6    0   0.749   1.3438  -0.4344  -3.8582
 UDX  O2    O  O      0  -0.462   0.6457  -1.3289  -3.4359
 UDX  N3    N  NR16   0  -0.734   2.7096  -0.5456  -3.9096
 UDX  C4    C  CR6    0   0.567   3.6318   0.3788  -4.3746
 UDX  O4    O  O      0  -0.464   4.8225   0.1283  -4.3584
 UDX  C5    C  CR16   0  -0.511   3.0259   1.6000  -4.8430
 UDX  H1'   H  HCH1   0   0.235  -1.1531  -0.7176   5.3457
 UDX  H2'1  H  HCH1   0   0.218   0.1021   0.9503   6.5549
 UDX  HO'2  H  HOH1   0   0.453  -1.5649   1.8089   5.2593
 UDX  H3'1  H  HCH1   0   0.211   1.7076   1.3856   4.0018
 UDX  HO'3  H  HOH1   0   0.448   2.8411   2.7781   5.4738
 UDX  H4'1  H  HCH1   0   0.217   2.4730   0.2426   6.7135
 UDX  HO'4  H  HOH1   0   0.459   4.4651   0.0826   5.7551
 UDX  H5'1  H  HCH2   0   0.221   2.2296  -1.1968   4.0237
 UDX  H5'2  H  HCH2   0   0.238   2.6604  -1.9154   5.5760
 UDX  H5A1  H  HCH2   0   0.222  -1.8604  -1.5734  -2.6337
 UDX  H5A2  H  HCH2   0   0.212  -3.4520  -1.0847  -2.0448
 UDX  H4A1  H  HCH1   0   0.251  -3.0020   1.2466  -2.3951
 UDX  H3A1  H  HCH1   0   0.247  -3.4950  -0.5355  -4.4503
 UDX  HOA3  H  HOH1   0   0.448  -3.3836   1.5250  -5.7490
 UDX  H2A1  H  HCH1   0   0.269  -1.1801  -0.9433  -4.9283
 UDX  HOC2  H  HOH1   0   0.469  -1.7560  -0.2999  -6.9427
 UDX  H1'1  H  HCH1   0   0.250  -0.6830   2.0462  -4.7279
 UDX  H61   H  HCR6   0   0.329   1.2150   2.6468  -5.1276
 UDX  HN3   H  HNR6   0   0.426   3.0782  -1.4234  -3.5639
 UDX  H51   H  HCR6   0   0.294   3.6449   2.3981  -5.2222
 UDX  PB    P  P      0   1.353  -0.6560  -1.7338   2.7100

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
 UDX  C1'  C2'   single  1.535  0.020  1.535
 UDX  C1'  O5'   single  1.398  0.020  1.398
 UDX  C1'  O3B   single  1.393  0.020  1.393
 UDX  C1'  H1'   single  0.970  0.020  1.090
 UDX  C2'  O2'   single  1.402  0.020  1.402
 UDX  C2'  C3'   single  1.520  0.020  1.520
 UDX  C2'  H2'1  single  0.970  0.020  1.090
 UDX  O2'  HO'2  single  0.850  0.020  0.980
 UDX  C3'  O3'   single  1.408  0.020  1.408
 UDX  C3'  C4'   single  1.524  0.020  1.524
 UDX  C3'  H3'1  single  0.970  0.020  1.090
 UDX  O3'  HO'3  single  0.850  0.020  0.980
 UDX  C4'  O4'   single  1.411  0.020  1.411
 UDX  C4'  C5'   single  1.524  0.020  1.524
 UDX  C4'  H4'1  single  0.970  0.020  1.090
 UDX  O4'  HO'4  single  0.850  0.020  0.980
 UDX  C5'  O5'   single  1.417  0.020  1.417
 UDX  C5'  H5'1  single  0.970  0.020  1.090
 UDX  C5'  H5'2  single  0.970  0.020  1.090
 UDX  PB   O1B   deloc   1.495  0.020  1.495
 UDX  PB   O2B   deloc   1.494  0.020  1.494
 UDX  PB   O3B   single  1.657  0.020  1.657
 UDX  PB   O3A   single  1.644  0.020  1.644
 UDX  O3A  PA    single  1.641  0.020  1.641
 UDX  PA   O1A   deloc   1.497  0.020  1.497
 UDX  PA   O2A   deloc   1.496  0.020  1.496
 UDX  PA   O5D   single  1.645  0.020  1.645
 UDX  O5D  C5D   single  1.410  0.020  1.410
 UDX  C5D  C4D   single  1.515  0.020  1.515
 UDX  C5D  H5A1  single  0.970  0.020  1.090
 UDX  C5D  H5A2  single  0.970  0.020  1.090
 UDX  C4D  O4D   single  1.431  0.020  1.431
 UDX  C4D  C3D   single  1.525  0.020  1.525
 UDX  C4D  H4A1  single  0.970  0.020  1.090
 UDX  O4D  C1D   single  1.393  0.020  1.393
 UDX  C3D  O3D   single  1.405  0.020  1.405
 UDX  C3D  C2D   single  1.534  0.020  1.534
 UDX  C3D  H3A1  single  0.970  0.020  1.090
 UDX  O3D  HOA3  single  0.850  0.020  0.980
 UDX  C2D  O2D   single  1.400  0.020  1.400
 UDX  C2D  C1D   single  1.528  0.020  1.528
 UDX  C2D  H2A1  single  0.970  0.020  1.090
 UDX  O2D  HOC2  single  0.850  0.020  0.980
 UDX  C1D  N1    single  1.456  0.020  1.456
 UDX  C1D  H1'1  single  0.970  0.020  1.090
 UDX  N1   C6    single  1.368  0.020  1.368
 UDX  N1   C2    single  1.385  0.020  1.385
 UDX  C6   C5    double  1.342  0.020  1.342
 UDX  C6   H61   single  0.930  0.020  1.080
 UDX  C2   O2    double  1.211  0.020  1.211
 UDX  C2   N3    single  1.371  0.020  1.371
 UDX  N3   C4    single  1.386  0.020  1.386
 UDX  N3   HN3   single  0.860  0.020  1.020
 UDX  C4   O4    double  1.217  0.020  1.217
 UDX  C4   C5    single  1.441  0.020  1.441
 UDX  C5   H51   single  0.930  0.020  1.080

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
 UDX  H1'   C1'  O3B   110.82  3.000
 UDX  H1'   C1'  O5'   105.09  3.000
 UDX  O3B   C1'  O5'   112.35  3.000
 UDX  H1'   C1'  C2'   109.57  3.000
 UDX  O3B   C1'  C2'   108.19  3.000
 UDX  O5'   C1'  C2'   110.80  3.000
 UDX  H2'1  C2'  C3'   107.93  3.000
 UDX  H2'1  C2'  O2'   111.10  3.000
 UDX  C3'   C2'  O2'   108.84  3.000
 UDX  H2'1  C2'  C1'   106.43  3.000
 UDX  C3'   C2'  C1'   110.51  3.000
 UDX  O2'   C2'  C1'   111.94  3.000
 UDX  HO'2  O2'  C2'   108.54  3.000
 UDX  H3'1  C3'  C4'   108.43  3.000
 UDX  H3'1  C3'  O3'   110.63  3.000
 UDX  C4'   C3'  O3'   111.49  3.000
 UDX  H3'1  C3'  C2'   109.12  3.000
 UDX  C4'   C3'  C2'   108.79  3.000
 UDX  O3'   C3'  C2'   108.34  3.000
 UDX  HO'3  O3'  C3'   107.53  3.000
 UDX  H4'1  C4'  C5'   108.72  3.000
 UDX  H4'1  C4'  O4'   110.87  3.000
 UDX  C5'   C4'  O4'   111.14  3.000
 UDX  H4'1  C4'  C3'   107.79  3.000
 UDX  C5'   C4'  C3'   110.53  3.000
 UDX  O4'   C4'  C3'   107.73  3.000
 UDX  HO'4  O4'  C4'   108.69  3.000
 UDX  H5'2  C5'  H5'1  107.55  3.000
 UDX  H5'2  C5'  O5'   106.27  3.000
 UDX  H5'1  C5'  O5'   111.29  3.000
 UDX  H5'2  C5'  C4'   110.18  3.000
 UDX  H5'1  C5'  C4'   110.48  3.000
 UDX  O5'   C5'  C4'   110.92  3.000
 UDX  C5'   O5'  C1'   114.16  3.000
 UDX  PB    O3B  C1'   119.82  3.000
 UDX  PA    O3A  PB    123.68  3.000
 UDX  O5D   PA   O2A   109.97  3.000
 UDX  O5D   PA   O1A   109.23  3.000
 UDX  O2A   PA   O1A   120.22  3.000
 UDX  O5D   PA   O3A    93.81  3.000
 UDX  O2A   PA   O3A   110.98  3.000
 UDX  O1A   PA   O3A   109.43  3.000
 UDX  C5D   O5D  PA    117.22  3.000
 UDX  H5A2  C5D  H5A1  107.48  3.000
 UDX  H5A2  C5D  C4D   106.87  3.000
 UDX  H5A1  C5D  C4D   111.02  3.000
 UDX  H5A2  C5D  O5D   112.08  3.000
 UDX  H5A1  C5D  O5D   110.52  3.000
 UDX  C4D   C5D  O5D   108.83  3.000
 UDX  H4A1  C4D  C3D   110.26  3.000
 UDX  H4A1  C4D  O4D   108.03  3.000
 UDX  C3D   C4D  O4D   106.11  3.000
 UDX  H4A1  C4D  C5D   108.53  3.000
 UDX  C3D   C4D  C5D   112.51  3.000
 UDX  O4D   C4D  C5D   111.31  3.000
 UDX  C1D   O4D  C4D   110.45  3.000
 UDX  H3A1  C3D  C2D   111.68  3.000
 UDX  H3A1  C3D  O3D   111.50  3.000
 UDX  C2D   C3D  O3D   110.88  3.000
 UDX  H3A1  C3D  C4D   111.73  3.000
 UDX  C2D   C3D  C4D   101.77  3.000
 UDX  O3D   C3D  C4D   108.87  3.000
 UDX  HOA3  O3D  C3D   107.65  3.000
 UDX  H2A1  C2D  C1D   111.19  3.000
 UDX  H2A1  C2D  O2D   111.75  3.000
 UDX  C1D   C2D  O2D   109.35  3.000
 UDX  H2A1  C2D  C3D   109.22  3.000
 UDX  C1D   C2D  C3D   100.41  3.000
 UDX  O2D   C2D  C3D   114.39  3.000
 UDX  HOC2  O2D  C2D   108.76  3.000
 UDX  H1'1  C1D  N1    104.58  3.000
 UDX  H1'1  C1D  C2D   107.93  3.000
 UDX  N1    C1D  C2D   116.46  3.000
 UDX  H1'1  C1D  O4D   110.67  3.000
 UDX  N1    C1D  O4D   110.47  3.000
 UDX  C2D   C1D  O4D   106.70  3.000
 UDX  C2    N1   C6    120.45  3.000
 UDX  C2    N1   C1D   120.70  3.000
 UDX  C6    N1   C1D   118.80  3.000
 UDX  H61   C6   C5    120.85  3.000
 UDX  H61   C6   N1    115.34  3.000
 UDX  C5    C6   N1    123.81  3.000
 UDX  N3    C2   O2    121.84  3.000
 UDX  N3    C2   N1    114.63  3.000
 UDX  O2    C2   N1    123.53  3.000
 UDX  HN3   N3   C4    116.76  3.000
 UDX  HN3   N3   C2    114.83  3.000
 UDX  C4    N3   C2    128.40  3.000
 UDX  C5    C4   O4    126.16  3.000
 UDX  C5    C4   N3    113.23  3.000
 UDX  O4    C4   N3    120.62  3.000
 UDX  H51   C5   C4    119.99  3.000
 UDX  H51   C5   C6    120.54  3.000
 UDX  C4    C5   C6    119.46  3.000
 UDX  O3A   PB   O3B    93.59  3.000
 UDX  O3A   PB   O2B   109.39  3.000
 UDX  O3B   PB   O2B   108.77  3.000
 UDX  O3A   PB   O1B   110.37  3.000
 UDX  O3B   PB   O1B   109.54  3.000
 UDX  O2B   PB   O1B   121.58  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
 UDX  CONST_01  N3   C2   N1   C1D  180.00   0.0  0
 UDX  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 UDX  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 UDX  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 UDX  CONST_05  O2   C2   N1   C1D    0.00   0.0  0
 UDX  CONST_06  O2   C2   N1   C6   180.00   0.0  0
 UDX  CONST_07  O4   C4   N3   C2   180.00   0.0  0
 UDX  CONST_08  C4   N3   C2   O2   180.00   0.0  0
 UDX  CONST_09  HN3  N3   C2   N1   180.00   0.0  0
 UDX  Var_01    C4'  C5'  O5'  C1'   58.93  30.0  1
 UDX  Var_02    O1B  PB   O3B  C1'   34.76  30.0  1
 UDX  Var_03    C4D  C5D  O5D  PA   150.18  30.0  3
 UDX  Var_04    O1A  PA   O3A  PB   101.61  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
 UDX  chir_01  C1'  C2'  O5'  O3B  positiv
 UDX  chir_02  C2'  O2'  C1'  C3'  negativ
 UDX  chir_03  C3'  O3'  C2'  C4'  positiv
 UDX  chir_04  C4'  O4'  C3'  C5'  negativ
 UDX  chir_07  C4D  C5D  O4D  C3D  negativ
 UDX  chir_08  C3D  O3D  C4D  C2D  positiv
 UDX  chir_09  C2D  O2D  C3D  C1D  positiv
 UDX  chir_10  C1D  O4D  N1   C2D  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
 UDX  plan-1  C1D  0.020
 UDX  plan-1  N1   0.020
 UDX  plan-1  C6   0.020
 UDX  plan-1  C2   0.020
 UDX  plan-1  O2   0.020
 UDX  plan-1  N3   0.020
 UDX  plan-1  C4   0.020
 UDX  plan-1  O4   0.020
 UDX  plan-1  C5   0.020
 UDX  plan-1  H61  0.020
 UDX  plan-1  HN3  0.020
 UDX  plan-1  H51  0.020

