# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 23 03:56:16 2022
#   Inital geometry file: a 144 line input string
#   Ligand name: (2S,3S,4S,5R,6R)-6-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)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
#
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
 UGA  UGA  '(2S,3S,4S,5R,6R)-6-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)'  ligand  56  37  .  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_UGA
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
 UGA  C1'   C  CH1    0   0.125   0.2013   0.8338   4.5879
 UGA  C2'   C  CH1    0  -0.021   0.5038  -0.4736   5.3346
 UGA  O2'   O  OH1    0  -0.592   1.8609  -0.8257   5.3682
 UGA  C3'   C  CH1    0  -0.020  -0.3685  -1.6040   4.7916
 UGA  O3'   O  OH1    0  -0.659  -0.1663  -2.7893   5.5261
 UGA  C4'   C  CH1    0   0.075  -1.8259  -1.1954   4.9041
 UGA  O4'   O  OH1    0  -0.619  -2.6481  -2.1799   4.3397
 UGA  C5'   C  CH1    0  -0.102  -2.0340   0.1560   4.1973
 UGA  O5'   O  O2     0  -0.450  -1.1470   1.1429   4.6926
 UGA  C6'   C  C      0   0.374  -3.4827   0.6563   4.3575
 UGA  O'P   O  O      0  -0.537  -3.6810   1.8446   4.6170
 UGA  O'Q   O  OC    -1  -0.757  -4.3600  -0.2355   4.2015
 UGA  O1B   O  O      0  -0.829   2.9025  -0.1435   3.0168
 UGA  O2B   O  OP    -1  -0.790   2.4859   2.4250   3.1168
 UGA  O3B   O  O2     0  -0.580   0.5313   0.7518   3.2189
 UGA  O3A   O  O2     0  -0.753   1.6477   1.0198   1.1102
 UGA  PA    P  P      0   1.327   2.5119   1.7824  -0.0728
 UGA  O1A   O  O      0  -0.752   3.9761   1.6305   0.1864
 UGA  O2A   O  OP    -1  -0.853   1.9160   3.1242  -0.3513
 UGA  O5D   O  O2     0  -0.587   2.0400   0.7190  -1.2351
 UGA  C5D   C  CH2    0  -0.199   2.4135   1.0252  -2.5617
 UGA  C4D   C  CR15   0   0.006   2.4219  -0.2567  -3.3670
 UGA  O4D   O  O      0  -0.476   1.1402  -0.8934  -3.3296
 UGA  C3D   C  CR15   0  -0.035   2.7345  -0.0222  -4.8413
 UGA  O3D   O  OH1    0  -0.692   3.3913  -1.1543  -5.3524
 UGA  C2D   C  CR15   0  -0.003   1.3290   0.1090  -5.4410
 UGA  O2D   O  OH1    0  -0.694   1.2414  -0.2411  -6.7932
 UGA  C1D   C  CR15   0   0.169   0.5751  -0.9224  -4.6024
 UGA  N1    N  NR6    0  -0.512  -0.8685  -0.7546  -4.5222
 UGA  C6    C  CR16   0   0.061  -1.6794  -1.7765  -4.9325
 UGA  C2    C  CR6    0   0.713  -1.4123   0.4075  -4.0020
 UGA  O2    O  OC     0  -0.472  -0.7493   1.3467  -3.6253
 UGA  N3    N  NR16   0  -0.677  -2.7830   0.4250  -3.9552
 UGA  C4    C  CR6    0   0.491  -3.6730  -0.5608  -4.3546
 UGA  O4    O  OC     0  -0.443  -4.8746  -0.3899  -4.2574
 UGA  C5    C  CR16   0  -0.471  -3.0205  -1.7332  -4.8818
 UGA  H1'1  H  HCH1   0   0.277   0.7431   1.6635   5.0581
 UGA  H2'1  H  HCH1   0   0.156   0.2070  -0.2971   6.3766
 UGA  HO'2  H  HOH1   0   0.468   2.2642  -0.7382   4.4701
 UGA  H3'1  H  HCH1   0   0.171  -0.1296  -1.7638   3.7276
 UGA  HO'3  H  HOH1   0   0.451   0.7860  -2.9296   5.5759
 UGA  H4'1  H  HCH1   0   0.177  -2.0488  -1.0536   5.9772
 UGA  HO'4  H  HOH1   0   0.439  -3.4986  -1.7036   4.1980
 UGA  H5'1  H  HCH1   0   0.257  -1.8676  -0.0057   3.1208
 UGA  H5A1  H  HCH2   0   0.250   1.7284   1.7560  -2.9991
 UGA  H5'2  H  HCH2   0   0.267   3.4249   1.4468  -2.6141
 UGA  H4A1  H  HCR5   0   0.219   3.1558  -0.9406  -2.9280
 UGA  H3A1  H  HCR5   0   0.212   3.3285   0.8889  -4.9916
 UGA  HOA3  H  HOH1   0   0.449   3.2479  -1.1685  -6.3062
 UGA  H2A1  H  HCR5   0   0.283   0.9552   1.1187  -5.2583
 UGA  HOC2  H  HOH1   0   0.460   1.4054   0.5417  -7.3277
 UGA  H1A1  H  HCR5   0   0.311   0.7170  -1.9051  -5.0669
 UGA  H61   H  HCR6   0   0.304  -1.1682  -2.6509  -5.3100
 UGA  HN3   H  HNR6   0   0.436  -3.1809   1.2746  -3.5733
 UGA  H51   H  HCR6   0   0.280  -3.6080  -2.5709  -5.2235
 UGA  PB    P  P      0   1.366   2.0566   1.0634   2.6856

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
 UGA  C1'  C2'   single    1.536  0.020  1.536
 UGA  C1'  O5'   single    1.387  0.020  1.387
 UGA  C1'  O3B   single    1.411  0.020  1.411
 UGA  C1'  H1'1  single    0.970  0.020  1.090
 UGA  C2'  O2'   single    1.403  0.020  1.403
 UGA  C2'  C3'   single    1.528  0.020  1.528
 UGA  C2'  H2'1  single    0.970  0.020  1.090
 UGA  O2'  HO'2  single    0.850  0.020  0.980
 UGA  C3'  O3'   single    1.409  0.020  1.409
 UGA  C3'  C4'   single    1.518  0.020  1.518
 UGA  C3'  H3'1  single    0.970  0.020  1.090
 UGA  O3'  HO'3  single    0.850  0.020  0.980
 UGA  C4'  O4'   single    1.401  0.020  1.401
 UGA  C4'  C5'   single    1.539  0.020  1.539
 UGA  C4'  H4'1  single    0.970  0.020  1.090
 UGA  O4'  HO'4  single    0.850  0.020  0.980
 UGA  C5'  O5'   single    1.416  0.020  1.416
 UGA  C5'  C6'   single    1.541  0.020  1.541
 UGA  C5'  H5'1  single    0.970  0.020  1.090
 UGA  C6'  O'P   deloc     1.232  0.020  1.232
 UGA  C6'  O'Q   deloc     1.261  0.020  1.261
 UGA  PB   O1B   deloc     1.511  0.020  1.511
 UGA  PB   O2B   deloc     1.491  0.020  1.491
 UGA  PB   O3B   single    1.646  0.020  1.646
 UGA  PB   O3A   single    1.628  0.020  1.628
 UGA  O3A  PA    single    1.652  0.020  1.652
 UGA  PA   O1A   deloc     1.495  0.020  1.495
 UGA  PA   O2A   deloc     1.494  0.020  1.494
 UGA  PA   O5D   single    1.645  0.020  1.645
 UGA  O5D  C5D   single    1.412  0.020  1.412
 UGA  C5D  C4D   single    1.514  0.020  1.514
 UGA  C5D  H5A1  single    0.970  0.020  1.090
 UGA  C5D  H5'2  single    0.970  0.020  1.090
 UGA  C4D  O4D   single    1.432  0.020  1.432
 UGA  C4D  C3D   single    1.525  0.020  1.525
 UGA  C4D  H4A1  single    0.970  0.020  1.090
 UGA  O4D  C1D   single    1.393  0.020  1.393
 UGA  C3D  O3D   single    1.405  0.020  1.405
 UGA  C3D  C2D   single    1.534  0.020  1.534
 UGA  C3D  H3A1  single    0.970  0.020  1.090
 UGA  O3D  HOA3  single    0.850  0.020  0.980
 UGA  C2D  O2D   single    1.400  0.020  1.400
 UGA  C2D  C1D   single    1.528  0.020  1.528
 UGA  C2D  H2A1  single    0.970  0.020  1.090
 UGA  O2D  HOC2  single    0.850  0.020  0.980
 UGA  C1D  N1    single    1.455  0.020  1.455
 UGA  C1D  H1A1  single    0.970  0.020  1.090
 UGA  N1   C6    aromatic  1.368  0.020  1.368
 UGA  N1   C2    aromatic  1.384  0.020  1.384
 UGA  C6   C5    aromatic  1.343  0.020  1.343
 UGA  C6   H61   single    0.930  0.020  1.080
 UGA  C2   O2    double    1.210  0.020  1.210
 UGA  C2   N3    aromatic  1.372  0.020  1.372
 UGA  N3   C4    aromatic  1.387  0.020  1.387
 UGA  N3   HN3   single    0.860  0.020  1.020
 UGA  C4   O4    double    1.218  0.020  1.218
 UGA  C4   C5    aromatic  1.442  0.020  1.442
 UGA  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
 UGA  H1'1  C1'  O3B   110.15  3.000
 UGA  H1'1  C1'  O5'   106.21  3.000
 UGA  O3B   C1'  O5'   108.28  3.000
 UGA  H1'1  C1'  C2'   109.77  3.000
 UGA  O3B   C1'  C2'   112.11  3.000
 UGA  O5'   C1'  C2'   110.14  3.000
 UGA  H2'1  C2'  C3'   107.58  3.000
 UGA  H2'1  C2'  O2'   106.21  3.000
 UGA  C3'   C2'  O2'   112.04  3.000
 UGA  H2'1  C2'  C1'   105.75  3.000
 UGA  C3'   C2'  C1'   110.16  3.000
 UGA  O2'   C2'  C1'   114.58  3.000
 UGA  HO'2  O2'  C2'   110.54  3.000
 UGA  H3'1  C3'  C4'   108.59  3.000
 UGA  H3'1  C3'  O3'   110.50  3.000
 UGA  C4'   C3'  O3'   109.01  3.000
 UGA  H3'1  C3'  C2'   109.06  3.000
 UGA  C4'   C3'  C2'   108.83  3.000
 UGA  O3'   C3'  C2'   110.81  3.000
 UGA  HO'3  O3'  C3'   106.93  3.000
 UGA  H4'1  C4'  C5'   107.82  3.000
 UGA  H4'1  C4'  O4'   111.28  3.000
 UGA  C5'   C4'  O4'   110.65  3.000
 UGA  H4'1  C4'  C3'   107.46  3.000
 UGA  C5'   C4'  C3'   109.40  3.000
 UGA  O4'   C4'  C3'   110.14  3.000
 UGA  HO'4  O4'  C4'   102.99  3.000
 UGA  H5'1  C5'  C6'   106.94  3.000
 UGA  H5'1  C5'  O5'   110.47  3.000
 UGA  C6'   C5'  O5'   109.04  3.000
 UGA  H5'1  C5'  C4'   107.43  3.000
 UGA  C6'   C5'  C4'   111.37  3.000
 UGA  O5'   C5'  C4'   111.50  3.000
 UGA  C5'   O5'  C1'   115.28  3.000
 UGA  O'Q   C6'  O'P   126.60  3.000
 UGA  O'Q   C6'  C5'   114.31  3.000
 UGA  O'P   C6'  C5'   119.09  3.000
 UGA  PB    O3B  C1'   121.36  3.000
 UGA  PA    O3A  PB    123.32  3.000
 UGA  O5D   PA   O2A   109.54  3.000
 UGA  O5D   PA   O1A   109.75  3.000
 UGA  O2A   PA   O1A   120.95  3.000
 UGA  O5D   PA   O3A    93.30  3.000
 UGA  O2A   PA   O3A   109.84  3.000
 UGA  O1A   PA   O3A   109.96  3.000
 UGA  C5D   O5D  PA    116.61  3.000
 UGA  H5'2  C5D  H5A1  107.57  3.000
 UGA  H5'2  C5D  C4D   107.15  3.000
 UGA  H5A1  C5D  C4D   110.90  3.000
 UGA  H5'2  C5D  O5D   111.85  3.000
 UGA  H5A1  C5D  O5D   110.81  3.000
 UGA  C4D   C5D  O5D   108.52  3.000
 UGA  H4A1  C4D  C3D   110.26  3.000
 UGA  H4A1  C4D  O4D   108.16  3.000
 UGA  C3D   C4D  O4D   106.09  3.000
 UGA  H4A1  C4D  C5D   108.63  3.000
 UGA  C3D   C4D  C5D   112.65  3.000
 UGA  O4D   C4D  C5D   110.96  3.000
 UGA  C1D   O4D  C4D   110.40  3.000
 UGA  H3A1  C3D  C2D   111.79  3.000
 UGA  H3A1  C3D  O3D   111.46  3.000
 UGA  C2D   C3D  O3D   110.80  3.000
 UGA  H3A1  C3D  C4D   111.76  3.000
 UGA  C2D   C3D  C4D   101.73  3.000
 UGA  O3D   C3D  C4D   108.87  3.000
 UGA  HOA3  O3D  C3D   107.58  3.000
 UGA  H2A1  C2D  C1D   111.30  3.000
 UGA  H2A1  C2D  O2D   111.81  3.000
 UGA  C1D   C2D  O2D   109.30  3.000
 UGA  H2A1  C2D  C3D   109.11  3.000
 UGA  C1D   C2D  C3D   100.35  3.000
 UGA  O2D   C2D  C3D   114.44  3.000
 UGA  HOC2  O2D  C2D   108.82  3.000
 UGA  H1A1  C1D  N1    104.78  3.000
 UGA  H1A1  C1D  C2D   107.98  3.000
 UGA  N1    C1D  C2D   116.21  3.000
 UGA  H1A1  C1D  O4D   110.69  3.000
 UGA  N1    C1D  O4D   110.47  3.000
 UGA  C2D   C1D  O4D   106.69  3.000
 UGA  C2    N1   C6    120.47  3.000
 UGA  C2    N1   C1D   120.47  3.000
 UGA  C6    N1   C1D   119.04  3.000
 UGA  H61   C6   C5    120.76  3.000
 UGA  H61   C6   N1    115.40  3.000
 UGA  C5    C6   N1    123.84  3.000
 UGA  N3    C2   O2    121.81  3.000
 UGA  N3    C2   N1    114.58  3.000
 UGA  O2    C2   N1    123.60  3.000
 UGA  HN3   N3   C4    116.91  3.000
 UGA  HN3   N3   C2    114.59  3.000
 UGA  C4    N3   C2    128.49  3.000
 UGA  C5    C4   O4    126.16  3.000
 UGA  C5    C4   N3    113.14  3.000
 UGA  O4    C4   N3    120.70  3.000
 UGA  H51   C5   C4    120.06  3.000
 UGA  H51   C5   C6    120.46  3.000
 UGA  C4    C5   C6    119.47  3.000
 UGA  O3A   PB   O3B    94.34  3.000
 UGA  O3A   PB   O2B   112.12  3.000
 UGA  O3B   PB   O2B   110.24  3.000
 UGA  O3A   PB   O1B   109.35  3.000
 UGA  O3B   PB   O1B   107.26  3.000
 UGA  O2B   PB   O1B   120.33  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
 UGA  CONST_01  C4   C5   C6   N1     0.00   0.0  0
 UGA  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 UGA  CONST_03  N3   C2   N1   C6     0.00   0.0  0
 UGA  CONST_04  N3   C4   C5   C6     0.00   0.0  0
 UGA  CONST_05  C5   C6   N1   C2     0.00   0.0  0
 UGA  CONST_06  C5   C4   N3   C2     0.00   0.0  0
 UGA  CONST_07  C5   C6   N1   C1D  180.00   0.0  0
 UGA  CONST_08  N3   C2   N1   C1D  180.00   0.0  0
 UGA  CONST_09  O2   C2   N1   C1D    0.00   0.0  0
 UGA  CONST_10  O2   C2   N1   C6   180.00   0.0  0
 UGA  CONST_11  O4   C4   C5   C6   180.00   0.0  0
 UGA  CONST_12  O4   C4   N3   C2   180.00   0.0  0
 UGA  CONST_13  C4   N3   C2   O2   180.00   0.0  0
 UGA  CONST_14  H61  C6   N1   C1D    0.00   0.0  0
 UGA  CONST_15  H51  C5   C6   N1   180.00   0.0  0
 UGA  CONST_16  HN3  N3   C2   N1   180.00   0.0  0
 UGA  Var_01    O1B  PB   O3B  C1'   76.55  30.0  2
 UGA  Var_02    C4D  C5D  O5D  PA   156.87  30.0  3
 UGA  Var_03    O1A  PA   O3A  PB    40.35  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
 UGA  chir_01  C1'  C2'  O5'  O3B  positiv
 UGA  chir_02  C2'  O2'  C1'  C3'  negativ
 UGA  chir_03  C3'  O3'  C2'  C4'  positiv
 UGA  chir_04  C4'  O4'  C3'  C5'  negativ
 UGA  chir_05  C5'  O5'  C4'  C6'  negativ
 UGA  chir_08  C4D  C5D  O4D  C3D  negativ
 UGA  chir_09  C3D  O3D  C4D  C2D  positiv
 UGA  chir_10  C2D  O2D  C3D  C1D  positiv
 UGA  chir_11  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
 UGA  plan-1  C1D  0.020
 UGA  plan-1  N1   0.020
 UGA  plan-1  C6   0.020
 UGA  plan-1  C2   0.020
 UGA  plan-1  O2   0.020
 UGA  plan-1  N3   0.020
 UGA  plan-1  C4   0.020
 UGA  plan-1  O4   0.020
 UGA  plan-1  C5   0.020
 UGA  plan-1  H61  0.020
 UGA  plan-1  HN3  0.020
 UGA  plan-1  H51  0.020
 UGA  plan-2  C5'  0.020
 UGA  plan-2  C6'  0.020
 UGA  plan-2  O'P  0.020
 UGA  plan-2  O'Q  0.020

