# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 27 00:30:04 2022
#   Inital geometry file: a 142 line input string
#   Ligand name: (2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid
#   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]1F)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
 UGF  UGF  '(2~{R},3~{S},4~{R},5~{R},6~{R})-6-[[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3-fluoranyl-4,5-bis(oxidanyl)oxane-2-carboxylic acid'  ligand  55  37  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_UGF
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
 UGF  O2   O  O      0  -0.471  -5.1967  16.3915   -9.2196
 UGF  C2   C  CR6    0   0.729  -4.1336  15.9144   -8.8835
 UGF  N3   N  NR16   0  -0.735  -2.9665  16.2140   -9.5378
 UGF  C4   C  CR6    0   0.565  -1.6881  15.7397   -9.2783
 UGF  O4   O  O      0  -0.456  -0.7468  16.0964   -9.9609
 UGF  C5   C  CR16   0  -0.520  -1.6363  14.8271   -8.1636
 UGF  C6   C  CR16   0   0.077  -2.7630  14.5225   -7.5001
 UGF  N1   N  NR6    0  -0.568  -3.9890  15.0326   -7.8289
 UGF  C1D  C  CH1    0   0.193  -5.1635  14.6414   -7.0614
 UGF  O4D  O  O2     0  -0.494  -4.9449  14.9051   -5.7052
 UGF  C2D  C  CH1    0  -0.023  -5.4990  13.1543   -7.1624
 UGF  O2D  O  OH1    0  -0.655  -6.2098  12.9256   -8.3412
 UGF  C3D  C  CH1    0  -0.059  -6.2592  12.9365   -5.8548
 UGF  O3D  O  OH1    0  -0.668  -7.5849  13.3626   -6.0576
 UGF  C4D  C  CH1    0  -0.025  -5.5008  13.8647   -4.8934
 UGF  C5D  C  CH2    0  -0.165  -4.4183  13.2024   -4.0654
 UGF  O5D  O  O2     0  -0.631  -3.4434  12.6630   -4.9225
 UGF  PA   P  P      0   1.378  -2.1651  11.7794   -4.3753
 UGF  O1A  O  O      0  -0.780  -1.1233  11.8838   -5.4405
 UGF  O2A  O  OP    -1  -0.780  -1.8833  12.1228   -2.9485
 UGF  O3A  O  O2     0  -0.747  -2.8099  10.2643   -4.3539
 UGF  PB   P  P      0   1.356  -3.8390   9.5623   -5.4292
 UGF  O1B  O  OP    -1  -0.777  -5.2169   9.5860   -4.8425
 UGF  O2B  O  O      0  -0.772  -3.5643  10.0318   -6.8206
 UGF  O3B  O  O2     0  -0.621  -3.2224   8.0331   -5.3264
 UGF  C1'  C  CH1    0   0.251  -3.8565   7.0094   -4.6259
 UGF  O5'  O  O2     0  -0.504  -4.7357   6.2882   -5.4399
 UGF  C5'  C  CH1    0  -0.140  -4.1246   5.6180   -6.5347
 UGF  C6'  C  C      0   0.389  -5.2632   4.9297   -7.3336
 UGF  O'P  O  OC    -1  -0.595  -5.8382   3.9904   -6.7542
 UGF  O'Q  O  O      0  -0.591  -5.4977   5.3911   -8.4638
 UGF  C4'  C  CH1    0   0.184  -3.1132   4.6180   -6.0006
 UGF  F4'  F  F      0  -0.380  -2.4992   3.9905   -7.0852
 UGF  C3'  C  CH1    0  -0.022  -2.0680   5.3041   -5.1506
 UGF  O3'  O  OH1    0  -0.668  -1.2028   4.3301   -4.6211
 UGF  C2'  C  CH1    0  -0.026  -2.7926   6.0702   -4.0465
 UGF  O2'  O  OH1    0  -0.663  -1.8246   6.7553   -3.2947
 UGF  H1   H  HNR6   0   0.422  -3.0644  16.8584  -10.3130
 UGF  H2   H  HCR6   0   0.285  -0.6931  14.3956   -7.8657
 UGF  H3   H  HCR6   0   0.348  -2.7437  13.8477   -6.6560
 UGF  H4   H  HCH1   0   0.266  -5.9946  15.2334   -7.4503
 UGF  H5   H  HCH1   0   0.255  -4.5852  12.5511   -7.1267
 UGF  H6   H  HOH1   0   0.458  -6.2199  11.9796   -8.5154
 UGF  H7   H  HCH1   0   0.251  -6.2163  11.8935   -5.5203
 UGF  H8   H  HOH1   0   0.452  -8.0661  13.2561   -5.2312
 UGF  H9   H  HCH1   0   0.251  -6.2068  14.3140   -4.1846
 UGF  H10  H  HCH2   0   0.225  -3.9787  13.9413   -3.3879
 UGF  H11  H  HCH2   0   0.213  -4.8928  12.4354   -3.4423
 UGF  H14  H  HCH1   0   0.231  -4.4758   7.4077   -3.8159
 UGF  H15  H  HCH1   0   0.208  -3.6108   6.3356   -7.1856
 UGF  H17  H  HCH1   0   0.205  -3.6249   3.8454   -5.4183
 UGF  H18  H  HCH1   0   0.217  -1.5160   6.0196   -5.7789
 UGF  H19  H  HOH1   0   0.448  -0.5569   4.7794   -4.0659
 UGF  H20  H  HCH1   0   0.223  -3.3251   5.3350   -3.4255
 UGF  H21  H  HOH1   0   0.457  -2.2001   6.9878   -2.4400

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
 UGF  O2D  C2D  single  1.395  0.020  1.395
 UGF  C2D  C1D  single  1.528  0.020  1.528
 UGF  C2D  C3D  single  1.528  0.020  1.528
 UGF  O2   C2   double  1.213  0.020  1.213
 UGF  O4   C4   double  1.216  0.020  1.216
 UGF  N3   C2   single  1.371  0.020  1.371
 UGF  N3   C4   single  1.388  0.020  1.388
 UGF  O3D  C3D  single  1.407  0.020  1.407
 UGF  C2   N1   single  1.382  0.020  1.382
 UGF  C4   C5   single  1.442  0.020  1.442
 UGF  N1   C6   single  1.368  0.020  1.368
 UGF  N1   C1D  single  1.457  0.020  1.457
 UGF  C5   C6   double  1.343  0.020  1.343
 UGF  C1D  O4D  single  1.399  0.020  1.399
 UGF  C3D  C4D  single  1.537  0.020  1.537
 UGF  O2B  PB   deloc   1.494  0.020  1.494
 UGF  O1A  PA   deloc   1.494  0.020  1.494
 UGF  O4D  C4D  single  1.432  0.020  1.432
 UGF  F4'  C4'  single  1.395  0.020  1.395
 UGF  C4D  C5D  single  1.515  0.020  1.515
 UGF  PB   O3B  single  1.652  0.020  1.652
 UGF  PB   O1B  deloc   1.498  0.020  1.498
 UGF  PB   O3A  single  1.646  0.020  1.646
 UGF  O5D  PA   single  1.647  0.020  1.647
 UGF  O5D  C5D  single  1.406  0.020  1.406
 UGF  O3B  C1'  single  1.393  0.020  1.393
 UGF  C3'  O3'  single  1.406  0.020  1.406
 UGF  C3'  C4'  single  1.512  0.020  1.512
 UGF  C3'  C2'  single  1.527  0.020  1.527
 UGF  O2'  C2'  single  1.404  0.020  1.404
 UGF  PA   O3A  single  1.647  0.020  1.647
 UGF  PA   O2A  deloc   1.494  0.020  1.494
 UGF  C4'  C5'  single  1.519  0.020  1.519
 UGF  C5'  C6'  single  1.552  0.020  1.552
 UGF  C5'  O5'  single  1.422  0.020  1.422
 UGF  C2'  C1'  single  1.533  0.020  1.533
 UGF  O'Q  C6'  deloc   1.243  0.020  1.243
 UGF  C1'  O5'  single  1.398  0.020  1.398
 UGF  C6'  O'P  deloc   1.244  0.020  1.244
 UGF  N3   H1   single  0.860  0.020  1.020
 UGF  C5   H2   single  0.930  0.020  1.080
 UGF  C6   H3   single  0.930  0.020  1.080
 UGF  C1D  H4   single  0.970  0.020  1.090
 UGF  C2D  H5   single  0.970  0.020  1.090
 UGF  O2D  H6   single  0.850  0.020  0.980
 UGF  C3D  H7   single  0.970  0.020  1.090
 UGF  O3D  H8   single  0.850  0.020  0.980
 UGF  C4D  H9   single  0.970  0.020  1.090
 UGF  C5D  H10  single  0.970  0.020  1.090
 UGF  C5D  H11  single  0.970  0.020  1.090
 UGF  C1'  H14  single  0.970  0.020  1.090
 UGF  C5'  H15  single  0.970  0.020  1.090
 UGF  C4'  H17  single  0.970  0.020  1.090
 UGF  C3'  H18  single  0.970  0.020  1.090
 UGF  O3'  H19  single  0.850  0.020  0.980
 UGF  C2'  H20  single  0.970  0.020  1.090
 UGF  O2'  H21  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
 UGF  N1   C2   N3   114.48  3.000
 UGF  N1   C2   O2   123.65  3.000
 UGF  N3   C2   O2   121.87  3.000
 UGF  H1   N3   C4   116.71  3.000
 UGF  H1   N3   C2   114.96  3.000
 UGF  C4   N3   C2   128.33  3.000
 UGF  C5   C4   O4   126.29  3.000
 UGF  C5   C4   N3   113.20  3.000
 UGF  O4   C4   N3   120.51  3.000
 UGF  H2   C5   C6   120.42  3.000
 UGF  H2   C5   C4   119.86  3.000
 UGF  C6   C5   C4   119.71  3.000
 UGF  H3   C6   N1   115.88  3.000
 UGF  H3   C6   C5   120.83  3.000
 UGF  N1   C6   C5   123.28  3.000
 UGF  C1D  N1   C6   119.73  3.000
 UGF  C1D  N1   C2   119.28  3.000
 UGF  C6   N1   C2   121.00  3.000
 UGF  H4   C1D  C2D  109.70  3.000
 UGF  H4   C1D  O4D  111.23  3.000
 UGF  C2D  C1D  O4D  106.38  3.000
 UGF  H4   C1D  N1   106.28  3.000
 UGF  O4D  C1D  N1   109.52  3.000
 UGF  C2D  C1D  N1   113.81  3.000
 UGF  C4D  O4D  C1D  110.61  3.000
 UGF  H5   C2D  C3D  107.98  3.000
 UGF  H5   C2D  O2D  111.23  3.000
 UGF  C3D  C2D  O2D  116.50  3.000
 UGF  H5   C2D  C1D  110.52  3.000
 UGF  C3D  C2D  C1D  101.03  3.000
 UGF  O2D  C2D  C1D  109.10  3.000
 UGF  H6   O2D  C2D  108.63  3.000
 UGF  H7   C3D  C4D  111.38  3.000
 UGF  H7   C3D  O3D  111.65  3.000
 UGF  C4D  C3D  O3D  111.85  3.000
 UGF  H7   C3D  C2D  112.16  3.000
 UGF  C4D  C3D  C2D  101.76  3.000
 UGF  O3D  C3D  C2D  107.59  3.000
 UGF  H8   O3D  C3D  108.29  3.000
 UGF  H9   C4D  C5D  106.61  3.000
 UGF  H9   C4D  C3D  109.52  3.000
 UGF  C5D  C4D  C3D  115.50  3.000
 UGF  H9   C4D  O4D  108.58  3.000
 UGF  C5D  C4D  O4D  110.49  3.000
 UGF  C3D  C4D  O4D  106.01  3.000
 UGF  H11  C5D  H10  107.12  3.000
 UGF  H11  C5D  O5D  112.23  3.000
 UGF  H10  C5D  O5D  110.97  3.000
 UGF  H11  C5D  C4D  107.89  3.000
 UGF  H10  C5D  C4D  109.28  3.000
 UGF  O5D  C5D  C4D  109.27  3.000
 UGF  PA   O5D  C5D  122.78  3.000
 UGF  O3A  PA   O2A  105.84  3.000
 UGF  O2A  PA   O1A  122.23  3.000
 UGF  O3A  PA   O1A  110.28  3.000
 UGF  O2A  PA   O5D  109.89  3.000
 UGF  O3A  PA   O5D  101.19  3.000
 UGF  O1A  PA   O5D  105.47  3.000
 UGF  PB   O3A  PA   128.97  3.000
 UGF  O3B  PB   O2B  106.27  3.000
 UGF  O3B  PB   O1B  109.49  3.000
 UGF  O2B  PB   O1B  121.94  3.000
 UGF  O1B  PB   O3A  108.21  3.000
 UGF  O3B  PB   O3A   96.94  3.000
 UGF  O2B  PB   O3A  111.07  3.000
 UGF  C1'  O3B  PB   122.79  3.000
 UGF  H14  C1'  C2'  109.63  3.000
 UGF  H14  C1'  O5'  105.23  3.000
 UGF  C2'  C1'  O5'  109.90  3.000
 UGF  H14  C1'  O3B  111.24  3.000
 UGF  O5'  C1'  O3B  111.87  3.000
 UGF  C2'  C1'  O3B  108.93  3.000
 UGF  C5'  O5'  C1'  114.91  3.000
 UGF  H15  C5'  C4'  109.12  3.000
 UGF  H15  C5'  C6'  109.17  3.000
 UGF  C4'  C5'  C6'  112.18  3.000
 UGF  H15  C5'  O5'  110.49  3.000
 UGF  C6'  C5'  O5'  106.87  3.000
 UGF  C4'  C5'  O5'  109.01  3.000
 UGF  O'Q  C6'  O'P  128.05  3.000
 UGF  O'P  C6'  C5'  115.72  3.000
 UGF  O'Q  C6'  C5'  116.22  3.000
 UGF  H17  C4'  C3'  110.15  3.000
 UGF  H17  C4'  F4'  107.57  3.000
 UGF  C3'  C4'  F4'  109.68  3.000
 UGF  H17  C4'  C5'  109.90  3.000
 UGF  C3'  C4'  C5'  111.05  3.000
 UGF  F4'  C4'  C5'  108.40  3.000
 UGF  H18  C3'  C2'  108.94  3.000
 UGF  H18  C3'  O3'  110.89  3.000
 UGF  C2'  C3'  O3'  111.55  3.000
 UGF  H18  C3'  C4'  108.71  3.000
 UGF  C2'  C3'  C4'  107.83  3.000
 UGF  O3'  C3'  C4'  108.83  3.000
 UGF  H19  O3'  C3'  107.86  3.000
 UGF  H20  C2'  O2'  110.95  3.000
 UGF  H20  C2'  C3'  107.62  3.000
 UGF  O2'  C2'  C3'  107.75  3.000
 UGF  H20  C2'  C1'  106.68  3.000
 UGF  O2'  C2'  C1'  112.45  3.000
 UGF  C3'  C2'  C1'  111.31  3.000
 UGF  H21  O2'  C2'  108.93  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
 UGF  CONST_01  C6   N1   C2   N3      0.00   0.0  0
 UGF  CONST_02  C1D  N1   C2   N3    180.00   0.0  0
 UGF  CONST_03  N1   C2   N3   C4      0.00   0.0  0
 UGF  CONST_04  C4   N3   C2   O2    180.00   0.0  0
 UGF  CONST_05  C6   N1   C2   O2    180.00   0.0  0
 UGF  CONST_06  C1D  N1   C2   O2      0.00   0.0  0
 UGF  CONST_07  H1   N3   C2   N1    180.00   0.0  0
 UGF  Var_01    O1A  PA   O5D  C5D  -157.26  30.0  3
 UGF  Var_02    O2B  PB   O3A  PA     34.31  30.0  2
 UGF  Var_03    H10  C5D  O5D  PA     63.61  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
 UGF  chir_01  C1D  C2D  N1   O4D  positiv
 UGF  chir_02  C2D  O2D  C3D  C1D  positiv
 UGF  chir_03  C3D  O3D  C4D  C2D  positiv
 UGF  chir_04  C4D  O4D  C3D  C5D  negativ
 UGF  chir_07  C1'  O3B  C2'  O5'  positiv
 UGF  chir_08  C5'  O5'  C6'  C4'  positiv
 UGF  chir_09  C4'  F4'  C5'  C3'  positiv
 UGF  chir_10  C3'  O3'  C4'  C2'  negativ
 UGF  chir_11  C2'  O2'  C3'  C1'  positiv

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
 UGF  plan-1  O2   0.020
 UGF  plan-1  C2   0.020
 UGF  plan-1  N3   0.020
 UGF  plan-1  C4   0.020
 UGF  plan-1  O4   0.020
 UGF  plan-1  C5   0.020
 UGF  plan-1  C6   0.020
 UGF  plan-1  N1   0.020
 UGF  plan-1  C1D  0.020
 UGF  plan-1  H1   0.020
 UGF  plan-1  H2   0.020
 UGF  plan-1  H3   0.020
 UGF  plan-2  C5'  0.020
 UGF  plan-2  C6'  0.020
 UGF  plan-2  O'P  0.020
 UGF  plan-2  O'Q  0.020

