# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Sep 23 06:14:31 2022
#   Inital geometry file: a 141 line input string
#   Ligand name: [[(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] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[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](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
 AWU  AWU  "[[(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] [(2~{R},3~{R},4~{R},5~{R},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate"  ligand  59  35  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AWU
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
 AWU  PA   P  P     0   1.494  -16.3343  -19.2614  -49.9056
 AWU  O1A  O  O     0  -0.650  -17.5019  -18.9307  -50.7318
 AWU  O2A  O  OH1   0  -0.733  -16.5713  -19.6114  -48.3758
 AWU  O3A  O  O2    0  -0.710  -15.1821  -18.1228  -49.9260
 AWU  PB   P  P     0   1.477  -14.5426  -16.9720  -48.9921
 AWU  O1B  O  O     0  -0.653  -13.0767  -16.9688  -49.0681
 AWU  O2B  O  OH1   0  -0.722  -15.1890  -17.1354  -47.5524
 AWU  O3B  O  O2    0  -0.602  -15.1995  -15.6300  -49.5355
 AWU  C5'  C  CH1   0   0.005  -18.7333  -15.9906  -49.7111
 AWU  O5'  O  O2    0  -0.499  -17.4008  -16.0258  -49.2110
 AWU  C4'  C  CH1   0   0.036  -19.1568  -14.5396  -49.9918
 AWU  O4'  O  OH1   0  -0.665  -20.4163  -14.5086  -50.6178
 AWU  C3'  C  CH1   0   0.018  -18.1500  -13.8906  -50.9342
 AWU  O3'  O  OH1   0  -0.659  -18.5108  -12.5507  -51.1311
 AWU  C2'  C  CH1   0  -0.061  -16.7310  -14.0283  -50.3763
 AWU  C1'  C  CH1   0   0.302  -16.4821  -15.5097  -50.1133
 AWU  N1   N  NR6   0  -0.571  -11.5156  -23.6135  -48.1705
 AWU  C2   C  CR6   0   0.736  -10.7235  -24.7349  -47.9864
 AWU  O2   O  O     0  -0.465  -11.0801  -25.8571  -48.2712
 AWU  N3   N  NR16  0  -0.736   -9.4916  -24.4782  -47.4456
 AWU  C4   C  CR6   0   0.567   -8.9497  -23.2529  -47.0850
 AWU  O4   O  O     0  -0.449   -7.8293  -23.1848  -46.6201
 AWU  C5   C  CR16  0  -0.509   -9.8405  -22.1421  -47.3235
 AWU  C6   C  CR16  0   0.101  -11.0549  -22.3661  -47.8468
 AWU  C1C  C  CH1   0   0.178  -12.8290  -23.7709  -48.7673
 AWU  C2C  C  CH1   0  -0.016  -14.0059  -23.3694  -47.8732
 AWU  C3C  C  CH1   0  -0.045  -15.0805  -23.1247  -48.9310
 AWU  C4C  C  CH1   0  -0.008  -14.2630  -22.4709  -50.0439
 AWU  C5C  C  CH2   0  -0.204  -14.2618  -20.9520  -49.9881
 AWU  C6'  C  CH3   0  -0.698  -19.6171  -16.6734  -48.6914
 AWU  O2'  O  OH1   0  -0.659  -16.6281  -13.2698  -49.2044
 AWU  O2C  O  OH1   0  -0.652  -14.4054  -24.3465  -46.9663
 AWU  O3C  O  OH1   0  -0.661  -15.6037  -24.3288  -49.4271
 AWU  O4C  O  O2    0  -0.491  -12.9202  -22.9269  -49.8856
 AWU  O5C  O  O2    0  -0.569  -15.5513  -20.5254  -50.4394
 AWU  H1   H  HOH1  0   0.509  -17.2245  -19.0661  -47.9145
 AWU  H2   H  HOH1  0   0.505  -14.6773  -17.6899  -46.9449
 AWU  H3   H  HCH1  0   0.224  -18.7774  -16.5491  -50.6568
 AWU  H4   H  HCH1  0   0.221  -19.1700  -13.9862  -49.0426
 AWU  H5   H  HOH1  0   0.455  -21.0991  -14.5979  -49.9470
 AWU  H6   H  HCH1  0   0.220  -18.1744  -14.4520  -51.8818
 AWU  H7   H  HOH1  0   0.451  -17.9753  -12.1905  -51.8453
 AWU  H8   H  HCH1  0   0.246  -16.0174  -13.6914  -51.1435
 AWU  H9   H  HCH1  0   0.226  -16.5097  -16.0640  -51.0641
 AWU  H10  H  HNR6  0   0.425   -8.9083  -25.2942  -47.3031
 AWU  H11  H  HCR6  0   0.292   -9.5211  -21.1394  -47.0850
 AWU  H12  H  HCR6  0   0.329  -11.7285  -21.5445  -48.0430
 AWU  H13  H  HCH1  0   0.275  -12.9209  -24.8214  -49.0485
 AWU  H14  H  HCH1  0   0.246  -13.7827  -22.4159  -47.3735
 AWU  H15  H  HCH1  0   0.259  -15.8721  -22.4643  -48.5573
 AWU  H16  H  HCH1  0   0.270  -14.6362  -22.7858  -51.0237
 AWU  H17  H  HCH2  0   0.252  -14.0472  -20.5926  -48.9774
 AWU  H18  H  HCH2  0   0.274  -13.5037  -20.5488  -50.6616
 AWU  H19  H  HCH3  0   0.249  -19.2924  -17.7000  -48.5244
 AWU  H20  H  HCH3  0   0.232  -19.6030  -16.1445  -47.7370
 AWU  H21  H  HCH3  0   0.236  -20.6472  -16.7162  -49.0429
 AWU  H22  H  HOH1  0   0.455  -15.7052  -13.2377  -48.9338
 AWU  H23  H  HOH1  0   0.467  -13.7993  -24.3580  -46.2188
 AWU  H24  H  HOH1  0   0.454  -15.9995  -24.8168  -48.6968

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
 AWU  O3'  C3'  single  1.402  0.020  1.402
 AWU  O4'  C4'  single  1.407  0.020  1.407
 AWU  C3'  C4'  single  1.524  0.020  1.524
 AWU  C3'  C2'  single  1.531  0.020  1.531
 AWU  C4'  C5'  single  1.537  0.020  1.537
 AWU  O3C  C3C  single  1.404  0.020  1.404
 AWU  C2'  O2'  single  1.400  0.020  1.400
 AWU  C2'  C1'  single  1.525  0.020  1.525
 AWU  C4C  C5C  single  1.520  0.020  1.520
 AWU  C4C  O4C  single  1.427  0.020  1.427
 AWU  C4C  C3C  single  1.528  0.020  1.528
 AWU  O1B  PB   double  1.468  0.020  1.468
 AWU  C5C  O5C  single  1.431  0.020  1.431
 AWU  C5'  C6'  single  1.512  0.020  1.512
 AWU  C5'  O5'  single  1.424  0.020  1.424
 AWU  O4C  C1C  single  1.404  0.020  1.404
 AWU  C1'  O5'  single  1.387  0.020  1.387
 AWU  C1'  O3B  single  1.412  0.020  1.412
 AWU  O5C  PA   single  1.580  0.020  1.580
 AWU  C3C  C2C  single  1.528  0.020  1.528
 AWU  O3A  PB   single  1.614  0.020  1.614
 AWU  O3A  PA   single  1.620  0.020  1.620
 AWU  C1C  C2C  single  1.532  0.020  1.532
 AWU  C1C  N1   single  1.451  0.020  1.451
 AWU  O3B  PB   single  1.590  0.020  1.590
 AWU  PB   O2B  single  1.587  0.020  1.587
 AWU  O2   C2   double  1.211  0.020  1.211
 AWU  O1A  PA   double  1.468  0.020  1.468
 AWU  PA   O2A  single  1.587  0.020  1.587
 AWU  C2C  O2C  single  1.392  0.020  1.392
 AWU  N1   C2   single  1.385  0.020  1.385
 AWU  N1   C6   single  1.369  0.020  1.369
 AWU  C2   N3   single  1.370  0.020  1.370
 AWU  C6   C5   double  1.341  0.020  1.341
 AWU  N3   C4   single  1.387  0.020  1.387
 AWU  C5   C4   single  1.444  0.020  1.444
 AWU  C4   O4   double  1.215  0.020  1.215
 AWU  O2A  H1   single  0.850  0.020  0.980
 AWU  O2B  H2   single  0.850  0.020  0.980
 AWU  C5'  H3   single  0.970  0.020  1.090
 AWU  C4'  H4   single  0.970  0.020  1.090
 AWU  O4'  H5   single  0.850  0.020  0.980
 AWU  C3'  H6   single  0.970  0.020  1.090
 AWU  O3'  H7   single  0.850  0.020  0.980
 AWU  C2'  H8   single  0.970  0.020  1.090
 AWU  C1'  H9   single  0.970  0.020  1.090
 AWU  N3   H10  single  0.860  0.020  1.020
 AWU  C5   H11  single  0.930  0.020  1.080
 AWU  C6   H12  single  0.930  0.020  1.080
 AWU  C1C  H13  single  0.970  0.020  1.090
 AWU  C2C  H14  single  0.970  0.020  1.090
 AWU  C3C  H15  single  0.970  0.020  1.090
 AWU  C4C  H16  single  0.970  0.020  1.090
 AWU  C5C  H17  single  0.970  0.020  1.090
 AWU  C5C  H18  single  0.970  0.020  1.090
 AWU  C6'  H19  single  0.970  0.020  1.090
 AWU  C6'  H20  single  0.970  0.020  1.090
 AWU  C6'  H21  single  0.970  0.020  1.090
 AWU  O2'  H22  single  0.850  0.020  0.980
 AWU  O2C  H23  single  0.850  0.020  0.980
 AWU  O3C  H24  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
 AWU  O5C  PA   O3A  101.86  3.000
 AWU  O3A  PA   O2A  105.86  3.000
 AWU  O5C  PA   O2A  102.90  3.000
 AWU  O2A  PA   O1A  118.25  3.000
 AWU  O3A  PA   O1A  113.59  3.000
 AWU  O5C  PA   O1A  112.60  3.000
 AWU  H1   O2A  PA   115.84  3.000
 AWU  PB   O3A  PA   140.85  3.000
 AWU  O3B  PB   O2B  103.22  3.000
 AWU  O2B  PB   O1B  117.01  3.000
 AWU  O3B  PB   O1B  113.14  3.000
 AWU  O2B  PB   O3A  106.87  3.000
 AWU  O3B  PB   O3A  103.91  3.000
 AWU  O1B  PB   O3A  111.54  3.000
 AWU  H2   O2B  PB   114.38  3.000
 AWU  C1'  O3B  PB   125.95  3.000
 AWU  H3   C5'  C6'  109.10  3.000
 AWU  H3   C5'  C4'  108.15  3.000
 AWU  C6'  C5'  C4'  112.85  3.000
 AWU  H3   C5'  O5'  109.10  3.000
 AWU  C6'  C5'  O5'  107.39  3.000
 AWU  C4'  C5'  O5'  110.20  3.000
 AWU  C1'  O5'  C5'  112.47  3.000
 AWU  H4   C4'  C3'  109.12  3.000
 AWU  H4   C4'  O4'  111.26  3.000
 AWU  C3'  C4'  O4'  107.87  3.000
 AWU  H4   C4'  C5'  108.72  3.000
 AWU  C3'  C4'  C5'  109.44  3.000
 AWU  O4'  C4'  C5'  110.41  3.000
 AWU  H5   O4'  C4'  108.87  3.000
 AWU  H6   C3'  C2'  106.75  3.000
 AWU  H6   C3'  O3'  111.14  3.000
 AWU  C2'  C3'  O3'  112.08  3.000
 AWU  H6   C3'  C4'  107.46  3.000
 AWU  C2'  C3'  C4'  110.40  3.000
 AWU  O3'  C3'  C4'  108.90  3.000
 AWU  H7   O3'  C3'  108.59  3.000
 AWU  H8   C2'  O2'  111.72  3.000
 AWU  H8   C2'  C1'  108.16  3.000
 AWU  O2'  C2'  C1'  111.71  3.000
 AWU  H8   C2'  C3'  108.63  3.000
 AWU  C1'  C2'  C3'  107.55  3.000
 AWU  O2'  C2'  C3'  108.93  3.000
 AWU  H9   C1'  C2'  109.64  3.000
 AWU  H9   C1'  O5'  110.97  3.000
 AWU  C2'  C1'  O5'  111.43  3.000
 AWU  H9   C1'  O3B  109.47  3.000
 AWU  O5'  C1'  O3B  107.68  3.000
 AWU  C2'  C1'  O3B  107.56  3.000
 AWU  C1C  N1   C6   120.05  3.000
 AWU  C6   N1   C2   120.92  3.000
 AWU  C1C  N1   C2   118.98  3.000
 AWU  N3   C2   O2   122.09  3.000
 AWU  N3   C2   N1   114.52  3.000
 AWU  O2   C2   N1   123.38  3.000
 AWU  H10  N3   C4   116.74  3.000
 AWU  H10  N3   C2   114.98  3.000
 AWU  C4   N3   C2   128.28  3.000
 AWU  C5   C4   O4   126.09  3.000
 AWU  O4   C4   N3   120.60  3.000
 AWU  C5   C4   N3   113.30  3.000
 AWU  H11  C5   C6   120.63  3.000
 AWU  H11  C5   C4   119.72  3.000
 AWU  C6   C5   C4   119.64  3.000
 AWU  H12  C6   C5   120.56  3.000
 AWU  H12  C6   N1   116.12  3.000
 AWU  C5   C6   N1   123.32  3.000
 AWU  H13  C1C  O4C  111.59  3.000
 AWU  H13  C1C  C2C  109.76  3.000
 AWU  O4C  C1C  C2C  104.92  3.000
 AWU  H13  C1C  N1   106.65  3.000
 AWU  C2C  C1C  N1   115.28  3.000
 AWU  O4C  C1C  N1   108.73  3.000
 AWU  H14  C2C  O2C  111.78  3.000
 AWU  H14  C2C  C3C  108.58  3.000
 AWU  O2C  C2C  C3C  111.21  3.000
 AWU  H14  C2C  C1C  109.67  3.000
 AWU  O2C  C2C  C1C  114.64  3.000
 AWU  C3C  C2C  C1C  100.27  3.000
 AWU  H15  C3C  O3C  111.59  3.000
 AWU  H15  C3C  C4C  112.13  3.000
 AWU  O3C  C3C  C4C  108.01  3.000
 AWU  H15  C3C  C2C  111.61  3.000
 AWU  C4C  C3C  C2C  101.34  3.000
 AWU  O3C  C3C  C2C  111.69  3.000
 AWU  H16  C4C  O4C  109.16  3.000
 AWU  H16  C4C  C5C  108.70  3.000
 AWU  O4C  C4C  C5C  108.33  3.000
 AWU  H16  C4C  C3C  110.27  3.000
 AWU  O4C  C4C  C3C  106.62  3.000
 AWU  C5C  C4C  C3C  113.66  3.000
 AWU  H18  C5C  H17  108.22  3.000
 AWU  H18  C5C  O5C  108.73  3.000
 AWU  H17  C5C  O5C  111.72  3.000
 AWU  H18  C5C  C4C  110.31  3.000
 AWU  H17  C5C  C4C  111.25  3.000
 AWU  O5C  C5C  C4C  106.59  3.000
 AWU  H21  C6'  H20  108.28  3.000
 AWU  H21  C6'  H19  107.11  3.000
 AWU  H20  C6'  H19  108.58  3.000
 AWU  H21  C6'  C5'  110.66  3.000
 AWU  H20  C6'  C5'  111.31  3.000
 AWU  H19  C6'  C5'  110.77  3.000
 AWU  H22  O2'  C2'  108.91  3.000
 AWU  H23  O2C  C2C  109.49  3.000
 AWU  H24  O3C  C3C  108.65  3.000
 AWU  C4C  O4C  C1C  109.97  3.000
 AWU  C5C  O5C  PA   125.34  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
 AWU  CONST_01  C4   N3   C2   N1      0.00   0.0  0
 AWU  CONST_02  C5   C4   N3   C2      0.00   0.0  0
 AWU  CONST_03  C1C  N1   C2   N3    180.00   0.0  0
 AWU  CONST_04  C6   N1   C2   N3      0.00   0.0  0
 AWU  CONST_05  O4   C4   N3   C2    180.00   0.0  0
 AWU  CONST_06  C1C  N1   C2   O2      0.00   0.0  0
 AWU  CONST_07  C6   N1   C2   O2    180.00   0.0  0
 AWU  CONST_08  C4   N3   C2   O2    180.00   0.0  0
 AWU  CONST_09  H10  N3   C2   N1    180.00   0.0  0
 AWU  CONST_10  H10  N3   C4   C5    180.00   0.0  0
 AWU  CONST_11  H10  N3   C2   O2      0.00   0.0  0
 AWU  CONST_12  H10  N3   C4   O4      0.00   0.0  0
 AWU  Var_01    H11  C5   C6   N1    179.96  30.0  1
 AWU  Var_02    H12  C6   N1   C2    178.66  30.0  1
 AWU  Var_03    H11  C5   C4   N3   -179.67  30.0  1
 AWU  Var_04    H12  C6   C5   C4   -179.22  30.0  1
 AWU  Var_05    H12  C6   N1   C1C     1.25  30.0  1
 AWU  Var_06    H11  C5   C4   O4      0.26  30.0  1
 AWU  Var_07    C4C  C5C  O5C  PA    145.78  30.0  1
 AWU  Var_08    C1'  O3B  PB   O3A    30.50  30.0  1
 AWU  Var_09    C1'  O3B  PB   O1B   151.65  30.0  1
 AWU  Var_10    C1'  O3B  PB   O2B   -80.93  30.0  1
 AWU  Var_11    O1B  PB   O3A  PA    136.75  30.0  3
 AWU  Var_12    O3B  PB   O3A  PA   -101.04  30.0  3
 AWU  Var_13    O2B  PB   O3A  PA      7.71  30.0  3
 AWU  Var_14    C5C  O5C  PA   O1A   168.86  30.0  2
 AWU  Var_15    PB   O3A  PA   O1A   107.06  30.0  1
 AWU  Var_16    C5C  O5C  PA   O2A   -62.73  30.0  2
 AWU  Var_17    PB   O3A  PA   O2A   -24.33  30.0  1
 AWU  Var_18    C5C  O5C  PA   O3A    46.82  30.0  2
 AWU  Var_19    O5C  PA   O3A  PB   -131.60  30.0  3
 AWU  Var_20    H17  C5C  O5C  PA     24.06  30.0  1
 AWU  Var_21    H18  C5C  O5C  PA    -95.31  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
 AWU  chir_03  C5'  C4'  C6'  O5'  positiv
 AWU  chir_04  C4'  O4'  C5'  C3'  negativ
 AWU  chir_05  C3'  O3'  C4'  C2'  positiv
 AWU  chir_06  C2'  O2'  C3'  C1'  positiv
 AWU  chir_07  C1'  O5'  O3B  C2'  positiv
 AWU  chir_08  C1C  O4C  C2C  N1   positiv
 AWU  chir_09  C2C  O2C  C1C  C3C  negativ
 AWU  chir_10  C3C  O3C  C4C  C2C  positiv
 AWU  chir_11  C4C  O4C  C3C  C5C  negativ
 AWU  chir_12  PA   O3A  O1A  O2A  both
 AWU  chir_13  PB   O3A  O3B  O2B  both

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
 AWU  plan-1  N1   0.020
 AWU  plan-1  C2   0.020
 AWU  plan-1  O2   0.020
 AWU  plan-1  N3   0.020
 AWU  plan-1  C4   0.020
 AWU  plan-1  O4   0.020
 AWU  plan-1  C5   0.020
 AWU  plan-1  C6   0.020
 AWU  plan-1  C1C  0.020
 AWU  plan-1  H10  0.020

