# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 05:00:39 2021
#   Inital geometry file: a 133 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-2-fluoro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc(F)nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4OC[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O
#
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
 AVV  AVV  '[(2R,3S,4R,5R)-5-(6-amino-2-fluoro-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  58  36  .  2021-08-06  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_AVV
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
 AVV  PA    P  P     0   1.473  3.9966   1.2710  -19.8639
 AVV  PN    P  P     0   1.493  5.6314  -1.0599  -20.1161
 AVV  F1A   F  F     0  -0.286  5.9699  11.2290  -21.1386
 AVV  N1A   N  N     0  -0.503  6.8837  10.0475  -22.7762
 AVV  O1A   O  OH1   0  -0.716  2.6777   1.3093  -18.9882
 AVV  O1N   O  OH1   0  -0.723  5.0331  -2.3949  -20.7318
 AVV  C2A   C  CR6   0   0.573  6.3621  10.0337  -21.5723
 AVV  O2A   O  O     0  -0.680  3.9651   1.8458  -21.2177
 AVV  O2N   O  O     0  -0.677  6.5682  -0.2607  -20.9190
 AVV  O3    O  O2    0  -0.685  4.2147  -0.3325  -19.8051
 AVV  N3A   N  N     0  -0.490  6.1628   9.0550  -20.7337
 AVV  C4A   C  CR56  0   0.498  6.5903   7.9029  -21.2577
 AVV  C5A   C  CR56  0  -0.005  7.1606   7.7260  -22.5065
 AVV  C6A   C  CR6   0   0.478  7.3059   8.8855  -23.2941
 AVV  N6A   N  NH2   0  -0.807  7.8389   8.8740  -24.5096
 AVV  N7A   N  N     0  -0.444  7.4847   6.4109  -22.7069
 AVV  C8A   C  CR15  0   0.103  7.1194   5.8152  -21.6112
 AVV  N9A   N  NR5   0  -0.533  6.5660   6.6680  -20.6907
 AVV  C1'A  C  CH1   0   0.171  6.0528   6.3765  -19.3586
 AVV  C1'N  C  CH2   0  -0.166  7.8713  -3.6551  -15.8459
 AVV  C2'A  C  CH1   0  -0.046  4.5293   6.2614  -19.3440
 AVV  O2'A  O  OH1   0  -0.658  4.1023   6.6175  -18.0600
 AVV  C2'N  C  CH1   0  -0.009  6.4943  -3.8535  -15.2220
 AVV  O2'N  O  OH1   0  -0.660  6.5784  -4.7132  -14.1260
 AVV  C3'A  C  CH1   0  -0.034  4.3512   4.7611  -19.6018
 AVV  O3'A  O  OH1   0  -0.672  3.1225   4.2527  -19.1490
 AVV  C3'N  C  CH1   0  -0.039  5.6836  -4.3657  -16.4175
 AVV  O3'N  O  OH1   0  -0.665  5.9541  -5.7333  -16.5738
 AVV  C4'A  C  CH1   0   0.031  5.5166   4.1799  -18.8023
 AVV  O4'A  O  O2    0  -0.494  6.5551   5.1442  -18.9355
 AVV  C4'N  C  CH1   0  -0.028  6.2835  -3.5250  -17.5468
 AVV  O4'N  O  O2    0  -0.496  7.6390  -3.2982  -17.1982
 AVV  C5'A  C  CH2   0  -0.211  6.0604   2.8464  -19.2834
 AVV  O5'A  O  O2    0  -0.591  5.1541   1.8077  -18.9095
 AVV  C5'N  C  CH2   0  -0.210  5.5480  -2.2096  -17.7154
 AVV  O5'N  O  O2    0  -0.568  6.2248  -1.4014  -18.6901
 AVV  HAO1  H  HOH1  0   0.503  2.3846   2.2191  -18.8170
 AVV  HNO1  H  HOH1  0   0.512  5.6773  -2.9505  -21.1930
 AVV  HAN6  H  HNH2  0   0.411  7.9316   9.7262  -25.0357
 AVV  HANA  H  HNH2  0   0.418  8.1487   8.0161  -24.9321
 AVV  HC1'  H  HCH1  0   0.293  6.3971   7.1791  -18.7010
 AVV  HC1A  H  HCH2  0   0.214  8.4522  -4.5824  -15.7835
 AVV  HC1B  H  HCH2  0   0.233  8.4417  -2.8640  -15.3551
 AVV  HC2'  H  HCH1  0   0.270  4.0623   6.8772  -20.1222
 AVV  HO2'  H  HOH1  0   0.456  3.2433   6.2095  -17.8987
 AVV  HC2A  H  HCH1  0   0.227  6.0806  -2.8781  -14.9319
 AVV  HO2A  H  HOH1  0   0.458  5.7217  -4.7429  -13.6891
 AVV  HC3'  H  HCH1  0   0.252  4.4878   4.5591  -20.6715
 AVV  HO3'  H  HOH1  0   0.480  2.4390   4.5006  -19.7831
 AVV  HC3A  H  HCH1  0   0.244  4.6080  -4.1784  -16.2981
 AVV  HO3A  H  HOH1  0   0.455  5.4878  -6.0476  -17.3548
 AVV  HC4'  H  HCH1  0   0.262  5.2310   4.0848  -17.7475
 AVV  HC4A  H  HCH1  0   0.252  6.2455  -4.0713  -18.4970
 AVV  HC5'  H  HCH2  0   0.242  6.2364   2.8461  -20.3611
 AVV  HC5A  H  HCH2  0   0.281  7.0023   2.6212  -18.7845
 AVV  HC5B  H  HCH2  0   0.253  4.5100  -2.4021  -17.9960
 AVV  HC5C  H  HCH2  0   0.261  5.5383  -1.6308  -16.7908
 AVV  HC8   H  HCR5  0   0.298  7.2441   4.7620  -21.4168

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
 AVV  O2A   PA    double    1.471  0.020  1.471
 AVV  PA    O3    single    1.619  0.020  1.619
 AVV  PA    O5'A  single    1.593  0.020  1.593
 AVV  PA    O1A   single    1.584  0.020  1.584
 AVV  O2N   PN    double    1.470  0.020  1.470
 AVV  O1N   PN    single    1.587  0.020  1.587
 AVV  PN    O3    single    1.623  0.020  1.623
 AVV  PN    O5'N  single    1.582  0.020  1.582
 AVV  C2A   F1A   single    1.331  0.020  1.331
 AVV  C6A   N1A   aromatic  1.340  0.020  1.340
 AVV  N1A   C2A   aromatic  1.312  0.020  1.312
 AVV  O1A   HAO1  single    0.850  0.020  0.980
 AVV  O1N   HNO1  single    0.850  0.020  0.980
 AVV  N3A   C2A   aromatic  1.304  0.020  1.304
 AVV  C4A   N3A   aromatic  1.336  0.020  1.336
 AVV  C5A   C4A   aromatic  1.384  0.020  1.384
 AVV  N9A   C4A   aromatic  1.359  0.020  1.359
 AVV  N7A   C5A   aromatic  1.369  0.020  1.369
 AVV  C5A   C6A   aromatic  1.409  0.020  1.409
 AVV  N6A   C6A   single    1.327  0.020  1.327
 AVV  N6A   HAN6  single    0.860  0.020  1.020
 AVV  N6A   HANA  single    0.860  0.020  1.020
 AVV  N7A   C8A   aromatic  1.300  0.020  1.300
 AVV  C8A   N9A   aromatic  1.371  0.020  1.371
 AVV  C8A   HC8   single    0.930  0.020  1.080
 AVV  N9A   C1'A  single    1.457  0.020  1.457
 AVV  C2'A  C1'A  single    1.528  0.020  1.528
 AVV  C1'A  O4'A  single    1.396  0.020  1.396
 AVV  C1'A  HC1'  single    0.970  0.020  1.090
 AVV  O4'N  C1'N  single    1.418  0.020  1.418
 AVV  C1'N  C2'N  single    1.525  0.020  1.525
 AVV  C1'N  HC1A  single    0.970  0.020  1.090
 AVV  C1'N  HC1B  single    0.970  0.020  1.090
 AVV  C2'A  C3'A  single    1.533  0.020  1.533
 AVV  C2'A  O2'A  single    1.399  0.020  1.399
 AVV  C2'A  HC2'  single    0.970  0.020  1.090
 AVV  O2'A  HO2'  single    0.850  0.020  0.980
 AVV  C3'N  C2'N  single    1.533  0.020  1.533
 AVV  C2'N  O2'N  single    1.395  0.020  1.395
 AVV  C2'N  HC2A  single    0.970  0.020  1.090
 AVV  O2'N  HO2A  single    0.850  0.020  0.980
 AVV  C3'A  C4'A  single    1.528  0.020  1.528
 AVV  C3'A  O3'A  single    1.405  0.020  1.405
 AVV  C3'A  HC3'  single    0.970  0.020  1.090
 AVV  O3'A  HO3'  single    0.850  0.020  0.980
 AVV  C4'N  C3'N  single    1.530  0.020  1.530
 AVV  O3'N  C3'N  single    1.403  0.020  1.403
 AVV  C3'N  HC3A  single    0.970  0.020  1.090
 AVV  O3'N  HO3A  single    0.850  0.020  0.980
 AVV  C5'A  C4'A  single    1.518  0.020  1.518
 AVV  O4'A  C4'A  single    1.423  0.020  1.423
 AVV  C4'A  HC4'  single    0.970  0.020  1.090
 AVV  O4'N  C4'N  single    1.418  0.020  1.418
 AVV  C5'N  C4'N  single    1.516  0.020  1.516
 AVV  C4'N  HC4A  single    0.970  0.020  1.090
 AVV  C5'A  O5'A  single    1.428  0.020  1.428
 AVV  C5'A  HC5'  single    0.970  0.020  1.090
 AVV  C5'A  HC5A  single    0.970  0.020  1.090
 AVV  O5'N  C5'N  single    1.436  0.020  1.436
 AVV  C5'N  HC5B  single    0.970  0.020  1.090
 AVV  C5'N  HC5C  single    0.970  0.020  1.090

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
 AVV  O5'A  PA    O3    102.35  3.000
 AVV  O5'A  PA    O2A   115.79  3.000
 AVV  O3    PA    O2A   115.04  3.000
 AVV  O5'A  PA    O1A   105.41  3.000
 AVV  O3    PA    O1A    96.67  3.000
 AVV  O2A   PA    O1A   118.79  3.000
 AVV  O5'N  PN    O3    104.57  3.000
 AVV  O5'N  PN    O2N   111.76  3.000
 AVV  O3    PN    O2N   114.67  3.000
 AVV  O5'N  PN    O1N   108.03  3.000
 AVV  O3    PN    O1N    97.03  3.000
 AVV  O2N   PN    O1N   119.06  3.000
 AVV  C6A   N1A   C2A   118.08  3.000
 AVV  HAO1  O1A   PA    111.81  3.000
 AVV  HNO1  O1N   PN    114.63  3.000
 AVV  N3A   C2A   N1A   131.19  3.000
 AVV  N3A   C2A   F1A   114.81  3.000
 AVV  N1A   C2A   F1A   114.00  3.000
 AVV  PN    O3    PA    123.68  3.000
 AVV  C4A   N3A   C2A   110.25  3.000
 AVV  N9A   C4A   C5A   105.52  3.000
 AVV  N9A   C4A   N3A   127.90  3.000
 AVV  C5A   C4A   N3A   126.58  3.000
 AVV  N7A   C5A   C6A   133.16  3.000
 AVV  C6A   C5A   C4A   116.20  3.000
 AVV  N7A   C5A   C4A   110.63  3.000
 AVV  N6A   C6A   C5A   123.10  3.000
 AVV  N6A   C6A   N1A   119.20  3.000
 AVV  C5A   C6A   N1A   117.70  3.000
 AVV  HANA  N6A   HAN6  118.35  3.000
 AVV  HANA  N6A   C6A   121.07  3.000
 AVV  HAN6  N6A   C6A   120.58  3.000
 AVV  C8A   N7A   C5A   104.50  3.000
 AVV  HC8   C8A   N9A   122.22  3.000
 AVV  HC8   C8A   N7A   124.56  3.000
 AVV  N9A   C8A   N7A   113.22  3.000
 AVV  C1'A  N9A   C8A   129.15  3.000
 AVV  C1'A  N9A   C4A   124.72  3.000
 AVV  C8A   N9A   C4A   106.13  3.000
 AVV  HC1'  C1'A  O4'A  110.63  3.000
 AVV  HC1'  C1'A  C2'A  111.32  3.000
 AVV  O4'A  C1'A  C2'A  106.82  3.000
 AVV  HC1'  C1'A  N9A   106.98  3.000
 AVV  O4'A  C1'A  N9A   109.08  3.000
 AVV  C2'A  C1'A  N9A   112.03  3.000
 AVV  HC1B  C1'N  HC1A  108.09  3.000
 AVV  HC1B  C1'N  O4'N  109.39  3.000
 AVV  HC1A  C1'N  O4'N  110.75  3.000
 AVV  HC1B  C1'N  C2'N  112.47  3.000
 AVV  HC1A  C1'N  C2'N  110.20  3.000
 AVV  O4'N  C1'N  C2'N  105.97  3.000
 AVV  HC2'  C2'A  C3'A  112.38  3.000
 AVV  HC2'  C2'A  O2'A  112.23  3.000
 AVV  C3'A  C2'A  O2'A  111.59  3.000
 AVV  HC2'  C2'A  C1'A  112.06  3.000
 AVV  O2'A  C2'A  C1'A  107.09  3.000
 AVV  C3'A  C2'A  C1'A  100.84  3.000
 AVV  HO2'  O2'A  C2'A  108.51  3.000
 AVV  HC2A  C2'N  C3'N  107.67  3.000
 AVV  HC2A  C2'N  O2'N  111.25  3.000
 AVV  C3'N  C2'N  O2'N  116.02  3.000
 AVV  HC2A  C2'N  C1'N  109.43  3.000
 AVV  O2'N  C2'N  C1'N  110.31  3.000
 AVV  C3'N  C2'N  C1'N  101.65  3.000
 AVV  HO2A  O2'N  C2'N  108.78  3.000
 AVV  HC3'  C3'A  C4'A  110.19  3.000
 AVV  HC3'  C3'A  O3'A  110.89  3.000
 AVV  C4'A  C3'A  O3'A  111.15  3.000
 AVV  HC3'  C3'A  C2'A  109.25  3.000
 AVV  O3'A  C3'A  C2'A  113.69  3.000
 AVV  C4'A  C3'A  C2'A  101.28  3.000
 AVV  HO3'  O3'A  C3'A  108.34  3.000
 AVV  HC3A  C3'N  C4'N  111.74  3.000
 AVV  HC3A  C3'N  O3'N  111.54  3.000
 AVV  C4'N  C3'N  O3'N  112.19  3.000
 AVV  HC3A  C3'N  C2'N  112.10  3.000
 AVV  O3'N  C3'N  C2'N  108.10  3.000
 AVV  C4'N  C3'N  C2'N  100.64  3.000
 AVV  HO3A  O3'N  C3'N  108.38  3.000
 AVV  HC4'  C4'A  C5'A  108.77  3.000
 AVV  HC4'  C4'A  O4'A  109.80  3.000
 AVV  C5'A  C4'A  O4'A  107.69  3.000
 AVV  HC4'  C4'A  C3'A  109.73  3.000
 AVV  O4'A  C4'A  C3'A  104.47  3.000
 AVV  C5'A  C4'A  C3'A  116.19  3.000
 AVV  C4'A  O4'A  C1'A  111.33  3.000
 AVV  HC4A  C4'N  C5'N  108.59  3.000
 AVV  HC4A  C4'N  O4'N  109.02  3.000
 AVV  C5'N  C4'N  O4'N  110.62  3.000
 AVV  HC4A  C4'N  C3'N  110.62  3.000
 AVV  C5'N  C4'N  C3'N  111.62  3.000
 AVV  O4'N  C4'N  C3'N  106.33  3.000
 AVV  C4'N  O4'N  C1'N  110.54  3.000
 AVV  HC5A  C5'A  HC5'  108.22  3.000
 AVV  HC5A  C5'A  O5'A  106.16  3.000
 AVV  HC5'  C5'A  O5'A  111.13  3.000
 AVV  HC5A  C5'A  C4'A  110.25  3.000
 AVV  HC5'  C5'A  C4'A  111.76  3.000
 AVV  O5'A  C5'A  C4'A  109.18  3.000
 AVV  C5'A  O5'A  PA    123.31  3.000
 AVV  HC5C  C5'N  HC5B  107.62  3.000
 AVV  HC5C  C5'N  O5'N  106.31  3.000
 AVV  HC5B  C5'N  O5'N  111.89  3.000
 AVV  HC5C  C5'N  C4'N  111.74  3.000
 AVV  HC5B  C5'N  C4'N  109.67  3.000
 AVV  O5'N  C5'N  C4'N  109.58  3.000
 AVV  C5'N  O5'N  PN    123.83  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
 AVV  CONST_01  C4A   C5A   C6A   N1A     0.00   0.0  0
 AVV  CONST_02  N7A   C5A   C6A   N1A   180.00   0.0  0
 AVV  CONST_03  C4A   N3A   C2A   N1A     0.00   0.0  0
 AVV  CONST_04  C5A   C6A   N1A   C2A     0.00   0.0  0
 AVV  CONST_05  C5A   C4A   N3A   C2A     0.00   0.0  0
 AVV  CONST_06  N9A   C4A   N3A   C2A   180.00   0.0  0
 AVV  CONST_07  C6A   N1A   C2A   N3A     0.00   0.0  0
 AVV  CONST_08  N7A   C5A   C4A   N3A   180.00   0.0  0
 AVV  CONST_09  C6A   C5A   C4A   N3A     0.00   0.0  0
 AVV  CONST_10  C8A   N9A   C4A   N3A   180.00   0.0  0
 AVV  CONST_11  C8A   N7A   C5A   C4A     0.00   0.0  0
 AVV  CONST_12  N7A   C8A   N9A   C4A     0.00   0.0  0
 AVV  CONST_13  C8A   N9A   C4A   C5A     0.00   0.0  0
 AVV  CONST_14  N9A   C8A   N7A   C5A     0.00   0.0  0
 AVV  CONST_15  N9A   C4A   C5A   C6A   180.00   0.0  0
 AVV  CONST_16  C8A   N7A   C5A   C6A   180.00   0.0  0
 AVV  CONST_17  N9A   C4A   C5A   N7A     0.00   0.0  0
 AVV  CONST_18  C1'A  N9A   C4A   N3A     0.00   0.0  0
 AVV  CONST_19  C1'A  N9A   C4A   C5A   180.00   0.0  0
 AVV  CONST_20  C1'A  N9A   C8A   N7A   180.00   0.0  0
 AVV  CONST_21  C6A   N1A   C2A   F1A   180.00   0.0  0
 AVV  CONST_22  C4A   N3A   C2A   F1A   180.00   0.0  0
 AVV  CONST_23  N6A   C6A   N1A   C2A   180.00   0.0  0
 AVV  CONST_24  N6A   C6A   C5A   C4A   180.00   0.0  0
 AVV  CONST_25  N7A   C5A   C6A   N6A     0.00   0.0  0
 AVV  CONST_26  HC8   C8A   N9A   C4A   180.00   0.0  0
 AVV  CONST_27  HAN6  N6A   C6A   N1A     0.00   0.0  0
 AVV  CONST_28  HANA  N6A   C6A   N1A   180.00   0.0  0
 AVV  Var_01    HC1A  C1'N  O4'N  C4'N  107.35  30.0  1
 AVV  Var_02    C4'A  C5'A  O5'A  PA     93.27  30.0  2
 AVV  Var_03    C4'N  C5'N  O5'N  PN    111.19  30.0  3
 AVV  Var_04    O2N   PN    O3    PA    -21.45  30.0  2
 AVV  Var_05    O2A   PA    O3    PN     73.25  30.0  2

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
 AVV  chir_03  C1'A  N9A   C2'A  O4'A  negativ
 AVV  chir_04  C2'A  O2'A  C3'A  C1'A  positiv
 AVV  chir_05  C2'N  C1'N  C3'N  O2'N  negativ
 AVV  chir_06  C3'A  C2'A  C4'A  O3'A  negativ
 AVV  chir_07  C3'N  O3'N  C4'N  C2'N  positiv
 AVV  chir_08  C4'A  O4'A  C3'A  C5'A  negativ
 AVV  chir_09  C4'N  O4'N  C3'N  C5'N  negativ
 AVV  chir_10  PA    O3    O5'A  O1A   both
 AVV  chir_11  PN    O1N   O3    O5'N  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
 AVV  plan-1  C6A   0.020
 AVV  plan-1  N6A   0.020
 AVV  plan-1  HAN6  0.020
 AVV  plan-1  HANA  0.020
 AVV  plan-2  F1A   0.020
 AVV  plan-2  N1A   0.020
 AVV  plan-2  C2A   0.020
 AVV  plan-2  N3A   0.020
 AVV  plan-2  C4A   0.020
 AVV  plan-2  C5A   0.020
 AVV  plan-2  C6A   0.020
 AVV  plan-2  N6A   0.020
 AVV  plan-2  N7A   0.020
 AVV  plan-2  C8A   0.020
 AVV  plan-2  N9A   0.020
 AVV  plan-2  C1'A  0.020
 AVV  plan-2  HC8   0.020

