# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Tue Jun 23 02:37:15 2020
#   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  56  36  .  2021-08-06  2021-08-06  
;
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   1.363  -0.8601  -1.5369   0.4957
 AVV  PN    P  P      0   1.345  -2.3738   0.8778   1.0405
 AVV  F1A   F  F      0  -0.289   7.8769   2.3429  -0.1873
 AVV  N1A   N  N      0  -0.505   6.5309   2.6794   1.5428
 AVV  O1A   O  OP    -1  -0.788  -1.8964  -2.6135   0.5300
 AVV  O1N   O  OP    -1  -0.798  -2.8962   0.1210   2.2197
 AVV  C2A   C  CR6    0   0.572   6.7366   2.0256   0.4240
 AVV  O2A   O  O      0  -0.785   0.0711  -1.3489   1.6567
 AVV  O2N   O  O      0  -0.788  -1.6152   2.1527   1.2313
 AVV  O3    O  O2     0  -0.734  -1.5219  -0.1076   0.0434
 AVV  N3A   N  N      0  -0.487   6.0218   1.1248  -0.1891
 AVV  C4A   C  CR56   0   0.497   4.9015   0.8733   0.4936
 AVV  C5A   C  CR56   0  -0.016   4.5187   1.4652   1.6859
 AVV  C6A   C  CR6    0   0.471   5.4024   2.4227   2.2197
 AVV  N6A   N  NH2    0  -0.809   5.1668   3.0719   3.3548
 AVV  N7A   N  N      0  -0.453   3.3061   0.9789   2.0997
 AVV  C8A   C  CR15   0   0.072   2.9673   0.1165   1.1871
 AVV  N9A   N  NR5    0  -0.539   3.8993   0.0090   0.1828
 AVV  C1'A  C  CH1    0   0.223   3.8526  -0.8597  -0.9705
 AVV  C1'N  C  CH2    0  -0.177  -7.4615   0.8379  -1.1719
 AVV  C2'A  C  CH1    0  -0.047   4.1455  -2.3256  -0.6507
 AVV  O2'A  O  OH1    0  -0.652   5.5229  -2.5485  -0.6417
 AVV  C2'N  C  CH1    0  -0.017  -7.8073   1.8879  -0.1199
 AVV  O2'N  O  OH1    0  -0.668  -9.1161   2.3824  -0.1697
 AVV  C3'A  C  CH1    0  -0.034   3.3782  -3.0293  -1.7748
 AVV  O3'A  O  OH1    0  -0.668   4.0804  -2.9548  -2.9876
 AVV  C3'N  C  CH1    0  -0.038  -6.8029   2.9870  -0.4659
 AVV  O3'N  O  OH1    0  -0.671  -7.2073   3.7200  -1.5964
 AVV  C4'A  C  CH1    0  -0.043   2.1381  -2.1523  -1.8660
 AVV  O4'A  O  O2     0  -0.488   2.5660  -0.8341  -1.5089
 AVV  C4'N  C  CH1    0  -0.021  -5.5741   2.1632  -0.8351
 AVV  O4'N  O  O2     0  -0.498  -6.0553   0.9086  -1.3118
 AVV  C5'A  C  CH2    0  -0.150   1.0437  -2.6347  -0.9311
 AVV  O5'A  O  O2     0  -0.616   0.0176  -1.6737  -0.8931
 AVV  C5'N  C  CH2    0  -0.145  -4.6532   1.9574   0.3516
 AVV  O5'N  O  O2     0  -0.617  -3.5875   1.1246  -0.0461
 AVV  HAN6  H  HNH2   0   0.417   4.3154   2.9228   3.8679
 AVV  HANA  H  HNH2   0   0.409   5.8093   3.7697   3.6886
 AVV  HC1'  H  HCH1   0   0.260   4.5957  -0.4718  -1.6768
 AVV  HC1B  H  HCH2   0   0.203  -7.9719   1.0701  -2.1153
 AVV  HC2'  H  HCH1   0   0.249   3.6883  -2.5842   0.3126
 AVV  HO2'  H  HOH1   0   0.469   5.7017  -3.3601  -0.1565
 AVV  HC2A  H  HCH1   0   0.222  -7.5650   1.4981   0.8781
 AVV  HO2A  H  HOH1   0   0.463  -9.7270   1.6753   0.0589
 AVV  HC3'  H  HCH1   0   0.252   3.1270  -4.0658  -1.5116
 AVV  HO3'  H  HOH1   0   0.450   4.9886  -3.2345  -2.8239
 AVV  HC3A  H  HCH1   0   0.241  -6.6109   3.6495   0.3892
 AVV  HO3A  H  HOH1   0   0.450  -8.0990   4.0487  -1.4393
 AVV  HC4'  H  HCH1   0   0.262   1.7539  -2.1168  -2.8897
 AVV  HC4A  H  HCH1   0   0.242  -5.0099   2.6611  -1.6326
 AVV  HC5'  H  HCH2   0   0.227   0.6733  -3.5956  -1.3078
 AVV  HC5A  H  HCH2   0   0.206   1.4555  -2.8214   0.0678
 AVV  HC5B  H  HCH2   0   0.212  -4.2928   2.9391   0.6819
 AVV  HC5C  H  HCH2   0   0.206  -5.2069   1.5142   1.1892
 AVV  HC8   H  HCR5   0   0.327   2.0436  -0.4519   1.1893
 AVV  HC1A  H  HCH2   0   0.232  -7.7408  -0.1752  -0.8743

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    deloc     1.500  0.020  1.500
 AVV  PA    O3    single    1.639  0.020  1.639
 AVV  PA    O5'A  single    1.649  0.020  1.649
 AVV  PA    O1A   deloc     1.495  0.020  1.495
 AVV  O2N   PN    deloc     1.496  0.020  1.496
 AVV  O1N   PN    deloc     1.495  0.020  1.495
 AVV  PN    O3    single    1.640  0.020  1.640
 AVV  PN    O5'N  single    1.648  0.020  1.648
 AVV  C2A   F1A   single    1.332  0.020  1.332
 AVV  C6A   N1A   aromatic  1.341  0.020  1.341
 AVV  N1A   C2A   aromatic  1.312  0.020  1.312
 AVV  N3A   C2A   aromatic  1.303  0.020  1.303
 AVV  C4A   N3A   aromatic  1.336  0.020  1.336
 AVV  C5A   C4A   aromatic  1.385  0.020  1.385
 AVV  N9A   C4A   aromatic  1.359  0.020  1.359
 AVV  N7A   C5A   aromatic  1.370  0.020  1.370
 AVV  C5A   C6A   aromatic  1.408  0.020  1.408
 AVV  N6A   C6A   single    1.329  0.020  1.329
 AVV  N6A   HAN6  single    0.860  0.020  1.020
 AVV  N6A   HANA  single    0.860  0.020  1.020
 AVV  N7A   C8A   aromatic  1.301  0.020  1.301
 AVV  C8A   N9A   aromatic  1.374  0.020  1.374
 AVV  C8A   HC8   single    0.930  0.020  1.080
 AVV  N9A   C1'A  single    1.445  0.020  1.445
 AVV  C2'A  C1'A  single    1.529  0.020  1.529
 AVV  C1'A  O4'A  single    1.395  0.020  1.395
 AVV  C1'A  HC1'  single    0.970  0.020  1.090
 AVV  O4'N  C1'N  single    1.415  0.020  1.415
 AVV  C1'N  C2'N  single    1.526  0.020  1.526
 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    1.532  0.020  1.532
 AVV  C2'A  O2'A  single    1.395  0.020  1.395
 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    1.529  0.020  1.529
 AVV  C2'N  O2'N  single    1.400  0.020  1.400
 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    1.522  0.020  1.522
 AVV  C3'A  O3'A  single    1.403  0.020  1.403
 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    1.525  0.020  1.525
 AVV  O3'N  C3'N  single    1.407  0.020  1.407
 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    1.431  0.020  1.431
 AVV  C4'A  HC4'  single    0.970  0.020  1.090
 AVV  O4'N  C4'N  single    1.426  0.020  1.426
 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    1.406  0.020  1.406
 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    1.410  0.020  1.410
 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     93.15  3.000
 AVV  O5'A  PA    O2A   109.39  3.000
 AVV  O3    PA    O2A   110.80  3.000
 AVV  O5'A  PA    O1A   109.18  3.000
 AVV  O3    PA    O1A   110.76  3.000
 AVV  O2A   PA    O1A   120.19  3.000
 AVV  O5'N  PN    O3     94.11  3.000
 AVV  O5'N  PN    O2N   109.27  3.000
 AVV  O3    PN    O2N   109.04  3.000
 AVV  O5'N  PN    O1N   109.78  3.000
 AVV  O3    PN    O1N   110.90  3.000
 AVV  O2N   PN    O1N   120.53  3.000
 AVV  C6A   N1A   C2A   117.84  3.000
 AVV  N3A   C2A   N1A   131.27  3.000
 AVV  N3A   C2A   F1A   114.73  3.000
 AVV  N1A   C2A   F1A   114.00  3.000
 AVV  PN    O3    PA    124.46  3.000
 AVV  C4A   N3A   C2A   110.47  3.000
 AVV  N9A   C4A   C5A   105.35  3.000
 AVV  N9A   C4A   N3A   128.40  3.000
 AVV  C5A   C4A   N3A   126.25  3.000
 AVV  N7A   C5A   C6A   133.01  3.000
 AVV  C6A   C5A   C4A   116.33  3.000
 AVV  N7A   C5A   C4A   110.66  3.000
 AVV  N6A   C6A   C5A   123.01  3.000
 AVV  N6A   C6A   N1A   119.15  3.000
 AVV  C5A   C6A   N1A   117.84  3.000
 AVV  HANA  N6A   HAN6  118.33  3.000
 AVV  HANA  N6A   C6A   120.62  3.000
 AVV  HAN6  N6A   C6A   120.92  3.000
 AVV  C8A   N7A   C5A   104.71  3.000
 AVV  HC8   C8A   N9A   122.55  3.000
 AVV  HC8   C8A   N7A   124.61  3.000
 AVV  N9A   C8A   N7A   112.83  3.000
 AVV  C1'A  N9A   C8A   127.48  3.000
 AVV  C1'A  N9A   C4A   126.06  3.000
 AVV  C8A   N9A   C4A   106.45  3.000
 AVV  HC1'  C1'A  O4'A  111.72  3.000
 AVV  HC1'  C1'A  C2'A  110.14  3.000
 AVV  O4'A  C1'A  C2'A  105.97  3.000
 AVV  HC1'  C1'A  N9A   106.25  3.000
 AVV  O4'A  C1'A  N9A   109.08  3.000
 AVV  C2'A  C1'A  N9A   113.79  3.000
 AVV  HC1B  C1'N  HC1A  108.16  3.000
 AVV  HC1B  C1'N  O4'N  111.51  3.000
 AVV  HC1A  C1'N  O4'N  109.11  3.000
 AVV  HC1B  C1'N  C2'N  109.97  3.000
 AVV  HC1A  C1'N  C2'N  113.10  3.000
 AVV  O4'N  C1'N  C2'N  105.01  3.000
 AVV  HC2'  C2'A  C3'A  109.10  3.000
 AVV  HC2'  C2'A  O2'A  111.59  3.000
 AVV  C3'A  C2'A  O2'A  115.20  3.000
 AVV  HC2'  C2'A  C1'A  109.26  3.000
 AVV  O2'A  C2'A  C1'A  110.10  3.000
 AVV  C3'A  C2'A  C1'A  101.01  3.000
 AVV  HO2'  O2'A  C2'A  108.74  3.000
 AVV  HC2A  C2'N  C3'N  108.41  3.000
 AVV  HC2A  C2'N  O2'N  111.34  3.000
 AVV  C3'N  C2'N  O2'N  110.63  3.000
 AVV  HC2A  C2'N  C1'N  109.40  3.000
 AVV  O2'N  C2'N  C1'N  115.49  3.000
 AVV  C3'N  C2'N  C1'N  100.94  3.000
 AVV  HO2A  O2'N  C2'N  109.00  3.000
 AVV  HC3'  C3'A  C4'A  111.83  3.000
 AVV  HC3'  C3'A  O3'A  111.81  3.000
 AVV  C4'A  C3'A  O3'A  108.99  3.000
 AVV  HC3'  C3'A  C2'A  111.84  3.000
 AVV  O3'A  C3'A  C2'A  111.04  3.000
 AVV  C4'A  C3'A  C2'A  100.80  3.000
 AVV  HO3'  O3'A  C3'A  108.01  3.000
 AVV  HC3A  C3'N  C4'N  111.93  3.000
 AVV  HC3A  C3'N  O3'N  111.19  3.000
 AVV  C4'N  C3'N  O3'N  108.58  3.000
 AVV  HC3A  C3'N  C2'N  111.85  3.000
 AVV  O3'N  C3'N  C2'N  111.57  3.000
 AVV  C4'N  C3'N  C2'N  101.30  3.000
 AVV  HO3A  O3'N  C3'N  108.23  3.000
 AVV  HC4'  C4'A  C5'A  109.48  3.000
 AVV  HC4'  C4'A  O4'A  107.97  3.000
 AVV  C5'A  C4'A  O4'A  110.77  3.000
 AVV  HC4'  C4'A  C3'A  111.16  3.000
 AVV  O4'A  C4'A  C3'A  105.80  3.000
 AVV  C5'A  C4'A  C3'A  111.56  3.000
 AVV  C4'A  O4'A  C1'A  110.80  3.000
 AVV  HC4A  C4'N  C5'N  108.56  3.000
 AVV  HC4A  C4'N  O4'N  109.28  3.000
 AVV  C5'N  C4'N  O4'N  110.31  3.000
 AVV  HC4A  C4'N  C3'N  110.21  3.000
 AVV  C5'N  C4'N  C3'N  111.92  3.000
 AVV  O4'N  C4'N  C3'N  106.52  3.000
 AVV  C4'N  O4'N  C1'N  110.26  3.000
 AVV  HC5A  C5'A  HC5'  106.90  3.000
 AVV  HC5A  C5'A  O5'A  111.45  3.000
 AVV  HC5'  C5'A  O5'A  111.20  3.000
 AVV  HC5A  C5'A  C4'A  110.14  3.000
 AVV  HC5'  C5'A  C4'A  108.09  3.000
 AVV  O5'A  C5'A  C4'A  108.99  3.000
 AVV  C5'A  O5'A  PA    117.90  3.000
 AVV  HC5C  C5'N  HC5B  107.30  3.000
 AVV  HC5C  C5'N  O5'N  110.99  3.000
 AVV  HC5B  C5'N  O5'N  111.43  3.000
 AVV  HC5C  C5'N  C4'N  110.23  3.000
 AVV  HC5B  C5'N  C4'N  108.29  3.000
 AVV  O5'N  C5'N  C4'N  108.58  3.000
 AVV  C5'N  O5'N  PN    117.34  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
 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    180.00   0.0  0
 AVV  CONST_28  HANA  N6A   C6A   N1A      0.00   0.0  0
 AVV  Var_01    HC1A  C1'N  O4'N  C4'N  -141.95  30.0  1
 AVV  Var_02    C4'A  C5'A  O5'A  PA    -150.03  30.0  2
 AVV  Var_03    C4'N  C5'N  O5'N  PN     174.17  30.0  3
 AVV  Var_04    O2N   PN    O3    PA     114.14  30.0  2
 AVV  Var_05    O2A   PA    O3    PN     -56.60  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

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

