# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 29 16:56:13 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4OC[C@@H](F)[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
 AVU  AVU  '[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)'  ligand  57  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 (reasonable std)
;

data_comp_AVU
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
 AVU  N1    N  N     0  -0.472   1.1838  -2.7569   4.8754
 AVU  C2    C  CR16  0   0.042   2.3350  -3.0560   5.4730
 AVU  N3    N  N     0  -0.457   3.5659  -2.8801   5.0230
 AVU  C4    C  CR56  0   0.504   3.5708  -2.3528   3.8016
 AVU  C5    C  CR56  0  -0.001   2.4593  -2.0210   3.0461
 AVU  C6    C  CR6   0   0.457   1.2060  -2.2219   3.6505
 AVU  N6    N  NH2   0  -0.820   0.0558  -1.9103   3.0467
 AVU  N7    N  N     0  -0.442   2.8308  -1.5161   1.8283
 AVU  C8    C  CR15  0   0.104   4.1280  -1.5298   1.8531
 AVU  N9    N  NR5   0  -0.548   4.6475  -2.0297   3.0216
 AVU  PA    P  P     0   1.520   7.0859   3.6653   4.1517
 AVU  PB    P  P     0   1.511   4.2829   4.6058   4.5337
 AVU  C1'   C  CH1   0   0.168   6.0288  -2.1920   3.4401
 AVU  O1A   O  O     0  -0.660   7.9520   4.5058   3.3181
 AVU  O1B   O  O     0  -0.669   4.4851   6.0486   4.7109
 AVU  C1R   C  CH2   0  -0.209   1.7748   2.9312  -0.0890
 AVU  C2'   C  CH1   0  -0.054   7.0251  -1.9035   2.3226
 AVU  O2'   O  OH1   0  -0.661   8.1936  -2.6020   2.6494
 AVU  O2A   O  OH1   0  -0.739   7.1039   3.8968   5.7213
 AVU  O2B   O  OH1   0  -0.736   4.0689   3.7153   5.8311
 AVU  C2R   C  CH1   0   0.149   2.0217   1.5133   0.3637
 AVU  F2R   F  F     0  -0.371   3.3910   1.3137   0.5314
 AVU  C3'   C  CH1   0  -0.013   7.2131  -0.3917   2.4747
 AVU  O3'   O  OH1   0  -0.658   8.4113  -0.0015   1.8776
 AVU  O3A   O  O2    0  -0.720   5.5065   3.7966   3.8508
 AVU  C3R   C  CH1   0  -0.072   1.3410   1.4954   1.7268
 AVU  O3R   O  OH1   0  -0.669  -0.0166   1.2194   1.4916
 AVU  C4'   C  CH1   0   0.004   7.1592  -0.2324   4.0012
 AVU  O4'   O  O2    0  -0.487   6.3360  -1.2906   4.4715
 AVU  C4R   C  CH1   0  -0.016   1.5956   2.9281   2.2272
 AVU  O4R   O  O2    0  -0.498   1.8604   3.7229   1.0852
 AVU  C5'   C  CH2   0  -0.200   6.5495   1.0739   4.4709
 AVU  O5'   O  O2    0  -0.583   7.3316   2.1186   3.8811
 AVU  C5R   C  CH2   0  -0.195   2.7807   2.9250   3.1699
 AVU  O5R   O  O2    0  -0.567   3.1091   4.2738   3.5216
 AVU  H2    H  HCR6  0   0.253   2.2458  -3.4948   6.4610
 AVU  HN6   H  HNH2  0   0.404  -0.8088  -1.9850   3.5552
 AVU  HN6A  H  HNH2  0   0.406   0.0486  -1.3840   2.1893
 AVU  H8    H  HCR5  0   0.297   4.7540  -1.2023   1.0379
 AVU  H1'   H  HCH1  0   0.291   6.1320  -3.2100   3.8195
 AVU  H1RA  H  HCH2  0   0.227   0.7818   3.0025  -0.5462
 AVU  H2'   H  HCH1  0   0.270   6.6537  -2.1864   1.3314
 AVU  HO2'  H  HOH1  0   0.461   8.9223  -2.2358   2.1357
 AVU  HO2A  H  HOH1  0   0.513   7.9617   4.1638   6.0820
 AVU  HO2B  H  HOH1  0   0.509   3.5275   4.1279   6.5189
 AVU  H2R   H  HCH1  0   0.254   1.6441   0.7519  -0.3188
 AVU  H3'   H  HCH1  0   0.225   6.3561   0.1257   2.0174
 AVU  HO3'  H  HOH1  0   0.463   8.5195   0.9499   1.9761
 AVU  H3R   H  HCH1  0   0.253   1.7914   0.7482   2.3885
 AVU  HO3R  H  HOH1  0   0.461  -0.5098   1.3708   2.3042
 AVU  H4'   H  HCH1  0   0.259   8.1683  -0.3398   4.4154
 AVU  H4R   H  HCH1  0   0.260   0.7177   3.3208   2.7550
 AVU  H5'   H  HCH2  0   0.232   5.5096   1.1446   4.1387
 AVU  H5'A  H  HCH2  0   0.275   6.5698   1.1451   5.5604
 AVU  H5R   H  HCH2  0   0.252   2.5131   2.3569   4.0643
 AVU  H5RA  H  HCH2  0   0.235   3.6409   2.4475   2.6970
 AVU  H1R   H  HCH2  0   0.256   2.5095   3.2783  -0.8175

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
 AVU  C6   N1    aromatic  1.337  0.020  1.337
 AVU  N1   C2    aromatic  1.331  0.020  1.331
 AVU  N3   C2    aromatic  1.322  0.020  1.322
 AVU  C2   H2    single    0.930  0.020  1.080
 AVU  C4   N3    aromatic  1.330  0.020  1.330
 AVU  N9   C4    aromatic  1.368  0.020  1.368
 AVU  C5   C4    aromatic  1.384  0.020  1.384
 AVU  N7   C5    aromatic  1.370  0.020  1.370
 AVU  C5   C6    aromatic  1.406  0.020  1.406
 AVU  N6   C6    single    1.336  0.020  1.336
 AVU  N6   HN6   single    0.860  0.020  1.020
 AVU  N6   HN6A  single    0.860  0.020  1.020
 AVU  C8   N7    aromatic  1.298  0.020  1.298
 AVU  C8   N9    aromatic  1.373  0.020  1.373
 AVU  C8   H8    single    0.930  0.020  1.080
 AVU  N9   C1'   single    1.452  0.020  1.452
 AVU  O3A  PA    single    1.613  0.020  1.613
 AVU  O1A  PA    double    1.467  0.020  1.467
 AVU  O5'  PA    single    1.589  0.020  1.589
 AVU  PA   O2A   single    1.587  0.020  1.587
 AVU  O5R  PB    single    1.585  0.020  1.585
 AVU  O3A  PB    single    1.618  0.020  1.618
 AVU  O1B  PB    double    1.468  0.020  1.468
 AVU  PB   O2B   single    1.588  0.020  1.588
 AVU  C2'  C1'   single    1.525  0.020  1.525
 AVU  C1'  O4'   single    1.404  0.020  1.404
 AVU  C1'  H1'   single    0.970  0.020  1.090
 AVU  C1R  C2R   single    1.509  0.020  1.509
 AVU  C1R  O4R   single    1.419  0.020  1.419
 AVU  C1R  H1R   single    0.970  0.020  1.090
 AVU  C1R  H1RA  single    0.970  0.020  1.090
 AVU  O2'  C2'   single    1.400  0.020  1.400
 AVU  C2'  C3'   single    1.531  0.020  1.531
 AVU  C2'  H2'   single    0.970  0.020  1.090
 AVU  O2'  HO2'  single    0.850  0.020  0.980
 AVU  O2A  HO2A  single    0.850  0.020  0.980
 AVU  O2B  HO2B  single    0.850  0.020  0.980
 AVU  C2R  F2R   single    1.394  0.020  1.394
 AVU  C2R  C3R   single    1.524  0.020  1.524
 AVU  C2R  H2R   single    0.970  0.020  1.090
 AVU  O3'  C3'   single    1.394  0.020  1.394
 AVU  C3'  C4'   single    1.536  0.020  1.536
 AVU  C3'  H3'   single    0.970  0.020  1.090
 AVU  O3'  HO3'  single    0.850  0.020  0.980
 AVU  O3R  C3R   single    1.405  0.020  1.405
 AVU  C3R  C4R   single    1.539  0.020  1.539
 AVU  C3R  H3R   single    0.970  0.020  1.090
 AVU  O3R  HO3R  single    0.850  0.020  0.980
 AVU  C4'  O4'   single    1.421  0.020  1.421
 AVU  C4'  C5'   single    1.516  0.020  1.516
 AVU  C4'  H4'   single    0.970  0.020  1.090
 AVU  O4R  C4R   single    1.416  0.020  1.416
 AVU  C4R  C5R   single    1.514  0.020  1.514
 AVU  C4R  H4R   single    0.970  0.020  1.090
 AVU  O5'  C5'   single    1.432  0.020  1.432
 AVU  C5'  H5'   single    0.970  0.020  1.090
 AVU  C5'  H5'A  single    0.970  0.020  1.090
 AVU  C5R  O5R   single    1.432  0.020  1.432
 AVU  C5R  H5R   single    0.970  0.020  1.090
 AVU  C5R  H5RA  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
 AVU  C6    N1   C2   119.14  3.000
 AVU  H2    C2   N3   116.12  3.000
 AVU  H2    C2   N1   115.38  3.000
 AVU  N3    C2   N1   128.49  3.000
 AVU  C4    N3   C2   111.63  3.000
 AVU  N9    C4   C5   105.31  3.000
 AVU  C5    C4   N3   126.37  3.000
 AVU  N9    C4   N3   128.32  3.000
 AVU  N7    C5   C6   132.59  3.000
 AVU  C6    C5   C4   116.54  3.000
 AVU  N7    C5   C4   110.85  3.000
 AVU  N6    C6   C5   122.68  3.000
 AVU  N6    C6   N1   119.55  3.000
 AVU  C5    C6   N1   117.77  3.000
 AVU  HN6A  N6   HN6  117.62  3.000
 AVU  HN6A  N6   C6   120.89  3.000
 AVU  HN6   N6   C6   119.63  3.000
 AVU  C8    N7   C5   104.50  3.000
 AVU  H8    C8   N9   122.28  3.000
 AVU  H8    C8   N7   124.23  3.000
 AVU  N9    C8   N7   113.47  3.000
 AVU  C1'   N9   C8   130.22  3.000
 AVU  C1'   N9   C4   123.90  3.000
 AVU  C8    N9   C4   105.87  3.000
 AVU  O5'   PA   O3A  101.47  3.000
 AVU  O5'   PA   O2A  107.98  3.000
 AVU  O3A   PA   O2A  100.59  3.000
 AVU  O2A   PA   O1A  118.16  3.000
 AVU  O5'   PA   O1A  111.69  3.000
 AVU  O3A   PA   O1A  115.18  3.000
 AVU  O5R   PB   O3A  100.70  3.000
 AVU  O3A   PB   O2B   99.57  3.000
 AVU  O5R   PB   O2B  107.72  3.000
 AVU  O2B   PB   O1B  118.11  3.000
 AVU  O3A   PB   O1B  116.00  3.000
 AVU  O5R   PB   O1B  112.65  3.000
 AVU  H1'   C1'  O4'  108.83  3.000
 AVU  H1'   C1'  C2'  111.69  3.000
 AVU  O4'   C1'  C2'  105.90  3.000
 AVU  H1'   C1'  N9   107.11  3.000
 AVU  O4'   C1'  N9   110.37  3.000
 AVU  C2'   C1'  N9   112.90  3.000
 AVU  H1RA  C1R  H1R  108.11  3.000
 AVU  H1RA  C1R  O4R  111.33  3.000
 AVU  H1R   C1R  O4R  109.53  3.000
 AVU  H1RA  C1R  C2R  109.56  3.000
 AVU  H1R   C1R  C2R  112.90  3.000
 AVU  O4R   C1R  C2R  105.44  3.000
 AVU  H2'   C2'  C3'  112.73  3.000
 AVU  H2'   C2'  O2'  111.42  3.000
 AVU  C3'   C2'  O2'  111.53  3.000
 AVU  H2'   C2'  C1'  113.12  3.000
 AVU  C3'   C2'  C1'  101.21  3.000
 AVU  O2'   C2'  C1'  106.26  3.000
 AVU  HO2'  O2'  C2'  108.49  3.000
 AVU  HO2A  O2A  PA   114.76  3.000
 AVU  HO2B  O2B  PB   114.64  3.000
 AVU  H2R   C2R  C3R  113.40  3.000
 AVU  H2R   C2R  F2R  108.40  3.000
 AVU  C3R   C2R  F2R  109.24  3.000
 AVU  H2R   C2R  C1R  114.32  3.000
 AVU  C3R   C2R  C1R  101.91  3.000
 AVU  F2R   C2R  C1R  109.35  3.000
 AVU  H3'   C3'  C4'  109.69  3.000
 AVU  H3'   C3'  O3'  111.08  3.000
 AVU  C4'   C3'  O3'  115.26  3.000
 AVU  H3'   C3'  C2'  109.11  3.000
 AVU  C4'   C3'  C2'  101.35  3.000
 AVU  O3'   C3'  C2'  109.83  3.000
 AVU  HO3'  O3'  C3'  109.23  3.000
 AVU  PB    O3A  PA   134.61  3.000
 AVU  H3R   C3R  C4R  111.76  3.000
 AVU  H3R   C3R  O3R  111.38  3.000
 AVU  C4R   C3R  O3R  113.40  3.000
 AVU  H3R   C3R  C2R  111.39  3.000
 AVU  C4R   C3R  C2R  101.89  3.000
 AVU  O3R   C3R  C2R  106.51  3.000
 AVU  HO3R  O3R  C3R  108.84  3.000
 AVU  H4'   C4'  C5'  109.73  3.000
 AVU  H4'   C4'  O4'  109.60  3.000
 AVU  C5'   C4'  O4'  107.83  3.000
 AVU  H4'   C4'  C3'  109.46  3.000
 AVU  C5'   C4'  C3'  114.29  3.000
 AVU  O4'   C4'  C3'  105.79  3.000
 AVU  C4'   O4'  C1'  111.21  3.000
 AVU  H4R   C4R  C5R  109.11  3.000
 AVU  H4R   C4R  O4R  109.67  3.000
 AVU  C5R   C4R  O4R  110.91  3.000
 AVU  H4R   C4R  C3R  110.93  3.000
 AVU  C5R   C4R  C3R  109.27  3.000
 AVU  O4R   C4R  C3R  106.94  3.000
 AVU  C4R   O4R  C1R  110.05  3.000
 AVU  H5'A  C5'  H5'  108.45  3.000
 AVU  H5'A  C5'  O5'  110.68  3.000
 AVU  H5'   C5'  O5'  110.30  3.000
 AVU  H5'A  C5'  C4'  110.96  3.000
 AVU  H5'   C5'  C4'  110.11  3.000
 AVU  O5'   C5'  C4'  106.34  3.000
 AVU  C5'   O5'  PA   123.74  3.000
 AVU  H5RA  C5R  H5R  108.67  3.000
 AVU  H5RA  C5R  O5R  109.74  3.000
 AVU  H5R   C5R  O5R  110.18  3.000
 AVU  H5RA  C5R  C4R  110.35  3.000
 AVU  H5R   C5R  C4R  108.59  3.000
 AVU  O5R   C5R  C4R  109.29  3.000
 AVU  C5R   O5R  PB   121.59  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
 AVU  CONST_01  C4    C5   C6   N1      0.00   0.0  0
 AVU  CONST_02  N7    C5   C6   N1    180.00   0.0  0
 AVU  CONST_03  C4    N3   C2   N1      0.00   0.0  0
 AVU  CONST_04  C5    C6   N1   C2      0.00   0.0  0
 AVU  CONST_05  N9    C4   N3   C2    180.00   0.0  0
 AVU  CONST_06  C5    C4   N3   C2      0.00   0.0  0
 AVU  CONST_07  C6    N1   C2   N3      0.00   0.0  0
 AVU  CONST_08  C8    N9   C4   N3    180.00   0.0  0
 AVU  CONST_09  N7    C5   C4   N3    180.00   0.0  0
 AVU  CONST_10  C6    C5   C4   N3      0.00   0.0  0
 AVU  CONST_11  N7    C8   N9   C4      0.00   0.0  0
 AVU  CONST_12  C8    N7   C5   C4      0.00   0.0  0
 AVU  CONST_13  C8    N9   C4   C5      0.00   0.0  0
 AVU  CONST_14  N9    C8   N7   C5      0.00   0.0  0
 AVU  CONST_15  N9    C4   C5   C6    180.00   0.0  0
 AVU  CONST_16  C8    N7   C5   C6    180.00   0.0  0
 AVU  CONST_17  N9    C4   C5   N7      0.00   0.0  0
 AVU  CONST_18  C1'   N9   C4   N3      0.00   0.0  0
 AVU  CONST_19  C1'   N9   C4   C5    180.00   0.0  0
 AVU  CONST_20  C1'   N9   C8   N7    180.00   0.0  0
 AVU  CONST_21  N6    C6   N1   C2    180.00   0.0  0
 AVU  CONST_22  N6    C6   C5   C4    180.00   0.0  0
 AVU  CONST_23  N7    C5   C6   N6      0.00   0.0  0
 AVU  CONST_24  H2    C2   N3   C4    180.00   0.0  0
 AVU  CONST_25  H8    C8   N9   C4    180.00   0.0  0
 AVU  CONST_26  HN6   N6   C6   N1      0.00   0.0  0
 AVU  CONST_27  HN6A  N6   C6   N1    180.00   0.0  0
 AVU  Var_01    H1R   C1R  O4R  C4R  -145.31  30.0  1
 AVU  Var_02    C4'   C5'  O5'  PA   -177.36  30.0  3
 AVU  Var_03    C4R   C5R  O5R  PB    178.15  30.0  1
 AVU  Var_04    O5R   PB   O3A  PA    174.86  30.0  3
 AVU  Var_05    O1A   PA   O3A  PB    -99.02  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
 AVU  chir_03  C1'  N9   C2'  O4'  negativ
 AVU  chir_04  C2'  O2'  C3'  C1'  positiv
 AVU  chir_05  C2R  C1R  F2R  C3R  negativ
 AVU  chir_06  C3'  C2'  O3'  C4'  positiv
 AVU  chir_07  C3R  C2R  O3R  C4R  positiv
 AVU  chir_08  C4'  O4'  C3'  C5'  negativ
 AVU  chir_09  C4R  C3R  O4R  C5R  positiv
 AVU  chir_10  PA   O1A  O5'  O2A  both
 AVU  chir_11  PB   O1B  O3A  O5R  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
 AVU  plan-1  C6    0.020
 AVU  plan-1  N6    0.020
 AVU  plan-1  HN6   0.020
 AVU  plan-1  HN6A  0.020
 AVU  plan-2  N1    0.020
 AVU  plan-2  C2    0.020
 AVU  plan-2  N3    0.020
 AVU  plan-2  C4    0.020
 AVU  plan-2  C5    0.020
 AVU  plan-2  C6    0.020
 AVU  plan-2  N6    0.020
 AVU  plan-2  N7    0.020
 AVU  plan-2  C8    0.020
 AVU  plan-2  N9    0.020
 AVU  plan-2  C1'   0.020
 AVU  plan-2  H2    0.020
 AVU  plan-2  H8    0.020

