# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 14:52:29 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: [[(1~{R},3~{S},5~{S})-3-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1
#
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
 ET9  ET9  '[[(1~{R},3~{S},5~{S})-3-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate'  ligand  50  32  .  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_ET9
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
 ET9  C1'  C  CR15  0  -0.204  180.3134  276.3601  -124.1898
 ET9  C2   C  CR6   0   0.667  181.2476  272.1752  -125.2713
 ET9  C2'  C  CH2   0  -0.487  180.2929  276.2353  -122.6628
 ET9  C3'  C  CR15  0   0.080  180.9933  277.5078  -122.1901
 ET9  C4   C  CR56  0   0.638  181.6707  274.4367  -125.0395
 ET9  C4'  C  CR15  0  -0.353  180.4099  278.5748  -123.1168
 ET9  C5   C  CR56  0  -0.113  182.9528  274.2626  -125.4851
 ET9  C5'  C  CH2   0  -0.211  181.1620  279.8835  -123.1455
 ET9  C6   C  CR6   0   0.415  183.3995  272.9367  -125.8501
 ET9  C6'  C  CR5   0   0.165  180.2693  277.8595  -124.4394
 ET9  C8   C  CR15  0   0.090  182.7202  276.3294  -125.0687
 ET9  N1   N  N     0  -0.539  182.4576  271.9457  -125.7059
 ET9  N2   N  NH2   0  -0.827  180.3861  271.1600  -125.1264
 ET9  N3   N  NR16  0  -0.742  180.7880  273.4126  -124.9143
 ET9  N7   N  N     0  -0.442  183.5969  275.4721  -125.4948
 ET9  N9   N  NR5   0  -0.491  181.5057  275.7513  -124.7774
 ET9  O1A  O  OH1   0  -0.766  183.5194  281.7134  -122.7198
 ET9  O1B  O  O     0  -0.670  182.4982  280.9637  -119.8015
 ET9  O1G  O  OH1   0  -0.695  186.9711  282.0989  -119.2401
 ET9  O2A  O  O     0  -0.661  185.0170  279.8004  -123.7193
 ET9  O2B  O  OH1   0  -0.693  183.5464  278.5902  -119.2851
 ET9  O2G  O  OH1   0  -0.708  184.8310  282.8429  -118.4389
 ET9  O3'  O  OH1   0  -0.662  180.7678  277.8604  -120.8533
 ET9  O3A  O  O2    0  -0.697  183.8034  279.4686  -121.5082
 ET9  O3B  O  O2    0  -0.680  185.0295  280.5744  -119.6102
 ET9  O3G  O  O     0  -0.713  185.1555  282.7086  -121.0284
 ET9  O5'  O  O2    0  -0.573  182.4853  279.6613  -123.6652
 ET9  PA   P  P     0   1.486  183.8067  280.1935  -122.9871
 ET9  PB   P  P     0   1.477  183.5709  279.9831  -120.0165
 ET9  PG   P  P     0   1.513  185.4679  282.1350  -119.6932
 ET9  H1   H  HCR5  0   0.309  179.4529  275.8703  -124.6475
 ET9  H2   H  HCH2  0   0.263  179.2539  276.2456  -122.3248
 ET9  H3   H  HCH2  0   0.270  180.7581  275.3173  -122.3017
 ET9  H4   H  HCR5  0   0.217  182.0690  277.4009  -122.3847
 ET9  H5   H  HCR5  0   0.288  179.4030  278.8086  -122.7435
 ET9  H6   H  H     0   0.253  180.0834  279.4757  -125.7838
 ET9  H7   H  H     0   0.258  180.0001  277.7912  -126.5229
 ET9  H8   H  HCH2  0   0.261  181.1929  280.3083  -122.1401
 ET9  H9   H  HCH2  0   0.270  180.6706  280.6106  -123.7919
 ET9  H10  H  HCR5  0   0.289  182.8797  277.3894  -124.9525
 ET9  H11  H  HNH2  0   0.412  180.6486  270.2646  -125.5006
 ET9  H12  H  HNH2  0   0.414  179.4075  271.3155  -124.9543
 ET9  H13  H  HNR6  0   0.441  179.8349  273.5476  -124.6085
 ET9  H14  H  HOH1  0   0.502  184.1696  282.2005  -122.1282
 ET9  H15  H  HOH1  0   0.522  187.6035  281.8090  -119.9137
 ET9  H16  H  HOH1  0   0.522  183.2522  278.6228  -118.3624
 ET9  H17  H  HOH1  0   0.516  183.9584  283.2364  -118.5817
 ET9  H18  H  HOH1  0   0.455  181.2960  277.2878  -120.2895
 ET9  C44  C  C2    0  -0.574  180.1089  278.4034  -125.6361
 ET9  O6   O  O     0  -0.495  184.5270  272.6841  -126.2596

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
 ET9  O6   C6   double    1.226  0.020  1.226
 ET9  C6   C5   single    1.446  0.020  1.446
 ET9  C6   N1   single    1.375  0.020  1.375
 ET9  N7   C5   aromatic  1.370  0.020  1.370
 ET9  N7   C8   aromatic  1.298  0.020  1.298
 ET9  C5   C4   aromatic  1.368  0.020  1.368
 ET9  N1   C2   double    1.306  0.020  1.306
 ET9  C44  C6'  double    1.324  0.020  1.324
 ET9  C8   N9   aromatic  1.376  0.020  1.376
 ET9  C4   N9   aromatic  1.351  0.020  1.351
 ET9  C4   N3   single    1.358  0.020  1.358
 ET9  C2   N3   single    1.367  0.020  1.367
 ET9  C2   N2   single    1.339  0.020  1.339
 ET9  N9   C1'  single    1.462  0.020  1.462
 ET9  C6'  C1'  single    1.521  0.020  1.521
 ET9  C6'  C4'  single    1.510  0.020  1.510
 ET9  C1'  C2'  single    1.532  0.020  1.532
 ET9  O2A  PA   double    1.468  0.020  1.468
 ET9  O5'  C5'  single    1.439  0.020  1.439
 ET9  O5'  PA   single    1.578  0.020  1.578
 ET9  C5'  C4'  single    1.510  0.020  1.510
 ET9  PA   O1A  single    1.570  0.020  1.570
 ET9  PA   O3A  single    1.647  0.020  1.647
 ET9  C4'  C3'  single    1.529  0.020  1.529
 ET9  C2'  C3'  single    1.527  0.020  1.527
 ET9  C3'  O3'  single    1.401  0.020  1.401
 ET9  O3A  PB   single    1.595  0.020  1.595
 ET9  O1B  PB   double    1.469  0.020  1.469
 ET9  PB   O2B  single    1.573  0.020  1.573
 ET9  PB   O3B  single    1.625  0.020  1.625
 ET9  O3G  PG   double    1.486  0.020  1.486
 ET9  O1G  PG   single    1.570  0.020  1.570
 ET9  O3B  PG   single    1.623  0.020  1.623
 ET9  PG   O2G  single    1.575  0.020  1.575
 ET9  C1'  H1   single    0.970  0.020  1.090
 ET9  C2'  H2   single    0.970  0.020  1.090
 ET9  C2'  H3   single    0.970  0.020  1.090
 ET9  C3'  H4   single    0.970  0.020  1.090
 ET9  C4'  H5   single    0.970  0.020  1.090
 ET9  C44  H6   single    0.930  0.020  1.080
 ET9  C44  H7   single    0.930  0.020  1.080
 ET9  C5'  H8   single    0.970  0.020  1.090
 ET9  C5'  H9   single    0.970  0.020  1.090
 ET9  C8   H10  single    0.930  0.020  1.080
 ET9  N2   H11  single    0.890  0.020  1.040
 ET9  N2   H12  single    0.890  0.020  1.040
 ET9  N3   H13  single    0.860  0.020  1.020
 ET9  O1A  H14  single    0.850  0.020  0.980
 ET9  O1G  H15  single    0.850  0.020  0.980
 ET9  O2B  H16  single    0.850  0.020  0.980
 ET9  O2G  H17  single    0.850  0.020  0.980
 ET9  O3'  H18  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
 ET9  H1   C1'  N9   106.72  3.000
 ET9  H1   C1'  C6'  110.55  3.000
 ET9  N9   C1'  C6'  111.60  3.000
 ET9  H1   C1'  C2'  111.79  3.000
 ET9  C6'  C1'  C2'  104.09  3.000
 ET9  N9   C1'  C2'  112.18  3.000
 ET9  N3   C2   N2   116.20  3.000
 ET9  N2   C2   N1   119.92  3.000
 ET9  N3   C2   N1   123.87  3.000
 ET9  H3   C2'  H2   108.12  3.000
 ET9  H3   C2'  C3'  113.78  3.000
 ET9  H2   C2'  C3'  109.42  3.000
 ET9  H3   C2'  C1'  113.13  3.000
 ET9  H2   C2'  C1'  108.67  3.000
 ET9  C3'  C2'  C1'  103.56  3.000
 ET9  H4   C3'  O3'  110.56  3.000
 ET9  H4   C3'  C4'  109.53  3.000
 ET9  O3'  C3'  C4'  109.95  3.000
 ET9  H4   C3'  C2'  108.25  3.000
 ET9  O3'  C3'  C2'  115.55  3.000
 ET9  C4'  C3'  C2'  102.64  3.000
 ET9  N9   C4   N3   129.56  3.000
 ET9  N3   C4   C5   122.90  3.000
 ET9  N9   C4   C5   107.54  3.000
 ET9  H5   C4'  C6'  108.24  3.000
 ET9  H5   C4'  C5'  106.17  3.000
 ET9  C6'  C4'  C5'  116.12  3.000
 ET9  H5   C4'  C3'  107.00  3.000
 ET9  C5'  C4'  C3'  115.24  3.000
 ET9  C6'  C4'  C3'  103.64  3.000
 ET9  N7   C5   C6   131.47  3.000
 ET9  N7   C5   C4   109.30  3.000
 ET9  C6   C5   C4   119.23  3.000
 ET9  H9   C5'  H8   107.41  3.000
 ET9  H9   C5'  O5'  107.67  3.000
 ET9  H8   C5'  O5'  111.51  3.000
 ET9  H9   C5'  C4'  111.41  3.000
 ET9  H8   C5'  C4'  109.50  3.000
 ET9  O5'  C5'  C4'  109.34  3.000
 ET9  O6   C6   N1   121.11  3.000
 ET9  N1   C6   C5   115.01  3.000
 ET9  O6   C6   C5   123.88  3.000
 ET9  C44  C6'  C4'  127.46  3.000
 ET9  C4'  C6'  C1'  108.70  3.000
 ET9  C44  C6'  C1'  123.84  3.000
 ET9  H10  C8   N9   121.38  3.000
 ET9  H10  C8   N7   125.78  3.000
 ET9  N9   C8   N7   112.83  3.000
 ET9  C6   N1   C2   122.89  3.000
 ET9  H12  N2   H11  117.10  3.000
 ET9  H12  N2   C2   121.81  3.000
 ET9  H11  N2   C2   117.83  3.000
 ET9  H13  N3   C4   122.72  3.000
 ET9  H13  N3   C2   121.14  3.000
 ET9  C4   N3   C2   116.10  3.000
 ET9  C8   N7   C5   105.25  3.000
 ET9  C8   N9   C4   105.07  3.000
 ET9  C4   N9   C1'  125.66  3.000
 ET9  C8   N9   C1'  129.03  3.000
 ET9  H14  O1A  PA   116.82  3.000
 ET9  H15  O1G  PG   115.55  3.000
 ET9  H16  O2B  PB   114.68  3.000
 ET9  H17  O2G  PG   115.46  3.000
 ET9  H18  O3'  C3'  108.73  3.000
 ET9  PB   O3A  PA   134.27  3.000
 ET9  PG   O3B  PB   125.40  3.000
 ET9  PA   O5'  C5'  124.26  3.000
 ET9  O5'  PA   O3A  103.64  3.000
 ET9  O3A  PA   O2A  109.37  3.000
 ET9  O5'  PA   O2A  112.69  3.000
 ET9  O3A  PA   O1A  105.84  3.000
 ET9  O5'  PA   O1A  104.27  3.000
 ET9  O2A  PA   O1A  119.67  3.000
 ET9  O3B  PB   O3A  102.73  3.000
 ET9  O3B  PB   O2B  102.70  3.000
 ET9  O3A  PB   O2B   98.71  3.000
 ET9  O3B  PB   O1B  112.07  3.000
 ET9  O2B  PB   O1B  120.76  3.000
 ET9  O3A  PB   O1B  117.30  3.000
 ET9  O3G  PG   O3B  111.11  3.000
 ET9  O3B  PG   O2G  106.40  3.000
 ET9  O3G  PG   O2G  117.19  3.000
 ET9  O2G  PG   O1G   99.65  3.000
 ET9  O3B  PG   O1G  102.81  3.000
 ET9  O3G  PG   O1G  117.98  3.000
 ET9  H7   C44  H6   116.48  3.000
 ET9  H7   C44  C6'  121.32  3.000
 ET9  H6   C44  C6'  122.20  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
 ET9  CONST_01  C8   N7   C5   C4      0.00   0.0  0
 ET9  CONST_02  N7   C8   N9   C4      0.00   0.0  0
 ET9  CONST_03  N9   C8   N7   C5      0.00   0.0  0
 ET9  CONST_04  C8   N9   C4   C5      0.00   0.0  0
 ET9  CONST_05  N9   C4   C5   N7      0.00   0.0  0
 ET9  CONST_06  N7   C8   N9   C1'   180.00   0.0  0
 ET9  CONST_07  C5   C4   N9   C1'   180.00   0.0  0
 ET9  CONST_08  N3   C4   N9   C1'     0.00   0.0  0
 ET9  CONST_09  N1   C2   N3   C4      0.00   0.0  0
 ET9  CONST_10  N3   C2   N1   C6      0.00   0.0  0
 ET9  CONST_11  N2   C2   N3   C4    180.00   0.0  0
 ET9  CONST_12  N2   C2   N1   C6    180.00   0.0  0
 ET9  CONST_13  H10  C8   N9   C1'     0.00   0.0  0
 ET9  CONST_14  H13  N3   C2   N1    180.00   0.0  0
 ET9  CONST_15  H11  N2   C2   N1      0.00   0.0  0
 ET9  CONST_16  H12  N2   C2   N1    180.00   0.0  0
 ET9  Var_01    H6   C44  C6'  C1'  -179.87   0.0  2
 ET9  Var_02    O2A  PA   O5'  C5'   179.00  30.0  3
 ET9  Var_03    H8   C5'  O5'  PA    -10.10  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
 ET9  chir_01  C1'  N9   C6'  C2'  positiv
 ET9  chir_02  C3'  O3'  C4'  C2'  positiv
 ET9  chir_03  C4'  C3'  C5'  C6'  negativ
 ET9  chir_04  PA   O5'  O1A  O3A  both
 ET9  chir_05  PB   O2B  O1B  O3A  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
 ET9  plan-1  C1'  0.020
 ET9  plan-1  C2   0.020
 ET9  plan-1  C4   0.020
 ET9  plan-1  C5   0.020
 ET9  plan-1  C6   0.020
 ET9  plan-1  C8   0.020
 ET9  plan-1  N1   0.020
 ET9  plan-1  N2   0.020
 ET9  plan-1  N3   0.020
 ET9  plan-1  N7   0.020
 ET9  plan-1  N9   0.020
 ET9  plan-1  H10  0.020
 ET9  plan-1  H11  0.020
 ET9  plan-1  H12  0.020
 ET9  plan-1  H13  0.020
 ET9  plan-1  O6   0.020
 ET9  plan-2  C1'  0.020
 ET9  plan-2  C4'  0.020
 ET9  plan-2  C6'  0.020
 ET9  plan-2  H6   0.020
 ET9  plan-2  H7   0.020
 ET9  plan-2  C44  0.020

