# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 10:14:10 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine
#   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)O[P](O)(O)=O)[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
 HEJ  HEJ  9-{5-O-[(S)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine  ligand  47  31  .  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_HEJ
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
 HEJ  N6   N  NH2   0  -0.817  22.7877   0.8639  137.5731
 HEJ  C6   C  CR6   0   0.459  23.9946   1.1533  137.0848
 HEJ  N1   N  N     0  -0.474  25.0105   0.3112  137.3066
 HEJ  C2   C  CR16  0   0.044  26.2146   0.6055  136.8237
 HEJ  N3   N  N     0  -0.456  26.5806   1.6601  136.1156
 HEJ  C4   C  CR56  0   0.482  25.5601   2.4885  135.9068
 HEJ  C5   C  CR56  0  -0.007  24.2560   2.3205  136.3437
 HEJ  N7   N  N     0  -0.452  23.4698   3.3707  135.9447
 HEJ  C8   C  CR15  0   0.109  24.2749   4.1446  135.2788
 HEJ  N9   N  NR5   0  -0.537  25.5583   3.6709  135.2243
 HEJ  C1'  C  CR15  0   0.203  26.6773   4.2418  134.5202
 HEJ  O4'  O  O     0  -0.497  26.6181   5.6384  134.6365
 HEJ  C4'  C  CR15  0  -0.029  26.9193   6.2647  133.3957
 HEJ  C5'  C  CH2   0  -0.225  25.7042   6.9769  132.8359
 HEJ  O5'  O  O2    0  -0.582  25.1860   7.9215  133.7905
 HEJ  PA   P  P     0   1.497  25.6978   9.4168  133.8312
 HEJ  O2A  O  O     0  -0.668  27.1302   9.6796  133.6387
 HEJ  O1A  O  OH1   0  -0.710  24.9979   9.8653  135.1726
 HEJ  O3A  O  O2    0  -0.681  24.8801  10.1718  132.6310
 HEJ  PB   P  P     0   1.489  23.3950  10.1157  132.0504
 HEJ  O1B  O  O     0  -0.671  23.1693  11.1059  130.9850
 HEJ  O2B  O  OH1   0  -0.709  22.5227  10.1685  133.3600
 HEJ  O3B  O  O2    0  -0.695  23.2579   8.5954  131.5381
 HEJ  PG   P  P     0   1.482  23.1234   8.0361  130.0035
 HEJ  O3G  O  O     0  -0.663  23.5610   6.6372  129.9557
 HEJ  O2G  O  OH1   0  -0.725  21.6338   8.3892  129.5909
 HEJ  O1G  O  OH1   0  -0.733  23.9887   9.0077  129.1063
 HEJ  C3'  C  CR15  0  -0.027  27.4136   5.1448  132.4701
 HEJ  O3'  O  OH1   0  -0.668  28.7825   4.8898  132.6527
 HEJ  C2'  C  CR15  0  -0.035  26.6694   3.9289  133.0116
 HEJ  O31  O  OH1   0  -0.651  25.3761   3.9123  132.4800
 HEJ  H1   H  HNH2  0   0.404  22.6332   0.0007  138.0646
 HEJ  H2   H  HNH2  0   0.411  21.9961   1.4525  137.3825
 HEJ  H3   H  HCR6  0   0.252  26.9936  -0.1173  137.0413
 HEJ  H4   H  HCR5  0   0.293  23.9952   5.0842  134.8300
 HEJ  H5   H  HCR5  0   0.269  27.5830   3.8427  134.9875
 HEJ  H6   H  HCR5  0   0.269  27.7123   7.0006  133.5642
 HEJ  H7   H  HCH2  0   0.259  25.9783   7.4654  131.8979
 HEJ  H8   H  HCH2  0   0.280  24.8867   6.2912  132.6292
 HEJ  H9   H  HOH1  0   0.514  25.2649  10.7361  135.5000
 HEJ  H10  H  HOH1  0   0.519  21.5709  10.2928  133.2290
 HEJ  H11  H  HOH1  0   0.511  20.9535   7.8116  129.9658
 HEJ  H12  H  HOH1  0   0.499  23.7719   9.9532  129.1538
 HEJ  H13  H  HCR5  0   0.263  27.1670   5.3343  131.4183
 HEJ  H14  H  HOH1  0   0.462  29.2818   5.6695  132.3894
 HEJ  H15  H  HCR5  0   0.274  27.2126   3.0022  132.8025
 HEJ  H16  H  HOH1  0   0.469  25.0051   3.0300  132.5765

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
 HEJ  O3G  PG   double    1.467  0.020  1.467
 HEJ  O1G  PG   single    1.580  0.020  1.580
 HEJ  PG   O2G  single    1.586  0.020  1.586
 HEJ  PG   O3B  single    1.639  0.020  1.639
 HEJ  O1B  PB   double    1.472  0.020  1.472
 HEJ  O3B  PB   single    1.610  0.020  1.610
 HEJ  O31  C2'  single    1.398  0.020  1.398
 HEJ  PB   O3A  single    1.596  0.020  1.596
 HEJ  PB   O2B  single    1.574  0.020  1.574
 HEJ  C3'  O3'  single    1.404  0.020  1.404
 HEJ  C3'  C2'  single    1.525  0.020  1.525
 HEJ  C3'  C4'  single    1.535  0.020  1.535
 HEJ  C5'  C4'  single    1.516  0.020  1.516
 HEJ  C5'  O5'  single    1.439  0.020  1.439
 HEJ  O3A  PA   single    1.637  0.020  1.637
 HEJ  C2'  C1'  single    1.541  0.020  1.541
 HEJ  C4'  O4'  single    1.422  0.020  1.422
 HEJ  O5'  PA   single    1.581  0.020  1.581
 HEJ  O2A  PA   double    1.469  0.020  1.469
 HEJ  PA   O1A  single    1.578  0.020  1.578
 HEJ  C1'  O4'  single    1.403  0.020  1.403
 HEJ  C1'  N9   single    1.440  0.020  1.440
 HEJ  C8   N9   aromatic  1.369  0.020  1.369
 HEJ  C8   N7   aromatic  1.300  0.020  1.300
 HEJ  N9   C4   aromatic  1.365  0.020  1.365
 HEJ  N7   C5   aromatic  1.371  0.020  1.371
 HEJ  C4   C5   aromatic  1.386  0.020  1.386
 HEJ  C4   N3   aromatic  1.331  0.020  1.331
 HEJ  C5   C6   aromatic  1.407  0.020  1.407
 HEJ  N3   C2   aromatic  1.322  0.020  1.322
 HEJ  C6   N6   single    1.334  0.020  1.334
 HEJ  C6   N1   aromatic  1.338  0.020  1.338
 HEJ  C2   N1   aromatic  1.330  0.020  1.330
 HEJ  N6   H1   single    0.860  0.020  1.020
 HEJ  N6   H2   single    0.860  0.020  1.020
 HEJ  C2   H3   single    0.930  0.020  1.080
 HEJ  C8   H4   single    0.930  0.020  1.080
 HEJ  C1'  H5   single    0.970  0.020  1.090
 HEJ  C4'  H6   single    0.970  0.020  1.090
 HEJ  C5'  H7   single    0.970  0.020  1.090
 HEJ  C5'  H8   single    0.970  0.020  1.090
 HEJ  O1A  H9   single    0.850  0.020  0.980
 HEJ  O2B  H10  single    0.850  0.020  0.980
 HEJ  O2G  H11  single    0.850  0.020  0.980
 HEJ  O1G  H12  single    0.850  0.020  0.980
 HEJ  C3'  H13  single    0.970  0.020  1.090
 HEJ  O3'  H14  single    0.850  0.020  0.980
 HEJ  C2'  H15  single    0.970  0.020  1.090
 HEJ  O31  H16  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
 HEJ  H2   N6   H1   118.34  3.000
 HEJ  H2   N6   C6   121.10  3.000
 HEJ  H1   N6   C6   120.29  3.000
 HEJ  C5   C6   N1   117.92  3.000
 HEJ  N1   C6   N6   119.33  3.000
 HEJ  C5   C6   N6   122.74  3.000
 HEJ  C2   N1   C6   119.20  3.000
 HEJ  H3   C2   N3   116.12  3.000
 HEJ  H3   C2   N1   115.46  3.000
 HEJ  N3   C2   N1   128.43  3.000
 HEJ  C4   N3   C2   111.61  3.000
 HEJ  N9   C4   C5   105.15  3.000
 HEJ  C5   C4   N3   126.64  3.000
 HEJ  N9   C4   N3   128.21  3.000
 HEJ  N7   C5   C4   110.80  3.000
 HEJ  C4   C5   C6   116.20  3.000
 HEJ  N7   C5   C6   133.01  3.000
 HEJ  C8   N7   C5   104.47  3.000
 HEJ  H4   C8   N9   121.87  3.000
 HEJ  H4   C8   N7   124.84  3.000
 HEJ  N9   C8   N7   113.26  3.000
 HEJ  C1'  N9   C8   127.64  3.000
 HEJ  C8   N9   C4   106.32  3.000
 HEJ  C1'  N9   C4   125.93  3.000
 HEJ  H5   C1'  C2'  110.38  3.000
 HEJ  H5   C1'  O4'  111.26  3.000
 HEJ  C2'  C1'  O4'  106.45  3.000
 HEJ  H5   C1'  N9   106.84  3.000
 HEJ  O4'  C1'  N9   108.75  3.000
 HEJ  C2'  C1'  N9   113.21  3.000
 HEJ  C4'  O4'  C1'  110.93  3.000
 HEJ  H6   C4'  C3'  110.48  3.000
 HEJ  H6   C4'  C5'  108.76  3.000
 HEJ  C3'  C4'  C5'  112.24  3.000
 HEJ  H6   C4'  O4'  108.37  3.000
 HEJ  C5'  C4'  O4'  111.06  3.000
 HEJ  C3'  C4'  O4'  105.85  3.000
 HEJ  H8   C5'  H7   107.91  3.000
 HEJ  H8   C5'  O5'  105.63  3.000
 HEJ  H7   C5'  O5'  111.49  3.000
 HEJ  H8   C5'  C4'  112.13  3.000
 HEJ  H7   C5'  C4'  109.03  3.000
 HEJ  O5'  C5'  C4'  110.61  3.000
 HEJ  PA   O5'  C5'  121.41  3.000
 HEJ  O3A  PA   O1A  105.70  3.000
 HEJ  O1A  PA   O2A  119.54  3.000
 HEJ  O3A  PA   O2A  107.97  3.000
 HEJ  O1A  PA   O5'   98.47  3.000
 HEJ  O2A  PA   O5'  118.78  3.000
 HEJ  O3A  PA   O5'  104.82  3.000
 HEJ  H9   O1A  PA   114.90  3.000
 HEJ  PB   O3A  PA   135.69  3.000
 HEJ  O3B  PB   O2B  104.43  3.000
 HEJ  O2B  PB   O1B  119.64  3.000
 HEJ  O3B  PB   O1B  113.07  3.000
 HEJ  O2B  PB   O3A  102.23  3.000
 HEJ  O3B  PB   O3A  103.19  3.000
 HEJ  O1B  PB   O3A  112.48  3.000
 HEJ  H10  O2B  PB   115.86  3.000
 HEJ  PG   O3B  PB   128.84  3.000
 HEJ  O1G  PG   O2G  103.28  3.000
 HEJ  O2G  PG   O3G  118.97  3.000
 HEJ  O1G  PG   O3G  113.87  3.000
 HEJ  O2G  PG   O3B  104.17  3.000
 HEJ  O1G  PG   O3B  106.07  3.000
 HEJ  O3G  PG   O3B  109.36  3.000
 HEJ  H11  O2G  PG   115.26  3.000
 HEJ  H12  O1G  PG   116.66  3.000
 HEJ  H13  C3'  C2'  111.63  3.000
 HEJ  H13  C3'  O3'  112.04  3.000
 HEJ  C2'  C3'  O3'  106.54  3.000
 HEJ  H13  C3'  C4'  112.32  3.000
 HEJ  C2'  C3'  C4'  102.15  3.000
 HEJ  O3'  C3'  C4'  111.59  3.000
 HEJ  H14  O3'  C3'  108.84  3.000
 HEJ  H15  C2'  O31  112.11  3.000
 HEJ  H15  C2'  C3'  111.41  3.000
 HEJ  O31  C2'  C3'  109.01  3.000
 HEJ  H15  C2'  C1'  110.89  3.000
 HEJ  C3'  C2'  C1'  100.56  3.000
 HEJ  O31  C2'  C1'  112.30  3.000
 HEJ  H16  O31  C2'  109.24  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
 HEJ  CONST_01  C8   N7   C5   C6   180.00   0.0  0
 HEJ  CONST_02  N9   C4   C5   C6   180.00   0.0  0
 HEJ  CONST_03  N3   C4   C5   C6     0.00   0.0  0
 HEJ  CONST_04  N3   C2   N1   C6     0.00   0.0  0
 HEJ  CONST_05  N7   C5   C6   N1   180.00   0.0  0
 HEJ  CONST_06  C4   C5   C6   N1     0.00   0.0  0
 HEJ  CONST_07  C4   N3   C2   N1     0.00   0.0  0
 HEJ  CONST_08  N9   C4   N3   C2   180.00   0.0  0
 HEJ  CONST_09  C5   C4   N3   C2     0.00   0.0  0
 HEJ  CONST_10  C5   C6   N1   C2     0.00   0.0  0
 HEJ  CONST_11  C8   N9   C4   N3   180.00   0.0  0
 HEJ  CONST_12  N7   C5   C4   N3   180.00   0.0  0
 HEJ  CONST_13  N7   C8   N9   C4     0.00   0.0  0
 HEJ  CONST_14  C8   N7   C5   C4     0.00   0.0  0
 HEJ  CONST_15  N9   C8   N7   C5     0.00   0.0  0
 HEJ  CONST_16  C8   N9   C4   C5     0.00   0.0  0
 HEJ  CONST_17  N9   C4   C5   N7     0.00   0.0  0
 HEJ  CONST_18  C1'  N9   C4   N3     0.00   0.0  0
 HEJ  CONST_19  C1'  N9   C4   C5   180.00   0.0  0
 HEJ  CONST_20  C1'  N9   C8   N7   180.00   0.0  0
 HEJ  CONST_21  N7   C5   C6   N6     0.00   0.0  0
 HEJ  CONST_22  C4   C5   C6   N6   180.00   0.0  0
 HEJ  CONST_23  C2   N1   C6   N6   180.00   0.0  0
 HEJ  CONST_24  H3   C2   N1   C6   180.00   0.0  0
 HEJ  CONST_25  H4   C8   N9   C4   180.00   0.0  0
 HEJ  CONST_26  H1   N6   C6   N1     0.00   0.0  0
 HEJ  CONST_27  H2   N6   C6   N1   180.00   0.0  0
 HEJ  Var_01    O3A  PA   O5'  C5'   80.44  30.0  3
 HEJ  Var_02    O1B  PB   O3A  PA   176.18  30.0  1
 HEJ  Var_03    O3G  PG   O3B  PB   157.26  30.0  1
 HEJ  Var_04    H7   C5'  O5'  PA   -32.08  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
 HEJ  chir_01  C1'  C2'  O4'  N9   negativ
 HEJ  chir_02  C4'  O4'  C5'  C3'  positiv
 HEJ  chir_05  C3'  O3'  C2'  C4'  negativ
 HEJ  chir_06  C2'  O31  C1'  C3'  positiv
 HEJ  chir_07  PA   O5'  O2A  O1A  both
 HEJ  chir_08  PB   O3B  O3A  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
 HEJ  plan-1  N6   0.020
 HEJ  plan-1  C6   0.020
 HEJ  plan-1  N1   0.020
 HEJ  plan-1  C2   0.020
 HEJ  plan-1  N3   0.020
 HEJ  plan-1  C4   0.020
 HEJ  plan-1  C5   0.020
 HEJ  plan-1  N7   0.020
 HEJ  plan-1  C8   0.020
 HEJ  plan-1  N9   0.020
 HEJ  plan-1  C1'  0.020
 HEJ  plan-1  H3   0.020
 HEJ  plan-1  H4   0.020
 HEJ  plan-2  N6   0.020
 HEJ  plan-2  C6   0.020
 HEJ  plan-2  H1   0.020
 HEJ  plan-2  H2   0.020

