# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 01:17:23 2021
#   Inital geometry file: a 118 line input string
#   Ligand name: 9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-methyl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)c2ncn([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@@H]3F)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
 HDV  HDV  9-{2-deoxy-2-fluoro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-2-methyl-9H-purin-6-amine  ligand  49  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_HDV
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
 HDV  O2A  O  O     0  -0.668  -39.1519   9.7224  58.0253
 HDV  PA   P  P     0   1.508  -37.7708  10.1915  57.8710
 HDV  O1A  O  OH1   0  -0.724  -37.4335  11.7131  58.1660
 HDV  O3A  O  O2    0  -0.694  -37.1978  10.1845  56.3477
 HDV  PB   P  P     0   1.514  -37.6059   9.2961  55.0762
 HDV  O1B  O  OH1   0  -0.713  -37.5902   7.8493  55.7045
 HDV  O2B  O  O     0  -0.661  -36.7788   9.5908  53.9023
 HDV  O3B  O  O2    0  -0.688  -39.1755   9.5983  54.8893
 HDV  PG   P  P     0   1.465  -39.8699  10.5992  53.8071
 HDV  O3G  O  O     0  -0.678  -39.8495  10.1014  52.4247
 HDV  O2G  O  OH1   0  -0.732  -39.1000  11.9449  54.1392
 HDV  O1G  O  OH1   0  -0.714  -41.2853  10.8301  54.4811
 HDV  O5'  O  O2    0  -0.568  -36.7478   9.2975  58.6802
 HDV  C5'  C  CH2   0  -0.213  -35.3487   9.5680  58.7923
 HDV  C4'  C  CH1   0  -0.010  -34.6295   8.2950  59.1690
 HDV  C3'  C  CH1   0  -0.086  -34.7840   7.1215  58.1777
 HDV  O3'  O  OH1   0  -0.669  -33.5858   6.4014  58.0355
 HDV  C2'  C  CH1   0   0.171  -35.7495   6.1816  58.8848
 HDV  F2'  F  F     0  -0.349  -37.0571   6.4838  58.5694
 HDV  C1'  C  CH1   0   0.154  -35.4717   6.4803  60.3583
 HDV  O4'  O  O2    0  -0.496  -35.0970   7.8291  60.4272
 HDV  N9   N  NR5   0  -0.547  -36.5969   6.2639  61.2201
 HDV  C4   C  CR56  0   0.494  -36.7251   5.2602  62.1396
 HDV  C5   C  CR56  0  -0.019  -37.9700   5.4512  62.7101
 HDV  N7   N  N     0  -0.452  -38.5948   6.5463  62.1671
 HDV  C8   C  CR15  0   0.113  -37.7544   6.9993  61.2872
 HDV  N3   N  N     0  -0.474  -35.8545   4.2989  62.4306
 HDV  C2   C  CR6   0   0.348  -36.2957   3.4837  63.3792
 HDV  CL2  C  CH3   0  -0.729  -35.3866   2.3760  63.8112
 HDV  N1   N  N     0  -0.487  -37.4737   3.5538  64.0074
 HDV  C6   C  CR6   0   0.448  -38.3383   4.5234  63.7008
 HDV  N6   N  NH2   0  -0.819  -39.5050   4.5868  64.3483
 HDV  H1   H  HOH1  0   0.512  -37.7685  12.0446  59.0114
 HDV  H2   H  HOH1  0   0.517  -37.6796   7.1159  55.0786
 HDV  H3   H  HOH1  0   0.512  -39.0256  12.5598  53.3959
 HDV  H4   H  HOH1  0   0.510  -41.9716  10.2064  54.2056
 HDV  H5   H  HCH2  0   0.257  -34.9313   9.9354  57.8513
 HDV  H6   H  HCH2  0   0.272  -35.1887  10.3317  59.5558
 HDV  H7   H  HCH1  0   0.271  -33.5686   8.5607  59.2488
 HDV  H8   H  HCH1  0   0.267  -35.1812   7.4494  57.2104
 HDV  H9   H  HOH1  0   0.464  -32.9333   6.9650  57.6076
 HDV  H10  H  HCH1  0   0.262  -35.5710   5.1345  58.6381
 HDV  H11  H  HCH1  0   0.278  -34.6706   5.8211  60.7109
 HDV  H12  H  HCR5  0   0.294  -37.9119   7.8706  60.6716
 HDV  H13  H  HCH3  0   0.245  -34.5429   2.2748  63.1331
 HDV  H14  H  HCH3  0   0.255  -34.9986   2.5744  64.8123
 HDV  H15  H  HCH3  0   0.249  -35.9230   1.4287  63.8576
 HDV  H16  H  HNH2  0   0.401  -39.7676   3.8501  64.9804
 HDV  H17  H  HNH2  0   0.409  -40.2165   5.2355  64.0605

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
 HDV  O3G  PG   double    1.469  0.020  1.469
 HDV  O2B  PB   double    1.466  0.020  1.466
 HDV  O1G  PG   single    1.585  0.020  1.585
 HDV  O1B  PB   single    1.577  0.020  1.577
 HDV  PG   O3B  single    1.629  0.020  1.629
 HDV  PG   O2G  single    1.586  0.020  1.586
 HDV  PB   O3B  single    1.609  0.020  1.609
 HDV  PB   O3A  single    1.604  0.020  1.604
 HDV  O3A  PA   single    1.627  0.020  1.627
 HDV  O2A  PA   double    1.467  0.020  1.467
 HDV  PA   O5'  single    1.581  0.020  1.581
 HDV  PA   O1A  single    1.586  0.020  1.586
 HDV  O5'  C5'  single    1.429  0.020  1.429
 HDV  F2'  C2'  single    1.379  0.020  1.379
 HDV  C3'  O3'  single    1.405  0.020  1.405
 HDV  C3'  C2'  single    1.522  0.020  1.522
 HDV  C3'  C4'  single    1.544  0.020  1.544
 HDV  C5'  C4'  single    1.510  0.020  1.510
 HDV  C2'  C1'  single    1.529  0.020  1.529
 HDV  C4'  O4'  single    1.421  0.020  1.421
 HDV  O4'  C1'  single    1.402  0.020  1.402
 HDV  C8   N9   aromatic  1.373  0.020  1.373
 HDV  C8   N7   aromatic  1.298  0.020  1.298
 HDV  C1'  N9   single    1.434  0.020  1.434
 HDV  N9   C4   aromatic  1.367  0.020  1.367
 HDV  N7   C5   aromatic  1.373  0.020  1.373
 HDV  C4   C5   aromatic  1.383  0.020  1.383
 HDV  C4   N3   aromatic  1.329  0.020  1.329
 HDV  C5   C6   aromatic  1.406  0.020  1.406
 HDV  N3   C2   aromatic  1.326  0.020  1.326
 HDV  C6   N6   single    1.336  0.020  1.336
 HDV  C6   N1   aromatic  1.335  0.020  1.335
 HDV  C2   N1   aromatic  1.337  0.020  1.337
 HDV  C2   CL2  single    1.497  0.020  1.497
 HDV  O1A  H1   single    0.850  0.020  0.980
 HDV  O1B  H2   single    0.850  0.020  0.980
 HDV  O2G  H3   single    0.850  0.020  0.980
 HDV  O1G  H4   single    0.850  0.020  0.980
 HDV  C5'  H5   single    0.970  0.020  1.090
 HDV  C5'  H6   single    0.970  0.020  1.090
 HDV  C4'  H7   single    0.970  0.020  1.090
 HDV  C3'  H8   single    0.970  0.020  1.090
 HDV  O3'  H9   single    0.850  0.020  0.980
 HDV  C2'  H10  single    0.970  0.020  1.090
 HDV  C1'  H11  single    0.970  0.020  1.090
 HDV  C8   H12  single    0.930  0.020  1.080
 HDV  CL2  H13  single    0.970  0.020  1.090
 HDV  CL2  H14  single    0.970  0.020  1.090
 HDV  CL2  H15  single    0.970  0.020  1.090
 HDV  N6   H16  single    0.860  0.020  1.020
 HDV  N6   H17  single    0.860  0.020  1.020

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
 HDV  O5'  PA   O3A  104.41  3.000
 HDV  O5'  PA   O1A  108.03  3.000
 HDV  O3A  PA   O1A   95.93  3.000
 HDV  O1A  PA   O2A  119.17  3.000
 HDV  O5'  PA   O2A  111.99  3.000
 HDV  O3A  PA   O2A  115.38  3.000
 HDV  H1   O1A  PA   114.67  3.000
 HDV  PB   O3A  PA   130.90  3.000
 HDV  O3B  PB   O2B  114.80  3.000
 HDV  O3B  PB   O1B  103.19  3.000
 HDV  O2B  PB   O1B  119.85  3.000
 HDV  O3B  PB   O3A  103.66  3.000
 HDV  O1B  PB   O3A  100.94  3.000
 HDV  O2B  PB   O3A  112.33  3.000
 HDV  H2   O1B  PB   115.87  3.000
 HDV  PG   O3B  PB   127.45  3.000
 HDV  O1G  PG   O2G  102.77  3.000
 HDV  O2G  PG   O3G  118.54  3.000
 HDV  O1G  PG   O3G  117.51  3.000
 HDV  O2G  PG   O3B  100.10  3.000
 HDV  O1G  PG   O3B  100.82  3.000
 HDV  O3G  PG   O3B  114.26  3.000
 HDV  H3   O2G  PG   114.57  3.000
 HDV  H4   O1G  PG   114.75  3.000
 HDV  C5'  O5'  PA   124.50  3.000
 HDV  H6   C5'  H5   108.12  3.000
 HDV  H6   C5'  C4'  110.21  3.000
 HDV  H5   C5'  C4'  108.44  3.000
 HDV  H6   C5'  O5'  109.31  3.000
 HDV  H5   C5'  O5'  111.70  3.000
 HDV  C4'  C5'  O5'  109.04  3.000
 HDV  H7   C4'  O4'  109.47  3.000
 HDV  H7   C4'  C3'  109.13  3.000
 HDV  O4'  C4'  C3'  106.64  3.000
 HDV  H7   C4'  C5'  105.95  3.000
 HDV  O4'  C4'  C5'  109.92  3.000
 HDV  C3'  C4'  C5'  115.65  3.000
 HDV  H8   C3'  C2'  111.41  3.000
 HDV  H8   C3'  O3'  111.91  3.000
 HDV  C2'  C3'  O3'  105.76  3.000
 HDV  H8   C3'  C4'  112.06  3.000
 HDV  C2'  C3'  C4'  103.57  3.000
 HDV  O3'  C3'  C4'  111.66  3.000
 HDV  H9   O3'  C3'  108.85  3.000
 HDV  H10  C2'  C1'  112.08  3.000
 HDV  H10  C2'  F2'  108.30  3.000
 HDV  C1'  C2'  F2'  110.49  3.000
 HDV  H10  C2'  C3'  112.59  3.000
 HDV  C1'  C2'  C3'  102.23  3.000
 HDV  F2'  C2'  C3'  111.11  3.000
 HDV  H11  C1'  N9   106.83  3.000
 HDV  H11  C1'  O4'  111.57  3.000
 HDV  N9   C1'  O4'  109.00  3.000
 HDV  H11  C1'  C2'  108.99  3.000
 HDV  N9   C1'  C2'  114.03  3.000
 HDV  O4'  C1'  C2'  106.49  3.000
 HDV  C1'  O4'  C4'  111.11  3.000
 HDV  C8   N9   C4   106.34  3.000
 HDV  C4   N9   C1'  126.05  3.000
 HDV  C8   N9   C1'  127.60  3.000
 HDV  N3   C4   C5   126.82  3.000
 HDV  N3   C4   N9   128.08  3.000
 HDV  C5   C4   N9   105.10  3.000
 HDV  C6   C5   N7   133.30  3.000
 HDV  C6   C5   C4   115.80  3.000
 HDV  N7   C5   C4   110.90  3.000
 HDV  C8   N7   C5   104.59  3.000
 HDV  H12  C8   N7   125.05  3.000
 HDV  H12  C8   N9   121.87  3.000
 HDV  N7   C8   N9   113.07  3.000
 HDV  C2   N3   C4   112.54  3.000
 HDV  N1   C2   CL2  116.00  3.000
 HDV  CL2  C2   N3   117.34  3.000
 HDV  N1   C2   N3   126.65  3.000
 HDV  H15  CL2  H14  107.10  3.000
 HDV  H15  CL2  H13  109.12  3.000
 HDV  H14  CL2  H13  108.24  3.000
 HDV  H15  CL2  C2   110.89  3.000
 HDV  H14  CL2  C2   110.24  3.000
 HDV  H13  CL2  C2   111.12  3.000
 HDV  C6   N1   C2   120.06  3.000
 HDV  N6   C6   N1   119.27  3.000
 HDV  N1   C6   C5   118.13  3.000
 HDV  N6   C6   C5   122.60  3.000
 HDV  H17  N6   H16  117.90  3.000
 HDV  H17  N6   C6   120.68  3.000
 HDV  H16  N6   C6   119.87  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
 HDV  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 HDV  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 HDV  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 HDV  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 HDV  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 HDV  CONST_06  C8   N7   C5   C4      0.00   0.0  0
 HDV  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 HDV  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 HDV  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 HDV  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 HDV  CONST_11  C2   N1   C6   C5      0.00   0.0  0
 HDV  CONST_12  N3   C4   C5   N7    180.00   0.0  0
 HDV  CONST_13  N1   C6   C5   N7    180.00   0.0  0
 HDV  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 HDV  CONST_15  C6   C5   N7   C8    180.00   0.0  0
 HDV  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 HDV  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 HDV  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 HDV  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 HDV  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 HDV  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 HDV  CONST_22  CL2  C2   N3   C4    180.00   0.0  0
 HDV  CONST_23  N6   C6   C5   N7      0.00   0.0  0
 HDV  CONST_24  N6   C6   N1   C2    180.00   0.0  0
 HDV  CONST_25  C6   N1   C2   CL2   180.00   0.0  0
 HDV  CONST_26  H12  C8   N9   C1'     0.00   0.0  0
 HDV  CONST_27  H16  N6   C6   C5    180.00   0.0  0
 HDV  CONST_28  H17  N6   C6   C5      0.00   0.0  0
 HDV  Var_01    H13  CL2  C2   N3    -11.33  30.0  2
 HDV  Var_02    C4'  C5'  O5'  PA   -159.08  30.0  3
 HDV  Var_03    O2B  PB   O3A  PA   -177.58  30.0  2
 HDV  Var_04    O3G  PG   O3B  PB     72.50  30.0  2
 HDV  Var_05    O5'  PA   O3A  PB     97.40  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
 HDV  chir_03  C4'  C3'  C5'  O4'  negativ
 HDV  chir_04  C3'  O3'  C2'  C4'  negativ
 HDV  chir_05  C2'  F2'  C1'  C3'  positiv
 HDV  chir_06  C1'  O4'  N9   C2'  negativ
 HDV  chir_07  PA   O2A  O5'  O1A  both
 HDV  chir_08  PB   O1B  O3B  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
 HDV  plan-1  C1'  0.020
 HDV  plan-1  N9   0.020
 HDV  plan-1  C4   0.020
 HDV  plan-1  C5   0.020
 HDV  plan-1  N7   0.020
 HDV  plan-1  C8   0.020
 HDV  plan-1  N3   0.020
 HDV  plan-1  C2   0.020
 HDV  plan-1  CL2  0.020
 HDV  plan-1  N1   0.020
 HDV  plan-1  C6   0.020
 HDV  plan-1  N6   0.020
 HDV  plan-1  H12  0.020
 HDV  plan-2  C6   0.020
 HDV  plan-2  N6   0.020
 HDV  plan-2  H16  0.020
 HDV  plan-2  H17  0.020

