# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 13:47:15 2021
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-fluoro-9-{5-O-[(R)-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: Nc1nc(F)nc2n(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
 HFD  HFD  2-fluoro-9-{5-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine  ligand  47  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_HFD
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
 HFD  O2A  O  O     0  -0.658  -1.3010   2.2449  -5.8068
 HFD  PA   P  P     0   1.497  -0.8497   3.2458  -4.8346
 HFD  O1A  O  OH1   0  -0.740  -1.4740   3.2081  -3.3726
 HFD  O3A  O  O2    0  -0.695  -1.1042   4.7823  -5.3398
 HFD  PB   P  P     0   1.505  -2.4026   5.6918  -5.0510
 HFD  O1B  O  OH1   0  -0.715  -2.4013   6.7282  -6.2385
 HFD  O2B  O  O     0  -0.667  -3.6096   4.9073  -4.7602
 HFD  O3B  O  O2    0  -0.689  -1.9462   6.6055  -3.8195
 HFD  PG   P  P     0   1.474  -1.0304   7.9503  -3.7232
 HFD  O3G  O  OH1   0  -0.715  -0.5955   7.8992  -2.2002
 HFD  O2G  O  OH1   0  -0.730   0.2561   7.4423  -4.4958
 HFD  O1G  O  O     0  -0.674  -1.6988   9.1716  -4.1915
 HFD  O5'  O  O2    0  -0.559   0.7005   3.2479  -4.5839
 HFD  C5'  C  CH2   0  -0.224   1.4016   4.1334  -3.7030
 HFD  C4'  C  CH1   0   0.032   2.2421   3.3539  -2.7241
 HFD  C3'  C  CH1   0  -0.048   3.1782   2.2932  -3.3401
 HFD  O3'  O  OH1   0  -0.666   4.4616   2.5161  -2.8098
 HFD  C2'  C  CH1   0  -0.024   2.5889   0.9679  -2.8442
 HFD  O2'  O  OH1   0  -0.649   1.6162   0.5162  -3.7419
 HFD  C1'  C  CH1   0   0.204   1.9741   1.4253  -1.5148
 HFD  O4'  O  O2    0  -0.493   1.4138   2.6792  -1.7897
 HFD  N9   N  NR5   0  -0.547   0.9422   0.5668  -1.0072
 HFD  C4   C  CR56  0   0.495   1.0531  -0.2855   0.0487
 HFD  C5   C  CR56  0  -0.012  -0.1746  -0.9180   0.1399
 HFD  N7   N  N     0  -0.449  -1.0280  -0.4631  -0.8317
 HFD  C8   C  CR15  0   0.109  -0.3324   0.4103  -1.4945
 HFD  N3   N  N     0  -0.489   2.1089  -0.4873   0.8405
 HFD  C2   C  CR6   0   0.576   1.8321  -1.3820   1.7481
 HFD  F2   F  F     0  -0.286   2.8281  -1.6496   2.5896
 HFD  N1   N  N     0  -0.504   0.7386  -2.0691   1.9787
 HFD  C6   C  CR6   0   0.475  -0.3150  -1.8603   1.1768
 HFD  N6   N  NH2   0  -0.808  -1.4334  -2.5466   1.3842
 HFD  H1   H  HOH1  0   0.505  -2.4233   3.0215  -3.3304
 HFD  H2   H  HOH1  0   0.520  -2.7924   6.4171  -7.0683
 HFD  H3   H  HOH1  0   0.511  -1.1089   8.4744  -1.6158
 HFD  H4   H  HOH1  0   0.512   0.8642   8.1402  -4.7775
 HFD  H5   H  HCH2  0   0.270   2.0533   4.7598  -4.3118
 HFD  H6   H  HCH2  0   0.257   0.7204   4.7918  -3.1599
 HFD  H7   H  HCH1  0   0.260   2.8614   4.0952  -2.2038
 HFD  H8   H  HCH1  0   0.260   3.1821   2.3257  -4.4352
 HFD  H9   H  HOH1  0   0.459   5.0685   1.8808  -3.2031
 HFD  H10  H  HCH1  0   0.264   3.3707   0.2207  -2.6751
 HFD  H11  H  HOH1  0   0.465   1.5022  -0.4318  -3.6266
 HFD  H12  H  HCH1  0   0.266   2.7523   1.4829  -0.7442
 HFD  H13  H  HCR5  0   0.297  -0.6953   0.9899  -2.3261
 HFD  H14  H  HNH2  0   0.410  -1.5109  -3.1717   2.1681
 HFD  H15  H  HNH2  0   0.417  -2.2541  -2.3745   0.8300

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
 HFD  O2B  PB   double    1.469  0.020  1.469
 HFD  O1B  PB   single    1.576  0.020  1.576
 HFD  PB   O3A  single    1.611  0.020  1.611
 HFD  PB   O3B  single    1.600  0.020  1.600
 HFD  O3A  PA   single    1.637  0.020  1.637
 HFD  O3B  PG   single    1.630  0.020  1.630
 HFD  O2A  PA   double    1.467  0.020  1.467
 HFD  PA   O5'  single    1.570  0.020  1.570
 HFD  PA   O1A  single    1.590  0.020  1.590
 HFD  O1G  PG   double    1.469  0.020  1.469
 HFD  C3'  O3'  single    1.406  0.020  1.406
 HFD  C3'  C4'  single    1.543  0.020  1.543
 HFD  C3'  C2'  single    1.533  0.020  1.533
 HFD  O2'  C2'  single    1.399  0.020  1.399
 HFD  C5'  O5'  single    1.432  0.020  1.432
 HFD  C5'  C4'  single    1.507  0.020  1.507
 HFD  PG   O2G  single    1.584  0.020  1.584
 HFD  PG   O3G  single    1.585  0.020  1.585
 HFD  C4'  O4'  single    1.419  0.020  1.419
 HFD  C2'  C1'  single    1.534  0.020  1.534
 HFD  O4'  C1'  single    1.401  0.020  1.401
 HFD  C1'  N9   single    1.435  0.020  1.435
 HFD  C8   N9   aromatic  1.374  0.020  1.374
 HFD  C8   N7   aromatic  1.298  0.020  1.298
 HFD  N9   C4   aromatic  1.362  0.020  1.362
 HFD  N7   C5   aromatic  1.371  0.020  1.371
 HFD  C4   C5   aromatic  1.384  0.020  1.384
 HFD  C4   N3   aromatic  1.335  0.020  1.335
 HFD  C5   C6   aromatic  1.408  0.020  1.408
 HFD  N3   C2   aromatic  1.304  0.020  1.304
 HFD  C6   N1   aromatic  1.340  0.020  1.340
 HFD  C6   N6   single    1.328  0.020  1.328
 HFD  C2   N1   aromatic  1.312  0.020  1.312
 HFD  C2   F2   single    1.331  0.020  1.331
 HFD  O1A  H1   single    0.850  0.020  0.980
 HFD  O1B  H2   single    0.850  0.020  0.980
 HFD  O3G  H3   single    0.850  0.020  0.980
 HFD  O2G  H4   single    0.850  0.020  0.980
 HFD  C5'  H5   single    0.970  0.020  1.090
 HFD  C5'  H6   single    0.970  0.020  1.090
 HFD  C4'  H7   single    0.970  0.020  1.090
 HFD  C3'  H8   single    0.970  0.020  1.090
 HFD  O3'  H9   single    0.850  0.020  0.980
 HFD  C2'  H10  single    0.970  0.020  1.090
 HFD  O2'  H11  single    0.850  0.020  0.980
 HFD  C1'  H12  single    0.970  0.020  1.090
 HFD  C8   H13  single    0.930  0.020  1.080
 HFD  N6   H14  single    0.860  0.020  1.020
 HFD  N6   H15  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
 HFD  O5'  PA   O3A  101.62  3.000
 HFD  O5'  PA   O1A  103.94  3.000
 HFD  O3A  PA   O1A  104.17  3.000
 HFD  O1A  PA   O2A  118.20  3.000
 HFD  O5'  PA   O2A  114.24  3.000
 HFD  O3A  PA   O2A  112.84  3.000
 HFD  H1   O1A  PA   115.44  3.000
 HFD  PB   O3A  PA   126.84  3.000
 HFD  O3B  PB   O2B  112.77  3.000
 HFD  O3B  PB   O1B  101.78  3.000
 HFD  O2B  PB   O1B  120.08  3.000
 HFD  O3B  PB   O3A  103.32  3.000
 HFD  O1B  PB   O3A  103.62  3.000
 HFD  O2B  PB   O3A  113.34  3.000
 HFD  H2   O1B  PB   115.72  3.000
 HFD  PG   O3B  PB   132.61  3.000
 HFD  O1G  PG   O2G  118.73  3.000
 HFD  O2G  PG   O3G  103.62  3.000
 HFD  O1G  PG   O3G  117.26  3.000
 HFD  O3G  PG   O3B  100.63  3.000
 HFD  O2G  PG   O3B   99.37  3.000
 HFD  O1G  PG   O3B  114.30  3.000
 HFD  H3   O3G  PG   114.57  3.000
 HFD  H4   O2G  PG   114.90  3.000
 HFD  C5'  O5'  PA   125.61  3.000
 HFD  H6   C5'  H5   107.72  3.000
 HFD  H6   C5'  C4'  109.68  3.000
 HFD  H5   C5'  C4'  109.06  3.000
 HFD  H6   C5'  O5'  111.91  3.000
 HFD  H5   C5'  O5'  107.72  3.000
 HFD  C4'  C5'  O5'  110.64  3.000
 HFD  H7   C4'  O4'  109.77  3.000
 HFD  H7   C4'  C3'  108.15  3.000
 HFD  O4'  C4'  C3'  106.86  3.000
 HFD  H7   C4'  C5'  105.86  3.000
 HFD  O4'  C4'  C5'  110.36  3.000
 HFD  C3'  C4'  C5'  115.76  3.000
 HFD  H8   C3'  C2'  110.51  3.000
 HFD  H8   C3'  O3'  111.65  3.000
 HFD  C2'  C3'  O3'  111.46  3.000
 HFD  H8   C3'  C4'  112.38  3.000
 HFD  C2'  C3'  C4'  103.41  3.000
 HFD  O3'  C3'  C4'  107.10  3.000
 HFD  H9   O3'  C3'  108.46  3.000
 HFD  H10  C2'  C1'  110.85  3.000
 HFD  H10  C2'  O2'  112.05  3.000
 HFD  C1'  C2'  O2'  111.94  3.000
 HFD  H10  C2'  C3'  111.44  3.000
 HFD  C1'  C2'  C3'  100.17  3.000
 HFD  O2'  C2'  C3'  109.82  3.000
 HFD  H11  O2'  C2'  108.90  3.000
 HFD  H12  C1'  N9   107.04  3.000
 HFD  H12  C1'  O4'  112.01  3.000
 HFD  N9   C1'  O4'  108.50  3.000
 HFD  H12  C1'  C2'  109.88  3.000
 HFD  N9   C1'  C2'  114.60  3.000
 HFD  O4'  C1'  C2'  104.90  3.000
 HFD  C1'  O4'  C4'  108.74  3.000
 HFD  C8   N9   C4   106.23  3.000
 HFD  C4   N9   C1'  126.18  3.000
 HFD  C8   N9   C1'  127.58  3.000
 HFD  N3   C4   C5   126.39  3.000
 HFD  N3   C4   N9   128.25  3.000
 HFD  C5   C4   N9   105.36  3.000
 HFD  C6   C5   N7   132.99  3.000
 HFD  C6   C5   C4   116.28  3.000
 HFD  N7   C5   C4   110.72  3.000
 HFD  C8   N7   C5   104.57  3.000
 HFD  H13  C8   N7   125.16  3.000
 HFD  H13  C8   N9   121.70  3.000
 HFD  N7   C8   N9   113.12  3.000
 HFD  C2   N3   C4   110.41  3.000
 HFD  N1   C2   F2   114.04  3.000
 HFD  F2   C2   N3   114.78  3.000
 HFD  N1   C2   N3   131.19  3.000
 HFD  C6   N1   C2   117.93  3.000
 HFD  N6   C6   N1   119.20  3.000
 HFD  N6   C6   C5   123.00  3.000
 HFD  N1   C6   C5   117.80  3.000
 HFD  H15  N6   H14  118.24  3.000
 HFD  H15  N6   C6   120.85  3.000
 HFD  H14  N6   C6   120.52  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
 HFD  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 HFD  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 HFD  CONST_03  C6   C5   C4   N9    180.00   0.0  0
 HFD  CONST_04  C2   N3   C4   N9    180.00   0.0  0
 HFD  CONST_05  N7   C8   N9   C4      0.00   0.0  0
 HFD  CONST_06  C8   N7   C5   C4      0.00   0.0  0
 HFD  CONST_07  N1   C6   C5   C4      0.00   0.0  0
 HFD  CONST_08  N1   C2   N3   C4      0.00   0.0  0
 HFD  CONST_09  C8   N9   C4   C5      0.00   0.0  0
 HFD  CONST_10  C2   N3   C4   C5      0.00   0.0  0
 HFD  CONST_11  C2   N1   C6   C5      0.00   0.0  0
 HFD  CONST_12  N3   C4   C5   N7    180.00   0.0  0
 HFD  CONST_13  N1   C6   C5   N7    180.00   0.0  0
 HFD  CONST_14  N3   C4   N9   C8    180.00   0.0  0
 HFD  CONST_15  C6   C5   N7   C8    180.00   0.0  0
 HFD  CONST_16  C6   C5   C4   N3      0.00   0.0  0
 HFD  CONST_17  C6   N1   C2   N3      0.00   0.0  0
 HFD  CONST_18  N7   C8   N9   C1'   180.00   0.0  0
 HFD  CONST_19  C5   C4   N9   C1'   180.00   0.0  0
 HFD  CONST_20  N3   C4   N9   C1'     0.00   0.0  0
 HFD  CONST_21  N6   C6   C5   C4    180.00   0.0  0
 HFD  CONST_22  F2   C2   N3   C4    180.00   0.0  0
 HFD  CONST_23  N6   C6   C5   N7      0.00   0.0  0
 HFD  CONST_24  N6   C6   N1   C2    180.00   0.0  0
 HFD  CONST_25  C6   N1   C2   F2    180.00   0.0  0
 HFD  CONST_26  H13  C8   N9   C1'     0.00   0.0  0
 HFD  CONST_27  H14  N6   C6   C5    180.00   0.0  0
 HFD  CONST_28  H15  N6   C6   C5      0.00   0.0  0
 HFD  Var_01    C4'  C5'  O5'  PA    126.09  30.0  2
 HFD  Var_02    O2B  PB   O3A  PA    -23.81  30.0  2
 HFD  Var_03    O5'  PA   O3A  PB   -145.41  30.0  3
 HFD  Var_04    O1G  PG   O3B  PB     74.53  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
 HFD  chir_03  C4'  C3'  C5'  O4'  negativ
 HFD  chir_04  C3'  O3'  C2'  C4'  negativ
 HFD  chir_05  C2'  O2'  C1'  C3'  positiv
 HFD  chir_06  C1'  O4'  N9   C2'  negativ
 HFD  chir_07  PA   O2A  O5'  O1A  both
 HFD  chir_08  PB   O1B  O3A  O3B  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
 HFD  plan-1  C1'  0.020
 HFD  plan-1  N9   0.020
 HFD  plan-1  C4   0.020
 HFD  plan-1  C5   0.020
 HFD  plan-1  N7   0.020
 HFD  plan-1  C8   0.020
 HFD  plan-1  N3   0.020
 HFD  plan-1  C2   0.020
 HFD  plan-1  F2   0.020
 HFD  plan-1  N1   0.020
 HFD  plan-1  C6   0.020
 HFD  plan-1  N6   0.020
 HFD  plan-1  H13  0.020
 HFD  plan-2  C6   0.020
 HFD  plan-2  N6   0.020
 HFD  plan-2  H14  0.020
 HFD  plan-2  H15  0.020

