# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 10:56:11 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)[C@H](F)[P](O)(O)=O)O3
#
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
 GFH  GFH  2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  45  32  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GFH
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
 GFH  PA    P  P      0   1.368   1.2678  -2.2479  -1.6284
 GFH  O1A   O  OP    -1  -0.798   0.2454  -1.8075  -2.6377
 GFH  O2A   O  O      0  -0.808   2.6268  -2.6869  -2.0822
 GFH  O3A   O  O2     0  -0.742   1.3955  -1.1954  -0.4053
 GFH  O5'   O  O2     0  -0.619   0.6614  -3.5320  -0.7826
 GFH  PB    P  P      0   1.243   2.3014   0.2141  -0.3848
 GFH  O1B   O  O      0  -0.821   2.3450   0.7534  -1.7869
 GFH  O2B   O  OP    -1  -0.810   3.5798  -0.1059   0.3399
 GFH  C3B   C  CH1    0  -0.339   1.2260   1.2054   0.7119
 GFH  F3B   F  F      0  -0.401   0.0878   1.5751  -0.0392
 GFH  PG    P  P      0   1.125   2.0115   2.7342   1.4604
 GFH  O1G   O  OP    -1  -0.906   2.8178   3.3847   0.3330
 GFH  O2G   O  OP    -1  -0.911   0.8130   3.5715   1.9219
 GFH  O3G   O  O      0  -0.905   2.8558   2.1881   2.6138
 GFH  C5'   C  CH2    0  -0.160  -0.7174  -3.7682  -0.6292
 GFH  C4'   C  CH1    0  -0.019  -1.2582  -3.2738   0.7034
 GFH  O4'   O  O2     0  -0.478  -1.2622  -1.8505   0.7849
 GFH  C1'   C  CH1    0   0.241  -2.5707  -1.3543   0.7828
 GFH  N9    N  NR5    0  -0.537  -2.6564  -0.1997  -0.0847
 GFH  C4    C  CR56   0   0.494  -3.4496   0.8808   0.1307
 GFH  N3    N  N      0  -0.515  -4.2174   1.1011   1.2101
 GFH  C2    C  CR6    0   0.680  -4.8762   2.2294   1.1518
 GFH  N2    N  NH2    0  -0.834  -5.6476   2.6121   2.1844
 GFH  N1    N  NR16   0  -0.726  -4.7967   3.0830   0.0898
 GFH  C6    C  CR6    0   0.490  -4.0248   2.8945  -1.0656
 GFH  O6    O  O      0  -0.484  -4.0389   3.7291  -1.9579
 GFH  C5    C  CR56   0  -0.089  -3.3040   1.6709  -0.9944
 GFH  N7    N  N      0  -0.468  -2.4369   1.0884  -1.8823
 GFH  C8    C  CR15   0   0.082  -2.0647  -0.0171  -1.3104
 GFH  C2'   C  CH2    0  -0.553  -3.4578  -2.5125   0.3421
 GFH  C3'   C  CH1    0  -0.014  -2.7103  -3.7034   0.9195
 GFH  O3'   O  OH1    0  -0.672  -2.9191  -3.8399   2.3077
 GFH  H3B   H  HCH1   0   0.174   0.8660   0.5600   1.5217
 GFH  H5'1  H  HCH2   0   0.209  -1.2915  -3.3400  -1.4578
 GFH  H5'2  H  HCH2   0   0.219  -0.8650  -4.8525  -0.6599
 GFH  H4'   H  HCH1   0   0.244  -0.6233  -3.6631   1.5069
 GFH  H1'   H  HCH1   0   0.245  -2.8550  -1.0023   1.7797
 GFH  HN21  H  HNH2   0   0.409  -5.8616   1.9169   2.8794
 GFH  HN22  H  HNH2   0   0.411  -6.3262   3.3457   2.0714
 GFH  HN1   H  HNR6   0   0.422  -5.3377   3.9380   0.1186
 GFH  H8    H  HCR5   0   0.320  -1.3407  -0.7149  -1.7126
 GFH  H2'1  H  HCH2   0   0.277  -4.4851  -2.4179   0.6956
 GFH  H2'2  H  HCH2   0   0.260  -3.4863  -2.5765  -0.7485
 GFH  H3'   H  HCH1   0   0.244  -2.9457  -4.6339   0.3887
 GFH  HO3'  H  HOH1   0   0.453  -3.8602  -3.9727   2.4601

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
 GFH  PA   O5'   single    1.653  0.020  1.653
 GFH  PA   O3A   single    1.619  0.020  1.619
 GFH  PA   O2A   deloc     1.499  0.020  1.499
 GFH  PA   O1A   deloc     1.503  0.020  1.503
 GFH  O3A  PB    single    1.676  0.020  1.676
 GFH  O5'  C5'   single    1.407  0.020  1.407
 GFH  PB   O1B   deloc     1.503  0.020  1.503
 GFH  PB   O2B   deloc     1.504  0.020  1.504
 GFH  PB   C3B   single    1.828  0.020  1.828
 GFH  C3B  F3B   single    1.413  0.020  1.413
 GFH  C3B  PG    single    1.875  0.020  1.875
 GFH  C3B  H3B   single    0.970  0.020  1.090
 GFH  PG   O3G   deloc     1.530  0.020  1.530
 GFH  PG   O1G   deloc     1.531  0.020  1.531
 GFH  PG   O2G   deloc     1.533  0.020  1.533
 GFH  C5'  C4'   single    1.521  0.020  1.521
 GFH  C5'  H5'1  single    0.970  0.020  1.090
 GFH  C5'  H5'2  single    0.970  0.020  1.090
 GFH  C4'  C3'   single    1.530  0.020  1.530
 GFH  C4'  O4'   single    1.426  0.020  1.426
 GFH  C4'  H4'   single    0.970  0.020  1.090
 GFH  O4'  C1'   single    1.400  0.020  1.400
 GFH  C1'  C2'   single    1.524  0.020  1.524
 GFH  C1'  N9    single    1.447  0.020  1.447
 GFH  C1'  H1'   single    0.970  0.020  1.090
 GFH  N9   C4    aromatic  1.358  0.020  1.358
 GFH  N9   C8    aromatic  1.373  0.020  1.373
 GFH  C4   N3    single    1.343  0.020  1.343
 GFH  C4   C5    aromatic  1.382  0.020  1.382
 GFH  N3   C2    double    1.308  0.020  1.308
 GFH  C2   N2    single    1.344  0.020  1.344
 GFH  C2   N1    single    1.365  0.020  1.365
 GFH  N2   HN21  single    0.890  0.020  1.040
 GFH  N2   HN22  single    0.890  0.020  1.040
 GFH  N1   C6    single    1.402  0.020  1.402
 GFH  N1   HN1   single    0.860  0.020  1.020
 GFH  C6   O6    double    1.222  0.020  1.222
 GFH  C6   C5    single    1.422  0.020  1.422
 GFH  C5   N7    aromatic  1.371  0.020  1.371
 GFH  N7   C8    aromatic  1.299  0.020  1.299
 GFH  C8   H8    single    0.930  0.020  1.080
 GFH  C2'  C3'   single    1.520  0.020  1.520
 GFH  C2'  H2'1  single    0.970  0.020  1.090
 GFH  C2'  H2'2  single    0.970  0.020  1.090
 GFH  C3'  O3'   single    1.410  0.020  1.410
 GFH  C3'  H3'   single    0.970  0.020  1.090
 GFH  O3'  HO3'  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
 GFH  O5'   PA   O3A    98.48  3.000
 GFH  O3A   PA   O2A   110.35  3.000
 GFH  O5'   PA   O2A   105.07  3.000
 GFH  O2A   PA   O1A   119.97  3.000
 GFH  O3A   PA   O1A   111.76  3.000
 GFH  O5'   PA   O1A   108.77  3.000
 GFH  PB    O3A  PA    126.79  3.000
 GFH  C5'   O5'  PA    123.07  3.000
 GFH  C3B   PB   O2B   109.05  3.000
 GFH  C3B   PB   O1B   112.47  3.000
 GFH  O2B   PB   O1B   120.08  3.000
 GFH  C3B   PB   O3A    98.36  3.000
 GFH  O2B   PB   O3A   106.65  3.000
 GFH  O1B   PB   O3A   107.82  3.000
 GFH  H3B   C3B  PG    108.83  3.000
 GFH  H3B   C3B  F3B   106.39  3.000
 GFH  PG    C3B  F3B   109.66  3.000
 GFH  H3B   C3B  PB    108.48  3.000
 GFH  PG    C3B  PB    115.80  3.000
 GFH  F3B   C3B  PB    107.27  3.000
 GFH  O3G   PG   O2G   113.54  3.000
 GFH  O2G   PG   O1G   113.66  3.000
 GFH  O3G   PG   O1G   114.59  3.000
 GFH  O2G   PG   C3B   103.76  3.000
 GFH  O1G   PG   C3B   105.85  3.000
 GFH  O3G   PG   C3B   103.95  3.000
 GFH  H5'2  C5'  H5'1  107.17  3.000
 GFH  H5'2  C5'  C4'   107.37  3.000
 GFH  H5'1  C5'  C4'   110.45  3.000
 GFH  H5'2  C5'  O5'   107.18  3.000
 GFH  H5'1  C5'  O5'   111.44  3.000
 GFH  C4'   C5'  O5'   112.92  3.000
 GFH  H4'   C4'  C3'   110.29  3.000
 GFH  H4'   C4'  O4'   108.33  3.000
 GFH  C3'   C4'  O4'   105.65  3.000
 GFH  H4'   C4'  C5'   108.73  3.000
 GFH  O4'   C4'  C5'   112.06  3.000
 GFH  C3'   C4'  C5'   111.72  3.000
 GFH  C1'   O4'  C4'   110.89  3.000
 GFH  H1'   C1'  C2'   110.88  3.000
 GFH  H1'   C1'  N9    105.91  3.000
 GFH  C2'   C1'  N9    113.50  3.000
 GFH  H1'   C1'  O4'   110.82  3.000
 GFH  N9    C1'  O4'   109.83  3.000
 GFH  C2'   C1'  O4'   105.97  3.000
 GFH  C8    N9   C4    106.71  3.000
 GFH  C8    N9   C1'   128.01  3.000
 GFH  C4    N9   C1'   125.08  3.000
 GFH  C5    C4   N3    128.36  3.000
 GFH  C5    C4   N9    105.32  3.000
 GFH  N3    C4   N9    126.31  3.000
 GFH  C2    N3   C4    113.19  3.000
 GFH  N1    C2   N2    116.94  3.000
 GFH  N1    C2   N3    123.01  3.000
 GFH  N2    C2   N3    120.02  3.000
 GFH  HN22  N2   HN21  115.98  3.000
 GFH  HN22  N2   C2    120.56  3.000
 GFH  HN21  N2   C2    117.13  3.000
 GFH  HN1   N1   C6    115.55  3.000
 GFH  HN1   N1   C2    118.36  3.000
 GFH  C6    N1   C2    126.10  3.000
 GFH  C5    C6   O6    129.06  3.000
 GFH  C5    C6   N1    110.70  3.000
 GFH  O6    C6   N1    120.24  3.000
 GFH  N7    C5   C6    130.83  3.000
 GFH  N7    C5   C4    110.54  3.000
 GFH  C6    C5   C4    118.63  3.000
 GFH  C8    N7   C5    104.93  3.000
 GFH  H8    C8   N7    125.19  3.000
 GFH  H8    C8   N9    122.27  3.000
 GFH  N7    C8   N9    112.50  3.000
 GFH  H2'2  C2'  H2'1  107.70  3.000
 GFH  H2'2  C2'  C3'   110.24  3.000
 GFH  H2'1  C2'  C3'   114.09  3.000
 GFH  H2'2  C2'  C1'   110.38  3.000
 GFH  H2'1  C2'  C1'   112.87  3.000
 GFH  C3'   C2'  C1'   101.50  3.000
 GFH  H3'   C3'  O3'   111.25  3.000
 GFH  H3'   C3'  C2'   112.04  3.000
 GFH  O3'   C3'  C2'   112.14  3.000
 GFH  H3'   C3'  C4'   111.94  3.000
 GFH  O3'   C3'  C4'   107.87  3.000
 GFH  C2'   C3'  C4'   101.14  3.000
 GFH  HO3'  O3'  C3'   108.30  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
 GFH  CONST_01  N7    C5   C4   N9     0.00   0.0  0
 GFH  CONST_02  C5    N7   C8   N9     0.00   0.0  0
 GFH  CONST_03  N7    C8   N9   C4     0.00   0.0  0
 GFH  CONST_04  C8    N7   C5   C4     0.00   0.0  0
 GFH  CONST_05  C8    N9   C4   C5     0.00   0.0  0
 GFH  CONST_06  N3    C4   N9   C1'    0.00   0.0  0
 GFH  CONST_07  C5    C4   N9   C1'  180.00   0.0  0
 GFH  CONST_08  N7    C8   N9   C1'  180.00   0.0  0
 GFH  CONST_09  N1    C2   N3   C4     0.00   0.0  0
 GFH  CONST_10  C6    N1   C2   N3     0.00   0.0  0
 GFH  CONST_11  C5    C6   N1   C2     0.00   0.0  0
 GFH  CONST_12  N2    C2   N3   C4   180.00   0.0  0
 GFH  CONST_13  O6    C6   N1   C2   180.00   0.0  0
 GFH  CONST_14  C6    N1   C2   N2   180.00   0.0  0
 GFH  CONST_15  H8    C8   N9   C1'    0.00   0.0  0
 GFH  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 GFH  CONST_17  HN21  N2   C2   N3     0.00   0.0  0
 GFH  Var_01    C4'   C5'  O5'  PA   -98.48  30.0  3
 GFH  Var_02    O1B   PB   O3A  PA    31.13  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
 GFH  chir_03  C3B  PB   F3B  PG   positiv
 GFH  chir_04  C4'  O4'  C5'  C3'  positiv
 GFH  chir_05  C1'  O4'  N9   C2'  negativ
 GFH  chir_06  C3'  O3'  C4'  C2'  positiv

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
 GFH  plan-1  C1'   0.020
 GFH  plan-1  N9    0.020
 GFH  plan-1  C4    0.020
 GFH  plan-1  N3    0.020
 GFH  plan-1  C2    0.020
 GFH  plan-1  N2    0.020
 GFH  plan-1  N1    0.020
 GFH  plan-1  C6    0.020
 GFH  plan-1  O6    0.020
 GFH  plan-1  C5    0.020
 GFH  plan-1  N7    0.020
 GFH  plan-1  C8    0.020
 GFH  plan-1  HN21  0.020
 GFH  plan-1  HN22  0.020
 GFH  plan-1  HN1   0.020
 GFH  plan-1  H8    0.020

