# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 02:52:22 2021
#   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  49  32  .  2021-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   1.516   5.2436   4.9243  14.5270
 GFH  O1A   O  OH1   0  -0.738   4.0108   4.9209  15.5251
 GFH  O2A   O  O     0  -0.661   6.5997   5.0890  15.0612
 GFH  O3A   O  O2    0  -0.711   5.0485   3.4947  13.8043
 GFH  O5'   O  O2    0  -0.577   4.9355   5.9923  13.3962
 GFH  PB    P  P     0   1.353   3.9696   2.3289  13.4849
 GFH  O1B   O  O     0  -0.642   4.0592   1.8606  12.0956
 GFH  O2B   O  OH1   0  -0.754   2.5463   2.8639  13.9163
 GFH  C3B   C  CH1   0  -0.336   4.4486   1.0572  14.7250
 GFH  F3B   F  F     0  -0.352   3.7060  -0.0725  14.4100
 GFH  PG    P  P     0   1.371   4.0025   1.5021  16.4473
 GFH  O1G   O  OH1   0  -0.722   5.2825   2.3482  16.8570
 GFH  O2G   O  OH1   0  -0.709   3.9666   0.1622  17.2936
 GFH  O3G   O  O     0  -0.703   2.6741   2.1757  16.4864
 GFH  C5'   C  CH2   0  -0.220   3.6415   6.2566  12.8429
 GFH  C4'   C  CH1   0   0.006   3.7767   6.5835  11.3785
 GFH  O4'   O  O2    0  -0.495   4.6021   7.7227  11.1962
 GFH  C1'   C  CH1   0   0.191   5.3057   7.6380   9.9855
 GFH  N9    N  NR5   0  -0.528   6.7304   7.7270  10.2720
 GFH  C4    C  CR56  0   0.504   7.6645   8.2125   9.4128
 GFH  N3    N  N     0  -0.516   7.4289   8.7169   8.1932
 GFH  C2    C  CR6   0   0.689   8.5186   9.1085   7.5803
 GFH  N2    N  NH2   0  -0.832   8.4484   9.5956   6.3338
 GFH  N1    N  NR16  0  -0.727   9.7611   9.0139   8.1393
 GFH  C6    C  CR6   0   0.502  10.0617   8.4963   9.4059
 GFH  O6    O  O     0  -0.474  11.2145   8.4588   9.8027
 GFH  C5    C  CR56  0  -0.089   8.8745   8.0660  10.0653
 GFH  N7    N  N     0  -0.445   8.6917   7.4994  11.2992
 GFH  C8    C  CR15  0   0.084   7.4104   7.3068  11.3883
 GFH  C2'   C  CH2   0  -0.548   4.9067   6.3195   9.3273
 GFH  C3'   C  CH1   0   0.002   4.3940   5.4903  10.5011
 GFH  O3'   O  OH1   0  -0.644   3.5135   4.4548  10.1876
 GFH  HO1A  H  HOH1  0   0.513   4.0471   5.5844  16.2289
 GFH  HO2B  H  HOH1  0   0.501   2.3631   2.7785  14.8892
 GFH  H3B   H  HCH1  0   0.326   5.5134   0.8312  14.6218
 GFH  HO1G  H  HOH1  0   0.514   5.2035   2.8818  17.6622
 GFH  HO2G  H  HOH1  0   0.509   4.8154  -0.2700  17.4640
 GFH  H5'1  H  HCH2  0   0.249   2.9700   5.3999  12.9347
 GFH  H5'2  H  HCH2  0   0.279   3.1957   7.0879  13.3909
 GFH  H4'   H  HCH1  0   0.251   2.7585   6.7956  11.0183
 GFH  H1'   H  HCH1  0   0.272   5.0733   8.4927   9.3463
 GFH  HN21  H  HNH2  0   0.413   7.5369   9.8005   5.9612
 GFH  HN22  H  HNH2  0   0.415   9.2232  10.0864   5.9217
 GFH  HN1   H  HNR6  0   0.425  10.5558   9.3258   7.5954
 GFH  H8    H  HCR5  0   0.287   6.9048   6.8810  12.2390
 GFH  H2'1  H  HCH2  0   0.267   4.0955   6.5019   8.6171
 GFH  H2'2  H  HCH2  0   0.284   5.7286   5.8564   8.7832
 GFH  H3'   H  HCH1  0   0.253   5.2345   5.0212  11.0204
 GFH  HO3'  H  HOH1  0   0.446   2.7837   4.8140   9.6702

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    1.586  0.020  1.586
 GFH  PA   O3A   single    1.614  0.020  1.614
 GFH  PA   O2A   double    1.467  0.020  1.467
 GFH  PA   O1A   single    1.586  0.020  1.586
 GFH  O1A  HO1A  single    0.850  0.020  0.980
 GFH  O3A  PB    single    1.620  0.020  1.620
 GFH  O5'  C5'   single    1.432  0.020  1.432
 GFH  PB   O1B   double    1.469  0.020  1.469
 GFH  PB   O2B   single    1.581  0.020  1.581
 GFH  PB   C3B   single    1.840  0.020  1.840
 GFH  O2B  HO2B  single    0.850  0.020  0.980
 GFH  C3B  F3B   single    1.388  0.020  1.388
 GFH  C3B  PG    single    1.834  0.020  1.834
 GFH  C3B  H3B   single    0.970  0.020  1.090
 GFH  PG   O3G   double    1.490  0.020  1.490
 GFH  PG   O1G   single    1.588  0.020  1.588
 GFH  PG   O2G   single    1.585  0.020  1.585
 GFH  O1G  HO1G  single    0.850  0.020  0.980
 GFH  O2G  HO2G  single    0.850  0.020  0.980
 GFH  C5'  C4'   single    1.507  0.020  1.507
 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    1.532  0.020  1.532
 GFH  C4'  O4'   single    1.419  0.020  1.419
 GFH  C4'  H4'   single    0.970  0.020  1.090
 GFH  O4'  C1'   single    1.403  0.020  1.403
 GFH  C1'  C2'   single    1.527  0.020  1.527
 GFH  C1'  N9    single    1.456  0.020  1.456
 GFH  C1'  H1'   single    0.970  0.020  1.090
 GFH  N9   C4    aromatic  1.359  0.020  1.359
 GFH  N9   C8    aromatic  1.373  0.020  1.373
 GFH  C4   N3    single    1.341  0.020  1.341
 GFH  C4   C5    aromatic  1.383  0.020  1.383
 GFH  N3   C2    double    1.310  0.020  1.310
 GFH  C2   N2    single    1.340  0.020  1.340
 GFH  C2   N1    single    1.366  0.020  1.366
 GFH  N2   HN21  single    0.890  0.020  1.040
 GFH  N2   HN22  single    0.890  0.020  1.040
 GFH  N1   C6    single    1.401  0.020  1.401
 GFH  N1   HN1   single    0.860  0.020  1.020
 GFH  C6   O6    double    1.220  0.020  1.220
 GFH  C6   C5    single    1.424  0.020  1.424
 GFH  C5   N7    aromatic  1.370  0.020  1.370
 GFH  N7   C8    aromatic  1.299  0.020  1.299
 GFH  C8   H8    single    0.930  0.020  1.080
 GFH  C2'  C3'   single    1.526  0.020  1.526
 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    1.395  0.020  1.395
 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   104.70  3.000
 GFH  O3A   PA   O2A   111.99  3.000
 GFH  O5'   PA   O2A   111.33  3.000
 GFH  O2A   PA   O1A   119.32  3.000
 GFH  O3A   PA   O1A   100.71  3.000
 GFH  O5'   PA   O1A   107.41  3.000
 GFH  HO1A  O1A  PA    115.27  3.000
 GFH  PB    O3A  PA    143.73  3.000
 GFH  C5'   O5'  PA    125.13  3.000
 GFH  C3B   PB   O2B   106.53  3.000
 GFH  C3B   PB   O1B   113.66  3.000
 GFH  O2B   PB   O1B   114.90  3.000
 GFH  C3B   PB   O3A   101.02  3.000
 GFH  O2B   PB   O3A   107.59  3.000
 GFH  O1B   PB   O3A   112.04  3.000
 GFH  HO2B  O2B  PB    113.84  3.000
 GFH  H3B   C3B  PG    112.07  3.000
 GFH  H3B   C3B  F3B   109.35  3.000
 GFH  PG    C3B  F3B   106.28  3.000
 GFH  H3B   C3B  PB    109.44  3.000
 GFH  PG    C3B  PB    113.70  3.000
 GFH  F3B   C3B  PB    105.68  3.000
 GFH  O3G   PG   O2G   110.36  3.000
 GFH  O2G   PG   O1G   109.32  3.000
 GFH  O3G   PG   O1G   118.10  3.000
 GFH  O2G   PG   C3B   107.57  3.000
 GFH  O1G   PG   C3B   100.10  3.000
 GFH  O3G   PG   C3B   110.56  3.000
 GFH  HO1G  O1G  PG    116.23  3.000
 GFH  HO2G  O2G  PG    116.85  3.000
 GFH  H5'2  C5'  H5'1  107.72  3.000
 GFH  H5'2  C5'  C4'   111.07  3.000
 GFH  H5'1  C5'  C4'   107.88  3.000
 GFH  H5'2  C5'  O5'   108.41  3.000
 GFH  H5'1  C5'  O5'   112.23  3.000
 GFH  C4'   C5'  O5'   109.54  3.000
 GFH  H4'   C4'  C3'   108.84  3.000
 GFH  H4'   C4'  O4'   109.96  3.000
 GFH  C3'   C4'  O4'   105.37  3.000
 GFH  H4'   C4'  C5'   106.07  3.000
 GFH  O4'   C4'  C5'   110.58  3.000
 GFH  C3'   C4'  C5'   115.98  3.000
 GFH  C1'   O4'  C4'   110.75  3.000
 GFH  H1'   C1'  C2'   111.58  3.000
 GFH  H1'   C1'  N9    105.99  3.000
 GFH  C2'   C1'  N9    113.16  3.000
 GFH  H1'   C1'  O4'   110.55  3.000
 GFH  N9    C1'  O4'   108.50  3.000
 GFH  C2'   C1'  O4'   107.05  3.000
 GFH  C8    N9   C4    106.44  3.000
 GFH  C8    N9   C1'   128.75  3.000
 GFH  C4    N9   C1'   124.76  3.000
 GFH  C5    C4   N3    128.53  3.000
 GFH  C5    C4   N9    105.39  3.000
 GFH  N3    C4   N9    126.08  3.000
 GFH  C2    N3   C4    113.07  3.000
 GFH  N1    C2   N2    116.97  3.000
 GFH  N1    C2   N3    122.99  3.000
 GFH  N2    C2   N3    120.01  3.000
 GFH  HN22  N2   HN21  116.55  3.000
 GFH  HN22  N2   C2    121.21  3.000
 GFH  HN21  N2   C2    117.78  3.000
 GFH  HN1   N1   C6    115.55  3.000
 GFH  HN1   N1   C2    118.23  3.000
 GFH  C6    N1   C2    126.22  3.000
 GFH  C5    C6   O6    128.89  3.000
 GFH  C5    C6   N1    110.57  3.000
 GFH  O6    C6   N1    120.54  3.000
 GFH  N7    C5   C6    130.77  3.000
 GFH  N7    C5   C4    110.61  3.000
 GFH  C6    C5   C4    118.62  3.000
 GFH  C8    N7   C5    104.76  3.000
 GFH  H8    C8   N7    125.16  3.000
 GFH  H8    C8   N9    122.04  3.000
 GFH  N7    C8   N9    112.79  3.000
 GFH  H2'2  C2'  H2'1  107.84  3.000
 GFH  H2'2  C2'  C3'   114.01  3.000
 GFH  H2'1  C2'  C3'   109.94  3.000
 GFH  H2'2  C2'  C1'   112.67  3.000
 GFH  H2'1  C2'  C1'   109.26  3.000
 GFH  C3'   C2'  C1'   103.03  3.000
 GFH  H3'   C3'  O3'   105.86  3.000
 GFH  H3'   C3'  C2'   109.89  3.000
 GFH  O3'   C3'  C2'   116.27  3.000
 GFH  H3'   C3'  C4'   110.11  3.000
 GFH  O3'   C3'  C4'   113.84  3.000
 GFH  C2'   C3'  C4'   100.85  3.000
 GFH  HO3'  O3'  C3'   108.77  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  CONST_18  HN22  N2   C2   N3    180.00   0.0  0
 GFH  Var_01    C4'   C5'  O5'  PA   -144.76  30.0  3
 GFH  Var_02    O1B   PB   O3A  PA    136.25  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
 GFH  chir_07  PA   O3A  O2A  O1A  both
 GFH  chir_08  PB   O1B  O3A  C3B  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
 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

