# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 30 21:27:30 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 2'-deoxy-5'-O-[(S)-{[(S)-[(1R)-1-fluoro-1-phosphonoethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@](F)([P](O)(O)=O)[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H](C[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
#
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
 GFM  GFM  2'-deoxy-5'-O-[(S)-{[(S)-[(1R)-1-fluoro-1-phosphonoethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  52  33  .  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_GFM
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
 GFM  N1    N  NR16  0  -0.728   9.5434   8.4472   7.9570
 GFM  C2    C  CR6   0   0.689   8.2686   8.6049   7.4921
 GFM  N2    N  NH2   0  -0.833   8.1307   9.0357   6.2318
 GFM  N3    N  N     0  -0.516   7.2081   8.3806   8.2286
 GFM  C4    C  CR56  0   0.504   7.5085   7.9938   9.4767
 GFM  C5    C  CR56  0  -0.088   8.7549   7.8010  10.0436
 GFM  C6    C  CR6   0   0.502   9.9107   8.0377   9.2454
 GFM  O6    O  O     0  -0.474  11.0869   7.9278   9.5490
 GFM  N7    N  N     0  -0.445   8.6343   7.3951  11.3463
 GFM  C8    C  CR15  0   0.084   7.3540   7.3415  11.5588
 GFM  N9    N  NR5   0  -0.526   6.6163   7.6986  10.4575
 GFM  PA    P  P     0   1.536   5.2444   5.0758  14.9592
 GFM  PB    P  P     0   1.404   4.8736   2.5969  13.4838
 GFM  PG    P  P     0   1.347   3.3328   1.4813  15.9292
 GFM  C1'   C  CH1   0   0.189   5.1668   7.7287  10.2935
 GFM  O1A   O  O     0  -0.707   4.0898   4.8901  15.8739
 GFM  O1B   O  OH1   0  -0.710   5.9901   2.1477  12.4544
 GFM  O1G   O  OH1   0  -0.769   3.9436   2.5209  16.9523
 GFM  C2'   C  CH2   0  -0.534   4.6191   6.4477   9.6710
 GFM  O2A   O  OH1   0  -0.690   6.6328   5.5148  15.5511
 GFM  O2B   O  O     0  -0.668   3.6072   3.1300  12.9340
 GFM  O2G   O  OH1   0  -0.733   3.4055   0.1692  16.8361
 GFM  C3'   C  CH1   0   0.006   4.2427   5.6252  10.8925
 GFM  O3'   O  OH1   0  -0.682   3.2951   4.6462  10.5962
 GFM  O3A   O  O2    0  -0.686   5.7488   3.6788  14.3143
 GFM  C3B   C  CT    0  -0.135   4.6770   1.2033  14.6703
 GFM  F3B2  F  F     0  -0.369   4.1736   0.1876  13.8425
 GFM  C3B3  C  CH3   0  -0.719   5.9932   0.7535  15.2684
 GFM  O3G   O  O     0  -0.680   2.0359   1.7822  15.2908
 GFM  C4'   C  CH1   0   0.007   3.7273   6.7365  11.8148
 GFM  O4'   O  O2    0  -0.496   4.5783   7.8473  11.5599
 GFM  C5'   C  CH2   0  -0.214   3.6748   6.4451  13.2908
 GFM  O5'   O  O2    0  -0.578   4.9830   6.0465  13.7464
 GFM  HN1   H  HNR6  0   0.425  10.3103   8.6461   7.3270
 GFM  HN2   H  HNH2  0   0.413   7.2079   9.0404   5.8325
 GFM  HN2A  H  HNH2  0   0.416   8.9053   9.0461   5.5908
 GFM  H8    H  HCR5  0   0.283   6.8927   7.0634  12.4916
 GFM  H1'   H  HCH1  0   0.275   4.9438   8.6076   9.6845
 GFM  H2'   H  HCH2  0   0.268   3.7207   6.6796   9.0940
 GFM  H2'A  H  HCH2  0   0.283   5.3341   5.9619   9.0083
 GFM  H3'   H  HCH1  0   0.214   5.1536   5.1816  11.3200
 GFM  HO3'  H  HOH1  0   0.460   3.2757   4.0237  11.3400
 GFM  HC3B  H  HCH3  0   0.284   5.8502  -0.1649  15.8357
 GFM  HC3A  H  HCH3  0   0.276   6.7309   0.5574  14.4911
 GFM  HC3C  H  HCH3  0   0.265   6.4013   1.5041  15.9422
 GFM  H4'   H  HCH1  0   0.254   2.6963   6.9767  11.5192
 GFM  H5'   H  HCH2  0   0.283   3.3725   7.3300  13.8516
 GFM  H5'A  H  HCH2  0   0.264   2.9379   5.6614  13.4694
 GFM  H16   H  HOH1  0   0.518   5.6810   1.6553  11.6799
 GFM  H17   H  HOH1  0   0.506   3.9302   3.4710  16.6531
 GFM  H18   H  HOH1  0   0.523   6.6171   6.3150  16.0973
 GFM  H19   H  HOH1  0   0.505   2.8159  -0.5425  16.5531

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
 GFM  N1    C2    single    1.366  0.020  1.366
 GFM  N1    C6    single    1.401  0.020  1.401
 GFM  N1    HN1   single    0.860  0.020  1.020
 GFM  C2    N2    single    1.339  0.020  1.339
 GFM  C2    N3    double    1.311  0.020  1.311
 GFM  N2    HN2   single    0.890  0.020  1.040
 GFM  N2    HN2A  single    0.890  0.020  1.040
 GFM  N3    C4    single    1.341  0.020  1.341
 GFM  C4    C5    aromatic  1.383  0.020  1.383
 GFM  C4    N9    aromatic  1.358  0.020  1.358
 GFM  C5    C6    single    1.424  0.020  1.424
 GFM  C5    N7    aromatic  1.370  0.020  1.370
 GFM  C6    O6    double    1.220  0.020  1.220
 GFM  N7    C8    aromatic  1.299  0.020  1.299
 GFM  C8    N9    aromatic  1.373  0.020  1.373
 GFM  C8    H8    single    0.930  0.020  1.080
 GFM  N9    C1'   single    1.459  0.020  1.459
 GFM  PA    O1A   double    1.485  0.020  1.485
 GFM  PA    O2A   single    1.572  0.020  1.572
 GFM  PA    O3A   single    1.619  0.020  1.619
 GFM  PA    O5'   single    1.575  0.020  1.575
 GFM  PB    O1B   single    1.584  0.020  1.584
 GFM  PB    O2B   double    1.480  0.020  1.480
 GFM  PB    O3A   single    1.621  0.020  1.621
 GFM  PB    C3B   single    1.841  0.020  1.841
 GFM  PG    O1G   single    1.581  0.020  1.581
 GFM  PG    O2G   single    1.597  0.020  1.597
 GFM  PG    C3B   single    1.863  0.020  1.863
 GFM  PG    O3G   double    1.477  0.020  1.477
 GFM  C1'   C2'   single    1.526  0.020  1.526
 GFM  C1'   O4'   single    1.401  0.020  1.401
 GFM  C1'   H1'   single    0.970  0.020  1.090
 GFM  C2'   C3'   single    1.520  0.020  1.520
 GFM  C2'   H2'   single    0.970  0.020  1.090
 GFM  C2'   H2'A  single    0.970  0.020  1.090
 GFM  C3'   O3'   single    1.394  0.020  1.394
 GFM  C3'   C4'   single    1.533  0.020  1.533
 GFM  C3'   H3'   single    0.970  0.020  1.090
 GFM  O3'   HO3'  single    0.850  0.020  0.980
 GFM  C3B   F3B2  single    1.404  0.020  1.404
 GFM  C3B   C3B3  single    1.514  0.020  1.514
 GFM  C3B3  HC3B  single    0.970  0.020  1.090
 GFM  C3B3  HC3A  single    0.970  0.020  1.090
 GFM  C3B3  HC3C  single    0.970  0.020  1.090
 GFM  C4'   O4'   single    1.422  0.020  1.422
 GFM  C4'   C5'   single    1.505  0.020  1.505
 GFM  C4'   H4'   single    0.970  0.020  1.090
 GFM  C5'   O5'   single    1.441  0.020  1.441
 GFM  C5'   H5'   single    0.970  0.020  1.090
 GFM  C5'   H5'A  single    0.970  0.020  1.090
 GFM  O1B   H16   single    0.850  0.020  0.980
 GFM  O1G   H17   single    0.850  0.020  0.980
 GFM  O2A   H18   single    0.850  0.020  0.980
 GFM  O2G   H19   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
 GFM  HN1   N1    C6    115.54  3.000
 GFM  HN1   N1    C2    118.20  3.000
 GFM  C6    N1    C2    126.26  3.000
 GFM  N3    C2    N2    120.04  3.000
 GFM  N3    C2    N1    122.97  3.000
 GFM  N2    C2    N1    116.97  3.000
 GFM  HN2A  N2    HN2   116.98  3.000
 GFM  HN2A  N2    C2    121.60  3.000
 GFM  HN2   N2    C2    118.03  3.000
 GFM  C4    N3    C2    113.03  3.000
 GFM  N9    C4    C5    105.41  3.000
 GFM  N9    C4    N3    125.99  3.000
 GFM  C5    C4    N3    128.60  3.000
 GFM  N7    C5    C6    130.81  3.000
 GFM  N7    C5    C4    110.60  3.000
 GFM  C6    C5    C4    118.59  3.000
 GFM  O6    C6    C5    128.90  3.000
 GFM  O6    C6    N1    120.54  3.000
 GFM  C5    C6    N1    110.56  3.000
 GFM  C8    N7    C5    104.75  3.000
 GFM  H8    C8    N9    122.13  3.000
 GFM  H8    C8    N7    125.06  3.000
 GFM  N9    C8    N7    112.81  3.000
 GFM  C1'   N9    C8    129.00  3.000
 GFM  C1'   N9    C4    124.54  3.000
 GFM  C8    N9    C4    106.43  3.000
 GFM  O5'   PA    O3A   106.06  3.000
 GFM  O5'   PA    O2A   105.33  3.000
 GFM  O3A   PA    O2A    96.65  3.000
 GFM  O5'   PA    O1A   114.98  3.000
 GFM  O3A   PA    O1A   112.32  3.000
 GFM  O2A   PA    O1A   119.33  3.000
 GFM  C3B   PB    O3A   103.46  3.000
 GFM  C3B   PB    O2B   114.88  3.000
 GFM  O3A   PB    O2B   114.34  3.000
 GFM  C3B   PB    O1B   106.23  3.000
 GFM  O3A   PB    O1B    98.15  3.000
 GFM  O2B   PB    O1B   117.65  3.000
 GFM  O3G   PG    C3B   111.85  3.000
 GFM  O3G   PG    O2G   116.94  3.000
 GFM  C3B   PG    O2G   103.20  3.000
 GFM  O3G   PG    O1G   119.01  3.000
 GFM  C3B   PG    O1G   104.88  3.000
 GFM  O2G   PG    O1G    98.93  3.000
 GFM  H1'   C1'   O4'   110.49  3.000
 GFM  H1'   C1'   C2'   112.01  3.000
 GFM  O4'   C1'   C2'   106.80  3.000
 GFM  H1'   C1'   N9    106.39  3.000
 GFM  O4'   C1'   N9    108.50  3.000
 GFM  C2'   C1'   N9    112.65  3.000
 GFM  H16   O1B   PB    116.04  3.000
 GFM  H17   O1G   PG    115.31  3.000
 GFM  H2'A  C2'   H2'   108.25  3.000
 GFM  H2'A  C2'   C3'   114.21  3.000
 GFM  H2'   C2'   C3'   109.61  3.000
 GFM  H2'A  C2'   C1'   112.77  3.000
 GFM  H2'   C2'   C1'   109.41  3.000
 GFM  C3'   C2'   C1'   102.43  3.000
 GFM  H18   O2A   PA    115.38  3.000
 GFM  H19   O2G   PG    114.27  3.000
 GFM  H3'   C3'   C4'   109.69  3.000
 GFM  H3'   C3'   O3'   111.24  3.000
 GFM  C4'   C3'   O3'   114.10  3.000
 GFM  H3'   C3'   C2'   109.00  3.000
 GFM  C4'   C3'   C2'   100.05  3.000
 GFM  O3'   C3'   C2'   112.18  3.000
 GFM  HO3'  O3'   C3'   107.53  3.000
 GFM  PB    O3A   PA    127.72  3.000
 GFM  C3B3  C3B   F3B2  109.26  3.000
 GFM  C3B3  C3B   PG    113.87  3.000
 GFM  F3B2  C3B   PG    104.35  3.000
 GFM  C3B3  C3B   PB    112.75  3.000
 GFM  F3B2  C3B   PB    101.89  3.000
 GFM  PG    C3B   PB    113.56  3.000
 GFM  HC3C  C3B3  HC3A  108.19  3.000
 GFM  HC3C  C3B3  HC3B  107.98  3.000
 GFM  HC3A  C3B3  HC3B  107.99  3.000
 GFM  HC3C  C3B3  C3B   111.45  3.000
 GFM  HC3A  C3B3  C3B   111.11  3.000
 GFM  HC3B  C3B3  C3B   110.01  3.000
 GFM  H4'   C4'   C5'   105.86  3.000
 GFM  H4'   C4'   O4'   110.02  3.000
 GFM  C5'   C4'   O4'   110.35  3.000
 GFM  H4'   C4'   C3'   108.17  3.000
 GFM  C5'   C4'   C3'   117.47  3.000
 GFM  O4'   C4'   C3'   104.90  3.000
 GFM  C4'   O4'   C1'   110.31  3.000
 GFM  H5'A  C5'   H5'   108.16  3.000
 GFM  H5'A  C5'   O5'   111.27  3.000
 GFM  H5'   C5'   O5'   108.27  3.000
 GFM  H5'A  C5'   C4'   108.86  3.000
 GFM  H5'   C5'   C4'   110.91  3.000
 GFM  O5'   C5'   C4'   109.38  3.000
 GFM  C5'   O5'   PA    124.36  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
 GFM  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 GFM  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 GFM  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 GFM  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 GFM  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 GFM  CONST_06  C1'   N9   C4   N3     0.00   0.0  0
 GFM  CONST_07  C1'   N9   C4   C5   180.00   0.0  0
 GFM  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 GFM  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 GFM  CONST_10  C5    C6   N1   C2     0.00   0.0  0
 GFM  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 GFM  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 GFM  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 GFM  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 GFM  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 GFM  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 GFM  CONST_17  HN2   N2   C2   N1   180.00   0.0  0
 GFM  CONST_18  HN2A  N2   C2   N1     0.00   0.0  0
 GFM  Var_01    C4'   C5'  O5'  PA  -151.00  30.0  1
 GFM  Var_02    O1B   PB   O3A  PA   144.38  30.0  2
 GFM  Var_03    O1A   PA   O3A  PB    54.97  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
 GFM  chir_03  C1'  N9   C2'   O4'   negativ
 GFM  chir_04  C3'  O3'  C4'   C2'   positiv
 GFM  chir_05  C3B  PG   F3B2  C3B3  positiv
 GFM  chir_06  C4'  O4'  C3'   C5'   negativ
 GFM  chir_07  PA   O2A  O3A   O5'   both
 GFM  chir_08  PB   O2B  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
 GFM  plan-1  N1    0.020
 GFM  plan-1  C2    0.020
 GFM  plan-1  N2    0.020
 GFM  plan-1  N3    0.020
 GFM  plan-1  C4    0.020
 GFM  plan-1  C5    0.020
 GFM  plan-1  C6    0.020
 GFM  plan-1  O6    0.020
 GFM  plan-1  N7    0.020
 GFM  plan-1  C8    0.020
 GFM  plan-1  N9    0.020
 GFM  plan-1  C1'   0.020
 GFM  plan-1  HN1   0.020
 GFM  plan-1  HN2   0.020
 GFM  plan-1  HN2A  0.020
 GFM  plan-1  H8    0.020

