# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 09:14:58 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 5'-O-[(S)-{[(S)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine
#   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@@](F)(Cl)[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
 GFC  GFC  5'-O-[(S)-{[(S)-[(S)-chloro(fluoro)phosphonomethyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2'-deoxyguanosine  ligand  49  33  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GFC
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
 GFC  N1    N   NR16  0  -0.727   9.5012   8.6953   7.9724
 GFC  C2    C   CR6   0   0.689   8.2231   8.8480   7.5154
 GFC  N2    N   NH2   0  -0.833   8.0730   9.3809   6.2955
 GFC  N3    N   N     0  -0.516   7.1688   8.5270   8.2242
 GFC  C4    C   CR56  0   0.505   7.4777   8.0494   9.4383
 GFC  C5    C   CR56  0  -0.089   8.7282   7.8559   9.9955
 GFC  C6    C   CR6   0   0.503   9.8780   8.1958   9.2261
 GFC  O6    O   O     0  -0.474  11.0560   8.1011   9.5271
 GFC  N7    N   N     0  -0.444   8.6185   7.3383  11.2592
 GFC  C8    C   CR15  0   0.088   7.3408   7.2190  11.4575
 GFC  N9    N   NR5   0  -0.525   6.5937   7.6411  10.3858
 GFC  PA    P   P     0   1.541   5.1061   5.0846  15.0077
 GFC  PB    P   P     0   1.414   4.9084   2.5092  13.6547
 GFC  PG    P   P     0   1.361   3.0547   1.5734  16.0483
 GFC  C1'   C   CH1   0   0.185   5.1480   7.6022  10.2124
 GFC  O1A   O   O     0  -0.706   3.9138   4.9182  15.8750
 GFC  O1B   O   OH1   0  -0.696   6.1347   1.9235  12.8553
 GFC  O1G   O   OH1   0  -0.753   3.5988   2.6446  17.0640
 GFC  C2'   C   CH2   0  -0.536   4.6587   6.2894   9.6035
 GFC  O2A   O   OH1   0  -0.683   6.3959   5.7529  15.5994
 GFC  O2B   O   O     0  -0.656   3.7223   2.9797  12.9116
 GFC  O2G   O   OH1   0  -0.721   3.0421   0.2919  16.9877
 GFC  C3'   C   CH1   0   0.009   4.2756   5.4779  10.8302
 GFC  O3'   O   OH1   0  -0.680   3.3618   4.4675  10.5324
 GFC  O3A   O   O2    0  -0.680   5.6711   3.6353  14.5189
 GFC  C3B   C   CT    0  -0.170   4.5017   1.2200  14.9179
 GFC  F3B   F   F     0  -0.322   4.1481   0.1181  14.1789
 GFC  CL3B  CL  CL    0  -0.049   5.9478   0.8361  15.8510
 GFC  O3G   O   O     0  -0.665   1.8519   1.8639  15.2473
 GFC  C4'   C   CH1   0   0.004   3.7090   6.5917  11.7189
 GFC  O4'   O   O2    0  -0.495   4.5477   7.7125  11.4756
 GFC  C5'   C   CH2   0  -0.213   3.6126   6.3180  13.1947
 GFC  O5'   O   O2    0  -0.577   4.9074   5.9126  13.6900
 GFC  HN1   H   HNR6  0   0.425  10.2633   8.9679   7.3641
 GFC  HN2   H   HNH2  0   0.413   7.1517   9.3783   5.8926
 GFC  HN2A  H   HNH2  0   0.416   8.8463   9.4511   5.6567
 GFC  H8    H   HCR5  0   0.281   6.8869   6.8496  12.3622
 GFC  H1'   H   HCH1  0   0.274   4.8917   8.4611   9.5883
 GFC  H2'   H   HCH2  0   0.269   3.7702   6.4779   8.9961
 GFC  H2'A  H   HCH2  0   0.283   5.4077   5.8146   8.9711
 GFC  H3'   H   HCH1  0   0.217   5.1865   5.0677  11.2889
 GFC  HO3'  H   HOH1  0   0.461   3.3596   3.8465  11.2759
 GFC  H4'   H   HCH1  0   0.256   2.6829   6.8077  11.3889
 GFC  H5'   H   HCH2  0   0.287   3.2968   7.2091  13.7379
 GFC  H5'A  H   HCH2  0   0.265   2.8712   5.5355  13.3588
 GFC  H13   H   HOH1  0   0.523   5.9252   1.4644  12.0281
 GFC  H14   H   HOH1  0   0.510   3.6446   3.5773  16.7099
 GFC  H15   H   HOH1  0   0.523   6.6369   5.5029  16.5038
 GFC  H16   H   HOH1  0   0.510   2.4409  -0.4103  16.7033

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
 GFC  N1   C2    single    1.366  0.020  1.366
 GFC  N1   C6    single    1.401  0.020  1.401
 GFC  N1   HN1   single    0.860  0.020  1.020
 GFC  C2   N2    single    1.340  0.020  1.340
 GFC  C2   N3    double    1.310  0.020  1.310
 GFC  N2   HN2   single    0.890  0.020  1.040
 GFC  N2   HN2A  single    0.890  0.020  1.040
 GFC  N3   C4    single    1.341  0.020  1.341
 GFC  C4   C5    aromatic  1.383  0.020  1.383
 GFC  C4   N9    aromatic  1.359  0.020  1.359
 GFC  C5   C6    single    1.425  0.020  1.425
 GFC  C5   N7    aromatic  1.370  0.020  1.370
 GFC  C6   O6    double    1.220  0.020  1.220
 GFC  N7   C8    aromatic  1.299  0.020  1.299
 GFC  C8   N9    aromatic  1.373  0.020  1.373
 GFC  C8   H8    single    0.930  0.020  1.080
 GFC  N9   C1'   single    1.457  0.020  1.457
 GFC  PA   O1A   double    1.484  0.020  1.484
 GFC  PA   O2A   single    1.569  0.020  1.569
 GFC  PA   O3A   single    1.631  0.020  1.631
 GFC  PA   O5'   single    1.569  0.020  1.569
 GFC  PB   O1B   single    1.577  0.020  1.577
 GFC  PB   O2B   double    1.477  0.020  1.477
 GFC  PB   O3A   single    1.611  0.020  1.611
 GFC  PB   C3B   single    1.850  0.020  1.850
 GFC  PG   O1G   single    1.573  0.020  1.573
 GFC  PG   O2G   single    1.589  0.020  1.589
 GFC  PG   C3B   single    1.870  0.020  1.870
 GFC  PG   O3G   double    1.474  0.020  1.474
 GFC  C1'  C2'   single    1.528  0.020  1.528
 GFC  C1'  O4'   single    1.403  0.020  1.403
 GFC  C1'  H1'   single    0.970  0.020  1.090
 GFC  C2'  C3'   single    1.520  0.020  1.520
 GFC  C2'  H2'   single    0.970  0.020  1.090
 GFC  C2'  H2'A  single    0.970  0.020  1.090
 GFC  C3'  O3'   single    1.395  0.020  1.395
 GFC  C3'  C4'   single    1.533  0.020  1.533
 GFC  C3'  H3'   single    0.970  0.020  1.090
 GFC  O3'  HO3'  single    0.850  0.020  0.980
 GFC  C3B  F3B   single    1.373  0.020  1.373
 GFC  C3B  CL3B  single    1.763  0.020  1.763
 GFC  C4'  O4'   single    1.421  0.020  1.421
 GFC  C4'  C5'   single    1.504  0.020  1.504
 GFC  C4'  H4'   single    0.970  0.020  1.090
 GFC  C5'  O5'   single    1.444  0.020  1.444
 GFC  C5'  H5'   single    0.970  0.020  1.090
 GFC  C5'  H5'A  single    0.970  0.020  1.090
 GFC  O1B  H13   single    0.850  0.020  0.980
 GFC  O1G  H14   single    0.850  0.020  0.980
 GFC  O2A  H15   single    0.850  0.020  0.980
 GFC  O2G  H16   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
 GFC  HN1   N1   C6   115.54  3.000
 GFC  HN1   N1   C2   118.24  3.000
 GFC  C6    N1   C2   126.22  3.000
 GFC  N3    C2   N2   119.99  3.000
 GFC  N3    C2   N1   122.99  3.000
 GFC  N2    C2   N1   117.00  3.000
 GFC  HN2A  N2   HN2  116.76  3.000
 GFC  HN2A  N2   C2   121.35  3.000
 GFC  HN2   N2   C2   117.81  3.000
 GFC  C4    N3   C2   113.06  3.000
 GFC  N9    C4   C5   105.39  3.000
 GFC  N9    C4   N3   126.06  3.000
 GFC  C5    C4   N3   128.55  3.000
 GFC  N7    C5   C6   130.76  3.000
 GFC  N7    C5   C4   110.62  3.000
 GFC  C6    C5   C4   118.61  3.000
 GFC  O6    C6   C5   128.89  3.000
 GFC  O6    C6   N1   120.55  3.000
 GFC  C5    C6   N1   110.57  3.000
 GFC  C8    N7   C5   104.74  3.000
 GFC  H8    C8   N9   122.12  3.000
 GFC  H8    C8   N7   125.05  3.000
 GFC  N9    C8   N7   112.83  3.000
 GFC  C1'   N9   C8   128.67  3.000
 GFC  C1'   N9   C4   124.81  3.000
 GFC  C8    N9   C4   106.42  3.000
 GFC  O5'   PA   O3A  105.14  3.000
 GFC  O5'   PA   O2A  101.31  3.000
 GFC  O3A   PA   O2A  101.94  3.000
 GFC  O5'   PA   O1A  116.64  3.000
 GFC  O3A   PA   O1A  110.73  3.000
 GFC  O2A   PA   O1A  119.21  3.000
 GFC  C3B   PB   O3A  102.99  3.000
 GFC  C3B   PB   O2B  112.89  3.000
 GFC  O3A   PB   O2B  115.30  3.000
 GFC  C3B   PB   O1B  104.97  3.000
 GFC  O3A   PB   O1B   99.40  3.000
 GFC  O2B   PB   O1B  119.21  3.000
 GFC  O3G   PG   C3B  109.89  3.000
 GFC  O3G   PG   O2G  118.28  3.000
 GFC  C3B   PG   O2G  102.19  3.000
 GFC  O3G   PG   O1G  119.92  3.000
 GFC  C3B   PG   O1G  104.56  3.000
 GFC  O2G   PG   O1G   99.80  3.000
 GFC  H1'   C1'  O4'  110.62  3.000
 GFC  H1'   C1'  C2'  111.90  3.000
 GFC  O4'   C1'  C2'  106.82  3.000
 GFC  H1'   C1'  N9   106.26  3.000
 GFC  O4'   C1'  N9   108.38  3.000
 GFC  C2'   C1'  N9   112.85  3.000
 GFC  H13   O1B  PB   116.15  3.000
 GFC  H14   O1G  PG   115.02  3.000
 GFC  H2'A  C2'  H2'  108.16  3.000
 GFC  H2'A  C2'  C3'  114.15  3.000
 GFC  H2'   C2'  C3'  109.63  3.000
 GFC  H2'A  C2'  C1'  112.69  3.000
 GFC  H2'   C2'  C1'  109.50  3.000
 GFC  C3'   C2'  C1'  102.58  3.000
 GFC  H15   O2A  PA   116.54  3.000
 GFC  H16   O2G  PG   114.62  3.000
 GFC  H3'   C3'  C4'  109.60  3.000
 GFC  H3'   C3'  O3'  111.21  3.000
 GFC  C4'   C3'  O3'  114.07  3.000
 GFC  H3'   C3'  C2'  109.10  3.000
 GFC  C4'   C3'  C2'   99.97  3.000
 GFC  O3'   C3'  C2'  112.31  3.000
 GFC  HO3'  O3'  C3'  107.58  3.000
 GFC  PB    O3A  PA   128.16  3.000
 GFC  CL3B  C3B  F3B  108.74  3.000
 GFC  CL3B  C3B  PG   110.85  3.000
 GFC  F3B   C3B  PG   106.13  3.000
 GFC  CL3B  C3B  PB   109.43  3.000
 GFC  F3B   C3B  PB   104.38  3.000
 GFC  PG    C3B  PB   116.82  3.000
 GFC  H4'   C4'  C5'  105.69  3.000
 GFC  H4'   C4'  O4'  110.15  3.000
 GFC  C5'   C4'  O4'  110.44  3.000
 GFC  H4'   C4'  C3'  108.28  3.000
 GFC  C5'   C4'  C3'  117.40  3.000
 GFC  O4'   C4'  C3'  104.81  3.000
 GFC  C4'   O4'  C1'  110.17  3.000
 GFC  H5'A  C5'  H5'  108.34  3.000
 GFC  H5'A  C5'  O5'  110.88  3.000
 GFC  H5'   C5'  O5'  108.55  3.000
 GFC  H5'A  C5'  C4'  108.77  3.000
 GFC  H5'   C5'  C4'  111.02  3.000
 GFC  O5'   C5'  C4'  109.28  3.000
 GFC  C5'   O5'  PA   123.35  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
 GFC  CONST_01  C8    N7   C5   C4     0.00   0.0  0
 GFC  CONST_02  N7    C8   N9   C4     0.00   0.0  0
 GFC  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 GFC  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 GFC  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 GFC  CONST_06  C1'   N9   C4   N3     0.00   0.0  0
 GFC  CONST_07  C1'   N9   C4   C5   180.00   0.0  0
 GFC  CONST_08  C1'   N9   C8   N7   180.00   0.0  0
 GFC  CONST_09  C4    N3   C2   N1     0.00   0.0  0
 GFC  CONST_10  C5    C6   N1   C2     0.00   0.0  0
 GFC  CONST_11  C6    N1   C2   N3     0.00   0.0  0
 GFC  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 GFC  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 GFC  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 GFC  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 GFC  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 GFC  CONST_17  HN2   N2   C2   N1   180.00   0.0  0
 GFC  CONST_18  HN2A  N2   C2   N1     0.00   0.0  0
 GFC  Var_01    C4'   C5'  O5'  PA  -157.89  30.0  1
 GFC  Var_02    O1B   PB   O3A  PA   147.02  30.0  1
 GFC  Var_03    O1A   PA   O3A  PB    60.34  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
 GFC  chir_03  C1'  N9   C2'  O4'   negativ
 GFC  chir_04  C3'  O3'  C4'  C2'   positiv
 GFC  chir_05  C3B  PG   F3B  CL3B  positiv
 GFC  chir_06  C4'  O4'  C3'  C5'   negativ
 GFC  chir_07  PA   O2A  O3A  O5'   both
 GFC  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
 GFC  plan-1  N1    0.020
 GFC  plan-1  C2    0.020
 GFC  plan-1  N2    0.020
 GFC  plan-1  N3    0.020
 GFC  plan-1  C4    0.020
 GFC  plan-1  C5    0.020
 GFC  plan-1  C6    0.020
 GFC  plan-1  O6    0.020
 GFC  plan-1  N7    0.020
 GFC  plan-1  C8    0.020
 GFC  plan-1  N9    0.020
 GFC  plan-1  C1'   0.020
 GFC  plan-1  HN1   0.020
 GFC  plan-1  HN2   0.020
 GFC  plan-1  HN2A  0.020
 GFC  plan-1  H8    0.020

