# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 06:37:42 2021
#   Inital geometry file: a 125 line input string
#   Ligand name: 2'-deoxy-5'-O-[(R)-{[(S)-[difluoro(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(F)(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
 GFF  GFF  2'-deoxy-5'-O-[(R)-{[(S)-[difluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine  ligand  49  33  .  2022-07-25  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GFF
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
 GFF  P1    P  P     0   1.503   5.0285   5.0366  14.7077
 GFF  O1A   O  OH1   0  -0.733   3.7835   5.1977  15.6715
 GFF  O2A   O  O     0  -0.657   6.3820   5.1116  15.2666
 GFF  O3A   O  O2    0  -0.715   4.8326   3.6256  13.9202
 GFF  O5'   O  O2    0  -0.576   4.7520   6.1350  13.6028
 GFF  P2    P  P     0   1.310   3.6227   2.5952  13.6108
 GFF  O1B   O  OH1   0  -0.754   3.8848   2.1570  12.1298
 GFF  O2B   O  O     0  -0.654   2.2889   3.0716  14.0153
 GFF  C3B   C  CT    0   0.278   4.1866   1.0840  14.5280
 GFF  F1B   F  F     0  -0.327   3.4600   0.0357  14.0634
 GFF  F2B   F  F     0  -0.327   5.4890   0.8497  14.2283
 GFF  P3    P  P     0   1.347   4.0600   1.0937  16.3817
 GFF  O1G   O  OH1   0  -0.756   4.6353   2.5438  16.7544
 GFF  O2G   O  O     0  -0.664   4.7326  -0.0575  17.0081
 GFF  O3G   O  OH1   0  -0.723   2.4940   1.2587  16.5323
 GFF  C5'   C  CH2   0  -0.236   3.5046   6.3256  12.9236
 GFF  C4'   C  CH1   0   0.013   3.7294   6.4508  11.4391
 GFF  O4'   O  O2    0  -0.490   4.5168   7.5933  11.1545
 GFF  C1'   C  CH1   0   0.181   5.2679   7.4031   9.9822
 GFF  N9    N  NR5   0  -0.528   6.6702   7.6063  10.3007
 GFF  C4    C  CR56  0   0.507   7.5945   8.1336   9.4543
 GFF  N3    N  N     0  -0.515   7.3617   8.5921   8.2165
 GFF  C2    C  CR6   0   0.689   8.4377   9.0531   7.6286
 GFF  N2    N  NH2   0  -0.831   8.3691   9.5187   6.3730
 GFF  N1    N  NR16  0  -0.727   9.6671   9.0553   8.2232
 GFF  C6    C  CR6   0   0.504   9.9645   8.5894   9.5103
 GFF  O6    O  O     0  -0.473  11.1039   8.6412   9.9414
 GFF  C5    C  CR56  0  -0.090   8.7902   8.0923  10.1462
 GFF  N7    N  N     0  -0.442   8.6091   7.5518  11.3920
 GFF  C8    C  CR15  0   0.091   7.3433   7.2713  11.4507
 GFF  C2'   C  CH2   0  -0.541   4.9561   5.9918   9.4821
 GFF  C3'   C  CH1   0   0.017   4.4609   5.3010  10.7431
 GFF  O3'   O  OH1   0  -0.695   3.6671   4.1563  10.5316
 GFF  HN21  H  HNH2  0   0.412   7.4538   9.6671   5.9827
 GFF  HN22  H  HNH2  0   0.414   9.1098  10.0832   5.9930
 GFF  HN1   H  HNR6  0   0.426  10.4533   9.4139   7.6957
 GFF  H8    H  HCR5  0   0.281   6.8439   6.8451  12.3056
 GFF  H1'   H  HCH1  0   0.280   5.0145   8.1567   9.2340
 GFF  H2'1  H  HCH2  0   0.279   4.1539   6.0414   8.7420
 GFF  H2'2  H  HCH2  0   0.295   5.8157   5.5092   9.0207
 GFF  H3'   H  HCH1  0   0.271   5.3092   4.9591  11.3406
 GFF  H1    H  HOH1  0   0.484   2.8633   4.3675  10.0395
 GFF  H4'   H  HCH1  0   0.263   2.7290   6.5591  10.9929
 GFF  H5'1  H  HCH2  0   0.255   2.8042   5.5060  13.0989
 GFF  H5'2  H  HCH2  0   0.292   3.0432   7.2328  13.3150
 GFF  H1A   H  HOH1  0   0.506   3.7746   4.6171  16.4474
 GFF  H1B   H  HOH1  0   0.519   3.7495   2.8774  11.4385
 GFF  H1G   H  HOH1  0   0.517   5.5222   2.5434  17.1444
 GFF  H3G   H  HOH1  0   0.514   2.1240   0.9870  17.3856

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
 GFF  P1   O5'   single    1.582  0.020  1.582
 GFF  P1   O1A   single    1.583  0.020  1.583
 GFF  P1   O2A   double    1.466  0.020  1.466
 GFF  P1   O3A   single    1.628  0.020  1.628
 GFF  O1A  H1A   single    0.850  0.020  0.980
 GFF  O3A  P2    single    1.619  0.020  1.619
 GFF  O5'  C5'   single    1.433  0.020  1.433
 GFF  P2   O1B   single    1.567  0.020  1.567
 GFF  P2   O2B   double    1.473  0.020  1.473
 GFF  P2   C3B   single    1.856  0.020  1.856
 GFF  O1B  H1B   single    0.850  0.020  0.980
 GFF  C3B  F1B   single    1.358  0.020  1.358
 GFF  C3B  F2B   single    1.357  0.020  1.357
 GFF  C3B  P3    single    1.858  0.020  1.858
 GFF  P3   O1G   single    1.604  0.020  1.604
 GFF  P3   O2G   double    1.473  0.020  1.473
 GFF  P3   O3G   single    1.582  0.020  1.582
 GFF  O1G  H1G   single    0.850  0.020  0.980
 GFF  O3G  H3G   single    0.850  0.020  0.980
 GFF  C5'  C4'   single    1.507  0.020  1.507
 GFF  C5'  H5'1  single    0.970  0.020  1.090
 GFF  C5'  H5'2  single    0.970  0.020  1.090
 GFF  C4'  C3'   single    1.530  0.020  1.530
 GFF  C4'  O4'   single    1.416  0.020  1.416
 GFF  C4'  H4'   single    0.970  0.020  1.090
 GFF  O4'  C1'   single    1.405  0.020  1.405
 GFF  C1'  N9    single    1.452  0.020  1.452
 GFF  C1'  C2'   single    1.529  0.020  1.529
 GFF  C1'  H1'   single    0.970  0.020  1.090
 GFF  N9   C8    aromatic  1.374  0.020  1.374
 GFF  N9   C4    aromatic  1.360  0.020  1.360
 GFF  C4   C5    aromatic  1.382  0.020  1.382
 GFF  C4   N3    single    1.340  0.020  1.340
 GFF  N3   C2    double    1.310  0.020  1.310
 GFF  C2   N2    single    1.341  0.020  1.341
 GFF  C2   N1    single    1.366  0.020  1.366
 GFF  N2   HN21  single    0.890  0.020  1.040
 GFF  N2   HN22  single    0.890  0.020  1.040
 GFF  N1   C6    single    1.401  0.020  1.401
 GFF  N1   HN1   single    0.860  0.020  1.020
 GFF  C6   O6    double    1.219  0.020  1.219
 GFF  C6   C5    single    1.425  0.020  1.425
 GFF  C5   N7    aromatic  1.370  0.020  1.370
 GFF  N7   C8    aromatic  1.298  0.020  1.298
 GFF  C8   H8    single    0.930  0.020  1.080
 GFF  C2'  C3'   single    1.521  0.020  1.521
 GFF  C2'  H2'1  single    0.970  0.020  1.090
 GFF  C2'  H2'2  single    0.970  0.020  1.090
 GFF  C3'  O3'   single    1.409  0.020  1.409
 GFF  C3'  H3'   single    0.970  0.020  1.090
 GFF  O3'  H1    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
 GFF  O5'   P1   O3A   104.06  3.000
 GFF  O3A   P1   O2A   109.86  3.000
 GFF  O5'   P1   O2A   113.07  3.000
 GFF  O3A   P1   O1A   106.75  3.000
 GFF  O2A   P1   O1A   119.26  3.000
 GFF  O5'   P1   O1A   102.54  3.000
 GFF  H1A   O1A  P1    115.70  3.000
 GFF  P2    O3A  P1    137.22  3.000
 GFF  C5'   O5'  P1    125.12  3.000
 GFF  C3B   P2   O2B   113.76  3.000
 GFF  C3B   P2   O1B   100.87  3.000
 GFF  O2B   P2   O1B   120.10  3.000
 GFF  C3B   P2   O3A   101.35  3.000
 GFF  O2B   P2   O3A   114.74  3.000
 GFF  O1B   P2   O3A   103.51  3.000
 GFF  H1B   O1B  P2    115.22  3.000
 GFF  P3    C3B  F2B   106.66  3.000
 GFF  P3    C3B  F1B   108.00  3.000
 GFF  F2B   C3B  F1B   107.75  3.000
 GFF  P3    C3B  P2    117.92  3.000
 GFF  F2B   C3B  P2    108.85  3.000
 GFF  F1B   C3B  P2    107.28  3.000
 GFF  O3G   P3   O2G   119.54  3.000
 GFF  O3G   P3   O1G   103.80  3.000
 GFF  O2G   P3   O1G   116.36  3.000
 GFF  O3G   P3   C3B    99.38  3.000
 GFF  O2G   P3   C3B   112.90  3.000
 GFF  O1G   P3   C3B   102.24  3.000
 GFF  H1G   O1G  P3    114.92  3.000
 GFF  H3G   O3G  P3    115.64  3.000
 GFF  H5'2  C5'  H5'1  107.18  3.000
 GFF  H5'2  C5'  C4'   110.34  3.000
 GFF  H5'1  C5'  C4'   108.43  3.000
 GFF  H5'2  C5'  O5'   107.98  3.000
 GFF  H5'1  C5'  O5'   112.48  3.000
 GFF  C4'   C5'  O5'   110.38  3.000
 GFF  H4'   C4'  C3'   108.91  3.000
 GFF  H4'   C4'  O4'   110.15  3.000
 GFF  C3'   C4'  O4'   104.41  3.000
 GFF  H4'   C4'  C5'   105.79  3.000
 GFF  O4'   C4'  C5'   110.36  3.000
 GFF  C3'   C4'  C5'   117.19  3.000
 GFF  C1'   O4'  C4'   110.83  3.000
 GFF  H1'   C1'  C2'   111.44  3.000
 GFF  H1'   C1'  N9    106.13  3.000
 GFF  C2'   C1'  N9    113.44  3.000
 GFF  H1'   C1'  O4'   110.74  3.000
 GFF  C2'   C1'  O4'   106.78  3.000
 GFF  N9    C1'  O4'   108.31  3.000
 GFF  C8    N9   C4    106.41  3.000
 GFF  C4    N9   C1'   125.04  3.000
 GFF  C8    N9   C1'   128.50  3.000
 GFF  C5    C4   N3    128.53  3.000
 GFF  N3    C4   N9    126.12  3.000
 GFF  C5    C4   N9    105.36  3.000
 GFF  C2    N3   C4    113.09  3.000
 GFF  N1    C2   N2    116.95  3.000
 GFF  N1    C2   N3    123.00  3.000
 GFF  N2    C2   N3    120.03  3.000
 GFF  HN22  N2   HN21  116.15  3.000
 GFF  HN22  N2   C2    120.73  3.000
 GFF  HN21  N2   C2    117.45  3.000
 GFF  HN1   N1   C6    115.57  3.000
 GFF  HN1   N1   C2    118.21  3.000
 GFF  C6    N1   C2    126.21  3.000
 GFF  C5    C6   O6    128.84  3.000
 GFF  C5    C6   N1    110.55  3.000
 GFF  O6    C6   N1    120.61  3.000
 GFF  N7    C5   C6    130.72  3.000
 GFF  N7    C5   C4    110.65  3.000
 GFF  C6    C5   C4    118.63  3.000
 GFF  C8    N7   C5    104.79  3.000
 GFF  H8    C8   N7    124.97  3.000
 GFF  H8    C8   N9    122.22  3.000
 GFF  N7    C8   N9    112.79  3.000
 GFF  H2'2  C2'  H2'1  108.23  3.000
 GFF  H2'2  C2'  C3'   114.03  3.000
 GFF  H2'1  C2'  C3'   110.07  3.000
 GFF  H2'2  C2'  C1'   112.75  3.000
 GFF  H2'1  C2'  C1'   109.23  3.000
 GFF  C3'   C2'  C1'   102.38  3.000
 GFF  H3'   C3'  O3'   105.38  3.000
 GFF  H3'   C3'  C2'   110.05  3.000
 GFF  O3'   C3'  C2'   115.34  3.000
 GFF  H3'   C3'  C4'   110.95  3.000
 GFF  O3'   C3'  C4'   114.17  3.000
 GFF  C2'   C3'  C4'   101.04  3.000
 GFF  H1    O3'  C3'   111.57  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
 GFF  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GFF  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GFF  CONST_03  N7    C8   N9   C4      0.00   0.0  0
 GFF  CONST_04  C8    N7   C5   C4      0.00   0.0  0
 GFF  CONST_05  C8    N9   C4   C5      0.00   0.0  0
 GFF  CONST_06  N7    C8   N9   C1'   180.00   0.0  0
 GFF  CONST_07  C5    C4   N9   C1'   180.00   0.0  0
 GFF  CONST_08  N3    C4   N9   C1'     0.00   0.0  0
 GFF  CONST_09  N1    C2   N3   C4      0.00   0.0  0
 GFF  CONST_10  C6    N1   C2   N3      0.00   0.0  0
 GFF  CONST_11  C5    C6   N1   C2      0.00   0.0  0
 GFF  CONST_12  N2    C2   N3   C4    180.00   0.0  0
 GFF  CONST_13  O6    C6   N1   C2    180.00   0.0  0
 GFF  CONST_14  C6    N1   C2   N2    180.00   0.0  0
 GFF  CONST_15  H8    C8   N9   C1'     0.00   0.0  0
 GFF  CONST_16  HN1   N1   C2   N3    180.00   0.0  0
 GFF  CONST_17  HN21  N2   C2   N3      0.00   0.0  0
 GFF  Var_01    C4'   C5'  O5'  P1   -132.64  30.0  3
 GFF  Var_02    O1B   P2   O3A  P1    140.33  30.0  3
 GFF  Var_03    F1B   C3B  P2   O3A  -163.67  30.0  3
 GFF  Var_04    O1G   P3   C3B  P2    -44.89  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
 GFF  chir_03  C4'  C5'  C3'  O4'  positiv
 GFF  chir_04  C1'  O4'  N9   C2'  negativ
 GFF  chir_05  C3'  O3'  C4'  C2'  positiv
 GFF  chir_06  P1   O1A  O2A  O3A  both
 GFF  chir_07  P2   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
 GFF  plan-1  C1'   0.020
 GFF  plan-1  N9    0.020
 GFF  plan-1  C4    0.020
 GFF  plan-1  N3    0.020
 GFF  plan-1  C2    0.020
 GFF  plan-1  N2    0.020
 GFF  plan-1  N1    0.020
 GFF  plan-1  C6    0.020
 GFF  plan-1  O6    0.020
 GFF  plan-1  C5    0.020
 GFF  plan-1  N7    0.020
 GFF  plan-1  C8    0.020
 GFF  plan-1  HN21  0.020
 GFF  plan-1  HN22  0.020
 GFF  plan-1  HN1   0.020
 GFF  plan-1  H8    0.020

