# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 08:18:11 2020
#   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  45  33  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

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   1.355   1.8470  -0.9429  -4.7861
 GFF  O1A   O  OP    -1  -0.809   1.2302  -2.2352  -5.2200
 GFF  O2A   O  O      0  -0.806   3.0116  -0.3664  -5.5303
 GFF  O3A   O  O2     0  -0.739   0.7023   0.2034  -4.5677
 GFF  O5'   O  O2     0  -0.625   2.3354  -1.0628  -3.2230
 GFF  P2    P  P      0   1.202  -0.2694   0.9133  -5.6866
 GFF  O1B   O  OP    -1  -0.802  -0.8477  -0.1076  -6.6199
 GFF  O2B   O  O      0  -0.816   0.4549   2.0996  -6.2659
 GFF  C3B   C  CT     0   0.202  -1.5766   1.5577  -4.5384
 GFF  F1B   F  F      0  -0.413  -2.4968   2.1471  -5.4122
 GFF  F2B   F  F      0  -0.385  -1.0232   2.6298  -3.8575
 GFF  P3    P  P      0   1.133  -2.5560   0.5056  -3.3217
 GFF  O1G   O  OP    -1  -0.881  -3.0901  -0.6424  -4.1684
 GFF  O2G   O  O      0  -0.900  -3.6237   1.4812  -2.8276
 GFF  O3G   O  OP    -1  -0.811  -1.5515   0.0896  -2.2407
 GFF  C5'   C  CH2    0  -0.191   1.4072  -1.5530  -2.2734
 GFF  C4'   C  CH1    0  -0.022   2.0144  -1.4268  -0.8909
 GFF  O4'   O  O2     0  -0.498   2.3623  -0.0757  -0.5956
 GFF  C1'   C  CH1    0   0.235   1.5129   0.4482   0.3993
 GFF  N9    N  NR5    0  -0.544   1.1505   1.8018   0.0652
 GFF  C4    C  CR56   0   0.496   1.6356   2.9205   0.6702
 GFF  N3    N  N      0  -0.514   2.4697   2.9612   1.7206
 GFF  C2    C  CR6    0   0.682   2.7563   4.1782   2.1057
 GFF  N2    N  NH2    0  -0.833   3.6118   4.3771   3.1231
 GFF  N1    N  NR16   0  -0.725   2.2520   5.2901   1.4954
 GFF  C6    C  CR6    0   0.495   1.3801   5.3048   0.3980
 GFF  O6    O  O      0  -0.481   0.9885   6.3646  -0.0652
 GFF  C5    C  CR56   0  -0.101   1.0755   3.9788  -0.0183
 GFF  N7    N  N      0  -0.451   0.2707   3.5240  -1.0323
 GFF  C8    C  CR15   0   0.040   0.3365   2.2282  -0.9639
 GFF  C2'   C  CH2    0  -0.595   0.3418  -0.5182   0.5015
 GFF  C3'   C  CH1    0  -0.008   1.0220  -1.8443   0.1925
 GFF  O3'   O  OH1    0  -0.675   1.7552  -2.3427   1.2904
 GFF  HN21  H  HNH2   0   0.409   3.8395   3.5797   3.6929
 GFF  HN22  H  HNH2   0   0.411   3.6637   5.2721   3.5792
 GFF  HN1   H  HNR6   0   0.422   2.5162   6.1977   1.8568
 GFF  H8    H  HCR5   0   0.349  -0.2053   1.5285  -1.5983
 GFF  H1'   H  HCH1   0   0.243   2.0464   0.5118   1.3522
 GFF  H2'1  H  HCH2   0   0.292  -0.4174  -0.3078  -0.2547
 GFF  H2'2  H  HCH2   0   0.268  -0.1325  -0.4918   1.4836
 GFF  H3'   H  HCH1   0   0.240   0.3095  -2.5898  -0.1811
 GFF  H1    H  HOH1   0   0.452   1.1439  -2.4742   2.0219
 GFF  H4'   H  HCH1   0   0.238   2.9240  -2.0358  -0.8363
 GFF  H5'1  H  HCH2   0   0.268   0.4562  -1.0107  -2.3318
 GFF  H5'2  H  HCH2   0   0.192   1.1996  -2.6164  -2.4474

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    1.642  0.020  1.642
 GFF  P1   O1A   deloc     1.496  0.020  1.496
 GFF  P1   O2A   deloc     1.498  0.020  1.498
 GFF  P1   O3A   single    1.635  0.020  1.635
 GFF  O3A  P2    single    1.643  0.020  1.643
 GFF  O5'  C5'   single    1.416  0.020  1.416
 GFF  P2   O1B   deloc     1.499  0.020  1.499
 GFF  P2   O2B   deloc     1.506  0.020  1.506
 GFF  P2   C3B   single    1.855  0.020  1.855
 GFF  C3B  F1B   single    1.399  0.020  1.399
 GFF  C3B  F2B   single    1.385  0.020  1.385
 GFF  C3B  P3    single    1.883  0.020  1.883
 GFF  P3   O1G   deloc     1.523  0.020  1.523
 GFF  P3   O2G   deloc     1.528  0.020  1.528
 GFF  P3   O3G   deloc     1.533  0.020  1.533
 GFF  C5'  C4'   single    1.515  0.020  1.515
 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    1.527  0.020  1.527
 GFF  C4'  O4'   single    1.426  0.020  1.426
 GFF  C4'  H4'   single    0.970  0.020  1.090
 GFF  O4'  C1'   single    1.409  0.020  1.409
 GFF  C1'  N9    single    1.441  0.020  1.441
 GFF  C1'  C2'   single    1.522  0.020  1.522
 GFF  C1'  H1'   single    0.970  0.020  1.090
 GFF  N9   C8    aromatic  1.380  0.020  1.380
 GFF  N9   C4    aromatic  1.361  0.020  1.361
 GFF  C4   C5    aromatic  1.381  0.020  1.381
 GFF  C4   N3    single    1.342  0.020  1.342
 GFF  N3   C2    double    1.308  0.020  1.308
 GFF  C2   N2    single    1.344  0.020  1.344
 GFF  C2   N1    single    1.365  0.020  1.365
 GFF  N2   HN21  single    0.890  0.020  1.040
 GFF  N2   HN22  single    0.890  0.020  1.040
 GFF  N1   C6    single    1.402  0.020  1.402
 GFF  N1   HN1   single    0.860  0.020  1.020
 GFF  C6   O6    double    1.221  0.020  1.221
 GFF  C6   C5    single    1.423  0.020  1.423
 GFF  C5   N7    aromatic  1.372  0.020  1.372
 GFF  N7   C8    aromatic  1.299  0.020  1.299
 GFF  C8   H8    single    0.930  0.020  1.080
 GFF  C2'  C3'   single    1.522  0.020  1.522
 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    1.411  0.020  1.411
 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    97.60  3.000
 GFF  O3A   P1   O2A   109.94  3.000
 GFF  O5'   P1   O2A   105.66  3.000
 GFF  O3A   P1   O1A   110.84  3.000
 GFF  O2A   P1   O1A   120.59  3.000
 GFF  O5'   P1   O1A   109.61  3.000
 GFF  P2    O3A  P1    128.77  3.000
 GFF  C5'   O5'  P1    117.96  3.000
 GFF  C3B   P2   O2B   107.66  3.000
 GFF  C3B   P2   O1B   110.49  3.000
 GFF  O2B   P2   O1B   118.85  3.000
 GFF  C3B   P2   O3A    98.36  3.000
 GFF  O2B   P2   O3A   108.54  3.000
 GFF  O1B   P2   O3A   110.96  3.000
 GFF  P3    C3B  F2B   108.82  3.000
 GFF  P3    C3B  F1B   107.27  3.000
 GFF  F2B   C3B  F1B   104.10  3.000
 GFF  P3    C3B  P2    124.90  3.000
 GFF  F2B   C3B  P2    106.95  3.000
 GFF  F1B   C3B  P2    102.90  3.000
 GFF  O3G   P3   O2G   113.76  3.000
 GFF  O3G   P3   O1G   114.65  3.000
 GFF  O2G   P3   O1G   114.58  3.000
 GFF  O3G   P3   C3B   105.45  3.000
 GFF  O2G   P3   C3B   102.45  3.000
 GFF  O1G   P3   C3B   104.14  3.000
 GFF  H5'2  C5'  H5'1  107.87  3.000
 GFF  H5'2  C5'  C4'   107.53  3.000
 GFF  H5'1  C5'  C4'   110.79  3.000
 GFF  H5'2  C5'  O5'   110.69  3.000
 GFF  H5'1  C5'  O5'   111.21  3.000
 GFF  C4'   C5'  O5'   108.69  3.000
 GFF  H4'   C4'  C3'   110.61  3.000
 GFF  H4'   C4'  O4'   108.28  3.000
 GFF  C3'   C4'  O4'   105.70  3.000
 GFF  H4'   C4'  C5'   109.38  3.000
 GFF  O4'   C4'  C5'   111.45  3.000
 GFF  C3'   C4'  C5'   111.35  3.000
 GFF  C1'   O4'  C4'   110.57  3.000
 GFF  H1'   C1'  C2'   110.72  3.000
 GFF  H1'   C1'  N9    105.67  3.000
 GFF  C2'   C1'  N9    114.75  3.000
 GFF  H1'   C1'  O4'   110.04  3.000
 GFF  C2'   C1'  O4'   105.97  3.000
 GFF  N9    C1'  O4'   109.71  3.000
 GFF  C8    N9   C4    106.73  3.000
 GFF  C4    N9   C1'   125.42  3.000
 GFF  C8    N9   C1'   127.72  3.000
 GFF  C5    C4   N3    128.24  3.000
 GFF  N3    C4   N9    126.47  3.000
 GFF  C5    C4   N9    105.28  3.000
 GFF  C2    N3   C4    113.26  3.000
 GFF  N1    C2   N2    116.94  3.000
 GFF  N1    C2   N3    123.04  3.000
 GFF  N2    C2   N3    119.99  3.000
 GFF  HN22  N2   HN21  115.89  3.000
 GFF  HN22  N2   C2    120.51  3.000
 GFF  HN21  N2   C2    117.10  3.000
 GFF  HN1   N1   C6    115.63  3.000
 GFF  HN1   N1   C2    118.32  3.000
 GFF  C6    N1   C2    126.05  3.000
 GFF  C5    C6   O6    128.99  3.000
 GFF  C5    C6   N1    110.64  3.000
 GFF  O6    C6   N1    120.37  3.000
 GFF  N7    C5   C6    130.59  3.000
 GFF  N7    C5   C4    110.63  3.000
 GFF  C6    C5   C4    118.78  3.000
 GFF  C8    N7   C5    105.18  3.000
 GFF  H8    C8   N7    125.80  3.000
 GFF  H8    C8   N9    121.98  3.000
 GFF  N7    C8   N9    112.18  3.000
 GFF  H2'2  C2'  H2'1  108.44  3.000
 GFF  H2'2  C2'  C3'   113.46  3.000
 GFF  H2'1  C2'  C3'   109.75  3.000
 GFF  H2'2  C2'  C1'   112.31  3.000
 GFF  H2'1  C2'  C1'   111.48  3.000
 GFF  C3'   C2'  C1'   101.29  3.000
 GFF  H3'   C3'  O3'   111.25  3.000
 GFF  H3'   C3'  C2'   111.78  3.000
 GFF  O3'   C3'  C2'   112.46  3.000
 GFF  H3'   C3'  C4'   111.48  3.000
 GFF  O3'   C3'  C4'   108.11  3.000
 GFF  C2'   C3'  C4'   101.32  3.000
 GFF  H1    O3'  C3'   108.04  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   -173.56  30.0  3
 GFF  Var_02    O1B   P2   O3A  P1     45.03  30.0  3
 GFF  Var_03    F1B   C3B  P2   O3A  -177.80  30.0  3
 GFF  Var_04    O1G   P3   C3B  P2    -51.18  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

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

