# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:15:48 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: 2-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-3-fluoranyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(cnc2C(=O)N1)[C@@H]3O[C@H](CO)[C@@H](O)[C@H]3F
#
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
 GF0  GF0  2-azanyl-9-[(2~{R},3~{R},4~{R},5~{R})-3-fluoranyl-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-1~{H}-purin-6-one  ligand  32  20  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GF0
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
 GF0  F     F  F     0  -0.366  -1.9570  -2.5998  -0.5139
 GF0  N1    N  NR16  0  -0.729   3.8334  -0.0907   0.1293
 GF0  C2    C  CR6   0   0.692   3.1140  -1.1669  -0.3064
 GF0  N2    N  NH2   0  -0.832   3.7862  -2.3014  -0.5273
 GF0  N3    N  N     0  -0.518   1.8230  -1.1176  -0.5327
 GF0  C4    C  CR56  0   0.506   1.2964   0.0911  -0.2958
 GF0  C5    C  CR56  0  -0.085   1.9278   1.2386   0.1444
 GF0  C6    C  CR6   0   0.505   3.3300   1.1902   0.3938
 GF0  O6    O  O     0  -0.472   4.0699   2.0785   0.7810
 GF0  N7    N  N     0  -0.442   1.0323   2.2692   0.2570
 GF0  C8    C  CR15  0   0.086  -0.1066   1.7616  -0.1032
 GF0  N9    N  NR5   0  -0.541  -0.0104   0.4340  -0.4470
 GF0  C1'   C  CH1   0   0.140  -1.0546  -0.4622  -0.9291
 GF0  C2'   C  CH1   0   0.109  -1.4232  -1.4948   0.1307
 GF0  C3'   C  CH1   0  -0.029  -2.5311  -0.7740   0.8880
 GF0  O3'   O  OH1   0  -0.655  -3.4157  -1.5937   1.5827
 GF0  C4'   C  CH1   0  -0.007  -3.2447  -0.0390  -0.2444
 GF0  O4'   O  O2    0  -0.496  -2.2116   0.2706  -1.1856
 GF0  C5'   C  CH2   0  -0.152  -3.9413   1.2191   0.2082
 GF0  O5'   O  OH1   0  -0.668  -4.5733   1.8139  -0.8970
 GF0  HN2   H  HNH2  0   0.417   4.7386  -2.4211  -0.2290
 GF0  HN2A  H  HNH2  0   0.415   3.2612  -3.1337  -0.7332
 GF0  H8    H  HCR5  0   0.294  -1.0378   2.3024  -0.1513
 GF0  H1'   H  HCH1  0   0.295  -0.6875  -0.9392  -1.8421
 GF0  H2'   H  HCH1  0   0.270  -0.5832  -1.8259   0.7417
 GF0  H3'   H  HCH1  0   0.241  -2.0506  -0.0381   1.5496
 GF0  H1    H  HOH1  0   0.466  -3.0127  -1.8494   2.4182
 GF0  H4'   H  HCH1  0   0.252  -3.9723  -0.7085  -0.7199
 GF0  H5'A  H  HCH2  0   0.216  -4.6587   0.9362   0.9895
 GF0  H5'   H  HCH2  0   0.200  -3.2103   1.8911   0.6774
 GF0  H5T   H  HOH1  0   0.460  -5.0008   2.6220  -0.5996
 GF0  HN1   H  HNR6  0   0.426   4.8278  -0.2079   0.2801

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
 GF0  O6   C6    double    1.219  0.020  1.219
 GF0  C6   C5    single    1.425  0.020  1.425
 GF0  C6   N1    single    1.401  0.020  1.401
 GF0  N7   C5    aromatic  1.370  0.020  1.370
 GF0  N7   C8    aromatic  1.298  0.020  1.298
 GF0  C5   C4    aromatic  1.382  0.020  1.382
 GF0  N1   C2    single    1.366  0.020  1.366
 GF0  C8   N9    aromatic  1.375  0.020  1.375
 GF0  C4   N9    aromatic  1.359  0.020  1.359
 GF0  C4   N3    single    1.340  0.020  1.340
 GF0  C2   N3    double    1.312  0.020  1.312
 GF0  C2   N2    single    1.337  0.020  1.337
 GF0  N9   C1'   single    1.458  0.020  1.458
 GF0  C5'  O5'   single    1.405  0.020  1.405
 GF0  C5'  C4'   single    1.508  0.020  1.508
 GF0  C3'  C4'   single    1.527  0.020  1.527
 GF0  C3'  C2'   single    1.523  0.020  1.523
 GF0  C3'  O3'   single    1.392  0.020  1.392
 GF0  O4'  C1'   single    1.393  0.020  1.393
 GF0  O4'  C4'   single    1.432  0.020  1.432
 GF0  C1'  C2'   single    1.525  0.020  1.525
 GF0  C2'  F     single    1.386  0.020  1.386
 GF0  N1   HN1   single    0.860  0.020  1.020
 GF0  N2   HN2   single    0.860  0.020  1.020
 GF0  N2   HN2A  single    0.860  0.020  1.020
 GF0  C8   H8    single    0.930  0.020  1.080
 GF0  C1'  H1'   single    0.970  0.020  1.090
 GF0  C2'  H2'   single    0.970  0.020  1.090
 GF0  C3'  H3'   single    0.970  0.020  1.090
 GF0  O3'  H1    single    0.850  0.020  0.980
 GF0  C4'  H4'   single    0.970  0.020  1.090
 GF0  C5'  H5'A  single    0.970  0.020  1.090
 GF0  C5'  H5'   single    0.970  0.020  1.090
 GF0  O5'  H5T   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
 GF0  HN1   N1   C6    115.50  3.000
 GF0  HN1   N1   C2    118.26  3.000
 GF0  C6    N1   C2    126.24  3.000
 GF0  N3    C2   N2    119.88  3.000
 GF0  N2    C2   N1    117.16  3.000
 GF0  N3    C2   N1    122.95  3.000
 GF0  HN2A  N2   HN2   117.19  3.000
 GF0  HN2A  N2   C2    118.28  3.000
 GF0  HN2   N2   C2    121.90  3.000
 GF0  C4    N3   C2    112.98  3.000
 GF0  N9    C4   C5    105.38  3.000
 GF0  N9    C4   N3    125.86  3.000
 GF0  C5    C4   N3    128.76  3.000
 GF0  N7    C5   C6    130.87  3.000
 GF0  N7    C5   C4    110.62  3.000
 GF0  C6    C5   C4    118.50  3.000
 GF0  O6    C6   C5    128.90  3.000
 GF0  C5    C6   N1    110.58  3.000
 GF0  O6    C6   N1    120.52  3.000
 GF0  C8    N7   C5    104.86  3.000
 GF0  H8    C8   N9    122.26  3.000
 GF0  H8    C8   N7    125.04  3.000
 GF0  N9    C8   N7    112.69  3.000
 GF0  C1'   N9   C8    128.76  3.000
 GF0  C1'   N9   C4    124.76  3.000
 GF0  C8    N9   C4    106.44  3.000
 GF0  H1'   C1'  O4'   110.76  3.000
 GF0  H1'   C1'  C2'   111.47  3.000
 GF0  O4'   C1'  C2'   106.46  3.000
 GF0  H1'   C1'  N9    107.69  3.000
 GF0  C2'   C1'  N9    111.07  3.000
 GF0  O4'   C1'  N9    109.41  3.000
 GF0  H2'   C2'  C3'   115.18  3.000
 GF0  H2'   C2'  C1'   114.13  3.000
 GF0  C3'   C2'  C1'   101.59  3.000
 GF0  H2'   C2'  F     108.37  3.000
 GF0  C1'   C2'  F     108.04  3.000
 GF0  C3'   C2'  F     109.17  3.000
 GF0  H3'   C3'  C4'   109.15  3.000
 GF0  H3'   C3'  O3'   111.81  3.000
 GF0  C4'   C3'  O3'   110.89  3.000
 GF0  H3'   C3'  C2'   107.33  3.000
 GF0  O3'   C3'  C2'   115.58  3.000
 GF0  C4'   C3'  C2'   101.47  3.000
 GF0  H1    O3'  C3'   108.89  3.000
 GF0  H4'   C4'  C5'   109.45  3.000
 GF0  H4'   C4'  O4'   109.01  3.000
 GF0  C5'   C4'  O4'   110.51  3.000
 GF0  H4'   C4'  C3'   109.73  3.000
 GF0  O4'   C4'  C3'   104.74  3.000
 GF0  C5'   C4'  C3'   113.26  3.000
 GF0  C4'   O4'  C1'   111.38  3.000
 GF0  H5'   C5'  H5'A  106.78  3.000
 GF0  H5'   C5'  O5'   112.11  3.000
 GF0  H5'A  C5'  O5'   112.01  3.000
 GF0  H5'   C5'  C4'   109.35  3.000
 GF0  H5'A  C5'  C4'   107.49  3.000
 GF0  O5'   C5'  C4'   108.96  3.000
 GF0  H5T   O5'  C5'   108.21  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
 GF0  CONST_01  C8    N7  C5  C4    0.00  0.0  0
 GF0  CONST_02  N7    C8  N9  C4    0.00  0.0  0
 GF0  CONST_03  N9    C8  N7  C5    0.00  0.0  0
 GF0  CONST_04  C8    N9  C4  C5    0.00  0.0  0
 GF0  CONST_05  N9    C4  C5  N7    0.00  0.0  0
 GF0  CONST_06  C1'   N9  C4  N3    0.00  0.0  0
 GF0  CONST_07  C1'   N9  C4  C5  180.00  0.0  0
 GF0  CONST_08  C1'   N9  C8  N7  180.00  0.0  0
 GF0  CONST_09  C4    N3  C2  N1    0.00  0.0  0
 GF0  CONST_10  C5    C6  N1  C2    0.00  0.0  0
 GF0  CONST_11  C6    N1  C2  N3    0.00  0.0  0
 GF0  CONST_12  O6    C6  N1  C2  180.00  0.0  0
 GF0  CONST_13  C6    N1  C2  N2  180.00  0.0  0
 GF0  CONST_14  C4    N3  C2  N2  180.00  0.0  0
 GF0  CONST_15  H8    C8  N9  C4  180.00  0.0  0
 GF0  CONST_16  HN1   N1  C2  N3  180.00  0.0  0
 GF0  CONST_17  HN2   N2  C2  N1    0.00  0.0  0
 GF0  CONST_18  HN2A  N2  C2  N1  180.00  0.0  0

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
 GF0  chir_01  C1'  N9   O4'  C2'  positiv
 GF0  chir_02  C2'  F    C3'  C1'  positiv
 GF0  chir_03  C3'  O3'  C4'  C2'  positiv
 GF0  chir_04  C4'  O4'  C3'  C5'  negativ

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
 GF0  plan-1  N1    0.020
 GF0  plan-1  C2    0.020
 GF0  plan-1  N2    0.020
 GF0  plan-1  N3    0.020
 GF0  plan-1  C4    0.020
 GF0  plan-1  C5    0.020
 GF0  plan-1  C6    0.020
 GF0  plan-1  O6    0.020
 GF0  plan-1  N7    0.020
 GF0  plan-1  C8    0.020
 GF0  plan-1  N9    0.020
 GF0  plan-1  C1'   0.020
 GF0  plan-1  HN2   0.020
 GF0  plan-1  HN2A  0.020
 GF0  plan-1  H8    0.020
 GF0  plan-1  HN1   0.020

