# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 08:41:23 2020
#   Inital geometry file: a 93 line input string
#   Ligand name: [5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1,1-difluoropentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CCCCC(F)(F)[P](O)(O)=O)cnc2C(=O)N1
#
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
 HA1  HA1  '[5-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-1,1-difluoropentyl]phosphonic acid'  ligand  34  22  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HA1
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
 HA1  N9    N  NR5    0  -0.494  -1.3112   0.6263  -2.5204
 HA1  C8    C  CR15   0   0.090  -2.4603   0.2245  -3.1460
 HA1  N7    N  N      0  -0.449  -2.2519  -0.2988  -4.3167
 HA1  C5    C  CR56   0  -0.088  -0.8913  -0.2469  -4.4742
 HA1  C6    C  CR6    0   0.499  -0.0658  -0.6640  -5.5570
 HA1  O6    O  O      0  -0.477  -0.3905  -1.1788  -6.6146
 HA1  N1    N  NR16   0  -0.727   1.2820  -0.4062  -5.2760
 HA1  C2    C  CR6    0   0.683   1.7743   0.1640  -4.1359
 HA1  N2    N  NH2    0  -0.834   3.1004   0.3583  -4.0793
 HA1  N3    N  N      0  -0.512   1.0120   0.5453  -3.1424
 HA1  C4    C  CR56   0   0.496  -0.2924   0.3225  -3.3635
 HA1  C10   C  CH2    0  -0.300  -1.1970   1.2112  -1.1991
 HA1  C11   C  CH2    0  -0.431  -0.7504   0.2083  -0.1451
 HA1  C12   C  CH2    0  -0.439  -0.6619   0.8570   1.2297
 HA1  C13   C  CH2    0  -0.540  -0.1716  -0.1233   2.2904
 HA1  C14   C  CT     0   0.449  -0.0740   0.4375   3.6883
 HA1  F15   F  F      0  -0.395   0.6981   1.5920   3.6468
 HA1  F16   F  F      0  -0.395  -1.3311   0.8974   4.0640
 HA1  P     P  P      0   1.110   0.5983  -0.7267   5.0035
 HA1  O2P   O  OP    -1  -0.891  -0.4074  -1.8768   4.9913
 HA1  O1P   O  O      0  -0.893   0.5990   0.1120   6.2801
 HA1  O3P   O  OP    -1  -0.891   1.9857  -1.0817   4.4699
 HA1  H8    H  HCR5   0   0.285  -3.4242   0.3566  -2.6770
 HA1  HN1   H  HNR6   0   0.424   1.9376  -0.6691  -6.0006
 HA1  HN21  H  HNH2   0   0.412   3.4954   0.6340  -3.1965
 HA1  HN22  H  HNH2   0   0.414   3.7215  -0.0953  -4.7274
 HA1  H101  H  HCH2   0   0.260  -0.4956   2.0451  -1.2545
 HA1  H102  H  HCH2   0   0.265  -2.1718   1.6274  -0.9426
 HA1  H111  H  HCH2   0   0.231  -1.4531  -0.6295  -0.1214
 HA1  H112  H  HCH2   0   0.233   0.2233  -0.2016  -0.4275
 HA1  H121  H  HCH2   0   0.224   0.0130   1.7154   1.1763
 HA1  H122  H  HCH2   0   0.223  -1.6446   1.2494   1.5058
 HA1  H131  H  HCH2   0   0.230  -0.8309  -0.9943   2.3342
 HA1  H132  H  HCH2   0   0.230   0.8152  -0.5065   2.0184

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
 HA1  N9   C8    aromatic  1.369  0.020  1.369
 HA1  N9   C4    aromatic  1.357  0.020  1.357
 HA1  N9   C10   single    1.450  0.020  1.450
 HA1  C8   N7    aromatic  1.299  0.020  1.299
 HA1  C8   H8    single    0.930  0.020  1.080
 HA1  N7   C5    aromatic  1.371  0.020  1.371
 HA1  C5   C6    single    1.424  0.020  1.424
 HA1  C5   C4    aromatic  1.384  0.020  1.384
 HA1  C6   O6    double    1.220  0.020  1.220
 HA1  C6   N1    single    1.401  0.020  1.401
 HA1  N1   C2    single    1.366  0.020  1.366
 HA1  N1   HN1   single    0.860  0.020  1.020
 HA1  C2   N2    single    1.341  0.020  1.341
 HA1  C2   N3    double    1.309  0.020  1.309
 HA1  N2   HN21  single    0.890  0.020  1.040
 HA1  N2   HN22  single    0.890  0.020  1.040
 HA1  N3   C4    single    1.342  0.020  1.342
 HA1  C10  C11   single    1.522  0.020  1.522
 HA1  C10  H101  single    0.970  0.020  1.090
 HA1  C10  H102  single    0.970  0.020  1.090
 HA1  C11  C12   single    1.523  0.020  1.523
 HA1  C11  H111  single    0.970  0.020  1.090
 HA1  C11  H112  single    0.970  0.020  1.090
 HA1  C12  C13   single    1.525  0.020  1.525
 HA1  C12  H121  single    0.970  0.020  1.090
 HA1  C12  H122  single    0.970  0.020  1.090
 HA1  C13  C14   single    1.509  0.020  1.509
 HA1  C13  H131  single    0.970  0.020  1.090
 HA1  C13  H132  single    0.970  0.020  1.090
 HA1  C14  F15   single    1.389  0.020  1.389
 HA1  C14  F16   single    1.390  0.020  1.390
 HA1  C14  P     single    1.881  0.020  1.881
 HA1  P    O2P   deloc     1.528  0.020  1.528
 HA1  P    O1P   deloc     1.527  0.020  1.527
 HA1  P    O3P   deloc     1.528  0.020  1.528

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
 HA1  C10   N9   C4    126.70  3.000
 HA1  C10   N9   C8    126.96  3.000
 HA1  C4    N9   C8    106.30  3.000
 HA1  H8    C8   N7    125.71  3.000
 HA1  H8    C8   N9    121.00  3.000
 HA1  N7    C8   N9    113.29  3.000
 HA1  C5    N7   C8    104.33  3.000
 HA1  C4    C5   C6    118.67  3.000
 HA1  C4    C5   N7    110.66  3.000
 HA1  C6    C5   N7    130.67  3.000
 HA1  N1    C6   O6    120.50  3.000
 HA1  N1    C6   C5    110.57  3.000
 HA1  O6    C6   C5    128.93  3.000
 HA1  HN1   N1   C2    118.19  3.000
 HA1  HN1   N1   C6    115.59  3.000
 HA1  C2    N1   C6    126.21  3.000
 HA1  N3    C2   N2    120.10  3.000
 HA1  N3    C2   N1    123.02  3.000
 HA1  N2    C2   N1    116.86  3.000
 HA1  HN22  N2   HN21  116.54  3.000
 HA1  HN22  N2   C2    121.20  3.000
 HA1  HN21  N2   C2    117.71  3.000
 HA1  C4    N3   C2    113.12  3.000
 HA1  N3    C4   C5    128.40  3.000
 HA1  N3    C4   N9    126.19  3.000
 HA1  C5    C4   N9    105.42  3.000
 HA1  H102  C10  H101  107.16  3.000
 HA1  H102  C10  C11   110.54  3.000
 HA1  H101  C10  C11   110.50  3.000
 HA1  H102  C10  N9    107.34  3.000
 HA1  H101  C10  N9    108.22  3.000
 HA1  C11   C10  N9    112.86  3.000
 HA1  H112  C11  H111  106.89  3.000
 HA1  H112  C11  C12   109.94  3.000
 HA1  H111  C11  C12   110.13  3.000
 HA1  H112  C11  C10   109.23  3.000
 HA1  H111  C11  C10   109.34  3.000
 HA1  C12   C11  C10   111.20  3.000
 HA1  H122  C12  H121  106.58  3.000
 HA1  H122  C12  C13   110.12  3.000
 HA1  H121  C12  C13   109.88  3.000
 HA1  H122  C12  C11   109.18  3.000
 HA1  H121  C12  C11   109.04  3.000
 HA1  C13   C12  C11   111.88  3.000
 HA1  H132  C13  H131  105.97  3.000
 HA1  H132  C13  C14   107.60  3.000
 HA1  H131  C13  C14   107.33  3.000
 HA1  H132  C13  C12   110.03  3.000
 HA1  H131  C13  C12   110.24  3.000
 HA1  C14   C13  C12   115.21  3.000
 HA1  P     C14  F16   109.82  3.000
 HA1  P     C14  F15   109.67  3.000
 HA1  F16   C14  F15   103.64  3.000
 HA1  P     C14  C13   116.15  3.000
 HA1  F16   C14  C13   108.34  3.000
 HA1  F15   C14  C13   108.48  3.000
 HA1  O3P   P    O1P   114.77  3.000
 HA1  O3P   P    O2P   114.83  3.000
 HA1  O1P   P    O2P   114.85  3.000
 HA1  O3P   P    C14   102.95  3.000
 HA1  O1P   P    C14   104.17  3.000
 HA1  O2P   P    C14   103.01  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
 HA1  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 HA1  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 HA1  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 HA1  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 HA1  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 HA1  CONST_06  C2    N1   C6   C5      0.00   0.0  0
 HA1  CONST_07  N3    C2   N1   C6      0.00   0.0  0
 HA1  CONST_08  C4    N3   C2   N1      0.00   0.0  0
 HA1  CONST_09  C10   N9   C8   N7    180.00   0.0  0
 HA1  CONST_10  C10   N9   C4   C5    180.00   0.0  0
 HA1  CONST_11  C10   N9   C4   N3      0.00   0.0  0
 HA1  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 HA1  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 HA1  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 HA1  CONST_15  H8    C8   N7   C5    180.00   0.0  0
 HA1  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 HA1  CONST_17  HN21  N2   C2   N1    180.00   0.0  0
 HA1  CONST_18  HN22  N2   C2   N1      0.00   0.0  0
 HA1  Var_01    C11   C10  N9   C8    100.64  30.0  2
 HA1  Var_02    C12   C11  C10  N9   -179.21  30.0  3
 HA1  Var_03    C13   C12  C11  C10  -178.13  30.0  3
 HA1  Var_04    C14   C13  C12  C11  -179.19  30.0  3
 HA1  Var_05    F15   C14  C13  C12   -53.44  30.0  3
 HA1  Var_06    O2P   P    C14  C13   -60.63  30.0  3

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
 HA1  plan-1  N9    0.020
 HA1  plan-1  C8    0.020
 HA1  plan-1  N7    0.020
 HA1  plan-1  C5    0.020
 HA1  plan-1  C6    0.020
 HA1  plan-1  O6    0.020
 HA1  plan-1  N1    0.020
 HA1  plan-1  C2    0.020
 HA1  plan-1  N2    0.020
 HA1  plan-1  N3    0.020
 HA1  plan-1  C4    0.020
 HA1  plan-1  C10   0.020
 HA1  plan-1  H8    0.020
 HA1  plan-1  HN1   0.020
 HA1  plan-1  HN21  0.020
 HA1  plan-1  HN22  0.020

