# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:07:08 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  36  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  -0.495  -1.2931   0.6487  -2.5305
 HA1  C8    C  CR15  0   0.090  -2.4429   0.2623  -3.1654
 HA1  N7    N  N     0  -0.448  -2.2301  -0.2822  -4.3253
 HA1  C5    C  CR56  0  -0.088  -0.8666  -0.2612  -4.4660
 HA1  C6    C  CR6   0   0.500  -0.0353  -0.7144  -5.5298
 HA1  O6    O  O     0  -0.477  -0.3568  -1.2369  -6.5846
 HA1  N1    N  NR16  0  -0.728   1.3144  -0.4849  -5.2328
 HA1  C2    C  CR6   0   0.688   1.8033   0.0912  -4.0940
 HA1  N2    N  NH2   0  -0.836   3.1337   0.1928  -3.9889
 HA1  N3    N  N     0  -0.513   1.0348   0.5127  -3.1206
 HA1  C4    C  CR56  0   0.497  -0.2701   0.3123  -3.3563
 HA1  C10   C  CH2   0  -0.301  -1.1803   1.2452  -1.2152
 HA1  C11   C  CH2   0  -0.437  -0.7454   0.2420  -0.1560
 HA1  C12   C  CH2   0  -0.448  -0.6507   0.8991   1.2146
 HA1  C13   C  CH2   0  -0.569  -0.1729  -0.0990   2.2674
 HA1  C14   C  CT    0   0.504  -0.0802   0.4901   3.6508
 HA1  F15   F  F     0  -0.347   0.7517   1.5750   3.6562
 HA1  F16   F  F     0  -0.345  -1.3008   0.9483   4.0596
 HA1  P     P  P     0   1.333   0.5480  -0.6079   5.0088
 HA1  O2P   O  OH1   0  -0.741  -0.4687  -1.8293   4.8731
 HA1  O1P   O  O     0  -0.687   0.6477   0.0804   6.3109
 HA1  O3P   O  OH1   0  -0.739   1.9804  -1.1096   4.5048
 HA1  H8    H  HCR5  0   0.286  -3.4098   0.4218  -2.7113
 HA1  HN1   H  HNR6  0   0.424   1.9746  -0.7839  -5.9398
 HA1  HN21  H  HNH2  0   0.413   3.5140   0.7066  -3.2131
 HA1  HN22  H  HNH2  0   0.416   3.7442   0.0102  -4.7657
 HA1  H101  H  HCH2  0   0.264  -0.4717   2.0728  -1.2728
 HA1  H102  H  HCH2  0   0.268  -2.1529   1.6697  -0.9648
 HA1  H111  H  HCH2  0   0.239  -1.4588  -0.5860  -0.1263
 HA1  H112  H  HCH2  0   0.242   0.2237  -0.1802  -0.4342
 HA1  H121  H  HCH2  0   0.244   0.0377   1.7456   1.1622
 HA1  H122  H  HCH2  0   0.244  -1.6279   1.3003   1.4926
 HA1  H131  H  HCH2  0   0.274  -0.8487  -0.9567   2.3027
 HA1  H132  H  HCH2  0   0.265   0.8094  -0.4855   1.9845
 HA1  H2P   H  HOH1  0   0.508  -0.4900  -2.4322   5.6308
 HA1  H3P   H  HOH1  0   0.500   1.9943  -1.8450   3.8779

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    1.449  0.020  1.449
 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    1.367  0.020  1.367
 HA1  N1   HN1   single    0.860  0.020  1.020
 HA1  C2   N2    single    1.338  0.020  1.338
 HA1  C2   N3    double    1.310  0.020  1.310
 HA1  N2   HN21  single    0.860  0.020  1.020
 HA1  N2   HN22  single    0.860  0.020  1.020
 HA1  N3   C4    single    1.341  0.020  1.341
 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    1.527  0.020  1.527
 HA1  C12  H121  single    0.970  0.020  1.090
 HA1  C12  H122  single    0.970  0.020  1.090
 HA1  C13  C14   single    1.507  0.020  1.507
 HA1  C13  H131  single    0.970  0.020  1.090
 HA1  C13  H132  single    0.970  0.020  1.090
 HA1  C14  F15   single    1.367  0.020  1.367
 HA1  C14  F16   single    1.366  0.020  1.366
 HA1  C14  P     single    1.856  0.020  1.856
 HA1  P    O2P   single    1.595  0.020  1.595
 HA1  P    O1P   double    1.476  0.020  1.476
 HA1  P    O3P   single    1.599  0.020  1.599
 HA1  O2P  H2P   single    0.850  0.020  0.980
 HA1  O3P  H3P   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
 HA1  C10   N9   C4    126.58  3.000
 HA1  C10   N9   C8    127.06  3.000
 HA1  C4    N9   C8    106.31  3.000
 HA1  H8    C8   N7    125.74  3.000
 HA1  H8    C8   N9    121.01  3.000
 HA1  N7    C8   N9    113.25  3.000
 HA1  C5    N7   C8    104.37  3.000
 HA1  C4    C5   C6    118.63  3.000
 HA1  C4    C5   N7    110.66  3.000
 HA1  C6    C5   N7    130.72  3.000
 HA1  N1    C6   O6    120.48  3.000
 HA1  N1    C6   C5    110.60  3.000
 HA1  O6    C6   C5    128.92  3.000
 HA1  HN1   N1   C2    118.23  3.000
 HA1  HN1   N1   C6    115.58  3.000
 HA1  C2    N1   C6    126.19  3.000
 HA1  N3    C2   N2    120.02  3.000
 HA1  N3    C2   N1    123.02  3.000
 HA1  N2    C2   N1    116.94  3.000
 HA1  HN22  N2   HN21  117.37  3.000
 HA1  HN22  N2   C2    121.97  3.000
 HA1  HN21  N2   C2    118.40  3.000
 HA1  C4    N3   C2    113.09  3.000
 HA1  N3    C4   C5    128.47  3.000
 HA1  N3    C4   N9    126.12  3.000
 HA1  C5    C4   N9    105.41  3.000
 HA1  H102  C10  H101  107.23  3.000
 HA1  H102  C10  C11   110.59  3.000
 HA1  H101  C10  C11   110.55  3.000
 HA1  H102  C10  N9    107.42  3.000
 HA1  H101  C10  N9    108.36  3.000
 HA1  C11   C10  N9    112.50  3.000
 HA1  H112  C11  H111  107.03  3.000
 HA1  H112  C11  C12   109.91  3.000
 HA1  H111  C11  C12   110.05  3.000
 HA1  H112  C11  C10   109.31  3.000
 HA1  H111  C11  C10   109.36  3.000
 HA1  C12   C11  C10   111.08  3.000
 HA1  H122  C12  H121  106.94  3.000
 HA1  H122  C12  C13   110.15  3.000
 HA1  H121  C12  C13   110.02  3.000
 HA1  H122  C12  C11   109.39  3.000
 HA1  H121  C12  C11   109.29  3.000
 HA1  C13   C12  C11   110.97  3.000
 HA1  H132  C13  H131  106.66  3.000
 HA1  H132  C13  C14   108.71  3.000
 HA1  H131  C13  C14   108.38  3.000
 HA1  H132  C13  C12   109.51  3.000
 HA1  H131  C13  C12   109.98  3.000
 HA1  C14   C13  C12   113.37  3.000
 HA1  P     C14  F16   106.37  3.000
 HA1  P     C14  F15   105.11  3.000
 HA1  F16   C14  F15   106.04  3.000
 HA1  P     C14  C13   117.48  3.000
 HA1  F16   C14  C13   110.54  3.000
 HA1  F15   C14  C13   110.57  3.000
 HA1  O3P   P    O1P   111.34  3.000
 HA1  O3P   P    O2P   107.69  3.000
 HA1  O1P   P    O2P   118.37  3.000
 HA1  O3P   P    C14   104.96  3.000
 HA1  O1P   P    C14   113.11  3.000
 HA1  O2P   P    C14   100.08  3.000
 HA1  H2P   O2P  P     115.10  3.000
 HA1  H3P   O3P  P     117.13  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    101.43  30.0  2
 HA1  Var_02    C12   C11  C10  N9   -179.44  30.0  3
 HA1  Var_03    C13   C12  C11  C10  -178.26  30.0  3
 HA1  Var_04    C14   C13  C12  C11  -179.10  30.0  3
 HA1  Var_05    F15   C14  C13  C12   -57.26  30.0  3
 HA1  Var_06    O2P   P    C14  C13   -55.28  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

