# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 23:03:31 2020
#   Inital geometry file: a 74 line input string
#   Ligand name: {[2-(6-amino-9H-purin-9-yl)ethoxy]methyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCOC[P](O)(O)=O)cnc12
#
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
 5HG  5HG  '{[2-(6-amino-9H-purin-9-yl)ethoxy]methyl}phosphonic acid'  ligand  28  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5HG
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
 5HG  O36   O  O      0  -0.909  -4.8104  -0.5551   0.8217
 5HG  P30   P  P      0   1.136  -4.2000  -0.1499  -0.5241
 5HG  O32   O  OP    -1  -0.909  -5.2126   0.4261  -1.5241
 5HG  O34   O  OP    -1  -0.897  -3.2732  -1.2154  -1.1272
 5HG  C28   C  CH2    0  -0.454  -3.1287   1.3352  -0.1571
 5HG  O26   O  O2     0  -0.503  -2.1041   1.1440   0.8161
 5HG  C24   C  CH2    0  -0.119  -0.9768   0.4749   0.3339
 5HG  C22   C  CH2    0  -0.356   0.0490   0.4610   1.4573
 5HG  N17   N  NR5    0  -0.496   1.2707  -0.1973   1.0455
 5HG  C15   C  CR15   0   0.108   1.5984  -1.5098   1.2232
 5HG  N13   N  N      0  -0.455   2.7509  -1.8364   0.7125
 5HG  C2    C  CR56   0  -0.004   3.2108  -0.6711   0.1574
 5HG  C3    C  CR56   0   0.480   2.3017   0.3589   0.3504
 5HG  N4    N  N      0  -0.456   2.4346   1.6198  -0.0589
 5HG  C5    C  CR16   0   0.037   3.5742   1.8071  -0.6996
 5HG  N6    N  N      0  -0.476   4.5350   0.9219  -0.9576
 5HG  C1    C  CR6    0   0.452   4.3880  -0.3397  -0.5383
 5HG  N20   N  NH2    0  -0.818   5.3552  -1.2260  -0.7841
 5HG  H281  H  HCH2   0   0.193  -3.7569   2.1405   0.2396
 5HG  H282  H  HCH2   0   0.166  -2.6829   1.7261  -1.0863
 5HG  H241  H  HCH2   0   0.186  -0.5517   0.9923  -0.5410
 5HG  H242  H  HCH2   0   0.208  -1.2083  -0.5481   0.0206
 5HG  H221  H  HCH2   0   0.271  -0.3403  -0.0676   2.3277
 5HG  H222  H  HCH2   0   0.263   0.2959   1.4765   1.7672
 5HG  H15   H  HCR5   0   0.293   0.9373  -2.1806   1.7525
 5HG  H5    H  HCR6   0   0.249   3.7570   2.8112  -1.0676
 5HG  H201  H  HNH2   0   0.402   6.1567  -0.9630  -1.3311
 5HG  H202  H  HNH2   0   0.410   5.2531  -2.1910  -0.5240

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
 5HG  O36  P30   deloc     1.532  0.020  1.532
 5HG  P30  O32   deloc     1.535  0.020  1.535
 5HG  P30  O34   deloc     1.536  0.020  1.536
 5HG  P30  C28   single    1.868  0.020  1.868
 5HG  C28  O26   single    1.426  0.020  1.426
 5HG  C28  H281  single    0.970  0.020  1.090
 5HG  C28  H282  single    0.970  0.020  1.090
 5HG  O26  C24   single    1.397  0.020  1.397
 5HG  C24  C22   single    1.521  0.020  1.521
 5HG  C24  H241  single    0.970  0.020  1.090
 5HG  C24  H242  single    0.970  0.020  1.090
 5HG  C22  N17   single    1.448  0.020  1.448
 5HG  C22  H221  single    0.970  0.020  1.090
 5HG  C22  H222  single    0.970  0.020  1.090
 5HG  N17  C15   aromatic  1.364  0.020  1.364
 5HG  N17  C3    aromatic  1.362  0.020  1.362
 5HG  C15  N13   aromatic  1.302  0.020  1.302
 5HG  C15  H15   single    0.930  0.020  1.080
 5HG  N13  C2    aromatic  1.370  0.020  1.370
 5HG  C2   C3    aromatic  1.387  0.020  1.387
 5HG  C2   C1    aromatic  1.407  0.020  1.407
 5HG  C3   N4    aromatic  1.332  0.020  1.332
 5HG  N4   C5    aromatic  1.321  0.020  1.321
 5HG  C5   N6    aromatic  1.332  0.020  1.332
 5HG  C5   H5    single    0.930  0.020  1.080
 5HG  N6   C1    aromatic  1.338  0.020  1.338
 5HG  C1   N20   single    1.335  0.020  1.335
 5HG  N20  H201  single    0.860  0.020  1.020
 5HG  N20  H202  single    0.860  0.020  1.020

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
 5HG  C28   P30  O34   106.43  3.000
 5HG  C28   P30  O32   102.01  3.000
 5HG  O34   P30  O32   113.74  3.000
 5HG  C28   P30  O36   105.44  3.000
 5HG  O34   P30  O36   113.70  3.000
 5HG  O32   P30  O36   114.11  3.000
 5HG  H282  C28  H281  106.05  3.000
 5HG  H282  C28  O26   109.41  3.000
 5HG  H281  C28  O26   105.27  3.000
 5HG  H282  C28  P30   110.39  3.000
 5HG  H281  C28  P30   109.07  3.000
 5HG  O26   C28  P30   116.08  3.000
 5HG  C24   O26  C28   114.11  3.000
 5HG  H242  C24  H241  107.05  3.000
 5HG  H242  C24  C22   110.21  3.000
 5HG  H241  C24  C22   109.30  3.000
 5HG  H242  C24  O26   112.07  3.000
 5HG  H241  C24  O26   111.14  3.000
 5HG  C22   C24  O26   107.08  3.000
 5HG  H222  C22  H221  107.80  3.000
 5HG  H222  C22  N17   108.27  3.000
 5HG  H221  C22  N17   107.94  3.000
 5HG  H222  C22  C24   110.74  3.000
 5HG  H221  C22  C24   110.68  3.000
 5HG  N17   C22  C24   111.29  3.000
 5HG  C3    N17  C15   106.11  3.000
 5HG  C3    N17  C22   126.75  3.000
 5HG  C15   N17  C22   127.09  3.000
 5HG  H15   C15  N13   125.31  3.000
 5HG  H15   C15  N17   120.94  3.000
 5HG  N13   C15  N17   113.75  3.000
 5HG  C2    N13  C15   104.04  3.000
 5HG  C1    C2   C3    116.25  3.000
 5HG  C1    C2   N13   132.95  3.000
 5HG  C3    C2   N13   110.80  3.000
 5HG  N4    C3   C2    126.48  3.000
 5HG  N4    C3   N17   128.22  3.000
 5HG  C2    C3   N17   105.30  3.000
 5HG  C5    N4   C3    111.67  3.000
 5HG  H5    C5   N6    115.34  3.000
 5HG  H5    C5   N4    116.18  3.000
 5HG  N6    C5   N4    128.49  3.000
 5HG  C1    N6   C5    119.14  3.000
 5HG  N20   C1   N6    119.27  3.000
 5HG  N20   C1   C2    122.75  3.000
 5HG  N6    C1   C2    117.98  3.000
 5HG  H202  N20  H201  118.24  3.000
 5HG  H202  N20  C1    121.10  3.000
 5HG  H201  N20  C1    120.28  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
 5HG  CONST_01  C2    N13  C15  N17     0.00   0.0  0
 5HG  CONST_02  N13   C2   C3   N17     0.00   0.0  0
 5HG  CONST_03  C1    C2   C3   N17   180.00   0.0  0
 5HG  CONST_04  C5    N4   C3   N17   180.00   0.0  0
 5HG  CONST_05  C2    C3   N17  C15     0.00   0.0  0
 5HG  CONST_06  N4    C3   N17  C15   180.00   0.0  0
 5HG  CONST_07  C3    C2   N13  C15     0.00   0.0  0
 5HG  CONST_08  C1    C2   N13  C15   180.00   0.0  0
 5HG  CONST_09  C3    N17  C15  N13     0.00   0.0  0
 5HG  CONST_10  N4    C3   C2   N13   180.00   0.0  0
 5HG  CONST_11  N6    C1   C2   N13   180.00   0.0  0
 5HG  CONST_12  C5    N4   C3   C2      0.00   0.0  0
 5HG  CONST_13  C5    N6   C1   C2      0.00   0.0  0
 5HG  CONST_14  N6    C1   C2   C3      0.00   0.0  0
 5HG  CONST_15  N6    C5   N4   C3      0.00   0.0  0
 5HG  CONST_16  C1    C2   C3   N4      0.00   0.0  0
 5HG  CONST_17  C1    N6   C5   N4      0.00   0.0  0
 5HG  CONST_18  N13   C15  N17  C22   180.00   0.0  0
 5HG  CONST_19  C2    C3   N17  C22   180.00   0.0  0
 5HG  CONST_20  N4    C3   N17  C22     0.00   0.0  0
 5HG  CONST_21  N20   C1   C2   N13     0.00   0.0  0
 5HG  CONST_22  N20   C1   C2   C3    180.00   0.0  0
 5HG  CONST_23  N20   C1   N6   C5    180.00   0.0  0
 5HG  CONST_24  H15   C15  N13  C2    180.00   0.0  0
 5HG  CONST_25  H5    C5   N4   C3    180.00   0.0  0
 5HG  CONST_26  H201  N20  C1   C2    180.00   0.0  0
 5HG  CONST_27  H202  N20  C1   C2      0.00   0.0  0
 5HG  Var_01    C15   N17  C22  C24   -93.69  30.0  2
 5HG  Var_02    N17   C22  C24  O26  -179.09  30.0  3
 5HG  Var_03    O26   C28  P30  O36    57.46  30.0  3
 5HG  Var_04    C22   C24  O26  C28   175.39  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
 5HG  plan-1  C22   0.020
 5HG  plan-1  N17   0.020
 5HG  plan-1  C15   0.020
 5HG  plan-1  N13   0.020
 5HG  plan-1  C2    0.020
 5HG  plan-1  C3    0.020
 5HG  plan-1  N4    0.020
 5HG  plan-1  C5    0.020
 5HG  plan-1  N6    0.020
 5HG  plan-1  C1    0.020
 5HG  plan-1  N20   0.020
 5HG  plan-1  H15   0.020
 5HG  plan-1  H5    0.020
 5HG  plan-2  C1    0.020
 5HG  plan-2  N20   0.020
 5HG  plan-2  H201  0.020
 5HG  plan-2  H202  0.020

