# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 13:14:07 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: {[(1S)-2-(2,6-diamino-9H-purin-9-yl)-1-methylethoxy]methyl}phosphonate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Cn1cnc2c(N)nc(N)nc12)OC[P]([O-])([O-])=O
#
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
 9PP  9PP  {[(1S)-2-(2,6-diamino-9H-purin-9-yl)-1-methylethoxy]methyl}phosphonate  ligand  33  20  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9PP
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
 9PP  N9    N  NR5    0  -0.497   0.1165   1.2889   0.7848
 9PP  C8    C  CR15   0   0.141   0.1305   0.6485   1.9927
 9PP  N7    N  N      0  -0.471   1.1740  -0.1017   2.1733
 9PP  C5    C  CR56   0  -0.033   1.8759   0.0163   0.9984
 9PP  C6    C  CR6    0   0.429   3.0942  -0.5107   0.5432
 9PP  N6    N  NH2    0  -0.824   3.8284  -1.3638   1.2772
 9PP  N1    N  N      0  -0.523   3.5289  -0.1717  -0.6696
 9PP  C2    C  CR6    0   0.506   2.7947   0.6666  -1.4165
 9PP  N2    N  NH2    0  -0.828   3.2813   0.9264  -2.6644
 9PP  N3    N  N      0  -0.518   1.6387   1.2358  -1.0892
 9PP  C4    C  CR56   0   0.515   1.2269   0.8724   0.1216
 9PP  C10   C  CH2    0  -0.325  -0.8816   2.2067   0.2861
 9PP  C11   C  CH1    0   0.042  -2.0704   1.4922  -0.3347
 9PP  C12   C  CH3    0  -0.680  -3.0209   2.4936  -0.9788
 9PP  O13   O  O2     0  -0.508  -2.7041   0.7788   0.7004
 9PP  P     P  P      0   1.154  -2.1987  -1.8549  -0.1588
 9PP  C14   C  CH2    0  -0.462  -3.3292  -0.4331   0.2916
 9PP  O2P   O  O      0  -0.881  -1.2922  -2.0639   1.0548
 9PP  O3P   O  OP    -1  -0.919  -3.2191  -2.9886  -0.3739
 9PP  O1P   O  OP    -1  -0.888  -1.4678  -1.4516  -1.4474
 9PP  H81   H  HCR5   0   0.262  -0.6625   0.7966   2.7084
 9PP  HN61  H  HNH2   0   0.400   3.6100  -1.4966   2.2490
 9PP  HN62  H  HNH2   0   0.392   4.7672  -1.5754   0.9859
 9PP  HN21  H  HNH2   0   0.381   4.2647   0.7674  -2.8046
 9PP  HN22  H  HNH2   0   0.381   2.9174   1.7433  -3.1257
 9PP  H101  H  HCH2   0   0.255  -0.3992   2.8504  -0.4497
 9PP  H102  H  HCH2   0   0.252  -1.2089   2.8442   1.1104
 9PP  H111  H  HCH1   0   0.237  -1.6941   0.7987  -1.0932
 9PP  H121  H  HCH3   0   0.220  -2.5347   3.0263  -1.7979
 9PP  H122  H  HCH3   0   0.232  -3.8936   1.9867  -1.3930
 9PP  H123  H  HCH3   0   0.215  -3.3742   3.2343  -0.2577
 9PP  H141  H  HCH2   0   0.183  -3.9460  -0.7352   1.1455
 9PP  H142  H  HCH2   0   0.159  -4.0388  -0.2408  -0.5301

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
 9PP  N9   C8    aromatic  1.367  0.020  1.367
 9PP  N9   C4    aromatic  1.359  0.020  1.359
 9PP  N9   C10   single    1.445  0.020  1.445
 9PP  C8   N7    aromatic  1.298  0.020  1.298
 9PP  C8   H81   single    0.930  0.020  1.080
 9PP  N7   C5    aromatic  1.374  0.020  1.374
 9PP  C5   C6    aromatic  1.403  0.020  1.403
 9PP  C5   C4    aromatic  1.387  0.020  1.387
 9PP  C6   N6    single    1.344  0.020  1.344
 9PP  C6   N1    aromatic  1.332  0.020  1.332
 9PP  N6   HN61  single    0.890  0.020  1.040
 9PP  N6   HN62  single    0.890  0.020  1.040
 9PP  N1   C2    aromatic  1.342  0.020  1.342
 9PP  C2   N2    single    1.364  0.020  1.364
 9PP  C2   N3    aromatic  1.330  0.020  1.330
 9PP  N2   HN21  single    0.890  0.020  1.040
 9PP  N2   HN22  single    0.890  0.020  1.040
 9PP  N3   C4    aromatic  1.329  0.020  1.329
 9PP  C10  C11   single    1.520  0.020  1.520
 9PP  C10  H101  single    0.970  0.020  1.090
 9PP  C10  H102  single    0.970  0.020  1.090
 9PP  C11  C12   single    1.523  0.020  1.523
 9PP  C11  O13   single    1.408  0.020  1.408
 9PP  C11  H111  single    0.970  0.020  1.090
 9PP  C12  H121  single    0.970  0.020  1.090
 9PP  C12  H122  single    0.970  0.020  1.090
 9PP  C12  H123  single    0.970  0.020  1.090
 9PP  O13  C14   single    1.424  0.020  1.424
 9PP  P    C14   single    1.872  0.020  1.872
 9PP  P    O2P   deloc     1.529  0.020  1.529
 9PP  P    O3P   deloc     1.540  0.020  1.540
 9PP  P    O1P   deloc     1.535  0.020  1.535
 9PP  C14  H141  single    0.970  0.020  1.090
 9PP  C14  H142  single    0.970  0.020  1.090

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
 9PP  C10   N9   C4    126.21  3.000
 9PP  C10   N9   C8    127.56  3.000
 9PP  C4    N9   C8    106.22  3.000
 9PP  H81   C8   N7    125.33  3.000
 9PP  H81   C8   N9    120.96  3.000
 9PP  N7    C8   N9    113.69  3.000
 9PP  C5    N7   C8    104.02  3.000
 9PP  C4    C5   C6    115.67  3.000
 9PP  C4    C5   N7    110.77  3.000
 9PP  C6    C5   N7    133.54  3.000
 9PP  N1    C6   N6    118.72  3.000
 9PP  N1    C6   C5    118.88  3.000
 9PP  N6    C6   C5    122.38  3.000
 9PP  HN62  N6   HN61  117.09  3.000
 9PP  HN62  N6   C6    119.04  3.000
 9PP  HN61  N6   C6    119.57  3.000
 9PP  C2    N1   C6    119.16  3.000
 9PP  N3    C2   N2    116.99  3.000
 9PP  N3    C2   N1    127.32  3.000
 9PP  N2    C2   N1    115.66  3.000
 9PP  HN22  N2   HN21  114.70  3.000
 9PP  HN22  N2   C2    116.42  3.000
 9PP  HN21  N2   C2    116.48  3.000
 9PP  C4    N3   C2    112.12  3.000
 9PP  N3    C4   C5    126.84  3.000
 9PP  N3    C4   N9    127.87  3.000
 9PP  C5    C4   N9    105.25  3.000
 9PP  H102  C10  H101  107.30  3.000
 9PP  H102  C10  C11   110.38  3.000
 9PP  H101  C10  C11   110.36  3.000
 9PP  H102  C10  N9    108.50  3.000
 9PP  H101  C10  N9    107.60  3.000
 9PP  C11   C10  N9    112.51  3.000
 9PP  H111  C11  O13   110.07  3.000
 9PP  H111  C11  C12   109.76  3.000
 9PP  O13   C11  C12   111.29  3.000
 9PP  H111  C11  C10   108.18  3.000
 9PP  O13   C11  C10   106.86  3.000
 9PP  C12   C11  C10   110.60  3.000
 9PP  H123  C12  H122  107.88  3.000
 9PP  H123  C12  H121  107.97  3.000
 9PP  H122  C12  H121  107.35  3.000
 9PP  H123  C12  C11   111.62  3.000
 9PP  H122  C12  C11   110.75  3.000
 9PP  H121  C12  C11   111.11  3.000
 9PP  C14   O13  C11   114.70  3.000
 9PP  O1P   P    O3P   113.05  3.000
 9PP  O1P   P    O2P   114.82  3.000
 9PP  O3P   P    O2P   113.77  3.000
 9PP  O1P   P    C14   106.86  3.000
 9PP  O3P   P    C14   101.10  3.000
 9PP  O2P   P    C14   105.72  3.000
 9PP  H142  C14  H141  105.46  3.000
 9PP  H142  C14  P     109.99  3.000
 9PP  H141  C14  P     108.55  3.000
 9PP  H142  C14  O13   110.37  3.000
 9PP  H141  C14  O13   104.96  3.000
 9PP  P     C14  O13   116.78  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
 9PP  CONST_01  C5    N7   C8   N9     0.00   0.0  0
 9PP  CONST_02  N7    C5   C4   N9     0.00   0.0  0
 9PP  CONST_03  C6    C5   C4   N9   180.00   0.0  0
 9PP  CONST_04  C2    N3   C4   N9   180.00   0.0  0
 9PP  CONST_05  C5    C4   N9   C8     0.00   0.0  0
 9PP  CONST_06  N3    C4   N9   C8   180.00   0.0  0
 9PP  CONST_07  C6    C5   N7   C8   180.00   0.0  0
 9PP  CONST_08  C4    C5   N7   C8     0.00   0.0  0
 9PP  CONST_09  C4    N9   C8   N7     0.00   0.0  0
 9PP  CONST_10  N1    C6   C5   N7   180.00   0.0  0
 9PP  CONST_11  N3    C4   C5   N7   180.00   0.0  0
 9PP  CONST_12  C2    N1   C6   C5     0.00   0.0  0
 9PP  CONST_13  C2    N3   C4   C5     0.00   0.0  0
 9PP  CONST_14  N3    C4   C5   C6     0.00   0.0  0
 9PP  CONST_15  N3    C2   N1   C6     0.00   0.0  0
 9PP  CONST_16  C4    C5   C6   N1     0.00   0.0  0
 9PP  CONST_17  C4    N3   C2   N1     0.00   0.0  0
 9PP  CONST_18  C10   N9   C8   N7   180.00   0.0  0
 9PP  CONST_19  N6    C6   C5   N7     0.00   0.0  0
 9PP  CONST_20  C10   N9   C4   C5   180.00   0.0  0
 9PP  CONST_21  N2    C2   N1   C6   180.00   0.0  0
 9PP  CONST_22  C4    C5   C6   N6   180.00   0.0  0
 9PP  CONST_23  C2    N1   C6   N6   180.00   0.0  0
 9PP  CONST_24  C4    N3   C2   N2   180.00   0.0  0
 9PP  CONST_25  C10   N9   C4   N3     0.00   0.0  0
 9PP  CONST_26  H81   C8   N7   C5   180.00   0.0  0
 9PP  CONST_27  HN61  N6   C6   C5     0.00   0.0  0
 9PP  CONST_28  HN62  N6   C6   C5   180.00   0.0  0
 9PP  Var_01    C11   C10  N9   C8   -83.36  30.0  2
 9PP  Var_02    P     C14  O13  C11   71.88  30.0  3
 9PP  Var_03    O2P   P    C14  O13   54.91  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
 9PP  chir_01  C11  C10  C12  O13  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
 9PP  plan-1  N9    0.020
 9PP  plan-1  C8    0.020
 9PP  plan-1  N7    0.020
 9PP  plan-1  C5    0.020
 9PP  plan-1  C6    0.020
 9PP  plan-1  N6    0.020
 9PP  plan-1  N1    0.020
 9PP  plan-1  C2    0.020
 9PP  plan-1  N2    0.020
 9PP  plan-1  N3    0.020
 9PP  plan-1  C4    0.020
 9PP  plan-1  C10   0.020
 9PP  plan-1  H81   0.020
 9PP  plan-2  C6    0.020
 9PP  plan-2  N6    0.020
 9PP  plan-2  HN61  0.020
 9PP  plan-2  HN62  0.020
 9PP  plan-3  C2    0.020
 9PP  plan-3  N2    0.020
 9PP  plan-3  HN21  0.020
 9PP  plan-3  HN22  0.020

