# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 07:01:22 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: (2~{S})-2-[2-(6-aminopurin-9-yl)ethoxy]-3-phosphono-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2n(CCO[C@H](C[P](O)(O)=O)C(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
 1IO  1IO  "(S)-2-(2-(6-amino-9H-purin-9-yl)ethoxy)-3-phosphonopropanoic acid"  ligand  33  22  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1IO
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
 1IO  C02  C  CR6    0   0.448  -5.7132  -50.0576  133.9665
 1IO  C04  C  CR16   0   0.037  -4.3237  -51.5081  132.8456
 1IO  C06  C  CR56   0   0.478  -3.3462  -49.8973  133.9715
 1IO  C07  C  CR56   0  -0.009  -4.5591  -49.3971  134.4225
 1IO  C09  C  CR15   0   0.100  -3.0714  -48.1571  135.2518
 1IO  C12  C  CH2    0  -0.141  -0.4943  -47.9191  133.4844
 1IO  C14  C  CH1    0  -0.025  -1.2052  -46.5104  131.7421
 1IO  C15  C  CH2    0  -0.761  -2.1379  -46.4589  130.5393
 1IO  C20  C  C      0   0.366   0.1981  -46.0035  131.3365
 1IO  N01  N  NH2    0  -0.819  -6.9478  -49.6533  134.2773
 1IO  N03  N  N      0  -0.474  -5.5549  -51.1257  133.1778
 1IO  N05  N  N      0  -0.454  -3.1726  -50.9604  133.1881
 1IO  N08  N  N      0  -0.451  -4.3647  -48.3078  135.2296
 1IO  N10  N  NR5    0  -0.485  -2.3981  -49.0882  134.5162
 1IO  O13  O  O2     0  -0.487  -1.1874  -47.8233  132.2773
 1IO  O17  O  O      0  -0.912  -4.6553  -46.1733  129.6276
 1IO  O18  O  OP    -1  -0.905  -4.3171  -46.3032  132.1759
 1IO  O19  O  OP    -1  -0.904  -4.0633  -48.4157  130.7129
 1IO  O21  O  O      0  -0.610   1.0419  -46.8516  130.9835
 1IO  O22  O  OC    -1  -0.619   0.3452  -44.7626  131.3516
 1IO  P16  P  P      0   1.170  -3.9552  -46.8857  130.7981
 1IO  H1   H  HCR6   0   0.244  -4.2661  -52.3863  132.2106
 1IO  H2   H  HCR5   0   0.289  -2.5455  -47.3859  135.7962
 1IO  H3   H  HCH2   0   0.268  -0.7722  -50.0527  133.7130
 1IO  H4   H  HCH2   0   0.270  -0.4337  -49.1903  135.2069
 1IO  H5   H  HCH2   0   0.210   0.5890  -48.0164  133.3423
 1IO  H6   H  HCH2   0   0.194  -0.6465  -47.0209  134.1019
 1IO  H7   H  HCH1   0   0.157  -1.6052  -45.8296  132.5084
 1IO  H8   H  HCH2   0   0.181  -1.7237  -47.0749  129.7304
 1IO  H9   H  HCH2   0   0.188  -2.0968  -45.4284  130.1731
 1IO  H10  H  HNH2   0   0.399  -7.7460  -50.1801  133.9675
 1IO  H11  H  HNH2   0   0.408  -7.0985  -48.8781  134.8981
 1IO  C11  C  CH2    0  -0.351  -0.9724  -49.1323  134.2600

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
 1IO  O17  P16  deloc     1.539  0.020  1.539
 1IO  P16  C15  single    1.885  0.020  1.885
 1IO  P16  O19  deloc     1.536  0.020  1.536
 1IO  P16  O18  deloc     1.539  0.020  1.539
 1IO  C15  C14  single    1.523  0.020  1.523
 1IO  C14  O13  single    1.418  0.020  1.418
 1IO  C14  C20  single    1.546  0.020  1.546
 1IO  O13  C12  single    1.395  0.020  1.395
 1IO  C20  O21  deloc     1.247  0.020  1.247
 1IO  C20  O22  deloc     1.250  0.020  1.250
 1IO  C12  C11  single    1.517  0.020  1.517
 1IO  C11  N10  single    1.449  0.020  1.449
 1IO  N05  C04  aromatic  1.320  0.020  1.320
 1IO  N05  C06  aromatic  1.332  0.020  1.332
 1IO  C04  N03  aromatic  1.331  0.020  1.331
 1IO  N10  C06  aromatic  1.360  0.020  1.360
 1IO  N10  C09  aromatic  1.364  0.020  1.364
 1IO  C06  C07  aromatic  1.387  0.020  1.387
 1IO  N03  C02  aromatic  1.337  0.020  1.337
 1IO  C09  N08  aromatic  1.302  0.020  1.302
 1IO  C07  C02  aromatic  1.406  0.020  1.406
 1IO  C07  N08  aromatic  1.370  0.020  1.370
 1IO  C02  N01  single    1.336  0.020  1.336
 1IO  C04  H1   single    0.930  0.020  1.080
 1IO  C09  H2   single    0.930  0.020  1.080
 1IO  C11  H3   single    0.970  0.020  1.090
 1IO  C11  H4   single    0.970  0.020  1.090
 1IO  C12  H5   single    0.970  0.020  1.090
 1IO  C12  H6   single    0.970  0.020  1.090
 1IO  C14  H7   single    0.970  0.020  1.090
 1IO  C15  H8   single    0.970  0.020  1.090
 1IO  C15  H9   single    0.970  0.020  1.090
 1IO  N01  H10  single    0.860  0.020  1.020
 1IO  N01  H11  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
 1IO  N03  C02  N01  119.24  3.000
 1IO  N01  C02  C07  122.76  3.000
 1IO  N03  C02  C07  118.00  3.000
 1IO  H1   C04  N05  116.19  3.000
 1IO  H1   C04  N03  115.31  3.000
 1IO  N05  C04  N03  128.50  3.000
 1IO  N10  C06  N05  128.27  3.000
 1IO  N10  C06  C07  105.35  3.000
 1IO  N05  C06  C07  126.37  3.000
 1IO  N08  C07  C06  110.75  3.000
 1IO  N08  C07  C02  132.95  3.000
 1IO  C06  C07  C02  116.29  3.000
 1IO  H2   C09  N10  121.24  3.000
 1IO  H2   C09  N08  125.07  3.000
 1IO  N10  C09  N08  113.70  3.000
 1IO  H6   C12  H5   106.36  3.000
 1IO  H6   C12  O13  111.15  3.000
 1IO  H5   C12  O13  112.62  3.000
 1IO  H6   C12  C11  108.80  3.000
 1IO  H5   C12  C11  107.85  3.000
 1IO  O13  C12  C11  109.92  3.000
 1IO  H7   C14  O13  108.33  3.000
 1IO  H7   C14  C20  108.04  3.000
 1IO  O13  C14  C20  113.03  3.000
 1IO  H7   C14  C15  107.85  3.000
 1IO  C20  C14  C15  109.73  3.000
 1IO  O13  C14  C15  109.70  3.000
 1IO  H9   C15  H8   105.52  3.000
 1IO  H9   C15  P16  107.18  3.000
 1IO  H8   C15  P16  109.75  3.000
 1IO  H9   C15  C14  105.85  3.000
 1IO  H8   C15  C14  109.38  3.000
 1IO  P16  C15  C14  118.33  3.000
 1IO  O22  C20  O21  126.79  3.000
 1IO  O22  C20  C14  115.42  3.000
 1IO  O21  C20  C14  117.73  3.000
 1IO  H11  N01  H10  118.41  3.000
 1IO  H11  N01  C02  121.06  3.000
 1IO  H10  N01  C02  120.24  3.000
 1IO  C04  N03  C02  119.08  3.000
 1IO  C06  N05  C04  111.72  3.000
 1IO  C09  N08  C07  104.07  3.000
 1IO  C11  N10  C09  126.98  3.000
 1IO  C09  N10  C06  106.13  3.000
 1IO  C11  N10  C06  126.65  3.000
 1IO  C14  O13  C12  113.35  3.000
 1IO  O19  P16  O18  114.21  3.000
 1IO  O18  P16  O17  113.50  3.000
 1IO  O19  P16  O17  112.76  3.000
 1IO  O18  P16  C15  105.31  3.000
 1IO  O19  P16  C15  106.61  3.000
 1IO  O17  P16  C15  103.26  3.000
 1IO  H4   C11  H3   107.47  3.000
 1IO  H4   C11  N10  109.52  3.000
 1IO  H3   C11  N10  107.18  3.000
 1IO  H4   C11  C12  109.30  3.000
 1IO  H3   C11  C12  111.16  3.000
 1IO  N10  C11  C12  112.09  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
 1IO  CONST_01  N05  C04  N03  C02     0.00   0.0  0
 1IO  CONST_02  N05  C06  C07  C02     0.00   0.0  0
 1IO  CONST_03  N10  C06  C07  C02   180.00   0.0  0
 1IO  CONST_04  C09  N08  C07  C02   180.00   0.0  0
 1IO  CONST_05  N10  C06  N05  C04   180.00   0.0  0
 1IO  CONST_06  C07  C06  N05  C04     0.00   0.0  0
 1IO  CONST_07  C07  C02  N03  C04     0.00   0.0  0
 1IO  CONST_08  N03  C04  N05  C06     0.00   0.0  0
 1IO  CONST_09  N08  C09  N10  C06     0.00   0.0  0
 1IO  CONST_10  N03  C02  C07  C06     0.00   0.0  0
 1IO  CONST_11  C09  N08  C07  C06     0.00   0.0  0
 1IO  CONST_12  C09  N10  C06  C07     0.00   0.0  0
 1IO  CONST_13  N10  C09  N08  C07     0.00   0.0  0
 1IO  CONST_14  N05  C06  N10  C09   180.00   0.0  0
 1IO  CONST_15  N08  C07  C02  N03   180.00   0.0  0
 1IO  CONST_16  N08  C07  C06  N05   180.00   0.0  0
 1IO  CONST_17  N10  C06  C07  N08     0.00   0.0  0
 1IO  CONST_18  N01  C02  N03  C04   180.00   0.0  0
 1IO  CONST_19  N01  C02  C07  C06   180.00   0.0  0
 1IO  CONST_20  C11  N10  C06  C07   180.00   0.0  0
 1IO  CONST_21  N05  C06  N10  C11     0.00   0.0  0
 1IO  CONST_22  N08  C09  N10  C11   180.00   0.0  0
 1IO  CONST_23  N08  C07  C02  N01     0.00   0.0  0
 1IO  CONST_24  H1   C04  N03  C02   180.00   0.0  0
 1IO  CONST_25  H1   C04  N05  C06   180.00   0.0  0
 1IO  CONST_26  H2   C09  N10  C06   180.00   0.0  0
 1IO  CONST_27  H2   C09  N08  C07   180.00   0.0  0
 1IO  CONST_28  H10  N01  C02  C07   180.00   0.0  0
 1IO  CONST_29  H11  N01  C02  C07     0.00   0.0  0
 1IO  CONST_30  H10  N01  C02  N03     0.00   0.0  0
 1IO  CONST_31  H11  N01  C02  N03   180.00   0.0  0
 1IO  Var_01    C12  C11  N10  C06   110.97  30.0  2
 1IO  Var_02    C12  C11  N10  C09   -62.59  30.0  2
 1IO  Var_03    H3   C11  N10  C06   -11.25  30.0  2
 1IO  Var_04    H4   C11  N10  C06  -127.54  30.0  2
 1IO  Var_05    H3   C11  N10  C09   175.19  30.0  2
 1IO  Var_06    H4   C11  N10  C09    58.90  30.0  2
 1IO  Var_07    O13  C12  C11  N10   -57.67  30.0  1
 1IO  Var_08    H5   C12  C11  N10   179.21  30.0  1
 1IO  Var_09    H6   C12  C11  N10    64.24  30.0  1
 1IO  Var_10    C14  O13  C12  C11   156.97  30.0  2
 1IO  Var_11    O17  P16  C15  C14   156.58  30.0  3
 1IO  Var_12    O19  P16  C15  C14   -84.40  30.0  3
 1IO  Var_13    O18  P16  C15  C14    37.29  30.0  3
 1IO  Var_14    H5   C12  O13  C14   -82.76  30.0  3
 1IO  Var_15    H6   C12  O13  C14    36.46  30.0  3
 1IO  Var_16    H3   C11  C12  O13    62.26  30.0  3
 1IO  Var_17    H4   C11  C12  O13  -179.28  30.0  3
 1IO  Var_18    H8   C15  P16  O17   -76.97  30.0  3
 1IO  Var_19    H9   C15  P16  O17    37.15  30.0  3
 1IO  Var_20    H8   C15  P16  O18   163.74  30.0  3
 1IO  Var_21    H9   C15  P16  O18   -82.14  30.0  3
 1IO  Var_22    H8   C15  P16  O19    42.05  30.0  3
 1IO  Var_23    H9   C15  P16  O19   156.17  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
 1IO  chir_01  C14  C15  O13  C20  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
 1IO  plan-1  C02  0.020
 1IO  plan-1  C04  0.020
 1IO  plan-1  C06  0.020
 1IO  plan-1  C07  0.020
 1IO  plan-1  C09  0.020
 1IO  plan-1  N01  0.020
 1IO  plan-1  N03  0.020
 1IO  plan-1  N05  0.020
 1IO  plan-1  N08  0.020
 1IO  plan-1  N10  0.020
 1IO  plan-1  H1   0.020
 1IO  plan-1  H2   0.020
 1IO  plan-1  C11  0.020
 1IO  plan-2  C02  0.020
 1IO  plan-2  N01  0.020
 1IO  plan-2  H10  0.020
 1IO  plan-2  H11  0.020
 1IO  plan-3  C14  0.020
 1IO  plan-3  C20  0.020
 1IO  plan-3  O21  0.020
 1IO  plan-3  O22  0.020

