# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 19 21:45:40 2022
#   Inital geometry file: a 120 line input string
#   Ligand name: [(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COC[P](O)(O)=O)n2cnc3c(NC4CCCC4)nc(Cl)nc23
#
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
 OO2  OO2  '[(2~{R},3~{S},4~{R},5~{R})-5-[2-chloranyl-6-(cyclopentylamino)purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxymethylphosphonic acid'  ligand  51  30  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OO2
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
 OO2  C1   C   CR6    0   0.265  24.3523  31.6949   0.0534
 OO2  C2   C   CR56   0   0.500  23.6145  30.0631   1.2984
 OO2  N1   N   N      0  -0.467  25.1578  30.9447  -0.6717
 OO2  N2   N   N      0  -0.438  23.5556  31.3749   1.0400
 OO2  C3   C   CR6    0   0.521  25.2176  29.6328  -0.4022
 OO2  O1   O   OH1    0  -0.653  18.5773  29.9555   2.2417
 OO2  C4   C   CH1    0  -0.000  19.8941  29.5070   2.3707
 OO2  C5   C   CH1    0  -0.052  20.8547  30.6578   2.6406
 OO2  O2   O   OH1    0  -0.657  20.2816  31.5084   3.5943
 OO2  C6   C   CH1    0  -0.021  20.1426  28.5801   3.5691
 OO2  C7   C   CH2    0  -0.138  19.9865  27.1200   3.2172
 OO2  O3   O   O2     0  -0.500  20.2278  26.3463   4.3534
 OO2  C8   C   CH2    0  -0.457  20.3738  24.9509   4.1028
 OO2  P1   P   P      0   1.162  21.9007  24.3974   3.1499
 OO2  O4   O   O      0  -0.893  21.6634  24.7603   1.6752
 OO2  O5   O   OP    -1  -0.890  21.9052  22.8872   3.4176
 OO2  O6   O   OP    -1  -0.883  23.0694  25.1611   3.7985
 OO2  O7   O   O2     0  -0.488  21.4849  28.8562   3.9928
 OO2  C9   C   CH1    0   0.167  22.0348  29.8998   3.2636
 OO2  N3   N   NR5    0  -0.548  22.9423  29.3530   2.2471
 OO2  C10  C   CR15   0   0.066  23.3825  28.0580   2.1392
 OO2  N4   N   N      0  -0.455  24.2534  27.8949   1.1826
 OO2  C11  C   CR56   0  -0.000  24.4104  29.1400   0.6433
 OO2  CL1  CL  CL     0  -0.117  24.3560  33.3810  -0.3751
 OO2  N5   N   NH1    0  -0.651  26.0139  28.8417  -1.1164
 OO2  C12  C   CH1    0  -0.114  26.9216  29.2963  -2.1583
 OO2  C13  C   CH2    0  -0.440  28.1722  29.9557  -1.5746
 OO2  C14  C   CH2    0  -0.449  29.0048  28.7780  -1.0561
 OO2  C15  C   CH2    0  -0.457  28.6339  27.5795  -1.9612
 OO2  C16  C   CH2    0  -0.473  27.5036  28.0827  -2.8787
 OO2  H1   H   HOH1   0   0.457  18.0562  29.2539   1.8404
 OO2  H2   H   HCH1   0   0.236  20.2332  29.0045   1.4533
 OO2  H3   H   HCH1   0   0.266  21.1328  31.1924   1.7279
 OO2  H4   H   HOH1   0   0.459  20.8569  32.2723   3.7060
 OO2  H5   H   HCH1   0   0.233  19.4647  28.8451   4.3888
 OO2  H6   H   HCH2   0   0.185  18.9601  26.9693   2.8368
 OO2  H7   H   HCH2   0   0.206  20.6631  26.8615   2.3953
 OO2  H8   H   HCH2   0   0.158  19.4633  24.5609   3.6172
 OO2  H9   H   HCH2   0   0.187  20.4071  24.4942   5.0969
 OO2  H12  H   HCH1   0   0.284  22.6275  30.5420   3.9221
 OO2  H13  H   HCR5   0   0.311  23.0553  27.2664   2.8033
 OO2  H14  H   HNH1   0   0.409  26.0180  27.8640  -0.8677
 OO2  H15  H   HCH1   0   0.258  26.3780  29.9594  -2.8334
 OO2  H16  H   HCH2   0   0.232  28.6961  30.4715  -2.3837
 OO2  H17  H   HCH2   0   0.244  27.9471  30.7001  -0.8105
 OO2  H18  H   HCH2   0   0.230  28.7467  28.5643  -0.0177
 OO2  H19  H   HCH2   0   0.235  30.0723  28.9974  -1.0738
 OO2  H20  H   HCH2   0   0.234  28.3031  26.7295  -1.3623
 OO2  H21  H   HCH2   0   0.237  29.4847  27.2304  -2.5461
 OO2  H22  H   HCH2   0   0.250  27.9081  28.4187  -3.8346
 OO2  H23  H   HCH2   0   0.248  26.7523  27.3225  -3.0996

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
 OO2  C16  C15  single    1.540  0.020  1.540
 OO2  C16  C12  single    1.527  0.020  1.527
 OO2  C15  C14  single    1.547  0.020  1.547
 OO2  C12  C13  single    1.530  0.020  1.530
 OO2  C12  N5   single    1.455  0.020  1.455
 OO2  C14  C13  single    1.533  0.020  1.533
 OO2  N5   C3   single    1.330  0.020  1.330
 OO2  C3   N1   aromatic  1.341  0.020  1.341
 OO2  C3   C11  aromatic  1.410  0.020  1.410
 OO2  N1   C1   aromatic  1.318  0.020  1.318
 OO2  C11  N4   aromatic  1.366  0.020  1.366
 OO2  C11  C2   aromatic  1.384  0.020  1.384
 OO2  N4   C10  aromatic  1.304  0.020  1.304
 OO2  C1   CL1  single    1.740  0.020  1.740
 OO2  C1   N2   aromatic  1.308  0.020  1.308
 OO2  C2   N2   aromatic  1.338  0.020  1.338
 OO2  C2   N3   aromatic  1.362  0.020  1.362
 OO2  C10  N3   aromatic  1.372  0.020  1.372
 OO2  N3   C9   single    1.468  0.020  1.468
 OO2  O1   C4   single    1.397  0.020  1.397
 OO2  C4   C5   single    1.523  0.020  1.523
 OO2  C4   C6   single    1.535  0.020  1.535
 OO2  C5   O2   single    1.400  0.020  1.400
 OO2  C5   C9   single    1.535  0.020  1.535
 OO2  C9   O7   single    1.387  0.020  1.387
 OO2  O4   P1   deloc     1.537  0.020  1.537
 OO2  C7   C6   single    1.510  0.020  1.510
 OO2  C7   O3   single    1.396  0.020  1.396
 OO2  C6   O7   single    1.434  0.020  1.434
 OO2  P1   O6   deloc     1.539  0.020  1.539
 OO2  P1   C8   single    1.883  0.020  1.883
 OO2  P1   O5   deloc     1.534  0.020  1.534
 OO2  C8   O3   single    1.425  0.020  1.425
 OO2  O1   H1   single    0.850  0.020  0.980
 OO2  C4   H2   single    0.970  0.020  1.090
 OO2  C5   H3   single    0.970  0.020  1.090
 OO2  O2   H4   single    0.850  0.020  0.980
 OO2  C6   H5   single    0.970  0.020  1.090
 OO2  C7   H6   single    0.970  0.020  1.090
 OO2  C7   H7   single    0.970  0.020  1.090
 OO2  C8   H8   single    0.970  0.020  1.090
 OO2  C8   H9   single    0.970  0.020  1.090
 OO2  C9   H12  single    0.970  0.020  1.090
 OO2  C10  H13  single    0.930  0.020  1.080
 OO2  N5   H14  single    0.860  0.020  1.020
 OO2  C12  H15  single    0.970  0.020  1.090
 OO2  C13  H16  single    0.970  0.020  1.090
 OO2  C13  H17  single    0.970  0.020  1.090
 OO2  C14  H18  single    0.970  0.020  1.090
 OO2  C14  H19  single    0.970  0.020  1.090
 OO2  C15  H20  single    0.970  0.020  1.090
 OO2  C15  H21  single    0.970  0.020  1.090
 OO2  C16  H22  single    0.970  0.020  1.090
 OO2  C16  H23  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
 OO2  CL1  C1   N2   115.11  3.000
 OO2  N2   C1   N1   130.39  3.000
 OO2  CL1  C1   N1   114.51  3.000
 OO2  C11  C2   N3   105.41  3.000
 OO2  N3   C2   N2   128.58  3.000
 OO2  C11  C2   N2   126.00  3.000
 OO2  C3   N1   C1   118.27  3.000
 OO2  C2   N2   C1   111.02  3.000
 OO2  N5   C3   C11  122.20  3.000
 OO2  C11  C3   N1   117.75  3.000
 OO2  N5   C3   N1   120.05  3.000
 OO2  H1   O1   C4   108.36  3.000
 OO2  H2   C4   C6   108.99  3.000
 OO2  H2   C4   C5   107.38  3.000
 OO2  C6   C4   C5   102.46  3.000
 OO2  H2   C4   O1   111.12  3.000
 OO2  C6   C4   O1   114.74  3.000
 OO2  C5   C4   O1   111.61  3.000
 OO2  H3   C5   C9   112.62  3.000
 OO2  H3   C5   O2   112.05  3.000
 OO2  C9   C5   O2   109.77  3.000
 OO2  H3   C5   C4   112.44  3.000
 OO2  C9   C5   C4   100.59  3.000
 OO2  O2   C5   C4   108.75  3.000
 OO2  H4   O2   C5   108.44  3.000
 OO2  H5   C6   O7   108.14  3.000
 OO2  H5   C6   C7   110.13  3.000
 OO2  O7   C6   C7   110.59  3.000
 OO2  H5   C6   C4   109.73  3.000
 OO2  O7   C6   C4   105.42  3.000
 OO2  C7   C6   C4   112.65  3.000
 OO2  H7   C7   H6   106.46  3.000
 OO2  H7   C7   O3   111.91  3.000
 OO2  H6   C7   O3   111.42  3.000
 OO2  H7   C7   C6   109.83  3.000
 OO2  H6   C7   C6   107.95  3.000
 OO2  O3   C7   C6   109.17  3.000
 OO2  C8   O3   C7   114.66  3.000
 OO2  H9   C8   H8   106.10  3.000
 OO2  H9   C8   P1   108.20  3.000
 OO2  H8   C8   P1   110.03  3.000
 OO2  H9   C8   O3   104.59  3.000
 OO2  H8   C8   O3   109.82  3.000
 OO2  P1   C8   O3   117.38  3.000
 OO2  O6   P1   O5   114.38  3.000
 OO2  O5   P1   O4   113.61  3.000
 OO2  O6   P1   O4   113.85  3.000
 OO2  O5   P1   C8   101.74  3.000
 OO2  O6   P1   C8   104.86  3.000
 OO2  O4   P1   C8   106.91  3.000
 OO2  C9   O7   C6   111.13  3.000
 OO2  H12  C9   N3   107.48  3.000
 OO2  H12  C9   O7   109.87  3.000
 OO2  N3   C9   O7   109.20  3.000
 OO2  H12  C9   C5   111.78  3.000
 OO2  O7   C9   C5   106.28  3.000
 OO2  N3   C9   C5   112.22  3.000
 OO2  C10  N3   C9   127.18  3.000
 OO2  C9   N3   C2   126.37  3.000
 OO2  C10  N3   C2   106.19  3.000
 OO2  H13  C10  N4   124.04  3.000
 OO2  H13  C10  N3   122.97  3.000
 OO2  N4   C10  N3   112.96  3.000
 OO2  C11  N4   C10  104.62  3.000
 OO2  N4   C11  C3   132.63  3.000
 OO2  N4   C11  C2   110.80  3.000
 OO2  C3   C11  C2   116.57  3.000
 OO2  H14  N5   C12  118.49  3.000
 OO2  H14  N5   C3   116.51  3.000
 OO2  C12  N5   C3   124.90  3.000
 OO2  H15  C12  C16  112.40  3.000
 OO2  H15  C12  C13  112.42  3.000
 OO2  C16  C12  C13  102.19  3.000
 OO2  H15  C12  N5   108.79  3.000
 OO2  C13  C12  N5   111.81  3.000
 OO2  C16  C12  N5   109.11  3.000
 OO2  H17  C13  H16  107.19  3.000
 OO2  H17  C13  C14  113.56  3.000
 OO2  H16  C13  C14  110.64  3.000
 OO2  H17  C13  C12  113.14  3.000
 OO2  H16  C13  C12  108.23  3.000
 OO2  C14  C13  C12  104.00  3.000
 OO2  H19  C14  H18  106.65  3.000
 OO2  H19  C14  C15  112.41  3.000
 OO2  H18  C14  C15  110.39  3.000
 OO2  H19  C14  C13  111.83  3.000
 OO2  H18  C14  C13  110.12  3.000
 OO2  C15  C14  C13  105.49  3.000
 OO2  H21  C15  H20  106.36  3.000
 OO2  H21  C15  C16  110.97  3.000
 OO2  H20  C15  C16  111.04  3.000
 OO2  H21  C15  C14  112.02  3.000
 OO2  H20  C15  C14  110.80  3.000
 OO2  C16  C15  C14  105.75  3.000
 OO2  H23  C16  H22  107.01  3.000
 OO2  H23  C16  C15  113.46  3.000
 OO2  H22  C16  C15  110.51  3.000
 OO2  H23  C16  C12  112.76  3.000
 OO2  H22  C16  C12  108.06  3.000
 OO2  C15  C16  C12  104.97  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
 OO2  CONST_01  C11  C3   N1   C1     0.00   0.0  0
 OO2  CONST_02  C11  C2   N2   C1     0.00   0.0  0
 OO2  CONST_03  N3   C2   N2   C1   180.00   0.0  0
 OO2  CONST_04  N1   C3   C11  C2     0.00   0.0  0
 OO2  CONST_05  C10  N4   C11  C2     0.00   0.0  0
 OO2  CONST_06  N1   C1   N2   C2     0.00   0.0  0
 OO2  CONST_07  N4   C10  N3   C2     0.00   0.0  0
 OO2  CONST_08  N4   C11  C3   N1   180.00   0.0  0
 OO2  CONST_09  C3   N1   C1   N2     0.00   0.0  0
 OO2  CONST_10  C3   C11  C2   N2     0.00   0.0  0
 OO2  CONST_11  N4   C11  C2   N2   180.00   0.0  0
 OO2  CONST_12  C10  N3   C2   N2   180.00   0.0  0
 OO2  CONST_13  C10  N4   C11  C3   180.00   0.0  0
 OO2  CONST_14  N3   C2   C11  C3   180.00   0.0  0
 OO2  CONST_15  N4   C11  C2   N3     0.00   0.0  0
 OO2  CONST_16  C11  N4   C10  N3     0.00   0.0  0
 OO2  CONST_17  C11  C2   N3   C10    0.00   0.0  0
 OO2  CONST_18  C9   N3   C2   N2     0.00   0.0  0
 OO2  CONST_19  C11  C2   N3   C9   180.00   0.0  0
 OO2  CONST_20  N4   C10  N3   C9   180.00   0.0  0
 OO2  CONST_21  N5   C3   N1   C1   180.00   0.0  0
 OO2  CONST_22  N5   C3   C11  C2   180.00   0.0  0
 OO2  CONST_23  CL1  C1   N2   C2   180.00   0.0  0
 OO2  CONST_24  CL1  C1   N1   C3   180.00   0.0  0
 OO2  CONST_25  N5   C3   C11  N4     0.00   0.0  0
 OO2  CONST_26  C12  N5   C3   N1     0.00   0.0  0
 OO2  CONST_27  C12  N5   C3   C11  180.00   0.0  0
 OO2  CONST_28  H13  C10  N3   C2   180.00   0.0  0
 OO2  CONST_29  H14  N5   C3   N1   180.00   0.0  0
 OO2  Var_01    C14  C15  C16  C12  -20.54  30.0  1
 OO2  Var_02    C15  C14  C13  C12   28.98  30.0  1
 OO2  Var_03    C16  C15  C14  C13   -5.22  30.0  1
 OO2  Var_04    P1   C8   O3   C7    68.12  30.0  2
 OO2  Var_05    O4   P1   C8   O3   -75.55  30.0  2
 OO2  Var_06    H6   C7   O3   C8    72.71  30.0  2

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
 OO2  chir_01  C4   O1   C5   C6  negativ
 OO2  chir_02  C5   O2   C9   C4  negativ
 OO2  chir_03  C6   O7   C7   C4  positiv
 OO2  chir_04  C9   O7   N3   C5  negativ
 OO2  chir_05  C12  C16  C13  N5  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
 OO2  plan-1  C3   0.020
 OO2  plan-1  N5   0.020
 OO2  plan-1  C12  0.020
 OO2  plan-1  H14  0.020
 OO2  plan-2  C1   0.020
 OO2  plan-2  C2   0.020
 OO2  plan-2  N1   0.020
 OO2  plan-2  N2   0.020
 OO2  plan-2  C3   0.020
 OO2  plan-2  C9   0.020
 OO2  plan-2  N3   0.020
 OO2  plan-2  C10  0.020
 OO2  plan-2  N4   0.020
 OO2  plan-2  C11  0.020
 OO2  plan-2  CL1  0.020
 OO2  plan-2  N5   0.020
 OO2  plan-2  H13  0.020

