# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 31 21:41:09 2021
#   Inital geometry file: a 131 line input string
#   Ligand name: 3-[3-[9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c2ncnc3c4cccc(CCC(O)=O)c4
#
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
 K2R  K2R  '3-[3-[9-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]purin-6-yl]phenyl]propanoic acid'  ligand  54  33  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_K2R
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
 K2R  OZ1  O  OH1   0  -0.590  -7.2417  -19.4242  -11.8161
 K2R  CZ   C  C     0   0.536  -8.1802  -18.4845  -11.8033
 K2R  OZ2  O  O     0  -0.447  -9.2639  -18.6469  -11.2982
 K2R  CE   C  CH2   0  -0.553  -7.7487  -17.2251  -12.5053
 K2R  CD2  C  CH2   0  -0.522  -6.3150  -16.7774  -12.2003
 K2R  CG1  C  CR6   0   0.149  -6.0164  -15.4625  -12.8662
 K2R  CB1  C  CR16  0  -0.338  -5.5090  -15.4260  -14.1577
 K2R  CD1  C  CR16  0  -0.304  -6.2779  -14.2590  -12.2149
 K2R  CG2  C  CR16  0  -0.222  -6.0259  -13.0497  -12.8454
 K2R  CB2  C  CR16  0  -0.339  -5.5101  -13.0211  -14.1318
 K2R  CA   C  CR6   0   0.074  -5.2458  -14.2161  -14.8051
 K2R  C6   C  CR6   0   0.225  -4.7018  -14.2321  -16.1740
 K2R  N1   N  N     0  -0.449  -4.6625  -15.4066  -16.8069
 K2R  C2   C  CR16  0   0.036  -4.1768  -15.4944  -18.0381
 K2R  N3   N  N     0  -0.423  -3.6948  -14.5098  -18.7820
 K2R  C4   C  CR56  0   0.504  -3.7339  -13.3485  -18.1564
 K2R  C5   C  CR56  0   0.068  -4.2130  -13.1152  -16.8593
 K2R  N7   N  N     0  -0.465  -4.0600  -11.7890  -16.5457
 K2R  C8   C  CR15  0   0.134  -3.5174  -11.2549  -17.6006
 K2R  N9   N  NR5   0  -0.545  -3.3069  -12.1402  -18.6178
 K2R  C1'  C  CR15  0   0.167  -2.6486  -11.9158  -19.9057
 K2R  C2'  C  CR15  0  -0.067  -3.6125  -12.1117  -21.0841
 K2R  O2'  O  OH1   0  -0.656  -2.9005  -12.3773  -22.2577
 K2R  O4'  O  O     0  -0.492  -2.2093  -10.5955  -19.9642
 K2R  C4'  C  CR15  0  -0.005  -2.9842   -9.8366  -20.8906
 K2R  C3'  C  CR15  0   0.004  -4.2038  -10.7045  -21.1930
 K2R  O3'  O  OH1   0  -0.655  -4.7463  -10.3642  -22.4289
 K2R  C5'  C  CH2   0  -0.172  -3.3555   -8.5007  -20.3000
 K2R  O5'  O  O2    0  -0.588  -2.1555   -7.7752  -20.0249
 K2R  P    P  P     0   1.449  -2.1172   -6.7361  -18.8130
 K2R  O3P  O  OH1   0  -0.727  -0.6299   -6.1785  -18.9224
 K2R  O2P  O  OH1   0  -0.735  -2.0203   -7.7130  -17.5548
 K2R  O1P  O  O     0  -0.708  -3.2060   -5.7402  -18.7830
 K2R  H1   H  HOH1  0   0.482  -7.5609  -20.2194  -11.3628
 K2R  H2   H  HCH2  0   0.273  -8.4574  -16.4389  -12.2441
 K2R  H3   H  HCH2  0   0.286  -7.8550  -17.3956  -13.5821
 K2R  H4   H  HCH2  0   0.261  -5.6065  -17.5319  -12.5441
 K2R  H5   H  HCH2  0   0.260  -6.1813  -16.6793  -11.1209
 K2R  H6   H  HCR6  0   0.251  -5.3043  -16.3563  -14.6725
 K2R  H7   H  HCR6  0   0.255  -6.6743  -14.2692  -11.2061
 K2R  H8   H  HCR6  0   0.260  -6.2287  -12.1197  -12.3305
 K2R  H9   H  HCR6  0   0.269  -5.3121  -12.0701  -14.6043
 K2R  H10  H  HCR6  0   0.262  -4.1755  -16.4824  -18.4837
 K2R  H11  H  HCR5  0   0.296  -3.2341  -10.2171  -17.6779
 K2R  H12  H  HCR5  0   0.292  -1.7976  -12.6011  -19.9538
 K2R  H13  H  HCR5  0   0.273  -4.3712  -12.8745  -20.8796
 K2R  H14  H  HOH1  0   0.463  -2.5627  -13.2779  -22.2174
 K2R  H15  H  HCR5  0   0.261  -2.4002   -9.6826  -21.8058
 K2R  H16  H  HCR5  0   0.244  -4.9394  -10.5857  -20.3847
 K2R  H17  H  HOH1  0   0.464  -5.6320  -10.7351  -22.4903
 K2R  H18  H  HCH2  0   0.264  -3.9598   -7.9475  -21.0224
 K2R  H19  H  HCH2  0   0.236  -3.9591   -8.6374  -19.3976
 K2R  H20  H  HOH1  0   0.504  -0.5366   -5.4071  -19.4975
 K2R  H21  H  HOH1  0   0.502  -2.3201   -7.3211  -16.7236

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
 K2R  O3'  C3'  single    1.392  0.020  1.392
 K2R  O2'  C2'  single    1.398  0.020  1.398
 K2R  C3'  C2'  single    1.530  0.020  1.530
 K2R  C3'  C4'  single    1.527  0.020  1.527
 K2R  C2'  C1'  single    1.535  0.020  1.535
 K2R  C4'  C5'  single    1.507  0.020  1.507
 K2R  C4'  O4'  single    1.426  0.020  1.426
 K2R  C5'  O5'  single    1.429  0.020  1.429
 K2R  O1P  P    double    1.476  0.020  1.476
 K2R  O5'  P    single    1.597  0.020  1.597
 K2R  C1'  O4'  single    1.393  0.020  1.393
 K2R  C1'  N9   single    1.464  0.020  1.464
 K2R  O3P  P    single    1.592  0.020  1.592
 K2R  P    O2P  single    1.596  0.020  1.596
 K2R  N9   C4   aromatic  1.362  0.020  1.362
 K2R  N9   C8   aromatic  1.365  0.020  1.365
 K2R  N3   C4   aromatic  1.320  0.020  1.320
 K2R  N3   C2   aromatic  1.325  0.020  1.325
 K2R  C4   C5   aromatic  1.402  0.020  1.402
 K2R  C2   N1   aromatic  1.326  0.020  1.326
 K2R  C8   N7   aromatic  1.301  0.020  1.301
 K2R  C5   N7   aromatic  1.371  0.020  1.371
 K2R  C5   C6   aromatic  1.399  0.020  1.399
 K2R  N1   C6   aromatic  1.335  0.020  1.335
 K2R  C6   CA   single    1.473  0.020  1.473
 K2R  CA   CB2  aromatic  1.397  0.020  1.397
 K2R  CA   CB1  aromatic  1.397  0.020  1.397
 K2R  CB2  CG2  aromatic  1.386  0.020  1.386
 K2R  CB1  CG1  aromatic  1.388  0.020  1.388
 K2R  CG2  CD1  aromatic  1.387  0.020  1.387
 K2R  CG1  CD1  aromatic  1.393  0.020  1.393
 K2R  CG1  CD2  single    1.504  0.020  1.504
 K2R  CE   CD2  single    1.533  0.020  1.533
 K2R  CE   CZ   single    1.505  0.020  1.505
 K2R  OZ2  CZ   double    1.207  0.020  1.207
 K2R  CZ   OZ1  single    1.328  0.020  1.328
 K2R  OZ1  H1   single    0.850  0.020  0.980
 K2R  CE   H2   single    0.970  0.020  1.090
 K2R  CE   H3   single    0.970  0.020  1.090
 K2R  CD2  H4   single    0.970  0.020  1.090
 K2R  CD2  H5   single    0.970  0.020  1.090
 K2R  CB1  H6   single    0.930  0.020  1.080
 K2R  CD1  H7   single    0.930  0.020  1.080
 K2R  CG2  H8   single    0.930  0.020  1.080
 K2R  CB2  H9   single    0.930  0.020  1.080
 K2R  C2   H10  single    0.930  0.020  1.080
 K2R  C8   H11  single    0.930  0.020  1.080
 K2R  C1'  H12  single    0.970  0.020  1.090
 K2R  C2'  H13  single    0.970  0.020  1.090
 K2R  O2'  H14  single    0.850  0.020  0.980
 K2R  C4'  H15  single    0.970  0.020  1.090
 K2R  C3'  H16  single    0.970  0.020  1.090
 K2R  O3'  H17  single    0.850  0.020  0.980
 K2R  C5'  H18  single    0.970  0.020  1.090
 K2R  C5'  H19  single    0.970  0.020  1.090
 K2R  O3P  H20  single    0.850  0.020  0.980
 K2R  O2P  H21  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
 K2R  H1   OZ1  CZ   110.07  3.000
 K2R  CE   CZ   OZ2  124.43  3.000
 K2R  OZ2  CZ   OZ1  122.92  3.000
 K2R  CE   CZ   OZ1  112.64  3.000
 K2R  H3   CE   H2   106.54  3.000
 K2R  H3   CE   CD2  109.38  3.000
 K2R  H2   CE   CD2  110.47  3.000
 K2R  H3   CE   CZ   107.49  3.000
 K2R  H2   CE   CZ   107.78  3.000
 K2R  CD2  CE   CZ   114.82  3.000
 K2R  H5   CD2  H4   107.11  3.000
 K2R  H5   CD2  CG1  109.56  3.000
 K2R  H4   CD2  CG1  109.66  3.000
 K2R  H5   CD2  CE   109.72  3.000
 K2R  H4   CD2  CE   110.05  3.000
 K2R  CG1  CD2  CE   110.67  3.000
 K2R  CD1  CG1  CB1  118.74  3.000
 K2R  CD1  CG1  CD2  120.74  3.000
 K2R  CB1  CG1  CD2  120.50  3.000
 K2R  H6   CB1  CA   119.21  3.000
 K2R  H6   CB1  CG1  119.27  3.000
 K2R  CA   CB1  CG1  121.52  3.000
 K2R  H7   CD1  CG2  119.85  3.000
 K2R  H7   CD1  CG1  119.71  3.000
 K2R  CG2  CD1  CG1  120.44  3.000
 K2R  H8   CG2  CB2  119.57  3.000
 K2R  H8   CG2  CD1  119.93  3.000
 K2R  CB2  CG2  CD1  120.50  3.000
 K2R  H9   CB2  CA   120.50  3.000
 K2R  H9   CB2  CG2  119.50  3.000
 K2R  CA   CB2  CG2  120.00  3.000
 K2R  C6   CA   CB2  121.81  3.000
 K2R  CB2  CA   CB1  118.80  3.000
 K2R  C6   CA   CB1  119.39  3.000
 K2R  C5   C6   N1   117.40  3.000
 K2R  N1   C6   CA   117.46  3.000
 K2R  C5   C6   CA   125.15  3.000
 K2R  C2   N1   C6   120.61  3.000
 K2R  H10  C2   N3   116.50  3.000
 K2R  H10  C2   N1   116.26  3.000
 K2R  N3   C2   N1   127.24  3.000
 K2R  C4   N3   C2   112.16  3.000
 K2R  N9   C4   C5   105.83  3.000
 K2R  C5   C4   N3   126.52  3.000
 K2R  N9   C4   N3   127.65  3.000
 K2R  N7   C5   C4   109.53  3.000
 K2R  N7   C5   C6   134.37  3.000
 K2R  C4   C5   C6   116.08  3.000
 K2R  C8   N7   C5   104.96  3.000
 K2R  H11  C8   N9   122.02  3.000
 K2R  H11  C8   N7   124.24  3.000
 K2R  N9   C8   N7   113.73  3.000
 K2R  C1'  N9   C8   128.73  3.000
 K2R  C8   N9   C4   105.94  3.000
 K2R  C1'  N9   C4   125.10  3.000
 K2R  H12  C1'  O4'  110.29  3.000
 K2R  H12  C1'  C2'  112.02  3.000
 K2R  O4'  C1'  C2'  106.67  3.000
 K2R  H12  C1'  N9   107.01  3.000
 K2R  O4'  C1'  N9   108.92  3.000
 K2R  C2'  C1'  N9   111.93  3.000
 K2R  H13  C2'  C3'  112.72  3.000
 K2R  H13  C2'  O2'  112.16  3.000
 K2R  C3'  C2'  O2'  108.16  3.000
 K2R  H13  C2'  C1'  112.37  3.000
 K2R  C3'  C2'  C1'  100.36  3.000
 K2R  O2'  C2'  C1'  110.42  3.000
 K2R  H14  O2'  C2'  108.74  3.000
 K2R  C4'  O4'  C1'  111.12  3.000
 K2R  H15  C4'  C5'  109.50  3.000
 K2R  H15  C4'  C3'  109.87  3.000
 K2R  C5'  C4'  C3'  112.62  3.000
 K2R  H15  C4'  O4'  109.11  3.000
 K2R  C5'  C4'  O4'  110.54  3.000
 K2R  C3'  C4'  O4'  105.08  3.000
 K2R  H16  C3'  O3'  111.45  3.000
 K2R  H16  C3'  C4'  109.11  3.000
 K2R  O3'  C3'  C4'  110.37  3.000
 K2R  H16  C3'  C2'  107.79  3.000
 K2R  C4'  C3'  C2'  101.54  3.000
 K2R  O3'  C3'  C2'  116.01  3.000
 K2R  H17  O3'  C3'  108.74  3.000
 K2R  H19  C5'  H18  107.66  3.000
 K2R  H19  C5'  O5'  111.58  3.000
 K2R  H18  C5'  O5'  109.56  3.000
 K2R  H19  C5'  C4'  110.39  3.000
 K2R  H18  C5'  C4'  109.03  3.000
 K2R  O5'  C5'  C4'  108.58  3.000
 K2R  P    O5'  C5'  119.78  3.000
 K2R  O1P  P    O2P  116.22  3.000
 K2R  O2P  P    O3P  102.23  3.000
 K2R  O1P  P    O3P  117.02  3.000
 K2R  O2P  P    O5'  101.62  3.000
 K2R  O3P  P    O5'  101.43  3.000
 K2R  O1P  P    O5'  115.90  3.000
 K2R  H20  O3P  P    114.24  3.000
 K2R  H21  O2P  P    114.26  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
 K2R  CONST_01  C6   CA   CB1  CG1   180.00   0.0  0
 K2R  CONST_02  CB2  CA   CB1  CG1     0.00   0.0  0
 K2R  CONST_03  CB2  CG2  CD1  CG1     0.00   0.0  0
 K2R  CONST_04  C5   C6   CA   CB1   180.00   0.0  0
 K2R  CONST_05  N1   C6   CA   CB1     0.00   0.0  0
 K2R  CONST_06  CG2  CB2  CA   CB1     0.00   0.0  0
 K2R  CONST_07  CG2  CD1  CG1  CB1     0.00   0.0  0
 K2R  CONST_08  CA   CB2  CG2  CD1     0.00   0.0  0
 K2R  CONST_09  CA   CB1  CG1  CD1     0.00   0.0  0
 K2R  CONST_10  C6   CA   CB2  CG2   180.00   0.0  0
 K2R  CONST_11  C5   C6   CA   CB2     0.00   0.0  0
 K2R  CONST_12  N1   C6   CA   CB2   180.00   0.0  0
 K2R  CONST_13  C4   C5   C6   CA    180.00   0.0  0
 K2R  CONST_14  N7   C5   C6   CA      0.00   0.0  0
 K2R  CONST_15  C2   N1   C6   CA    180.00   0.0  0
 K2R  CONST_16  N9   C4   C5   C6    180.00   0.0  0
 K2R  CONST_17  N3   C4   C5   C6      0.00   0.0  0
 K2R  CONST_18  C8   N7   C5   C6    180.00   0.0  0
 K2R  CONST_19  N3   C2   N1   C6      0.00   0.0  0
 K2R  CONST_20  C4   N3   C2   N1      0.00   0.0  0
 K2R  CONST_21  C4   C5   C6   N1      0.00   0.0  0
 K2R  CONST_22  N7   C5   C6   N1    180.00   0.0  0
 K2R  CONST_23  N9   C4   N3   C2    180.00   0.0  0
 K2R  CONST_24  C5   C4   N3   C2      0.00   0.0  0
 K2R  CONST_25  C5   C6   N1   C2      0.00   0.0  0
 K2R  CONST_26  C8   N9   C4   N3    180.00   0.0  0
 K2R  CONST_27  N7   C5   C4   N3    180.00   0.0  0
 K2R  CONST_28  N7   C8   N9   C4      0.00   0.0  0
 K2R  CONST_29  C8   N7   C5   C4      0.00   0.0  0
 K2R  CONST_30  C8   N9   C4   C5      0.00   0.0  0
 K2R  CONST_31  N9   C8   N7   C5      0.00   0.0  0
 K2R  CONST_32  N9   C4   C5   N7      0.00   0.0  0
 K2R  CONST_33  C1'  N9   C4   N3      0.00   0.0  0
 K2R  CONST_34  C1'  N9   C4   C5    180.00   0.0  0
 K2R  CONST_35  C1'  N9   C8   N7    180.00   0.0  0
 K2R  CONST_36  CA   CB1  CG1  CD2   180.00   0.0  0
 K2R  CONST_37  CG2  CD1  CG1  CD2   180.00   0.0  0
 K2R  CONST_38  H8   CG2  CD1  CG1   180.00   0.0  0
 K2R  CONST_39  H9   CB2  CA   CB1   180.00   0.0  0
 K2R  CONST_40  H7   CD1  CG1  CB1   180.00   0.0  0
 K2R  CONST_41  H6   CB1  CG1  CD1   180.00   0.0  0
 K2R  CONST_42  H10  C2   N1   C6    180.00   0.0  0
 K2R  CONST_43  H11  C8   N9   C4    180.00   0.0  0
 K2R  CONST_44  H1   OZ1  CZ   OZ2     0.00   0.0  0
 K2R  Var_01    CB1  CG1  CD2  CE    -88.96  30.0  3
 K2R  Var_02    CG1  CD2  CE   CZ   -175.82  30.0  3
 K2R  Var_03    CD2  CE   CZ   OZ1   -42.86  30.0  3
 K2R  Var_04    O1P  P    O5'  C5'   -51.13  30.0  3
 K2R  Var_05    H18  C5'  O5'  P      91.35  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
 K2R  chir_01  C1'  C2'  O4'  N9   negativ
 K2R  chir_02  C2'  O2'  C3'  C1'  positiv
 K2R  chir_03  C4'  O4'  C5'  C3'  positiv
 K2R  chir_04  C3'  O3'  C4'  C2'  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
 K2R  plan-1  CD2  0.020
 K2R  plan-1  CG1  0.020
 K2R  plan-1  CB1  0.020
 K2R  plan-1  CD1  0.020
 K2R  plan-1  CG2  0.020
 K2R  plan-1  CB2  0.020
 K2R  plan-1  CA   0.020
 K2R  plan-1  C6   0.020
 K2R  plan-1  H6   0.020
 K2R  plan-1  H7   0.020
 K2R  plan-1  H8   0.020
 K2R  plan-1  H9   0.020
 K2R  plan-2  CA   0.020
 K2R  plan-2  C6   0.020
 K2R  plan-2  N1   0.020
 K2R  plan-2  C2   0.020
 K2R  plan-2  N3   0.020
 K2R  plan-2  C4   0.020
 K2R  plan-2  C5   0.020
 K2R  plan-2  N7   0.020
 K2R  plan-2  C8   0.020
 K2R  plan-2  N9   0.020
 K2R  plan-2  C1'  0.020
 K2R  plan-2  H10  0.020
 K2R  plan-2  H11  0.020
 K2R  plan-3  OZ1  0.020
 K2R  plan-3  CZ   0.020
 K2R  plan-3  OZ2  0.020
 K2R  plan-3  CE   0.020
 K2R  plan-3  H1   0.020

