# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 19:46:25 2020
#   Inital geometry file: a 122 line input string
#   Ligand name: {[(2R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(C[C@H](COCC[P](O)(O)=O)OCC[P](O)(O)=O)cnc2C(=O)N1
#
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
 3QE  3QE  '{[(2R)-3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)propane-1,2-diyl]bis(oxyethane-2,1-diyl)}bis(phosphonic acid)'  ligand  49  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3QE
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
 3QE  OAE  O  O     0  -0.715  -6.9849   0.2068  -1.0680
 3QE  PBA  P  P     0   1.357  -6.4346   0.0847   0.3031
 3QE  OAF  O  OH1   0  -0.743  -6.9487   1.1616   1.3776
 3QE  OAC  O  OH1   0  -0.749  -6.8011  -1.3706   0.8852
 3QE  CAL  C  CH2   0  -0.777  -4.6485   0.2758   0.4505
 3QE  CAJ  C  CH2   0  -0.130  -3.9082  -0.6312  -0.5194
 3QE  OAS  O  O2    0  -0.481  -2.5294  -0.4359  -0.3302
 3QE  CAN  C  CH2   0  -0.131  -1.7480  -1.1353  -1.2621
 3QE  CAY  C  CH1   0  -0.012  -0.2873  -0.8718  -0.9576
 3QE  OAT  O  O2    0  -0.492   0.0038   0.4969  -1.1228
 3QE  CAK  C  CH2   0  -0.145   0.5144   1.1418   0.0207
 3QE  CAM  C  CH2   0  -0.779   0.9962   2.5187  -0.4043
 3QE  PBB  P  P     0   1.357   1.7389   3.4194   0.9686
 3QE  OAG  O  OH1   0  -0.744   2.0720   4.8233   0.2634
 3QE  OAH  O  OH1   0  -0.750   0.5687   3.6956   2.0393
 3QE  OAD  O  O     0  -0.711   2.8671   2.7419   1.6496
 3QE  CAO  C  CH2   0  -0.326   0.6082  -1.6761  -1.8968
 3QE  N9   N  NR5   0  -0.491   1.9998  -1.3734  -1.6601
 3QE  C4   C  CR56  0   0.490   2.7823  -1.8906  -0.6779
 3QE  N3   N  N     0  -0.514   2.4333  -2.8603   0.1792
 3QE  C2   C  CR6   0   0.690   3.3871  -3.1654   1.0243
 3QE  N2   N  NH2   0  -0.835   3.1776  -4.0918   1.9669
 3QE  N1   N  NR16  0  -0.727   4.6099  -2.5560   1.0162
 3QE  C6   C  CR6   0   0.500   5.0229  -1.5383   0.1467
 3QE  O6   O  O     0  -0.477   6.1435  -1.0638   0.2373
 3QE  C5   C  CR56  0  -0.083   3.9808  -1.2050  -0.7647
 3QE  N7   N  N     0  -0.446   3.9346  -0.2758  -1.7727
 3QE  C8   C  CR15  0   0.096   2.7432  -0.3991  -2.2730
 3QE  H1   H  HOH1  0   0.495  -7.9038   1.3141   1.3588
 3QE  H2   H  HOH1  0   0.490  -6.5233  -1.5367   1.7956
 3QE  H3   H  HCH2  0   0.293  -4.4043   1.3203   0.2427
 3QE  H4   H  HCH2  0   0.291  -4.3461   0.0647   1.4795
 3QE  H5   H  HCH2  0   0.213  -4.1760  -1.6823  -0.3471
 3QE  H6   H  HCH2  0   0.216  -4.1967  -0.3892  -1.5499
 3QE  H7   H  HCH2  0   0.210  -1.9363  -2.2169  -1.2093
 3QE  H8   H  HCH2  0   0.210  -1.9814  -0.8170  -2.2885
 3QE  H9   H  HCH1  0   0.242  -0.0859  -1.1931   0.0728
 3QE  H10  H  HCH2  0   0.227  -0.2555   1.2257   0.7968
 3QE  H11  H  HCH2  0   0.218   1.3501   0.5773   0.4506
 3QE  H12  H  HCH2  0   0.290   1.7586   2.4200  -1.1814
 3QE  H13  H  HCH2  0   0.292   0.1732   3.1043  -0.8215
 3QE  H14  H  HOH1  0   0.495   2.6201   5.4154   0.7969
 3QE  H15  H  HOH1  0   0.490  -0.2035   4.1666   1.6998
 3QE  H16  H  HCH2  0   0.278   0.4503  -2.7452  -1.7570
 3QE  H17  H  HCH2  0   0.279   0.3840  -1.4409  -2.9382
 3QE  H18  H  HNH2  0   0.414   2.3290  -4.6296   1.9309
 3QE  H19  H  HNH2  0   0.416   3.9255  -4.4473   2.5362
 3QE  H20  H  HNR6  0   0.424   5.2935  -2.8468   1.7034
 3QE  H21  H  HCR5  0   0.285   2.3427   0.1725  -3.0968

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
 3QE  OAD  PBB  double    1.482  0.020  1.482
 3QE  CAL  CAJ  single    1.520  0.020  1.520
 3QE  CAL  PBA  single    1.802  0.020  1.802
 3QE  OAE  PBA  double    1.482  0.020  1.482
 3QE  PBB  OAH  single    1.610  0.020  1.610
 3QE  PBB  OAG  single    1.606  0.020  1.606
 3QE  PBB  CAM  single    1.802  0.020  1.802
 3QE  CAJ  OAS  single    1.405  0.020  1.405
 3QE  OAS  CAN  single    1.403  0.020  1.403
 3QE  PBA  OAF  single    1.606  0.020  1.606
 3QE  PBA  OAC  single    1.610  0.020  1.610
 3QE  CAK  CAM  single    1.519  0.020  1.519
 3QE  CAK  OAT  single    1.409  0.020  1.409
 3QE  OAT  CAY  single    1.409  0.020  1.409
 3QE  CAN  CAY  single    1.515  0.020  1.515
 3QE  CAO  CAY  single    1.527  0.020  1.527
 3QE  CAO  N9   single    1.444  0.020  1.444
 3QE  N9   C8   aromatic  1.370  0.020  1.370
 3QE  N9   C4   aromatic  1.358  0.020  1.358
 3QE  C8   N7   aromatic  1.298  0.020  1.298
 3QE  C4   N3   single    1.340  0.020  1.340
 3QE  C4   C5   aromatic  1.383  0.020  1.383
 3QE  N3   C2   double    1.310  0.020  1.310
 3QE  N7   C5   aromatic  1.372  0.020  1.372
 3QE  C5   C6   single    1.424  0.020  1.424
 3QE  C2   N2   single    1.338  0.020  1.338
 3QE  C2   N1   single    1.366  0.020  1.366
 3QE  C6   N1   single    1.401  0.020  1.401
 3QE  C6   O6   double    1.220  0.020  1.220
 3QE  OAF  H1   single    0.850  0.020  0.980
 3QE  OAC  H2   single    0.850  0.020  0.980
 3QE  CAL  H3   single    0.970  0.020  1.090
 3QE  CAL  H4   single    0.970  0.020  1.090
 3QE  CAJ  H5   single    0.970  0.020  1.090
 3QE  CAJ  H6   single    0.970  0.020  1.090
 3QE  CAN  H7   single    0.970  0.020  1.090
 3QE  CAN  H8   single    0.970  0.020  1.090
 3QE  CAY  H9   single    0.970  0.020  1.090
 3QE  CAK  H10  single    0.970  0.020  1.090
 3QE  CAK  H11  single    0.970  0.020  1.090
 3QE  CAM  H12  single    0.970  0.020  1.090
 3QE  CAM  H13  single    0.970  0.020  1.090
 3QE  OAG  H14  single    0.850  0.020  0.980
 3QE  OAH  H15  single    0.850  0.020  0.980
 3QE  CAO  H16  single    0.970  0.020  1.090
 3QE  CAO  H17  single    0.970  0.020  1.090
 3QE  N2   H18  single    0.860  0.020  1.020
 3QE  N2   H19  single    0.860  0.020  1.020
 3QE  N1   H20  single    0.860  0.020  1.020
 3QE  C8   H21  single    0.930  0.020  1.080

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
 3QE  CAL  PBA  OAC  106.97  3.000
 3QE  OAC  PBA  OAF  106.94  3.000
 3QE  CAL  PBA  OAF  101.03  3.000
 3QE  OAC  PBA  OAE  108.93  3.000
 3QE  OAF  PBA  OAE  116.41  3.000
 3QE  CAL  PBA  OAE  115.77  3.000
 3QE  H1   OAF  PBA  114.13  3.000
 3QE  H2   OAC  PBA  115.51  3.000
 3QE  H4   CAL  H3   107.57  3.000
 3QE  H4   CAL  CAJ  110.52  3.000
 3QE  H3   CAL  CAJ  109.89  3.000
 3QE  H4   CAL  PBA  109.31  3.000
 3QE  H3   CAL  PBA  107.90  3.000
 3QE  CAJ  CAL  PBA  111.54  3.000
 3QE  H6   CAJ  H5   107.11  3.000
 3QE  H6   CAJ  OAS  110.72  3.000
 3QE  H5   CAJ  OAS  110.56  3.000
 3QE  H6   CAJ  CAL  109.85  3.000
 3QE  H5   CAJ  CAL  110.62  3.000
 3QE  OAS  CAJ  CAL  108.00  3.000
 3QE  CAN  OAS  CAJ  112.81  3.000
 3QE  H8   CAN  H7   107.05  3.000
 3QE  H8   CAN  CAY  109.98  3.000
 3QE  H7   CAN  CAY  109.06  3.000
 3QE  H8   CAN  OAS  110.95  3.000
 3QE  H7   CAN  OAS  111.31  3.000
 3QE  CAY  CAN  OAS  108.47  3.000
 3QE  H9   CAY  CAO  108.40  3.000
 3QE  H9   CAY  OAT  110.88  3.000
 3QE  CAO  CAY  OAT  108.57  3.000
 3QE  H9   CAY  CAN  108.33  3.000
 3QE  CAO  CAY  CAN  110.50  3.000
 3QE  OAT  CAY  CAN  110.15  3.000
 3QE  CAK  OAT  CAY  115.11  3.000
 3QE  H11  CAK  H10  107.29  3.000
 3QE  H11  CAK  CAM  109.55  3.000
 3QE  H10  CAK  CAM  110.57  3.000
 3QE  H11  CAK  OAT  111.03  3.000
 3QE  H10  CAK  OAT  110.80  3.000
 3QE  CAM  CAK  OAT  107.62  3.000
 3QE  H13  CAM  H12  107.60  3.000
 3QE  H13  CAM  PBB  109.47  3.000
 3QE  H12  CAM  PBB  107.42  3.000
 3QE  H13  CAM  CAK  110.70  3.000
 3QE  H12  CAM  CAK  109.77  3.000
 3QE  PBB  CAM  CAK  111.75  3.000
 3QE  OAD  PBB  OAH  109.04  3.000
 3QE  OAH  PBB  OAG  107.03  3.000
 3QE  OAD  PBB  OAG  116.33  3.000
 3QE  OAG  PBB  CAM  100.83  3.000
 3QE  OAH  PBB  CAM  107.03  3.000
 3QE  OAD  PBB  CAM  115.81  3.000
 3QE  H14  OAG  PBB  114.24  3.000
 3QE  H15  OAH  PBB  115.52  3.000
 3QE  H17  CAO  H16  107.71  3.000
 3QE  H17  CAO  N9   108.03  3.000
 3QE  H16  CAO  N9   108.92  3.000
 3QE  H17  CAO  CAY  110.68  3.000
 3QE  H16  CAO  CAY  110.67  3.000
 3QE  N9   CAO  CAY  110.73  3.000
 3QE  C8   N9   C4   106.36  3.000
 3QE  C4   N9   CAO  126.45  3.000
 3QE  C8   N9   CAO  126.78  3.000
 3QE  C5   C4   N3   128.63  3.000
 3QE  C5   C4   N9   105.37  3.000
 3QE  N3   C4   N9   126.01  3.000
 3QE  C2   N3   C4   113.04  3.000
 3QE  N1   C2   N2   116.94  3.000
 3QE  N1   C2   N3   122.94  3.000
 3QE  N2   C2   N3   120.10  3.000
 3QE  H19  N2   H18  117.34  3.000
 3QE  H19  N2   C2   121.83  3.000
 3QE  H18  N2   C2   118.51  3.000
 3QE  H20  N1   C6   115.54  3.000
 3QE  H20  N1   C2   118.19  3.000
 3QE  C6   N1   C2   126.27  3.000
 3QE  C5   C6   O6   128.94  3.000
 3QE  O6   C6   N1   120.47  3.000
 3QE  C5   C6   N1   110.59  3.000
 3QE  N7   C5   C6   130.81  3.000
 3QE  C6   C5   C4   118.54  3.000
 3QE  N7   C5   C4   110.65  3.000
 3QE  C8   N7   C5   104.47  3.000
 3QE  H21  C8   N7   125.75  3.000
 3QE  H21  C8   N9   121.10  3.000
 3QE  N7   C8   N9   113.15  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
 3QE  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 3QE  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 3QE  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 3QE  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 3QE  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3QE  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3QE  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3QE  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 3QE  CONST_09  N7   C8   N9   CAO   180.00   0.0  0
 3QE  CONST_10  N3   C4   N9   CAO     0.00   0.0  0
 3QE  CONST_11  C5   C4   N9   CAO   180.00   0.0  0
 3QE  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 3QE  CONST_13  O6   C6   N1   C2    180.00   0.0  0
 3QE  CONST_14  C6   N1   C2   N2    180.00   0.0  0
 3QE  CONST_15  H21  C8   N9   C4    180.00   0.0  0
 3QE  CONST_16  H20  N1   C2   N3    180.00   0.0  0
 3QE  CONST_17  H18  N2   C2   N3      0.00   0.0  0
 3QE  CONST_18  H19  N2   C2   N3    180.00   0.0  0
 3QE  Var_01    C8   N9   CAO  CAY   -90.52  30.0  2
 3QE  Var_02    CAJ  CAL  PBA  OAE   -51.65  30.0  2
 3QE  Var_03    OAS  CAJ  CAL  PBA  -179.25  30.0  3
 3QE  Var_04    CAY  CAN  OAS  CAJ  -179.23  30.0  3
 3QE  Var_05    CAM  CAK  OAT  CAY   170.08  30.0  2
 3QE  Var_06    PBB  CAM  CAK  OAT  -177.61  30.0  3
 3QE  Var_07    OAD  PBB  CAM  CAK    56.40  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
 3QE  chir_01  CAY  OAT  CAN  CAO  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
 3QE  plan-1  CAO  0.020
 3QE  plan-1  N9   0.020
 3QE  plan-1  C4   0.020
 3QE  plan-1  N3   0.020
 3QE  plan-1  C2   0.020
 3QE  plan-1  N2   0.020
 3QE  plan-1  N1   0.020
 3QE  plan-1  C6   0.020
 3QE  plan-1  O6   0.020
 3QE  plan-1  C5   0.020
 3QE  plan-1  N7   0.020
 3QE  plan-1  C8   0.020
 3QE  plan-1  H18  0.020
 3QE  plan-1  H19  0.020
 3QE  plan-1  H20  0.020
 3QE  plan-1  H21  0.020

