# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:56:29 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: [2-([2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl]{2-[(2-oxoethyl)(2-phosphonoethyl)amino]ethyl}amino)ethyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CCN(CCN(CC[P](O)(O)=O)CC=O)CC[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
 3QF  3QF  '[2-([2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl]{2-[(2-oxoethyl)(2-phosphonoethyl)amino]ethyl}amino)ethyl]phosphonic acid'  ligand  59  32  .  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_3QF
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
 3QF  OAF  O  OH1   0  -0.744  -6.5882  -2.8720  -1.6415
 3QF  PBE  P  P     0   1.369  -5.1308  -3.0122  -0.9794
 3QF  OAG  O  O     0  -0.717  -4.9178  -4.1968  -0.1136
 3QF  OAC  O  OH1   0  -0.751  -4.0695  -3.0540  -2.1904
 3QF  CAS  C  CH2   0  -0.763  -4.9528  -1.4074  -0.1812
 3QF  CAP  C  CH2   0  -0.284  -3.6043  -1.2736   0.5219
 3QF  NBB  N  NT    0  -0.436  -3.4322   0.0424   1.1164
 3QF  CAL  C  CH2   0  -0.404  -4.2015   0.2142   2.3264
 3QF  CAK  C  C1    0   0.169  -4.3917   1.6756   2.6336
 3QF  OAE  O  O     0  -0.376  -4.6000   2.1220   3.7325
 3QF  CAM  C  CH2   0  -0.302  -2.0281   0.3661   1.3236
 3QF  CAN  C  CH2   0  -0.300  -1.3534   0.8535   0.0462
 3QF  NBC  N  NT    0  -0.427   0.0610   1.0823   0.2815
 3QF  CAQ  C  CH2   0  -0.281   0.6388   2.1455  -0.5188
 3QF  CAT  C  CH2   0  -0.759   0.2153   3.5241  -0.0156
 3QF  PBF  P  P     0   1.367   1.0652   4.8501  -0.8882
 3QF  OAH  O  O     0  -0.719   2.5467   4.7802  -0.8859
 3QF  OAI  O  OH1   0  -0.751   0.5450   4.8300  -2.4121
 3QF  OAD  O  OH1   0  -0.745   0.4163   6.1445  -0.1901
 3QF  CAO  C  CH2   0  -0.307   0.8577  -0.1291   0.2428
 3QF  CAR  C  CH2   0  -0.320   1.8899  -0.1081   1.3650
 3QF  N9   N  NR5   0  -0.493   2.7730  -1.2529   1.3092
 3QF  C4   C  CR56  0   0.495   3.8767  -1.3820   0.5303
 3QF  N3   N  N     0  -0.508   4.3816  -0.4442  -0.2844
 3QF  C2   C  CR6   0   0.682   5.4670  -0.8347  -0.9038
 3QF  N2   N  NH2   0  -0.833   6.1159   0.0091  -1.7203
 3QF  N1   N  NR16  0  -0.727   6.0140  -2.0756  -0.7371
 3QF  C6   C  CR6   0   0.500   5.5251  -3.0917   0.0941
 3QF  O6   O  O     0  -0.476   6.1001  -4.1654   0.1641
 3QF  C5   C  CR56  0  -0.088   4.3474  -2.6613   0.7695
 3QF  N7   N  N     0  -0.447   3.5454  -3.3108   1.6720
 3QF  C8   C  CR15  0   0.091   2.6216  -2.4461   1.9642
 3QF  H1   H  HOH1  0   0.494  -6.9484  -3.7028  -1.9817
 3QF  H2   H  HOH1  0   0.490  -4.1637  -2.3528  -2.8482
 3QF  H3   H  HCH2  0   0.289  -5.0686  -0.6131  -0.9227
 3QF  H4   H  HCH2  0   0.288  -5.7806  -1.3119   0.5253
 3QF  H5   H  HCH2  0   0.229  -3.4869  -2.0733   1.2678
 3QF  H6   H  HCH2  0   0.249  -2.8107  -1.4180  -0.2126
 3QF  H8   H  HCH2  0   0.285  -5.2135  -0.1815   2.1819
 3QF  H9   H  HCH2  0   0.247  -3.7897  -0.3088   3.2023
 3QF  H10  H  H     0   0.192  -4.3577   2.3254   1.7395
 3QF  H11  H  HCH2  0   0.246  -1.9468   1.1728   2.0567
 3QF  H12  H  HCH2  0   0.220  -1.4795  -0.4859   1.7557
 3QF  H13  H  HCH2  0   0.221  -1.5195   0.1542  -0.7865
 3QF  H14  H  HCH2  0   0.242  -1.8320   1.7894  -0.2454
 3QF  H16  H  HCH2  0   0.246   1.7259   2.0718  -0.4454
 3QF  H17  H  HCH2  0   0.224   0.3929   2.0366  -1.5855
 3QF  H18  H  HCH2  0   0.284  -0.8628   3.6732  -0.1136
 3QF  H19  H  HCH2  0   0.289   0.4575   3.6114   1.0460
 3QF  H20  H  HOH1  0   0.490  -0.4118   4.9008  -2.5247
 3QF  H21  H  HOH1  0   0.493   0.8345   6.9802  -0.4394
 3QF  H22  H  HCH2  0   0.250   0.2152  -1.0022   0.3741
 3QF  H23  H  HCH2  0   0.238   1.3575  -0.2638  -0.7265
 3QF  H24  H  HCH2  0   0.266   2.4992   0.7945   1.3157
 3QF  H25  H  HCH2  0   0.273   1.3876  -0.1091   2.3321
 3QF  H26  H  HNH2  0   0.411   5.6481   0.8624  -1.9752
 3QF  H27  H  HNH2  0   0.414   6.8144  -0.3262  -2.3614
 3QF  H28  H  HNR6  0   0.424   6.8609  -2.2977  -1.2447
 3QF  H29  H  HCR5  0   0.287   1.8049  -2.6036   2.6537

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
 3QF  OAE  CAK  double    1.204  0.020  1.204
 3QF  CAK  CAL  single    1.505  0.020  1.505
 3QF  CAL  NBB  single    1.444  0.020  1.444
 3QF  OAH  PBF  double    1.483  0.020  1.483
 3QF  NBB  CAM  single    1.456  0.020  1.456
 3QF  NBB  CAP  single    1.454  0.020  1.454
 3QF  CAM  CAN  single    1.525  0.020  1.525
 3QF  PBF  OAI  single    1.610  0.020  1.610
 3QF  PBF  OAD  single    1.607  0.020  1.607
 3QF  PBF  CAT  single    1.801  0.020  1.801
 3QF  CAS  CAP  single    1.527  0.020  1.527
 3QF  CAS  PBE  single    1.801  0.020  1.801
 3QF  CAT  CAQ  single    1.527  0.020  1.527
 3QF  CAQ  NBC  single    1.451  0.020  1.451
 3QF  CAN  NBC  single    1.452  0.020  1.452
 3QF  NBC  CAO  single    1.450  0.020  1.450
 3QF  OAG  PBE  double    1.483  0.020  1.483
 3QF  PBE  OAC  single    1.611  0.020  1.611
 3QF  PBE  OAF  single    1.607  0.020  1.607
 3QF  CAO  CAR  single    1.525  0.020  1.525
 3QF  CAR  N9   single    1.447  0.020  1.447
 3QF  N9   C8   aromatic  1.370  0.020  1.370
 3QF  N9   C4   aromatic  1.357  0.020  1.357
 3QF  C8   N7   aromatic  1.299  0.020  1.299
 3QF  C4   N3   single    1.341  0.020  1.341
 3QF  C4   C5   aromatic  1.384  0.020  1.384
 3QF  N3   C2   double    1.309  0.020  1.309
 3QF  N7   C5   aromatic  1.371  0.020  1.371
 3QF  C5   C6   single    1.424  0.020  1.424
 3QF  C2   N2   single    1.342  0.020  1.342
 3QF  C2   N1   single    1.366  0.020  1.366
 3QF  C6   N1   single    1.401  0.020  1.401
 3QF  C6   O6   double    1.220  0.020  1.220
 3QF  OAF  H1   single    0.850  0.020  0.980
 3QF  OAC  H2   single    0.850  0.020  0.980
 3QF  CAS  H3   single    0.970  0.020  1.090
 3QF  CAS  H4   single    0.970  0.020  1.090
 3QF  CAP  H5   single    0.970  0.020  1.090
 3QF  CAP  H6   single    0.970  0.020  1.090
 3QF  CAL  H8   single    0.970  0.020  1.090
 3QF  CAL  H9   single    0.970  0.020  1.090
 3QF  CAK  H10  single    0.930  0.020  1.080
 3QF  CAM  H11  single    0.970  0.020  1.090
 3QF  CAM  H12  single    0.970  0.020  1.090
 3QF  CAN  H13  single    0.970  0.020  1.090
 3QF  CAN  H14  single    0.970  0.020  1.090
 3QF  CAQ  H16  single    0.970  0.020  1.090
 3QF  CAQ  H17  single    0.970  0.020  1.090
 3QF  CAT  H18  single    0.970  0.020  1.090
 3QF  CAT  H19  single    0.970  0.020  1.090
 3QF  OAI  H20  single    0.850  0.020  0.980
 3QF  OAD  H21  single    0.850  0.020  0.980
 3QF  CAO  H22  single    0.970  0.020  1.090
 3QF  CAO  H23  single    0.970  0.020  1.090
 3QF  CAR  H24  single    0.970  0.020  1.090
 3QF  CAR  H25  single    0.970  0.020  1.090
 3QF  N2   H26  single    0.890  0.020  1.040
 3QF  N2   H27  single    0.890  0.020  1.040
 3QF  N1   H28  single    0.860  0.020  1.020
 3QF  C8   H29  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
 3QF  H1   OAF  PBE  114.06  3.000
 3QF  CAS  PBE  OAC  106.93  3.000
 3QF  OAC  PBE  OAG  108.88  3.000
 3QF  CAS  PBE  OAG  116.04  3.000
 3QF  OAC  PBE  OAF  106.86  3.000
 3QF  OAG  PBE  OAF  116.14  3.000
 3QF  CAS  PBE  OAF  101.21  3.000
 3QF  H2   OAC  PBE  115.40  3.000
 3QF  H4   CAS  H3   107.16  3.000
 3QF  H4   CAS  CAP  111.33  3.000
 3QF  H3   CAS  CAP  110.02  3.000
 3QF  H4   CAS  PBE  106.83  3.000
 3QF  H3   CAS  PBE  109.66  3.000
 3QF  CAP  CAS  PBE  111.68  3.000
 3QF  H6   CAP  H5   106.42  3.000
 3QF  H6   CAP  NBB  107.99  3.000
 3QF  H5   CAP  NBB  111.60  3.000
 3QF  H6   CAP  CAS  108.72  3.000
 3QF  H5   CAP  CAS  110.05  3.000
 3QF  NBB  CAP  CAS  111.85  3.000
 3QF  CAM  NBB  CAL  111.60  3.000
 3QF  CAM  NBB  CAP  111.94  3.000
 3QF  CAL  NBB  CAP  112.77  3.000
 3QF  H9   CAL  H8   106.20  3.000
 3QF  H9   CAL  CAK  110.26  3.000
 3QF  H8   CAL  CAK  105.11  3.000
 3QF  H9   CAL  NBB  114.28  3.000
 3QF  H8   CAL  NBB  109.78  3.000
 3QF  CAK  CAL  NBB  110.72  3.000
 3QF  H10  CAK  OAE  121.68  3.000
 3QF  H10  CAK  CAL  113.68  3.000
 3QF  OAE  CAK  CAL  124.61  3.000
 3QF  H12  CAM  H11  105.70  3.000
 3QF  H12  CAM  CAN  110.82  3.000
 3QF  H11  CAM  CAN  107.04  3.000
 3QF  H12  CAM  NBB  111.36  3.000
 3QF  H11  CAM  NBB  109.35  3.000
 3QF  CAN  CAM  NBB  112.25  3.000
 3QF  H14  CAN  H13  106.07  3.000
 3QF  H14  CAN  NBC  109.61  3.000
 3QF  H13  CAN  NBC  111.71  3.000
 3QF  H14  CAN  CAM  107.70  3.000
 3QF  H13  CAN  CAM  111.36  3.000
 3QF  NBC  CAN  CAM  110.22  3.000
 3QF  CAO  NBC  CAQ  112.25  3.000
 3QF  CAO  NBC  CAN  113.53  3.000
 3QF  CAQ  NBC  CAN  114.46  3.000
 3QF  H17  CAQ  H16  106.32  3.000
 3QF  H17  CAQ  CAT  110.29  3.000
 3QF  H16  CAQ  CAT  108.34  3.000
 3QF  H17  CAQ  NBC  111.92  3.000
 3QF  H16  CAQ  NBC  108.05  3.000
 3QF  CAT  CAQ  NBC  111.68  3.000
 3QF  H19  CAT  H18  107.15  3.000
 3QF  H19  CAT  PBF  107.91  3.000
 3QF  H18  CAT  PBF  108.77  3.000
 3QF  H19  CAT  CAQ  109.32  3.000
 3QF  H18  CAT  CAQ  111.54  3.000
 3QF  PBF  CAT  CAQ  111.98  3.000
 3QF  OAD  PBF  OAI  106.89  3.000
 3QF  OAD  PBF  OAH  116.14  3.000
 3QF  OAI  PBF  OAH  108.88  3.000
 3QF  OAD  PBF  CAT  101.08  3.000
 3QF  OAI  PBF  CAT  107.27  3.000
 3QF  OAH  PBF  CAT  115.85  3.000
 3QF  H20  OAI  PBF  115.43  3.000
 3QF  H21  OAD  PBF  114.17  3.000
 3QF  H23  CAO  H22  106.00  3.000
 3QF  H23  CAO  CAR  110.06  3.000
 3QF  H22  CAO  CAR  108.71  3.000
 3QF  H23  CAO  NBC  112.07  3.000
 3QF  H22  CAO  NBC  109.96  3.000
 3QF  CAR  CAO  NBC  109.92  3.000
 3QF  H25  CAR  H24  107.37  3.000
 3QF  H25  CAR  N9   108.35  3.000
 3QF  H24  CAR  N9   108.19  3.000
 3QF  H25  CAR  CAO  109.94  3.000
 3QF  H24  CAR  CAO  110.88  3.000
 3QF  N9   CAR  CAO  111.95  3.000
 3QF  C8   N9   C4   106.35  3.000
 3QF  C4   N9   CAR  126.43  3.000
 3QF  C8   N9   CAR  127.11  3.000
 3QF  C5   C4   N3   128.56  3.000
 3QF  C5   C4   N9   105.39  3.000
 3QF  N3   C4   N9   126.05  3.000
 3QF  C2   N3   C4   113.02  3.000
 3QF  N1   C2   N2   116.86  3.000
 3QF  N1   C2   N3   123.03  3.000
 3QF  N2   C2   N3   120.09  3.000
 3QF  H27  N2   H26  116.38  3.000
 3QF  H27  N2   C2   120.94  3.000
 3QF  H26  N2   C2   117.57  3.000
 3QF  H28  N1   C6   115.50  3.000
 3QF  H28  N1   C2   118.24  3.000
 3QF  C6   N1   C2   126.26  3.000
 3QF  C5   C6   O6   128.94  3.000
 3QF  O6   C6   N1   120.53  3.000
 3QF  C5   C6   N1   110.54  3.000
 3QF  N7   C5   C6   130.75  3.000
 3QF  C6   C5   C4   118.60  3.000
 3QF  N7   C5   C4   110.65  3.000
 3QF  C8   N7   C5   104.41  3.000
 3QF  H29  C8   N7   125.75  3.000
 3QF  H29  C8   N9   121.05  3.000
 3QF  N7   C8   N9   113.19  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
 3QF  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 3QF  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 3QF  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 3QF  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 3QF  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3QF  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3QF  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3QF  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 3QF  CONST_09  N7   C8   N9   CAR   180.00   0.0  0
 3QF  CONST_10  N3   C4   N9   CAR     0.00   0.0  0
 3QF  CONST_11  C5   C4   N9   CAR   180.00   0.0  0
 3QF  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 3QF  CONST_13  O6   C6   N1   C2    180.00   0.0  0
 3QF  CONST_14  C6   N1   C2   N2    180.00   0.0  0
 3QF  CONST_15  H29  C8   N9   C4    180.00   0.0  0
 3QF  CONST_16  H28  N1   C2   N3    180.00   0.0  0
 3QF  CONST_17  H26  N2   C2   N3      0.00   0.0  0
 3QF  CONST_18  H27  N2   C2   N3    180.00   0.0  0
 3QF  Var_01    C8   N9   CAR  CAO   -93.07  30.0  2
 3QF  Var_02    N9   CAR  CAO  NBC  -175.86  30.0  3
 3QF  Var_03    CAP  CAS  PBE  OAF  -179.12  30.0  2
 3QF  Var_04    NBB  CAP  CAS  PBE   177.42  30.0  3
 3QF  Var_05    CAL  NBB  CAP  CAS    75.22  30.0  1
 3QF  Var_06    CAK  CAL  NBB  CAP  -159.92  30.0  3
 3QF  Var_07    CAN  CAM  NBB  CAP    80.46  30.0  3
 3QF  Var_08    OAE  CAK  CAL  NBB  -155.39  30.0  2
 3QF  Var_09    NBC  CAN  CAM  NBB  -176.40  30.0  3
 3QF  Var_10    CAQ  NBC  CAN  CAM  -148.67  30.0  3
 3QF  Var_11    CAT  CAQ  NBC  CAN    74.41  30.0  1
 3QF  Var_12    CAR  CAO  NBC  CAN  -138.42  30.0  3
 3QF  Var_13    PBF  CAT  CAQ  NBC   173.85  30.0  1
 3QF  Var_14    OAH  PBF  CAT  CAQ   -54.71  30.0  3

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
 3QF  plan-1  CAR  0.020
 3QF  plan-1  N9   0.020
 3QF  plan-1  C4   0.020
 3QF  plan-1  N3   0.020
 3QF  plan-1  C2   0.020
 3QF  plan-1  N2   0.020
 3QF  plan-1  N1   0.020
 3QF  plan-1  C6   0.020
 3QF  plan-1  O6   0.020
 3QF  plan-1  C5   0.020
 3QF  plan-1  N7   0.020
 3QF  plan-1  C8   0.020
 3QF  plan-1  H26  0.020
 3QF  plan-1  H27  0.020
 3QF  plan-1  H28  0.020
 3QF  plan-1  H29  0.020
 3QF  plan-2  CAL  0.020
 3QF  plan-2  CAK  0.020
 3QF  plan-2  OAE  0.020
 3QF  plan-2  H10  0.020

