# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:59:36 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: [(2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-phosphonoethyl)amino}ethoxy)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[P](O)(=O)CCN(CCOC[P](O)(O)=O)CCn1cnc2C(=O)NC=Nc12
#
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
 3L8  3L8  '[(2-{[2-(6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](2-phosphonoethyl)amino}ethoxy)methyl]phosphonic acid'  ligand  48  27  .  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_3L8
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
 3L8  OAF  O  OH1   0  -0.750  -4.0745  -2.9050  -2.0279
 3L8  PBA  P  P     0   1.354  -2.9001  -2.0238  -1.3676
 3L8  OAG  O  O     0  -0.703  -1.8331  -1.5687  -2.2888
 3L8  OAC  O  OH1   0  -0.738  -3.6125  -0.7475  -0.6952
 3L8  CAP  C  CH2   0  -0.450  -2.3924  -3.1701  -0.0397
 3L8  OAT  O  O2    0  -0.474  -1.3195  -2.6444   0.6856
 3L8  CAJ  C  CH2   0  -0.138  -1.6541  -1.9347   1.8611
 3L8  CAK  C  CH2   0  -0.338  -0.5428  -0.9503   2.1562
 3L8  NAX  N  NT    0  -0.407  -0.4796   0.1015   1.1577
 3L8  CAM  C  CH2   0  -0.273  -1.2376   1.2794   1.5180
 3L8  CAO  C  CH2   0  -0.771  -1.6812   2.0671   0.2867
 3L8  PAZ  P  P     0   1.363  -2.7514   3.4479   0.7144
 3L8  OAD  O  OH1   0  -0.745  -2.9772   4.1207  -0.7289
 3L8  OAE  O  O     0  -0.718  -3.9811   3.1211   1.4769
 3L8  OAB  O  OH1   0  -0.752  -1.8682   4.4830   1.5784
 3L8  CAL  C  CH2   0  -0.297   0.8428   0.3495   0.6369
 3L8  CAN  C  CH2   0  -0.330   1.1998  -0.7124  -0.3994
 3L8  N9   N  NR5   0  -0.482   2.5342  -0.5091  -0.9294
 3L8  C4   C  CR56  0   0.475   3.7002  -0.8595  -0.3320
 3L8  N3   N  N     0  -0.445   3.8384  -1.5058   0.8444
 3L8  C2   C  CR16  0   0.157   5.0765  -1.7087   1.1549
 3L8  N1   N  NR16  0  -0.664   6.1327  -1.3267   0.4007
 3L8  C6   C  CR6   0   0.508   6.0681  -0.6587  -0.8268
 3L8  O6   O  O     0  -0.469   7.0768  -0.3574  -1.4403
 3L8  C5   C  CR56  0  -0.057   4.7017  -0.4242  -1.1808
 3L8  N7   N  N     0  -0.447   4.1661   0.1868  -2.2776
 3L8  C8   C  CR15  0   0.103   2.8781   0.1193  -2.0885
 3L8  H1   H  HOH1  0   0.494  -4.3798  -2.5843  -2.8878
 3L8  H2   H  HOH1  0   0.489  -4.3788  -0.9391  -0.1396
 3L8  H3   H  HCH2  0   0.259  -3.2532  -3.4370   0.5862
 3L8  H4   H  HCH2  0   0.281  -2.0622  -4.0932  -0.5251
 3L8  H5   H  HCH2  0   0.207  -2.6008  -1.3944   1.7531
 3L8  H6   H  HCH2  0   0.214  -1.7737  -2.6290   2.7026
 3L8  H7   H  HCH2  0   0.234  -0.6880  -0.5485   3.1677
 3L8  H8   H  HCH2  0   0.242   0.4086  -1.4885   2.1893
 3L8  H10  H  HCH2  0   0.245  -2.1311   0.9473   2.0510
 3L8  H11  H  HCH2  0   0.214  -0.6888   1.9347   2.2125
 3L8  H12  H  HCH2  0   0.279  -0.8261   2.4560  -0.2711
 3L8  H13  H  HCH2  0   0.302  -2.2272   1.3996  -0.3816
 3L8  H14  H  HOH1  0   0.493  -3.6198   4.8435  -0.7319
 3L8  H15  H  HOH1  0   0.489  -1.0488   4.7788   1.1611
 3L8  H16  H  HCH2  0   0.243   0.8674   1.3244   0.1459
 3L8  H17  H  HCH2  0   0.225   1.6111   0.3841   1.4248
 3L8  H18  H  HCH2  0   0.265   1.1559  -1.7124   0.0287
 3L8  H19  H  HCH2  0   0.282   0.4846  -0.6863  -1.2201
 3L8  H20  H  HCR6  0   0.303   5.3260  -2.2178   2.0764
 3L8  H21  H  HNR6  0   0.434   7.0565  -1.5399   0.7543
 3L8  H22  H  HCR5  0   0.293   2.1248   0.5008  -2.7620

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
 3L8  O6   C6   double    1.218  0.020  1.218
 3L8  C6   C5   single    1.431  0.020  1.431
 3L8  C6   N1   single    1.399  0.020  1.399
 3L8  N7   C5   aromatic  1.365  0.020  1.365
 3L8  N7   C8   aromatic  1.304  0.020  1.304
 3L8  C5   C4   aromatic  1.383  0.020  1.383
 3L8  N1   C2   single    1.353  0.020  1.353
 3L8  C8   N9   aromatic  1.363  0.020  1.363
 3L8  OAE  PAZ  double    1.483  0.020  1.483
 3L8  C4   N9   aromatic  1.356  0.020  1.356
 3L8  C4   N3   single    1.349  0.020  1.349
 3L8  OAB  PAZ  single    1.612  0.020  1.612
 3L8  C2   N3   double    1.292  0.020  1.292
 3L8  N9   CAN  single    1.450  0.020  1.450
 3L8  PAZ  CAO  single    1.799  0.020  1.799
 3L8  PAZ  OAD  single    1.608  0.020  1.608
 3L8  CAO  CAM  single    1.527  0.020  1.527
 3L8  CAN  CAL  single    1.526  0.020  1.526
 3L8  CAL  NAX  single    1.443  0.020  1.443
 3L8  CAM  NAX  single    1.446  0.020  1.446
 3L8  NAX  CAK  single    1.452  0.020  1.452
 3L8  CAK  CAJ  single    1.514  0.020  1.514
 3L8  CAJ  OAT  single    1.413  0.020  1.413
 3L8  OAT  CAP  single    1.398  0.020  1.398
 3L8  OAG  PBA  double    1.481  0.020  1.481
 3L8  OAC  PBA  single    1.609  0.020  1.609
 3L8  CAP  PBA  single    1.826  0.020  1.826
 3L8  PBA  OAF  single    1.610  0.020  1.610
 3L8  OAF  H1   single    0.850  0.020  0.980
 3L8  OAC  H2   single    0.850  0.020  0.980
 3L8  CAP  H3   single    0.970  0.020  1.090
 3L8  CAP  H4   single    0.970  0.020  1.090
 3L8  CAJ  H5   single    0.970  0.020  1.090
 3L8  CAJ  H6   single    0.970  0.020  1.090
 3L8  CAK  H7   single    0.970  0.020  1.090
 3L8  CAK  H8   single    0.970  0.020  1.090
 3L8  CAM  H10  single    0.970  0.020  1.090
 3L8  CAM  H11  single    0.970  0.020  1.090
 3L8  CAO  H12  single    0.970  0.020  1.090
 3L8  CAO  H13  single    0.970  0.020  1.090
 3L8  OAD  H14  single    0.850  0.020  0.980
 3L8  OAB  H15  single    0.850  0.020  0.980
 3L8  CAL  H16  single    0.970  0.020  1.090
 3L8  CAL  H17  single    0.970  0.020  1.090
 3L8  CAN  H18  single    0.970  0.020  1.090
 3L8  CAN  H19  single    0.970  0.020  1.090
 3L8  C2   H20  single    0.930  0.020  1.080
 3L8  N1   H21  single    0.860  0.020  1.020
 3L8  C8   H22  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
 3L8  H1   OAF  PBA  114.42  3.000
 3L8  CAP  PBA  OAC  108.49  3.000
 3L8  CAP  PBA  OAG  116.41  3.000
 3L8  OAC  PBA  OAG  109.58  3.000
 3L8  CAP  PBA  OAF   99.06  3.000
 3L8  OAC  PBA  OAF  106.42  3.000
 3L8  OAG  PBA  OAF  116.01  3.000
 3L8  H2   OAC  PBA  115.75  3.000
 3L8  H4   CAP  H3   106.54  3.000
 3L8  H4   CAP  OAT  108.42  3.000
 3L8  H3   CAP  OAT  113.44  3.000
 3L8  H4   CAP  PBA  106.91  3.000
 3L8  H3   CAP  PBA  110.44  3.000
 3L8  OAT  CAP  PBA  110.77  3.000
 3L8  CAJ  OAT  CAP  116.03  3.000
 3L8  H6   CAJ  H5   107.07  3.000
 3L8  H6   CAJ  CAK  109.99  3.000
 3L8  H5   CAJ  CAK  109.45  3.000
 3L8  H6   CAJ  OAT  110.23  3.000
 3L8  H5   CAJ  OAT  111.73  3.000
 3L8  CAK  CAJ  OAT  108.36  3.000
 3L8  H8   CAK  H7   105.50  3.000
 3L8  H8   CAK  NAX  109.85  3.000
 3L8  H7   CAK  NAX  111.98  3.000
 3L8  H8   CAK  CAJ  108.94  3.000
 3L8  H7   CAK  CAJ  108.69  3.000
 3L8  NAX  CAK  CAJ  111.66  3.000
 3L8  CAL  NAX  CAM  115.48  3.000
 3L8  CAM  NAX  CAK  113.32  3.000
 3L8  CAL  NAX  CAK  114.38  3.000
 3L8  H11  CAM  H10  106.31  3.000
 3L8  H11  CAM  CAO  110.26  3.000
 3L8  H10  CAM  CAO  108.22  3.000
 3L8  H11  CAM  NAX  112.36  3.000
 3L8  H10  CAM  NAX  107.62  3.000
 3L8  CAO  CAM  NAX  111.80  3.000
 3L8  H13  CAO  H12  107.26  3.000
 3L8  H13  CAO  PAZ  108.52  3.000
 3L8  H12  CAO  PAZ  108.29  3.000
 3L8  H13  CAO  CAM  108.88  3.000
 3L8  H12  CAO  CAM  111.59  3.000
 3L8  PAZ  CAO  CAM  112.15  3.000
 3L8  OAB  PAZ  OAE  108.67  3.000
 3L8  OAB  PAZ  OAD  106.82  3.000
 3L8  OAE  PAZ  OAD  115.92  3.000
 3L8  OAD  PAZ  CAO  101.03  3.000
 3L8  OAB  PAZ  CAO  107.13  3.000
 3L8  OAE  PAZ  CAO  116.51  3.000
 3L8  H14  OAD  PAZ  114.12  3.000
 3L8  H15  OAB  PAZ  115.46  3.000
 3L8  H17  CAL  H16  106.14  3.000
 3L8  H17  CAL  CAN  110.15  3.000
 3L8  H16  CAL  CAN  108.10  3.000
 3L8  H17  CAL  NAX  112.75  3.000
 3L8  H16  CAL  NAX  109.66  3.000
 3L8  CAN  CAL  NAX  109.87  3.000
 3L8  H19  CAN  H18  106.97  3.000
 3L8  H19  CAN  N9   109.00  3.000
 3L8  H18  CAN  N9   108.03  3.000
 3L8  H19  CAN  CAL  109.96  3.000
 3L8  H18  CAN  CAL  111.27  3.000
 3L8  N9   CAN  CAL  111.47  3.000
 3L8  C8   N9   C4   106.08  3.000
 3L8  C4   N9   CAN  126.43  3.000
 3L8  C8   N9   CAN  127.43  3.000
 3L8  C5   C4   N3   127.71  3.000
 3L8  N3   C4   N9   126.58  3.000
 3L8  C5   C4   N9   105.72  3.000
 3L8  C2   N3   C4   112.51  3.000
 3L8  H20  C2   N1   115.32  3.000
 3L8  H20  C2   N3   119.96  3.000
 3L8  N1   C2   N3   124.72  3.000
 3L8  H21  N1   C6   116.71  3.000
 3L8  H21  N1   C2   117.28  3.000
 3L8  C6   N1   C2   126.01  3.000
 3L8  C5   C6   O6   128.72  3.000
 3L8  C5   C6   N1   109.84  3.000
 3L8  O6   C6   N1   121.44  3.000
 3L8  N7   C5   C6   130.31  3.000
 3L8  N7   C5   C4   110.48  3.000
 3L8  C6   C5   C4   119.21  3.000
 3L8  C8   N7   C5   104.36  3.000
 3L8  H22  C8   N7   125.48  3.000
 3L8  H22  C8   N9   121.15  3.000
 3L8  N7   C8   N9   113.37  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
 3L8  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 3L8  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 3L8  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 3L8  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 3L8  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3L8  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3L8  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3L8  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 3L8  CONST_09  N7   C8   N9   CAN   180.00   0.0  0
 3L8  CONST_10  C5   C4   N9   CAN   180.00   0.0  0
 3L8  CONST_11  N3   C4   N9   CAN     0.00   0.0  0
 3L8  CONST_12  O6   C6   N1   C2    180.00   0.0  0
 3L8  CONST_13  H22  C8   N9   C4    180.00   0.0  0
 3L8  CONST_14  H20  C2   N3   C4    180.00   0.0  0
 3L8  CONST_15  H21  N1   C2   N3    180.00   0.0  0
 3L8  Var_01    C8   N9   CAN  CAL   -97.25  30.0  3
 3L8  Var_02    N9   CAN  CAL  NAX  -179.00  30.0  1
 3L8  Var_03    OAT  CAP  PBA  OAF   178.14  30.0  3
 3L8  Var_04    CAK  CAJ  OAT  CAP  -154.72  30.0  3
 3L8  Var_05    NAX  CAK  CAJ  OAT    67.70  30.0  1
 3L8  Var_06    CAL  NAX  CAK  CAJ  -131.60  30.0  1
 3L8  Var_07    CAN  CAL  NAX  CAK    78.74  30.0  1
 3L8  Var_08    CAO  CAM  NAX  CAK  -154.33  30.0  1
 3L8  Var_09    PAZ  CAO  CAM  NAX   174.72  30.0  1
 3L8  Var_10    OAE  PAZ  CAO  CAM   -56.66  30.0  1

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
 3L8  plan-1  CAN  0.020
 3L8  plan-1  N9   0.020
 3L8  plan-1  C4   0.020
 3L8  plan-1  N3   0.020
 3L8  plan-1  C2   0.020
 3L8  plan-1  N1   0.020
 3L8  plan-1  C6   0.020
 3L8  plan-1  O6   0.020
 3L8  plan-1  C5   0.020
 3L8  plan-1  N7   0.020
 3L8  plan-1  C8   0.020
 3L8  plan-1  H20  0.020
 3L8  plan-1  H21  0.020
 3L8  plan-1  H22  0.020

