# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 12:07:22 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: (2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC(=O)c2ncn(CCN(CCOCC[P](O)(O)=O)CC[P](O)(O)=O)c2N1
#
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
 3L5  3L5  '(2-{[2-(2-amino-6-oxo-3,6-dihydro-9H-purin-9-yl)ethyl][2-(2-phosphonoethoxy)ethyl]amino}ethyl)phosphonic acid'  ligand  53  29  .  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_3L5
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
 3L5  OAE  O  O     0  -0.716  -5.5589  -3.5327   0.4697
 3L5  PBB  P  P     0   1.356  -4.6782  -3.0639  -0.6269
 3L5  OAF  O  OH1   0  -0.744  -4.3189  -4.1443  -1.7600
 3L5  OAC  O  OH1   0  -0.750  -5.3852  -1.8221  -1.3683
 3L5  CAP  C  CH2   0  -0.777  -3.0321  -2.5183  -0.1391
 3L5  CAK  C  CH2   0  -0.123  -3.0859  -1.4548   0.9461
 3L5  OAU  O  O2    0  -0.473  -1.7698  -1.0677   1.2355
 3L5  CAJ  C  CH2   0  -0.129  -1.6828  -0.0977   2.2496
 3L5  CAL  C  CH2   0  -0.335  -0.2822   0.4779   2.2528
 3L5  NAZ  N  NT    0  -0.408  -0.0134   1.2609   1.0618
 3L5  CAN  C  CH2   0  -0.286  -0.3809   2.6555   1.1709
 3L5  CAQ  C  CH2   0  -0.755  -0.8261   3.2153  -0.1803
 3L5  PBC  P  P     0   1.366  -1.3126   4.9460  -0.0807
 3L5  OAG  O  OH1   0  -0.745  -1.8367   5.2085  -1.5777
 3L5  OAH  O  OH1   0  -0.752  -2.6013   5.0150   0.8840
 3L5  OAD  O  O     0  -0.718  -0.2847   5.8888   0.4227
 3L5  CAM  C  CH2   0  -0.309   1.2590   1.0021   0.4349
 3L5  CAO  C  CH2   0  -0.345   1.1231  -0.1670  -0.5392
 3L5  N9   N  NR5   0  -0.485   2.3982  -0.5415  -1.1200
 3L5  C4   C  CR56  0   0.624   3.3773  -1.2792  -0.5566
 3L5  N3   N  NR16  0  -0.735   3.3983  -1.9196   0.6404
 3L5  C2   C  CR6   0   0.666   4.5445  -2.6033   0.9369
 3L5  N2   N  NH2   0  -0.826   4.5811  -3.2058   2.1355
 3L5  N1   N  N     0  -0.538   5.5794  -2.6648   0.1445
 3L5  C6   C  CR6   0   0.414   5.6225  -2.0402  -1.0809
 3L5  O6   O  O     0  -0.494   6.6121  -2.1240  -1.7991
 3L5  C5   C  CR56  0  -0.105   4.4300  -1.3019  -1.4318
 3L5  N7   N  N     0  -0.442   4.1103  -0.5691  -2.5457
 3L5  C8   C  CR15  0   0.089   2.9083  -0.1302  -2.3267
 3L5  H1   H  HOH1  0   0.495  -5.0780  -4.6560  -2.0725
 3L5  H2   H  HOH1  0   0.490  -4.9093  -1.4643  -2.1291
 3L5  H3   H  HCH2  0   0.292  -2.4825  -3.3925   0.2187
 3L5  H4   H  HCH2  0   0.289  -2.5046  -2.1366  -1.0172
 3L5  H5   H  HCH2  0   0.207  -3.6744  -0.5909   0.6076
 3L5  H6   H  HCH2  0   0.211  -3.5877  -1.8541   1.8373
 3L5  H7   H  HCH2  0   0.198  -2.4155   0.7062   2.0879
 3L5  H8   H  HCH2  0   0.204  -1.9053  -0.5356   3.2327
 3L5  H9   H  HCH2  0   0.233  -0.1436   1.0648   3.1710
 3L5  H10  H  HCH2  0   0.237   0.4336  -0.3462   2.3166
 3L5  H12  H  HCH2  0   0.246  -1.2152   2.7313   1.8707
 3L5  H13  H  HCH2  0   0.227   0.4305   3.2703   1.5873
 3L5  H14  H  HCH2  0   0.284  -0.0193   3.1510  -0.9144
 3L5  H15  H  HCH2  0   0.287  -1.6579   2.6198  -0.5641
 3L5  H16  H  HOH1  0   0.493  -2.0044   6.1393  -1.7801
 3L5  H17  H  HOH1  0   0.489  -3.3498   4.4666   0.6149
 3L5  H18  H  HCH2  0   0.255   1.5888   1.8812  -0.1221
 3L5  H19  H  HCH2  0   0.233   2.0544   0.8003   1.1680
 3L5  H20  H  HCH2  0   0.273   0.6822  -1.0371  -0.0507
 3L5  H21  H  HCH2  0   0.283   0.4499   0.1050  -1.3507
 3L5  H22  H  HNR6  0   0.433   2.6213  -1.8946   1.2846
 3L5  H23  H  HNH2  0   0.410   5.3459  -3.8353   2.3090
 3L5  H24  H  HNH2  0   0.413   3.7382  -3.3724   2.6588
 3L5  H25  H  HCR5  0   0.292   2.3235   0.4877  -2.9916

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
 3L5  OAE  PBB  double    1.483  0.020  1.483
 3L5  OAF  PBB  single    1.606  0.020  1.606
 3L5  OAC  PBB  single    1.610  0.020  1.610
 3L5  PBB  CAP  single    1.801  0.020  1.801
 3L5  N2   C2   single    1.342  0.020  1.342
 3L5  C2   N1   double    1.305  0.020  1.305
 3L5  C2   N3   single    1.367  0.020  1.367
 3L5  N1   C6   single    1.376  0.020  1.376
 3L5  N3   C4   single    1.358  0.020  1.358
 3L5  C6   O6   double    1.226  0.020  1.226
 3L5  C6   C5   single    1.446  0.020  1.446
 3L5  C4   C5   aromatic  1.369  0.020  1.369
 3L5  C4   N9   aromatic  1.349  0.020  1.349
 3L5  C5   N7   aromatic  1.371  0.020  1.371
 3L5  CAP  CAK  single    1.520  0.020  1.520
 3L5  CAK  OAU  single    1.402  0.020  1.402
 3L5  N9   CAO  single    1.450  0.020  1.450
 3L5  N9   C8   aromatic  1.373  0.020  1.373
 3L5  N7   C8   aromatic  1.298  0.020  1.298
 3L5  CAO  CAM  single    1.528  0.020  1.528
 3L5  OAU  CAJ  single    1.406  0.020  1.406
 3L5  CAM  NAZ  single    1.442  0.020  1.442
 3L5  NAZ  CAN  single    1.446  0.020  1.446
 3L5  NAZ  CAL  single    1.450  0.020  1.450
 3L5  CAJ  CAL  single    1.514  0.020  1.514
 3L5  CAN  CAQ  single    1.529  0.020  1.529
 3L5  OAD  PBC  double    1.483  0.020  1.483
 3L5  CAQ  PBC  single    1.800  0.020  1.800
 3L5  PBC  OAG  single    1.608  0.020  1.608
 3L5  PBC  OAH  single    1.611  0.020  1.611
 3L5  OAF  H1   single    0.850  0.020  0.980
 3L5  OAC  H2   single    0.850  0.020  0.980
 3L5  CAP  H3   single    0.970  0.020  1.090
 3L5  CAP  H4   single    0.970  0.020  1.090
 3L5  CAK  H5   single    0.970  0.020  1.090
 3L5  CAK  H6   single    0.970  0.020  1.090
 3L5  CAJ  H7   single    0.970  0.020  1.090
 3L5  CAJ  H8   single    0.970  0.020  1.090
 3L5  CAL  H9   single    0.970  0.020  1.090
 3L5  CAL  H10  single    0.970  0.020  1.090
 3L5  CAN  H12  single    0.970  0.020  1.090
 3L5  CAN  H13  single    0.970  0.020  1.090
 3L5  CAQ  H14  single    0.970  0.020  1.090
 3L5  CAQ  H15  single    0.970  0.020  1.090
 3L5  OAG  H16  single    0.850  0.020  0.980
 3L5  OAH  H17  single    0.850  0.020  0.980
 3L5  CAM  H18  single    0.970  0.020  1.090
 3L5  CAM  H19  single    0.970  0.020  1.090
 3L5  CAO  H20  single    0.970  0.020  1.090
 3L5  CAO  H21  single    0.970  0.020  1.090
 3L5  N3   H22  single    0.860  0.020  1.020
 3L5  N2   H23  single    0.890  0.020  1.040
 3L5  N2   H24  single    0.890  0.020  1.040
 3L5  C8   H25  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
 3L5  CAP  PBB  OAC  107.00  3.000
 3L5  CAP  PBB  OAF  100.97  3.000
 3L5  OAC  PBB  OAF  106.99  3.000
 3L5  CAP  PBB  OAE  115.99  3.000
 3L5  OAC  PBB  OAE  108.89  3.000
 3L5  OAF  PBB  OAE  116.23  3.000
 3L5  H1   OAF  PBB  114.09  3.000
 3L5  H2   OAC  PBB  115.59  3.000
 3L5  H4   CAP  H3   107.43  3.000
 3L5  H4   CAP  CAK  110.25  3.000
 3L5  H3   CAP  CAK  110.10  3.000
 3L5  H4   CAP  PBB  109.22  3.000
 3L5  H3   CAP  PBB  107.81  3.000
 3L5  CAK  CAP  PBB  111.89  3.000
 3L5  H6   CAK  H5   106.93  3.000
 3L5  H6   CAK  OAU  111.22  3.000
 3L5  H5   CAK  OAU  110.45  3.000
 3L5  H6   CAK  CAP  109.94  3.000
 3L5  H5   CAK  CAP  110.42  3.000
 3L5  OAU  CAK  CAP  107.90  3.000
 3L5  CAJ  OAU  CAK  113.41  3.000
 3L5  H8   CAJ  H7   106.74  3.000
 3L5  H8   CAJ  CAL  109.68  3.000
 3L5  H7   CAJ  CAL  109.80  3.000
 3L5  H8   CAJ  OAU  110.97  3.000
 3L5  H7   CAJ  OAU  110.92  3.000
 3L5  CAL  CAJ  OAU  108.72  3.000
 3L5  H10  CAL  H9   105.74  3.000
 3L5  H10  CAL  NAZ  109.48  3.000
 3L5  H9   CAL  NAZ  111.99  3.000
 3L5  H10  CAL  CAJ  108.61  3.000
 3L5  H9   CAL  CAJ  108.75  3.000
 3L5  NAZ  CAL  CAJ  112.02  3.000
 3L5  CAM  NAZ  CAN  115.48  3.000
 3L5  CAN  NAZ  CAL  114.30  3.000
 3L5  CAM  NAZ  CAL  115.06  3.000
 3L5  H13  CAN  H12  106.40  3.000
 3L5  H13  CAN  CAQ  110.17  3.000
 3L5  H12  CAN  CAQ  108.58  3.000
 3L5  H13  CAN  NAZ  112.34  3.000
 3L5  H12  CAN  NAZ  108.03  3.000
 3L5  CAQ  CAN  NAZ  111.12  3.000
 3L5  H15  CAQ  H14  107.09  3.000
 3L5  H15  CAQ  PBC  109.74  3.000
 3L5  H14  CAQ  PBC  107.05  3.000
 3L5  H15  CAQ  CAN  109.43  3.000
 3L5  H14  CAQ  CAN  110.93  3.000
 3L5  PBC  CAQ  CAN  112.44  3.000
 3L5  OAD  PBC  OAH  108.90  3.000
 3L5  OAH  PBC  OAG  106.85  3.000
 3L5  OAD  PBC  OAG  115.99  3.000
 3L5  OAH  PBC  CAQ  106.88  3.000
 3L5  OAG  PBC  CAQ  101.16  3.000
 3L5  OAD  PBC  CAQ  116.27  3.000
 3L5  H16  OAG  PBC  114.11  3.000
 3L5  H17  OAH  PBC  115.38  3.000
 3L5  H19  CAM  H18  105.62  3.000
 3L5  H19  CAM  CAO  110.42  3.000
 3L5  H18  CAM  CAO  108.53  3.000
 3L5  H19  CAM  NAZ  112.40  3.000
 3L5  H18  CAM  NAZ  110.11  3.000
 3L5  CAO  CAM  NAZ  109.63  3.000
 3L5  H21  CAO  H20  106.45  3.000
 3L5  H21  CAO  N9   108.04  3.000
 3L5  H20  CAO  N9   109.19  3.000
 3L5  H21  CAO  CAM  109.82  3.000
 3L5  H20  CAO  CAM  111.15  3.000
 3L5  N9   CAO  CAM  112.00  3.000
 3L5  C8   N9   C4   105.14  3.000
 3L5  C8   N9   CAO  126.96  3.000
 3L5  C4   N9   CAO  127.73  3.000
 3L5  C5   C4   N3   122.95  3.000
 3L5  C5   C4   N9   107.46  3.000
 3L5  N3   C4   N9   129.59  3.000
 3L5  H22  N3   C2   121.28  3.000
 3L5  H22  N3   C4   122.61  3.000
 3L5  C2   N3   C4   116.10  3.000
 3L5  N1   C2   N2   119.97  3.000
 3L5  N1   C2   N3   123.84  3.000
 3L5  N2   C2   N3   116.17  3.000
 3L5  H24  N2   H23  116.35  3.000
 3L5  H24  N2   C2   121.07  3.000
 3L5  H23  N2   C2   117.12  3.000
 3L5  C6   N1   C2   122.97  3.000
 3L5  C5   C6   O6   123.96  3.000
 3L5  C5   C6   N1   114.97  3.000
 3L5  O6   C6   N1   121.07  3.000
 3L5  N7   C5   C6   131.48  3.000
 3L5  N7   C5   C4   109.34  3.000
 3L5  C6   C5   C4   119.18  3.000
 3L5  C8   N7   C5   105.04  3.000
 3L5  H25  C8   N7   126.23  3.000
 3L5  H25  C8   N9   120.76  3.000
 3L5  N7   C8   N9   113.01  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
 3L5  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 3L5  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 3L5  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 3L5  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 3L5  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3L5  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3L5  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3L5  CONST_08  N3   C4   N9   CAO     0.00   0.0  0
 3L5  CONST_09  C5   C4   N9   CAO   180.00   0.0  0
 3L5  CONST_10  N7   C8   N9   CAO   180.00   0.0  0
 3L5  CONST_11  N2   C2   N3   C4    180.00   0.0  0
 3L5  CONST_12  C6   N1   C2   N2    180.00   0.0  0
 3L5  CONST_13  H25  C8   N9   C4    180.00   0.0  0
 3L5  CONST_14  H22  N3   C2   N1    180.00   0.0  0
 3L5  CONST_15  H23  N2   C2   N3    180.00   0.0  0
 3L5  Var_01    C4   N9   CAO  CAM    78.86  30.0  3
 3L5  Var_02    N9   CAO  CAM  NAZ  -175.38  30.0  1
 3L5  Var_03    CAK  CAP  PBB  OAE   -53.92  30.0  3
 3L5  Var_04    OAU  CAK  CAP  PBB  -178.48  30.0  3
 3L5  Var_05    CAL  CAJ  OAU  CAK  -166.78  30.0  3
 3L5  Var_06    NAZ  CAL  CAJ  OAU    68.02  30.0  3
 3L5  Var_07    CAM  NAZ  CAL  CAJ  -134.47  30.0  2
 3L5  Var_08    CAO  CAM  NAZ  CAL    86.74  30.0  2
 3L5  Var_09    CAQ  CAN  NAZ  CAL  -148.02  30.0  3
 3L5  Var_10    PBC  CAQ  CAN  NAZ   179.26  30.0  3
 3L5  Var_11    OAD  PBC  CAQ  CAN    58.09  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
 3L5  plan-1  CAO  0.020
 3L5  plan-1  N9   0.020
 3L5  plan-1  C4   0.020
 3L5  plan-1  N3   0.020
 3L5  plan-1  C2   0.020
 3L5  plan-1  N2   0.020
 3L5  plan-1  N1   0.020
 3L5  plan-1  C6   0.020
 3L5  plan-1  O6   0.020
 3L5  plan-1  C5   0.020
 3L5  plan-1  N7   0.020
 3L5  plan-1  C8   0.020
 3L5  plan-1  H22  0.020
 3L5  plan-1  H23  0.020
 3L5  plan-1  H24  0.020
 3L5  plan-1  H25  0.020

