# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 06:05:40 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCN(CCn1cnc2C(=O)NC(=Nc12)N)CC[P](O)(O)=O
#
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
 3L6  3L6  '(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl](3-aminopropyl)amino}ethyl)phosphonic acid'  ligand  46  24  .  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_3L6
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
 3L6  NAA  N  NH2   0  -0.799   0.1437   5.3743  -0.0043
 3L6  CAG  C  CH2   0  -0.275   0.9469   4.3918   0.7099
 3L6  CAI  C  CH2   0  -0.441   0.8024   3.0139   0.0815
 3L6  CAJ  C  CH2   0  -0.280   1.6238   1.9637   0.8166
 3L6  NAV  N  NT    0  -0.426   1.4462   0.6280   0.2679
 3L6  CAL  C  CH2   0  -0.285   2.5738  -0.2490   0.5273
 3L6  CAN  C  CH2   0  -0.754   3.7262   0.0276  -0.4375
 3L6  PAX  P  P     0   1.364   5.1103  -1.0932  -0.1771
 3L6  OAD  O  O     0  -0.719   5.6641  -1.1313   1.1980
 3L6  OAF  O  OH1   0  -0.752   4.6061  -2.5705  -0.5773
 3L6  OAE  O  OH1   0  -0.745   6.1192  -0.6196  -1.3357
 3L6  CAK  C  CH2   0  -0.302   0.1832   0.0291   0.6492
 3L6  CAM  C  CH2   0  -0.314  -0.3302  -0.8928  -0.4532
 3L6  N9   N  NR5   0  -0.493  -1.6497  -1.4014  -0.1457
 3L6  C4   C  CR56  0   0.494  -2.8109  -0.7054  -0.2447
 3L6  N3   N  N     0  -0.504  -2.9391   0.5520  -0.6924
 3L6  C2   C  CR6   0   0.683  -4.1790   0.9712  -0.6934
 3L6  N2   N  NH2   0  -0.832  -4.4712   2.1977  -1.1505
 3L6  N1   N  NR16  0  -0.728  -5.2260   0.2001  -0.2741
 3L6  C6   C  CR6   0   0.500  -5.1469  -1.1141   0.2061
 3L6  O6   O  O     0  -0.476  -6.1545  -1.7072   0.5543
 3L6  C5   C  CR56  0  -0.086  -3.7960  -1.5667   0.2047
 3L6  N7   N  N     0  -0.448  -3.2522  -2.7681   0.5804
 3L6  C8   C  CR15  0   0.091  -1.9792  -2.6293   0.3624
 3L6  H1   H  HNH2  0   0.335  -0.8376   5.1832   0.1587
 3L6  H2   H  HNH2  0   0.346   0.3067   6.2923   0.3890
 3L6  H4   H  HCH2  0   0.214   1.9940   4.7024   0.6534
 3L6  H5   H  HCH2  0   0.190   0.7055   4.3246   1.7808
 3L6  H6   H  HCH2  0   0.215  -0.2568   2.7332   0.0755
 3L6  H7   H  HCH2  0   0.221   1.1198   3.0541  -0.9635
 3L6  H8   H  HCH2  0   0.233   2.6785   2.2363   0.7309
 3L6  H9   H  HCH2  0   0.203   1.3940   1.9892   1.8945
 3L6  H11  H  HCH2  0   0.226   2.9243  -0.1715   1.5672
 3L6  H12  H  HCH2  0   0.242   2.2449  -1.2813   0.3928
 3L6  H13  H  HCH2  0   0.286   3.3724  -0.0565  -1.4676
 3L6  H14  H  HCH2  0   0.287   4.1060   1.0443  -0.3101
 3L6  H15  H  HOH1  0   0.489   4.2753  -2.6659  -1.4798
 3L6  H16  H  HOH1  0   0.494   6.9861  -1.0477  -1.3061
 3L6  H17  H  HCH2  0   0.223   0.2425  -0.5208   1.6008
 3L6  H18  H  HCH2  0   0.256  -0.5563   0.8171   0.7937
 3L6  H19  H  HCH2  0   0.266  -0.3765  -0.3429  -1.3929
 3L6  H20  H  HCH2  0   0.266   0.3296  -1.7477  -0.6042
 3L6  H21  H  HNH2  0   0.408  -3.7047   2.8248  -1.3258
 3L6  H22  H  HNH2  0   0.414  -5.3686   2.6191  -0.9827
 3L6  H23  H  HNR6  0   0.424  -6.1582   0.5906  -0.3214
 3L6  H24  H  HCR5  0   0.287  -1.2231  -3.3798   0.5403

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
 3L6  O6   C6   double    1.220  0.020  1.220
 3L6  C6   N1   single    1.401  0.020  1.401
 3L6  C6   C5   single    1.425  0.020  1.425
 3L6  N1   C2   single    1.366  0.020  1.366
 3L6  N2   C2   single    1.341  0.020  1.341
 3L6  C2   N3   double    1.309  0.020  1.309
 3L6  C5   N7   aromatic  1.371  0.020  1.371
 3L6  C5   C4   aromatic  1.384  0.020  1.384
 3L6  N7   C8   aromatic  1.299  0.020  1.299
 3L6  N3   C4   single    1.341  0.020  1.341
 3L6  C4   N9   aromatic  1.357  0.020  1.357
 3L6  C8   N9   aromatic  1.369  0.020  1.369
 3L6  N9   CAM  single    1.447  0.020  1.447
 3L6  CAM  CAK  single    1.526  0.020  1.526
 3L6  CAK  NAV  single    1.449  0.020  1.449
 3L6  CAN  PAX  single    1.800  0.020  1.800
 3L6  CAN  CAL  single    1.528  0.020  1.528
 3L6  OAD  PAX  double    1.483  0.020  1.483
 3L6  NAV  CAL  single    1.452  0.020  1.452
 3L6  NAV  CAJ  single    1.455  0.020  1.455
 3L6  OAE  PAX  single    1.608  0.020  1.608
 3L6  PAX  OAF  single    1.611  0.020  1.611
 3L6  CAJ  CAI  single    1.523  0.020  1.523
 3L6  CAI  CAG  single    1.521  0.020  1.521
 3L6  CAG  NAA  single    1.456  0.020  1.456
 3L6  NAA  H1   single    0.890  0.020  1.040
 3L6  NAA  H2   single    0.890  0.020  1.040
 3L6  CAG  H4   single    0.970  0.020  1.090
 3L6  CAG  H5   single    0.970  0.020  1.090
 3L6  CAI  H6   single    0.970  0.020  1.090
 3L6  CAI  H7   single    0.970  0.020  1.090
 3L6  CAJ  H8   single    0.970  0.020  1.090
 3L6  CAJ  H9   single    0.970  0.020  1.090
 3L6  CAL  H11  single    0.970  0.020  1.090
 3L6  CAL  H12  single    0.970  0.020  1.090
 3L6  CAN  H13  single    0.970  0.020  1.090
 3L6  CAN  H14  single    0.970  0.020  1.090
 3L6  OAF  H15  single    0.850  0.020  0.980
 3L6  OAE  H16  single    0.850  0.020  0.980
 3L6  CAK  H17  single    0.970  0.020  1.090
 3L6  CAK  H18  single    0.970  0.020  1.090
 3L6  CAM  H19  single    0.970  0.020  1.090
 3L6  CAM  H20  single    0.970  0.020  1.090
 3L6  N2   H21  single    0.890  0.020  1.040
 3L6  N2   H22  single    0.890  0.020  1.040
 3L6  N1   H23  single    0.860  0.020  1.020
 3L6  C8   H24  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
 3L6  H2   NAA  H1   105.35  3.000
 3L6  H2   NAA  CAG  109.42  3.000
 3L6  H1   NAA  CAG  109.16  3.000
 3L6  H5   CAG  H4   106.13  3.000
 3L6  H5   CAG  CAI  109.03  3.000
 3L6  H4   CAG  CAI  109.08  3.000
 3L6  H5   CAG  NAA  113.43  3.000
 3L6  H4   CAG  NAA  108.13  3.000
 3L6  CAI  CAG  NAA  110.86  3.000
 3L6  H7   CAI  H6   106.55  3.000
 3L6  H7   CAI  CAJ  109.29  3.000
 3L6  H6   CAI  CAJ  110.33  3.000
 3L6  H7   CAI  CAG  109.52  3.000
 3L6  H6   CAI  CAG  109.03  3.000
 3L6  CAJ  CAI  CAG  111.97  3.000
 3L6  H9   CAJ  H8   105.79  3.000
 3L6  H9   CAJ  NAV  111.38  3.000
 3L6  H8   CAJ  NAV  108.50  3.000
 3L6  H9   CAJ  CAI  110.10  3.000
 3L6  H8   CAJ  CAI  108.10  3.000
 3L6  NAV  CAJ  CAI  112.66  3.000
 3L6  CAK  NAV  CAL  112.35  3.000
 3L6  CAL  NAV  CAJ  113.10  3.000
 3L6  CAK  NAV  CAJ  112.75  3.000
 3L6  H12  CAL  H11  106.21  3.000
 3L6  H12  CAL  CAN  108.70  3.000
 3L6  H11  CAL  CAN  110.10  3.000
 3L6  H12  CAL  NAV  108.37  3.000
 3L6  H11  CAL  NAV  111.95  3.000
 3L6  CAN  CAL  NAV  111.31  3.000
 3L6  H14  CAN  H13  107.10  3.000
 3L6  H14  CAN  PAX  107.17  3.000
 3L6  H13  CAN  PAX  109.72  3.000
 3L6  H14  CAN  CAL  110.91  3.000
 3L6  H13  CAN  CAL  109.70  3.000
 3L6  PAX  CAN  CAL  112.08  3.000
 3L6  OAE  PAX  OAF  106.71  3.000
 3L6  OAF  PAX  OAD  108.88  3.000
 3L6  OAE  PAX  OAD  116.20  3.000
 3L6  OAF  PAX  CAN  107.12  3.000
 3L6  OAE  PAX  CAN  101.24  3.000
 3L6  OAD  PAX  CAN  115.93  3.000
 3L6  H15  OAF  PAX  115.45  3.000
 3L6  H16  OAE  PAX  114.21  3.000
 3L6  H18  CAK  H17  106.44  3.000
 3L6  H18  CAK  CAM  107.71  3.000
 3L6  H17  CAK  CAM  109.93  3.000
 3L6  H18  CAK  NAV  109.11  3.000
 3L6  H17  CAK  NAV  112.77  3.000
 3L6  CAM  CAK  NAV  110.66  3.000
 3L6  H20  CAM  H19  107.57  3.000
 3L6  H20  CAM  N9   107.80  3.000
 3L6  H19  CAM  N9   108.77  3.000
 3L6  H20  CAM  CAK  111.72  3.000
 3L6  H19  CAM  CAK  109.41  3.000
 3L6  N9   CAM  CAK  111.44  3.000
 3L6  C8   N9   C4   106.32  3.000
 3L6  C8   N9   CAM  127.84  3.000
 3L6  C4   N9   CAM  125.75  3.000
 3L6  C5   C4   N3   128.63  3.000
 3L6  N3   C4   N9   125.94  3.000
 3L6  C5   C4   N9   105.44  3.000
 3L6  C2   N3   C4   113.02  3.000
 3L6  N1   C2   N2   116.99  3.000
 3L6  N2   C2   N3   119.97  3.000
 3L6  N1   C2   N3   123.02  3.000
 3L6  H22  N2   H21  116.61  3.000
 3L6  H22  N2   C2   121.39  3.000
 3L6  H21  N2   C2   117.62  3.000
 3L6  H23  N1   C6   115.47  3.000
 3L6  H23  N1   C2   118.28  3.000
 3L6  C6   N1   C2   126.24  3.000
 3L6  C5   C6   O6   128.97  3.000
 3L6  C5   C6   N1   110.56  3.000
 3L6  O6   C6   N1   120.47  3.000
 3L6  N7   C5   C6   130.85  3.000
 3L6  N7   C5   C4   110.61  3.000
 3L6  C6   C5   C4   118.53  3.000
 3L6  C8   N7   C5   104.42  3.000
 3L6  H24  C8   N7   125.74  3.000
 3L6  H24  C8   N9   121.06  3.000
 3L6  N7   C8   N9   113.20  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
 3L6  CONST_01  N7   C5   C4   N9      0.00   0.0  0
 3L6  CONST_02  C5   N7   C8   N9      0.00   0.0  0
 3L6  CONST_03  C8   N7   C5   C4      0.00   0.0  0
 3L6  CONST_04  N7   C8   N9   C4      0.00   0.0  0
 3L6  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3L6  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3L6  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3L6  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 3L6  CONST_09  C5   C4   N9   CAM   180.00   0.0  0
 3L6  CONST_10  N3   C4   N9   CAM     0.00   0.0  0
 3L6  CONST_11  N7   C8   N9   CAM   180.00   0.0  0
 3L6  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 3L6  CONST_13  O6   C6   N1   C2    180.00   0.0  0
 3L6  CONST_14  C6   N1   C2   N2    180.00   0.0  0
 3L6  CONST_15  H24  C8   N9   C4    180.00   0.0  0
 3L6  CONST_16  H23  N1   C2   N3    180.00   0.0  0
 3L6  CONST_17  H21  N2   C2   N3      0.00   0.0  0
 3L6  CONST_18  H22  N2   C2   N3    180.00   0.0  0
 3L6  Var_01    C4   N9   CAM  CAK    75.99  30.0  2
 3L6  Var_02    N9   CAM  CAK  NAV  -174.56  30.0  1
 3L6  Var_03    CAJ  CAI  CAG  NAA  -179.53  30.0  2
 3L6  Var_04    NAV  CAJ  CAI  CAG   177.21  30.0  1
 3L6  Var_05    CAK  NAV  CAJ  CAI   -75.92  30.0  2
 3L6  Var_06    CAM  CAK  NAV  CAJ   147.99  30.0  2
 3L6  Var_07    CAN  CAL  NAV  CAJ   -79.05  30.0  3
 3L6  Var_08    PAX  CAN  CAL  NAV  -177.70  30.0  1
 3L6  Var_09    OAD  PAX  CAN  CAL   -55.43  30.0  3
 3L6  Var_10    H1   NAA  CAG  CAI    69.22  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
 3L6  plan-1  CAM  0.020
 3L6  plan-1  N9   0.020
 3L6  plan-1  C4   0.020
 3L6  plan-1  N3   0.020
 3L6  plan-1  C2   0.020
 3L6  plan-1  N2   0.020
 3L6  plan-1  N1   0.020
 3L6  plan-1  C6   0.020
 3L6  plan-1  O6   0.020
 3L6  plan-1  C5   0.020
 3L6  plan-1  N7   0.020
 3L6  plan-1  C8   0.020
 3L6  plan-1  H21  0.020
 3L6  plan-1  H22  0.020
 3L6  plan-1  H23  0.020
 3L6  plan-1  H24  0.020

