# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:22:41 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: [(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CCN(CCOC[P](O)(O)=O)/C=C/[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
 3L4  3L4  '[(2-{[2-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)methyl]phosphonic acid'  ligand  44  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 PERFECT
;

data_comp_3L4
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
 3L4  OAG  O  OP    -1  -0.905   1.2832  -4.6341   0.1896
 3L4  PBB  P  P      0   1.133   2.7077  -4.2430  -0.2270
 3L4  OAH  O  OP    -1  -0.914   3.7555  -5.3208   0.0949
 3L4  OAD  O  O      0  -0.910   2.8063  -3.6819  -1.6497
 3L4  CAP  C  CH2    0  -0.450   3.2333  -2.8538   0.9060
 3L4  OAT  O  O2     0  -0.487   2.5612  -1.6085   0.7779
 3L4  CAJ  C  CH2    0  -0.102   1.2272  -1.6197   1.1964
 3L4  CAK  C  CH2    0  -0.335   0.7573  -0.2008   1.4528
 3L4  NAY  N  NT     0  -0.420   0.7170   0.6355   0.2738
 3L4  CAM  C  C1     0   0.006   1.6827   1.5912   0.0255
 3L4  CAO  C  C1     0  -0.694   2.8591   1.7969   0.6330
 3L4  PBA  P  P      0   1.132   4.0194   3.1342   0.1603
 3L4  OAE  O  OP    -1  -0.909   3.3441   3.8886  -0.9951
 3L4  OAF  O  OP    -1  -0.919   4.1921   3.9808   1.4317
 3L4  OAC  O  O      0  -0.919   5.3177   2.4194  -0.2478
 3L4  CAL  C  CH2    0  -0.338  -0.5586   0.7696  -0.3758
 3L4  CAN  C  CH2    0  -0.317  -1.4636   1.7921   0.3217
 3L4  N9   N  NR5    0  -0.492  -2.8156   1.7591  -0.1910
 3L4  C4   C  CR56   0   0.495  -3.7742   0.8612   0.1501
 3L4  N3   N  N      0  -0.506  -3.6465  -0.1220   1.0529
 3L4  C2   C  CR6    0   0.683  -4.7368  -0.8327   1.1939
 3L4  N2   N  NH2    0  -0.834  -4.7757  -1.8299   2.0889
 3L4  N1   N  NR16   0  -0.728  -5.8806  -0.5908   0.4858
 3L4  C6   C  CR6    0   0.500  -6.0649   0.4183  -0.4689
 3L4  O6   O  O      0  -0.478  -7.1364   0.5433  -1.0394
 3L4  C5   C  CR56   0  -0.088  -4.8762   1.1882  -0.6200
 3L4  N7   N  N      0  -0.448  -4.6001   2.2624  -1.4263
 3L4  C8   C  CR15   0   0.092  -3.3690   2.5688  -1.1466
 3L4  H3   H  HCH2   0   0.156   3.1766  -3.1956   1.9541
 3L4  H4   H  HCH2   0   0.186   4.2892  -2.6286   0.7176
 3L4  H5   H  HCH2   0   0.184   0.5720  -2.1034   0.4615
 3L4  H6   H  HCH2   0   0.169   1.1110  -2.1886   2.1324
 3L4  H7   H  HCH2   0   0.230  -0.2482  -0.2661   1.8835
 3L4  H8   H  HCH2   0   0.229   1.3811   0.2686   2.2177
 3L4  H9   H  H      0   0.222   1.4196   2.2473  -0.8012
 3L4  H10  H  H      0   0.191   3.1618   1.1300   1.4381
 3L4  H13  H  HCH2   0   0.254  -0.4152   1.0646  -1.4180
 3L4  H14  H  HCH2   0   0.253  -1.0573  -0.2031  -0.3956
 3L4  H15  H  HCH2   0   0.267  -1.5037   1.5956   1.3936
 3L4  H16  H  HCH2   0   0.272  -1.0756   2.8016   0.1878
 3L4  H17  H  HNH2   0   0.412  -3.9109  -2.1038   2.5231
 3L4  H18  H  HNH2   0   0.414  -5.5145  -2.5113   2.0815
 3L4  H19  H  HNR6   0   0.424  -6.6863  -1.1778   0.6627
 3L4  H20  H  HCR5   0   0.287  -2.8028   3.3755  -1.5880

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
 3L4  OAC  PBA  deloc     1.537  0.020  1.537
 3L4  OAF  PBA  deloc     1.537  0.020  1.537
 3L4  OAE  PBA  deloc     1.536  0.020  1.536
 3L4  PBA  CAO  single    1.833  0.020  1.833
 3L4  CAO  CAM  double    1.340  0.020  1.340
 3L4  CAM  NAY  single    1.381  0.020  1.381
 3L4  NAY  CAK  single    1.446  0.020  1.446
 3L4  NAY  CAL  single    1.438  0.020  1.438
 3L4  C8   N7   aromatic  1.299  0.020  1.299
 3L4  C8   N9   aromatic  1.369  0.020  1.369
 3L4  CAK  CAJ  single    1.517  0.020  1.517
 3L4  CAN  CAL  single    1.533  0.020  1.533
 3L4  CAN  N9   single    1.446  0.020  1.446
 3L4  N7   C5   aromatic  1.371  0.020  1.371
 3L4  CAJ  OAT  single    1.398  0.020  1.398
 3L4  N9   C4   aromatic  1.357  0.020  1.357
 3L4  C5   C4   aromatic  1.384  0.020  1.384
 3L4  C5   C6   single    1.424  0.020  1.424
 3L4  C4   N3   single    1.341  0.020  1.341
 3L4  OAT  CAP  single    1.421  0.020  1.421
 3L4  CAP  PBB  single    1.868  0.020  1.868
 3L4  O6   C6   double    1.220  0.020  1.220
 3L4  C6   N1   single    1.401  0.020  1.401
 3L4  N3   C2   double    1.309  0.020  1.309
 3L4  N1   C2   single    1.367  0.020  1.367
 3L4  C2   N2   single    1.340  0.020  1.340
 3L4  PBB  OAD  deloc     1.533  0.020  1.533
 3L4  PBB  OAG  deloc     1.535  0.020  1.535
 3L4  PBB  OAH  deloc     1.537  0.020  1.537
 3L4  CAP  H3   single    0.970  0.020  1.090
 3L4  CAP  H4   single    0.970  0.020  1.090
 3L4  CAJ  H5   single    0.970  0.020  1.090
 3L4  CAJ  H6   single    0.970  0.020  1.090
 3L4  CAK  H7   single    0.970  0.020  1.090
 3L4  CAK  H8   single    0.970  0.020  1.090
 3L4  CAM  H9   single    0.930  0.020  1.080
 3L4  CAO  H10  single    0.930  0.020  1.080
 3L4  CAL  H13  single    0.970  0.020  1.090
 3L4  CAL  H14  single    0.970  0.020  1.090
 3L4  CAN  H15  single    0.970  0.020  1.090
 3L4  CAN  H16  single    0.970  0.020  1.090
 3L4  N2   H17  single    0.890  0.020  1.040
 3L4  N2   H18  single    0.890  0.020  1.040
 3L4  N1   H19  single    0.860  0.020  1.020
 3L4  C8   H20  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
 3L4  CAP  PBB  OAD  105.82  3.000
 3L4  OAD  PBB  OAH  114.03  3.000
 3L4  CAP  PBB  OAH  101.69  3.000
 3L4  OAH  PBB  OAG  113.40  3.000
 3L4  OAD  PBB  OAG  113.89  3.000
 3L4  CAP  PBB  OAG  106.62  3.000
 3L4  H4   CAP  H3   106.04  3.000
 3L4  H4   CAP  OAT  105.08  3.000
 3L4  H3   CAP  OAT  109.43  3.000
 3L4  H4   CAP  PBB  108.64  3.000
 3L4  H3   CAP  PBB  109.33  3.000
 3L4  OAT  CAP  PBB  117.65  3.000
 3L4  CAJ  OAT  CAP  114.66  3.000
 3L4  H6   CAJ  H5   106.17  3.000
 3L4  H6   CAJ  CAK  107.87  3.000
 3L4  H5   CAJ  CAK  109.92  3.000
 3L4  H6   CAJ  OAT  111.05  3.000
 3L4  H5   CAJ  OAT  111.89  3.000
 3L4  CAK  CAJ  OAT  109.80  3.000
 3L4  H8   CAK  H7   105.91  3.000
 3L4  H8   CAK  NAY  109.77  3.000
 3L4  H7   CAK  NAY  109.23  3.000
 3L4  H8   CAK  CAJ  110.08  3.000
 3L4  H7   CAK  CAJ  107.16  3.000
 3L4  NAY  CAK  CAJ  114.32  3.000
 3L4  CAL  NAY  CAM  118.33  3.000
 3L4  CAL  NAY  CAK  116.55  3.000
 3L4  CAM  NAY  CAK  121.82  3.000
 3L4  H9   CAM  CAO  117.67  3.000
 3L4  H9   CAM  NAY  112.64  3.000
 3L4  CAO  CAM  NAY  129.68  3.000
 3L4  H10  CAO  PBA  117.51  3.000
 3L4  H10  CAO  CAM  119.05  3.000
 3L4  PBA  CAO  CAM  123.43  3.000
 3L4  OAC  PBA  OAF  112.38  3.000
 3L4  OAF  PBA  OAE  113.64  3.000
 3L4  OAC  PBA  OAE  113.57  3.000
 3L4  OAE  PBA  CAO  105.90  3.000
 3L4  OAF  PBA  CAO  105.05  3.000
 3L4  OAC  PBA  CAO  105.30  3.000
 3L4  H14  CAL  H13  106.43  3.000
 3L4  H14  CAL  CAN  109.41  3.000
 3L4  H13  CAL  CAN  109.35  3.000
 3L4  H14  CAL  NAY  109.27  3.000
 3L4  H13  CAL  NAY  109.86  3.000
 3L4  CAN  CAL  NAY  112.36  3.000
 3L4  H16  CAN  H15  107.51  3.000
 3L4  H16  CAN  N9   108.08  3.000
 3L4  H15  CAN  N9   108.06  3.000
 3L4  H16  CAN  CAL  110.59  3.000
 3L4  H15  CAN  CAL  110.40  3.000
 3L4  N9   CAN  CAL  112.04  3.000
 3L4  C8   N9   C4   106.33  3.000
 3L4  C4   N9   CAN  125.89  3.000
 3L4  C8   N9   CAN  127.72  3.000
 3L4  C5   C4   N3   128.60  3.000
 3L4  N3   C4   N9   125.96  3.000
 3L4  C5   C4   N9   105.44  3.000
 3L4  C2   N3   C4   113.03  3.000
 3L4  N1   C2   N2   116.96  3.000
 3L4  N2   C2   N3   119.99  3.000
 3L4  N1   C2   N3   123.03  3.000
 3L4  H18  N2   H17  116.78  3.000
 3L4  H18  N2   C2   121.38  3.000
 3L4  H17  N2   C2   117.77  3.000
 3L4  H19  N1   C6   115.59  3.000
 3L4  H19  N1   C2   118.22  3.000
 3L4  C6   N1   C2   126.19  3.000
 3L4  C5   C6   O6   128.89  3.000
 3L4  O6   C6   N1   120.51  3.000
 3L4  C5   C6   N1   110.60  3.000
 3L4  N7   C5   C6   130.84  3.000
 3L4  C6   C5   C4   118.55  3.000
 3L4  N7   C5   C4   110.61  3.000
 3L4  C8   N7   C5   104.42  3.000
 3L4  H20  C8   N7   125.81  3.000
 3L4  H20  C8   N9   121.00  3.000
 3L4  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
 3L4  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 3L4  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 3L4  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 3L4  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 3L4  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3L4  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3L4  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3L4  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 3L4  CONST_09  N7   C8   N9   CAN   180.00   0.0  0
 3L4  CONST_10  C5   C4   N9   CAN   180.00   0.0  0
 3L4  CONST_11  N3   C4   N9   CAN     0.00   0.0  0
 3L4  CONST_12  N2   C2   N3   C4    180.00   0.0  0
 3L4  CONST_13  O6   C6   N1   C2    180.00   0.0  0
 3L4  CONST_14  C6   N1   C2   N2    180.00   0.0  0
 3L4  CONST_15  H20  C8   N9   C4    180.00   0.0  0
 3L4  CONST_16  H19  N1   C2   N3    180.00   0.0  0
 3L4  CONST_17  H17  N2   C2   N3      0.00   0.0  0
 3L4  CONST_18  H18  N2   C2   N3    180.00   0.0  0
 3L4  CONST_19  PBA  CAO  CAM  NAY   180.00   0.0  0
 3L4  CONST_20  H10  CAO  CAM  NAY     0.00   0.0  0
 3L4  CONST_21  H9   CAM  CAO  PBA     0.00   0.0  0
 3L4  Var_01    C8   N9   CAN  CAL   -96.73  30.0  2
 3L4  Var_02    N9   CAN  CAL  NAY  -170.17  30.0  2
 3L4  Var_03    OAT  CAP  PBB  OAG   -67.56  30.0  3
 3L4  Var_04    CAK  CAJ  OAT  CAP   161.32  30.0  1
 3L4  Var_05    NAY  CAK  CAJ  OAT    65.05  30.0  1
 3L4  Var_06    CAM  NAY  CAK  CAJ  -103.69  30.0  2
 3L4  Var_07    CAO  CAM  NAY  CAK    10.91  30.0  2
 3L4  Var_08    CAN  CAL  NAY  CAK    80.34  30.0  3
 3L4  Var_09    OAC  PBA  CAO  CAM  -120.16  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
 3L4  plan-1  CAN  0.020
 3L4  plan-1  N9   0.020
 3L4  plan-1  C4   0.020
 3L4  plan-1  N3   0.020
 3L4  plan-1  C2   0.020
 3L4  plan-1  N2   0.020
 3L4  plan-1  N1   0.020
 3L4  plan-1  C6   0.020
 3L4  plan-1  O6   0.020
 3L4  plan-1  C5   0.020
 3L4  plan-1  N7   0.020
 3L4  plan-1  C8   0.020
 3L4  plan-1  H17  0.020
 3L4  plan-1  H18  0.020
 3L4  plan-1  H19  0.020
 3L4  plan-1  H20  0.020
 3L4  plan-2  NAY  0.020
 3L4  plan-2  CAM  0.020
 3L4  plan-2  CAO  0.020
 3L4  plan-2  PBA  0.020
 3L4  plan-2  H9   0.020
 3L4  plan-2  H10  0.020

