# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 14:09:43 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: [(E)-2-(2-{[2-(2-amino-8-bromo-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)ethenyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CCN(CCO/C=C/[P](O)(O)=O)\C=C\[P](O)(O)=O)c(Br)nc2C(=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
 3L3  3L3  '[(E)-2-(2-{[2-(2-amino-8-bromo-6-oxo-1,6-dihydro-9H-purin-9-yl)ethyl][(E)-2-phosphonoethenyl]amino}ethoxy)ethenyl]phosphonic acid'  ligand  45  30  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3L3
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
 3L3  OAE  O   O      0  -0.902  -5.6314  -4.3988   0.7428
 3L3  PBC  P   P      0   1.140  -6.3026  -3.0274   0.8831
 3L3  OAF  O   OP    -1  -0.909  -7.5256  -2.8357  -0.0224
 3L3  OAC  O   OP    -1  -0.910  -6.5577  -2.6049   2.3356
 3L3  CAP  C   C1     0  -0.692  -5.0677  -1.8144   0.2581
 3L3  CAK  C   C1     0   0.077  -3.8687  -2.1592  -0.2010
 3L3  OAU  O   O2     0  -0.458  -2.9570  -1.2637  -0.6690
 3L3  CAJ  C   CH2    0  -0.142  -1.7327  -1.8163  -1.1004
 3L3  CAL  C   CH2    0  -0.344  -0.8522  -0.7195  -1.6623
 3L3  NBA  N   NT     0  -0.424  -0.4449   0.2655  -0.6885
 3L3  CAN  C   C1     0   0.004  -0.9836   1.5409  -0.6715
 3L3  CAQ  C   C1     0  -0.685  -2.0685   2.0180  -1.2939
 3L3  PBD  P   P      0   1.133  -2.6046   3.7680  -1.1688
 3L3  OAG  O   OP    -1  -0.916  -4.0116   3.7230  -0.5543
 3L3  OAH  O   O      0  -0.906  -1.5633   4.4578  -0.2749
 3L3  OAD  O   OP    -1  -0.918  -2.6109   4.2829  -2.6170
 3L3  CAM  C   CH2    0  -0.334   0.8251   0.0589  -0.0481
 3L3  CAO  C   CH2    0  -0.332   1.9998   0.5041  -0.9272
 3L3  N9   N   NR5    0  -0.508   3.2751   0.2104  -0.3066
 3L3  C4   C   CR56   0   0.518   3.9858  -0.9394  -0.4765
 3L3  N3   N   N      0  -0.511   3.6550  -1.9482  -1.2899
 3L3  C2   C   CR6    0   0.692   4.5202  -2.9330  -1.2641
 3L3  N2   N   NH2    0  -0.831   4.3430  -3.9990  -2.0544
 3L3  N1   N   NR16   0  -0.728   5.6379  -2.9205  -0.4792
 3L3  C6   C   CR6    0   0.505   6.0274  -1.8948   0.3915
 3L3  O6   O   O      0  -0.469   7.0486  -1.9913   1.0495
 3L3  C5   C   CR56   0  -0.085   5.0834  -0.8279   0.3547
 3L3  N7   N   N      0  -0.417   5.0550   0.3603   1.0383
 3L3  C8   C   CR5    0   0.269   3.9753   0.9336   0.6252
 3L3  BR8  BR  BR     0   0.028   3.3927   2.5972   1.2047
 3L3  H3   H   H      0   0.200  -5.3235  -0.7549   0.2615
 3L3  H4   H   H      0   0.209  -3.5630  -3.2038  -0.2269
 3L3  H5   H   HCH2   0   0.205  -1.2174  -2.3170  -0.2697
 3L3  H6   H   HCH2   0   0.209  -1.8962  -2.5707  -1.8807
 3L3  H7   H   HCH2   0   0.243   0.0321  -1.2066  -2.0866
 3L3  H8   H   HCH2   0   0.244  -1.3560  -0.2273  -2.4974
 3L3  H9   H   H      0   0.225  -0.4215   2.2248  -0.0400
 3L3  H10  H   H      0   0.192  -2.6741   1.3460  -1.8982
 3L3  H13  H   HCH2   0   0.252   0.8485   0.6024   0.8992
 3L3  H14  H   HCH2   0   0.258   0.9426  -0.9992   0.2010
 3L3  H15  H   HCH2   0   0.279   1.9814  -0.0177  -1.8833
 3L3  H16  H   HCH2   0   0.279   1.9419   1.5710  -1.1424
 3L3  H17  H   HNH2   0   0.414   3.4611  -4.0876  -2.5301
 3L3  H18  H   HNH2   0   0.416   4.8648  -4.8467  -1.9110
 3L3  H19  H   HNR6   0   0.427   6.2585  -3.7194  -0.5172

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
 3L3  BR8  C8   single    1.856  0.020  1.856
 3L3  OAH  PBD  deloc     1.536  0.020  1.536
 3L3  OAE  PBC  deloc     1.533  0.020  1.533
 3L3  C8   N7   aromatic  1.290  0.020  1.290
 3L3  C8   N9   aromatic  1.372  0.020  1.372
 3L3  N7   C5   aromatic  1.371  0.020  1.371
 3L3  OAG  PBD  deloc     1.536  0.020  1.536
 3L3  CAO  N9   single    1.448  0.020  1.448
 3L3  CAO  CAM  single    1.533  0.020  1.533
 3L3  N9   C4   aromatic  1.362  0.020  1.362
 3L3  CAN  NBA  single    1.385  0.020  1.385
 3L3  CAN  CAQ  double    1.339  0.020  1.339
 3L3  C5   C4   aromatic  1.381  0.020  1.381
 3L3  C5   C6   single    1.425  0.020  1.425
 3L3  PBD  CAQ  single    1.835  0.020  1.835
 3L3  PBD  OAD  deloc     1.537  0.020  1.537
 3L3  C4   N3   single    1.337  0.020  1.337
 3L3  OAF  PBC  deloc     1.534  0.020  1.534
 3L3  PBC  CAP  single    1.840  0.020  1.840
 3L3  PBC  OAC  deloc     1.534  0.020  1.534
 3L3  O6   C6   double    1.219  0.020  1.219
 3L3  C6   N1   single    1.401  0.020  1.401
 3L3  NBA  CAM  single    1.437  0.020  1.437
 3L3  NBA  CAL  single    1.444  0.020  1.444
 3L3  N3   C2   double    1.311  0.020  1.311
 3L3  CAP  CAK  double    1.329  0.020  1.329
 3L3  N1   C2   single    1.366  0.020  1.366
 3L3  C2   N2   single    1.339  0.020  1.339
 3L3  CAL  CAJ  single    1.515  0.020  1.515
 3L3  CAK  OAU  single    1.361  0.020  1.361
 3L3  CAJ  OAU  single    1.411  0.020  1.411
 3L3  CAP  H3   single    0.930  0.020  1.080
 3L3  CAK  H4   single    0.930  0.020  1.080
 3L3  CAJ  H5   single    0.970  0.020  1.090
 3L3  CAJ  H6   single    0.970  0.020  1.090
 3L3  CAL  H7   single    0.970  0.020  1.090
 3L3  CAL  H8   single    0.970  0.020  1.090
 3L3  CAN  H9   single    0.930  0.020  1.080
 3L3  CAQ  H10  single    0.930  0.020  1.080
 3L3  CAM  H13  single    0.970  0.020  1.090
 3L3  CAM  H14  single    0.970  0.020  1.090
 3L3  CAO  H15  single    0.970  0.020  1.090
 3L3  CAO  H16  single    0.970  0.020  1.090
 3L3  N2   H17  single    0.890  0.020  1.040
 3L3  N2   H18  single    0.890  0.020  1.040
 3L3  N1   H19  single    0.860  0.020  1.020

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
 3L3  CAP  PBC  OAC  104.58  3.000
 3L3  OAC  PBC  OAF  113.08  3.000
 3L3  CAP  PBC  OAF  104.61  3.000
 3L3  OAC  PBC  OAE  113.94  3.000
 3L3  CAP  PBC  OAE  105.35  3.000
 3L3  OAF  PBC  OAE  114.00  3.000
 3L3  H3   CAP  CAK  117.71  3.000
 3L3  H3   CAP  PBC  118.83  3.000
 3L3  CAK  CAP  PBC  123.47  3.000
 3L3  H4   CAK  OAU  115.79  3.000
 3L3  H4   CAK  CAP  120.68  3.000
 3L3  OAU  CAK  CAP  123.52  3.000
 3L3  CAJ  OAU  CAK  115.39  3.000
 3L3  H6   CAJ  H5   107.11  3.000
 3L3  H6   CAJ  CAL  108.70  3.000
 3L3  H5   CAJ  CAL  109.76  3.000
 3L3  H6   CAJ  OAU  110.94  3.000
 3L3  H5   CAJ  OAU  110.76  3.000
 3L3  CAL  CAJ  OAU  109.53  3.000
 3L3  H8   CAL  H7   106.06  3.000
 3L3  H8   CAL  NBA  109.77  3.000
 3L3  H7   CAL  NBA  109.69  3.000
 3L3  H8   CAL  CAJ  109.99  3.000
 3L3  H7   CAL  CAJ  106.92  3.000
 3L3  NBA  CAL  CAJ  114.07  3.000
 3L3  CAM  NBA  CAN  118.08  3.000
 3L3  CAM  NBA  CAL  116.86  3.000
 3L3  CAN  NBA  CAL  121.80  3.000
 3L3  H9   CAN  CAQ  117.69  3.000
 3L3  H9   CAN  NBA  112.67  3.000
 3L3  CAQ  CAN  NBA  129.64  3.000
 3L3  H10  CAQ  PBD  117.68  3.000
 3L3  H10  CAQ  CAN  119.29  3.000
 3L3  PBD  CAQ  CAN  123.03  3.000
 3L3  OAD  PBD  OAH  113.62  3.000
 3L3  OAD  PBD  OAG  112.52  3.000
 3L3  OAH  PBD  OAG  113.66  3.000
 3L3  OAD  PBD  CAQ  104.86  3.000
 3L3  OAG  PBD  CAQ  105.49  3.000
 3L3  OAH  PBD  CAQ  105.66  3.000
 3L3  H14  CAM  H13  106.36  3.000
 3L3  H14  CAM  CAO  109.22  3.000
 3L3  H13  CAM  CAO  109.65  3.000
 3L3  H14  CAM  NBA  109.61  3.000
 3L3  H13  CAM  NBA  109.51  3.000
 3L3  CAO  CAM  NBA  112.32  3.000
 3L3  H16  CAO  H15  107.14  3.000
 3L3  H16  CAO  N9   109.26  3.000
 3L3  H15  CAO  N9   107.08  3.000
 3L3  H16  CAO  CAM  110.90  3.000
 3L3  H15  CAO  CAM  110.56  3.000
 3L3  N9   CAO  CAM  111.72  3.000
 3L3  C8   N9   C4   105.27  3.000
 3L3  C4   N9   CAO  125.25  3.000
 3L3  C8   N9   CAO  129.31  3.000
 3L3  C5   C4   N3   128.56  3.000
 3L3  N3   C4   N9   125.69  3.000
 3L3  C5   C4   N9   105.75  3.000
 3L3  C2   N3   C4   113.04  3.000
 3L3  N1   C2   N2   117.06  3.000
 3L3  N2   C2   N3   119.94  3.000
 3L3  N1   C2   N3   122.99  3.000
 3L3  H18  N2   H17  116.62  3.000
 3L3  H18  N2   C2   121.22  3.000
 3L3  H17  N2   C2   117.73  3.000
 3L3  H19  N1   C6   115.52  3.000
 3L3  H19  N1   C2   118.22  3.000
 3L3  C6   N1   C2   126.27  3.000
 3L3  C5   C6   O6   128.93  3.000
 3L3  O6   C6   N1   120.71  3.000
 3L3  C5   C6   N1   110.36  3.000
 3L3  N7   C5   C6   130.51  3.000
 3L3  C6   C5   C4   118.78  3.000
 3L3  N7   C5   C4   110.70  3.000
 3L3  C8   N7   C5   104.05  3.000
 3L3  BR8  C8   N7   124.13  3.000
 3L3  N7   C8   N9   114.22  3.000
 3L3  BR8  C8   N9   121.64  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
 3L3  CONST_01  C5   N7   C8   N9      0.00   0.0  0
 3L3  CONST_02  N7   C5   C4   N9      0.00   0.0  0
 3L3  CONST_03  N7   C8   N9   C4      0.00   0.0  0
 3L3  CONST_04  C8   N7   C5   C4      0.00   0.0  0
 3L3  CONST_05  C8   N9   C4   C5      0.00   0.0  0
 3L3  CONST_06  N1   C2   N3   C4      0.00   0.0  0
 3L3  CONST_07  C6   N1   C2   N3      0.00   0.0  0
 3L3  CONST_08  C5   C6   N1   C2      0.00   0.0  0
 3L3  CONST_09  N7   C8   N9   CAO   180.00   0.0  0
 3L3  CONST_10  C5   C4   N9   CAO   180.00   0.0  0
 3L3  CONST_11  N3   C4   N9   CAO     0.00   0.0  0
 3L3  CONST_12  BR8  C8   N9   C4    180.00   0.0  0
 3L3  CONST_13  BR8  C8   N7   C5    180.00   0.0  0
 3L3  CONST_14  N2   C2   N3   C4    180.00   0.0  0
 3L3  CONST_15  O6   C6   N1   C2    180.00   0.0  0
 3L3  CONST_16  C6   N1   C2   N2    180.00   0.0  0
 3L3  CONST_17  H19  N1   C2   N3    180.00   0.0  0
 3L3  CONST_18  H17  N2   C2   N3      0.00   0.0  0
 3L3  CONST_19  H18  N2   C2   N3    180.00   0.0  0
 3L3  CONST_20  PBD  CAQ  CAN  NBA   180.00   0.0  0
 3L3  CONST_21  H10  CAQ  CAN  NBA     0.00   0.0  0
 3L3  CONST_22  H9   CAN  CAQ  PBD     0.00   0.0  0
 3L3  Var_01    C8   N9   CAO  CAM   -83.63  30.0  2
 3L3  Var_02    N9   CAO  CAM  NBA  -176.25  30.0  3
 3L3  Var_03    OAU  CAK  CAP  PBC   179.70   0.0  2
 3L3  Var_04    CAK  CAP  PBC  OAE     0.09  30.0  3
 3L3  Var_05    CAL  CAJ  OAU  CAK   176.89  30.0  2
 3L3  Var_06    NBA  CAL  CAJ  OAU    64.90  30.0  1
 3L3  Var_07    CAN  NBA  CAL  CAJ  -106.58  30.0  3
 3L3  Var_08    CAQ  CAN  NBA  CAL    13.94  30.0  3
 3L3  Var_09    CAO  CAM  NBA  CAL    79.95  30.0  3
 3L3  Var_10    OAH  PBD  CAQ  CAN     0.97  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
 3L3  plan-1  CAO  0.020
 3L3  plan-1  N9   0.020
 3L3  plan-1  C4   0.020
 3L3  plan-1  N3   0.020
 3L3  plan-1  C2   0.020
 3L3  plan-1  N2   0.020
 3L3  plan-1  N1   0.020
 3L3  plan-1  C6   0.020
 3L3  plan-1  O6   0.020
 3L3  plan-1  C5   0.020
 3L3  plan-1  N7   0.020
 3L3  plan-1  C8   0.020
 3L3  plan-1  BR8  0.020
 3L3  plan-1  H17  0.020
 3L3  plan-1  H18  0.020
 3L3  plan-1  H19  0.020
 3L3  plan-2  NBA  0.020
 3L3  plan-2  CAN  0.020
 3L3  plan-2  CAQ  0.020
 3L3  plan-2  PBD  0.020
 3L3  plan-2  H9   0.020
 3L3  plan-2  H10  0.020
 3L3  plan-3  PBC  0.020
 3L3  plan-3  CAP  0.020
 3L3  plan-3  CAK  0.020
 3L3  plan-3  OAU  0.020
 3L3  plan-3  H3   0.020
 3L3  plan-3  H4   0.020

