# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 21:06:13 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: 6-amino-3-benzyl-9H-purin-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nc[n+](Cc2ccccc2)c3[nH]cnc13
#
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
 A4V  A4V  6-amino-3-benzyl-9H-purin-3-ium  ligand  29  17  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_A4V
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
 A4V  N1   N  NR15  0  -0.646  -0.5992   1.6326  -0.0284
 A4V  C1   C  CR15  0   0.131  -1.5918   2.1707   0.7449
 A4V  N2   N  N     0  -0.422  -2.5530   1.3326   0.9882
 A4V  C2   C  CR56  0   0.032  -2.1821   0.1856   0.3472
 A4V  C3   C  CR6   0   0.508  -2.8017  -1.0762   0.2353
 A4V  N3   N  NH2   0  -0.779  -3.9533  -1.3652   0.7962
 A4V  N4   N  N     0  -0.459  -2.1709  -2.0291  -0.4873
 A4V  C4   C  CR16  0   0.185  -1.0319  -1.7800  -1.0560
 A4V  N5   N  NR6   1  -0.497  -0.3674  -0.6097  -1.0048
 A4V  C5   C  CR56  0   0.677  -0.9693   0.3662  -0.2858
 A4V  C6   C  CR16  0  -0.269   2.2798  -0.9711   0.3729
 A4V  C7   C  CR16  0  -0.238   3.2878  -0.6825   1.2797
 A4V  C8   C  CR16  0  -0.256   4.0386   0.4799   1.1426
 A4V  C9   C  CR16  0  -0.238   3.7792   1.3495   0.0939
 A4V  C10  C  CR16  0  -0.316   2.7672   1.0609  -0.8139
 A4V  C11  C  CR6   0   0.080   2.0131  -0.0985  -0.6795
 A4V  C12  C  CH2   0  -0.417   0.9227  -0.4053  -1.6701
 A4V  H1   H  HCR5  0   0.313  -1.5336   3.1900   1.0920
 A4V  H2   H  HNH2  0   0.434  -4.4504  -0.6856   1.3489
 A4V  H3   H  HNH2  0   0.428  -4.3530  -2.2852   0.6994
 A4V  H4   H  HCR6  0   0.330  -0.5504  -2.5635  -1.6273
 A4V  H6   H  HCR6  0   0.266   3.4890  -1.3666   2.0936
 A4V  H7   H  HCR6  0   0.265   4.8228   0.7040   1.8537
 A4V  H8   H  HCR6  0   0.266   4.3592   2.2559  -0.0178
 A4V  H9   H  HCR6  0   0.273   2.5712   1.7431  -1.6333
 A4V  H10  H  HCH2  0   0.319   1.1350  -1.3155  -2.2293
 A4V  H11  H  HCH2  0   0.318   0.8094   0.3999  -2.3966
 A4V  H12  H  HNR5  0   0.451   0.2370   2.1151  -0.3279
 A4V  H5   H  HCR6  0   0.262   1.7030  -1.8818   0.4871

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
 A4V  C1   N1   aromatic  1.369  0.020  1.369
 A4V  C1   N2   aromatic  1.298  0.020  1.298
 A4V  N1   C5   aromatic  1.344  0.020  1.344
 A4V  N2   C2   aromatic  1.365  0.020  1.365
 A4V  C12  N5   single    1.466  0.020  1.466
 A4V  C12  C11  single    1.505  0.020  1.505
 A4V  C5   C2   aromatic  1.380  0.020  1.380
 A4V  C5   N5   aromatic  1.353  0.020  1.353
 A4V  C2   C3   aromatic  1.410  0.020  1.410
 A4V  N5   C4   aromatic  1.347  0.020  1.347
 A4V  C3   N3   single    1.313  0.020  1.313
 A4V  C3   N4   aromatic  1.352  0.020  1.352
 A4V  C11  C6   aromatic  1.393  0.020  1.393
 A4V  C11  C10  aromatic  1.390  0.020  1.390
 A4V  C4   N4   aromatic  1.297  0.020  1.297
 A4V  C6   C7   aromatic  1.386  0.020  1.386
 A4V  C10  C9   aromatic  1.390  0.020  1.390
 A4V  C7   C8   aromatic  1.391  0.020  1.391
 A4V  C9   C8   aromatic  1.387  0.020  1.387
 A4V  C1   H1   single    0.930  0.020  1.080
 A4V  N3   H2   single    0.860  0.020  1.020
 A4V  N3   H3   single    0.860  0.020  1.020
 A4V  C4   H4   single    0.930  0.020  1.080
 A4V  C6   H5   single    0.930  0.020  1.080
 A4V  C7   H6   single    0.930  0.020  1.080
 A4V  C8   H7   single    0.930  0.020  1.080
 A4V  C9   H8   single    0.930  0.020  1.080
 A4V  C10  H9   single    0.930  0.020  1.080
 A4V  C12  H10  single    0.970  0.020  1.090
 A4V  C12  H11  single    0.970  0.020  1.090
 A4V  N1   H12  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
 A4V  H12  N1   C5   128.37  3.000
 A4V  H12  N1   C1   125.43  3.000
 A4V  C5   N1   C1   106.19  3.000
 A4V  H1   C1   N2   126.14  3.000
 A4V  H1   C1   N1   120.96  3.000
 A4V  N2   C1   N1   112.90  3.000
 A4V  C2   N2   C1   104.66  3.000
 A4V  C5   C2   C3   117.83  3.000
 A4V  C3   C2   N2   132.04  3.000
 A4V  C5   C2   N2   110.13  3.000
 A4V  N4   C3   N3   118.84  3.000
 A4V  N4   C3   C2   117.90  3.000
 A4V  N3   C3   C2   123.25  3.000
 A4V  H3   N3   H2   118.23  3.000
 A4V  H3   N3   C3   120.51  3.000
 A4V  H2   N3   C3   121.25  3.000
 A4V  C4   N4   C3   120.57  3.000
 A4V  H4   C4   N5   115.44  3.000
 A4V  H4   C4   N4   118.87  3.000
 A4V  N5   C4   N4   125.69  3.000
 A4V  C12  N5   C5   122.14  3.000
 A4V  C5   N5   C4   115.30  3.000
 A4V  C12  N5   C4   122.56  3.000
 A4V  N5   C5   C2   122.70  3.000
 A4V  N5   C5   N1   131.19  3.000
 A4V  C2   C5   N1   106.11  3.000
 A4V  H5   C6   C11  120.27  3.000
 A4V  H5   C6   C7   119.53  3.000
 A4V  C11  C6   C7   120.20  3.000
 A4V  H6   C7   C8   120.15  3.000
 A4V  H6   C7   C6   119.71  3.000
 A4V  C8   C7   C6   120.14  3.000
 A4V  H7   C8   C9   120.17  3.000
 A4V  H7   C8   C7   119.98  3.000
 A4V  C9   C8   C7   119.85  3.000
 A4V  H8   C9   C10  119.79  3.000
 A4V  H8   C9   C8   120.21  3.000
 A4V  C10  C9   C8   119.99  3.000
 A4V  H9   C10  C11  120.00  3.000
 A4V  H9   C10  C9   119.65  3.000
 A4V  C11  C10  C9   120.35  3.000
 A4V  C12  C11  C10  119.98  3.000
 A4V  C10  C11  C6   119.46  3.000
 A4V  C12  C11  C6   120.56  3.000
 A4V  H11  C12  H10  107.17  3.000
 A4V  H11  C12  C11  111.31  3.000
 A4V  H10  C12  C11  111.54  3.000
 A4V  H11  C12  N5   108.30  3.000
 A4V  H10  C12  N5   106.74  3.000
 A4V  C11  C12  N5   111.56  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
 A4V  CONST_01  C2   N2   C1   N1     0.00   0.0  0
 A4V  CONST_02  N2   C2   C5   N1     0.00   0.0  0
 A4V  CONST_03  C3   C2   C5   N1   180.00   0.0  0
 A4V  CONST_04  C4   N5   C5   N1   180.00   0.0  0
 A4V  CONST_05  C2   C5   N1   C1     0.00   0.0  0
 A4V  CONST_06  N5   C5   N1   C1   180.00   0.0  0
 A4V  CONST_07  C5   C2   N2   C1     0.00   0.0  0
 A4V  CONST_08  C3   C2   N2   C1   180.00   0.0  0
 A4V  CONST_09  C5   N1   C1   N2     0.00   0.0  0
 A4V  CONST_10  N5   C5   C2   N2   180.00   0.0  0
 A4V  CONST_11  N4   C3   C2   N2   180.00   0.0  0
 A4V  CONST_12  C4   N5   C5   C2     0.00   0.0  0
 A4V  CONST_13  C4   N4   C3   C2     0.00   0.0  0
 A4V  CONST_14  N5   C5   C2   C3     0.00   0.0  0
 A4V  CONST_15  N5   C4   N4   C3     0.00   0.0  0
 A4V  CONST_16  C5   C2   C3   N4     0.00   0.0  0
 A4V  CONST_17  C5   N5   C4   N4     0.00   0.0  0
 A4V  CONST_18  C9   C10  C11  C6     0.00   0.0  0
 A4V  CONST_19  C9   C8   C7   C6     0.00   0.0  0
 A4V  CONST_20  C10  C11  C6   C7     0.00   0.0  0
 A4V  CONST_21  C10  C9   C8   C7     0.00   0.0  0
 A4V  CONST_22  C11  C6   C7   C8     0.00   0.0  0
 A4V  CONST_23  C11  C10  C9   C8     0.00   0.0  0
 A4V  CONST_24  C12  N5   C5   N1     0.00   0.0  0
 A4V  CONST_25  N3   C3   C2   N2     0.00   0.0  0
 A4V  CONST_26  C12  N5   C5   C2   180.00   0.0  0
 A4V  CONST_27  C5   C2   C3   N3   180.00   0.0  0
 A4V  CONST_28  C4   N4   C3   N3   180.00   0.0  0
 A4V  CONST_29  C12  N5   C4   N4   180.00   0.0  0
 A4V  CONST_30  C12  C11  C6   C7   180.00   0.0  0
 A4V  CONST_31  C12  C11  C10  C9   180.00   0.0  0
 A4V  CONST_32  H12  N1   C1   N2   180.00   0.0  0
 A4V  CONST_33  H1   C1   N2   C2   180.00   0.0  0
 A4V  CONST_34  H4   C4   N4   C3   180.00   0.0  0
 A4V  CONST_35  H9   C10  C11  C6   180.00   0.0  0
 A4V  CONST_36  H7   C8   C7   C6   180.00   0.0  0
 A4V  CONST_37  H8   C9   C8   C7   180.00   0.0  0
 A4V  CONST_38  H5   C6   C7   C8   180.00   0.0  0
 A4V  CONST_39  H6   C7   C8   C9   180.00   0.0  0
 A4V  CONST_40  H2   N3   C3   C2     0.00   0.0  0
 A4V  CONST_41  H3   N3   C3   C2   180.00   0.0  0
 A4V  Var_01    C11  C12  N5   C4  -117.50  30.0  1
 A4V  Var_02    C6   C11  C12  N5    55.94  30.0  2

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
 A4V  plan-1  C6   0.020
 A4V  plan-1  C7   0.020
 A4V  plan-1  C8   0.020
 A4V  plan-1  C9   0.020
 A4V  plan-1  C10  0.020
 A4V  plan-1  C11  0.020
 A4V  plan-1  C12  0.020
 A4V  plan-1  H6   0.020
 A4V  plan-1  H7   0.020
 A4V  plan-1  H8   0.020
 A4V  plan-1  H9   0.020
 A4V  plan-1  H5   0.020
 A4V  plan-2  N1   0.020
 A4V  plan-2  C1   0.020
 A4V  plan-2  N2   0.020
 A4V  plan-2  C2   0.020
 A4V  plan-2  C3   0.020
 A4V  plan-2  N3   0.020
 A4V  plan-2  N4   0.020
 A4V  plan-2  C4   0.020
 A4V  plan-2  N5   0.020
 A4V  plan-2  C5   0.020
 A4V  plan-2  C12  0.020
 A4V  plan-2  H1   0.020
 A4V  plan-2  H4   0.020
 A4V  plan-2  H12  0.020
 A4V  plan-3  C3   0.020
 A4V  plan-3  N3   0.020
 A4V  plan-3  H2   0.020
 A4V  plan-3  H3   0.020

