# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 03:28:24 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 6-amino-3,9-dimethyl-9H-purin-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc2c(N)nc[n+](C)c12
#
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
 39A  39A  6-amino-3,9-dimethyl-9H-purin-3-ium  ligand  22  12  .  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_39A
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
 39A  N6    N  NH2   0  -0.782  -2.9829   0.8464   0.0599
 39A  C6    C  CR6   0   0.509  -1.8651   0.1549   0.0495
 39A  C5    C  CR56  0   0.026  -0.5899   0.7534   0.0057
 39A  N7    N  N     0  -0.428  -0.2146   2.0624  -0.0349
 39A  C4    C  CR56  0   0.675   0.5239  -0.0664  -0.0024
 39A  N9    N  NR5   0  -0.491   1.5960   0.7533  -0.0510
 39A  C8    C  CR15  0   0.125   1.0815   2.0232  -0.0671
 39A  C9M   C  CH3   0  -0.545   3.0166   0.4452  -0.0717
 39A  N3    N  NR6   1  -0.496   0.4175  -1.4194   0.0349
 39A  C3M   C  CH3   0  -0.547   1.5602  -2.3294   0.0350
 39A  C2    C  CR16  0   0.183  -0.8397  -1.8974   0.0742
 39A  N1    N  N     0  -0.455  -1.9293  -1.1922   0.0819
 39A  HN61  H  HNH2  0   0.433  -2.9742   1.8530   0.0361
 39A  HN62  H  HNH2  0   0.427  -3.8747   0.3782   0.0897
 39A  H8    H  HCR5  0   0.315   1.7384   2.8793  -0.1049
 39A  H9M1  H  HCH3  0   0.282   3.3240  -0.0255   0.8577
 39A  H9M2  H  HCH3  0   0.280   3.2628  -0.1922  -0.9155
 39A  H9M3  H  HCH3  0   0.294   3.5575   1.3800  -0.1803
 39A  H3M1  H  HCH3  0   0.287   2.1417  -2.2074  -0.8738
 39A  H3M2  H  HCH3  0   0.287   2.1812  -2.1580   0.9093
 39A  H3M3  H  HCH3  0   0.297   1.1852  -3.3468   0.0709
 39A  H2    H  HCR6  0   0.322  -0.9235  -2.9759   0.1020

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
 39A  N6   C6    single    1.314  0.020  1.314
 39A  N6   HN61  single    0.860  0.020  1.020
 39A  N6   HN62  single    0.860  0.020  1.020
 39A  C6   C5    aromatic  1.409  0.020  1.409
 39A  C6   N1    aromatic  1.349  0.020  1.349
 39A  C5   N7    aromatic  1.362  0.020  1.362
 39A  C5   C4    aromatic  1.383  0.020  1.383
 39A  N7   C8    aromatic  1.297  0.020  1.297
 39A  C4   N9    aromatic  1.350  0.020  1.350
 39A  C4   N3    aromatic  1.358  0.020  1.358
 39A  N9   C8    aromatic  1.370  0.020  1.370
 39A  N9   C9M   single    1.454  0.020  1.454
 39A  C8   H8    single    0.930  0.020  1.080
 39A  C9M  H9M1  single    0.970  0.020  1.090
 39A  C9M  H9M2  single    0.970  0.020  1.090
 39A  C9M  H9M3  single    0.970  0.020  1.090
 39A  N3   C3M   single    1.461  0.020  1.461
 39A  N3   C2    aromatic  1.346  0.020  1.346
 39A  C3M  H3M1  single    0.970  0.020  1.090
 39A  C3M  H3M2  single    0.970  0.020  1.090
 39A  C3M  H3M3  single    0.970  0.020  1.090
 39A  C2   N1    aromatic  1.298  0.020  1.298
 39A  C2   H2    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
 39A  HN62  N6   HN61  118.22  3.000
 39A  HN62  N6   C6    120.56  3.000
 39A  HN61  N6   C6    121.22  3.000
 39A  N1    C6   C5    117.89  3.000
 39A  N1    C6   N6    118.99  3.000
 39A  C5    C6   N6    123.12  3.000
 39A  C4    C5   N7    110.33  3.000
 39A  C4    C5   C6    118.50  3.000
 39A  N7    C5   C6    131.16  3.000
 39A  C8    N7   C5    104.30  3.000
 39A  N3    C4   N9    131.92  3.000
 39A  N3    C4   C5    121.83  3.000
 39A  N9    C4   C5    106.25  3.000
 39A  C9M   N9   C8    124.27  3.000
 39A  C9M   N9   C4    130.36  3.000
 39A  C8    N9   C4    105.36  3.000
 39A  H8    C8   N9    120.45  3.000
 39A  H8    C8   N7    125.79  3.000
 39A  N9    C8   N7    113.76  3.000
 39A  H9M3  C9M  H9M2  108.35  3.000
 39A  H9M3  C9M  H9M1  108.53  3.000
 39A  H9M2  C9M  H9M1  110.27  3.000
 39A  H9M3  C9M  N9    107.81  3.000
 39A  H9M2  C9M  N9    110.92  3.000
 39A  H9M1  C9M  N9    110.87  3.000
 39A  C2    N3   C3M   120.64  3.000
 39A  C2    N3   C4    115.34  3.000
 39A  C3M   N3   C4    124.02  3.000
 39A  H3M3  C3M  H3M2  108.60  3.000
 39A  H3M3  C3M  H3M1  108.56  3.000
 39A  H3M2  C3M  H3M1  110.48  3.000
 39A  H3M3  C3M  N3    108.29  3.000
 39A  H3M2  C3M  N3    110.43  3.000
 39A  H3M1  C3M  N3    110.42  3.000
 39A  H2    C2   N1    118.45  3.000
 39A  H2    C2   N3    115.28  3.000
 39A  N1    C2   N3    126.27  3.000
 39A  C2    N1   C6    120.16  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
 39A  CONST_01  C8    N7   C5  C6   180.00   0.0  0
 39A  CONST_02  N9    C4   C5  C6   180.00   0.0  0
 39A  CONST_03  N3    C4   C5  C6     0.00   0.0  0
 39A  CONST_04  N3    C2   N1  C6     0.00   0.0  0
 39A  CONST_05  C2    N1   C6  C5     0.00   0.0  0
 39A  CONST_06  N9    C8   N7  C5     0.00   0.0  0
 39A  CONST_07  C8    N9   C4  C5     0.00   0.0  0
 39A  CONST_08  C2    N3   C4  C5     0.00   0.0  0
 39A  CONST_09  N1    C6   C5  N7   180.00   0.0  0
 39A  CONST_10  N9    C4   C5  N7     0.00   0.0  0
 39A  CONST_11  N3    C4   C5  N7   180.00   0.0  0
 39A  CONST_12  C4    N9   C8  N7     0.00   0.0  0
 39A  CONST_13  N1    C6   C5  C4     0.00   0.0  0
 39A  CONST_14  C8    N7   C5  C4     0.00   0.0  0
 39A  CONST_15  N1    C2   N3  C4     0.00   0.0  0
 39A  CONST_16  C2    N3   C4  N9   180.00   0.0  0
 39A  CONST_17  N3    C4   N9  C8   180.00   0.0  0
 39A  CONST_18  N7    C5   C6  N6     0.00   0.0  0
 39A  CONST_19  C4    C5   C6  N6   180.00   0.0  0
 39A  CONST_20  C2    N1   C6  N6   180.00   0.0  0
 39A  CONST_21  C9M   N9   C4  C5   180.00   0.0  0
 39A  CONST_22  C3M   N3   C4  C5   180.00   0.0  0
 39A  CONST_23  C9M   N9   C8  N7   180.00   0.0  0
 39A  CONST_24  C3M   N3   C4  N9     0.00   0.0  0
 39A  CONST_25  N3    C4   N9  C9M    0.00   0.0  0
 39A  CONST_26  N1    C2   N3  C3M  180.00   0.0  0
 39A  CONST_27  H2    C2   N1  C6   180.00   0.0  0
 39A  CONST_28  H8    C8   N7  C5   180.00   0.0  0
 39A  CONST_29  HN61  N6   C6  C5     0.00   0.0  0
 39A  CONST_30  HN62  N6   C6  C5   180.00   0.0  0
 39A  Var_01    H9M1  C9M  N9  C4   -65.09  30.0  2
 39A  Var_02    H3M1  C3M  N3  C4   -61.37  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
 39A  plan-1  N6    0.020
 39A  plan-1  C6    0.020
 39A  plan-1  C5    0.020
 39A  plan-1  N7    0.020
 39A  plan-1  C4    0.020
 39A  plan-1  N9    0.020
 39A  plan-1  C8    0.020
 39A  plan-1  C9M   0.020
 39A  plan-1  N3    0.020
 39A  plan-1  C3M   0.020
 39A  plan-1  C2    0.020
 39A  plan-1  N1    0.020
 39A  plan-1  H8    0.020
 39A  plan-1  H2    0.020
 39A  plan-2  N6    0.020
 39A  plan-2  C6    0.020
 39A  plan-2  HN61  0.020
 39A  plan-2  HN62  0.020

