# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 09:04:21 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: 3-methyl-3H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cnc(N)c2ncnc12
#
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
 ADK  ADK  3-methyl-3H-purin-6-amine  ligand  18  11  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ADK
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
 ADK  N9    N  N     0  -0.487  -1.7192  -0.0043   1.1811
 ADK  C4    C  CR56  0   0.426  -0.4886  -0.0022   0.6886
 ADK  N3    N  NR6   0  -0.477   0.6992  -0.0003   1.3609
 ADK  C2    C  CR16  0   0.149   1.8094  -0.0012   0.6139
 ADK  N1    N  N     0  -0.471   1.8497  -0.0026  -0.6894
 ADK  C6    C  CR6   0   0.449   0.7004  -0.0036  -1.4028
 ADK  N6    N  NH2   0  -0.804   0.7890  -0.0097  -2.7275
 ADK  C5    C  CR56  0   0.040  -0.5149  -0.0047  -0.7089
 ADK  N7    N  N     0  -0.471  -1.8160  -0.0081  -1.1061
 ADK  C8    C  CR15  0   0.001  -2.4638  -0.0079   0.0481
 ADK  C3A   C  CH3   0  -0.523   0.7332   0.0006   2.8139
 ADK  HC2   H  HCR6  0   0.300   2.7452   0.0002   1.1588
 ADK  HN61  H  HNH2  0   0.409   1.6861   0.0380  -3.1798
 ADK  HN62  H  HNH2  0   0.416  -0.0367   0.0349  -3.2993
 ADK  H8    H  HCR5  0   0.237  -3.5455  -0.0100   0.0976
 ADK  H3A1  H  HCH3  0   0.268   1.7670  -0.0089   3.1463
 ADK  H3A2  H  HCH3  0   0.270   0.2415   0.8921   3.1959
 ADK  H3A3  H  HCH3  0   0.270   0.2255  -0.8813   3.1969

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
 ADK  N9   C4    aromatic  1.325  0.020  1.325
 ADK  N9   C8    aromatic  1.356  0.020  1.356
 ADK  C4   N3    aromatic  1.365  0.020  1.365
 ADK  C4   C5    aromatic  1.398  0.020  1.398
 ADK  N3   C2    aromatic  1.338  0.020  1.338
 ADK  N3   C3A   single    1.453  0.020  1.453
 ADK  C2   N1    aromatic  1.304  0.020  1.304
 ADK  C2   HC2   single    0.930  0.020  1.080
 ADK  N1   C6    aromatic  1.353  0.020  1.353
 ADK  C6   N6    single    1.328  0.020  1.328
 ADK  C6   C5    aromatic  1.399  0.020  1.399
 ADK  N6   HN61  single    0.860  0.020  1.020
 ADK  N6   HN62  single    0.860  0.020  1.020
 ADK  C5   N7    aromatic  1.360  0.020  1.360
 ADK  N7   C8    aromatic  1.324  0.020  1.324
 ADK  C8   H8    single    0.930  0.020  1.080
 ADK  C3A  H3A1  single    0.970  0.020  1.090
 ADK  C3A  H3A2  single    0.970  0.020  1.090
 ADK  C3A  H3A3  single    0.970  0.020  1.090

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
 ADK  C8    N9   C4    101.51  3.000
 ADK  C5    C4   N3    120.59  3.000
 ADK  C5    C4   N9    110.73  3.000
 ADK  N3    C4   N9    128.68  3.000
 ADK  C3A   N3   C2    122.60  3.000
 ADK  C3A   N3   C4    120.85  3.000
 ADK  C2    N3   C4    116.55  3.000
 ADK  HC2   C2   N1    118.44  3.000
 ADK  HC2   C2   N3    115.85  3.000
 ADK  N1    C2   N3    125.71  3.000
 ADK  C6    N1   C2    120.05  3.000
 ADK  C5    C6   N6    123.55  3.000
 ADK  C5    C6   N1    118.45  3.000
 ADK  N6    C6   N1    118.00  3.000
 ADK  HN62  N6   HN61  118.34  3.000
 ADK  HN62  N6   C6    120.83  3.000
 ADK  HN61  N6   C6    120.53  3.000
 ADK  N7    C5   C6    133.30  3.000
 ADK  N7    C5   C4    108.05  3.000
 ADK  C6    C5   C4    118.65  3.000
 ADK  C8    N7   C5    102.33  3.000
 ADK  H8    C8   N7    121.92  3.000
 ADK  H8    C8   N9    120.70  3.000
 ADK  N7    C8   N9    117.38  3.000
 ADK  H3A3  C3A  H3A2  109.27  3.000
 ADK  H3A3  C3A  H3A1  109.25  3.000
 ADK  H3A2  C3A  H3A1  109.28  3.000
 ADK  H3A3  C3A  N3    109.92  3.000
 ADK  H3A2  C3A  N3    109.95  3.000
 ADK  H3A1  C3A  N3    109.16  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
 ADK  CONST_01  C2    N3   C4  N9  180.00   0.0  0
 ADK  CONST_02  C6    C5   C4  N9  180.00   0.0  0
 ADK  CONST_03  N7    C5   C4  N9    0.00   0.0  0
 ADK  CONST_04  C5    N7   C8  N9    0.00   0.0  0
 ADK  CONST_05  N7    C8   N9  C4    0.00   0.0  0
 ADK  CONST_06  N1    C2   N3  C4    0.00   0.0  0
 ADK  CONST_07  N1    C6   C5  C4    0.00   0.0  0
 ADK  CONST_08  C8    N7   C5  C4    0.00   0.0  0
 ADK  CONST_09  C8    N9   C4  N3  180.00   0.0  0
 ADK  CONST_10  C6    C5   C4  N3    0.00   0.0  0
 ADK  CONST_11  N7    C5   C4  N3  180.00   0.0  0
 ADK  CONST_12  C6    N1   C2  N3    0.00   0.0  0
 ADK  CONST_13  C5    C4   N3  C2    0.00   0.0  0
 ADK  CONST_14  C5    C6   N1  C2    0.00   0.0  0
 ADK  CONST_15  N7    C5   C6  N1  180.00   0.0  0
 ADK  CONST_16  C8    N7   C5  C6  180.00   0.0  0
 ADK  CONST_17  C8    N9   C4  C5    0.00   0.0  0
 ADK  CONST_18  C3A   N3   C4  N9    0.00   0.0  0
 ADK  CONST_19  N6    C6   C5  C4  180.00   0.0  0
 ADK  CONST_20  N6    C6   N1  C2  180.00   0.0  0
 ADK  CONST_21  C3A   N3   C2  N1  180.00   0.0  0
 ADK  CONST_22  N7    C5   C6  N6    0.00   0.0  0
 ADK  CONST_23  C3A   N3   C4  C5  180.00   0.0  0
 ADK  CONST_24  H8    C8   N9  C4  180.00   0.0  0
 ADK  CONST_25  HC2   C2   N3  C4  180.00   0.0  0
 ADK  CONST_26  HN61  N6   C6  N1    0.00   0.0  0
 ADK  CONST_27  HN62  N6   C6  N1  180.00   0.0  0
 ADK  Var_01    H3A1  C3A  N3  C4  179.38  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
 ADK  plan-1  N9    0.020
 ADK  plan-1  C4    0.020
 ADK  plan-1  N3    0.020
 ADK  plan-1  C2    0.020
 ADK  plan-1  N1    0.020
 ADK  plan-1  C6    0.020
 ADK  plan-1  N6    0.020
 ADK  plan-1  C5    0.020
 ADK  plan-1  N7    0.020
 ADK  plan-1  C8    0.020
 ADK  plan-1  C3A   0.020
 ADK  plan-1  HC2   0.020
 ADK  plan-1  H8    0.020
 ADK  plan-2  C6    0.020
 ADK  plan-2  N6    0.020
 ADK  plan-2  HN61  0.020
 ADK  plan-2  HN62  0.020

