# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 20:39:52 2022
#   Inital geometry file: a 47 line input string
#   Ligand name: N-methyl-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2[nH]cnc12
#
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
 N6M  N6M  N-methyl-9H-purin-6-amine  ligand  18  11  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_N6M
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
 N6M  C6    C  CR6   0   0.489   0.9862  -0.1435   0.0073
 N6M  C5    C  CR56  0  -0.002  -0.3823  -0.4819   0.0011
 N6M  C4    C  CR56  0   0.460  -1.2778   0.5777   0.0068
 N6M  C2    C  CR16  0   0.038   0.3389   2.0646   0.0213
 N6M  C8    C  CR15  0   0.102  -2.3034  -1.3537  -0.0132
 N6M  C11   C  CH3   0  -0.512   3.3575  -0.7467   0.0021
 N6M  N6    N  NH1   0  -0.643   1.9510  -1.0646   0.0066
 N6M  N1    N  N     0  -0.486   1.3109   1.1534   0.0157
 N6M  N3    N  N     0  -0.449  -0.9676   1.8754   0.0176
 N6M  N9    N  NR15  0  -0.644  -2.5056  -0.0079  -0.0024
 N6M  N7    N  N     0  -0.447  -1.0429  -1.6826  -0.0116
 N6M  H9    H  HNR5  0   0.425  -3.3992   0.4601  -0.0030
 N6M  H8    H  HCR5  0   0.289  -3.1311  -2.0458  -0.0233
 N6M  H6    H  HNH1  0   0.406   1.6758  -2.0319  -0.0103
 N6M  H111  H  HCH3  0   0.236   3.6551  -0.2251  -0.9089
 N6M  H112  H  HCH3  0   0.238   3.6321  -0.1244   0.8541
 N6M  H113  H  HCH3  0   0.252   3.9150  -1.6769   0.0624
 N6M  H2    H  HCR6  0   0.248   0.6718   3.0973   0.0292

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
 N6M  N9   C8    aromatic  1.361  0.020  1.361
 N6M  N9   C4    aromatic  1.360  0.020  1.360
 N6M  C8   N7    aromatic  1.303  0.020  1.303
 N6M  N7   C5    aromatic  1.370  0.020  1.370
 N6M  C5   C6    aromatic  1.410  0.020  1.410
 N6M  C5   C4    aromatic  1.387  0.020  1.387
 N6M  C6   N6    single    1.334  0.020  1.334
 N6M  C6   N1    aromatic  1.337  0.020  1.337
 N6M  N1   C2    aromatic  1.332  0.020  1.332
 N6M  C2   N3    aromatic  1.320  0.020  1.320
 N6M  N3   C4    aromatic  1.334  0.020  1.334
 N6M  N9   H9    single    0.860  0.020  1.020
 N6M  C8   H8    single    0.930  0.020  1.080
 N6M  N6   H6    single    0.860  0.020  1.020
 N6M  N6   C11   single    1.442  0.020  1.442
 N6M  C11  H111  single    0.970  0.020  1.090
 N6M  C11  H112  single    0.970  0.020  1.090
 N6M  C11  H113  single    0.970  0.020  1.090
 N6M  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
 N6M  N1    C6   N6    119.62  3.000
 N6M  N1    C6   C5    117.95  3.000
 N6M  N6    C6   C5    122.44  3.000
 N6M  N7    C5   C4    110.98  3.000
 N6M  C4    C5   C6    116.31  3.000
 N6M  N7    C5   C6    132.71  3.000
 N6M  N9    C4   N3    128.94  3.000
 N6M  N3    C4   C5    126.36  3.000
 N6M  N9    C4   C5    104.70  3.000
 N6M  H2    C2   N3    116.11  3.000
 N6M  H2    C2   N1    115.29  3.000
 N6M  N3    C2   N1    128.61  3.000
 N6M  H8    C8   N7    125.47  3.000
 N6M  H8    C8   N9    121.36  3.000
 N6M  N7    C8   N9    113.17  3.000
 N6M  H113  C11  H112  108.43  3.000
 N6M  H113  C11  H111  108.41  3.000
 N6M  H112  C11  H111  108.11  3.000
 N6M  H113  C11  N6    108.16  3.000
 N6M  H112  C11  N6    111.66  3.000
 N6M  H111  C11  N6    111.96  3.000
 N6M  H6    N6   C11   118.61  3.000
 N6M  C11   N6   C6    123.59  3.000
 N6M  H6    N6   C6    117.79  3.000
 N6M  C2    N1   C6    119.09  3.000
 N6M  C2    N3   C4    111.68  3.000
 N6M  H9    N9   C8    126.19  3.000
 N6M  H9    N9   C4    126.86  3.000
 N6M  C8    N9   C4    106.95  3.000
 N6M  C8    N7   C5    104.19  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
 N6M  CONST_01  C8    N7   C5  C6   180.00   0.0  0
 N6M  CONST_02  N9    C4   C5  C6   180.00   0.0  0
 N6M  CONST_03  N3    C4   C5  C6     0.00   0.0  0
 N6M  CONST_04  N3    C2   N1  C6     0.00   0.0  0
 N6M  CONST_05  N9    C8   N7  C5     0.00   0.0  0
 N6M  CONST_06  C2    N1   C6  C5     0.00   0.0  0
 N6M  CONST_07  C8    N9   C4  C5     0.00   0.0  0
 N6M  CONST_08  C2    N3   C4  C5     0.00   0.0  0
 N6M  CONST_09  N7    C8   N9  C4     0.00   0.0  0
 N6M  CONST_10  C8    N7   C5  C4     0.00   0.0  0
 N6M  CONST_11  N1    C6   C5  C4     0.00   0.0  0
 N6M  CONST_12  N1    C2   N3  C4     0.00   0.0  0
 N6M  CONST_13  N9    C4   N3  C2   180.00   0.0  0
 N6M  CONST_14  N3    C4   N9  C8   180.00   0.0  0
 N6M  CONST_15  N7    C5   C6  N1   180.00   0.0  0
 N6M  CONST_16  N7    C5   C4  N3   180.00   0.0  0
 N6M  CONST_17  N7    C5   C4  N9     0.00   0.0  0
 N6M  CONST_18  N6    C6   C5  C4   180.00   0.0  0
 N6M  CONST_19  N6    C6   N1  C2   180.00   0.0  0
 N6M  CONST_20  N7    C5   C6  N6     0.00   0.0  0
 N6M  CONST_21  H2    C2   N1  C6   180.00   0.0  0
 N6M  CONST_22  H8    C8   N7  C5   180.00   0.0  0
 N6M  CONST_23  H9    N9   C4  C5   180.00   0.0  0
 N6M  CONST_24  C11   N6   C6  C5   180.00   0.0  0
 N6M  CONST_25  N1    C6   N6  C11    0.00   0.0  0
 N6M  CONST_26  H6    N6   C6  C5     0.00   0.0  0
 N6M  Var_01    H111  C11  N6  C6   -63.94  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
 N6M  plan-1  C6   0.020
 N6M  plan-1  C5   0.020
 N6M  plan-1  C4   0.020
 N6M  plan-1  C2   0.020
 N6M  plan-1  C8   0.020
 N6M  plan-1  N6   0.020
 N6M  plan-1  N1   0.020
 N6M  plan-1  N3   0.020
 N6M  plan-1  N9   0.020
 N6M  plan-1  N7   0.020
 N6M  plan-1  H9   0.020
 N6M  plan-1  H8   0.020
 N6M  plan-1  H2   0.020
 N6M  plan-2  C6   0.020
 N6M  plan-2  C11  0.020
 N6M  plan-2  N6   0.020
 N6M  plan-2  H6   0.020

