# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 14:49:02 2020
#   Inital geometry file: a 47 line input string
#   Ligand name: ~{N}-methylthieno[3,2-d]pyrimidin-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1ncnc2ccsc12
#
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
 M1E  M1E  ~{N}-methylthieno[3,2-d]pyrimidin-4-amine  ligand  18  11  .  2022-03-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M1E
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
 M1E  C01  C  CH3   0  -0.512   3.3605  -1.1293  -0.0265
 M1E  C03  C  CR6   0   0.560   1.1360  -0.1152  -0.0081
 M1E  C05  C  CR16  0   0.034   0.9152   2.1628   0.0006
 M1E  C07  C  CR56  0   0.286  -0.9963   1.0003  -0.0048
 M1E  C08  C  CR15  0  -0.197  -2.4085   0.7662  -0.0051
 M1E  C09  C  CR15  0  -0.446  -2.7032  -0.5544  -0.0064
 M1E  C11  C  CR56  0  -0.328  -0.2750  -0.1902  -0.0083
 M1E  N02  N  NH1   0  -0.654   1.9184  -1.1977  -0.0072
 M1E  N04  N  N     0  -0.479   1.7041   1.0891  -0.0045
 M1E  N06  N  N     0  -0.462  -0.3968   2.2071   0.0002
 M1E  S10  S  S2    0   0.222  -1.3101  -1.5707  -0.0083
 M1E  H1   H  HCH3  0   0.239   3.7341  -0.6677  -0.9415
 M1E  H2   H  HCH3  0   0.241   3.7445  -0.5646   0.8227
 M1E  H3   H  HCH3  0   0.253   3.7461  -2.1428   0.0313
 M1E  H4   H  HCR6  0   0.250   1.4310   3.1180   0.0049
 M1E  H5   H  HCR5  0   0.277  -3.1479   1.5532  -0.0031
 M1E  H6   H  HCR5  0   0.310  -3.6831  -1.0074  -0.0065
 M1E  H7   H  HNH1  0   0.407   1.4940  -2.1087  -0.0490

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
 M1E  S10  C09  aromatic  1.724  0.020  1.724
 M1E  S10  C11  aromatic  1.725  0.020  1.725
 M1E  C09  C08  aromatic  1.353  0.020  1.353
 M1E  N02  C01  single    1.444  0.020  1.444
 M1E  N02  C03  single    1.336  0.020  1.336
 M1E  C11  C03  aromatic  1.413  0.020  1.413
 M1E  C11  C07  aromatic  1.392  0.020  1.392
 M1E  C08  C07  aromatic  1.431  0.020  1.431
 M1E  C03  N04  aromatic  1.332  0.020  1.332
 M1E  C07  N06  aromatic  1.348  0.020  1.348
 M1E  N04  C05  aromatic  1.332  0.020  1.332
 M1E  N06  C05  aromatic  1.313  0.020  1.313
 M1E  C01  H1   single    0.970  0.020  1.090
 M1E  C01  H2   single    0.970  0.020  1.090
 M1E  C01  H3   single    0.970  0.020  1.090
 M1E  C05  H4   single    0.930  0.020  1.080
 M1E  C08  H5   single    0.930  0.020  1.080
 M1E  C09  H6   single    0.930  0.020  1.080
 M1E  N02  H7   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
 M1E  H3   C01  H2   108.48  3.000
 M1E  H3   C01  H1   108.54  3.000
 M1E  H2   C01  H1   108.28  3.000
 M1E  H3   C01  N02  108.04  3.000
 M1E  H2   C01  N02  111.48  3.000
 M1E  H1   C01  N02  111.92  3.000
 M1E  N04  C03  N02  118.89  3.000
 M1E  N04  C03  C11  118.30  3.000
 M1E  N02  C03  C11  122.82  3.000
 M1E  H4   C05  N06  116.44  3.000
 M1E  H4   C05  N04  115.33  3.000
 M1E  N06  C05  N04  128.24  3.000
 M1E  N06  C07  C11  122.37  3.000
 M1E  N06  C07  C08  125.82  3.000
 M1E  C11  C07  C08  111.80  3.000
 M1E  H5   C08  C09  124.20  3.000
 M1E  H5   C08  C07  123.81  3.000
 M1E  C09  C08  C07  111.99  3.000
 M1E  H6   C09  S10  119.08  3.000
 M1E  H6   C09  C08  127.39  3.000
 M1E  S10  C09  C08  113.53  3.000
 M1E  S10  C11  C07  111.93  3.000
 M1E  C07  C11  C03  118.17  3.000
 M1E  S10  C11  C03  129.90  3.000
 M1E  H7   N02  C03  119.14  3.000
 M1E  H7   N02  C01  117.63  3.000
 M1E  C03  N02  C01  123.14  3.000
 M1E  C05  N04  C03  118.44  3.000
 M1E  C07  N06  C05  114.48  3.000
 M1E  C11  S10  C09   90.75  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
 M1E  CONST_01  C09  S10  C11  C03  180.00   0.0  0
 M1E  CONST_02  C08  C07  C11  C03  180.00   0.0  0
 M1E  CONST_03  N06  C07  C11  C03    0.00   0.0  0
 M1E  CONST_04  N06  C05  N04  C03    0.00   0.0  0
 M1E  CONST_05  C11  C03  N04  C05    0.00   0.0  0
 M1E  CONST_06  C11  C07  N06  C05    0.00   0.0  0
 M1E  CONST_07  C08  C07  N06  C05  180.00   0.0  0
 M1E  CONST_08  C09  S10  C11  C07    0.00   0.0  0
 M1E  CONST_09  N04  C03  C11  C07    0.00   0.0  0
 M1E  CONST_10  S10  C09  C08  C07    0.00   0.0  0
 M1E  CONST_11  N04  C05  N06  C07    0.00   0.0  0
 M1E  CONST_12  C11  S10  C09  C08    0.00   0.0  0
 M1E  CONST_13  S10  C11  C07  C08    0.00   0.0  0
 M1E  CONST_14  C11  C07  C08  C09    0.00   0.0  0
 M1E  CONST_15  N06  C07  C08  C09  180.00   0.0  0
 M1E  CONST_16  S10  C11  C03  N04  180.00   0.0  0
 M1E  CONST_17  S10  C11  C07  N06  180.00   0.0  0
 M1E  CONST_18  N02  C03  N04  C05  180.00   0.0  0
 M1E  CONST_19  N02  C03  C11  C07  180.00   0.0  0
 M1E  CONST_20  S10  C11  C03  N02    0.00   0.0  0
 M1E  CONST_21  H4   C05  N04  C03  180.00   0.0  0
 M1E  CONST_22  H6   C09  C08  C07  180.00   0.0  0
 M1E  CONST_23  H5   C08  C07  C11  180.00   0.0  0
 M1E  CONST_24  C11  C03  N02  C01  180.00   0.0  0
 M1E  CONST_25  N04  C03  N02  C01    0.00   0.0  0
 M1E  CONST_26  H7   N02  C03  C11    0.00   0.0  0
 M1E  Var_01    H1   C01  N02  C03  -63.47  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
 M1E  plan-1  C03  0.020
 M1E  plan-1  C05  0.020
 M1E  plan-1  C07  0.020
 M1E  plan-1  C08  0.020
 M1E  plan-1  C09  0.020
 M1E  plan-1  C11  0.020
 M1E  plan-1  N02  0.020
 M1E  plan-1  N04  0.020
 M1E  plan-1  N06  0.020
 M1E  plan-1  S10  0.020
 M1E  plan-1  H4   0.020
 M1E  plan-1  H5   0.020
 M1E  plan-1  H6   0.020
 M1E  plan-2  C01  0.020
 M1E  plan-2  C03  0.020
 M1E  plan-2  N02  0.020
 M1E  plan-2  H7   0.020

