# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:22:41 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 2-amino-1,9-dihydro-6H-purine-6-thione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2[nH]cnc2C(=S)N1
#
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
 DX4  DX4  2-amino-1,9-dihydro-6H-purine-6-thione  ligand  16  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DX4
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
 DX4  C4    C  CR56  0   0.494  -0.5832   1.1968  -0.0132
 DX4  C5    C  CR56  0   0.024  -0.7982  -0.1809  -0.0226
 DX4  C6    C  CR6   0   0.156   0.3182  -1.0302  -0.0309
 DX4  C8    C  CR15  0   0.097  -2.7143   0.7071  -0.0074
 DX4  N1    N  NR16  0  -0.677   1.5011  -0.3224  -0.0304
 DX4  N3    N  N     0  -0.489   0.5836   1.8427  -0.0110
 DX4  C2    C  CR6   0   0.701   1.6214   1.0383  -0.0226
 DX4  N9    N  NR15  0  -0.644  -1.8200   1.7425  -0.0035
 DX4  N7    N  N     0  -0.424  -2.1418  -0.4571  -0.0187
 DX4  S6    S  S1    0  -0.387   0.3300  -2.6963  -0.0410
 DX4  H8    H  HCR5  0   0.290  -3.7784   0.8858  -0.0010
 DX4  HN2   H  HNH2  0   0.420   3.6687   0.9647   0.0977
 DX4  HN2A  H  HNH2  0   0.418   2.9732   2.5329   0.0629
 DX4  HN9   H  HNR5  0   0.428  -2.0435   2.7263   0.0066
 DX4  H5    H  HNR6  0   0.427   2.3457  -0.8804  -0.0415
 DX4  N2    N  NH2   0  -0.832   2.8589   1.5408  -0.0564

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
 DX4  C4  C5    aromatic  1.394  0.020  1.394
 DX4  C4  N3    single    1.334  0.020  1.334
 DX4  C4  N9    aromatic  1.352  0.020  1.352
 DX4  C5  C6    single    1.403  0.020  1.403
 DX4  C5  N7    aromatic  1.372  0.020  1.372
 DX4  C6  N1    single    1.379  0.020  1.379
 DX4  C6  S6    double    1.666  0.020  1.666
 DX4  C8  N9    aromatic  1.368  0.020  1.368
 DX4  C8  N7    aromatic  1.297  0.020  1.297
 DX4  C8  H8    single    0.930  0.020  1.080
 DX4  N1  C2    single    1.366  0.020  1.366
 DX4  N1  H5    single    0.860  0.020  1.020
 DX4  N2  C2    single    1.336  0.020  1.336
 DX4  N2  HN2   single    0.890  0.020  1.040
 DX4  N2  HN2A  single    0.890  0.020  1.040
 DX4  N3  C2    double    1.313  0.020  1.313
 DX4  N9  HN9   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
 DX4  N9    C4  N3   127.22  3.000
 DX4  N9    C4  C5   104.94  3.000
 DX4  N3    C4  C5   127.84  3.000
 DX4  N7    C5  C6   131.12  3.000
 DX4  N7    C5  C4   110.48  3.000
 DX4  C6    C5  C4   118.40  3.000
 DX4  S6    C6  N1   120.49  3.000
 DX4  S6    C6  C5   127.67  3.000
 DX4  N1    C6  C5   111.84  3.000
 DX4  H8    C8  N7   125.72  3.000
 DX4  H8    C8  N9   121.28  3.000
 DX4  N7    C8  N9   112.99  3.000
 DX4  H5    N1  C2   118.40  3.000
 DX4  H5    N1  C6   115.65  3.000
 DX4  C2    N1  C6   125.94  3.000
 DX4  C2    N3  C4   113.25  3.000
 DX4  N3    C2  N2   120.12  3.000
 DX4  N3    C2  N1   122.73  3.000
 DX4  N2    C2  N1   117.13  3.000
 DX4  HN9   N9  C8   126.38  3.000
 DX4  HN9   N9  C4   126.61  3.000
 DX4  C8    N9  C4   107.01  3.000
 DX4  C8    N7  C5   104.57  3.000
 DX4  HN2A  N2  HN2  117.08  3.000
 DX4  HN2A  N2  C2   118.25  3.000
 DX4  HN2   N2  C2   121.77  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
 DX4  CONST_01  C8    N7  C5  C4    0.00  0.0  0
 DX4  CONST_02  N7    C8  N9  C4    0.00  0.0  0
 DX4  CONST_03  C8    N9  C4  C5    0.00  0.0  0
 DX4  CONST_04  N9    C8  N7  C5    0.00  0.0  0
 DX4  CONST_05  N7    C5  C4  N9    0.00  0.0  0
 DX4  CONST_06  N1    C2  N3  C4    0.00  0.0  0
 DX4  CONST_07  N3    C2  N1  C6    0.00  0.0  0
 DX4  CONST_08  N2    C2  N3  C4  180.00  0.0  0
 DX4  CONST_09  N2    C2  N1  C6  180.00  0.0  0
 DX4  CONST_10  H8    C8  N9  C4  180.00  0.0  0
 DX4  CONST_11  HN9   N9  C4  C5  180.00  0.0  0
 DX4  CONST_12  H5    N1  C2  N3  180.00  0.0  0
 DX4  CONST_13  HN2   N2  C2  N1    0.00  0.0  0
 DX4  CONST_14  HN2A  N2  C2  N1  180.00  0.0  0

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
 DX4  plan-1  C4    0.020
 DX4  plan-1  C5    0.020
 DX4  plan-1  C6    0.020
 DX4  plan-1  C8    0.020
 DX4  plan-1  N1    0.020
 DX4  plan-1  N3    0.020
 DX4  plan-1  C2    0.020
 DX4  plan-1  N9    0.020
 DX4  plan-1  N7    0.020
 DX4  plan-1  S6    0.020
 DX4  plan-1  H8    0.020
 DX4  plan-1  HN2   0.020
 DX4  plan-1  HN2A  0.020
 DX4  plan-1  HN9   0.020
 DX4  plan-1  H5    0.020
 DX4  plan-1  N2    0.020

