# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 01:12:07 2020
#   Inital geometry file: a 39 line input string
#   Ligand name: 9H-purine-6-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Sc1ncnc2[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
 PM6  PM6  '9H-purine-6-thiol        '  ligand  14  10  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PM6
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
 PM6  N9   N  NR15  0  -0.642   2.4978   0.2836  -0.1009
 PM6  C4   C  CR56  0   0.487   1.3601  -0.4510  -0.0024
 PM6  N3   N  N     0  -0.416   1.2013  -1.7660  -0.0097
 PM6  C2   C  CR16  0   0.042  -0.0652  -2.1247   0.1071
 PM6  N1   N  N     0  -0.416  -1.1310  -1.3295   0.2237
 PM6  C6   C  CR6   0   0.020  -0.9495  -0.0177   0.2282
 PM6  C5   C  CR56  0   0.104   0.3376   0.4953   0.1131
 PM6  N7   N  N     0  -0.439   0.8431   1.7654   0.0852
 PM6  C8   C  CR15  0   0.122   2.1277   1.5919  -0.0429
 PM6  S6   S  S2    0  -0.122  -2.3063   1.0726   0.3756
 PM6  HN9  H  HNR5  0   0.434   3.4400  -0.0649  -0.1986
 PM6  H2   H  HCR6  0   0.267  -0.2704  -3.1886   0.1088
 PM6  H8   H  HCR5  0   0.300   2.8593   2.3828  -0.1020
 PM6  HS6  H  HSH1  0   0.259  -3.2445   0.1215   0.4447

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
 PM6  N9  C4   aromatic  1.358  0.020  1.358
 PM6  N9  C8   aromatic  1.361  0.020  1.361
 PM6  C4  N3   aromatic  1.325  0.020  1.325
 PM6  C4  C5   aromatic  1.398  0.020  1.398
 PM6  N3  C2   aromatic  1.321  0.020  1.321
 PM6  C2  N1   aromatic  1.335  0.020  1.335
 PM6  N1  C6   aromatic  1.324  0.020  1.324
 PM6  C6  C5   aromatic  1.390  0.020  1.390
 PM6  C6  S6   single    1.747  0.020  1.747
 PM6  C5  N7   aromatic  1.367  0.020  1.367
 PM6  N7  C8   aromatic  1.303  0.020  1.303
 PM6  N9  HN9  single    0.860  0.020  1.020
 PM6  C2  H2   single    0.930  0.020  1.080
 PM6  C8  H8   single    0.930  0.020  1.080
 PM6  S6  HS6  single    1.200  0.020  1.300

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
 PM6  HN9  N9  C8  126.15  3.000
 PM6  HN9  N9  C4  127.04  3.000
 PM6  C8   N9  C4  106.80  3.000
 PM6  C5   C4  N3  125.79  3.000
 PM6  C5   C4  N9  104.63  3.000
 PM6  N3   C4  N9  129.58  3.000
 PM6  C2   N3  C4  112.57  3.000
 PM6  H2   C2  N1  115.69  3.000
 PM6  H2   C2  N3  116.63  3.000
 PM6  N1   C2  N3  127.68  3.000
 PM6  C6   N1  C2  118.75  3.000
 PM6  S6   C6  C5  119.72  3.000
 PM6  S6   C6  N1  120.81  3.000
 PM6  C5   C6  N1  119.48  3.000
 PM6  N7   C5  C6  133.37  3.000
 PM6  N7   C5  C4  110.90  3.000
 PM6  C6   C5  C4  115.73  3.000
 PM6  C8   N7  C5  104.05  3.000
 PM6  H8   C8  N7  125.20  3.000
 PM6  H8   C8  N9  121.19  3.000
 PM6  N7   C8  N9  113.61  3.000
 PM6  HS6  S6  C6   96.04  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
 PM6  CONST_01  C2   N3  C4  N9  180.00  0.0  0
 PM6  CONST_02  C6   C5  C4  N9  180.00  0.0  0
 PM6  CONST_03  N7   C5  C4  N9    0.00  0.0  0
 PM6  CONST_04  C5   N7  C8  N9    0.00  0.0  0
 PM6  CONST_05  N7   C8  N9  C4    0.00  0.0  0
 PM6  CONST_06  N1   C2  N3  C4    0.00  0.0  0
 PM6  CONST_07  N1   C6  C5  C4    0.00  0.0  0
 PM6  CONST_08  C8   N7  C5  C4    0.00  0.0  0
 PM6  CONST_09  C8   N9  C4  N3  180.00  0.0  0
 PM6  CONST_10  C6   C5  C4  N3    0.00  0.0  0
 PM6  CONST_11  N7   C5  C4  N3  180.00  0.0  0
 PM6  CONST_12  C6   N1  C2  N3    0.00  0.0  0
 PM6  CONST_13  C5   C4  N3  C2    0.00  0.0  0
 PM6  CONST_14  C5   C6  N1  C2    0.00  0.0  0
 PM6  CONST_15  N7   C5  C6  N1  180.00  0.0  0
 PM6  CONST_16  C8   N7  C5  C6  180.00  0.0  0
 PM6  CONST_17  C8   N9  C4  C5    0.00  0.0  0
 PM6  CONST_18  S6   C6  C5  C4  180.00  0.0  0
 PM6  CONST_19  S6   C6  N1  C2  180.00  0.0  0
 PM6  CONST_20  S6   C6  C5  N7    0.00  0.0  0
 PM6  CONST_21  H8   C8  N9  C4  180.00  0.0  0
 PM6  CONST_22  H2   C2  N3  C4  180.00  0.0  0
 PM6  CONST_23  HN9  N9  C4  N3    0.00  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
 PM6  plan-1  N9   0.020
 PM6  plan-1  C4   0.020
 PM6  plan-1  N3   0.020
 PM6  plan-1  C2   0.020
 PM6  plan-1  N1   0.020
 PM6  plan-1  C6   0.020
 PM6  plan-1  C5   0.020
 PM6  plan-1  N7   0.020
 PM6  plan-1  C8   0.020
 PM6  plan-1  S6   0.020
 PM6  plan-1  HN9  0.020
 PM6  plan-1  H2   0.020
 PM6  plan-1  H8   0.020

