# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 07:19:19 2021
#   Inital geometry file: a 43 line input string
#   Ligand name: 6-azanyl-9~{H}-purine-8-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ncnc2[nH]c(S)nc12
#
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
 KB5  KB5  6-azanyl-9~{H}-purine-8-thiol  ligand  16  11  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KB5
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
 KB5  C4  C  CR56  0   0.003  89.1336  69.4419  57.1736
 KB5  N3  N  NR15  0  -0.667  91.0177  68.7037  56.3642
 KB5  C2  C  CR56  0   0.475  89.9481  68.3213  57.1196
 KB5  N1  N  N     0  -0.469  87.6903  68.1312  58.4865
 KB5  C3  C  CR5   0   0.251  90.8006  70.0035  56.0095
 KB5  N4  N  N     0  -0.443  89.6846  70.4862  56.4715
 KB5  C   C  CR6   0   0.440  87.9412  69.3102  57.9048
 KB5  N   N  NH2   0  -0.819  87.0668  70.3094  58.0497
 KB5  N2  N  N     0  -0.449  89.7135  67.1437  57.6910
 KB5  C1  C  CR16  0   0.038  88.5674  67.1415  58.3518
 KB5  H1  H  HNR5  0   0.430  91.8101  68.1295  56.1171
 KB5  H3  H  HNH2  0   0.402  86.1939  70.1493  58.5222
 KB5  H4  H  HNH2  0   0.410  87.1865  71.1763  57.5561
 KB5  H5  H  HCR6  0   0.252  88.3052  66.2140  58.8496
 KB5  H6  H  HSH1  0   0.270  91.3219  72.0128  55.0421
 KB5  S   S  S2    0  -0.124  91.9713  70.8443  55.0271

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
 KB5  S   C3  single    1.744  0.020  1.744
 KB5  C3  N4  aromatic  1.301  0.020  1.301
 KB5  C3  N3  aromatic  1.365  0.020  1.365
 KB5  N4  C4  aromatic  1.374  0.020  1.374
 KB5  N3  C2  aromatic  1.364  0.020  1.364
 KB5  C4  C2  aromatic  1.386  0.020  1.386
 KB5  C4  C   aromatic  1.405  0.020  1.405
 KB5  C2  N2  aromatic  1.330  0.020  1.330
 KB5  N2  C1  aromatic  1.323  0.020  1.323
 KB5  N   C   single    1.336  0.020  1.336
 KB5  C   N1  aromatic  1.338  0.020  1.338
 KB5  C1  N1  aromatic  1.329  0.020  1.329
 KB5  N3  H1  single    0.860  0.020  1.020
 KB5  N   H3  single    0.860  0.020  1.020
 KB5  N   H4  single    0.860  0.020  1.020
 KB5  C1  H5  single    0.930  0.020  1.080
 KB5  S   H6  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
 KB5  C   C4  N4  132.67  3.000
 KB5  C   C4  C2  116.30  3.000
 KB5  N4  C4  C2  111.04  3.000
 KB5  H1  N3  C3  127.09  3.000
 KB5  H1  N3  C2  126.27  3.000
 KB5  C3  N3  C2  106.63  3.000
 KB5  N2  C2  N3  128.65  3.000
 KB5  N2  C2  C4  126.55  3.000
 KB5  N3  C2  C4  104.81  3.000
 KB5  C1  N1  C   119.22  3.000
 KB5  N4  C3  S   126.66  3.000
 KB5  N4  C3  N3  113.43  3.000
 KB5  S   C3  N3  119.92  3.000
 KB5  C3  N4  C4  104.10  3.000
 KB5  N   C   N1  119.28  3.000
 KB5  N1  C   C4  117.90  3.000
 KB5  N   C   C4  122.81  3.000
 KB5  H4  N   H3  118.15  3.000
 KB5  H4  N   C   120.94  3.000
 KB5  H3  N   C   120.01  3.000
 KB5  C1  N2  C2  111.65  3.000
 KB5  H5  C1  N2  116.11  3.000
 KB5  H5  C1  N1  115.51  3.000
 KB5  N2  C1  N1  128.39  3.000
 KB5  H6  S   C3   95.11  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
 KB5  CONST_01  N3  C3  N4  C4    0.00  0.0  0
 KB5  CONST_02  C3  N3  C2  C4    0.00  0.0  0
 KB5  CONST_03  C1  N2  C2  C4    0.00  0.0  0
 KB5  CONST_04  C1  N1  C   C4    0.00  0.0  0
 KB5  CONST_05  N4  C4  C2  N3    0.00  0.0  0
 KB5  CONST_06  C   C4  C2  N3  180.00  0.0  0
 KB5  CONST_07  C1  N2  C2  N3  180.00  0.0  0
 KB5  CONST_08  N4  C3  N3  C2    0.00  0.0  0
 KB5  CONST_09  C3  N4  C4  C2    0.00  0.0  0
 KB5  CONST_10  N1  C   C4  C2    0.00  0.0  0
 KB5  CONST_11  N1  C1  N2  C2    0.00  0.0  0
 KB5  CONST_12  N4  C4  C   N1  180.00  0.0  0
 KB5  CONST_13  C   C4  N4  C3  180.00  0.0  0
 KB5  CONST_14  N2  C2  N3  C3  180.00  0.0  0
 KB5  CONST_15  N2  C2  C4  N4  180.00  0.0  0
 KB5  CONST_16  N2  C2  C4  C     0.00  0.0  0
 KB5  CONST_17  N2  C1  N1  C     0.00  0.0  0
 KB5  CONST_18  S   C3  N4  C4  180.00  0.0  0
 KB5  CONST_19  S   C3  N3  C2  180.00  0.0  0
 KB5  CONST_20  N   C   C4  C2  180.00  0.0  0
 KB5  CONST_21  N   C   C4  N4    0.00  0.0  0
 KB5  CONST_22  C1  N1  C   N   180.00  0.0  0
 KB5  CONST_23  H1  N3  C2  C4  180.00  0.0  0
 KB5  CONST_24  H5  C1  N2  C2  180.00  0.0  0
 KB5  CONST_25  H3  N   C   C4  180.00  0.0  0
 KB5  CONST_26  H4  N   C   C4    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
 KB5  plan-1  C4  0.020
 KB5  plan-1  N3  0.020
 KB5  plan-1  C2  0.020
 KB5  plan-1  N1  0.020
 KB5  plan-1  C3  0.020
 KB5  plan-1  N4  0.020
 KB5  plan-1  C   0.020
 KB5  plan-1  N   0.020
 KB5  plan-1  N2  0.020
 KB5  plan-1  C1  0.020
 KB5  plan-1  H1  0.020
 KB5  plan-1  H5  0.020
 KB5  plan-1  S   0.020
 KB5  plan-2  C   0.020
 KB5  plan-2  N   0.020
 KB5  plan-2  H3  0.020
 KB5  plan-2  H4  0.020

