# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 13:28:03 2020
#   Inital geometry file: a 34 line input string
#   Ligand name: 5-methyl-4H-1,2,4-triazole-3-thiol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(S)nn1
#
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
 YY1  YY1  5-methyl-4H-1,2,4-triazole-3-thiol  ligand  12  7  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_YY1
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
 YY1  CAG  C  CH3   0  -0.741   2.8937  -0.7099  -0.0026
 YY1  CAE  C  CR5   0   0.411   1.5516  -0.0853  -0.0480
 YY1  NAA  N  NR15  0  -0.585   0.3896  -0.7600   0.0848
 YY1  NAD  N  N     0  -0.335   1.2903   1.1855  -0.2129
 YY1  NAC  N  N     0  -0.295  -0.0542   1.3481  -0.1775
 YY1  CAB  C  CR5   0   0.196  -0.5870   0.1748   0.0051
 YY1  SAF  S  S2    0  -0.148  -2.2987  -0.1708   0.0379
 YY1  H1   H  HCH3  0   0.268   3.0728  -1.1839   0.9626
 YY1  H2   H  HCH3  0   0.267   3.0003  -1.4736  -0.7729
 YY1  H3   H  HCH3  0   0.267   3.6556   0.0492  -0.1602
 YY1  H4   H  HNR5  0   0.437   0.2688  -1.7539   0.2110
 YY1  H5   H  HSH1  0   0.258  -2.3879  -0.4732   1.3404

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
 YY1  CAG  CAE  single    1.481  0.020  1.481
 YY1  CAE  NAD  aromatic  1.308  0.020  1.308
 YY1  CAE  NAA  aromatic  1.350  0.020  1.350
 YY1  NAD  NAC  aromatic  1.355  0.020  1.355
 YY1  NAC  CAB  aromatic  1.302  0.020  1.302
 YY1  NAA  CAB  aromatic  1.354  0.020  1.354
 YY1  CAB  SAF  single    1.747  0.020  1.747
 YY1  CAG  H1   single    0.970  0.020  1.090
 YY1  CAG  H2   single    0.970  0.020  1.090
 YY1  CAG  H3   single    0.970  0.020  1.090
 YY1  NAA  H4   single    0.860  0.020  1.020
 YY1  SAF  H5   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
 YY1  H3   CAG  H2   108.56  3.000
 YY1  H3   CAG  H1   108.47  3.000
 YY1  H2   CAG  H1   107.76  3.000
 YY1  H3   CAG  CAE  109.64  3.000
 YY1  H2   CAG  CAE  111.25  3.000
 YY1  H1   CAG  CAE  111.06  3.000
 YY1  NAD  CAE  NAA  109.02  3.000
 YY1  NAA  CAE  CAG  124.48  3.000
 YY1  NAD  CAE  CAG  126.50  3.000
 YY1  H4   NAA  CAB  126.94  3.000
 YY1  H4   NAA  CAE  127.40  3.000
 YY1  CAB  NAA  CAE  105.66  3.000
 YY1  NAC  NAD  CAE  108.16  3.000
 YY1  CAB  NAC  NAD  107.56  3.000
 YY1  SAF  CAB  NAC  125.61  3.000
 YY1  SAF  CAB  NAA  124.69  3.000
 YY1  NAC  CAB  NAA  109.59  3.000
 YY1  H5   SAF  CAB   97.36  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
 YY1  CONST_01  CAB  NAC  NAD  CAE    0.00   0.0  0
 YY1  CONST_02  NAC  CAB  NAA  CAE    0.00   0.0  0
 YY1  CONST_03  NAC  NAD  CAE  NAA    0.00   0.0  0
 YY1  CONST_04  NAD  NAC  CAB  NAA    0.00   0.0  0
 YY1  CONST_05  CAB  NAA  CAE  NAD    0.00   0.0  0
 YY1  CONST_06  NAC  NAD  CAE  CAG  180.00   0.0  0
 YY1  CONST_07  CAB  NAA  CAE  CAG  180.00   0.0  0
 YY1  CONST_08  SAF  CAB  NAA  CAE  180.00   0.0  0
 YY1  CONST_09  SAF  CAB  NAC  NAD  180.00   0.0  0
 YY1  CONST_10  H4   NAA  CAE  NAD  180.00   0.0  0
 YY1  Var_01    H1   CAG  CAE  NAA  -61.56  30.0  2

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
 YY1  plan-1  CAG  0.020
 YY1  plan-1  CAE  0.020
 YY1  plan-1  NAA  0.020
 YY1  plan-1  NAD  0.020
 YY1  plan-1  NAC  0.020
 YY1  plan-1  CAB  0.020
 YY1  plan-1  SAF  0.020
 YY1  plan-1  H4   0.020

