# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 11:57:36 2020
#   Inital geometry file: a 70 line input string
#   Ligand name: 3-[(2-methylbenzyl)sulfanyl]-4H-1,2,4-triazol-4-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccccc1CSc2nncn2N
#
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
 1YO  1YO  3-[(2-methylbenzyl)sulfanyl]-4H-1,2,4-triazol-4-amine  ligand  27  15  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1YO
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
 1YO  CAA  C  CH3   0  -0.747   1.8791   2.0927  -0.9572
 1YO  CAC  C  CR16  0  -0.248   4.5766  -0.4761  -0.2239
 1YO  CAD  C  CR16  0  -0.260   3.9329  -1.3312   0.6581
 1YO  CAE  C  CR16  0  -0.295   3.9017   0.6221  -0.7392
 1YO  CAF  C  CR16  0  -0.276   2.6166  -1.0760   1.0139
 1YO  CAG  C  CR15  0   0.090  -4.2426   0.2345   0.2044
 1YO  CAH  C  CH2   0  -0.639   0.5110   0.2548   0.9051
 1YO  CAL  C  CR6   0   0.087   2.5806   0.8919  -0.3914
 1YO  CAM  C  CR6   0   0.061   1.9372   0.0261   0.5035
 1YO  CAN  C  CR5   0   0.301  -2.1073  -0.0187   0.1825
 1YO  NAI  N  N     0  -0.320  -3.7699   0.8087   1.2655
 1YO  NAJ  N  N     0  -0.336  -2.4128   0.6498   1.2566
 1YO  NAO  N  NR5   0  -0.332  -3.2334  -0.3067  -0.5199
 1YO  SAK  S  S2    0   0.071  -0.5409  -0.5219  -0.3734
 1YO  HAC  H  HCH3  0   0.245   0.9472   1.8202  -1.4557
 1YO  HAA  H  HCH3  0   0.252   1.6246   2.8107  -0.1741
 1YO  HAB  H  HCH3  0   0.256   2.5088   2.6062  -1.6818
 1YO  HAD  H  HCR6  0   0.257   5.6035  -0.6605  -0.5119
 1YO  HAE  H  HCR6  0   0.257   4.4496  -2.1891   1.0678
 1YO  HAF  H  HCR6  0   0.251   4.4119   1.2857  -1.4270
 1YO  HAG  H  HCR6  0   0.256   2.1076  -1.7399   1.7031
 1YO  HAH  H  HCR5  0   0.307  -5.2764   0.1729  -0.0964
 1YO  HAI  H  HCH2  0   0.312   0.2864  -0.2069   1.8650
 1YO  HAJ  H  HCH2  0   0.305   0.2568   1.3121   0.9641
 1YO  HAL  H  HNC2  0   0.394  -2.8515  -0.5188  -2.4373
 1YO  HAK  H  HNC2  0   0.394  -3.0382  -1.9346  -1.6071
 1YO  NAB  N  NC2   0  -0.642  -3.3764  -0.9859  -1.7086

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
 1YO  NAB  NAO  single    1.377  0.020  1.377
 1YO  NAO  CAG  aromatic  1.355  0.020  1.355
 1YO  NAO  CAN  aromatic  1.358  0.020  1.358
 1YO  SAK  CAN  single    1.737  0.020  1.737
 1YO  SAK  CAH  single    1.829  0.020  1.829
 1YO  CAG  NAI  aromatic  1.296  0.020  1.296
 1YO  CAA  CAL  single    1.501  0.020  1.501
 1YO  CAN  NAJ  aromatic  1.302  0.020  1.302
 1YO  CAL  CAE  aromatic  1.392  0.020  1.392
 1YO  CAL  CAM  aromatic  1.402  0.020  1.402
 1YO  CAE  CAC  aromatic  1.388  0.020  1.388
 1YO  CAM  CAH  single    1.499  0.020  1.499
 1YO  CAM  CAF  aromatic  1.392  0.020  1.392
 1YO  CAC  CAD  aromatic  1.387  0.020  1.387
 1YO  NAI  NAJ  aromatic  1.366  0.020  1.366
 1YO  CAF  CAD  aromatic  1.387  0.020  1.387
 1YO  CAA  HAC  single    0.970  0.020  1.090
 1YO  CAA  HAA  single    0.970  0.020  1.090
 1YO  CAA  HAB  single    0.970  0.020  1.090
 1YO  CAC  HAD  single    0.930  0.020  1.080
 1YO  CAD  HAE  single    0.930  0.020  1.080
 1YO  CAE  HAF  single    0.930  0.020  1.080
 1YO  CAF  HAG  single    0.930  0.020  1.080
 1YO  CAG  HAH  single    0.930  0.020  1.080
 1YO  CAH  HAI  single    0.970  0.020  1.090
 1YO  CAH  HAJ  single    0.970  0.020  1.090
 1YO  NAB  HAL  single    0.890  0.020  1.040
 1YO  NAB  HAK  single    0.890  0.020  1.040

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
 1YO  HAB  CAA  HAA  107.57  3.000
 1YO  HAB  CAA  HAC  107.92  3.000
 1YO  HAA  CAA  HAC  107.01  3.000
 1YO  HAB  CAA  CAL  110.97  3.000
 1YO  HAA  CAA  CAL  111.37  3.000
 1YO  HAC  CAA  CAL  111.80  3.000
 1YO  HAD  CAC  CAE  119.82  3.000
 1YO  HAD  CAC  CAD  120.30  3.000
 1YO  CAE  CAC  CAD  119.88  3.000
 1YO  HAE  CAD  CAF  120.13  3.000
 1YO  HAE  CAD  CAC  120.53  3.000
 1YO  CAF  CAD  CAC  119.35  3.000
 1YO  HAF  CAE  CAL  119.13  3.000
 1YO  HAF  CAE  CAC  119.42  3.000
 1YO  CAL  CAE  CAC  121.45  3.000
 1YO  HAG  CAF  CAM  119.28  3.000
 1YO  HAG  CAF  CAD  119.74  3.000
 1YO  CAM  CAF  CAD  120.99  3.000
 1YO  HAH  CAG  NAO  122.83  3.000
 1YO  HAH  CAG  NAI  127.12  3.000
 1YO  NAO  CAG  NAI  110.05  3.000
 1YO  HAJ  CAH  HAI  108.41  3.000
 1YO  HAJ  CAH  SAK  108.42  3.000
 1YO  HAI  CAH  SAK  108.51  3.000
 1YO  HAJ  CAH  CAM  112.63  3.000
 1YO  HAI  CAH  CAM  111.58  3.000
 1YO  SAK  CAH  CAM  107.17  3.000
 1YO  CAM  CAL  CAE  118.38  3.000
 1YO  CAM  CAL  CAA  121.34  3.000
 1YO  CAE  CAL  CAA  120.27  3.000
 1YO  CAL  CAM  CAH  120.90  3.000
 1YO  CAH  CAM  CAF  119.14  3.000
 1YO  CAL  CAM  CAF  119.95  3.000
 1YO  SAK  CAN  NAO  121.39  3.000
 1YO  SAK  CAN  NAJ  128.66  3.000
 1YO  NAO  CAN  NAJ  109.94  3.000
 1YO  NAJ  NAI  CAG  107.79  3.000
 1YO  NAI  NAJ  CAN  107.35  3.000
 1YO  NAB  NAO  CAN  129.60  3.000
 1YO  CAN  NAO  CAG  104.86  3.000
 1YO  NAB  NAO  CAG  125.54  3.000
 1YO  CAN  SAK  CAH   99.90  3.000
 1YO  HAK  NAB  HAL  109.35  3.000
 1YO  HAK  NAB  NAO  109.94  3.000
 1YO  HAL  NAB  NAO  109.88  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
 1YO  CONST_01  CAM  CAL  CAE  CAC    0.00   0.0  0
 1YO  CONST_02  CAM  CAF  CAD  CAC    0.00   0.0  0
 1YO  CONST_03  CAL  CAE  CAC  CAD    0.00   0.0  0
 1YO  CONST_04  CAL  CAM  CAF  CAD    0.00   0.0  0
 1YO  CONST_05  CAF  CAM  CAL  CAE    0.00   0.0  0
 1YO  CONST_06  CAF  CAD  CAC  CAE    0.00   0.0  0
 1YO  CONST_07  NAJ  CAN  NAO  CAG    0.00   0.0  0
 1YO  CONST_08  CAN  NAJ  NAI  CAG    0.00   0.0  0
 1YO  CONST_09  NAI  CAG  NAO  CAN    0.00   0.0  0
 1YO  CONST_10  NAO  CAN  NAJ  NAI    0.00   0.0  0
 1YO  CONST_11  NAO  CAG  NAI  NAJ    0.00   0.0  0
 1YO  CONST_12  CAC  CAE  CAL  CAA  180.00   0.0  0
 1YO  CONST_13  CAF  CAM  CAL  CAA  180.00   0.0  0
 1YO  CONST_14  CAH  CAM  CAF  CAD  180.00   0.0  0
 1YO  CONST_15  CAH  CAM  CAL  CAE  180.00   0.0  0
 1YO  CONST_16  SAK  CAN  NAO  CAG  180.00   0.0  0
 1YO  CONST_17  NAI  CAG  NAO  NAB  180.00   0.0  0
 1YO  CONST_18  NAJ  CAN  NAO  NAB  180.00   0.0  0
 1YO  CONST_19  SAK  CAN  NAJ  NAI  180.00   0.0  0
 1YO  CONST_20  HAG  CAF  CAD  CAC  180.00   0.0  0
 1YO  CONST_21  HAF  CAE  CAC  CAD  180.00   0.0  0
 1YO  CONST_22  HAE  CAD  CAC  CAE  180.00   0.0  0
 1YO  CONST_23  HAD  CAC  CAD  CAF  180.00   0.0  0
 1YO  CONST_24  HAH  CAG  NAO  CAN  180.00   0.0  0
 1YO  Var_01    SAK  CAH  CAM  CAF  -93.92  30.0  2
 1YO  Var_02    NAO  CAN  SAK  CAH  176.16  30.0  2
 1YO  Var_03    HAC  CAA  CAL  CAE  125.04  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
 1YO  plan-1  CAG  0.020
 1YO  plan-1  CAN  0.020
 1YO  plan-1  NAI  0.020
 1YO  plan-1  NAJ  0.020
 1YO  plan-1  NAO  0.020
 1YO  plan-1  SAK  0.020
 1YO  plan-1  HAH  0.020
 1YO  plan-1  NAB  0.020
 1YO  plan-2  CAA  0.020
 1YO  plan-2  CAC  0.020
 1YO  plan-2  CAD  0.020
 1YO  plan-2  CAE  0.020
 1YO  plan-2  CAF  0.020
 1YO  plan-2  CAH  0.020
 1YO  plan-2  CAL  0.020
 1YO  plan-2  CAM  0.020
 1YO  plan-2  HAD  0.020
 1YO  plan-2  HAE  0.020
 1YO  plan-2  HAF  0.020
 1YO  plan-2  HAG  0.020
 1YO  plan-3  NAO  0.020
 1YO  plan-3  HAL  0.020
 1YO  plan-3  HAK  0.020
 1YO  plan-3  NAB  0.020

