# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 22:18:57 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: 2-(methylsulfanyl)-5-(thiophen-2-ylmethyl)-1H-imidazol-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1[nH]c(Cc2sccc2)c(O)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
 ZYT  ZYT  2-(methylsulfanyl)-5-(thiophen-2-ylmethyl)-1H-imidazol-4-ol  ligand  24  14  .  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_ZYT
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
 ZYT  CAA   C  CH3   0  -0.760   4.5702  -0.1679   1.1132
 ZYT  SAI   S  S2    0   0.033   3.5134  -1.2200   0.0968
 ZYT  CAL   C  CR5   0   0.294   2.1813  -0.1278  -0.1879
 ZYT  NAG   N  NR15  0  -0.639   1.0444  -0.5375  -0.7719
 ZYT  NAH   N  N     0  -0.482   2.1470   1.1543   0.0898
 ZYT  CAM   C  CR5   0   0.302   0.9301   1.5766  -0.3397
 ZYT  OAB   O  OH1   0  -0.633   0.5210   2.8487  -0.2066
 ZYT  CAN   C  CR5   0   0.195   0.2096   0.5601  -0.8961
 ZYT  CAC   C  CH2   0  -0.607  -1.1737   0.4939  -1.4414
 ZYT  CAK   C  CR5   0  -0.114  -2.2140   0.1895  -0.4033
 ZYT  CAF   C  CR15  0  -0.243  -3.2849   0.9473  -0.0379
 ZYT  CAD   C  CR15  0  -0.181  -4.0639   0.3560   0.9972
 ZYT  CAE   C  CR15  0  -0.473  -3.5694  -0.8438   1.4024
 ZYT  SAJ   S  S2    0   0.196  -2.1524  -1.2617   0.5273
 ZYT  HAA1  H  HCH3  0   0.283   5.4559  -0.7584   1.3363
 ZYT  HAA2  H  HCH3  0   0.278   4.8630   0.7286   0.5736
 ZYT  HAA3  H  HCH3  0   0.277   4.0741   0.1022   2.0417
 ZYT  HAG   H  HNR5  0   0.418   0.8395  -1.4710  -1.0931
 ZYT  HAB   H  HOH1  0   0.472   1.2535   3.3790   0.1273
 ZYT  HAC1  H  HCH2  0   0.283  -1.4265   1.4542  -1.8937
 ZYT  HAC2  H  HCH2  0   0.283  -1.2203  -0.2413  -2.2506
 ZYT  HAF   H  HCR5  0   0.261  -3.5079   1.9039  -0.4908
 ZYT  HAD   H  HCR5  0   0.264  -4.9494   0.8086   1.4203
 ZYT  HAE   H  HCR5  0   0.293  -3.9555  -1.5024   2.1650

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
 ZYT  CAA  SAI   single    1.805  0.020  1.805
 ZYT  SAI  CAL   single    1.746  0.020  1.746
 ZYT  CAL  NAG   aromatic  1.342  0.020  1.342
 ZYT  CAL  NAH   aromatic  1.312  0.020  1.312
 ZYT  NAG  CAN   aromatic  1.385  0.020  1.385
 ZYT  NAH  CAM   aromatic  1.358  0.020  1.358
 ZYT  CAM  OAB   single    1.343  0.020  1.343
 ZYT  CAM  CAN   aromatic  1.365  0.020  1.365
 ZYT  CAN  CAC   single    1.488  0.020  1.488
 ZYT  CAC  CAK   single    1.501  0.020  1.501
 ZYT  CAK  CAF   aromatic  1.362  0.020  1.362
 ZYT  CAK  SAJ   aromatic  1.725  0.020  1.725
 ZYT  CAF  CAD   aromatic  1.424  0.020  1.424
 ZYT  CAD  CAE   aromatic  1.360  0.020  1.360
 ZYT  CAE  SAJ   aromatic  1.717  0.020  1.717
 ZYT  CAA  HAA1  single    0.970  0.020  1.090
 ZYT  CAA  HAA2  single    0.970  0.020  1.090
 ZYT  CAA  HAA3  single    0.970  0.020  1.090
 ZYT  NAG  HAG   single    0.860  0.020  1.020
 ZYT  OAB  HAB   single    0.850  0.020  0.980
 ZYT  CAC  HAC1  single    0.970  0.020  1.090
 ZYT  CAC  HAC2  single    0.970  0.020  1.090
 ZYT  CAF  HAF   single    0.930  0.020  1.080
 ZYT  CAD  HAD   single    0.930  0.020  1.080
 ZYT  CAE  HAE   single    0.930  0.020  1.080

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
 ZYT  HAA3  CAA  HAA2  110.01  3.000
 ZYT  HAA3  CAA  HAA1  109.36  3.000
 ZYT  HAA2  CAA  HAA1  109.30  3.000
 ZYT  HAA3  CAA  SAI   111.02  3.000
 ZYT  HAA2  CAA  SAI   111.05  3.000
 ZYT  HAA1  CAA  SAI   106.01  3.000
 ZYT  CAL   SAI  CAA   100.01  3.000
 ZYT  NAH   CAL  NAG   111.60  3.000
 ZYT  NAH   CAL  SAI   126.63  3.000
 ZYT  NAG   CAL  SAI   121.75  3.000
 ZYT  HAG   NAG  CAN   125.65  3.000
 ZYT  HAG   NAG  CAL   126.40  3.000
 ZYT  CAN   NAG  CAL   107.92  3.000
 ZYT  CAM   NAH  CAL   105.09  3.000
 ZYT  CAN   CAM  OAB   125.82  3.000
 ZYT  CAN   CAM  NAH   111.75  3.000
 ZYT  OAB   CAM  NAH   122.43  3.000
 ZYT  HAB   OAB  CAM   108.90  3.000
 ZYT  CAC   CAN  CAM   132.32  3.000
 ZYT  CAC   CAN  NAG   123.91  3.000
 ZYT  CAM   CAN  NAG   103.62  3.000
 ZYT  HAC2  CAC  HAC1  105.96  3.000
 ZYT  HAC2  CAC  CAK   110.22  3.000
 ZYT  HAC1  CAC  CAK   107.73  3.000
 ZYT  HAC2  CAC  CAN   109.90  3.000
 ZYT  HAC1  CAC  CAN   109.15  3.000
 ZYT  CAK   CAC  CAN   113.56  3.000
 ZYT  SAJ   CAK  CAF   110.58  3.000
 ZYT  SAJ   CAK  CAC   121.27  3.000
 ZYT  CAF   CAK  CAC   128.15  3.000
 ZYT  HAF   CAF  CAD   123.97  3.000
 ZYT  HAF   CAF  CAK   122.82  3.000
 ZYT  CAD   CAF  CAK   113.21  3.000
 ZYT  HAD   CAD  CAE   123.43  3.000
 ZYT  HAD   CAD  CAF   123.98  3.000
 ZYT  CAE   CAD  CAF   112.59  3.000
 ZYT  HAE   CAE  SAJ   120.46  3.000
 ZYT  HAE   CAE  CAD   128.25  3.000
 ZYT  SAJ   CAE  CAD   111.29  3.000
 ZYT  CAE   SAJ  CAK    92.33  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
 ZYT  CONST_01  CAM   CAN  NAG  CAL     0.00   0.0  0
 ZYT  CONST_02  CAN   CAM  NAH  CAL     0.00   0.0  0
 ZYT  CONST_03  CAM   NAH  CAL  NAG     0.00   0.0  0
 ZYT  CONST_04  NAH   CAM  CAN  NAG     0.00   0.0  0
 ZYT  CONST_05  CAN   NAG  CAL  NAH     0.00   0.0  0
 ZYT  CONST_06  CAE   CAD  CAF  CAK     0.00   0.0  0
 ZYT  CONST_07  CAD   CAE  SAJ  CAK     0.00   0.0  0
 ZYT  CONST_08  CAE   SAJ  CAK  CAF     0.00   0.0  0
 ZYT  CONST_09  SAJ   CAE  CAD  CAF     0.00   0.0  0
 ZYT  CONST_10  SAJ   CAK  CAF  CAD     0.00   0.0  0
 ZYT  CONST_11  CAN   NAG  CAL  SAI   180.00   0.0  0
 ZYT  CONST_12  CAM   NAH  CAL  SAI   180.00   0.0  0
 ZYT  CONST_13  CAC   CAN  NAG  CAL   180.00   0.0  0
 ZYT  CONST_14  OAB   CAM  NAH  CAL   180.00   0.0  0
 ZYT  CONST_15  OAB   CAM  CAN  NAG   180.00   0.0  0
 ZYT  CONST_16  CAC   CAN  CAM  NAH   180.00   0.0  0
 ZYT  CONST_17  CAD   CAF  CAK  CAC   180.00   0.0  0
 ZYT  CONST_18  CAE   SAJ  CAK  CAC   180.00   0.0  0
 ZYT  CONST_19  HAG   NAG  CAL  NAH   180.00   0.0  0
 ZYT  CONST_20  HAD   CAD  CAF  CAK   180.00   0.0  0
 ZYT  CONST_21  HAE   CAE  SAJ  CAK   180.00   0.0  0
 ZYT  CONST_22  HAF   CAF  CAD  CAE   180.00   0.0  0
 ZYT  Var_01    CAK   CAC  CAN  NAG    87.89  30.0  2
 ZYT  Var_02    CAF   CAK  CAC  CAN   120.04  30.0  2
 ZYT  Var_03    NAG   CAL  SAI  CAA  -171.20  30.0  2
 ZYT  Var_04    HAA1  CAA  SAI  CAL  -179.00  30.0  3

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
 ZYT  plan-1  SAI  0.020
 ZYT  plan-1  CAL  0.020
 ZYT  plan-1  NAG  0.020
 ZYT  plan-1  NAH  0.020
 ZYT  plan-1  CAM  0.020
 ZYT  plan-1  OAB  0.020
 ZYT  plan-1  CAN  0.020
 ZYT  plan-1  CAC  0.020
 ZYT  plan-1  HAG  0.020
 ZYT  plan-2  CAC  0.020
 ZYT  plan-2  CAK  0.020
 ZYT  plan-2  CAF  0.020
 ZYT  plan-2  CAD  0.020
 ZYT  plan-2  CAE  0.020
 ZYT  plan-2  SAJ  0.020
 ZYT  plan-2  HAF  0.020
 ZYT  plan-2  HAD  0.020
 ZYT  plan-2  HAE  0.020

