# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:29:11 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: [2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cn1c2ccccc2nc1c3cscn3
#
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
 9BY  9BY  '[2-(1,3-thiazol-4-yl)-1H-benzimidazol-1-yl]acetic acid'  ligand  27  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9BY
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
 9BY  N3   N  N     0  -0.386   2.2184   0.5291  -0.1959
 9BY  C4   C  CR56  0   0.347  -2.0139  -0.0844  -0.3077
 9BY  N2   N  NR5   0  -0.557  -0.7187   0.3470  -0.4599
 9BY  C7   C  CR5   0   0.473   0.0827  -0.6928  -0.0753
 9BY  C6   C  CR16  0  -0.340  -3.0632  -2.1534   0.3976
 9BY  C9   C  C     0   0.554   0.1176   2.5114   0.2844
 9BY  C1   C  CR16  0  -0.271  -4.2855  -1.5457   0.1806
 9BY  C2   C  CR16  0  -0.273  -4.3710  -0.2211  -0.2756
 9BY  C3   C  CR16  0  -0.315  -3.2392   0.5340  -0.5292
 9BY  C5   C  CR56  0   0.145  -1.9109  -1.4074   0.1479
 9BY  N1   N  N     0  -0.480  -0.5933  -1.7516   0.2830
 9BY  O1   O  OH1   0  -0.588   0.6490   3.6464  -0.1367
 9BY  O2   O  O     0  -0.431  -0.0260   2.2060   1.4375
 9BY  C10  C  CR5   0   0.277   1.5376  -0.6478  -0.0649
 9BY  C11  C  CR15  0  -0.533   2.3225  -1.7542   0.0927
 9BY  S1   S  S2    0   0.258   3.9637  -1.3005   0.0766
 9BY  C12  C  CR15  0  -0.220   3.4942   0.3372  -0.1412
 9BY  H1   H  HCR6  0   0.256  -2.9963  -3.1752   0.7485
 9BY  H2   H  HCH2  0   0.319   0.4455   1.6191  -1.6431
 9BY  H3   H  HCH2  0   0.321  -1.1939   2.1445  -1.3537
 9BY  H4   H  HCR6  0   0.255  -5.1975  -2.0981   0.3653
 9BY  H5   H  HCR6  0   0.258  -5.3455   0.2217  -0.4329
 9BY  H6   H  HCR6  0   0.271  -3.3212   1.5548  -0.8791
 9BY  H7   H  HOH1  0   0.487   0.9057   4.1985   0.6173
 9BY  H8   H  HCR5  0   0.314   2.0122  -2.7797   0.2108
 9BY  H9   H  HCR5  0   0.308   4.2289   1.1254  -0.2213
 9BY  C8   C  CH2   0  -0.452  -0.3330   1.6637  -0.8844

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
 9BY  S1   C11  aromatic  1.703  0.020  1.703
 9BY  S1   C12  aromatic  1.718  0.020  1.718
 9BY  C11  C10  aromatic  1.366  0.020  1.366
 9BY  C12  N3   aromatic  1.291  0.020  1.291
 9BY  C10  N3   aromatic  1.366  0.020  1.366
 9BY  C10  C7   single    1.456  0.020  1.456
 9BY  N1   C7   aromatic  1.306  0.020  1.306
 9BY  N1   C5   aromatic  1.369  0.020  1.369
 9BY  C7   N2   aromatic  1.368  0.020  1.368
 9BY  C5   C6   aromatic  1.395  0.020  1.395
 9BY  C5   C4   aromatic  1.403  0.020  1.403
 9BY  N2   C8   single    1.436  0.020  1.436
 9BY  N2   C4   aromatic  1.374  0.020  1.374
 9BY  C6   C1   aromatic  1.382  0.020  1.382
 9BY  O2   C9   double    1.201  0.020  1.201
 9BY  C8   C9   single    1.513  0.020  1.513
 9BY  C4   C3   aromatic  1.390  0.020  1.390
 9BY  C9   O1   single    1.322  0.020  1.322
 9BY  C1   C2   aromatic  1.404  0.020  1.404
 9BY  C3   C2   aromatic  1.384  0.020  1.384
 9BY  C6   H1   single    0.930  0.020  1.080
 9BY  C8   H2   single    0.970  0.020  1.090
 9BY  C8   H3   single    0.970  0.020  1.090
 9BY  C1   H4   single    0.930  0.020  1.080
 9BY  C2   H5   single    0.930  0.020  1.080
 9BY  C3   H6   single    0.930  0.020  1.080
 9BY  O1   H7   single    0.850  0.020  0.980
 9BY  C11  H8   single    0.930  0.020  1.080
 9BY  C12  H9   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
 9BY  C12  N3   C10  111.12  3.000
 9BY  C5   C4   C3   122.40  3.000
 9BY  C3   C4   N2   132.35  3.000
 9BY  C5   C4   N2   105.24  3.000
 9BY  C8   N2   C7   128.51  3.000
 9BY  C8   N2   C4   125.03  3.000
 9BY  C7   N2   C4   106.41  3.000
 9BY  C10  C7   N1   122.71  3.000
 9BY  N1   C7   N2   112.96  3.000
 9BY  C10  C7   N2   124.33  3.000
 9BY  H1   C6   C5   120.78  3.000
 9BY  H1   C6   C1   121.37  3.000
 9BY  C5   C6   C1   117.85  3.000
 9BY  O2   C9   O1   124.89  3.000
 9BY  O1   C9   C8   110.78  3.000
 9BY  O2   C9   C8   124.30  3.000
 9BY  H4   C1   C2   119.07  3.000
 9BY  H4   C1   C6   119.61  3.000
 9BY  C2   C1   C6   121.32  3.000
 9BY  H5   C2   C3   119.12  3.000
 9BY  H5   C2   C1   119.23  3.000
 9BY  C3   C2   C1   121.64  3.000
 9BY  H6   C3   C2   120.79  3.000
 9BY  H6   C3   C4   122.54  3.000
 9BY  C2   C3   C4   116.67  3.000
 9BY  N1   C5   C6   130.02  3.000
 9BY  C6   C5   C4   120.11  3.000
 9BY  N1   C5   C4   109.87  3.000
 9BY  C5   N1   C7   105.50  3.000
 9BY  H7   O1   C9   110.35  3.000
 9BY  C11  C10  C7   123.38  3.000
 9BY  C7   C10  N3   121.61  3.000
 9BY  C11  C10  N3   115.00  3.000
 9BY  H8   C11  S1   122.14  3.000
 9BY  H8   C11  C10  128.16  3.000
 9BY  S1   C11  C10  109.70  3.000
 9BY  C12  S1   C11   89.53  3.000
 9BY  H9   C12  S1   121.27  3.000
 9BY  H9   C12  N3   124.07  3.000
 9BY  S1   C12  N3   114.66  3.000
 9BY  H3   C8   H2   106.40  3.000
 9BY  H3   C8   C9   108.67  3.000
 9BY  H2   C8   C9   110.41  3.000
 9BY  H3   C8   N2   108.60  3.000
 9BY  H2   C8   N2   111.14  3.000
 9BY  C9   C8   N2   111.43  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
 9BY  CONST_01  C11  S1   C12  N3     0.00   0.0  0
 9BY  CONST_02  S1   C11  C10  N3     0.00   0.0  0
 9BY  CONST_03  N1   C7   C10  N3   180.00   0.0  0
 9BY  CONST_04  N2   C7   C10  N3     0.00   0.0  0
 9BY  CONST_05  C7   N1   C5   C4     0.00   0.0  0
 9BY  CONST_06  C1   C6   C5   C4     0.00   0.0  0
 9BY  CONST_07  C10  C7   N2   C4   180.00   0.0  0
 9BY  CONST_08  N1   C7   N2   C4     0.00   0.0  0
 9BY  CONST_09  C1   C2   C3   C4     0.00   0.0  0
 9BY  CONST_10  C11  C10  C7   N2   180.00   0.0  0
 9BY  CONST_11  C5   N1   C7   N2     0.00   0.0  0
 9BY  CONST_12  N1   C5   C4   N2     0.00   0.0  0
 9BY  CONST_13  C6   C5   C4   N2   180.00   0.0  0
 9BY  CONST_14  C2   C3   C4   N2   180.00   0.0  0
 9BY  CONST_15  S1   C11  C10  C7   180.00   0.0  0
 9BY  CONST_16  C12  N3   C10  C7   180.00   0.0  0
 9BY  CONST_17  C6   C5   N1   C7   180.00   0.0  0
 9BY  CONST_18  C5   C4   N2   C7     0.00   0.0  0
 9BY  CONST_19  C3   C4   N2   C7   180.00   0.0  0
 9BY  CONST_20  C3   C4   C5   C6     0.00   0.0  0
 9BY  CONST_21  C3   C2   C1   C6     0.00   0.0  0
 9BY  CONST_22  N1   C5   C6   C1   180.00   0.0  0
 9BY  CONST_23  C5   C6   C1   C2     0.00   0.0  0
 9BY  CONST_24  C5   C4   C3   C2     0.00   0.0  0
 9BY  CONST_25  N1   C5   C4   C3   180.00   0.0  0
 9BY  CONST_26  C10  C7   N1   C5   180.00   0.0  0
 9BY  CONST_27  C11  C10  C7   N1     0.00   0.0  0
 9BY  CONST_28  C12  S1   C11  C10    0.00   0.0  0
 9BY  CONST_29  S1   C12  N3   C10    0.00   0.0  0
 9BY  CONST_30  C12  N3   C10  C11    0.00   0.0  0
 9BY  CONST_31  C10  C7   N2   C8     0.00   0.0  0
 9BY  CONST_32  N1   C7   N2   C8   180.00   0.0  0
 9BY  CONST_33  C5   C4   N2   C8   180.00   0.0  0
 9BY  CONST_34  C3   C4   N2   C8     0.00   0.0  0
 9BY  CONST_35  H8   C11  C10  N3   180.00   0.0  0
 9BY  CONST_36  H1   C6   C5   C4   180.00   0.0  0
 9BY  CONST_37  H5   C2   C3   C4   180.00   0.0  0
 9BY  CONST_38  H6   C3   C4   N2     0.00   0.0  0
 9BY  CONST_39  H4   C1   C2   C3   180.00   0.0  0
 9BY  CONST_40  H9   C12  N3   C10  180.00   0.0  0
 9BY  CONST_41  H7   O1   C9   C8   180.00   0.0  0
 9BY  Var_01    C9   C8   N2   C4   102.24  30.0  2
 9BY  Var_02    O2   C9   C8   N2   -11.02  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
 9BY  plan-1  N3   0.020
 9BY  plan-1  C7   0.020
 9BY  plan-1  C10  0.020
 9BY  plan-1  C11  0.020
 9BY  plan-1  S1   0.020
 9BY  plan-1  C12  0.020
 9BY  plan-1  H8   0.020
 9BY  plan-1  H9   0.020
 9BY  plan-2  C4   0.020
 9BY  plan-2  N2   0.020
 9BY  plan-2  C7   0.020
 9BY  plan-2  C6   0.020
 9BY  plan-2  C1   0.020
 9BY  plan-2  C2   0.020
 9BY  plan-2  C3   0.020
 9BY  plan-2  C5   0.020
 9BY  plan-2  N1   0.020
 9BY  plan-2  C10  0.020
 9BY  plan-2  H1   0.020
 9BY  plan-2  H4   0.020
 9BY  plan-2  H5   0.020
 9BY  plan-2  H6   0.020
 9BY  plan-2  C8   0.020
 9BY  plan-3  C9   0.020
 9BY  plan-3  O1   0.020
 9BY  plan-3  O2   0.020
 9BY  plan-3  H7   0.020
 9BY  plan-3  C8   0.020

