# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 15:29:35 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: [3-(4-chlorophenyl)[1,3]thiazolo[3,2-a]benzimidazol-2-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)Cc1sc2nc3ccccc3n2c1c4ccc(Cl)cc4
#
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
 R2D  R2D  '[3-(4-chlorophenyl)[1,3]thiazolo[3,2-a]benzimidazol-2-yl]acetic acid'  ligand  34  23  .  2022-08-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_R2D
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
 R2D  C1   C   CR55  0   0.258  -2.8973  -20.1942  -36.4378
 R2D  C2   C   CR56  0   0.339  -5.0782  -20.2341  -36.7144
 R2D  C3   C   CR5   0  -0.316  -2.6465  -20.9971  -34.1211
 R2D  C4   C   CR6   0   0.008  -5.1080  -21.2201  -33.6524
 R2D  C6   C   CR56  0   0.121  -4.3880  -19.8065  -37.8685
 R2D  C7   C   CR16  0  -0.279  -6.4610  -20.3615  -36.6766
 R2D  C8   C   CH2   0  -0.699  -2.0949  -21.4010  -32.8029
 R2D  C9   C   CR16  0  -0.291  -6.0254  -20.2212  -33.3305
 R2D  C10  C   CR16  0  -0.281  -5.2988  -22.5061  -33.1562
 R2D  C11  C   CR16  0  -0.336  -5.1050  -19.4751  -39.0172
 R2D  C15  C   CR16  0  -0.193  -6.3872  -22.7974  -32.3480
 R2D  C16  C   CR16  0  -0.265  -6.4826  -19.5897  -38.9817
 R2D  O17  O   O     0  -0.427  -1.7487  -23.6161  -33.6808
 R2D  C18  C   CR6   0  -0.042  -7.2889  -21.7905  -32.0443
 R2D  N    N   N     0  -0.634  -4.0745  -20.4660  -35.7933
 R2D  C    C   CR5   0   0.545  -3.9395  -20.9166  -34.4879
 R2D  S    S   S2    0   0.259  -1.5527  -20.5087  -35.4046
 R2D  N5   N   N     0  -0.484  -3.0244  -19.7956  -37.6651
 R2D  C12  C   CR16  0  -0.278  -7.1500  -20.0298  -37.8307
 R2D  C13  C   C     0   0.569  -1.5609  -22.8161  -32.8016
 R2D  C14  C   CR16  0  -0.192  -7.1186  -20.5011  -32.5287
 R2D  O    O   OH1   0  -0.585  -0.8747  -23.0689  -31.6986
 R2D  CL   CL  CL    0  -0.115  -8.6521  -22.1446  -31.0404
 R2D  H1   H   HCR6  0   0.273  -6.9855  -20.7072  -35.7975
 R2D  H2   H   HCH2  0   0.321  -1.3071  -20.7160  -32.4790
 R2D  H3   H   HCH2  0   0.323  -2.8756  -21.3317  -32.0394
 R2D  H4   H   HCR6  0   0.284  -5.8857  -19.2124  -33.6977
 R2D  H5   H   HCR6  0   0.272  -4.5979  -23.2917  -33.4074
 R2D  H6   H   HCR6  0   0.260  -4.5918  -19.1412  -39.9094
 R2D  H7   H   HCR6  0   0.289  -6.5291  -23.7994  -31.9673
 R2D  H8   H   HCR6  0   0.258  -7.0599  -19.3368  -39.8614
 R2D  H9   H   HCR6  0   0.260  -8.2284  -20.1143  -37.8420
 R2D  H10  H   HCR6  0   0.289  -7.8248  -19.7210  -32.2798
 R2D  H11  H   HOH1  0   0.486  -0.5587  -23.9852  -31.7015

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
 R2D  C11  C16  aromatic  1.383  0.020  1.383
 R2D  C11  C6   aromatic  1.394  0.020  1.394
 R2D  C16  C12  aromatic  1.401  0.020  1.401
 R2D  C12  C7   aromatic  1.384  0.020  1.384
 R2D  C6   N5   aromatic  1.379  0.020  1.379
 R2D  C6   C2   aromatic  1.411  0.020  1.411
 R2D  N5   C1   aromatic  1.297  0.020  1.297
 R2D  C2   C7   aromatic  1.389  0.020  1.389
 R2D  C2   N    aromatic  1.382  0.020  1.382
 R2D  C1   N    aromatic  1.369  0.020  1.369
 R2D  C1   S    aromatic  1.725  0.020  1.725
 R2D  N    C    aromatic  1.388  0.020  1.388
 R2D  S    C3   aromatic  1.756  0.020  1.756
 R2D  C    C3   aromatic  1.346  0.020  1.346
 R2D  C    C4   single    1.468  0.020  1.468
 R2D  C3   C8   single    1.485  0.020  1.485
 R2D  C4   C9   aromatic  1.394  0.020  1.394
 R2D  C4   C10  aromatic  1.392  0.020  1.392
 R2D  O17  C13  double    1.203  0.020  1.203
 R2D  C9   C14  aromatic  1.384  0.020  1.384
 R2D  C10  C15  aromatic  1.387  0.020  1.387
 R2D  C13  C8   single    1.512  0.020  1.512
 R2D  C13  O    single    1.323  0.020  1.323
 R2D  C14  C18  aromatic  1.388  0.020  1.388
 R2D  C15  C18  aromatic  1.385  0.020  1.385
 R2D  C18  CL   single    1.730  0.020  1.730
 R2D  C7   H1   single    0.930  0.020  1.080
 R2D  C8   H2   single    0.970  0.020  1.090
 R2D  C8   H3   single    0.970  0.020  1.090
 R2D  C9   H4   single    0.930  0.020  1.080
 R2D  C10  H5   single    0.930  0.020  1.080
 R2D  C11  H6   single    0.930  0.020  1.080
 R2D  C15  H7   single    0.930  0.020  1.080
 R2D  C16  H8   single    0.930  0.020  1.080
 R2D  C12  H9   single    0.930  0.020  1.080
 R2D  C14  H10  single    0.930  0.020  1.080
 R2D  O    H11  single    0.850  0.020  0.980

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
 R2D  N5   C1   S    134.39  3.000
 R2D  S    C1   N    110.61  3.000
 R2D  N5   C1   N    114.98  3.000
 R2D  N    C2   C7   133.59  3.000
 R2D  N    C2   C6   103.93  3.000
 R2D  C7   C2   C6   122.47  3.000
 R2D  S    C3   C    112.49  3.000
 R2D  C    C3   C8   127.94  3.000
 R2D  S    C3   C8   119.55  3.000
 R2D  C    C4   C10  120.20  3.000
 R2D  C10  C4   C9   119.32  3.000
 R2D  C    C4   C9   120.47  3.000
 R2D  N5   C6   C11  128.93  3.000
 R2D  N5   C6   C2   111.44  3.000
 R2D  C11  C6   C2   119.63  3.000
 R2D  H1   C7   C12  120.88  3.000
 R2D  H1   C7   C2   122.32  3.000
 R2D  C12  C7   C2   116.80  3.000
 R2D  H3   C8   H2   105.53  3.000
 R2D  H3   C8   C13  108.09  3.000
 R2D  H2   C8   C13  109.37  3.000
 R2D  H3   C8   C3   109.70  3.000
 R2D  H2   C8   C3   111.12  3.000
 R2D  C13  C8   C3   112.73  3.000
 R2D  H4   C9   C14  119.13  3.000
 R2D  H4   C9   C4   120.30  3.000
 R2D  C14  C9   C4   120.57  3.000
 R2D  H5   C10  C15  119.41  3.000
 R2D  H5   C10  C4   119.95  3.000
 R2D  C15  C10  C4   120.64  3.000
 R2D  H6   C11  C16  121.28  3.000
 R2D  H6   C11  C6   120.58  3.000
 R2D  C16  C11  C6   118.14  3.000
 R2D  H7   C15  C18  120.73  3.000
 R2D  H7   C15  C10  120.19  3.000
 R2D  C18  C15  C10  119.08  3.000
 R2D  H8   C16  C12  119.14  3.000
 R2D  H8   C16  C11  119.42  3.000
 R2D  C12  C16  C11  121.44  3.000
 R2D  CL   C18  C14  119.31  3.000
 R2D  CL   C18  C15  119.44  3.000
 R2D  C14  C18  C15  121.26  3.000
 R2D  C    N    C2   138.78  3.000
 R2D  C    N    C1   115.07  3.000
 R2D  C2   N    C1   106.10  3.000
 R2D  N    C    C4   121.68  3.000
 R2D  C4   C    C3   126.65  3.000
 R2D  N    C    C3   111.66  3.000
 R2D  C3   S    C1    90.17  3.000
 R2D  C6   N5   C1   103.54  3.000
 R2D  H9   C12  C16  119.39  3.000
 R2D  H9   C12  C7   119.09  3.000
 R2D  C16  C12  C7   121.52  3.000
 R2D  O    C13  O17  124.25  3.000
 R2D  O    C13  C8   111.25  3.000
 R2D  O17  C13  C8   124.49  3.000
 R2D  H10  C14  C18  120.65  3.000
 R2D  H10  C14  C9   120.21  3.000
 R2D  C18  C14  C9   119.14  3.000
 R2D  H11  O    C13  110.31  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
 R2D  CONST_01  C11  C6   N5   C1   180.00   0.0  0
 R2D  CONST_02  C2   C6   N5   C1     0.00   0.0  0
 R2D  CONST_03  C6   C2   N    C1     0.00   0.0  0
 R2D  CONST_04  C7   C2   N    C1   180.00   0.0  0
 R2D  CONST_05  C3   C    N    C1     0.00   0.0  0
 R2D  CONST_06  C4   C    N    C1   180.00   0.0  0
 R2D  CONST_07  C    C3   S    C1     0.00   0.0  0
 R2D  CONST_08  C16  C11  C6   C2     0.00   0.0  0
 R2D  CONST_09  C16  C12  C7   C2     0.00   0.0  0
 R2D  CONST_10  N5   C1   N    C2     0.00   0.0  0
 R2D  CONST_11  S    C1   N    C2   180.00   0.0  0
 R2D  CONST_12  C3   C    N    C2   180.00   0.0  0
 R2D  CONST_13  C4   C    N    C2     0.00   0.0  0
 R2D  CONST_14  N5   C1   S    C3   180.00   0.0  0
 R2D  CONST_15  N    C1   S    C3     0.00   0.0  0
 R2D  CONST_18  S    C3   C    C4   180.00   0.0  0
 R2D  CONST_19  C18  C14  C9   C4     0.00   0.0  0
 R2D  CONST_20  C18  C15  C10  C4     0.00   0.0  0
 R2D  CONST_21  C12  C16  C11  C6     0.00   0.0  0
 R2D  CONST_22  N    C1   N5   C6     0.00   0.0  0
 R2D  CONST_23  S    C1   N5   C6   180.00   0.0  0
 R2D  CONST_24  C12  C7   C2   C6     0.00   0.0  0
 R2D  CONST_25  C    N    C2   C6   180.00   0.0  0
 R2D  CONST_26  C11  C16  C12  C7     0.00   0.0  0
 R2D  CONST_27  C11  C6   C2   C7     0.00   0.0  0
 R2D  CONST_28  N5   C6   C2   C7   180.00   0.0  0
 R2D  CONST_29  C    N    C2   C7     0.00   0.0  0
 R2D  CONST_31  C15  C10  C4   C9     0.00   0.0  0
 R2D  CONST_32  C15  C18  C14  C9     0.00   0.0  0
 R2D  CONST_34  C14  C9   C4   C10    0.00   0.0  0
 R2D  CONST_35  C14  C18  C15  C10    0.00   0.0  0
 R2D  CONST_36  N    C2   C6   C11  180.00   0.0  0
 R2D  CONST_37  C    C4   C10  C15  180.00   0.0  0
 R2D  CONST_38  N5   C6   C11  C16  180.00   0.0  0
 R2D  CONST_39  N5   C6   C2   N      0.00   0.0  0
 R2D  CONST_40  C12  C7   C2   N    180.00   0.0  0
 R2D  CONST_41  S    C3   C    N      0.00   0.0  0
 R2D  CONST_42  N5   C1   N    C    180.00   0.0  0
 R2D  CONST_43  S    C1   N    C      0.00   0.0  0
 R2D  CONST_44  C14  C9   C4   C    180.00   0.0  0
 R2D  CONST_45  C8   C3   S    C1   180.00   0.0  0
 R2D  CONST_46  C8   C3   C    C4     0.00   0.0  0
 R2D  CONST_47  N    C    C3   C8   180.00   0.0  0
 R2D  CONST_48  CL   C18  C14  C9   180.00   0.0  0
 R2D  CONST_49  CL   C18  C15  C10  180.00   0.0  0
 R2D  CONST_50  H6   C11  C6   C2   180.00   0.0  0
 R2D  CONST_51  H9   C12  C7   C2   180.00   0.0  0
 R2D  CONST_52  H10  C14  C9   C4   180.00   0.0  0
 R2D  CONST_53  H7   C15  C10  C4   180.00   0.0  0
 R2D  CONST_54  H8   C16  C11  C6   180.00   0.0  0
 R2D  CONST_55  H1   C7   C2   C6   180.00   0.0  0
 R2D  CONST_56  H5   C10  C4   C9   180.00   0.0  0
 R2D  CONST_57  H4   C9   C4   C10  180.00   0.0  0
 R2D  CONST_58  H11  O    C13  C8   180.00   0.0  0
 R2D  Var_01    C13  C8   C3   C    102.51  30.0  2
 R2D  Var_02    O17  C13  C8   C3   -11.68  30.0  1

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
 R2D  plan-1  C4   0.020
 R2D  plan-1  C9   0.020
 R2D  plan-1  C10  0.020
 R2D  plan-1  C15  0.020
 R2D  plan-1  C18  0.020
 R2D  plan-1  C    0.020
 R2D  plan-1  C14  0.020
 R2D  plan-1  CL   0.020
 R2D  plan-1  H4   0.020
 R2D  plan-1  H5   0.020
 R2D  plan-1  H7   0.020
 R2D  plan-1  H10  0.020
 R2D  plan-2  C1   0.020
 R2D  plan-2  C2   0.020
 R2D  plan-2  C3   0.020
 R2D  plan-2  C4   0.020
 R2D  plan-2  C6   0.020
 R2D  plan-2  C7   0.020
 R2D  plan-2  C8   0.020
 R2D  plan-2  C11  0.020
 R2D  plan-2  C16  0.020
 R2D  plan-2  N    0.020
 R2D  plan-2  C    0.020
 R2D  plan-2  S    0.020
 R2D  plan-2  N5   0.020
 R2D  plan-2  C12  0.020
 R2D  plan-2  H1   0.020
 R2D  plan-2  H6   0.020
 R2D  plan-2  H8   0.020
 R2D  plan-2  H9   0.020
 R2D  plan-3  C8   0.020
 R2D  plan-3  O17  0.020
 R2D  plan-3  C13  0.020
 R2D  plan-3  O    0.020
 R2D  plan-3  H11  0.020

