# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 04:01:42 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 2-[2-[[3-(1~{H}-benzimidazol-2-ylamino)propylamino]methyl]-4,6-bis(chloranyl)indol-1-yl]ethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCn1c(CNCCCNc2[nH]c3ccccc3n2)cc4c(Cl)cc(Cl)cc14
#
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
 I53  I53  2-[2-[[3-(1~{H}-benzimidazol-2-ylamino)propylamino]methyl]-4,6-bis(chloranyl)indol-1-yl]ethanol  ligand  52  29  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I53
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
 I53  C1   C   CH2   0  -0.349    2.4224   1.8518  -0.8179
 I53  C2   C   CR5   0   0.367    2.5140  -0.6572  -1.1090
 I53  C3   C   CH2   0  -0.369    1.1185  -0.7891  -1.6125
 I53  C4   C   CH2   0  -0.249   -1.2114  -0.4471  -1.0754
 I53  C6   C   CH2   0  -0.277   -3.6192  -0.0906  -0.4537
 I53  C7   C   CR5   0   0.673   -5.8657   0.1840   0.4943
 I53  C8   C   CR56  0   0.160   -7.9594   0.3879   0.8397
 I53  C9   C   CR16  0  -0.352   -9.2306   0.6690   1.3315
 I53  C11  C   CR16  0  -0.290  -10.1782  -0.4399  -0.6134
 I53  C12  C   CR16  0  -0.315   -8.9163  -0.7319  -1.1205
 I53  C13  C   CR56  0   0.334   -7.8297  -0.3081  -0.3764
 I53  C14  C   CR15  0  -0.457    3.4315  -1.6498  -0.9088
 I53  C15  C   CR56  0   0.207    4.6132  -1.0292  -0.4198
 I53  C16  C   CR6   0  -0.198    5.8772  -1.4748  -0.0392
 I53  C17  C   CR16  0  -0.205    6.8387  -0.5894   0.3979
 I53  C18  C   CR6   0  -0.079    6.5273   0.7750   0.4525
 I53  C20  C   CR56  0   0.353    4.3470   0.3553  -0.3409
 I53  CL1  CL  CL    0  -0.127    7.7558   1.8708   1.0011
 I53  CL   CL  CL    0  -0.126    6.2328  -3.1652  -0.1231
 I53  C19  C   CR16  0  -0.269    5.2954   1.2796   0.0928
 I53  N    N   NR5   0  -0.577    3.0655   0.5576  -0.7668
 I53  C    C   CH2   0  -0.150    1.9271   2.2984   0.5495
 I53  O    O   OH1   0  -0.670    1.3904   3.5911   0.3910
 I53  N1   N   NH1   0  -0.581    0.1544  -0.4281  -0.5908
 I53  C5   C   CH2   0  -0.483   -2.1820  -0.0913   0.0382
 I53  N2   N   NH1   0  -0.687   -4.5243   0.2141   0.6356
 I53  N4   N   NR15  0  -0.739   -6.4706  -0.4173  -0.5691
 I53  N3   N   N     0  -0.538   -6.7207   0.6830   1.3574
 I53  C10  C   CR16  0  -0.273  -10.3297   0.2481   0.5931
 I53  H1   H   HCH2  0   0.261    3.1351   2.5759  -1.2189
 I53  H2   H   HCH2  0   0.277    1.5886   1.8054  -1.5165
 I53  H3   H   HCH2  0   0.251    0.9710  -0.1267  -2.4718
 I53  H4   H   HCH2  0   0.240    0.9928  -1.8126  -1.9921
 I53  H5   H   HCH2  0   0.224   -1.2966   0.2862  -1.8832
 I53  H6   H   HCH2  0   0.196   -1.4935  -1.4202  -1.5083
 I53  H7   H   HCH2  0   0.234   -3.7294   0.6221  -1.2803
 I53  H8   H   HCH2  0   0.237   -3.8600  -1.0816  -0.8479
 I53  H9   H   HCR6  0   0.245   -9.3585   1.2025   2.2651
 I53  H10  H   HCR6  0   0.247  -11.0565  -0.7507  -1.1640
 I53  H11  H   HCR6  0   0.260   -8.7947  -1.2678  -2.0531
 I53  H12  H   HCR5  0   0.258    3.2714  -2.6997  -1.0949
 I53  H13  H   HCR6  0   0.292    7.8175  -0.9384   0.6953
 I53  H14  H   HCR6  0   0.289    5.0888   2.3401   0.1473
 I53  H15  H   HCH2  0   0.214    1.1793   1.5791   0.8978
 I53  H16  H   HCH2  0   0.197    2.7580   2.2890   1.2665
 I53  H17  H   HOH1  0   0.459    1.0462   3.8809   1.2403
 I53  H18  H   HNH1  0   0.346    0.2437  -1.0763   0.1832
 I53  H20  H   HCH2  0   0.237   -2.0852  -0.8098   0.8576
 I53  H21  H   HCH2  0   0.239   -1.9232   0.8932   0.4382
 I53  H22  H   HNH1  0   0.395   -4.1948   0.8643   1.3321
 I53  H23  H   HNR5  0   0.422   -6.0163  -0.8672  -1.3472
 I53  H25  H   HCR6  0   0.246  -11.3263   0.4558   0.9609

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
 I53  CL   C16  single    1.729  0.020  1.729
 I53  C16  C17  aromatic  1.378  0.020  1.378
 I53  C16  C15  aromatic  1.393  0.020  1.393
 I53  C17  C18  aromatic  1.401  0.020  1.401
 I53  C15  C14  aromatic  1.421  0.020  1.421
 I53  C15  C20  aromatic  1.412  0.020  1.412
 I53  C14  C2   aromatic  1.366  0.020  1.366
 I53  C18  CL1  single    1.735  0.020  1.735
 I53  C18  C19  aromatic  1.379  0.020  1.379
 I53  C2   C3   single    1.489  0.020  1.489
 I53  C2   N    aromatic  1.377  0.020  1.377
 I53  C20  C19  aromatic  1.393  0.020  1.393
 I53  C20  N    aromatic  1.366  0.020  1.366
 I53  C3   N1   single    1.450  0.020  1.450
 I53  N    C1   single    1.446  0.020  1.446
 I53  C1   C    single    1.521  0.020  1.521
 I53  N1   C4   single    1.449  0.020  1.449
 I53  C    O    single    1.409  0.020  1.409
 I53  C4   C5   single    1.520  0.020  1.520
 I53  C5   C6   single    1.519  0.020  1.519
 I53  C6   N2   single    1.449  0.020  1.449
 I53  N2   C7   single    1.349  0.020  1.349
 I53  C7   N3   aromatic  1.313  0.020  1.313
 I53  C7   N4   aromatic  1.363  0.020  1.363
 I53  N3   C8   aromatic  1.375  0.020  1.375
 I53  N4   C13  aromatic  1.377  0.020  1.377
 I53  C8   C13  aromatic  1.407  0.020  1.407
 I53  C8   C9   aromatic  1.392  0.020  1.392
 I53  C13  C12  aromatic  1.383  0.020  1.383
 I53  C9   C10  aromatic  1.389  0.020  1.389
 I53  C12  C11  aromatic  1.391  0.020  1.391
 I53  C10  C11  aromatic  1.397  0.020  1.397
 I53  C1   H1   single    0.970  0.020  1.090
 I53  C1   H2   single    0.970  0.020  1.090
 I53  C3   H3   single    0.970  0.020  1.090
 I53  C3   H4   single    0.970  0.020  1.090
 I53  C4   H5   single    0.970  0.020  1.090
 I53  C4   H6   single    0.970  0.020  1.090
 I53  C6   H7   single    0.970  0.020  1.090
 I53  C6   H8   single    0.970  0.020  1.090
 I53  C9   H9   single    0.930  0.020  1.080
 I53  C11  H10  single    0.930  0.020  1.080
 I53  C12  H11  single    0.930  0.020  1.080
 I53  C14  H12  single    0.930  0.020  1.080
 I53  C17  H13  single    0.930  0.020  1.080
 I53  C19  H14  single    0.930  0.020  1.080
 I53  C    H15  single    0.970  0.020  1.090
 I53  C    H16  single    0.970  0.020  1.090
 I53  O    H17  single    0.850  0.020  0.980
 I53  N1   H18  single    0.890  0.020  1.040
 I53  C5   H20  single    0.970  0.020  1.090
 I53  C5   H21  single    0.970  0.020  1.090
 I53  N2   H22  single    0.890  0.020  1.040
 I53  N4   H23  single    0.860  0.020  1.020
 I53  C10  H25  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
 I53  H2   C1   H1   107.00  3.000
 I53  H2   C1   C    109.87  3.000
 I53  H1   C1   C    110.36  3.000
 I53  H2   C1   N    108.97  3.000
 I53  H1   C1   N    108.43  3.000
 I53  C    C1   N    112.07  3.000
 I53  N    C2   C14  109.60  3.000
 I53  N    C2   C3   122.50  3.000
 I53  C14  C2   C3   127.91  3.000
 I53  H4   C3   H3   106.07  3.000
 I53  H4   C3   N1   113.52  3.000
 I53  H3   C3   N1   108.23  3.000
 I53  H4   C3   C2   107.85  3.000
 I53  H3   C3   C2   109.76  3.000
 I53  N1   C3   C2   111.26  3.000
 I53  H6   C4   H5   106.37  3.000
 I53  H6   C4   C5   109.34  3.000
 I53  H5   C4   C5   109.53  3.000
 I53  H6   C4   N1   112.60  3.000
 I53  H5   C4   N1   108.15  3.000
 I53  C5   C4   N1   110.72  3.000
 I53  H8   C6   H7   107.16  3.000
 I53  H8   C6   N2   108.92  3.000
 I53  H7   C6   N2   111.54  3.000
 I53  H8   C6   C5   108.95  3.000
 I53  H7   C6   C5   109.83  3.000
 I53  N2   C6   C5   110.35  3.000
 I53  N3   C7   N4   113.04  3.000
 I53  N4   C7   N2   122.19  3.000
 I53  N3   C7   N2   124.75  3.000
 I53  N3   C8   C13  110.40  3.000
 I53  C13  C8   C9   119.31  3.000
 I53  N3   C8   C9   130.29  3.000
 I53  H9   C9   C10  120.93  3.000
 I53  H9   C9   C8   120.80  3.000
 I53  C10  C9   C8   118.26  3.000
 I53  H10  C11  C10  119.52  3.000
 I53  H10  C11  C12  119.38  3.000
 I53  C10  C11  C12  121.10  3.000
 I53  H11  C12  C13  121.79  3.000
 I53  H11  C12  C11  121.33  3.000
 I53  C13  C12  C11  116.88  3.000
 I53  N4   C13  C12  132.50  3.000
 I53  C12  C13  C8   122.96  3.000
 I53  N4   C13  C8   104.54  3.000
 I53  H12  C14  C15  127.44  3.000
 I53  H12  C14  C2   125.62  3.000
 I53  C15  C14  C2   106.95  3.000
 I53  C20  C15  C16  117.99  3.000
 I53  C20  C15  C14  106.89  3.000
 I53  C16  C15  C14  135.12  3.000
 I53  CL   C16  C17  119.99  3.000
 I53  C17  C16  C15  120.94  3.000
 I53  CL   C16  C15  119.07  3.000
 I53  H13  C17  C18  120.35  3.000
 I53  H13  C17  C16  120.77  3.000
 I53  C18  C17  C16  118.89  3.000
 I53  C19  C18  CL1  118.94  3.000
 I53  C19  C18  C17  123.02  3.000
 I53  CL1  C18  C17  118.04  3.000
 I53  N    C20  C19  129.60  3.000
 I53  N    C20  C15  107.74  3.000
 I53  C19  C20  C15  122.65  3.000
 I53  H14  C19  C20  122.41  3.000
 I53  H14  C19  C18  121.07  3.000
 I53  C20  C19  C18  116.52  3.000
 I53  C20  N    C2   108.82  3.000
 I53  C20  N    C1   124.12  3.000
 I53  C2   N    C1   127.05  3.000
 I53  H16  C    H15  107.69  3.000
 I53  H16  C    O    111.70  3.000
 I53  H15  C    O    112.24  3.000
 I53  H16  C    C1   109.77  3.000
 I53  H15  C    C1   108.39  3.000
 I53  O    C    C1   106.99  3.000
 I53  H17  O    C    108.28  3.000
 I53  H18  N1   C4   109.27  3.000
 I53  H18  N1   C3   108.67  3.000
 I53  C4   N1   C3   112.81  3.000
 I53  H21  C5   H20  107.24  3.000
 I53  H21  C5   C6   109.99  3.000
 I53  H20  C5   C6   109.06  3.000
 I53  H21  C5   C4   109.13  3.000
 I53  H20  C5   C4   109.79  3.000
 I53  C6   C5   C4   111.54  3.000
 I53  H22  N2   C7   114.31  3.000
 I53  H22  N2   C6   116.80  3.000
 I53  C7   N2   C6   122.53  3.000
 I53  H23  N4   C13  126.07  3.000
 I53  H23  N4   C7   126.84  3.000
 I53  C13  N4   C7   107.09  3.000
 I53  C8   N3   C7   104.93  3.000
 I53  H25  C10  C11  119.19  3.000
 I53  H25  C10  C9   119.32  3.000
 I53  C11  C10  C9   121.49  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
 I53  CONST_01  C16  C15  C14  C2    180.00   0.0  0
 I53  CONST_02  C20  C15  C14  C2      0.00   0.0  0
 I53  CONST_03  C15  C20  N    C2      0.00   0.0  0
 I53  CONST_04  C19  C20  N    C2    180.00   0.0  0
 I53  CONST_05  C13  C8   N3   C7      0.00   0.0  0
 I53  CONST_06  C9   C8   N3   C7    180.00   0.0  0
 I53  CONST_07  C8   C13  N4   C7      0.00   0.0  0
 I53  CONST_08  C12  C13  N4   C7    180.00   0.0  0
 I53  CONST_09  N4   C7   N3   C8      0.00   0.0  0
 I53  CONST_10  C11  C12  C13  C8      0.00   0.0  0
 I53  CONST_11  C11  C10  C9   C8      0.00   0.0  0
 I53  CONST_12  N4   C13  C8   C9    180.00   0.0  0
 I53  CONST_13  C12  C13  C8   C9      0.00   0.0  0
 I53  CONST_14  C12  C11  C10  C9      0.00   0.0  0
 I53  CONST_15  N4   C13  C12  C11   180.00   0.0  0
 I53  CONST_16  N3   C8   C13  C12   180.00   0.0  0
 I53  CONST_17  N3   C7   N4   C13     0.00   0.0  0
 I53  CONST_18  C10  C9   C8   C13     0.00   0.0  0
 I53  CONST_19  C10  C11  C12  C13     0.00   0.0  0
 I53  CONST_20  C17  C16  C15  C14   180.00   0.0  0
 I53  CONST_21  C19  C20  C15  C14   180.00   0.0  0
 I53  CONST_22  N    C20  C15  C14     0.00   0.0  0
 I53  CONST_23  C20  N    C2   C14     0.00   0.0  0
 I53  CONST_24  C18  C17  C16  C15     0.00   0.0  0
 I53  CONST_25  N    C2   C14  C15     0.00   0.0  0
 I53  CONST_26  C18  C19  C20  C15     0.00   0.0  0
 I53  CONST_27  C19  C18  C17  C16     0.00   0.0  0
 I53  CONST_28  C19  C20  C15  C16     0.00   0.0  0
 I53  CONST_29  N    C20  C15  C16   180.00   0.0  0
 I53  CONST_30  C20  C15  C16  C17     0.00   0.0  0
 I53  CONST_31  C20  C19  C18  C17     0.00   0.0  0
 I53  CONST_32  N    C20  C19  C18   180.00   0.0  0
 I53  CONST_33  N3   C8   C13  N4      0.00   0.0  0
 I53  CONST_34  C10  C9   C8   N3    180.00   0.0  0
 I53  CONST_35  C14  C2   N    C1    180.00   0.0  0
 I53  CONST_36  C15  C20  N    C1    180.00   0.0  0
 I53  CONST_37  C19  C20  N    C1      0.00   0.0  0
 I53  CONST_38  C15  C14  C2   C3    180.00   0.0  0
 I53  CONST_39  C20  N    C2   C3    180.00   0.0  0
 I53  CONST_40  N2   C7   N3   C8    180.00   0.0  0
 I53  CONST_41  N2   C7   N4   C13   180.00   0.0  0
 I53  CONST_42  CL   C16  C15  C14     0.00   0.0  0
 I53  CONST_43  CL1  C18  C17  C16   180.00   0.0  0
 I53  CONST_44  CL   C16  C17  C18   180.00   0.0  0
 I53  CONST_45  CL   C16  C15  C20   180.00   0.0  0
 I53  CONST_46  CL1  C18  C19  C20   180.00   0.0  0
 I53  CONST_47  H23  N4   C13  C8    180.00   0.0  0
 I53  CONST_48  H11  C12  C13  C8    180.00   0.0  0
 I53  CONST_49  H25  C10  C9   C8    180.00   0.0  0
 I53  CONST_50  H10  C11  C10  C9    180.00   0.0  0
 I53  CONST_51  H9   C9   C10  C11   180.00   0.0  0
 I53  CONST_52  H13  C17  C16  C15   180.00   0.0  0
 I53  CONST_53  H14  C19  C20  C15   180.00   0.0  0
 I53  CONST_54  H12  C14  C15  C16     0.00   0.0  0
 I53  CONST_55  N3   C7   N2   C6    180.00   0.0  0
 I53  CONST_57  H22  N2   C7   N4    180.00   0.0  0
 I53  Var_01    C    C1   N    C2     99.77  30.0  2
 I53  Var_02    N1   C3   C2   C14   114.18  30.0  2
 I53  Var_03    C4   N1   C3   C2    175.63  30.0  3
 I53  Var_04    C5   C6   N2   C7   -175.09  30.0  1
 I53  Var_05    O    C    C1   N     176.84  30.0  3
 I53  Var_06    C5   C4   N1   C3    178.80  30.0  3
 I53  Var_07    N2   C6   C5   C4    178.39  30.0  3
 I53  Var_08    N1   C4   C5   C6    179.37  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
 I53  plan-1  C7   0.020
 I53  plan-1  C8   0.020
 I53  plan-1  C9   0.020
 I53  plan-1  C11  0.020
 I53  plan-1  C12  0.020
 I53  plan-1  C13  0.020
 I53  plan-1  N2   0.020
 I53  plan-1  N4   0.020
 I53  plan-1  N3   0.020
 I53  plan-1  C10  0.020
 I53  plan-1  H9   0.020
 I53  plan-1  H10  0.020
 I53  plan-1  H11  0.020
 I53  plan-1  H23  0.020
 I53  plan-1  H25  0.020
 I53  plan-2  C1   0.020
 I53  plan-2  C2   0.020
 I53  plan-2  C3   0.020
 I53  plan-2  C14  0.020
 I53  plan-2  C15  0.020
 I53  plan-2  C16  0.020
 I53  plan-2  C17  0.020
 I53  plan-2  C18  0.020
 I53  plan-2  C20  0.020
 I53  plan-2  CL1  0.020
 I53  plan-2  CL   0.020
 I53  plan-2  C19  0.020
 I53  plan-2  N    0.020
 I53  plan-2  H12  0.020
 I53  plan-2  H13  0.020
 I53  plan-2  H14  0.020
 I53  plan-3  C6   0.020
 I53  plan-3  C7   0.020
 I53  plan-3  N2   0.020
 I53  plan-3  H22  0.020

