# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 08:10:46 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)Cn1cc(Cc2ccccc2)c3cc(Br)ccc13
#
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
 6JU  6JU  2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide  ligand  37  22  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6JU
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
 6JU  C5   C   CR5   0   0.028  -0.2988   1.6641   0.6870
 6JU  C4   C   CR15  0  -0.076  -1.5814   2.0415   0.4207
 6JU  C6   C   CR56  0   0.031  -0.1218   0.3966   0.0449
 6JU  C7   C   CR16  0  -0.345   0.9584  -0.4849  -0.0497
 6JU  C8   C   CR6   0  -0.122   0.7729  -1.6561  -0.7550
 6JU  BR   BR  BR    0  -0.068   2.2117  -2.8808  -0.9021
 6JU  C9   C   CR16  0  -0.255  -0.4441  -1.9801  -1.3713
 6JU  C10  C   CR16  0  -0.300  -1.5164  -1.1118  -1.2914
 6JU  C11  C   CR56  0   0.392  -1.3426   0.0748  -0.5853
 6JU  N3   N   NR5   0  -0.521  -2.2106   1.1054  -0.3589
 6JU  C12  C   CH2   0  -0.470  -3.5983   1.1118  -0.7102
 6JU  C13  C   C     0   0.515  -4.4093   0.2603   0.2627
 6JU  O2   O   O     0  -0.456  -4.1092   0.1546   1.4347
 6JU  N1   N   NH1   0  -0.368  -5.4852  -0.3013  -0.3051
 6JU  O14  O   OH1   0  -0.539  -6.2882  -1.1300   0.4135
 6JU  H2   H   HCR5  0   0.292  -2.1051   2.9347   0.7265
 6JU  H3   H   HCR6  0   0.264   1.9069  -0.2476   0.4155
 6JU  H4   H   HCR6  0   0.275  -0.5533  -2.9093  -1.9139
 6JU  H5   H   HCR6  0   0.270  -2.4529  -1.3676  -1.7709
 6JU  H6   H   HCH2  0   0.320  -3.9681   2.1369  -0.6576
 6JU  H7   H   HCH2  0   0.296  -3.7258   0.7898  -1.7456
 6JU  H8   H   HNH1  0   0.422  -5.6536  -0.2941  -1.3008
 6JU  H9   H   HOH1  0   0.480  -7.0085  -0.5838   0.7553
 6JU  C1   C   CH2   0  -0.605   0.7211   2.4163   1.4764
 6JU  C2   C   CR6   0   0.135   1.9501   2.7813   0.6764
 6JU  C3   C   CR16  0  -0.285   1.8317   3.4029  -0.5652
 6JU  C14  C   CR16  0  -0.241   2.9586   3.7585  -1.2918
 6JU  C15  C   CR16  0  -0.273   4.2275   3.4927  -0.7895
 6JU  C16  C   CR16  0  -0.242   4.3566   2.8717   0.4444
 6JU  C17  C   CR16  0  -0.328   3.2242   2.5187   1.1694
 6JU  H1   H   HCH2  0   0.267   0.2624   3.3274   1.8711
 6JU  H10  H   HCH2  0   0.257   1.0277   1.8322   2.3491
 6JU  H11  H   HCR6  0   0.244   0.8468   3.6072  -0.9687
 6JU  H12  H   HCR6  0   0.252   2.8466   4.2438  -2.2532
 6JU  H13  H   HCR6  0   0.253   5.1078   3.7658  -1.3571
 6JU  H14  H   HCR6  0   0.253   5.3392   2.6580   0.8453
 6JU  H15  H   HCR6  0   0.248   3.3353   2.0308   2.1310

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
 6JU  BR   C8   single    1.895  0.020  1.895
 6JU  C8   C9   aromatic  1.402  0.020  1.402
 6JU  C8   C7   aromatic  1.380  0.020  1.380
 6JU  C9   C10  aromatic  1.382  0.020  1.382
 6JU  C7   C6   aromatic  1.397  0.020  1.397
 6JU  C10  C11  aromatic  1.392  0.020  1.392
 6JU  C6   C11  aromatic  1.411  0.020  1.411
 6JU  C6   C5   aromatic  1.432  0.020  1.432
 6JU  C11  N3   aromatic  1.366  0.020  1.366
 6JU  C5   C4   aromatic  1.363  0.020  1.363
 6JU  O14  N1   single    1.359  0.020  1.359
 6JU  N3   C4   aromatic  1.371  0.020  1.371
 6JU  N3   C12  single    1.431  0.020  1.431
 6JU  N1   C13  single    1.340  0.020  1.340
 6JU  C13  C12  single    1.526  0.020  1.526
 6JU  C13  O2   double    1.214  0.020  1.214
 6JU  C4   H2   single    0.930  0.020  1.080
 6JU  C7   H3   single    0.930  0.020  1.080
 6JU  C9   H4   single    0.930  0.020  1.080
 6JU  C10  H5   single    0.930  0.020  1.080
 6JU  C12  H6   single    0.970  0.020  1.090
 6JU  C12  H7   single    0.970  0.020  1.090
 6JU  N1   H8   single    0.860  0.020  1.020
 6JU  O14  H9   single    0.850  0.020  0.980
 6JU  C5   C1   single    1.493  0.020  1.493
 6JU  C1   C2   single    1.511  0.020  1.511
 6JU  C2   C3   aromatic  1.394  0.020  1.394
 6JU  C3   C14  aromatic  1.387  0.020  1.387
 6JU  C14  C15  aromatic  1.390  0.020  1.390
 6JU  C15  C16  aromatic  1.387  0.020  1.387
 6JU  C16  C17  aromatic  1.390  0.020  1.390
 6JU  C17  C2   aromatic  1.391  0.020  1.391
 6JU  C1   H1   single    0.970  0.020  1.090
 6JU  C1   H10  single    0.970  0.020  1.090
 6JU  C3   H11  single    0.930  0.020  1.080
 6JU  C14  H12  single    0.930  0.020  1.080
 6JU  C15  H13  single    0.930  0.020  1.080
 6JU  C16  H14  single    0.930  0.020  1.080
 6JU  C17  H15  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
 6JU  C1   C5   C6   126.78  3.000
 6JU  C1   C5   C4   127.34  3.000
 6JU  C6   C5   C4   105.88  3.000
 6JU  H2   C4   N3   120.22  3.000
 6JU  H2   C4   C5   129.05  3.000
 6JU  N3   C4   C5   110.73  3.000
 6JU  C11  C6   C7   119.65  3.000
 6JU  C11  C6   C5   107.17  3.000
 6JU  C7   C6   C5   133.17  3.000
 6JU  H3   C7   C8   121.57  3.000
 6JU  H3   C7   C6   120.65  3.000
 6JU  C8   C7   C6   117.78  3.000
 6JU  C9   C8   BR   118.39  3.000
 6JU  C9   C8   C7   122.52  3.000
 6JU  BR   C8   C7   119.09  3.000
 6JU  H4   C9   C10  119.37  3.000
 6JU  H4   C9   C8   120.45  3.000
 6JU  C10  C9   C8   120.19  3.000
 6JU  H5   C10  C11  122.29  3.000
 6JU  H5   C10  C9   119.80  3.000
 6JU  C11  C10  C9   117.91  3.000
 6JU  N3   C11  C10  130.37  3.000
 6JU  N3   C11  C6   107.68  3.000
 6JU  C10  C11  C6   121.95  3.000
 6JU  C12  N3   C11  125.35  3.000
 6JU  C12  N3   C4   125.55  3.000
 6JU  C11  N3   C4   108.52  3.000
 6JU  H7   C12  H6   106.45  3.000
 6JU  H7   C12  C13  112.20  3.000
 6JU  H6   C12  C13  108.26  3.000
 6JU  H7   C12  N3   110.17  3.000
 6JU  H6   C12  N3   108.72  3.000
 6JU  C13  C12  N3   110.87  3.000
 6JU  N1   C13  O2   124.82  3.000
 6JU  O2   C13  C12  122.17  3.000
 6JU  N1   C13  C12  112.98  3.000
 6JU  H8   N1   O14  115.27  3.000
 6JU  H8   N1   C13  123.29  3.000
 6JU  O14  N1   C13  120.38  3.000
 6JU  H9   O14  N1   106.42  3.000
 6JU  H10  C1   H1   105.93  3.000
 6JU  H10  C1   C2   108.87  3.000
 6JU  H1   C1   C2   109.33  3.000
 6JU  H10  C1   C5   110.13  3.000
 6JU  H1   C1   C5   108.90  3.000
 6JU  C2   C1   C5   113.41  3.000
 6JU  C17  C2   C3   118.54  3.000
 6JU  C17  C2   C1   120.77  3.000
 6JU  C3   C2   C1   120.69  3.000
 6JU  H11  C3   C14  119.66  3.000
 6JU  H11  C3   C2   119.54  3.000
 6JU  C14  C3   C2   120.80  3.000
 6JU  H12  C14  C15  120.06  3.000
 6JU  H12  C14  C3   119.73  3.000
 6JU  C15  C14  C3   120.21  3.000
 6JU  H13  C15  C16  120.24  3.000
 6JU  H13  C15  C14  120.30  3.000
 6JU  C16  C15  C14  119.46  3.000
 6JU  H14  C16  C17  119.74  3.000
 6JU  H14  C16  C15  120.14  3.000
 6JU  C17  C16  C15  120.11  3.000
 6JU  H15  C17  C16  119.57  3.000
 6JU  H15  C17  C2   119.55  3.000
 6JU  C16  C17  C2   120.89  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
 6JU  CONST_01  C8   C7   C6   C5    180.00   0.0  0
 6JU  CONST_02  C10  C11  C6   C5    180.00   0.0  0
 6JU  CONST_03  N3   C11  C6   C5      0.00   0.0  0
 6JU  CONST_04  C11  N3   C4   C5      0.00   0.0  0
 6JU  CONST_05  C7   C6   C5   C4    180.00   0.0  0
 6JU  CONST_06  C11  C6   C5   C4      0.00   0.0  0
 6JU  CONST_07  C10  C11  N3   C4    180.00   0.0  0
 6JU  CONST_08  C6   C11  N3   C4      0.00   0.0  0
 6JU  CONST_09  C9   C8   C7   C6      0.00   0.0  0
 6JU  CONST_10  C9   C10  C11  C6      0.00   0.0  0
 6JU  CONST_11  N3   C4   C5   C6      0.00   0.0  0
 6JU  CONST_12  C10  C9   C8   C7      0.00   0.0  0
 6JU  CONST_13  C10  C11  C6   C7      0.00   0.0  0
 6JU  CONST_14  N3   C11  C6   C7    180.00   0.0  0
 6JU  CONST_15  C11  C10  C9   C8      0.00   0.0  0
 6JU  CONST_16  C11  C6   C7   C8      0.00   0.0  0
 6JU  CONST_17  N3   C11  C10  C9    180.00   0.0  0
 6JU  CONST_18  C15  C14  C3   C2      0.00   0.0  0
 6JU  CONST_19  C15  C16  C17  C2      0.00   0.0  0
 6JU  CONST_20  C16  C17  C2   C3      0.00   0.0  0
 6JU  CONST_21  C16  C15  C14  C3      0.00   0.0  0
 6JU  CONST_22  C17  C2   C3   C14     0.00   0.0  0
 6JU  CONST_23  C17  C16  C15  C14     0.00   0.0  0
 6JU  CONST_24  C12  N3   C4   C5    180.00   0.0  0
 6JU  CONST_25  BR   C8   C7   C6    180.00   0.0  0
 6JU  CONST_26  C12  N3   C11  C6    180.00   0.0  0
 6JU  CONST_27  C1   C5   C6   C7      0.00   0.0  0
 6JU  CONST_28  C10  C9   C8   BR    180.00   0.0  0
 6JU  CONST_29  C12  N3   C11  C10     0.00   0.0  0
 6JU  CONST_30  C1   C5   C6   C11   180.00   0.0  0
 6JU  CONST_31  C1   C5   C4   N3    180.00   0.0  0
 6JU  CONST_32  C14  C3   C2   C1    180.00   0.0  0
 6JU  CONST_33  C16  C17  C2   C1    180.00   0.0  0
 6JU  CONST_34  H3   C7   C6   C5      0.00   0.0  0
 6JU  CONST_35  H5   C10  C11  C6    180.00   0.0  0
 6JU  CONST_36  H2   C4   C5   C6    180.00   0.0  0
 6JU  CONST_37  H4   C9   C8   C7    180.00   0.0  0
 6JU  CONST_38  H12  C14  C3   C2    180.00   0.0  0
 6JU  CONST_39  H14  C16  C17  C2    180.00   0.0  0
 6JU  CONST_40  H15  C17  C2   C3    180.00   0.0  0
 6JU  CONST_41  H13  C15  C14  C3    180.00   0.0  0
 6JU  CONST_42  H11  C3   C14  C15   180.00   0.0  0
 6JU  CONST_43  O14  N1   C13  C12   180.00   0.0  0
 6JU  CONST_44  O14  N1   C13  O2      0.00   0.0  0
 6JU  CONST_45  H8   N1   C13  C12     0.00   0.0  0
 6JU  Var_01    C3   C2   C1   C5     50.02  30.0  2
 6JU  Var_02    C2   C1   C5   C4   -119.02  30.0  2
 6JU  Var_03    C13  C12  N3   C4    -94.16  30.0  2
 6JU  Var_04    N1   C13  C12  N3   -149.53  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
 6JU  plan-1  C1   0.020
 6JU  plan-1  C2   0.020
 6JU  plan-1  C3   0.020
 6JU  plan-1  C14  0.020
 6JU  plan-1  C15  0.020
 6JU  plan-1  C16  0.020
 6JU  plan-1  C17  0.020
 6JU  plan-1  H11  0.020
 6JU  plan-1  H12  0.020
 6JU  plan-1  H13  0.020
 6JU  plan-1  H14  0.020
 6JU  plan-1  H15  0.020
 6JU  plan-2  C5   0.020
 6JU  plan-2  C4   0.020
 6JU  plan-2  C6   0.020
 6JU  plan-2  C7   0.020
 6JU  plan-2  C8   0.020
 6JU  plan-2  BR   0.020
 6JU  plan-2  C9   0.020
 6JU  plan-2  C10  0.020
 6JU  plan-2  C11  0.020
 6JU  plan-2  N3   0.020
 6JU  plan-2  C12  0.020
 6JU  plan-2  H2   0.020
 6JU  plan-2  H3   0.020
 6JU  plan-2  H4   0.020
 6JU  plan-2  H5   0.020
 6JU  plan-2  C1   0.020
 6JU  plan-3  C12  0.020
 6JU  plan-3  C13  0.020
 6JU  plan-3  O2   0.020
 6JU  plan-3  N1   0.020
 6JU  plan-3  O14  0.020
 6JU  plan-3  H8   0.020

