# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 09:07:00 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: N-(6-oxohexyl)-2-(4,5,6,7-tetrabromo-1H-benzimidazol-1-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1c(Br)c(Br)c2n(CC(=O)NCCCCCC=O)cnc2c1Br
#
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
 0TJ  0TJ  N-(6-oxohexyl)-2-(4,5,6,7-tetrabromo-1H-benzimidazol-1-yl)acetamide  ligand  39  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0TJ
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
 0TJ  BR1  BR  BR    0   0.034  -4.5315  -1.7850   0.1888
 0TJ  CAM  C   CR6   0  -0.208  -2.9265  -0.8882  -0.1229
 0TJ  CAK  C   CR6   0  -0.106  -2.7674   0.4741   0.0676
 0TJ  BR2  BR  BR    0   0.039  -4.2177   1.4960   0.6650
 0TJ  CAL  C   CR6   0  -0.127  -1.5214   1.0883  -0.1875
 0TJ  BR3  BR  BR    0   0.043  -1.3324   2.9313   0.0843
 0TJ  CAN  C   CR6   0  -0.144  -0.4303   0.3505  -0.6363
 0TJ  BR4  BR  BR    0   0.047   1.2197   1.1687  -0.9628
 0TJ  CAP  C   CR56  0   0.455  -0.6025  -1.0183  -0.8265
 0TJ  CAO  C   CR56  0   0.206  -1.8398  -1.6338  -0.5699
 0TJ  NAI  N   N     0  -0.431  -1.7740  -2.9716  -0.8211
 0TJ  CAG  C   CR15  0   0.134  -0.5526  -3.1663  -1.2157
 0TJ  N    N   NR5   0  -0.508   0.2050  -2.0414  -1.2597
 0TJ  CA   C   CH2   0  -0.466   1.6058  -2.0487  -1.5947
 0TJ  C    C   C     0   0.545   2.4740  -1.8587  -0.3549
 0TJ  O    O   O     0  -0.478   2.0293  -2.0502   0.7640
 0TJ  NAA  N   NH1   0  -0.639   3.7342  -1.5114  -0.6204
 0TJ  H1   H   HCR5  0   0.311  -0.1378  -4.1218  -1.5023
 0TJ  H2   H   HCH2  0   0.328   1.8295  -3.0310  -2.0155
 0TJ  H3   H   HCH2  0   0.307   1.8260  -1.3243  -2.3768
 0TJ  H4   H   HNH1  0   0.407   4.0118  -1.3857  -1.5813
 0TJ  C1   C   CH2   0  -0.234   4.7532  -1.3730   0.4015
 0TJ  C2   C   CH2   0  -0.474   5.9930  -0.7065  -0.1726
 0TJ  C3   C   CH2   0  -0.416   7.1121  -0.6064   0.8548
 0TJ  C4   C   CH2   0  -0.437   8.3560   0.0681   0.2910
 0TJ  C5   C   CH2   0  -0.548   9.4832   0.1560   1.3206
 0TJ  H5   H   HCH2  0   0.240   4.3590  -0.7770   1.2272
 0TJ  H6   H   HCH2  0   0.235   5.0129  -2.3549   0.8093
 0TJ  H7   H   HCH2  0   0.232   6.3455  -1.2771  -1.0383
 0TJ  H8   H   HCH2  0   0.234   5.7331   0.2920  -0.5360
 0TJ  H9   H   HCH2  0   0.225   6.7616  -0.0491   1.7293
 0TJ  H10  H   HCH2  0   0.224   7.3733  -1.6080   1.2103
 0TJ  H11  H   HCH2  0   0.230   8.7037  -0.4858  -0.5866
 0TJ  H12  H   HCH2  0   0.235   8.1003   1.0728  -0.0573
 0TJ  H13  H   HCH2  0   0.251   9.1785   0.7255   2.2005
 0TJ  H14  H   HCH2  0   0.264   9.7423  -0.8569   1.6521
 0TJ  C6   C   C1    0   0.190  10.7228   0.7458   0.7274
 0TJ  O1   O   O     0  -0.383  11.3599   1.6560   1.1979
 0TJ  H15  H   H     0   0.181  11.0404   0.2682  -0.2183

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
 0TJ  O    C    double    1.219  0.020  1.219
 0TJ  CAG  NAI  aromatic  1.298  0.020  1.298
 0TJ  CAG  N    aromatic  1.357  0.020  1.357
 0TJ  NAI  CAO  aromatic  1.363  0.020  1.363
 0TJ  CA   C    single    1.525  0.020  1.525
 0TJ  CA   N    single    1.440  0.020  1.440
 0TJ  C    NAA  single    1.334  0.020  1.334
 0TJ  N    CAP  aromatic  1.373  0.020  1.373
 0TJ  CAO  CAP  aromatic  1.406  0.020  1.406
 0TJ  CAO  CAM  aromatic  1.392  0.020  1.392
 0TJ  CAP  CAN  aromatic  1.393  0.020  1.393
 0TJ  BR1  CAM  single    1.865  0.020  1.865
 0TJ  CAM  CAK  aromatic  1.385  0.020  1.385
 0TJ  CAN  BR4  single    1.871  0.020  1.871
 0TJ  CAN  CAL  aromatic  1.392  0.020  1.392
 0TJ  CAK  CAL  aromatic  1.412  0.020  1.412
 0TJ  CAK  BR2  single    1.872  0.020  1.872
 0TJ  CAL  BR3  single    1.872  0.020  1.872
 0TJ  CAG  H1   single    0.930  0.020  1.080
 0TJ  CA   H2   single    0.970  0.020  1.090
 0TJ  CA   H3   single    0.970  0.020  1.090
 0TJ  NAA  H4   single    0.860  0.020  1.020
 0TJ  NAA  C1   single    1.450  0.020  1.450
 0TJ  C1   C2   single    1.520  0.020  1.520
 0TJ  C2   C3   single    1.522  0.020  1.522
 0TJ  C3   C4   single    1.523  0.020  1.523
 0TJ  C4   C5   single    1.529  0.020  1.529
 0TJ  C1   H5   single    0.970  0.020  1.090
 0TJ  C1   H6   single    0.970  0.020  1.090
 0TJ  C2   H7   single    0.970  0.020  1.090
 0TJ  C2   H8   single    0.970  0.020  1.090
 0TJ  C3   H9   single    0.970  0.020  1.090
 0TJ  C3   H10  single    0.970  0.020  1.090
 0TJ  C4   H11  single    0.970  0.020  1.090
 0TJ  C4   H12  single    0.970  0.020  1.090
 0TJ  C5   H13  single    0.970  0.020  1.090
 0TJ  C5   H14  single    0.970  0.020  1.090
 0TJ  C5   C6   single    1.495  0.020  1.495
 0TJ  C6   O1   double    1.207  0.020  1.207
 0TJ  C6   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
 0TJ  CAO  CAM  CAK  118.79  3.000
 0TJ  CAK  CAM  BR1  123.30  3.000
 0TJ  CAO  CAM  BR1  117.91  3.000
 0TJ  CAL  CAK  BR2  120.25  3.000
 0TJ  BR2  CAK  CAM  119.47  3.000
 0TJ  CAL  CAK  CAM  120.29  3.000
 0TJ  CAN  CAL  BR3  119.31  3.000
 0TJ  BR3  CAL  CAK  119.40  3.000
 0TJ  CAN  CAL  CAK  121.29  3.000
 0TJ  CAP  CAN  BR4  121.01  3.000
 0TJ  BR4  CAN  CAL  121.07  3.000
 0TJ  CAP  CAN  CAL  117.92  3.000
 0TJ  N    CAP  CAO  104.41  3.000
 0TJ  CAO  CAP  CAN  120.95  3.000
 0TJ  N    CAP  CAN  134.63  3.000
 0TJ  NAI  CAO  CAP  110.72  3.000
 0TJ  CAP  CAO  CAM  120.76  3.000
 0TJ  NAI  CAO  CAM  128.53  3.000
 0TJ  CAG  NAI  CAO  104.40  3.000
 0TJ  H1   CAG  N    120.68  3.000
 0TJ  H1   CAG  NAI  125.07  3.000
 0TJ  N    CAG  NAI  114.25  3.000
 0TJ  CA   N    CAG  123.11  3.000
 0TJ  CA   N    CAP  130.46  3.000
 0TJ  CAG  N    CAP  106.20  3.000
 0TJ  H3   CA   H2   106.29  3.000
 0TJ  H3   CA   C    112.70  3.000
 0TJ  H2   CA   C    107.98  3.000
 0TJ  H3   CA   N    111.12  3.000
 0TJ  H2   CA   N    107.07  3.000
 0TJ  C    CA   N    111.34  3.000
 0TJ  NAA  C    O    124.62  3.000
 0TJ  NAA  C    CA   114.10  3.000
 0TJ  O    C    CA   121.25  3.000
 0TJ  C1   NAA  H4   117.80  3.000
 0TJ  C1   NAA  C    123.28  3.000
 0TJ  H4   NAA  C    118.84  3.000
 0TJ  H6   C1   H5   107.07  3.000
 0TJ  H6   C1   C2   109.91  3.000
 0TJ  H5   C1   C2   109.92  3.000
 0TJ  H6   C1   NAA  110.11  3.000
 0TJ  H5   C1   NAA  109.35  3.000
 0TJ  C2   C1   NAA  110.42  3.000
 0TJ  H8   C2   H7   106.83  3.000
 0TJ  H8   C2   C3   109.80  3.000
 0TJ  H7   C2   C3   109.33  3.000
 0TJ  H8   C2   C1   109.39  3.000
 0TJ  H7   C2   C1   109.43  3.000
 0TJ  C3   C2   C1   111.93  3.000
 0TJ  H10  C3   H9   106.43  3.000
 0TJ  H10  C3   C4   109.30  3.000
 0TJ  H9   C3   C4   109.37  3.000
 0TJ  H10  C3   C2   109.54  3.000
 0TJ  H9   C3   C2   109.71  3.000
 0TJ  C4   C3   C2   112.31  3.000
 0TJ  H12  C4   H11  106.49  3.000
 0TJ  H12  C4   C5   109.51  3.000
 0TJ  H11  C4   C5   109.56  3.000
 0TJ  H12  C4   C3   109.49  3.000
 0TJ  H11  C4   C3   109.39  3.000
 0TJ  C5   C4   C3   112.22  3.000
 0TJ  C6   C5   H14  106.76  3.000
 0TJ  C6   C5   H13  110.21  3.000
 0TJ  H14  C5   H13  107.70  3.000
 0TJ  C6   C5   C4   111.51  3.000
 0TJ  H14  C5   C4   108.94  3.000
 0TJ  H13  C5   C4   111.53  3.000
 0TJ  H15  C6   O1   120.50  3.000
 0TJ  H15  C6   C5   114.01  3.000
 0TJ  O1   C6   C5   125.49  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
 0TJ  CONST_01  CAG  NAI  CAO  CAM   180.00   0.0  0
 0TJ  CONST_02  N    CAP  CAO  CAM   180.00   0.0  0
 0TJ  CONST_03  CAN  CAP  CAO  CAM     0.00   0.0  0
 0TJ  CONST_04  CAN  CAL  CAK  CAM     0.00   0.0  0
 0TJ  CONST_05  NAI  CAO  CAM  CAK   180.00   0.0  0
 0TJ  CONST_06  CAP  CAO  CAM  CAK     0.00   0.0  0
 0TJ  CONST_07  CAP  CAN  CAL  CAK     0.00   0.0  0
 0TJ  CONST_08  N    CAP  CAN  CAL   180.00   0.0  0
 0TJ  CONST_09  CAO  CAP  CAN  CAL     0.00   0.0  0
 0TJ  CONST_10  CAO  CAM  CAK  CAL     0.00   0.0  0
 0TJ  CONST_11  CAG  N    CAP  CAN   180.00   0.0  0
 0TJ  CONST_12  NAI  CAO  CAP  CAN   180.00   0.0  0
 0TJ  CONST_13  NAI  CAG  N    CAP     0.00   0.0  0
 0TJ  CONST_14  CAG  NAI  CAO  CAP     0.00   0.0  0
 0TJ  CONST_15  N    CAG  NAI  CAO     0.00   0.0  0
 0TJ  CONST_16  CAG  N    CAP  CAO     0.00   0.0  0
 0TJ  CONST_17  N    CAP  CAO  NAI     0.00   0.0  0
 0TJ  CONST_18  NAI  CAO  CAM  BR1     0.00   0.0  0
 0TJ  CONST_19  CAP  CAO  CAM  BR1   180.00   0.0  0
 0TJ  CONST_20  CAL  CAK  CAM  BR1   180.00   0.0  0
 0TJ  CONST_21  BR3  CAL  CAK  CAM   180.00   0.0  0
 0TJ  CONST_22  BR4  CAN  CAL  CAK   180.00   0.0  0
 0TJ  CONST_23  CAO  CAM  CAK  BR2   180.00   0.0  0
 0TJ  CONST_24  CAN  CAL  CAK  BR2   180.00   0.0  0
 0TJ  CONST_25  CAP  CAN  CAL  BR3   180.00   0.0  0
 0TJ  CONST_26  CA   N    CAP  CAN     0.00   0.0  0
 0TJ  CONST_27  N    CAP  CAN  BR4     0.00   0.0  0
 0TJ  CONST_28  CAO  CAP  CAN  BR4   180.00   0.0  0
 0TJ  CONST_29  CA   N    CAP  CAO   180.00   0.0  0
 0TJ  CONST_30  CA   N    CAG  NAI   180.00   0.0  0
 0TJ  CONST_31  H1   CAG  N    CAP   180.00   0.0  0
 0TJ  CONST_32  C1   NAA  C    CA    180.00   0.0  0
 0TJ  CONST_33  C1   NAA  C    O       0.00   0.0  0
 0TJ  CONST_34  H4   NAA  C    CA      0.00   0.0  0
 0TJ  Var_01    C    CA   N    CAP    69.28  30.0  2
 0TJ  Var_02    O    C    CA   N      18.27  30.0  3
 0TJ  Var_03    C2   C1   NAA  C    -168.74  30.0  3
 0TJ  Var_04    C3   C2   C1   NAA  -177.17  30.0  3
 0TJ  Var_05    C4   C3   C2   C1   -179.65  30.0  3
 0TJ  Var_06    C5   C4   C3   C2   -179.47  30.0  3
 0TJ  Var_07    C6   C5   C4   C3    176.59  30.0  3
 0TJ  Var_08    O1   C6   C5   C4    129.55  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
 0TJ  plan-1  BR1  0.020
 0TJ  plan-1  CAM  0.020
 0TJ  plan-1  CAK  0.020
 0TJ  plan-1  BR2  0.020
 0TJ  plan-1  CAL  0.020
 0TJ  plan-1  BR3  0.020
 0TJ  plan-1  CAN  0.020
 0TJ  plan-1  BR4  0.020
 0TJ  plan-1  CAP  0.020
 0TJ  plan-1  CAO  0.020
 0TJ  plan-1  NAI  0.020
 0TJ  plan-1  CAG  0.020
 0TJ  plan-1  N    0.020
 0TJ  plan-1  CA   0.020
 0TJ  plan-1  H1   0.020
 0TJ  plan-2  CA   0.020
 0TJ  plan-2  C    0.020
 0TJ  plan-2  O    0.020
 0TJ  plan-2  NAA  0.020
 0TJ  plan-2  H4   0.020
 0TJ  plan-2  C1   0.020
 0TJ  plan-3  C5   0.020
 0TJ  plan-3  C6   0.020
 0TJ  plan-3  O1   0.020
 0TJ  plan-3  H15  0.020

