# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 21:20:05 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N-[2-(1H-benzimidazol-2-yl)ethyl]-2-(2-bromophenoxy)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Brc1ccccc1OCC(=O)NCCc2[nH]c3ccccc3n2
#
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
 B95  B95  N-[2-(1H-benzimidazol-2-yl)ethyl]-2-(2-bromophenoxy)ethanamide  ligand  39  23  .  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_B95
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
 B95  OAA   O   O     0  -0.474   0.4428  -0.8413  -0.2845
 B95  CAC   C   CR16  0  -0.279   6.5850   1.9182  -0.2168
 B95  CAD   C   CR16  0  -0.237   5.5168   2.7788  -0.4063
 B95  CAE   C   CR16  0  -0.281  -8.7300  -0.6674   0.4918
 B95  CAF   C   CR16  0  -0.271  -8.3382  -1.4096  -0.6325
 B95  CAG   C   CR16  0  -0.220   6.3428   0.5824   0.0773
 B95  CAH   C   CR16  0  -0.382   4.2095   2.3203  -0.3078
 B95  CAI   C   CR16  0  -0.306  -7.8628   0.2136   1.1156
 B95  CAJ   C   CR16  0  -0.337  -7.0674  -1.2927  -1.1677
 B95  CAL   C   CH2   0  -0.600  -3.1643   1.4213   0.0880
 B95  CAM   C   CH2   0  -0.306   1.6112   1.2577  -0.1576
 B95  NAN   N   NR15  0  -0.703  -5.4923   1.0715   0.9097
 B95  NAO   N   NH1   0  -0.653  -0.7634   1.0312   0.0710
 B95  NAP   N   N     0  -0.475  -4.8761  -0.1010  -0.8675
 B95  OAQ   O   O2    0  -0.445   2.7292   0.4467   0.0928
 B95  CAR   C   C     0   0.520   0.3817   0.3631  -0.1179
 B95  CAS   C   CR6   0  -0.234   5.0410   0.1230   0.1747
 B95  CAT   C   CR5   0   0.475  -4.5072   0.7799   0.0229
 B95  CAU   C   CR6   0   0.455   3.9532   0.9819  -0.0190
 B95  CAV   C   CR56  0   0.326  -6.5889   0.3241   0.5712
 B95  CAW   C   CR56  0   0.134  -6.1783  -0.4107  -0.5540
 B95  HAC   H   HCR6  0   0.266   7.6029   2.2744  -0.2950
 B95  HAD   H   HCR6  0   0.269   5.6913   3.8224  -0.6317
 B95  HAF   H   HCR6  0   0.252  -9.0469  -2.0890  -1.0878
 B95  HAG   H   HCR6  0   0.280   7.1710  -0.0972   0.2282
 B95  HAH   H   HCR6  0   0.293   3.3977   3.0198  -0.4539
 B95  HAI   H   HCR6  0   0.266  -8.1659   0.7824   1.9848
 B95  HAJ   H   HCR6  0   0.253  -6.7695  -1.8656  -2.0366
 B95  HAL   H   HCH2  0   0.275  -3.0870   2.0188   0.9990
 B95  HALA  H   HCH2  0   0.284  -3.0560   2.1093  -0.7554
 B95  HAM   H   HCH2  0   0.261   1.5269   2.0643   0.5791
 B95  HAMA  H   HCH2  0   0.273   1.6647   1.7221  -1.1501
 B95  HNAO  H   HNH1  0   0.410  -0.7300   2.0238   0.2420
 B95  HNAN  H   HNR5  0   0.419  -5.4198   1.7156   1.6814
 B95  BRAB  BR  BR    0  -0.033   4.7162  -1.6893   0.5736
 B95  CAK   C   CH2   0  -0.230  -2.0550   0.3779   0.0452
 B95  HAE   H   HCR6  0   0.255  -9.7332  -0.7862   0.8798
 B95  HAK   H   HCH2  0   0.250  -2.1550  -0.3019   0.8955
 B95  HAKA  H   HCH2  0   0.251  -2.1486  -0.2224  -0.8608

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
 B95  OAA   CAR   double    1.217  0.020  1.217
 B95  BRAB  CAS   single    1.884  0.020  1.884
 B95  CAG   CAC   aromatic  1.389  0.020  1.389
 B95  CAC   CAD   aromatic  1.385  0.020  1.385
 B95  CAC   HAC   single    0.930  0.020  1.080
 B95  CAH   CAD   aromatic  1.389  0.020  1.389
 B95  CAD   HAD   single    0.930  0.020  1.080
 B95  CAI   CAE   aromatic  1.385  0.020  1.385
 B95  CAE   CAF   aromatic  1.403  0.020  1.403
 B95  CAE   HAE   single    0.930  0.020  1.080
 B95  CAJ   CAF   aromatic  1.384  0.020  1.384
 B95  CAF   HAF   single    0.930  0.020  1.080
 B95  CAS   CAG   aromatic  1.384  0.020  1.384
 B95  CAG   HAG   single    0.930  0.020  1.080
 B95  CAU   CAH   aromatic  1.393  0.020  1.393
 B95  CAH   HAH   single    0.930  0.020  1.080
 B95  CAV   CAI   aromatic  1.390  0.020  1.390
 B95  CAI   HAI   single    0.930  0.020  1.080
 B95  CAW   CAJ   aromatic  1.395  0.020  1.395
 B95  CAJ   HAJ   single    0.930  0.020  1.080
 B95  NAO   CAK   single    1.448  0.020  1.448
 B95  CAK   CAL   single    1.523  0.020  1.523
 B95  CAK   HAK   single    0.970  0.020  1.090
 B95  CAK   HAKA  single    0.970  0.020  1.090
 B95  CAL   CAT   single    1.490  0.020  1.490
 B95  CAL   HAL   single    0.970  0.020  1.090
 B95  CAL   HALA  single    0.970  0.020  1.090
 B95  CAM   CAR   single    1.521  0.020  1.521
 B95  CAM   OAQ   single    1.404  0.020  1.404
 B95  CAM   HAM   single    0.970  0.020  1.090
 B95  CAM   HAMA  single    0.970  0.020  1.090
 B95  CAT   NAN   aromatic  1.357  0.020  1.357
 B95  NAN   CAV   aromatic  1.370  0.020  1.370
 B95  CAR   NAO   single    1.339  0.020  1.339
 B95  NAO   HNAO  single    0.860  0.020  1.020
 B95  CAT   NAP   aromatic  1.306  0.020  1.306
 B95  NAP   CAW   aromatic  1.375  0.020  1.375
 B95  OAQ   CAU   single    1.341  0.020  1.341
 B95  CAS   CAU   aromatic  1.400  0.020  1.400
 B95  CAV   CAW   aromatic  1.405  0.020  1.405
 B95  NAN   HNAN  single    0.860  0.020  1.020

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
 B95  HAC   CAC  CAG   119.75  3.000
 B95  HAC   CAC  CAD   120.77  3.000
 B95  CAG   CAC  CAD   119.48  3.000
 B95  HAD   CAD  CAH   119.02  3.000
 B95  HAD   CAD  CAC   120.24  3.000
 B95  CAH   CAD  CAC   120.75  3.000
 B95  HAE   CAE  CAI   119.27  3.000
 B95  HAE   CAE  CAF   119.22  3.000
 B95  CAI   CAE  CAF   121.51  3.000
 B95  HAF   CAF  CAJ   119.46  3.000
 B95  HAF   CAF  CAE   119.10  3.000
 B95  CAJ   CAF  CAE   121.44  3.000
 B95  HAG   CAG  CAS   120.12  3.000
 B95  HAG   CAG  CAC   120.01  3.000
 B95  CAS   CAG  CAC   119.88  3.000
 B95  HAH   CAH  CAU   120.75  3.000
 B95  HAH   CAH  CAD   118.91  3.000
 B95  CAU   CAH  CAD   120.34  3.000
 B95  HAI   CAI  CAV   121.98  3.000
 B95  HAI   CAI  CAE   121.39  3.000
 B95  CAV   CAI  CAE   116.63  3.000
 B95  HAJ   CAJ  CAW   120.83  3.000
 B95  HAJ   CAJ  CAF   121.22  3.000
 B95  CAW   CAJ  CAF   117.95  3.000
 B95  HALA  CAL  HAL   106.98  3.000
 B95  HALA  CAL  CAT   109.05  3.000
 B95  HAL   CAL  CAT   109.62  3.000
 B95  HALA  CAL  CAK   109.70  3.000
 B95  HAL   CAL  CAK   110.28  3.000
 B95  CAT   CAL  CAK   111.12  3.000
 B95  HAMA  CAM  HAM   107.48  3.000
 B95  HAMA  CAM  CAR   108.18  3.000
 B95  HAM   CAM  CAR   110.68  3.000
 B95  HAMA  CAM  OAQ   111.54  3.000
 B95  HAM   CAM  OAQ   111.51  3.000
 B95  CAR   CAM  OAQ   107.42  3.000
 B95  HNAN  NAN  CAV   126.56  3.000
 B95  HNAN  NAN  CAT   125.84  3.000
 B95  CAV   NAN  CAT   107.60  3.000
 B95  HNAO  NAO  CAR   119.14  3.000
 B95  HNAO  NAO  CAK   118.50  3.000
 B95  CAR   NAO  CAK   122.36  3.000
 B95  CAW   NAP  CAT   105.32  3.000
 B95  CAU   OAQ  CAM   118.79  3.000
 B95  NAO   CAR  CAM   113.67  3.000
 B95  NAO   CAR  OAA   123.76  3.000
 B95  CAM   CAR  OAA   122.53  3.000
 B95  CAU   CAS  CAG   121.18  3.000
 B95  CAU   CAS  BRAB  119.06  3.000
 B95  CAG   CAS  BRAB  119.77  3.000
 B95  NAP   CAT  NAN   112.67  3.000
 B95  NAP   CAT  CAL   125.10  3.000
 B95  NAN   CAT  CAL   122.23  3.000
 B95  CAS   CAU  OAQ   116.94  3.000
 B95  CAS   CAU  CAH   118.38  3.000
 B95  OAQ   CAU  CAH   124.68  3.000
 B95  CAW   CAV  NAN   104.44  3.000
 B95  CAW   CAV  CAI   122.68  3.000
 B95  NAN   CAV  CAI   132.88  3.000
 B95  CAV   CAW  NAP   109.97  3.000
 B95  CAV   CAW  CAJ   119.79  3.000
 B95  NAP   CAW  CAJ   130.24  3.000
 B95  HAKA  CAK  HAK   107.22  3.000
 B95  HAKA  CAK  NAO   109.86  3.000
 B95  HAK   CAK  NAO   110.38  3.000
 B95  HAKA  CAK  CAL   109.74  3.000
 B95  HAK   CAK  CAL   109.72  3.000
 B95  NAO   CAK  CAL   109.88  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
 B95  CONST_01  CAU   CAS  CAG  CAC      0.00   0.0  0
 B95  CONST_02  CAU   CAH  CAD  CAC      0.00   0.0  0
 B95  CONST_03  CAS   CAG  CAC  CAD      0.00   0.0  0
 B95  CONST_04  CAS   CAU  CAH  CAD      0.00   0.0  0
 B95  CONST_05  NAN   CAV  CAI  CAE    180.00   0.0  0
 B95  CONST_06  CAW   CAV  CAI  CAE      0.00   0.0  0
 B95  CONST_07  CAW   CAJ  CAF  CAE      0.00   0.0  0
 B95  CONST_08  CAV   CAI  CAE  CAF      0.00   0.0  0
 B95  CONST_09  NAP   CAW  CAJ  CAF    180.00   0.0  0
 B95  CONST_10  CAV   CAW  CAJ  CAF      0.00   0.0  0
 B95  CONST_11  CAH   CAD  CAC  CAG      0.00   0.0  0
 B95  CONST_12  CAH   CAU  CAS  CAG      0.00   0.0  0
 B95  CONST_13  CAJ   CAF  CAE  CAI      0.00   0.0  0
 B95  CONST_14  CAT   NAN  CAV  CAI    180.00   0.0  0
 B95  CONST_15  CAJ   CAW  CAV  CAI      0.00   0.0  0
 B95  CONST_16  NAP   CAW  CAV  CAI    180.00   0.0  0
 B95  CONST_17  CAT   NAP  CAW  CAJ    180.00   0.0  0
 B95  CONST_18  NAN   CAV  CAW  CAJ    180.00   0.0  0
 B95  CONST_19  CAW   NAP  CAT  NAN      0.00   0.0  0
 B95  CONST_20  NAP   CAW  CAV  NAN      0.00   0.0  0
 B95  CONST_21  CAV   NAN  CAT  NAP      0.00   0.0  0
 B95  CONST_22  CAW   CAV  NAN  CAT      0.00   0.0  0
 B95  CONST_23  CAV   CAW  NAP  CAT      0.00   0.0  0
 B95  CONST_24  CAC   CAG  CAS  BRAB   180.00   0.0  0
 B95  CONST_25  CAH   CAU  CAS  BRAB   180.00   0.0  0
 B95  CONST_26  OAQ   CAU  CAH  CAD    180.00   0.0  0
 B95  CONST_27  OAQ   CAU  CAS  CAG    180.00   0.0  0
 B95  CONST_28  CAV   NAN  CAT  CAL    180.00   0.0  0
 B95  CONST_29  CAW   NAP  CAT  CAL    180.00   0.0  0
 B95  CONST_30  HAH   CAH  CAD  CAC    180.00   0.0  0
 B95  CONST_31  HAG   CAG  CAC  CAD    180.00   0.0  0
 B95  CONST_32  HAJ   CAJ  CAF  CAE    180.00   0.0  0
 B95  CONST_33  HAI   CAI  CAE  CAF    180.00   0.0  0
 B95  CONST_34  HAD   CAD  CAC  CAG    180.00   0.0  0
 B95  CONST_35  HAC   CAC  CAD  CAH    180.00   0.0  0
 B95  CONST_36  HAF   CAF  CAE  CAI    180.00   0.0  0
 B95  CONST_37  HNAN  NAN  CAV  CAI      0.00   0.0  0
 B95  CONST_38  HAE   CAE  CAF  CAJ    180.00   0.0  0
 B95  CONST_39  CAK   NAO  CAR  OAA      0.00   0.0  0
 B95  CONST_40  CAM   CAR  NAO  CAK    180.00   0.0  0
 B95  CONST_41  HNAO  NAO  CAR  OAA    180.00   0.0  0
 B95  Var_01    NAN   CAT  CAL  CAK    129.50  30.0  2
 B95  Var_02    CAS   CAU  OAQ  CAM   -176.95  30.0  2
 B95  Var_03    CAT   CAL  CAK  NAO    178.36  30.0  3
 B95  Var_04    HAM   CAM  OAQ  CAU    -65.03  30.0  1
 B95  Var_05    OAQ   CAM  CAR  OAA    -21.57  30.0  2
 B95  Var_06    CAR   NAO  CAK  CAL   -171.81  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
 B95  plan-1  CAC   0.020
 B95  plan-1  CAD   0.020
 B95  plan-1  CAG   0.020
 B95  plan-1  CAH   0.020
 B95  plan-1  OAQ   0.020
 B95  plan-1  CAS   0.020
 B95  plan-1  CAU   0.020
 B95  plan-1  HAC   0.020
 B95  plan-1  HAD   0.020
 B95  plan-1  HAG   0.020
 B95  plan-1  HAH   0.020
 B95  plan-1  BRAB  0.020
 B95  plan-2  CAE   0.020
 B95  plan-2  CAF   0.020
 B95  plan-2  CAI   0.020
 B95  plan-2  CAJ   0.020
 B95  plan-2  CAL   0.020
 B95  plan-2  NAN   0.020
 B95  plan-2  NAP   0.020
 B95  plan-2  CAT   0.020
 B95  plan-2  CAV   0.020
 B95  plan-2  CAW   0.020
 B95  plan-2  HAF   0.020
 B95  plan-2  HAI   0.020
 B95  plan-2  HAJ   0.020
 B95  plan-2  HNAN  0.020
 B95  plan-2  HAE   0.020
 B95  plan-3  OAA   0.020
 B95  plan-3  CAM   0.020
 B95  plan-3  NAO   0.020
 B95  plan-3  CAR   0.020
 B95  plan-3  HNAO  0.020
 B95  plan-3  CAK   0.020

