# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 03:26:23 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCc1cncnc1N2CCN(CC2)Cc3[nH]c4ccc(cc4n3)C(F)(F)F
#
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
 5FI  5FI  2-{[4-(5-ethylpyrimidin-4-yl)piperazin-1-yl]methyl}-5-(trifluoromethyl)-1H-benzimidazole  ligand  49  28  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5FI
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
 5FI  C4   C  CR6   0   0.476   4.7017  -0.7685   0.3119
 5FI  C5   C  CR6   0  -0.002   5.9513  -0.3828  -0.2269
 5FI  C6   C  CR16  0  -0.073   7.0394  -1.0752   0.2672
 5FI  N1   N  N     0  -0.417   6.9699  -2.0638   1.1592
 5FI  N3   N  N     0  -0.451   4.6272  -1.7894   1.1673
 5FI  FAB  F  F     0  -0.318  -7.0753  -1.5138   0.1786
 5FI  FAC  F  F     0  -0.312  -7.5389   0.3817  -0.7184
 5FI  FAD  F  F     0  -0.307  -7.6519   0.1449   1.4171
 5FI  CAU  C  CR6   0  -0.216  -5.5009   0.2148   0.4511
 5FI  CAE  C  CR16  0  -0.301  -4.9204   0.3598   1.7214
 5FI  CAF  C  CR16  0  -0.292  -3.5843   0.6832   1.8667
 5FI  CAI  C  CR16  0  -0.367  -4.7575   0.3805  -0.7084
 5FI  CAX  C  CR56  0   0.157  -3.4130   0.7038  -0.5759
 5FI  CAY  C  CR56  0   0.355  -2.8466   0.8522   0.7030
 5FI  NAS  N  NR15  0  -0.678  -1.5402   1.1638   0.4636
 5FI  NAR  N  N     0  -0.474  -2.4582   0.9138  -1.5425
 5FI  CAV  C  CR5   0   0.431  -1.3663   1.1840  -0.8834
 5FI  NAZ  N  NT    0  -0.439   1.0372   1.0643  -0.6442
 5FI  CAL  C  CH2   0  -0.276   2.2891   1.7410  -0.9252
 5FI  CAN  C  CH2   0  -0.337   3.3601   1.2663   0.0337
 5FI  CAK  C  CH2   0  -0.294   1.2015  -0.3767  -0.7293
 5FI  CAM  C  CH2   0  -0.298   2.2733  -0.8644   0.2282
 5FI  NBA  N  NT    0  -0.499   3.5197  -0.1776  -0.0616
 5FI  CAJ  C  CH2   0  -0.547   6.1629   0.6133  -1.3356
 5FI  CAA  C  CH3   0  -0.661   6.8213   1.9153  -0.8806
 5FI  C2   C  CR16  0   0.049   5.7468  -2.3827   1.5382
 5FI  H1   H  HCR6  0   0.265   8.0316  -0.8339  -0.1044
 5FI  H2   H  HCR6  0   0.270  -5.5172   0.2236   2.6127
 5FI  H3   H  HCR6  0   0.276  -3.1443   0.8010   2.8475
 5FI  H4   H  HCR6  0   0.271  -5.1928   0.2655  -1.6928
 5FI  H7   H  HCH2  0   0.241  -0.0069   1.1638  -2.5098
 5FI  H8   H  HCH2  0   0.281   0.0165   2.6298  -1.5394
 5FI  H10  H  HCH2  0   0.208   2.6283   1.5730  -1.9610
 5FI  H11  H  HCH2  0   0.251   2.1515   2.8162  -0.7942
 5FI  H12  H  HCH2  0   0.270   4.2905   1.7790  -0.1862
 5FI  H13  H  HCH2  0   0.243   3.0767   1.5398   1.0587
 5FI  H14  H  HCH2  0   0.253   0.2609  -0.8680  -0.4690
 5FI  H15  H  HCH2  0   0.211   1.4591  -0.6919  -1.7537
 5FI  H16  H  HCH2  0   0.223   1.9519  -0.6960   1.2643
 5FI  H17  H  HCH2  0   0.259   2.4046  -1.9361   0.0948
 5FI  H18  H  HCH2  0   0.265   6.8060   0.1469  -2.0860
 5FI  H19  H  HCH2  0   0.256   5.2214   0.8161  -1.8474
 5FI  H20  H  HCH3  0   0.238   6.9362   2.6005  -1.7206
 5FI  H21  H  HCH3  0   0.230   6.2409   2.4249  -0.1107
 5FI  H22  H  HCH3  0   0.233   7.8132   1.7273  -0.4687
 5FI  H23  H  HCR6  0   0.252   5.6460  -3.2118   2.2311
 5FI  H5   H  HNR5  0   0.417  -0.8062   1.3175   1.1385
 5FI  CAO  C  CH2   0  -0.368  -0.0445   1.5386  -1.4769
 5FI  CBB  C  CT    0   1.047  -6.9359  -0.1854   0.3354

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
 5FI  FAB  CBB  single    1.345  0.020  1.345
 5FI  FAD  CBB  single    1.339  0.020  1.339
 5FI  CBB  FAC  single    1.340  0.020  1.340
 5FI  CBB  CAU  single    1.494  0.020  1.494
 5FI  CAU  CAI  aromatic  1.387  0.020  1.387
 5FI  CAU  CAE  aromatic  1.404  0.020  1.404
 5FI  CAI  CAX  aromatic  1.389  0.020  1.389
 5FI  CAE  CAF  aromatic  1.382  0.020  1.382
 5FI  CAX  NAR  aromatic  1.375  0.020  1.375
 5FI  CAX  CAY  aromatic  1.407  0.020  1.407
 5FI  NAR  CAV  aromatic  1.304  0.020  1.304
 5FI  CAA  CAJ  single    1.528  0.020  1.528
 5FI  CAJ  C5   single    1.505  0.020  1.505
 5FI  CAF  CAY  aromatic  1.388  0.020  1.388
 5FI  CAY  NAS  aromatic  1.364  0.020  1.364
 5FI  CAV  NAS  aromatic  1.358  0.020  1.358
 5FI  CAV  CAO  single    1.492  0.020  1.492
 5FI  CAM  CAK  single    1.518  0.020  1.518
 5FI  CAM  NBA  single    1.452  0.020  1.452
 5FI  C5   C6   aromatic  1.381  0.020  1.381
 5FI  C5   C4   aromatic  1.414  0.020  1.414
 5FI  CAO  NAZ  single    1.445  0.020  1.445
 5FI  CAK  NAZ  single    1.453  0.020  1.453
 5FI  C6   N1   aromatic  1.333  0.020  1.333
 5FI  NAZ  CAL  single    1.451  0.020  1.451
 5FI  NBA  C4   single    1.373  0.020  1.373
 5FI  NBA  CAN  single    1.456  0.020  1.456
 5FI  C4   N3   aromatic  1.334  0.020  1.334
 5FI  N1   C2   aromatic  1.320  0.020  1.320
 5FI  CAN  CAL  single    1.514  0.020  1.514
 5FI  N3   C2   aromatic  1.320  0.020  1.320
 5FI  C6   H1   single    0.930  0.020  1.080
 5FI  CAE  H2   single    0.930  0.020  1.080
 5FI  CAF  H3   single    0.930  0.020  1.080
 5FI  CAI  H4   single    0.930  0.020  1.080
 5FI  CAO  H7   single    0.970  0.020  1.090
 5FI  CAO  H8   single    0.970  0.020  1.090
 5FI  CAL  H10  single    0.970  0.020  1.090
 5FI  CAL  H11  single    0.970  0.020  1.090
 5FI  CAN  H12  single    0.970  0.020  1.090
 5FI  CAN  H13  single    0.970  0.020  1.090
 5FI  CAK  H14  single    0.970  0.020  1.090
 5FI  CAK  H15  single    0.970  0.020  1.090
 5FI  CAM  H16  single    0.970  0.020  1.090
 5FI  CAM  H17  single    0.970  0.020  1.090
 5FI  CAJ  H18  single    0.970  0.020  1.090
 5FI  CAJ  H19  single    0.970  0.020  1.090
 5FI  CAA  H20  single    0.970  0.020  1.090
 5FI  CAA  H21  single    0.970  0.020  1.090
 5FI  CAA  H22  single    0.970  0.020  1.090
 5FI  C2   H23  single    0.930  0.020  1.080
 5FI  NAS  H5   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
 5FI  NBA  C4   N3   117.11  3.000
 5FI  N3   C4   C5   120.15  3.000
 5FI  NBA  C4   C5   122.65  3.000
 5FI  CAJ  C5   C6   118.98  3.000
 5FI  C6   C5   C4   115.03  3.000
 5FI  CAJ  C5   C4   125.81  3.000
 5FI  H1   C6   N1   116.17  3.000
 5FI  H1   C6   C5   119.06  3.000
 5FI  N1   C6   C5   124.75  3.000
 5FI  C2   N1   C6   114.81  3.000
 5FI  C2   N3   C4   118.47  3.000
 5FI  CAI  CAU  CAE  121.48  3.000
 5FI  CAE  CAU  CBB  119.65  3.000
 5FI  CAI  CAU  CBB  118.81  3.000
 5FI  H2   CAE  CAF  118.44  3.000
 5FI  H2   CAE  CAU  120.30  3.000
 5FI  CAF  CAE  CAU  121.25  3.000
 5FI  H3   CAF  CAY  122.06  3.000
 5FI  H3   CAF  CAE  120.94  3.000
 5FI  CAY  CAF  CAE  117.00  3.000
 5FI  H4   CAI  CAX  120.04  3.000
 5FI  H4   CAI  CAU  122.14  3.000
 5FI  CAX  CAI  CAU  117.83  3.000
 5FI  NAR  CAX  CAY  110.09  3.000
 5FI  CAY  CAX  CAI  120.06  3.000
 5FI  NAR  CAX  CAI  129.85  3.000
 5FI  NAS  CAY  CAX  104.49  3.000
 5FI  NAS  CAY  CAF  133.14  3.000
 5FI  CAX  CAY  CAF  122.37  3.000
 5FI  H5   NAS  CAV  124.60  3.000
 5FI  H5   NAS  CAY  127.89  3.000
 5FI  CAV  NAS  CAY  107.46  3.000
 5FI  CAV  NAR  CAX  104.95  3.000
 5FI  CAO  CAV  NAR  126.18  3.000
 5FI  CAO  CAV  NAS  120.77  3.000
 5FI  NAR  CAV  NAS  113.02  3.000
 5FI  CAK  NAZ  CAL  110.72  3.000
 5FI  CAL  NAZ  CAO  112.41  3.000
 5FI  CAK  NAZ  CAO  112.12  3.000
 5FI  H11  CAL  H10  107.54  3.000
 5FI  H11  CAL  CAN  108.78  3.000
 5FI  H10  CAL  CAN  109.24  3.000
 5FI  H11  CAL  NAZ  109.11  3.000
 5FI  H10  CAL  NAZ  112.11  3.000
 5FI  CAN  CAL  NAZ  109.98  3.000
 5FI  H13  CAN  H12  107.03  3.000
 5FI  H13  CAN  NBA  109.66  3.000
 5FI  H12  CAN  NBA  111.19  3.000
 5FI  H13  CAN  CAL  109.30  3.000
 5FI  H12  CAN  CAL  109.28  3.000
 5FI  NBA  CAN  CAL  110.31  3.000
 5FI  H15  CAK  H14  107.10  3.000
 5FI  H15  CAK  CAM  109.24  3.000
 5FI  H14  CAK  CAM  108.25  3.000
 5FI  H15  CAK  NAZ  111.37  3.000
 5FI  H14  CAK  NAZ  109.55  3.000
 5FI  CAM  CAK  NAZ  111.20  3.000
 5FI  H17  CAM  H16  107.59  3.000
 5FI  H17  CAM  NBA  109.74  3.000
 5FI  H16  CAM  NBA  111.53  3.000
 5FI  H17  CAM  CAK  108.93  3.000
 5FI  H16  CAM  CAK  109.84  3.000
 5FI  NBA  CAM  CAK  109.16  3.000
 5FI  CAM  NBA  CAN  111.21  3.000
 5FI  CAN  NBA  C4   120.22  3.000
 5FI  CAM  NBA  C4   118.75  3.000
 5FI  H19  CAJ  H18  105.37  3.000
 5FI  H19  CAJ  CAA  110.68  3.000
 5FI  H18  CAJ  CAA  108.33  3.000
 5FI  H19  CAJ  C5   110.33  3.000
 5FI  H18  CAJ  C5   107.83  3.000
 5FI  CAA  CAJ  C5   113.89  3.000
 5FI  H22  CAA  H21  107.34  3.000
 5FI  H22  CAA  H20  107.67  3.000
 5FI  H21  CAA  H20  107.84  3.000
 5FI  H22  CAA  CAJ  110.94  3.000
 5FI  H21  CAA  CAJ  112.27  3.000
 5FI  H20  CAA  CAJ  110.58  3.000
 5FI  H23  C2   N3   116.35  3.000
 5FI  H23  C2   N1   117.00  3.000
 5FI  N3   C2   N1   126.64  3.000
 5FI  H8   CAO  H7   106.52  3.000
 5FI  H8   CAO  NAZ  108.56  3.000
 5FI  H7   CAO  NAZ  113.82  3.000
 5FI  H8   CAO  CAV  108.01  3.000
 5FI  H7   CAO  CAV  108.85  3.000
 5FI  NAZ  CAO  CAV  110.85  3.000
 5FI  CAU  CBB  FAD  112.65  3.000
 5FI  CAU  CBB  FAC  112.32  3.000
 5FI  FAD  CBB  FAC  106.88  3.000
 5FI  CAU  CBB  FAB  111.91  3.000
 5FI  FAC  CBB  FAB  106.24  3.000
 5FI  FAD  CBB  FAB  106.41  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
 5FI  CONST_01  N1   C6   C5   C4      0.00   0.0  0
 5FI  CONST_02  N1   C2   N3   C4      0.00   0.0  0
 5FI  CONST_03  C2   N1   C6   C5      0.00   0.0  0
 5FI  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 5FI  CONST_05  N3   C4   C5   C6      0.00   0.0  0
 5FI  CONST_06  N3   C2   N1   C6      0.00   0.0  0
 5FI  CONST_07  NAR  CAX  CAI  CAU   180.00   0.0  0
 5FI  CONST_08  CAY  CAX  CAI  CAU     0.00   0.0  0
 5FI  CONST_09  CAY  CAF  CAE  CAU     0.00   0.0  0
 5FI  CONST_10  CAX  CAI  CAU  CAE     0.00   0.0  0
 5FI  CONST_11  CAX  CAY  CAF  CAE     0.00   0.0  0
 5FI  CONST_12  NAS  CAY  CAF  CAE   180.00   0.0  0
 5FI  CONST_13  CAI  CAU  CAE  CAF     0.00   0.0  0
 5FI  CONST_14  CAI  CAX  CAY  CAF     0.00   0.0  0
 5FI  CONST_15  NAR  CAX  CAY  CAF   180.00   0.0  0
 5FI  CONST_16  CAV  NAS  CAY  CAF   180.00   0.0  0
 5FI  CONST_17  CAV  NAR  CAX  CAI   180.00   0.0  0
 5FI  CONST_18  NAS  CAY  CAX  CAI   180.00   0.0  0
 5FI  CONST_19  NAS  CAV  NAR  CAX     0.00   0.0  0
 5FI  CONST_20  CAV  NAS  CAY  CAX     0.00   0.0  0
 5FI  CONST_21  CAV  NAR  CAX  CAY     0.00   0.0  0
 5FI  CONST_22  NAR  CAV  NAS  CAY     0.00   0.0  0
 5FI  CONST_23  NAR  CAX  CAY  NAS     0.00   0.0  0
 5FI  CONST_24  NBA  C4   C5   C6    180.00   0.0  0
 5FI  CONST_25  C2   N3   C4   NBA   180.00   0.0  0
 5FI  CONST_26  CAJ  C5   C6   N1    180.00   0.0  0
 5FI  CONST_27  CAJ  C5   C4   N3    180.00   0.0  0
 5FI  CONST_28  CAX  CAI  CAU  CBB   180.00   0.0  0
 5FI  CONST_29  CAF  CAE  CAU  CBB   180.00   0.0  0
 5FI  CONST_30  CAO  CAV  NAR  CAX   180.00   0.0  0
 5FI  CONST_31  CAO  CAV  NAS  CAY   180.00   0.0  0
 5FI  CONST_32  CAJ  C5   C4   NBA     0.00   0.0  0
 5FI  CONST_33  H1   C6   C5   C4    180.00   0.0  0
 5FI  CONST_34  H23  C2   N3   C4    180.00   0.0  0
 5FI  CONST_35  H3   CAF  CAE  CAU   180.00   0.0  0
 5FI  CONST_36  H4   CAI  CAU  CAE   180.00   0.0  0
 5FI  CONST_37  H5   NAS  CAY  CAF     0.00   0.0  0
 5FI  CONST_38  H2   CAE  CAU  CAI   180.00   0.0  0
 5FI  Var_01    CAK  CAM  NBA  C4   -156.56  30.0  1
 5FI  Var_02    CAL  CAN  NBA  C4    156.19  30.0  1
 5FI  Var_03    CAM  NBA  C4   C5    162.42  30.0  2
 5FI  Var_04    NBA  CAM  CAK  NAZ   -57.05  30.0  1
 5FI  Var_05    NBA  CAN  CAL  NAZ    57.47  30.0  1
 5FI  Var_06    CAM  CAK  NAZ  CAL    57.75  30.0  1
 5FI  Var_07    CAK  NAZ  CAL  CAN   -57.31  30.0  1
 5FI  Var_08    NAZ  CAO  CAV  NAS    34.40  30.0  2
 5FI  Var_09    CAA  CAJ  C5   C4    110.74  30.0  2
 5FI  Var_10    CAI  CAU  CBB  FAB    82.67  30.0  2
 5FI  Var_11    H20  CAA  CAJ  C5   -179.23  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
 5FI  plan-1  C4   0.020
 5FI  plan-1  C5   0.020
 5FI  plan-1  C6   0.020
 5FI  plan-1  N1   0.020
 5FI  plan-1  N3   0.020
 5FI  plan-1  NBA  0.020
 5FI  plan-1  CAJ  0.020
 5FI  plan-1  C2   0.020
 5FI  plan-1  H1   0.020
 5FI  plan-1  H23  0.020
 5FI  plan-2  CAU  0.020
 5FI  plan-2  CAE  0.020
 5FI  plan-2  CAF  0.020
 5FI  plan-2  CAI  0.020
 5FI  plan-2  CAX  0.020
 5FI  plan-2  CAY  0.020
 5FI  plan-2  NAS  0.020
 5FI  plan-2  NAR  0.020
 5FI  plan-2  CAV  0.020
 5FI  plan-2  H2   0.020
 5FI  plan-2  H3   0.020
 5FI  plan-2  H4   0.020
 5FI  plan-2  H5   0.020
 5FI  plan-2  CAO  0.020
 5FI  plan-2  CBB  0.020

