# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 21:07:48 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: 6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-4-(1,2,3,6-tetrahydropyridin-4-yl)-1H-benzimidazole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Cn2c3cc(Cl)cc(C4=CCNCC4)c3nc2N5CCNCC5)cc(C)c1F
#
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
 FVD  FVD  6-chloro-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-4-(1,2,3,6-tetrahydropyridin-4-yl)-1H-benzimidazole  ligand  61  32  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FVD
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
 FVD  N1   N   NR5   0  -0.553   0.4065  -0.3601   1.4279
 FVD  N3   N   NH1   0  -0.600   1.4531  -5.3359   1.0511
 FVD  C4   C   CR6   0   0.162   2.6210   0.3923   0.6850
 FVD  C5   C   CH2   0  -0.454   1.7897  -0.1485   1.8200
 FVD  C6   C   CR5   0   0.684  -0.1291  -1.4900   0.8599
 FVD  C7   C   CH2   0  -0.295   0.1934  -3.6425  -0.1501
 FVD  C8   C   CH2   0  -0.302   1.2868  -4.6914  -0.2375
 FVD  C10  C   CH2   0  -0.326   0.7359  -3.3249   2.1850
 FVD  C13  C   C     0   0.060  -3.7782   0.2418  -0.6909
 FVD  C15  C   CH2   0  -0.310  -4.6730  -1.3019  -2.4360
 FVD  C17  C   CH2   0  -0.491  -5.1791   0.6890  -0.3600
 FVD  C20  C   CR16  0  -0.289  -0.4788   1.9862   1.5484
 FVD  C21  C   CR56  0   0.370  -0.4951   0.6483   1.1895
 FVD  C22  C   CR16  0  -0.363   3.0446   1.7139   0.6813
 FVD  C14  C   C1    0  -0.293  -3.5720  -0.6549  -1.6601
 FVD  N5   N   NH1   0  -0.602  -5.9624  -1.0861  -1.8132
 FVD  C16  C   CH2   0  -0.303  -6.1528   0.3086  -1.4631
 FVD  C12  C   CR6   0   0.037  -2.6543   0.8159   0.0746
 FVD  C18  C   CR16  0  -0.321  -2.6494   2.1598   0.4488
 FVD  C19  C   CR6   0  -0.045  -1.5860   2.7169   1.1559
 FVD  CL1  CL  CL    0  -0.138  -1.6539   4.4065   1.5598
 FVD  C11  C   CR56  0   0.095  -1.5449   0.0546   0.4690
 FVD  N4   N   N     0  -0.478  -1.2852  -1.2825   0.2945
 FVD  N2   N   NT    0  -0.544   0.5514  -2.6803   0.8831
 FVD  C9   C   CH2   0  -0.296   1.8233  -4.3744   2.0714
 FVD  C3   C   CR16  0  -0.349   2.9642  -0.4319  -0.3826
 FVD  C2   C   CR6   0  -0.065   3.7092   0.0417  -1.4552
 FVD  C1   C   CH3   0  -0.718   4.0832  -0.8356  -2.6118
 FVD  C25  C   CR6   0   0.499   4.0983   1.3728  -1.4085
 FVD  F1   F   F     0  -0.310   4.8201   1.8544  -2.4389
 FVD  C23  C   CR6   0  -0.072   3.7962   2.2356  -0.3689
 FVD  H1   H   HNH1  0   0.358   2.1578  -6.0580   0.9855
 FVD  H3   H   HCH2  0   0.291   1.8066   0.5325   2.6722
 FVD  H4   H   HCH2  0   0.298   2.2005  -1.0930   2.1683
 FVD  H5   H   HCH2  0   0.252   0.1000  -3.1256  -1.1044
 FVD  H6   H   HCH2  0   0.222  -0.7696  -4.1220   0.0661
 FVD  H7   H   HCH2  0   0.197   2.2095  -4.2042  -0.5930
 FVD  H8   H   HCH2  0   0.242   1.0054  -5.4391  -0.9811
 FVD  H9   H   HCH2  0   0.259   1.0048  -2.5881   2.9408
 FVD  H10  H   HCH2  0   0.238  -0.2022  -3.7948   2.5095
 FVD  H11  H   HCH2  0   0.210  -4.6243  -0.9351  -3.4757
 FVD  H12  H   HCH2  0   0.239  -4.4774  -2.3773  -2.4951
 FVD  H13  H   HCH2  0   0.243  -5.4877   0.2405   0.5899
 FVD  H14  H   HCH2  0   0.241  -5.2220   1.7700  -0.2109
 FVD  H15  H   HCR6  0   0.281   0.3322   2.4382   2.1014
 FVD  H16  H   HCR6  0   0.256   2.7981   2.3619   1.5147
 FVD  H17  H   HCH3  0   0.251   3.8988   4.1967  -1.2591
 FVD  H18  H   HCH3  0   0.249   3.9001   4.1868   0.5012
 FVD  H19  H   HCH3  0   0.252   5.3496   3.7299  -0.3860
 FVD  H20  H   H     0   0.245  -2.5652  -0.9531  -1.9241
 FVD  H21  H   HNH1  0   0.356  -6.6920  -1.3830  -2.4469
 FVD  H23  H   HCH2  0   0.236  -7.1781   0.4513  -1.1186
 FVD  H24  H   HCH2  0   0.195  -6.0052   0.9864  -2.3191
 FVD  H25  H   HCR6  0   0.268  -3.4747   2.8001   0.1689
 FVD  H26  H   HCH2  0   0.242   1.9274  -4.8848   3.0303
 FVD  H27  H   HCH2  0   0.200   2.7783  -3.8674   1.8596
 FVD  H28  H   HCR6  0   0.253   2.6532  -1.4707  -0.3790
 FVD  H29  H   HCH3  0   0.252   5.1632  -0.8759  -2.7570
 FVD  H30  H   HCH3  0   0.246   3.7330  -1.8535  -2.4490
 FVD  H31  H   HCH3  0   0.253   3.6443  -0.4796  -3.5448
 FVD  C24  C   CH3   0  -0.716   4.2608   3.6609  -0.3808

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
 FVD  C1   C2   single    1.499  0.020  1.499
 FVD  N3   C9   single    1.450  0.020  1.450
 FVD  N3   C8   single    1.450  0.020  1.450
 FVD  C9   C10  single    1.516  0.020  1.516
 FVD  F1   C25  single    1.347  0.020  1.347
 FVD  C2   C25  aromatic  1.388  0.020  1.388
 FVD  C2   C3   aromatic  1.389  0.020  1.389
 FVD  C25  C23  aromatic  1.384  0.020  1.384
 FVD  C8   C7   single    1.518  0.020  1.518
 FVD  C10  N2   single    1.464  0.020  1.464
 FVD  C3   C4   aromatic  1.392  0.020  1.392
 FVD  C23  C24  single    1.499  0.020  1.499
 FVD  C23  C22  aromatic  1.393  0.020  1.393
 FVD  C4   C22  aromatic  1.388  0.020  1.388
 FVD  C4   C5   single    1.507  0.020  1.507
 FVD  C7   N2   single    1.457  0.020  1.457
 FVD  N2   C6   single    1.371  0.020  1.371
 FVD  C5   N1   single    1.453  0.020  1.453
 FVD  C6   N1   aromatic  1.373  0.020  1.373
 FVD  C6   N4   aromatic  1.304  0.020  1.304
 FVD  N1   C21  aromatic  1.374  0.020  1.374
 FVD  N4   C11  aromatic  1.373  0.020  1.373
 FVD  C21  C11  aromatic  1.405  0.020  1.405
 FVD  C21  C20  aromatic  1.385  0.020  1.385
 FVD  C11  C12  aromatic  1.402  0.020  1.402
 FVD  C20  C19  aromatic  1.383  0.020  1.383
 FVD  C14  C15  single    1.494  0.020  1.494
 FVD  C14  C13  double    1.336  0.020  1.336
 FVD  C12  C13  single    1.476  0.020  1.476
 FVD  C12  C18  aromatic  1.395  0.020  1.395
 FVD  C19  C18  aromatic  1.393  0.020  1.393
 FVD  C19  CL1  single    1.739  0.020  1.739
 FVD  C15  N5   single    1.448  0.020  1.448
 FVD  C13  C17  single    1.507  0.020  1.507
 FVD  N5   C16  single    1.450  0.020  1.450
 FVD  C17  C16  single    1.520  0.020  1.520
 FVD  N3   H1   single    0.890  0.020  1.040
 FVD  C5   H3   single    0.970  0.020  1.090
 FVD  C5   H4   single    0.970  0.020  1.090
 FVD  C7   H5   single    0.970  0.020  1.090
 FVD  C7   H6   single    0.970  0.020  1.090
 FVD  C8   H7   single    0.970  0.020  1.090
 FVD  C8   H8   single    0.970  0.020  1.090
 FVD  C10  H9   single    0.970  0.020  1.090
 FVD  C10  H10  single    0.970  0.020  1.090
 FVD  C15  H11  single    0.970  0.020  1.090
 FVD  C15  H12  single    0.970  0.020  1.090
 FVD  C17  H13  single    0.970  0.020  1.090
 FVD  C17  H14  single    0.970  0.020  1.090
 FVD  C20  H15  single    0.930  0.020  1.080
 FVD  C22  H16  single    0.930  0.020  1.080
 FVD  C24  H17  single    0.970  0.020  1.090
 FVD  C24  H18  single    0.970  0.020  1.090
 FVD  C24  H19  single    0.970  0.020  1.090
 FVD  C14  H20  single    0.930  0.020  1.080
 FVD  N5   H21  single    0.890  0.020  1.040
 FVD  C16  H23  single    0.970  0.020  1.090
 FVD  C16  H24  single    0.970  0.020  1.090
 FVD  C18  H25  single    0.930  0.020  1.080
 FVD  C9   H26  single    0.970  0.020  1.090
 FVD  C9   H27  single    0.970  0.020  1.090
 FVD  C3   H28  single    0.930  0.020  1.080
 FVD  C1   H29  single    0.970  0.020  1.090
 FVD  C1   H30  single    0.970  0.020  1.090
 FVD  C1   H31  single    0.970  0.020  1.090

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
 FVD  C21  N1   C6   106.03  3.000
 FVD  C21  N1   C5   124.38  3.000
 FVD  C6   N1   C5   127.06  3.000
 FVD  H1   N3   C9   109.95  3.000
 FVD  H1   N3   C8   109.86  3.000
 FVD  C9   N3   C8   111.09  3.000
 FVD  C3   C4   C22  119.12  3.000
 FVD  C22  C4   C5   120.80  3.000
 FVD  C3   C4   C5   120.08  3.000
 FVD  H4   C5   H3   106.63  3.000
 FVD  H4   C5   C4   110.15  3.000
 FVD  H3   C5   C4   110.84  3.000
 FVD  H4   C5   N1   108.64  3.000
 FVD  H3   C5   N1   108.45  3.000
 FVD  C4   C5   N1   111.97  3.000
 FVD  N2   C6   N4   125.84  3.000
 FVD  N4   C6   N1   113.22  3.000
 FVD  N2   C6   N1   120.91  3.000
 FVD  H6   C7   H5   107.74  3.000
 FVD  H6   C7   N2   111.38  3.000
 FVD  H5   C7   N2   109.21  3.000
 FVD  H6   C7   C8   109.98  3.000
 FVD  H5   C7   C8   109.83  3.000
 FVD  N2   C7   C8   108.68  3.000
 FVD  H8   C8   H7   107.39  3.000
 FVD  H8   C8   C7   109.09  3.000
 FVD  H7   C8   C7   108.43  3.000
 FVD  H8   C8   N3   109.30  3.000
 FVD  H7   C8   N3   112.76  3.000
 FVD  C7   C8   N3   109.79  3.000
 FVD  H10  C10  H9   107.18  3.000
 FVD  H10  C10  C9   109.80  3.000
 FVD  H9   C10  C9   110.08  3.000
 FVD  H10  C10  N2   110.08  3.000
 FVD  H9   C10  N2   110.50  3.000
 FVD  C9   C10  N2   109.18  3.000
 FVD  C12  C13  C14  121.30  3.000
 FVD  C12  C13  C17  118.58  3.000
 FVD  C14  C13  C17  120.12  3.000
 FVD  H12  C15  H11  105.53  3.000
 FVD  H12  C15  N5   109.19  3.000
 FVD  H11  C15  N5   113.26  3.000
 FVD  H12  C15  C14  108.77  3.000
 FVD  H11  C15  C14  108.23  3.000
 FVD  N5   C15  C14  111.61  3.000
 FVD  H14  C17  H13  106.02  3.000
 FVD  H14  C17  C16  108.77  3.000
 FVD  H13  C17  C16  110.28  3.000
 FVD  H14  C17  C13  111.11  3.000
 FVD  H13  C17  C13  109.32  3.000
 FVD  C16  C17  C13  111.21  3.000
 FVD  H15  C20  C19  121.66  3.000
 FVD  H15  C20  C21  123.05  3.000
 FVD  C19  C20  C21  115.29  3.000
 FVD  C11  C21  C20  123.35  3.000
 FVD  C20  C21  N1   131.02  3.000
 FVD  C11  C21  N1   105.62  3.000
 FVD  H16  C22  C23  118.58  3.000
 FVD  H16  C22  C4   119.86  3.000
 FVD  C23  C22  C4   121.56  3.000
 FVD  H20  C14  C15  116.06  3.000
 FVD  H20  C14  C13  120.34  3.000
 FVD  C15  C14  C13  123.60  3.000
 FVD  H21  N5   C16  109.81  3.000
 FVD  H21  N5   C15  109.23  3.000
 FVD  C16  N5   C15  111.35  3.000
 FVD  H24  C16  H23  106.90  3.000
 FVD  H24  C16  N5   112.73  3.000
 FVD  H23  C16  N5   108.99  3.000
 FVD  H24  C16  C17  108.91  3.000
 FVD  H23  C16  C17  109.89  3.000
 FVD  N5   C16  C17  109.38  3.000
 FVD  C11  C12  C18  116.41  3.000
 FVD  C18  C12  C13  121.10  3.000
 FVD  C11  C12  C13  122.49  3.000
 FVD  H25  C18  C19  118.50  3.000
 FVD  H25  C18  C12  119.88  3.000
 FVD  C19  C18  C12  121.60  3.000
 FVD  CL1  C19  C18  118.47  3.000
 FVD  CL1  C19  C20  118.60  3.000
 FVD  C18  C19  C20  122.93  3.000
 FVD  N4   C11  C12  129.98  3.000
 FVD  C12  C11  C21  120.40  3.000
 FVD  N4   C11  C21  109.60  3.000
 FVD  C11  N4   C6   105.52  3.000
 FVD  C10  N2   C7   111.77  3.000
 FVD  C7   N2   C6   116.07  3.000
 FVD  C10  N2   C6   117.37  3.000
 FVD  H27  C9   H26  107.55  3.000
 FVD  H27  C9   C10  108.52  3.000
 FVD  H26  C9   C10  109.05  3.000
 FVD  H27  C9   N3   113.03  3.000
 FVD  H26  C9   N3   109.43  3.000
 FVD  C10  C9   N3   109.19  3.000
 FVD  H28  C3   C2   118.88  3.000
 FVD  H28  C3   C4   119.61  3.000
 FVD  C2   C3   C4   121.51  3.000
 FVD  C25  C2   C1   121.16  3.000
 FVD  C25  C2   C3   116.83  3.000
 FVD  C1   C2   C3   122.01  3.000
 FVD  H31  C1   H30  107.67  3.000
 FVD  H31  C1   H29  107.26  3.000
 FVD  H30  C1   H29  107.70  3.000
 FVD  H31  C1   C2   111.62  3.000
 FVD  H30  C1   C2   110.58  3.000
 FVD  H29  C1   C2   111.81  3.000
 FVD  C23  C25  F1   117.94  3.000
 FVD  C23  C25  C2   124.20  3.000
 FVD  F1   C25  C2   117.86  3.000
 FVD  C25  C23  C24  121.26  3.000
 FVD  C24  C23  C22  121.96  3.000
 FVD  C25  C23  C22  116.77  3.000
 FVD  H19  C24  H18  107.70  3.000
 FVD  H19  C24  H17  107.24  3.000
 FVD  H18  C24  H17  107.77  3.000
 FVD  H19  C24  C23  111.69  3.000
 FVD  H18  C24  C23  110.50  3.000
 FVD  H17  C24  C23  111.75  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
 FVD  CONST_01  C11  N4   C6   N1      0.00   0.0  0
 FVD  CONST_02  N4   C11  C21  N1      0.00   0.0  0
 FVD  CONST_03  C12  C11  C21  N1    180.00   0.0  0
 FVD  CONST_04  C19  C20  C21  N1    180.00   0.0  0
 FVD  CONST_05  C25  C2   C3   C4      0.00   0.0  0
 FVD  CONST_06  C25  C23  C22  C4      0.00   0.0  0
 FVD  CONST_07  C11  C21  N1   C6      0.00   0.0  0
 FVD  CONST_08  C20  C21  N1   C6    180.00   0.0  0
 FVD  CONST_09  C21  C11  N4   C6      0.00   0.0  0
 FVD  CONST_10  C12  C11  N4   C6    180.00   0.0  0
 FVD  CONST_11  N4   C11  C21  C20   180.00   0.0  0
 FVD  CONST_12  C12  C11  C21  C20     0.00   0.0  0
 FVD  CONST_13  C12  C18  C19  C20     0.00   0.0  0
 FVD  CONST_14  N4   C6   N1   C21     0.00   0.0  0
 FVD  CONST_15  C18  C12  C11  C21     0.00   0.0  0
 FVD  CONST_16  C18  C19  C20  C21     0.00   0.0  0
 FVD  CONST_17  C2   C25  C23  C22     0.00   0.0  0
 FVD  CONST_18  C2   C3   C4   C22     0.00   0.0  0
 FVD  CONST_19  N4   C11  C12  C18   180.00   0.0  0
 FVD  CONST_20  C11  C21  C20  C19     0.00   0.0  0
 FVD  CONST_21  C11  C12  C18  C19     0.00   0.0  0
 FVD  CONST_22  C23  C25  C2   C3      0.00   0.0  0
 FVD  CONST_23  C23  C22  C4   C3      0.00   0.0  0
 FVD  CONST_24  N4   C11  C12  C13     0.00   0.0  0
 FVD  CONST_25  C21  C11  C12  C13   180.00   0.0  0
 FVD  CONST_26  C19  C18  C12  C13   180.00   0.0  0
 FVD  CONST_27  N2   C6   N1   C21   180.00   0.0  0
 FVD  CONST_28  N2   C6   N4   C11   180.00   0.0  0
 FVD  CONST_29  C1   C2   C3   C4    180.00   0.0  0
 FVD  CONST_30  C24  C23  C22  C4    180.00   0.0  0
 FVD  CONST_31  C2   C3   C4   C5    180.00   0.0  0
 FVD  CONST_32  C23  C22  C4   C5    180.00   0.0  0
 FVD  CONST_37  CL1  C19  C20  C21   180.00   0.0  0
 FVD  CONST_38  F1   C25  C23  C22   180.00   0.0  0
 FVD  CONST_39  C2   C25  C23  C24   180.00   0.0  0
 FVD  CONST_40  CL1  C19  C18  C12   180.00   0.0  0
 FVD  CONST_41  F1   C25  C2   C3    180.00   0.0  0
 FVD  CONST_42  C23  C25  C2   C1    180.00   0.0  0
 FVD  CONST_43  H15  C20  C21  N1      0.00   0.0  0
 FVD  CONST_44  H25  C18  C12  C13     0.00   0.0  0
 FVD  CONST_45  H28  C3   C4   C22   180.00   0.0  0
 FVD  CONST_46  H16  C22  C4   C3    180.00   0.0  0
 FVD  Var_01    C10  N2   C6   N1     67.57  30.0  2
 FVD  Var_02    N2   C10  C9   N3    -57.91  30.0  1
 FVD  Var_03    N2   C7   C8   N3     57.93  30.0  1
 FVD  Var_04    C9   C10  N2   C6   -163.65  30.0  1
 FVD  Var_05    C8   C7   N2   C6    163.45  30.0  1
 FVD  Var_06    C9   N3   C8   C7    -60.18  30.0  1
 FVD  Var_07    C10  C9   N3   C8     59.92  30.0  1
 FVD  Var_08    N5   C15  C14  C13   -13.47  30.0  1
 FVD  Var_09    N5   C16  C17  C13    48.70  30.0  1
 FVD  Var_10    C12  C13  C14  C15   177.92  30.0  1
 FVD  Var_11    C17  C16  N5   C15   -67.10  30.0  1
 FVD  Var_12    C11  C12  C13  C17   141.26  30.0  3
 FVD  Var_13    C16  N5   C15  C14    48.04  30.0  1
 FVD  Var_14    C16  C17  C13  C14   -15.51  30.0  1
 FVD  Var_15    C3   C4   C5   N1    -72.15  30.0  2
 FVD  Var_16    C6   N1   C5   C4     87.95  30.0  2
 FVD  Var_17    H17  C24  C23  C22  -121.86  30.0  2
 FVD  Var_18    H29  C1   C2   C3   -122.63  30.0  2

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
 FVD  plan-1  C4   0.020
 FVD  plan-1  C5   0.020
 FVD  plan-1  C22  0.020
 FVD  plan-1  C3   0.020
 FVD  plan-1  C2   0.020
 FVD  plan-1  C1   0.020
 FVD  plan-1  C25  0.020
 FVD  plan-1  F1   0.020
 FVD  plan-1  C23  0.020
 FVD  plan-1  H16  0.020
 FVD  plan-1  H28  0.020
 FVD  plan-1  C24  0.020
 FVD  plan-2  N1   0.020
 FVD  plan-2  C5   0.020
 FVD  plan-2  C6   0.020
 FVD  plan-2  C13  0.020
 FVD  plan-2  C20  0.020
 FVD  plan-2  C21  0.020
 FVD  plan-2  C12  0.020
 FVD  plan-2  C18  0.020
 FVD  plan-2  C19  0.020
 FVD  plan-2  CL1  0.020
 FVD  plan-2  C11  0.020
 FVD  plan-2  N4   0.020
 FVD  plan-2  N2   0.020
 FVD  plan-2  H15  0.020
 FVD  plan-2  H25  0.020

