# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 02:32:08 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: (E)-1-(1-methyl-6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}-1H-imidazo[4,5-c]pyridin-4-yl)methanimine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CCCOc2ccc(cc2C(F)(F)F)c3cc4n(C)cnc4c(C=N)n3)CC1
#
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
 EF3  EF3  (E)-1-(1-methyl-6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}-1H-imidazo[4,5-c]pyridin-4-yl)methanimine  ligand  60  33  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_EF3
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
 EF3  C1    C  CR56  0   0.063    6.5109  -0.5294  -0.0104
 EF3  C2    C  CR56  0   0.479    5.7727  -1.7210  -0.0792
 EF3  N3    N  NR5   0  -0.512    6.7037  -2.7125  -0.1652
 EF3  C4    C  CR15  0   0.113    7.9165  -2.0976  -0.1457
 EF3  N5    N  N     0  -0.454    7.8537  -0.8001  -0.0542
 EF3  C6    C  CR6   0  -0.290    0.3719   1.1337   0.0545
 EF3  C7    C  CR6   0   0.411   -0.4851   0.0251   0.1540
 EF3  C8    C  CR16  0  -0.364    0.0755  -1.2459   0.2339
 EF3  C9    C  CR16  0  -0.322    1.4506  -1.4073   0.2050
 EF3  C10   C  CR6   0   0.060    2.3134  -0.3209   0.0949
 EF3  C11   C  CR16  0  -0.322    1.7422   0.9505   0.0275
 EF3  C12   C  CR6   0   0.219    3.7857  -0.4685   0.0518
 EF3  C13   C  CR16  0  -0.387    4.3905  -1.7213  -0.0555
 EF3  C14   C  CR6   0   0.135    5.8068   0.6713   0.0799
 EF3  N15   N  N     0  -0.461    4.4857   0.6697   0.1116
 EF3  C16   C  CH3   0  -0.531    6.4478  -4.1296  -0.2802
 EF3  C18   C  CH2   0  -0.178   -2.7176  -0.8088   0.2354
 EF3  C19   C  CH2   0  -0.480   -4.1152  -0.2295   0.1809
 EF3  C20   C  CH2   0  -0.260   -5.1566  -1.3394   0.2362
 EF3  N21   N  NT    0  -0.425   -6.5167  -0.8393   0.2761
 EF3  C22   C  CT    0   1.065   -0.2108   2.5107  -0.0218
 EF3  F23   F  F     0  -0.303    0.7356   3.4528  -0.1153
 EF3  F24   F  F     0  -0.313   -1.0094   2.6682  -1.0865
 EF3  F25   F  F     0  -0.314   -0.9419   2.8133   1.0603
 EF3  C26   C  C1    0  -0.100    6.5368   1.9515   0.1374
 EF3  N27   N  N     0  -0.526    5.9363   3.0630   0.1974
 EF3  C28   C  CH2   0  -0.281   -8.3568   0.2722  -0.8823
 EF3  N29   N  NT    0  -0.411   -9.2833  -0.7536  -0.4501
 EF3  C30   C  CH2   0  -0.283   -8.8515  -1.3130   0.8141
 EF3  C31   C  CH2   0  -0.287   -7.4462  -1.8704   0.6992
 EF3  C32   C  CH2   0  -0.294   -6.9489  -0.2821  -0.9923
 EF3  C33   C  CH3   0  -0.518  -10.6387  -0.2605  -0.3832
 EF3  H4    H  HCR5  0   0.298    8.8300  -2.6728  -0.2014
 EF3  H8    H  HCR6  0   0.294   -0.5482  -2.1240   0.3225
 EF3  H9    H  HCR6  0   0.264    1.8326  -2.4166   0.2809
 EF3  H11   H  HCR6  0   0.270    2.4057   1.8002  -0.0474
 EF3  H13   H  HCR6  0   0.287    3.8191  -2.6359  -0.1262
 EF3  H16   H  HCH3  0   0.267    6.0212  -4.3676  -1.2531
 EF3  H16A  H  HCH3  0   0.274    7.3832  -4.6694  -0.1649
 EF3  H16B  H  HCH3  0   0.267    5.7621  -4.4519   0.5006
 EF3  H18   H  HCH2  0   0.232   -2.5524  -1.4968  -0.6011
 EF3  H18A  H  HCH2  0   0.231   -2.5698  -1.3722   1.1633
 EF3  H19   H  HCH2  0   0.238   -4.2680   0.4485   1.0240
 EF3  H19A  H  HCH2  0   0.242   -4.2164   0.3588  -0.7340
 EF3  H20   H  HCH2  0   0.195   -5.0060  -2.0361  -0.6070
 EF3  H20A  H  HCH2  0   0.233   -4.9931  -1.9248   1.1458
 EF3  H26   H  H     0   0.237    7.6236   1.8556   0.1206
 EF3  HN27  H  H     0   0.352    6.6135   3.8201   0.2264
 EF3  H28   H  HCH2  0   0.235   -8.6696   0.6481  -1.8596
 EF3  H28A  H  HCH2  0   0.187   -8.3503   1.1338  -0.1907
 EF3  H30   H  HCH2  0   0.187   -8.8788  -0.5612   1.6229
 EF3  H30A  H  HCH2  0   0.234   -9.5326  -2.1179   1.1027
 EF3  H31   H  HCH2  0   0.189   -7.4543  -2.7260   0.0011
 EF3  H31A  H  HCH2  0   0.237   -7.1332  -2.2533   1.6736
 EF3  H32   H  HCH2  0   0.240   -6.2834   0.5303  -1.2902
 EF3  H32A  H  HCH2  0   0.190   -6.9149  -1.0386  -1.7961
 EF3  H33   H  HCH3  0   0.232  -10.9505   0.1132  -1.3598
 EF3  H33A  H  HCH3  0   0.232  -11.3160  -1.0686  -0.1015
 EF3  H33B  H  HCH3  0   0.190  -10.7704   0.5543   0.3465
 EF3  O17   O  O2    0  -0.462   -1.7964   0.2732   0.1681

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
 EF3  C1   C2    aromatic  1.403  0.020  1.403
 EF3  C1   N5    aromatic  1.371  0.020  1.371
 EF3  C1   C14   aromatic  1.395  0.020  1.395
 EF3  C2   N3    aromatic  1.363  0.020  1.363
 EF3  C2   C13   aromatic  1.382  0.020  1.382
 EF3  N3   C4    aromatic  1.360  0.020  1.360
 EF3  N3   C16   single    1.445  0.020  1.445
 EF3  C4   N5    aromatic  1.302  0.020  1.302
 EF3  C6   C7    aromatic  1.405  0.020  1.405
 EF3  C6   C11   aromatic  1.383  0.020  1.383
 EF3  C6   C22   single    1.497  0.020  1.497
 EF3  C7   C8    aromatic  1.391  0.020  1.391
 EF3  C7   O17   single    1.335  0.020  1.335
 EF3  C8   C9    aromatic  1.385  0.020  1.385
 EF3  C9   C10   aromatic  1.392  0.020  1.392
 EF3  C10  C11   aromatic  1.395  0.020  1.395
 EF3  C10  C12   single    1.480  0.020  1.480
 EF3  C12  C13   aromatic  1.395  0.020  1.395
 EF3  C12  N15   aromatic  1.338  0.020  1.338
 EF3  C14  N15   aromatic  1.322  0.020  1.322
 EF3  C14  C26   single    1.475  0.020  1.475
 EF3  O17  C18   single    1.423  0.020  1.423
 EF3  C18  C19   single    1.514  0.020  1.514
 EF3  C19  C20   single    1.523  0.020  1.523
 EF3  C20  N21   single    1.450  0.020  1.450
 EF3  N21  C31   single    1.451  0.020  1.451
 EF3  N21  C32   single    1.451  0.020  1.451
 EF3  C22  F23   single    1.339  0.020  1.339
 EF3  C22  F24   single    1.340  0.020  1.340
 EF3  C22  F25   single    1.341  0.020  1.341
 EF3  C26  N27   double    1.265  0.020  1.265
 EF3  C28  N29   single    1.448  0.020  1.448
 EF3  C28  C32   single    1.517  0.020  1.517
 EF3  N29  C30   single    1.448  0.020  1.448
 EF3  N29  C33   single    1.444  0.020  1.444
 EF3  C30  C31   single    1.516  0.020  1.516
 EF3  C4   H4    single    0.930  0.020  1.080
 EF3  C8   H8    single    0.930  0.020  1.080
 EF3  C9   H9    single    0.930  0.020  1.080
 EF3  C11  H11   single    0.930  0.020  1.080
 EF3  C13  H13   single    0.930  0.020  1.080
 EF3  C16  H16   single    0.970  0.020  1.090
 EF3  C16  H16A  single    0.970  0.020  1.090
 EF3  C16  H16B  single    0.970  0.020  1.090
 EF3  C18  H18   single    0.970  0.020  1.090
 EF3  C18  H18A  single    0.970  0.020  1.090
 EF3  C19  H19   single    0.970  0.020  1.090
 EF3  C19  H19A  single    0.970  0.020  1.090
 EF3  C20  H20   single    0.970  0.020  1.090
 EF3  C20  H20A  single    0.970  0.020  1.090
 EF3  C26  H26   single    0.930  0.020  1.080
 EF3  N27  HN27  single    0.890  0.020  1.040
 EF3  C28  H28   single    0.970  0.020  1.090
 EF3  C28  H28A  single    0.970  0.020  1.090
 EF3  C30  H30   single    0.970  0.020  1.090
 EF3  C30  H30A  single    0.970  0.020  1.090
 EF3  C31  H31   single    0.970  0.020  1.090
 EF3  C31  H31A  single    0.970  0.020  1.090
 EF3  C32  H32   single    0.970  0.020  1.090
 EF3  C32  H32A  single    0.970  0.020  1.090
 EF3  C33  H33   single    0.970  0.020  1.090
 EF3  C33  H33A  single    0.970  0.020  1.090
 EF3  C33  H33B  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
 EF3  C14   C1   N5    131.81  3.000
 EF3  C14   C1   C2    117.94  3.000
 EF3  N5    C1   C2    110.25  3.000
 EF3  C13   C2   N3    133.16  3.000
 EF3  C13   C2   C1    121.68  3.000
 EF3  N3    C2   C1    105.16  3.000
 EF3  C16   N3   C4    127.06  3.000
 EF3  C16   N3   C2    126.70  3.000
 EF3  C4    N3   C2    106.23  3.000
 EF3  H4    C4   N5    125.07  3.000
 EF3  H4    C4   N3    120.82  3.000
 EF3  N5    C4   N3    114.11  3.000
 EF3  C4    N5   C1    104.26  3.000
 EF3  C22   C6   C11   120.44  3.000
 EF3  C22   C6   C7    119.47  3.000
 EF3  C11   C6   C7    120.10  3.000
 EF3  O17   C7   C8    124.40  3.000
 EF3  O17   C7   C6    116.97  3.000
 EF3  C8    C7   C6    118.63  3.000
 EF3  H8    C8   C9    118.69  3.000
 EF3  H8    C8   C7    120.96  3.000
 EF3  C9    C8   C7    120.35  3.000
 EF3  H9    C9   C10   120.99  3.000
 EF3  H9    C9   C8    117.25  3.000
 EF3  C10   C9   C8    121.75  3.000
 EF3  C12   C10  C11   119.77  3.000
 EF3  C12   C10  C9    122.76  3.000
 EF3  C11   C10  C9    117.47  3.000
 EF3  H11   C11  C10   117.94  3.000
 EF3  H11   C11  C6    120.37  3.000
 EF3  C10   C11  C6    121.69  3.000
 EF3  N15   C12  C13   122.73  3.000
 EF3  N15   C12  C10   115.74  3.000
 EF3  C13   C12  C10   121.53  3.000
 EF3  H13   C13  C12   122.39  3.000
 EF3  H13   C13  C2    121.85  3.000
 EF3  C12   C13  C2    115.76  3.000
 EF3  C26   C14  N15   119.67  3.000
 EF3  C26   C14  C1    119.99  3.000
 EF3  N15   C14  C1    120.34  3.000
 EF3  C14   N15  C12   121.54  3.000
 EF3  H16B  C16  H16A  108.62  3.000
 EF3  H16B  C16  H16   109.24  3.000
 EF3  H16A  C16  H16   108.89  3.000
 EF3  H16B  C16  N3    110.19  3.000
 EF3  H16A  C16  N3    109.06  3.000
 EF3  H16   C16  N3    110.80  3.000
 EF3  H18A  C18  H18   107.66  3.000
 EF3  H18A  C18  C19   110.60  3.000
 EF3  H18   C18  C19   110.61  3.000
 EF3  H18A  C18  O17   110.11  3.000
 EF3  H18   C18  O17   110.12  3.000
 EF3  C19   C18  O17   107.76  3.000
 EF3  H19A  C19  H19   107.41  3.000
 EF3  H19A  C19  C20   111.07  3.000
 EF3  H19   C19  C20   109.18  3.000
 EF3  H19A  C19  C18   108.77  3.000
 EF3  H19   C19  C18   109.81  3.000
 EF3  C20   C19  C18   110.55  3.000
 EF3  H20A  C20  H20   106.08  3.000
 EF3  H20A  C20  N21   107.57  3.000
 EF3  H20   C20  N21   111.51  3.000
 EF3  H20A  C20  C19   108.54  3.000
 EF3  H20   C20  C19   109.80  3.000
 EF3  N21   C20  C19   113.03  3.000
 EF3  C32   N21  C31   109.69  3.000
 EF3  C32   N21  C20   112.82  3.000
 EF3  C31   N21  C20   111.34  3.000
 EF3  F25   C22  F24   106.85  3.000
 EF3  F25   C22  F23   106.44  3.000
 EF3  F24   C22  F23   106.45  3.000
 EF3  F25   C22  C6    112.25  3.000
 EF3  F24   C22  C6    112.37  3.000
 EF3  F23   C22  C6    112.06  3.000
 EF3  H26   C26  N27   123.43  3.000
 EF3  H26   C26  C14   114.59  3.000
 EF3  N27   C26  C14   121.98  3.000
 EF3  HN27  N27  C26   109.85  3.000
 EF3  H28A  C28  H28   107.05  3.000
 EF3  H28A  C28  C32   108.96  3.000
 EF3  H28   C28  C32   109.06  3.000
 EF3  H28A  C28  N29   111.68  3.000
 EF3  H28   C28  N29   109.11  3.000
 EF3  C32   C28  N29   110.89  3.000
 EF3  C33   N29  C30   111.80  3.000
 EF3  C33   N29  C28   111.87  3.000
 EF3  C30   N29  C28   110.08  3.000
 EF3  H30A  C30  H30   107.00  3.000
 EF3  H30A  C30  C31   109.08  3.000
 EF3  H30   C30  C31   109.18  3.000
 EF3  H30A  C30  N29   109.21  3.000
 EF3  H30   C30  N29   111.64  3.000
 EF3  C31   C30  N29   110.62  3.000
 EF3  H31A  C31  H31   107.12  3.000
 EF3  H31A  C31  C30   109.07  3.000
 EF3  H31   C31  C30   109.02  3.000
 EF3  H31A  C31  N21   109.00  3.000
 EF3  H31   C31  N21   111.77  3.000
 EF3  C30   C31  N21   110.77  3.000
 EF3  H32A  C32  H32   107.01  3.000
 EF3  H32A  C32  C28   109.37  3.000
 EF3  H32   C32  C28   108.28  3.000
 EF3  H32A  C32  N21   111.34  3.000
 EF3  H32   C32  N21   110.04  3.000
 EF3  C28   C32  N21   110.69  3.000
 EF3  H33B  C33  H33A  107.61  3.000
 EF3  H33B  C33  H33   107.78  3.000
 EF3  H33A  C33  H33   107.90  3.000
 EF3  H33B  C33  N29   113.30  3.000
 EF3  H33A  C33  N29   109.98  3.000
 EF3  H33   C33  N29   110.10  3.000
 EF3  C18   O17  C7    119.69  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
 EF3  CONST_01  C4   N3   C2   C1      0.00   0.0  0
 EF3  CONST_02  C12  C13  C2   C1      0.00   0.0  0
 EF3  CONST_03  N3   C4   N5   C1      0.00   0.0  0
 EF3  CONST_04  C12  N15  C14  C1      0.00   0.0  0
 EF3  CONST_05  C4   N5   C1   C2      0.00   0.0  0
 EF3  CONST_06  N15  C14  C1   C2      0.00   0.0  0
 EF3  CONST_07  N5   C4   N3   C2      0.00   0.0  0
 EF3  CONST_08  C10  C12  C13  C2    180.00   0.0  0
 EF3  CONST_09  N15  C12  C13  C2      0.00   0.0  0
 EF3  CONST_10  N5   C1   C2   N3      0.00   0.0  0
 EF3  CONST_11  C14  C1   C2   N3    180.00   0.0  0
 EF3  CONST_12  C12  C13  C2   N3    180.00   0.0  0
 EF3  CONST_13  C13  C2   N3   C4    180.00   0.0  0
 EF3  CONST_14  C14  C1   N5   C4    180.00   0.0  0
 EF3  CONST_15  C13  C2   C1   N5    180.00   0.0  0
 EF3  CONST_16  N15  C14  C1   N5    180.00   0.0  0
 EF3  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 EF3  CONST_18  C9   C10  C11  C6      0.00   0.0  0
 EF3  CONST_19  C12  C10  C11  C6    180.00   0.0  0
 EF3  CONST_20  C10  C11  C6   C7      0.00   0.0  0
 EF3  CONST_21  C10  C9   C8   C7      0.00   0.0  0
 EF3  CONST_22  C11  C6   C7   C8      0.00   0.0  0
 EF3  CONST_23  C11  C10  C9   C8      0.00   0.0  0
 EF3  CONST_24  C12  C10  C9   C8    180.00   0.0  0
 EF3  CONST_25  C13  C12  C10  C9      0.00   0.0  0
 EF3  CONST_26  N15  C12  C10  C9    180.00   0.0  0
 EF3  CONST_27  C14  N15  C12  C10   180.00   0.0  0
 EF3  CONST_28  C13  C12  C10  C11   180.00   0.0  0
 EF3  CONST_29  N15  C12  C10  C11     0.00   0.0  0
 EF3  CONST_30  C14  C1   C2   C13     0.00   0.0  0
 EF3  CONST_31  C14  N15  C12  C13     0.00   0.0  0
 EF3  CONST_32  C16  N3   C2   C1    180.00   0.0  0
 EF3  CONST_33  C26  C14  C1   C2    180.00   0.0  0
 EF3  CONST_34  C26  C14  C1   N5      0.00   0.0  0
 EF3  CONST_35  C16  N3   C4   N5    180.00   0.0  0
 EF3  CONST_36  C22  C6   C7   C8    180.00   0.0  0
 EF3  CONST_37  O17  C7   C8   C9    180.00   0.0  0
 EF3  CONST_38  C22  C6   C11  C10   180.00   0.0  0
 EF3  CONST_39  O17  C7   C6   C11   180.00   0.0  0
 EF3  CONST_40  C26  C14  N15  C12   180.00   0.0  0
 EF3  CONST_41  C16  N3   C2   C13     0.00   0.0  0
 EF3  CONST_42  H13  C13  C2   C1    180.00   0.0  0
 EF3  CONST_43  H4   C4   N5   C1    180.00   0.0  0
 EF3  CONST_44  H8   C8   C7   C6    180.00   0.0  0
 EF3  CONST_45  H11  C11  C6   C7    180.00   0.0  0
 EF3  CONST_46  H9   C9   C8   C7    180.00   0.0  0
 EF3  Var_01    N29  C30  C31  N21    58.07  30.0  1
 EF3  Var_02    N29  C28  C32  N21   -57.61  30.0  1
 EF3  Var_03    C31  C30  N29  C28   -57.20  30.0  1
 EF3  Var_04    C31  N21  C32  C28    57.37  30.0  1
 EF3  Var_05    C32  C28  N29  C30    57.08  30.0  1
 EF3  Var_06    C32  N21  C31  C30   -57.70  30.0  1
 EF3  Var_07    N27  C26  C14  C1    178.81  30.0  2
 EF3  Var_08    F23  C22  C6   C7   -179.88  30.0  2
 EF3  Var_09    H16  C16  N3   C2     69.34  30.0  2
 EF3  Var_10    H33  C33  N29  C28    58.54  30.0  3
 EF3  Var_11    C19  C18  O17  C7   -177.81  30.0  3
 EF3  Var_12    N21  C20  C19  C18   176.18  30.0  3
 EF3  Var_13    C20  C19  C18  O17   179.49  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
 EF3  plan-1  C6    0.020
 EF3  plan-1  C7    0.020
 EF3  plan-1  C8    0.020
 EF3  plan-1  C9    0.020
 EF3  plan-1  C10   0.020
 EF3  plan-1  C11   0.020
 EF3  plan-1  C12   0.020
 EF3  plan-1  C22   0.020
 EF3  plan-1  H8    0.020
 EF3  plan-1  H9    0.020
 EF3  plan-1  H11   0.020
 EF3  plan-1  O17   0.020
 EF3  plan-2  C14   0.020
 EF3  plan-2  C26   0.020
 EF3  plan-2  N27   0.020
 EF3  plan-2  H26   0.020
 EF3  plan-2  HN27  0.020
 EF3  plan-3  C1    0.020
 EF3  plan-3  C2    0.020
 EF3  plan-3  N3    0.020
 EF3  plan-3  C4    0.020
 EF3  plan-3  N5    0.020
 EF3  plan-3  C10   0.020
 EF3  plan-3  C12   0.020
 EF3  plan-3  C13   0.020
 EF3  plan-3  C14   0.020
 EF3  plan-3  N15   0.020
 EF3  plan-3  C16   0.020
 EF3  plan-3  C26   0.020
 EF3  plan-3  H4    0.020
 EF3  plan-3  H13   0.020

