# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 14:40:39 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}pyridine-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CCCOc2ccc(cc2C(F)(F)F)c3cccc(n3)C#N)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
 93N  93N  6-{4-[3-(4-methylpiperazin-1-yl)propoxy]-3-(trifluoromethyl)phenyl}pyridine-2-carbonitrile  ligand  52  29  .  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_93N
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
 93N  N1    N  N     0  -0.453  -5.5029   0.1794  -0.0610
 93N  C2    C  CR6   0   0.267  -4.6712   1.2067   0.0653
 93N  C3    C  CR16  0  -0.324  -5.1587   2.5085   0.2430
 93N  C4    C  CR16  0  -0.135  -6.5212   2.7271   0.2830
 93N  C5    C  CR16  0  -0.284  -7.3880   1.6513   0.1507
 93N  C6    C  CR6   0   0.207  -6.8091   0.4038  -0.0171
 93N  C7    C  CR6   0   0.057  -3.2272   0.9008   0.0161
 93N  C8    C  CR16  0  -0.315  -2.7974  -0.4252  -0.0475
 93N  C9    C  CR6   0  -0.291  -1.4547  -0.7493  -0.0903
 93N  C10   C  CR6   0   0.418  -0.4840   0.2673  -0.0739
 93N  C11   C  CR16  0  -0.364  -0.9051   1.5928  -0.0137
 93N  C12   C  CR16  0  -0.315  -2.2546   1.8958   0.0308
 93N  O13   O  O2    0  -0.459   0.7924  -0.1131  -0.1181
 93N  C14   C  CH2   0  -0.180   1.8180   0.8747  -0.1146
 93N  C15   C  CH2   0  -0.479   3.1556   0.1685  -0.1710
 93N  C16   C  CH2   0  -0.262   4.2839   1.1926  -0.1970
 93N  N17   N  NT    0  -0.425   5.5998   0.5886  -0.2684
 93N  C18   C  CSP   0   0.055  -7.6450  -0.7593  -0.1575
 93N  N19   N  NS    0  -0.234  -8.3195  -1.6850  -0.2694
 93N  C20   C  CT    0   1.067  -1.0207  -2.1814  -0.1551
 93N  F21   F  F     0  -0.313  -0.3120  -2.4463  -1.2611
 93N  F22   F  F     0  -0.312  -0.2568  -2.5279   0.8896
 93N  F23   F  F     0  -0.302  -2.0618  -3.0221  -0.1601
 93N  C24   C  CH2   0  -0.282   7.3683  -0.6725   0.8492
 93N  N25   N  NT    0  -0.411   8.3621   0.2884   0.4164
 93N  C26   C  CH2   0  -0.283   7.9566   0.8908  -0.8367
 93N  C27   C  CH2   0  -0.287   6.5992   1.5516  -0.6958
 93N  C28   C  CH2   0  -0.294   6.0091  -0.0129   0.9879
 93N  C29   C  CH3   0  -0.517   9.6782  -0.2990   0.3304
 93N  H3    H  HCR6  0   0.286  -4.4869   3.3469   0.3540
 93N  H4    H  HCR6  0   0.293  -6.9083   3.7271   0.4207
 93N  H5    H  HCR6  0   0.298  -8.4614   1.7720   0.1779
 93N  H8    H  HCR6  0   0.275  -3.5432  -1.2066  -0.0608
 93N  H11   H  HCR6  0   0.298  -0.1939   2.4056  -0.0015
 93N  H12   H  HCR6  0   0.269  -2.5266   2.9412   0.0752
 93N  H14   H  HCH2  0   0.233   1.6982   1.5414  -0.9756
 93N  H14A  H  HCH2  0   0.234   1.7480   1.4849   0.7924
 93N  H15   H  HCH2  0   0.243   3.2458  -0.4925   0.6938
 93N  H15A  H  HCH2  0   0.239   3.2136  -0.4536  -1.0673
 93N  H16   H  HCH2  0   0.234   4.1580   1.8222  -1.0825
 93N  H16A  H  HCH2  0   0.195   4.1955   1.8676   0.6723
 93N  H24   H  HCH2  0   0.188   7.2901  -1.5219   0.1470
 93N  H24A  H  HCH2  0   0.234   7.6657  -1.0837   1.8172
 93N  H26   H  HCH2  0   0.234   8.6923   1.6446  -1.1282
 93N  H26A  H  HCH2  0   0.187   7.9130   0.1465  -1.6518
 93N  H27   H  HCH2  0   0.237   6.3023   1.9665  -1.6619
 93N  H27A  H  HCH2  0   0.190   6.6783   2.3969   0.0100
 93N  H28   H  HCH2  0   0.190   6.0537   0.7384   1.7960
 93N  H28A  H  HCH2  0   0.240   5.2860  -0.7704   1.2944
 93N  H29   H  HCH3  0   0.190   9.7437  -1.1193  -0.4021
 93N  H29A  H  HCH3  0   0.231  10.4076   0.4604   0.0435
 93N  H29B  H  HCH3  0   0.232   9.9747  -0.6970   1.3022

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
 93N  C2   N1    aromatic  1.328  0.020  1.328
 93N  N1   C6    aromatic  1.326  0.020  1.326
 93N  C7   C2    single    1.477  0.020  1.477
 93N  C2   C3    aromatic  1.401  0.020  1.401
 93N  C3   C4    aromatic  1.381  0.020  1.381
 93N  C3   H3    single    0.930  0.020  1.080
 93N  C4   C5    aromatic  1.388  0.020  1.388
 93N  C4   H4    single    0.930  0.020  1.080
 93N  C6   C5    aromatic  1.385  0.020  1.385
 93N  C5   H5    single    0.930  0.020  1.080
 93N  C6   C18   single    1.439  0.020  1.439
 93N  C12  C7    aromatic  1.392  0.020  1.392
 93N  C8   C7    aromatic  1.395  0.020  1.395
 93N  C9   C8    aromatic  1.382  0.020  1.382
 93N  C8   H8    single    0.930  0.020  1.080
 93N  C10  C9    aromatic  1.406  0.020  1.406
 93N  C20  C9    single    1.498  0.020  1.498
 93N  O13  C10   single    1.333  0.020  1.333
 93N  C10  C11   aromatic  1.392  0.020  1.392
 93N  C11  C12   aromatic  1.384  0.020  1.384
 93N  C11  H11   single    0.930  0.020  1.080
 93N  C12  H12   single    0.930  0.020  1.080
 93N  O13  C14   single    1.424  0.020  1.424
 93N  C15  C14   single    1.514  0.020  1.514
 93N  C14  H14   single    0.970  0.020  1.090
 93N  C14  H14A  single    0.970  0.020  1.090
 93N  C16  C15   single    1.524  0.020  1.524
 93N  C15  H15   single    0.970  0.020  1.090
 93N  C15  H15A  single    0.970  0.020  1.090
 93N  N17  C16   single    1.450  0.020  1.450
 93N  C16  H16   single    0.970  0.020  1.090
 93N  C16  H16A  single    0.970  0.020  1.090
 93N  C27  N17   single    1.452  0.020  1.452
 93N  C28  N17   single    1.452  0.020  1.452
 93N  C18  N19   triple    1.151  0.020  1.151
 93N  F21  C20   single    1.340  0.020  1.340
 93N  C20  F23   single    1.338  0.020  1.338
 93N  C20  F22   single    1.340  0.020  1.340
 93N  N25  C24   single    1.449  0.020  1.449
 93N  C24  C28   single    1.517  0.020  1.517
 93N  C24  H24   single    0.970  0.020  1.090
 93N  C24  H24A  single    0.970  0.020  1.090
 93N  C29  N25   single    1.444  0.020  1.444
 93N  N25  C26   single    1.448  0.020  1.448
 93N  C26  C27   single    1.516  0.020  1.516
 93N  C26  H26   single    0.970  0.020  1.090
 93N  C26  H26A  single    0.970  0.020  1.090
 93N  C27  H27   single    0.970  0.020  1.090
 93N  C27  H27A  single    0.970  0.020  1.090
 93N  C28  H28   single    0.970  0.020  1.090
 93N  C28  H28A  single    0.970  0.020  1.090
 93N  C29  H29   single    0.970  0.020  1.090
 93N  C29  H29A  single    0.970  0.020  1.090
 93N  C29  H29B  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
 93N  C6    N1   C2    118.88  3.000
 93N  C7    C2   C3    122.46  3.000
 93N  C3    C2   N1    120.86  3.000
 93N  C7    C2   N1    116.68  3.000
 93N  H3    C3   C4    119.21  3.000
 93N  H3    C3   C2    121.18  3.000
 93N  C4    C3   C2    119.61  3.000
 93N  H4    C4   C5    120.36  3.000
 93N  H4    C4   C3    120.24  3.000
 93N  C5    C4   C3    119.40  3.000
 93N  H5    C5   C6    121.25  3.000
 93N  H5    C5   C4    122.10  3.000
 93N  C6    C5   C4    116.65  3.000
 93N  C18   C6   C5    119.79  3.000
 93N  C18   C6   N1    115.60  3.000
 93N  C5    C6   N1    124.61  3.000
 93N  C12   C7   C8    117.69  3.000
 93N  C8    C7   C2    119.97  3.000
 93N  C12   C7   C2    122.34  3.000
 93N  H8    C8   C9    120.05  3.000
 93N  H8    C8   C7    118.38  3.000
 93N  C9    C8   C7    121.57  3.000
 93N  C20   C9   C10   119.46  3.000
 93N  C20   C9   C8    120.47  3.000
 93N  C10   C9   C8    120.06  3.000
 93N  O13   C10  C11   124.26  3.000
 93N  C11   C10  C9    118.70  3.000
 93N  O13   C10  C9    117.04  3.000
 93N  H11   C11  C12   118.49  3.000
 93N  H11   C11  C10   121.18  3.000
 93N  C12   C11  C10   120.32  3.000
 93N  H12   C12  C11   117.28  3.000
 93N  H12   C12  C7    121.07  3.000
 93N  C11   C12  C7    121.65  3.000
 93N  C14   O13  C10   119.46  3.000
 93N  H14A  C14  H14   107.74  3.000
 93N  H14A  C14  C15   110.32  3.000
 93N  H14   C14  C15   110.56  3.000
 93N  H14A  C14  O13   110.03  3.000
 93N  H14   C14  O13   109.97  3.000
 93N  C15   C14  O13   108.22  3.000
 93N  H15A  C15  H15   107.49  3.000
 93N  H15A  C15  C16   109.23  3.000
 93N  H15   C15  C16   111.04  3.000
 93N  H15A  C15  C14   110.07  3.000
 93N  H15   C15  C14   109.02  3.000
 93N  C16   C15  C14   109.96  3.000
 93N  H16A  C16  H16   106.03  3.000
 93N  H16A  C16  N17   111.48  3.000
 93N  H16   C16  N17   107.72  3.000
 93N  H16A  C16  C15   109.76  3.000
 93N  H16   C16  C15   108.39  3.000
 93N  N17   C16  C15   113.14  3.000
 93N  C28   N17  C27   109.60  3.000
 93N  C28   N17  C16   112.70  3.000
 93N  C27   N17  C16   111.28  3.000
 93N  N19   C18  C6    180.00  3.000
 93N  F23   C20  F22   106.50  3.000
 93N  F22   C20  F21   106.91  3.000
 93N  F23   C20  F21   106.51  3.000
 93N  F22   C20  C9    112.26  3.000
 93N  F23   C20  C9    112.05  3.000
 93N  F21   C20  C9    112.21  3.000
 93N  H24A  C24  H24   107.04  3.000
 93N  H24A  C24  C28   109.05  3.000
 93N  H24   C24  C28   109.21  3.000
 93N  H24A  C24  N25   109.12  3.000
 93N  H24   C24  N25   111.63  3.000
 93N  C28   C24  N25   110.70  3.000
 93N  C29   N25  C26   111.90  3.000
 93N  C26   N25  C24   110.02  3.000
 93N  C29   N25  C24   111.92  3.000
 93N  H26A  C26  H26   107.13  3.000
 93N  H26A  C26  C27   109.08  3.000
 93N  H26   C26  C27   109.08  3.000
 93N  H26A  C26  N25   111.67  3.000
 93N  H26   C26  N25   109.22  3.000
 93N  C27   C26  N25   110.58  3.000
 93N  H27A  C27  H27   107.10  3.000
 93N  H27A  C27  C26   109.20  3.000
 93N  H27   C27  C26   109.06  3.000
 93N  H27A  C27  N17   111.65  3.000
 93N  H27   C27  N17   108.97  3.000
 93N  C26   C27  N17   110.76  3.000
 93N  H28A  C28  H28   107.07  3.000
 93N  H28A  C28  C24   108.51  3.000
 93N  H28   C28  C24   109.06  3.000
 93N  H28A  C28  N17   110.11  3.000
 93N  H28   C28  N17   111.27  3.000
 93N  C24   C28  N17   110.70  3.000
 93N  H29B  C29  H29A  107.84  3.000
 93N  H29B  C29  H29   107.72  3.000
 93N  H29A  C29  H29   107.67  3.000
 93N  H29B  C29  N25   110.07  3.000
 93N  H29A  C29  N25   109.98  3.000
 93N  H29   C29  N25   113.37  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
 93N  CONST_01  C12  C7   C2   N1    180.00   0.0  0
 93N  CONST_02  C8   C7   C2   N1      0.00   0.0  0
 93N  CONST_03  C4   C3   C2   N1      0.00   0.0  0
 93N  CONST_04  C4   C5   C6   N1      0.00   0.0  0
 93N  CONST_05  C5   C6   N1   C2      0.00   0.0  0
 93N  CONST_06  C11  C12  C7   C2    180.00   0.0  0
 93N  CONST_07  C9   C8   C7   C2    180.00   0.0  0
 93N  CONST_08  C5   C4   C3   C2      0.00   0.0  0
 93N  CONST_09  C6   N1   C2   C3      0.00   0.0  0
 93N  CONST_10  C12  C7   C2   C3      0.00   0.0  0
 93N  CONST_11  C8   C7   C2   C3    180.00   0.0  0
 93N  CONST_12  C6   C5   C4   C3      0.00   0.0  0
 93N  CONST_13  C7   C2   C3   C4    180.00   0.0  0
 93N  CONST_14  C7   C2   N1   C6    180.00   0.0  0
 93N  CONST_15  C10  C11  C12  C7      0.00   0.0  0
 93N  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 93N  CONST_17  C11  C12  C7   C8      0.00   0.0  0
 93N  CONST_18  C11  C10  C9   C8      0.00   0.0  0
 93N  CONST_19  C12  C7   C8   C9      0.00   0.0  0
 93N  CONST_20  C12  C11  C10  C9      0.00   0.0  0
 93N  CONST_21  C18  C6   N1   C2    180.00   0.0  0
 93N  CONST_22  C18  C6   C5   C4    180.00   0.0  0
 93N  CONST_23  C20  C9   C8   C7    180.00   0.0  0
 93N  CONST_24  O13  C10  C9   C8    180.00   0.0  0
 93N  CONST_25  C20  C9   C10  C11   180.00   0.0  0
 93N  CONST_26  O13  C10  C11  C12   180.00   0.0  0
 93N  CONST_27  H3   C3   C2   N1    180.00   0.0  0
 93N  CONST_28  H5   C5   C6   N1    180.00   0.0  0
 93N  CONST_29  H12  C12  C7   C2      0.00   0.0  0
 93N  CONST_30  H8   C8   C7   C2      0.00   0.0  0
 93N  CONST_31  H4   C4   C3   C2    180.00   0.0  0
 93N  CONST_32  H11  C11  C12  C7    180.00   0.0  0
 93N  Var_01    N25  C26  C27  N17   -58.12  30.0  1
 93N  Var_02    N25  C24  C28  N17    57.90  30.0  1
 93N  Var_03    C27  C26  N25  C24    57.45  30.0  1
 93N  Var_04    C27  N17  C28  C24   -57.48  30.0  1
 93N  Var_05    C28  C24  N25  C26   -57.40  30.0  1
 93N  Var_06    C28  N17  C27  C26    57.65  30.0  1
 93N  Var_07    F21  C20  C9   C8    119.60  30.0  3
 93N  Var_08    H29  C29  N25  C24    61.79  30.0  3
 93N  Var_09    C15  C14  O13  C10  -179.96  30.0  3
 93N  Var_10    N17  C16  C15  C14  -179.27  30.0  1
 93N  Var_11    C16  C15  C14  O13   178.88  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
 93N  plan-1  N1   0.020
 93N  plan-1  C2   0.020
 93N  plan-1  C3   0.020
 93N  plan-1  C4   0.020
 93N  plan-1  C5   0.020
 93N  plan-1  C6   0.020
 93N  plan-1  C7   0.020
 93N  plan-1  C18  0.020
 93N  plan-1  N19  0.020
 93N  plan-1  H3   0.020
 93N  plan-1  H4   0.020
 93N  plan-1  H5   0.020
 93N  plan-2  C2   0.020
 93N  plan-2  C7   0.020
 93N  plan-2  C8   0.020
 93N  plan-2  C9   0.020
 93N  plan-2  C10  0.020
 93N  plan-2  C11  0.020
 93N  plan-2  C12  0.020
 93N  plan-2  O13  0.020
 93N  plan-2  C20  0.020
 93N  plan-2  H8   0.020
 93N  plan-2  H11  0.020
 93N  plan-2  H12  0.020

