# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 14:47:48 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 6-{[3-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenoxy]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(COc2cccc(CNCCc3cccc(F)c3)c2)c1
#
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
 Q05  Q05  6-{[3-({[2-(3-fluorophenyl)ethyl]amino}methyl)phenoxy]methyl}-4-methylpyridin-2-amine  ligand  51  27  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q05
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
 Q05  F23  F  F     0  -0.315   8.3692  -2.7577  -0.7270
 Q05  C23  C  CR6   0   0.548   7.9759  -1.5119  -0.4176
 Q05  C24  C  CR16  0  -0.410   8.8239  -0.7050   0.3144
 Q05  C25  C  CR16  0  -0.202   8.3987   0.5815   0.6154
 Q05  C22  C  CR16  0  -0.450   6.7354  -1.0833  -0.8492
 Q05  C21  C  CR6   0   0.150   6.3139   0.2078  -0.5463
 Q05  C26  C  CR16  0  -0.300   7.1591   1.0350   0.1901
 Q05  C20  C  CH2   0  -0.516   4.9523   0.6821  -0.9667
 Q05  C19  C  CH2   0  -0.234   3.9223   0.4843   0.1425
 Q05  N18  N  NH1   0  -0.581   2.6202   0.9591  -0.2781
 Q05  C17  C  CH2   0  -0.301   1.6088   0.8401   0.7510
 Q05  C15  C  CR6   0   0.117   0.2980   1.4252   0.2976
 Q05  C14  C  CR16  0  -0.285   0.2525   2.7015  -0.2660
 Q05  C13  C  CR16  0  -0.200  -0.9603   3.2406  -0.6487
 Q05  C12  C  CR16  0  -0.374  -2.1481   2.5312  -0.4924
 Q05  C16  C  CR16  0  -0.412  -0.8787   0.7104   0.4462
 Q05  C11  C  CR6   0   0.411  -2.1031   1.2552   0.0541
 Q05  O09  O  O2    0  -0.484  -3.1873   0.4648   0.2415
 Q05  C08  C  CH2   0  -0.196  -4.4427   0.9343  -0.1761
 Q05  C06  C  CR6   0   0.195  -5.4828  -0.1364   0.0031
 Q05  N01  N  N     0  -0.482  -6.7200   0.2937  -0.2431
 Q05  C02  C  CR6   0   0.484  -7.7180  -0.5745  -0.1600
 Q05  N02  N  NH2   0  -0.826  -8.9615  -0.1167  -0.4720
 Q05  C03  C  CR16  0  -0.415  -7.5132  -1.9185   0.1985
 Q05  C04  C  CR6   0   0.228  -6.2338  -2.3518   0.4655
 Q05  C05  C  CR16  0  -0.394  -5.1815  -1.4329   0.3597
 Q05  C07  C  CH3   0  -0.712  -5.9570  -3.7677   0.8667
 Q05  H1   H  HCR6  0   0.257   9.7894  -1.0684   0.6382
 Q05  H2   H  HCR6  0   0.246   9.0451   1.2346   1.1856
 Q05  H3   H  HCR6  0   0.245   6.1066  -1.7515  -1.4247
 Q05  H4   H  HCR6  0   0.229   6.8489   2.0443   0.4303
 Q05  H5   H  HCH2  0   0.243   4.9843   1.7400  -1.2346
 Q05  H6   H  HCH2  0   0.229   4.6317   0.1406  -1.8610
 Q05  H7   H  HCH2  0   0.198   3.9170  -0.5725   0.4505
 Q05  H8   H  HCH2  0   0.219   4.2289   1.0570   1.0230
 Q05  H9   H  HNH1  0   0.327   2.3204   0.4331  -1.0908
 Q05  H11  H  HCH2  0   0.202   1.4525  -0.1956   1.0888
 Q05  H12  H  HCH2  0   0.236   1.9563   1.3927   1.6299
 Q05  H13  H  HCR6  0   0.236   1.1671   3.2627  -0.4000
 Q05  H14  H  HCR6  0   0.241  -0.9984   4.2330  -1.0777
 Q05  H15  H  HCR6  0   0.254  -3.0775   2.9925  -0.7953
 Q05  H16  H  HCR6  0   0.232  -0.8587  -0.2867   0.8718
 Q05  H17  H  HCH2  0   0.231  -4.7429   1.8248   0.3902
 Q05  H18  H  HCH2  0   0.232  -4.4227   1.2266  -1.2341
 Q05  H19  H  HNH2  0   0.363  -9.0826   0.8776  -0.5428
 Q05  H20  H  HNH2  0   0.361  -9.7667  -0.6414  -0.1858
 Q05  H21  H  HCR6  0   0.219  -8.3516  -2.6017   0.2577
 Q05  H22  H  HCR6  0   0.232  -4.1643  -1.7403   0.5538
 Q05  H23  H  HCH3  0   0.242  -5.1513  -4.1935   0.2683
 Q05  H24  H  HCH3  0   0.246  -5.6413  -3.8185   1.9098
 Q05  H25  H  HCH3  0   0.235  -6.8333  -4.4034   0.7536

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
 Q05  C07  C04  single    1.497  0.020  1.497
 Q05  C04  C03  aromatic  1.377  0.020  1.377
 Q05  C04  C05  aromatic  1.401  0.020  1.401
 Q05  C03  C02  aromatic  1.406  0.020  1.406
 Q05  C05  C06  aromatic  1.378  0.020  1.378
 Q05  C02  N02  single    1.361  0.020  1.361
 Q05  C02  N01  aromatic  1.325  0.020  1.325
 Q05  C06  N01  aromatic  1.333  0.020  1.333
 Q05  C06  C08  single    1.503  0.020  1.503
 Q05  C13  C12  aromatic  1.392  0.020  1.392
 Q05  C13  C14  aromatic  1.381  0.020  1.381
 Q05  C12  C11  aromatic  1.389  0.020  1.389
 Q05  C14  C15  aromatic  1.396  0.020  1.396
 Q05  C11  O09  single    1.355  0.020  1.355
 Q05  C11  C16  aromatic  1.396  0.020  1.396
 Q05  O09  C08  single    1.404  0.020  1.404
 Q05  C15  C16  aromatic  1.385  0.020  1.385
 Q05  C15  C17  single    1.505  0.020  1.505
 Q05  C17  N18  single    1.448  0.020  1.448
 Q05  C20  C21  single    1.502  0.020  1.502
 Q05  C20  C19  single    1.526  0.020  1.526
 Q05  N18  C19  single    1.448  0.020  1.448
 Q05  C21  C22  aromatic  1.392  0.020  1.392
 Q05  C21  C26  aromatic  1.393  0.020  1.393
 Q05  C22  C23  aromatic  1.382  0.020  1.382
 Q05  C26  C25  aromatic  1.387  0.020  1.387
 Q05  C23  F23  single    1.343  0.020  1.343
 Q05  C23  C24  aromatic  1.381  0.020  1.381
 Q05  C25  C24  aromatic  1.388  0.020  1.388
 Q05  C24  H1   single    0.930  0.020  1.080
 Q05  C25  H2   single    0.930  0.020  1.080
 Q05  C22  H3   single    0.930  0.020  1.080
 Q05  C26  H4   single    0.930  0.020  1.080
 Q05  C20  H5   single    0.970  0.020  1.090
 Q05  C20  H6   single    0.970  0.020  1.090
 Q05  C19  H7   single    0.970  0.020  1.090
 Q05  C19  H8   single    0.970  0.020  1.090
 Q05  N18  H9   single    0.890  0.020  1.040
 Q05  C17  H11  single    0.970  0.020  1.090
 Q05  C17  H12  single    0.970  0.020  1.090
 Q05  C14  H13  single    0.930  0.020  1.080
 Q05  C13  H14  single    0.930  0.020  1.080
 Q05  C12  H15  single    0.930  0.020  1.080
 Q05  C16  H16  single    0.930  0.020  1.080
 Q05  C08  H17  single    0.970  0.020  1.090
 Q05  C08  H18  single    0.970  0.020  1.090
 Q05  N02  H19  single    0.890  0.020  1.040
 Q05  N02  H20  single    0.890  0.020  1.040
 Q05  C03  H21  single    0.930  0.020  1.080
 Q05  C05  H22  single    0.930  0.020  1.080
 Q05  C07  H23  single    0.970  0.020  1.090
 Q05  C07  H24  single    0.970  0.020  1.090
 Q05  C07  H25  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
 Q05  C22  C23  C24  122.40  3.000
 Q05  C24  C23  F23  118.98  3.000
 Q05  C22  C23  F23  118.61  3.000
 Q05  H1   C24  C25  121.34  3.000
 Q05  H1   C24  C23  120.72  3.000
 Q05  C25  C24  C23  117.94  3.000
 Q05  H2   C25  C26  119.90  3.000
 Q05  H2   C25  C24  119.40  3.000
 Q05  C26  C25  C24  120.69  3.000
 Q05  H3   C22  C21  120.81  3.000
 Q05  H3   C22  C23  119.73  3.000
 Q05  C21  C22  C23  119.46  3.000
 Q05  C20  C21  C26  120.70  3.000
 Q05  C26  C21  C22  118.83  3.000
 Q05  C20  C21  C22  120.44  3.000
 Q05  H4   C26  C21  119.79  3.000
 Q05  H4   C26  C25  119.53  3.000
 Q05  C21  C26  C25  120.68  3.000
 Q05  H6   C20  H5   106.72  3.000
 Q05  H6   C20  C19  109.41  3.000
 Q05  H5   C20  C19  108.88  3.000
 Q05  H6   C20  C21  109.78  3.000
 Q05  H5   C20  C21  110.37  3.000
 Q05  C19  C20  C21  111.56  3.000
 Q05  H8   C19  H7   106.18  3.000
 Q05  H8   C19  N18  108.30  3.000
 Q05  H7   C19  N18  113.05  3.000
 Q05  H8   C19  C20  109.14  3.000
 Q05  H7   C19  C20  109.33  3.000
 Q05  N18  C19  C20  110.68  3.000
 Q05  H9   N18  C17  108.70  3.000
 Q05  H9   N18  C19  109.19  3.000
 Q05  C17  N18  C19  113.25  3.000
 Q05  H12  C17  H11  105.88  3.000
 Q05  H12  C17  C15  108.78  3.000
 Q05  H11  C17  C15  109.55  3.000
 Q05  H12  C17  N18  107.90  3.000
 Q05  H11  C17  N18  113.25  3.000
 Q05  C15  C17  N18  111.24  3.000
 Q05  C16  C15  C14  119.18  3.000
 Q05  C16  C15  C17  120.46  3.000
 Q05  C14  C15  C17  120.35  3.000
 Q05  H13  C14  C13  120.38  3.000
 Q05  H13  C14  C15  119.80  3.000
 Q05  C13  C14  C15  119.82  3.000
 Q05  H14  C13  C12  118.81  3.000
 Q05  H14  C13  C14  119.93  3.000
 Q05  C12  C13  C14  121.27  3.000
 Q05  H15  C12  C11  122.02  3.000
 Q05  H15  C12  C13  118.99  3.000
 Q05  C11  C12  C13  118.99  3.000
 Q05  H16  C16  C11  119.02  3.000
 Q05  H16  C16  C15  120.07  3.000
 Q05  C11  C16  C15  120.90  3.000
 Q05  O09  C11  C16  115.80  3.000
 Q05  C16  C11  C12  119.83  3.000
 Q05  O09  C11  C12  124.37  3.000
 Q05  C08  O09  C11  118.65  3.000
 Q05  H18  C08  H17  106.64  3.000
 Q05  H18  C08  C06  108.49  3.000
 Q05  H17  C08  C06  109.10  3.000
 Q05  H18  C08  O09  111.07  3.000
 Q05  H17  C08  O09  111.25  3.000
 Q05  C06  C08  O09  110.18  3.000
 Q05  C05  C06  N01  123.67  3.000
 Q05  N01  C06  C08  112.98  3.000
 Q05  C05  C06  C08  123.34  3.000
 Q05  C02  N01  C06  118.43  3.000
 Q05  C03  C02  N02  120.86  3.000
 Q05  N02  C02  N01  116.95  3.000
 Q05  C03  C02  N01  122.17  3.000
 Q05  H20  N02  H19  116.20  3.000
 Q05  H20  N02  C02  119.47  3.000
 Q05  H19  N02  C02  117.34  3.000
 Q05  H21  C03  C04  120.67  3.000
 Q05  H21  C03  C02  120.27  3.000
 Q05  C04  C03  C02  119.05  3.000
 Q05  C07  C04  C05  120.10  3.000
 Q05  C05  C04  C03  118.48  3.000
 Q05  C07  C04  C03  121.42  3.000
 Q05  H22  C05  C04  120.47  3.000
 Q05  H22  C05  C06  121.34  3.000
 Q05  C04  C05  C06  118.19  3.000
 Q05  H25  C07  H24  107.76  3.000
 Q05  H25  C07  H23  108.05  3.000
 Q05  H24  C07  H23  107.03  3.000
 Q05  H25  C07  C04  112.06  3.000
 Q05  H24  C07  C04  110.71  3.000
 Q05  H23  C07  C04  111.03  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
 Q05  CONST_01  C26  C21  C22  C23     0.00   0.0  0
 Q05  CONST_02  C26  C25  C24  C23     0.00   0.0  0
 Q05  CONST_03  C21  C22  C23  C24     0.00   0.0  0
 Q05  CONST_04  C21  C26  C25  C24     0.00   0.0  0
 Q05  CONST_05  C22  C21  C26  C25     0.00   0.0  0
 Q05  CONST_06  C22  C23  C24  C25     0.00   0.0  0
 Q05  CONST_07  C12  C13  C14  C15     0.00   0.0  0
 Q05  CONST_08  C12  C11  C16  C15     0.00   0.0  0
 Q05  CONST_09  C11  C12  C13  C14     0.00   0.0  0
 Q05  CONST_10  C11  C16  C15  C14     0.00   0.0  0
 Q05  CONST_11  C16  C11  C12  C13     0.00   0.0  0
 Q05  CONST_12  C16  C15  C14  C13     0.00   0.0  0
 Q05  CONST_13  C03  C04  C05  C06     0.00   0.0  0
 Q05  CONST_14  C03  C02  N01  C06     0.00   0.0  0
 Q05  CONST_15  C04  C03  C02  N01     0.00   0.0  0
 Q05  CONST_16  C04  C05  C06  N01     0.00   0.0  0
 Q05  CONST_17  C05  C04  C03  C02     0.00   0.0  0
 Q05  CONST_18  C05  C06  N01  C02     0.00   0.0  0
 Q05  CONST_19  C21  C22  C23  F23   180.00   0.0  0
 Q05  CONST_20  C25  C24  C23  F23   180.00   0.0  0
 Q05  CONST_21  C20  C21  C22  C23   180.00   0.0  0
 Q05  CONST_22  C20  C21  C26  C25   180.00   0.0  0
 Q05  CONST_23  C13  C14  C15  C17   180.00   0.0  0
 Q05  CONST_24  C11  C16  C15  C17   180.00   0.0  0
 Q05  CONST_25  O09  C11  C16  C15   180.00   0.0  0
 Q05  CONST_26  O09  C11  C12  C13   180.00   0.0  0
 Q05  CONST_27  C04  C05  C06  C08   180.00   0.0  0
 Q05  CONST_28  C02  N01  C06  C08   180.00   0.0  0
 Q05  CONST_29  C07  C04  C05  C06   180.00   0.0  0
 Q05  CONST_30  N02  C02  N01  C06   180.00   0.0  0
 Q05  CONST_31  C07  C04  C03  C02   180.00   0.0  0
 Q05  CONST_32  C04  C03  C02  N02   180.00   0.0  0
 Q05  CONST_33  H2   C25  C24  C23   180.00   0.0  0
 Q05  CONST_34  H3   C22  C23  C24   180.00   0.0  0
 Q05  CONST_35  H4   C26  C25  C24   180.00   0.0  0
 Q05  CONST_36  H1   C24  C23  C22   180.00   0.0  0
 Q05  CONST_37  H14  C13  C14  C15   180.00   0.0  0
 Q05  CONST_38  H15  C12  C13  C14   180.00   0.0  0
 Q05  CONST_39  H16  C16  C15  C14   180.00   0.0  0
 Q05  CONST_40  H13  C14  C13  C12   180.00   0.0  0
 Q05  CONST_41  H21  C03  C02  N01   180.00   0.0  0
 Q05  CONST_42  H22  C05  C06  N01   180.00   0.0  0
 Q05  CONST_43  H19  N02  C02  N01     0.00   0.0  0
 Q05  Var_01    C19  C20  C21  C22    94.02  30.0  2
 Q05  Var_02    C14  C15  C17  N18   -49.49  30.0  2
 Q05  Var_03    C06  C08  O09  C11   174.74  30.0  3
 Q05  Var_04    C05  C06  C08  O09    -7.84  30.0  2
 Q05  Var_05    H23  C07  C04  C03   130.39  30.0  2
 Q05  Var_06    N18  C19  C20  C21   179.46  30.0  3
 Q05  Var_07    C15  C17  N18  C19   176.39  30.0  2
 Q05  Var_08    C17  N18  C19  C20  -178.00  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
 Q05  plan-1  F23  0.020
 Q05  plan-1  C23  0.020
 Q05  plan-1  C24  0.020
 Q05  plan-1  C25  0.020
 Q05  plan-1  C22  0.020
 Q05  plan-1  C21  0.020
 Q05  plan-1  C26  0.020
 Q05  plan-1  C20  0.020
 Q05  plan-1  H1   0.020
 Q05  plan-1  H2   0.020
 Q05  plan-1  H3   0.020
 Q05  plan-1  H4   0.020
 Q05  plan-2  C17  0.020
 Q05  plan-2  C15  0.020
 Q05  plan-2  C14  0.020
 Q05  plan-2  C13  0.020
 Q05  plan-2  C12  0.020
 Q05  plan-2  C16  0.020
 Q05  plan-2  C11  0.020
 Q05  plan-2  O09  0.020
 Q05  plan-2  H13  0.020
 Q05  plan-2  H14  0.020
 Q05  plan-2  H15  0.020
 Q05  plan-2  H16  0.020
 Q05  plan-3  C08  0.020
 Q05  plan-3  C06  0.020
 Q05  plan-3  N01  0.020
 Q05  plan-3  C02  0.020
 Q05  plan-3  N02  0.020
 Q05  plan-3  C03  0.020
 Q05  plan-3  C04  0.020
 Q05  plan-3  C05  0.020
 Q05  plan-3  C07  0.020
 Q05  plan-3  H21  0.020
 Q05  plan-3  H22  0.020
 Q05  plan-4  C02  0.020
 Q05  plan-4  N02  0.020
 Q05  plan-4  H19  0.020
 Q05  plan-4  H20  0.020

