# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 15:04:03 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 3,5-bis[2-(6-amino-4-methylpyridin-2-yl)ethyl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(CCc2cc(CCc3cc(C)cc(N)n3)cc(c2)C#N)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
 1EV  1EV  3,5-bis[2-(6-amino-4-methylpyridin-2-yl)ethyl]benzonitrile  ligand  53  28  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1EV
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
 1EV  N10  N  NS    0  -0.254   0.0160   5.9089   0.0116
 1EV  C10  C  CSP   0   0.049   0.0136   4.7565   0.0105
 1EV  C11  C  CR6   0   0.051   0.0112   3.3288   0.0085
 1EV  C16  C  CR16  0  -0.331  -1.1646   2.6463  -0.2984
 1EV  C12  C  CR16  0  -0.331   1.1840   2.6411   0.3141
 1EV  C13  C  CR6   0   0.168   1.1874   1.2524   0.3143
 1EV  C09  C  CH2   0  -0.514   2.4501   0.4867   0.5847
 1EV  C08  C  CH2   0  -0.490   3.2265   0.2089  -0.7097
 1EV  C06  C  CR6   0   0.279   4.4877  -0.5630  -0.4438
 1EV  N01  N  N     0  -0.485   5.4331   0.0803   0.2451
 1EV  C02  C  CR6   0   0.440   6.5607  -0.5593   0.5323
 1EV  N02  N  NH2   0  -0.838   7.4834   0.1152   1.2800
 1EV  C03  C  CR16  0  -0.447   6.7936  -1.8875   0.1316
 1EV  C04  C  CR6   0   0.205   5.8189  -2.5533  -0.5815
 1EV  C05  C  CR16  0  -0.434   4.6322  -1.8683  -0.8741
 1EV  C07  C  CH3   0  -0.726   6.0099  -3.9685  -1.0325
 1EV  C14  C  CR16  0  -0.351   0.0053   0.5840   0.0069
 1EV  C15  C  CR6   0   0.168  -1.1739   1.2579  -0.3003
 1EV  C29  C  CH2   0  -0.514  -2.4399   0.4983  -0.5737
 1EV  C28  C  CH2   0  -0.490  -3.2243   0.2296   0.7179
 1EV  C26  C  CR6   0   0.278  -4.4854  -0.5416   0.4484
 1EV  N21  N  N     0  -0.485  -5.4279   0.1021  -0.2442
 1EV  C22  C  CR6   0   0.441  -6.5535  -0.5382  -0.5377
 1EV  N22  N  NH2   0  -0.838  -7.4732   0.1352  -1.2896
 1EV  C23  C  CR16  0  -0.447  -6.7886  -1.8662  -0.1369
 1EV  C24  C  CR6   0   0.205  -5.8176  -2.5311   0.5817
 1EV  C27  C  CH3   0  -0.726  -6.0091  -3.9465   1.0330
 1EV  C25  C  CR16  0  -0.434  -4.6320  -1.8468   0.8789
 1EV  H1   H  HCR6  0   0.271  -2.0649   3.1997  -0.5350
 1EV  H2   H  HCR6  0   0.271   2.0864   3.1906   0.5516
 1EV  H3   H  HCH2  0   0.256   3.0913   1.0433   1.2708
 1EV  H4   H  HCH2  0   0.255   2.2083  -0.4618   1.0703
 1EV  H5   H  HCH2  0   0.251   2.5908  -0.3427  -1.4055
 1EV  H6   H  HCH2  0   0.251   3.4770   1.1600  -1.1876
 1EV  H7   H  HNH2  0   0.379   7.3852   1.1172   1.2989
 1EV  H8   H  HNH2  0   0.388   8.4383  -0.1986   1.2322
 1EV  H9   H  HCR6  0   0.255   7.7276  -2.3743   0.3855
 1EV  H10  H  HCR6  0   0.244   3.8414  -2.3532  -1.4326
 1EV  H11  H  HCH3  0   0.252   5.2703  -4.6251  -0.5709
 1EV  H12  H  HCH3  0   0.251   5.8802  -4.0548  -2.1120
 1EV  H13  H  HCH3  0   0.247   6.9989  -4.3457  -0.7780
 1EV  H14  H  HCR6  0   0.252   0.0033  -0.5012   0.0064
 1EV  H15  H  HCH2  0   0.256  -3.0735   1.0573  -1.2647
 1EV  H16  H  HCH2  0   0.255  -2.2011  -0.4534  -1.0543
 1EV  H17  H  HCH2  0   0.251  -2.5938  -0.3190   1.4206
 1EV  H18  H  HCH2  0   0.251  -3.4760   1.1837   1.1890
 1EV  H19  H  HNH2  0   0.379  -7.3765   1.1373  -1.3093
 1EV  H20  H  HNH2  0   0.388  -8.4270  -0.1833  -1.2528
 1EV  H21  H  HCR6  0   0.255  -7.7220  -2.3523  -0.3955
 1EV  H22  H  HCH3  0   0.252  -5.2871  -4.6061   0.5485
 1EV  H23  H  HCH3  0   0.251  -5.8492  -4.0378   2.1081
 1EV  H24  H  HCH3  0   0.247  -7.0076  -4.3159   0.8041
 1EV  H25  H  HCR6  0   0.244  -3.8428  -2.3310   1.4403

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
 1EV  C07  C04  single    1.498  0.020  1.498
 1EV  C04  C03  aromatic  1.379  0.020  1.379
 1EV  C04  C05  aromatic  1.401  0.020  1.401
 1EV  C03  C02  aromatic  1.407  0.020  1.407
 1EV  C05  C06  aromatic  1.382  0.020  1.382
 1EV  C02  N02  single    1.366  0.020  1.366
 1EV  C02  N01  aromatic  1.328  0.020  1.328
 1EV  C06  N01  aromatic  1.335  0.020  1.335
 1EV  C06  C08  single    1.502  0.020  1.502
 1EV  C09  C08  single    1.535  0.020  1.535
 1EV  C09  C13  single    1.501  0.020  1.501
 1EV  C13  C14  aromatic  1.392  0.020  1.392
 1EV  C13  C12  aromatic  1.389  0.020  1.389
 1EV  C14  C15  aromatic  1.393  0.020  1.393
 1EV  C12  C11  aromatic  1.394  0.020  1.394
 1EV  C15  C29  single    1.502  0.020  1.502
 1EV  C15  C16  aromatic  1.388  0.020  1.388
 1EV  C29  C28  single    1.535  0.020  1.535
 1EV  C11  C16  aromatic  1.394  0.020  1.394
 1EV  C11  C10  single    1.428  0.020  1.428
 1EV  C10  N10  triple    1.152  0.020  1.152
 1EV  C28  C26  single    1.503  0.020  1.503
 1EV  N21  C26  aromatic  1.335  0.020  1.335
 1EV  N21  C22  aromatic  1.328  0.020  1.328
 1EV  C26  C25  aromatic  1.382  0.020  1.382
 1EV  N22  C22  single    1.366  0.020  1.366
 1EV  C22  C23  aromatic  1.407  0.020  1.407
 1EV  C25  C24  aromatic  1.401  0.020  1.401
 1EV  C23  C24  aromatic  1.379  0.020  1.379
 1EV  C24  C27  single    1.498  0.020  1.498
 1EV  C16  H1   single    0.930  0.020  1.080
 1EV  C12  H2   single    0.930  0.020  1.080
 1EV  C09  H3   single    0.970  0.020  1.090
 1EV  C09  H4   single    0.970  0.020  1.090
 1EV  C08  H5   single    0.970  0.020  1.090
 1EV  C08  H6   single    0.970  0.020  1.090
 1EV  N02  H7   single    0.890  0.020  1.040
 1EV  N02  H8   single    0.890  0.020  1.040
 1EV  C03  H9   single    0.930  0.020  1.080
 1EV  C05  H10  single    0.930  0.020  1.080
 1EV  C07  H11  single    0.970  0.020  1.090
 1EV  C07  H12  single    0.970  0.020  1.090
 1EV  C07  H13  single    0.970  0.020  1.090
 1EV  C14  H14  single    0.930  0.020  1.080
 1EV  C29  H15  single    0.970  0.020  1.090
 1EV  C29  H16  single    0.970  0.020  1.090
 1EV  C28  H17  single    0.970  0.020  1.090
 1EV  C28  H18  single    0.970  0.020  1.090
 1EV  N22  H19  single    0.890  0.020  1.040
 1EV  N22  H20  single    0.890  0.020  1.040
 1EV  C23  H21  single    0.930  0.020  1.080
 1EV  C27  H22  single    0.970  0.020  1.090
 1EV  C27  H23  single    0.970  0.020  1.090
 1EV  C27  H24  single    0.970  0.020  1.090
 1EV  C25  H25  single    0.930  0.020  1.080

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
 1EV  C11  C10  N10  180.00  3.000
 1EV  C12  C11  C16  121.11  3.000
 1EV  C16  C11  C10  119.43  3.000
 1EV  C12  C11  C10  119.46  3.000
 1EV  H1   C16  C15  120.34  3.000
 1EV  H1   C16  C11  119.95  3.000
 1EV  C15  C16  C11  119.71  3.000
 1EV  H2   C12  C13  120.35  3.000
 1EV  H2   C12  C11  119.93  3.000
 1EV  C13  C12  C11  119.71  3.000
 1EV  C14  C13  C09  120.60  3.000
 1EV  C14  C13  C12  118.55  3.000
 1EV  C09  C13  C12  120.81  3.000
 1EV  H4   C09  H3   107.06  3.000
 1EV  H4   C09  C08  109.25  3.000
 1EV  H3   C09  C08  108.98  3.000
 1EV  H4   C09  C13  109.68  3.000
 1EV  H3   C09  C13  110.31  3.000
 1EV  C08  C09  C13  111.46  3.000
 1EV  H6   C08  H5   107.11  3.000
 1EV  H6   C08  C06  109.38  3.000
 1EV  H5   C08  C06  110.00  3.000
 1EV  H6   C08  C09  109.09  3.000
 1EV  H5   C08  C09  109.53  3.000
 1EV  C06  C08  C09  111.61  3.000
 1EV  C05  C06  N01  122.80  3.000
 1EV  N01  C06  C08  116.00  3.000
 1EV  C05  C06  C08  121.19  3.000
 1EV  C02  N01  C06  118.75  3.000
 1EV  C03  C02  N02  120.69  3.000
 1EV  N02  C02  N01  117.02  3.000
 1EV  C03  C02  N01  122.26  3.000
 1EV  H8   N02  H7   113.81  3.000
 1EV  H8   N02  C02  117.46  3.000
 1EV  H7   N02  C02  115.83  3.000
 1EV  H9   C03  C04  120.91  3.000
 1EV  H9   C03  C02  120.01  3.000
 1EV  C04  C03  C02  119.08  3.000
 1EV  C07  C04  C05  120.47  3.000
 1EV  C05  C04  C03  118.07  3.000
 1EV  C07  C04  C03  121.45  3.000
 1EV  H10  C05  C04  120.49  3.000
 1EV  H10  C05  C06  120.48  3.000
 1EV  C04  C05  C06  119.03  3.000
 1EV  H13  C07  H12  108.18  3.000
 1EV  H13  C07  H11  107.96  3.000
 1EV  H12  C07  H11  106.88  3.000
 1EV  H13  C07  C04  111.90  3.000
 1EV  H12  C07  C04  110.96  3.000
 1EV  H11  C07  C04  110.77  3.000
 1EV  H14  C14  C15  118.84  3.000
 1EV  H14  C14  C13  118.80  3.000
 1EV  C15  C14  C13  122.36  3.000
 1EV  C29  C15  C14  120.62  3.000
 1EV  C29  C15  C16  120.78  3.000
 1EV  C14  C15  C16  118.56  3.000
 1EV  H16  C29  H15  107.13  3.000
 1EV  H16  C29  C28  109.23  3.000
 1EV  H15  C29  C28  109.01  3.000
 1EV  H16  C29  C15  109.66  3.000
 1EV  H15  C29  C15  110.22  3.000
 1EV  C28  C29  C15  111.48  3.000
 1EV  H18  C28  H17  107.10  3.000
 1EV  H18  C28  C26  109.38  3.000
 1EV  H17  C28  C26  110.01  3.000
 1EV  H18  C28  C29  109.12  3.000
 1EV  H17  C28  C29  109.54  3.000
 1EV  C26  C28  C29  111.58  3.000
 1EV  C25  C26  N21  122.82  3.000
 1EV  C25  C26  C28  121.18  3.000
 1EV  N21  C26  C28  115.98  3.000
 1EV  C22  N21  C26  118.73  3.000
 1EV  C23  C22  N22  120.65  3.000
 1EV  C23  C22  N21  122.26  3.000
 1EV  N22  C22  N21  117.06  3.000
 1EV  H20  N22  H19  114.00  3.000
 1EV  H20  N22  C22  117.53  3.000
 1EV  H19  N22  C22  115.90  3.000
 1EV  H21  C23  C24  120.97  3.000
 1EV  H21  C23  C22  119.96  3.000
 1EV  C24  C23  C22  119.07  3.000
 1EV  C25  C24  C27  120.39  3.000
 1EV  C27  C24  C23  121.51  3.000
 1EV  C25  C24  C23  118.10  3.000
 1EV  H24  C27  H23  108.25  3.000
 1EV  H24  C27  H22  107.95  3.000
 1EV  H23  C27  H22  106.86  3.000
 1EV  H24  C27  C24  111.99  3.000
 1EV  H23  C27  C24  110.94  3.000
 1EV  H22  C27  C24  110.66  3.000
 1EV  H25  C25  C24  120.56  3.000
 1EV  H25  C25  C26  120.44  3.000
 1EV  C24  C25  C26  119.01  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
 1EV  CONST_01  C14  C13  C12  C11     0.00   0.0  0
 1EV  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 1EV  CONST_03  C13  C14  C15  C16     0.00   0.0  0
 1EV  CONST_04  C13  C12  C11  C16     0.00   0.0  0
 1EV  CONST_05  C15  C14  C13  C12     0.00   0.0  0
 1EV  CONST_06  C15  C16  C11  C12     0.00   0.0  0
 1EV  CONST_07  C03  C04  C05  C06     0.00   0.0  0
 1EV  CONST_08  C03  C02  N01  C06     0.00   0.0  0
 1EV  CONST_09  C04  C03  C02  N01     0.00   0.0  0
 1EV  CONST_10  C04  C05  C06  N01     0.00   0.0  0
 1EV  CONST_11  C05  C04  C03  C02     0.00   0.0  0
 1EV  CONST_12  C05  C06  N01  C02     0.00   0.0  0
 1EV  CONST_13  C23  C22  N21  C26     0.00   0.0  0
 1EV  CONST_14  C23  C24  C25  C26     0.00   0.0  0
 1EV  CONST_15  C24  C25  C26  N21     0.00   0.0  0
 1EV  CONST_16  C24  C23  C22  N21     0.00   0.0  0
 1EV  CONST_17  C25  C26  N21  C22     0.00   0.0  0
 1EV  CONST_18  C25  C24  C23  C22     0.00   0.0  0
 1EV  CONST_19  C13  C12  C11  C10   180.00   0.0  0
 1EV  CONST_20  C15  C16  C11  C10   180.00   0.0  0
 1EV  CONST_21  C09  C13  C12  C11   180.00   0.0  0
 1EV  CONST_22  C29  C15  C16  C11   180.00   0.0  0
 1EV  CONST_23  C29  C15  C14  C13   180.00   0.0  0
 1EV  CONST_24  C15  C14  C13  C09   180.00   0.0  0
 1EV  CONST_25  C04  C05  C06  C08   180.00   0.0  0
 1EV  CONST_26  C02  N01  C06  C08   180.00   0.0  0
 1EV  CONST_27  C07  C04  C05  C06   180.00   0.0  0
 1EV  CONST_28  N02  C02  N01  C06   180.00   0.0  0
 1EV  CONST_29  C07  C04  C03  C02   180.00   0.0  0
 1EV  CONST_30  C04  C03  C02  N02   180.00   0.0  0
 1EV  CONST_31  C22  N21  C26  C28   180.00   0.0  0
 1EV  CONST_32  C24  C25  C26  C28   180.00   0.0  0
 1EV  CONST_33  N22  C22  N21  C26   180.00   0.0  0
 1EV  CONST_34  C27  C24  C25  C26   180.00   0.0  0
 1EV  CONST_35  C27  C24  C23  C22   180.00   0.0  0
 1EV  CONST_36  C24  C23  C22  N22   180.00   0.0  0
 1EV  CONST_37  H14  C14  C15  C16   180.00   0.0  0
 1EV  CONST_38  H2   C12  C11  C16   180.00   0.0  0
 1EV  CONST_39  H1   C16  C11  C12   180.00   0.0  0
 1EV  CONST_40  H9   C03  C02  N01   180.00   0.0  0
 1EV  CONST_41  H10  C05  C06  N01   180.00   0.0  0
 1EV  CONST_42  H25  C25  C26  N21   180.00   0.0  0
 1EV  CONST_43  H21  C23  C22  N21   180.00   0.0  0
 1EV  Var_01    C28  C29  C15  C16   -89.28  30.0  2
 1EV  Var_02    C08  C09  C13  C12   -89.62  30.0  1
 1EV  Var_03    C06  C08  C09  C13  -179.74  30.0  3
 1EV  Var_04    C05  C06  C08  C09   111.83  30.0  2
 1EV  Var_05    C26  C28  C29  C15  -179.47  30.0  3
 1EV  Var_06    N21  C26  C28  C29   -67.40  30.0  2
 1EV  Var_07    H11  C07  C04  C03   117.29  30.0  2
 1EV  Var_08    H22  C27  C24  C23   115.35  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
 1EV  plan-1  N10  0.020
 1EV  plan-1  C10  0.020
 1EV  plan-1  C11  0.020
 1EV  plan-1  C16  0.020
 1EV  plan-1  C12  0.020
 1EV  plan-1  C13  0.020
 1EV  plan-1  C09  0.020
 1EV  plan-1  C14  0.020
 1EV  plan-1  C15  0.020
 1EV  plan-1  C29  0.020
 1EV  plan-1  H1   0.020
 1EV  plan-1  H2   0.020
 1EV  plan-1  H14  0.020
 1EV  plan-2  C08  0.020
 1EV  plan-2  C06  0.020
 1EV  plan-2  N01  0.020
 1EV  plan-2  C02  0.020
 1EV  plan-2  N02  0.020
 1EV  plan-2  C03  0.020
 1EV  plan-2  C04  0.020
 1EV  plan-2  C05  0.020
 1EV  plan-2  C07  0.020
 1EV  plan-2  H9   0.020
 1EV  plan-2  H10  0.020
 1EV  plan-3  C28  0.020
 1EV  plan-3  C26  0.020
 1EV  plan-3  N21  0.020
 1EV  plan-3  C22  0.020
 1EV  plan-3  N22  0.020
 1EV  plan-3  C23  0.020
 1EV  plan-3  C24  0.020
 1EV  plan-3  C27  0.020
 1EV  plan-3  C25  0.020
 1EV  plan-3  H21  0.020
 1EV  plan-3  H25  0.020
 1EV  plan-4  C02  0.020
 1EV  plan-4  N02  0.020
 1EV  plan-4  H7   0.020
 1EV  plan-4  H8   0.020
 1EV  plan-5  C22  0.020
 1EV  plan-5  N22  0.020
 1EV  plan-5  H19  0.020
 1EV  plan-5  H20  0.020

