# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 22 23:20:55 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: (2E)-N-benzyl-2-cyano-3-(pyridin-4-yl)prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCc1ccccc1)/C(=C/c2ccncc2)C#N
#
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
 1L7  1L7  (2E)-N-benzyl-2-cyano-3-(pyridin-4-yl)prop-2-enamide  ligand  33  20  .  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_1L7
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
 1L7  C10  C  C     0  -0.105   0.9981  -0.3840   0.0505
 1L7  N12  N  NS    0  -0.220   0.6060   2.0596   0.7654
 1L7  C13  C  C1    0  -0.197   2.2123  -0.8999  -0.1970
 1L7  C15  C  CR16  0  -0.352   4.6258  -0.9173   0.2382
 1L7  C01  C  CR16  0  -0.241  -5.0031   1.1686  -1.1231
 1L7  C02  C  CR16  0  -0.263  -5.8994   1.3192  -0.0705
 1L7  C03  C  CR16  0  -0.240  -5.7326   0.5740   1.0875
 1L7  C04  C  CR16  0  -0.298  -4.6745  -0.3216   1.1926
 1L7  C05  C  CR6   0   0.059  -3.7766  -0.4806   0.1438
 1L7  C06  C  CR16  0  -0.282  -3.9479   0.2761  -1.0145
 1L7  C07  C  CH2   0  -0.326  -2.6310  -1.4500   0.2483
 1L7  N08  N  NH1   0  -0.667  -1.3716  -0.7335   0.3224
 1L7  C09  C  C     0   0.618  -0.2088  -1.2792  -0.0497
 1L7  C11  C  CSP   0   0.002   0.8125   0.9738   0.4373
 1L7  C14  C  CR6   0   0.184   3.4992  -0.2125  -0.1842
 1L7  C16  C  CR16  0  -0.053   5.8506  -0.2714   0.2637
 1L7  N17  N  N     0  -0.395   6.0206   0.9870  -0.1243
 1L7  C18  C  CR16  0  -0.054   4.9533   1.6478  -0.5561
 1L7  C19  C  CR16  0  -0.360   3.6793   1.1039  -0.6029
 1L7  O20  O  O     0  -0.472  -0.0957  -2.4206  -0.4642
 1L7  H2   H  H     0   0.306   2.2467  -1.9638  -0.4063
 1L7  H4   H  HCR6  0   0.283   4.5506  -1.9499   0.5523
 1L7  H5   H  HCR6  0   0.258  -5.1295   1.7453  -2.0303
 1L7  H6   H  HCR6  0   0.259  -6.7263   2.0120  -0.1569
 1L7  H7   H  HCR6  0   0.258  -6.4259   0.6875   1.9107
 1L7  H8   H  HCR6  0   0.256  -4.5505  -0.9030   2.0984
 1L7  H9   H  HCR6  0   0.256  -3.2570   0.1563  -1.8410
 1L7  H10  H  HCH2  0   0.265  -2.7628  -2.0992   1.1187
 1L7  H11  H  HCH2  0   0.270  -2.6081  -2.0969  -0.6292
 1L7  H12  H  HNH1  0   0.416  -1.3928   0.1819   0.7450
 1L7  H13  H  HCR6  0   0.275   6.7333  -0.7997   0.6043
 1L7  H14  H  HCR6  0   0.276   5.1140   2.6665  -0.8895
 1L7  H15  H  HCR6  0   0.283   2.8667   1.6957  -0.9993

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
 1L7  C16  C15  aromatic  1.385  0.020  1.385
 1L7  C16  N17  aromatic  1.328  0.020  1.328
 1L7  C15  C14  aromatic  1.394  0.020  1.394
 1L7  N17  C18  aromatic  1.327  0.020  1.327
 1L7  C18  C19  aromatic  1.386  0.020  1.386
 1L7  C14  C19  aromatic  1.393  0.020  1.393
 1L7  C14  C13  single    1.459  0.020  1.459
 1L7  C13  C10  double    1.342  0.020  1.342
 1L7  O20  C09  double    1.220  0.020  1.220
 1L7  C10  C09  single    1.506  0.020  1.506
 1L7  C10  C11  single    1.424  0.020  1.424
 1L7  C09  N08  single    1.337  0.020  1.337
 1L7  N08  C07  single    1.451  0.020  1.451
 1L7  C07  C05  single    1.504  0.020  1.504
 1L7  C11  N12  triple    1.153  0.020  1.153
 1L7  C05  C06  aromatic  1.394  0.020  1.394
 1L7  C05  C04  aromatic  1.390  0.020  1.390
 1L7  C06  C01  aromatic  1.386  0.020  1.386
 1L7  C04  C03  aromatic  1.390  0.020  1.390
 1L7  C01  C02  aromatic  1.391  0.020  1.391
 1L7  C03  C02  aromatic  1.387  0.020  1.387
 1L7  C13  H2   single    0.930  0.020  1.080
 1L7  C15  H4   single    0.930  0.020  1.080
 1L7  C01  H5   single    0.930  0.020  1.080
 1L7  C02  H6   single    0.930  0.020  1.080
 1L7  C03  H7   single    0.930  0.020  1.080
 1L7  C04  H8   single    0.930  0.020  1.080
 1L7  C06  H9   single    0.930  0.020  1.080
 1L7  C07  H10  single    0.970  0.020  1.090
 1L7  C07  H11  single    0.970  0.020  1.090
 1L7  N08  H12  single    0.860  0.020  1.020
 1L7  C16  H13  single    0.930  0.020  1.080
 1L7  C18  H14  single    0.930  0.020  1.080
 1L7  C19  H15  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
 1L7  C11  C10  C09  118.71  3.000
 1L7  C11  C10  C13  122.31  3.000
 1L7  C09  C10  C13  118.96  3.000
 1L7  H2   C13  C14  115.83  3.000
 1L7  H2   C13  C10  116.18  3.000
 1L7  C14  C13  C10  127.96  3.000
 1L7  H4   C15  C16  120.08  3.000
 1L7  H4   C15  C14  120.94  3.000
 1L7  C16  C15  C14  118.98  3.000
 1L7  H5   C01  C06  119.83  3.000
 1L7  H5   C01  C02  120.10  3.000
 1L7  C06  C01  C02  120.07  3.000
 1L7  H6   C02  C03  120.16  3.000
 1L7  H6   C02  C01  120.09  3.000
 1L7  C03  C02  C01  119.75  3.000
 1L7  H7   C03  C04  119.84  3.000
 1L7  H7   C03  C02  120.11  3.000
 1L7  C04  C03  C02  120.05  3.000
 1L7  H8   C04  C05  119.71  3.000
 1L7  H8   C04  C03  119.74  3.000
 1L7  C05  C04  C03  120.55  3.000
 1L7  C07  C05  C06  120.07  3.000
 1L7  C06  C05  C04  119.05  3.000
 1L7  C07  C05  C04  120.88  3.000
 1L7  H9   C06  C05  119.69  3.000
 1L7  H9   C06  C01  119.78  3.000
 1L7  C05  C06  C01  120.54  3.000
 1L7  H11  C07  H10  106.90  3.000
 1L7  H11  C07  N08  108.41  3.000
 1L7  H10  C07  N08  110.92  3.000
 1L7  H11  C07  C05  110.02  3.000
 1L7  H10  C07  C05  110.25  3.000
 1L7  N08  C07  C05  110.27  3.000
 1L7  H12  N08  C09  120.36  3.000
 1L7  H12  N08  C07  116.83  3.000
 1L7  C09  N08  C07  122.62  3.000
 1L7  O20  C09  N08  123.86  3.000
 1L7  N08  C09  C10  115.83  3.000
 1L7  O20  C09  C10  120.31  3.000
 1L7  N12  C11  C10  180.00  3.000
 1L7  C19  C14  C15  117.66  3.000
 1L7  C19  C14  C13  123.82  3.000
 1L7  C15  C14  C13  118.50  3.000
 1L7  H13  C16  N17  116.72  3.000
 1L7  H13  C16  C15  119.92  3.000
 1L7  N17  C16  C15  123.36  3.000
 1L7  C18  N17  C16  117.64  3.000
 1L7  H14  C18  C19  119.65  3.000
 1L7  H14  C18  N17  116.66  3.000
 1L7  C19  C18  N17  123.69  3.000
 1L7  H15  C19  C18  119.25  3.000
 1L7  H15  C19  C14  122.04  3.000
 1L7  C18  C19  C14  118.66  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
 1L7  CONST_01  C18  N17  C16  C15     0.00   0.0  0
 1L7  CONST_02  C18  C19  C14  C15     0.00   0.0  0
 1L7  CONST_03  C04  C05  C06  C01     0.00   0.0  0
 1L7  CONST_04  C04  C03  C02  C01     0.00   0.0  0
 1L7  CONST_05  C05  C06  C01  C02     0.00   0.0  0
 1L7  CONST_06  C05  C04  C03  C02     0.00   0.0  0
 1L7  CONST_07  C06  C05  C04  C03     0.00   0.0  0
 1L7  CONST_08  C06  C01  C02  C03     0.00   0.0  0
 1L7  CONST_09  N17  C16  C15  C14     0.00   0.0  0
 1L7  CONST_10  N17  C18  C19  C14     0.00   0.0  0
 1L7  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 1L7  CONST_12  C19  C18  N17  C16     0.00   0.0  0
 1L7  CONST_13  C16  C15  C14  C13   180.00   0.0  0
 1L7  CONST_14  C18  C19  C14  C13   180.00   0.0  0
 1L7  CONST_15  C07  C05  C06  C01   180.00   0.0  0
 1L7  CONST_16  C07  C05  C04  C03   180.00   0.0  0
 1L7  CONST_17  H15  C19  C14  C15   180.00   0.0  0
 1L7  CONST_18  H7   C03  C02  C01   180.00   0.0  0
 1L7  CONST_19  H9   C06  C01  C02   180.00   0.0  0
 1L7  CONST_20  H8   C04  C03  C02   180.00   0.0  0
 1L7  CONST_21  H5   C01  C02  C03   180.00   0.0  0
 1L7  CONST_22  H6   C02  C03  C04   180.00   0.0  0
 1L7  CONST_23  H13  C16  C15  C14   180.00   0.0  0
 1L7  CONST_24  H14  C18  C19  C14   180.00   0.0  0
 1L7  CONST_25  H4   C15  C16  N17   180.00   0.0  0
 1L7  CONST_26  C07  N08  C09  C10   180.00   0.0  0
 1L7  CONST_27  O20  C09  N08  C07     0.00   0.0  0
 1L7  CONST_28  H12  N08  C09  C10     0.00   0.0  0
 1L7  Var_01    C15  C14  C13  C10   146.19  30.0  2
 1L7  Var_02    N08  C07  C05  C04  -110.96  30.0  2
 1L7  Var_03    C14  C13  C10  C09   178.64   0.0  2
 1L7  Var_04    C09  N08  C07  C05  -155.51  30.0  1
 1L7  Var_05    C13  C10  C11  N12  -167.33  30.0  1
 1L7  Var_06    O20  C09  C10  C13    -6.46  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
 1L7  plan-1  C01  0.020
 1L7  plan-1  C02  0.020
 1L7  plan-1  C03  0.020
 1L7  plan-1  C04  0.020
 1L7  plan-1  C05  0.020
 1L7  plan-1  C06  0.020
 1L7  plan-1  C07  0.020
 1L7  plan-1  H5   0.020
 1L7  plan-1  H6   0.020
 1L7  plan-1  H7   0.020
 1L7  plan-1  H8   0.020
 1L7  plan-1  H9   0.020
 1L7  plan-2  C13  0.020
 1L7  plan-2  C15  0.020
 1L7  plan-2  C14  0.020
 1L7  plan-2  C16  0.020
 1L7  plan-2  N17  0.020
 1L7  plan-2  C18  0.020
 1L7  plan-2  C19  0.020
 1L7  plan-2  H4   0.020
 1L7  plan-2  H13  0.020
 1L7  plan-2  H14  0.020
 1L7  plan-2  H15  0.020
 1L7  plan-3  C10  0.020
 1L7  plan-3  C07  0.020
 1L7  plan-3  N08  0.020
 1L7  plan-3  C09  0.020
 1L7  plan-3  O20  0.020
 1L7  plan-3  H12  0.020
 1L7  plan-4  C10  0.020
 1L7  plan-4  C13  0.020
 1L7  plan-4  C09  0.020
 1L7  plan-4  C11  0.020
 1L7  plan-4  C14  0.020
 1L7  plan-4  H2   0.020

