# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 19:02:11 2021
#   Inital geometry file: a 64 line input string
#   Ligand name: 2-cyano-~{N}-(pyridin-4-ylmethyl)ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(CC#N)NCc1ccncc1
#
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
 S34  S34  2-cyano-~{N}-(pyridin-4-ylmethyl)ethanamide  ligand  22  13  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_S34
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
 S34  N1  N  N     0  -0.411  14.9665  22.0099  11.9536
 S34  N3  N  NS    0  -0.263  18.8156  21.9914   4.7916
 S34  C4  C  CR16  0  -0.357  15.5523  20.6457  10.0746
 S34  C5  C  CR6   0   0.181  14.4375  21.0759   9.3672
 S34  C6  C  CH2   0  -0.336  14.1000  20.5577   7.9925
 S34  C7  C  C     0   0.575  16.1249  20.9488   6.7096
 S34  C8  C  CH2   0  -0.683  17.2616  20.2655   5.9573
 S34  C1  C  CR16  0  -0.367  13.5959  21.9879   9.9934
 S34  C2  C  CR16  0  -0.061  13.9005  22.4191  11.2745
 S34  C3  C  CR16  0  -0.059  15.7691  21.1394  11.3524
 S34  C9  C  CSP   0   0.144  18.1188  21.2394   5.3109
 S34  N2  N  NH1   0  -0.639  15.2381  20.0963   7.2391
 S34  O1  O  O     0  -0.459  16.0521  22.1578   6.8136
 S34  H1  H  HCR6  0   0.261  16.2519  19.9395   9.6473
 S34  H2  H  HCH2  0   0.270  13.5666  21.3280   7.4328
 S34  H3  H  HCH2  0   0.295  13.4138  19.7158   8.0910
 S34  H4  H  HCH2  0   0.347  16.8701  19.5792   5.2029
 S34  H5  H  HCH2  0   0.350  17.8645  19.6673   6.6454
 S34  H6  H  HCR6  0   0.267  12.7144  22.3674   9.4916
 S34  H7  H  HCR6  0   0.264  13.2538  23.1338  11.7714
 S34  H8  H  HCR6  0   0.263  16.6367  20.8117  11.9148
 S34  H9  H  HNH1  0   0.421  15.3589  19.1051   7.1091

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
 S34  N3  C9  triple    1.149  0.020  1.149
 S34  C9  C8  single    1.449  0.020  1.449
 S34  C8  C7  single    1.525  0.020  1.525
 S34  O1  C7  double    1.216  0.020  1.216
 S34  C7  N2  single    1.339  0.020  1.339
 S34  N2  C6  single    1.441  0.020  1.441
 S34  C6  C5  single    1.507  0.020  1.507
 S34  C5  C1  aromatic  1.390  0.020  1.390
 S34  C5  C4  aromatic  1.389  0.020  1.389
 S34  C1  C2  aromatic  1.386  0.020  1.386
 S34  C4  C3  aromatic  1.387  0.020  1.387
 S34  C2  N1  aromatic  1.329  0.020  1.329
 S34  C3  N1  aromatic  1.328  0.020  1.328
 S34  C4  H1  single    0.930  0.020  1.080
 S34  C6  H2  single    0.970  0.020  1.090
 S34  C6  H3  single    0.970  0.020  1.090
 S34  C8  H4  single    0.970  0.020  1.090
 S34  C8  H5  single    0.970  0.020  1.090
 S34  C1  H6  single    0.930  0.020  1.080
 S34  C2  H7  single    0.930  0.020  1.080
 S34  C3  H8  single    0.930  0.020  1.080
 S34  N2  H9  single    0.860  0.020  1.020

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
 S34  C3  N1  C2  117.10  3.000
 S34  H1  C4  C3  119.67  3.000
 S34  H1  C4  C5  121.34  3.000
 S34  C3  C4  C5  118.99  3.000
 S34  C1  C5  C6  120.06  3.000
 S34  C1  C5  C4  117.37  3.000
 S34  C6  C5  C4  122.53  3.000
 S34  H3  C6  H2  106.48  3.000
 S34  H3  C6  N2  107.28  3.000
 S34  H2  C6  N2  110.11  3.000
 S34  H3  C6  C5  108.90  3.000
 S34  H2  C6  C5  109.54  3.000
 S34  N2  C6  C5  114.22  3.000
 S34  O1  C7  N2  124.03  3.000
 S34  N2  C7  C8  113.79  3.000
 S34  O1  C7  C8  122.17  3.000
 S34  H5  C8  H4  106.77  3.000
 S34  H5  C8  C9  108.79  3.000
 S34  H4  C8  C9  109.03  3.000
 S34  H5  C8  C7  110.23  3.000
 S34  H4  C8  C7  110.80  3.000
 S34  C9  C8  C7  111.09  3.000
 S34  H6  C1  C2  119.88  3.000
 S34  H6  C1  C5  120.93  3.000
 S34  C2  C1  C5  119.18  3.000
 S34  H7  C2  C1  119.85  3.000
 S34  H7  C2  N1  116.57  3.000
 S34  C1  C2  N1  123.58  3.000
 S34  H8  C3  C4  119.69  3.000
 S34  H8  C3  N1  116.53  3.000
 S34  C4  C3  N1  123.78  3.000
 S34  C8  C9  N3  180.00  3.000
 S34  H9  N2  C7  119.74  3.000
 S34  H9  N2  C6  118.52  3.000
 S34  C7  N2  C6  121.74  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
 S34  CONST_01  C5  C1  C2  N1    0.00   0.0  0
 S34  CONST_02  C5  C4  C3  N1    0.00   0.0  0
 S34  CONST_03  C2  C1  C5  C4    0.00   0.0  0
 S34  CONST_04  C2  N1  C3  C4    0.00   0.0  0
 S34  CONST_05  C3  C4  C5  C1    0.00   0.0  0
 S34  CONST_06  C3  N1  C2  C1    0.00   0.0  0
 S34  CONST_07  C2  C1  C5  C6  180.00   0.0  0
 S34  CONST_08  C3  C4  C5  C6  180.00   0.0  0
 S34  CONST_09  H6  C1  C2  N1  180.00   0.0  0
 S34  CONST_10  H1  C4  C3  N1  180.00   0.0  0
 S34  CONST_11  H7  C2  C1  C5  180.00   0.0  0
 S34  CONST_12  H8  C3  C4  C5  180.00   0.0  0
 S34  CONST_13  C8  C7  N2  C6  180.00   0.0  0
 S34  CONST_14  O1  C7  N2  C6    0.00   0.0  0
 S34  CONST_15  H9  N2  C7  C8    0.00   0.0  0
 S34  Var_01    N2  C6  C5  C4  -26.60  30.0  2
 S34  Var_02    C7  N2  C6  C5  -73.34  30.0  1
 S34  Var_03    C7  C8  C9  N3  173.27  30.0  3
 S34  Var_04    O1  C7  C8  C9   -5.39  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
 S34  plan-1  N1  0.020
 S34  plan-1  C4  0.020
 S34  plan-1  C5  0.020
 S34  plan-1  C6  0.020
 S34  plan-1  C1  0.020
 S34  plan-1  C2  0.020
 S34  plan-1  C3  0.020
 S34  plan-1  H1  0.020
 S34  plan-1  H6  0.020
 S34  plan-1  H7  0.020
 S34  plan-1  H8  0.020
 S34  plan-2  C6  0.020
 S34  plan-2  C7  0.020
 S34  plan-2  C8  0.020
 S34  plan-2  N2  0.020
 S34  plan-2  O1  0.020
 S34  plan-2  H9  0.020

