# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 11:39:15 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: 3-pyridin-3-ylpropanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=CCCc1cccnc1
#
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
 SJW  SJW  "3-pyridin-3-ylpropanal"  ligand  19  10  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SJW
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
 SJW  C1   C  CH2   0  -0.514  -31.2420  59.4924  39.8899
 SJW  C3   C  CR6   0   0.035  -31.0067  60.1427  41.2216
 SJW  C4   C  CR16  0  -0.108  -31.7410  59.7692  42.3431
 SJW  C6   C  CR16  0  -0.074  -30.6425  61.2208  43.7043
 SJW  C7   C  CR16  0  -0.316  -29.8499  61.6733  42.6593
 SJW  C    C  C1    0   0.170  -30.3682  57.7291  38.2812
 SJW  O    O  O     0  -0.378  -31.2886  57.9083  37.5232
 SJW  CH3  C  CH2   0  -0.554  -30.1747  58.4504  39.5764
 SJW  C8   C  CR16  0  -0.187  -30.0368  61.1239  41.4013
 SJW  N5   N  N     0  -0.397  -31.5730  60.2864  43.5543
 SJW  H1   H  HCH2  0   0.258  -31.2509  60.2527  39.1058
 SJW  H2   H  HCH2  0   0.255  -32.2274  59.0229  39.8825
 SJW  H3   H  HCR6  0   0.254  -32.5113  59.0093  42.2460
 SJW  H4   H  HCR6  0   0.259  -30.5219  61.6320  44.7006
 SJW  H5   H  HCR6  0   0.268  -29.1070  62.4404  42.8308
 SJW  H6   H  HCH2  0   0.280  -30.1185  57.6880  40.3625
 SJW  H7   H  HCH2  0   0.278  -29.1735  58.8961  39.5545
 SJW  H8   H  HCR6  0   0.265  -29.4372  61.4586  40.5626
 SJW  H9   H  H     0   0.207  -29.5835  56.9853  38.0520

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
 SJW  O    C    double    1.206  0.020  1.206
 SJW  C    CH3  single    1.495  0.020  1.495
 SJW  CH3  C1   single    1.524  0.020  1.524
 SJW  C1   C3   single    1.501  0.020  1.501
 SJW  C3   C8   aromatic  1.391  0.020  1.391
 SJW  C3   C4   aromatic  1.392  0.020  1.392
 SJW  C8   C7   aromatic  1.385  0.020  1.385
 SJW  C4   N5   aromatic  1.328  0.020  1.328
 SJW  C7   C6   aromatic  1.387  0.020  1.387
 SJW  N5   C6   aromatic  1.327  0.020  1.327
 SJW  C1   H1   single    0.970  0.020  1.090
 SJW  C1   H2   single    0.970  0.020  1.090
 SJW  C4   H3   single    0.930  0.020  1.080
 SJW  C6   H4   single    0.930  0.020  1.080
 SJW  C7   H5   single    0.930  0.020  1.080
 SJW  CH3  H6   single    0.970  0.020  1.090
 SJW  CH3  H7   single    0.970  0.020  1.090
 SJW  C8   H8   single    0.930  0.020  1.080
 SJW  C    H9   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
 SJW  H2   C1   H1   106.68  3.000
 SJW  H2   C1   CH3  109.67  3.000
 SJW  H1   C1   CH3  109.51  3.000
 SJW  H2   C1   C3   109.52  3.000
 SJW  H1   C1   C3   109.68  3.000
 SJW  CH3  C1   C3   111.66  3.000
 SJW  C8   C3   C4   116.94  3.000
 SJW  C4   C3   C1   121.07  3.000
 SJW  C8   C3   C1   121.98  3.000
 SJW  H3   C4   N5   116.34  3.000
 SJW  H3   C4   C3   119.33  3.000
 SJW  N5   C4   C3   124.32  3.000
 SJW  H4   C6   N5   116.66  3.000
 SJW  H4   C6   C7   120.31  3.000
 SJW  N5   C6   C7   123.02  3.000
 SJW  H5   C7   C8   121.19  3.000
 SJW  H5   C7   C6   120.28  3.000
 SJW  C8   C7   C6   118.52  3.000
 SJW  H9   C    CH3  114.36  3.000
 SJW  H9   C    O    120.77  3.000
 SJW  CH3  C    O    124.87  3.000
 SJW  H7   CH3  H6   104.49  3.000
 SJW  H7   CH3  C    107.28  3.000
 SJW  H6   CH3  C    106.99  3.000
 SJW  H7   CH3  C1   111.45  3.000
 SJW  H6   CH3  C1   111.33  3.000
 SJW  C    CH3  C1   114.67  3.000
 SJW  H8   C8   C7   120.36  3.000
 SJW  H8   C8   C3   120.23  3.000
 SJW  C7   C8   C3   119.41  3.000
 SJW  C6   N5   C4   117.78  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
 SJW  CONST_01  C6   C7   C8   C3      0.00   0.0  0
 SJW  CONST_02  C6   N5   C4   C3      0.00   0.0  0
 SJW  CONST_03  C7   C8   C3   C4      0.00   0.0  0
 SJW  CONST_04  C7   C6   N5   C4      0.00   0.0  0
 SJW  CONST_05  N5   C4   C3   C8      0.00   0.0  0
 SJW  CONST_06  N5   C6   C7   C8      0.00   0.0  0
 SJW  CONST_07  C7   C8   C3   C1    180.00   0.0  0
 SJW  CONST_08  N5   C4   C3   C1    180.00   0.0  0
 SJW  CONST_09  H5   C7   C8   C3    180.00   0.0  0
 SJW  CONST_10  H8   C8   C3   C4    180.00   0.0  0
 SJW  CONST_11  H4   C6   N5   C4    180.00   0.0  0
 SJW  CONST_12  H8   C8   C7   C6    180.00   0.0  0
 SJW  CONST_13  H3   C4   N5   C6    180.00   0.0  0
 SJW  CONST_14  H3   C4   C3   C8    180.00   0.0  0
 SJW  CONST_15  H4   C6   C7   C8    180.00   0.0  0
 SJW  CONST_16  H5   C7   C6   N5    180.00   0.0  0
 SJW  Var_01    CH3  C1   C3   C4   -101.69  30.0  3
 SJW  Var_02    C8   C3   C1   CH3    77.18  30.0  2
 SJW  Var_03    H1   C1   C3   C4    136.74  30.0  3
 SJW  Var_04    H2   C1   C3   C4     19.98  30.0  3
 SJW  Var_05    H1   C1   C3   C8    -44.39  30.0  3
 SJW  Var_06    H2   C1   C3   C8   -161.15  30.0  3
 SJW  Var_07    C    CH3  C1   C3    178.20  30.0  1
 SJW  Var_08    H6   CH3  C1   C3     56.55  30.0  1
 SJW  Var_09    H7   CH3  C1   C3    -59.68  30.0  1
 SJW  Var_10    O    C    CH3  C1     -1.10  30.0  3
 SJW  Var_11    H9   C    CH3  C1    179.15  30.0  3
 SJW  Var_12    H1   C1   CH3  C     -60.13  30.0  3
 SJW  Var_13    H2   C1   CH3  C      56.62  30.0  3
 SJW  Var_14    H6   CH3  C    O     122.89  30.0  3
 SJW  Var_15    H7   CH3  C    O    -125.45  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
 SJW  plan-1  C1   0.020
 SJW  plan-1  C3   0.020
 SJW  plan-1  C4   0.020
 SJW  plan-1  C6   0.020
 SJW  plan-1  C7   0.020
 SJW  plan-1  C8   0.020
 SJW  plan-1  N5   0.020
 SJW  plan-1  H3   0.020
 SJW  plan-1  H4   0.020
 SJW  plan-1  H5   0.020
 SJW  plan-1  H8   0.020
 SJW  plan-2  C    0.020
 SJW  plan-2  O    0.020
 SJW  plan-2  CH3  0.020
 SJW  plan-2  H9   0.020

