# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 16:38:26 2020
#   Inital geometry file: a 63 line input string
#   Ligand name: ethyl 5-oxidanylidenehexanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCOC(=O)CCCC(C)=O
#
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
 BKN  BKN  'ethyl 5-oxidanylidenehexanoate'  ligand  25  11  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BKN
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
 BKN  CAA  C  CH3   0  -0.690   4.9447   0.6979  -0.0210
 BKN  CAE  C  CH2   0  -0.181   3.8546  -0.3458  -0.0020
 BKN  OAI  O  O2    0  -0.460   2.5923   0.3383  -0.0293
 BKN  CAK  C  C     0   0.604   1.4830  -0.3889   0.0037
 BKN  OAD  O  O     0  -0.455   1.4786  -1.5943   0.0500
 BKN  CAH  C  CH2   0  -0.582   0.2561   0.4831  -0.0238
 BKN  CAF  C  CH2   0  -0.421  -1.0472  -0.2993   0.0073
 BKN  CAG  C  CH2   0  -0.559  -2.2368   0.6462  -0.0148
 BKN  CAJ  C  C     0   0.393  -3.5859  -0.0268   0.0160
 BKN  OAC  O  O     0  -0.406  -3.7067  -1.2310   0.0464
 BKN  CAB  C  CH3   0  -0.767  -4.7719   0.8992   0.0119
 BKN  H1   H  HCH3  0   0.236   4.8865   1.3536   0.8477
 BKN  H2   H  HCH3  0   0.239   5.9147   0.2020   0.0002
 BKN  H3   H  HCH3  0   0.236   4.9017   1.3079  -0.9232
 BKN  H4   H  HCH2  0   0.234   3.9328  -1.0079  -0.8667
 BKN  H5   H  HCH2  0   0.234   3.9202  -0.9611   0.8976
 BKN  H6   H  HCH2  0   0.275   0.3118   1.1732   0.8244
 BKN  H7   H  HCH2  0   0.276   0.3066   1.1146  -0.9167
 BKN  H8   H  HCH2  0   0.238  -1.0953  -0.9755  -0.8480
 BKN  H9   H  HCH2  0   0.237  -1.0847  -0.9224   0.9028
 BKN  H10  H  HCH2  0   0.266  -2.1946   1.3430   0.8305
 BKN  H11  H  HCH2  0   0.267  -2.2066   1.2870  -0.9039
 BKN  H12  H  HCH3  0   0.258  -5.7102   0.3488  -0.0111
 BKN  H13  H  HCH3  0   0.265  -4.7510   1.5304   0.9024
 BKN  H14  H  HCH3  0   0.262  -4.7255   1.5695  -0.8477

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
 BKN  CAB  CAJ  single  1.505  0.020  1.505
 BKN  CAJ  OAC  double  1.211  0.020  1.211
 BKN  CAJ  CAG  single  1.508  0.020  1.508
 BKN  CAG  CAF  single  1.520  0.020  1.520
 BKN  CAF  CAH  single  1.520  0.020  1.520
 BKN  CAH  CAK  single  1.506  0.020  1.506
 BKN  OAD  CAK  double  1.206  0.020  1.206
 BKN  CAK  OAI  single  1.327  0.020  1.327
 BKN  OAI  CAE  single  1.436  0.020  1.436
 BKN  CAE  CAA  single  1.509  0.020  1.509
 BKN  CAA  H1   single  0.970  0.020  1.090
 BKN  CAA  H2   single  0.970  0.020  1.090
 BKN  CAA  H3   single  0.970  0.020  1.090
 BKN  CAE  H4   single  0.970  0.020  1.090
 BKN  CAE  H5   single  0.970  0.020  1.090
 BKN  CAH  H6   single  0.970  0.020  1.090
 BKN  CAH  H7   single  0.970  0.020  1.090
 BKN  CAF  H8   single  0.970  0.020  1.090
 BKN  CAF  H9   single  0.970  0.020  1.090
 BKN  CAG  H10  single  0.970  0.020  1.090
 BKN  CAG  H11  single  0.970  0.020  1.090
 BKN  CAB  H12  single  0.970  0.020  1.090
 BKN  CAB  H13  single  0.970  0.020  1.090
 BKN  CAB  H14  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
 BKN  H3   CAA  H2   107.81  3.000
 BKN  H3   CAA  H1   108.72  3.000
 BKN  H2   CAA  H1   107.81  3.000
 BKN  H3   CAA  CAE  111.65  3.000
 BKN  H2   CAA  CAE  109.15  3.000
 BKN  H1   CAA  CAE  111.56  3.000
 BKN  H5   CAE  H4   107.85  3.000
 BKN  H5   CAE  OAI  109.69  3.000
 BKN  H4   CAE  OAI  109.68  3.000
 BKN  H5   CAE  CAA  110.89  3.000
 BKN  H4   CAE  CAA  110.95  3.000
 BKN  OAI  CAE  CAA  107.77  3.000
 BKN  CAK  OAI  CAE  118.25  3.000
 BKN  CAH  CAK  OAD  125.21  3.000
 BKN  OAD  CAK  OAI  123.48  3.000
 BKN  CAH  CAK  OAI  111.31  3.000
 BKN  H7   CAH  H6   105.42  3.000
 BKN  H7   CAH  CAF  110.67  3.000
 BKN  H6   CAH  CAF  110.62  3.000
 BKN  H7   CAH  CAK  108.14  3.000
 BKN  H6   CAH  CAK  108.02  3.000
 BKN  CAF  CAH  CAK  113.59  3.000
 BKN  H9   CAF  H8   106.72  3.000
 BKN  H9   CAF  CAG  109.89  3.000
 BKN  H8   CAF  CAG  109.85  3.000
 BKN  H9   CAF  CAH  109.88  3.000
 BKN  H8   CAF  CAH  109.92  3.000
 BKN  CAG  CAF  CAH  110.52  3.000
 BKN  H11  CAG  H10  104.64  3.000
 BKN  H11  CAG  CAJ  107.58  3.000
 BKN  H10  CAG  CAJ  107.60  3.000
 BKN  H11  CAG  CAF  110.72  3.000
 BKN  H10  CAG  CAF  110.73  3.000
 BKN  CAJ  CAG  CAF  114.98  3.000
 BKN  CAB  CAJ  OAC  122.24  3.000
 BKN  OAC  CAJ  CAG  122.26  3.000
 BKN  CAB  CAJ  CAG  115.50  3.000
 BKN  H14  CAB  H13  106.66  3.000
 BKN  H14  CAB  H12  109.32  3.000
 BKN  H13  CAB  H12  109.04  3.000
 BKN  H14  CAB  CAJ  110.28  3.000
 BKN  H13  CAB  CAJ  109.78  3.000
 BKN  H12  CAB  CAJ  111.62  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
 BKN  Var_01  CAH  CAK  OAI  CAE   179.67  30.0  1
 BKN  Var_02  CAF  CAH  CAK  OAI   179.79  30.0  1
 BKN  Var_03  CAG  CAF  CAH  CAK   179.68  30.0  1
 BKN  Var_04  CAJ  CAG  CAF  CAH  -179.88  30.0  1
 BKN  Var_05  CAB  CAJ  CAG  CAF   179.27  30.0  1
 BKN  Var_06  H1   CAA  CAE  OAI    60.92  30.0  3
 BKN  Var_07  H4   CAE  OAI  CAK    60.21  30.0  3
 BKN  Var_08  H12  CAB  CAJ  CAG   177.39  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
 BKN  plan-1  CAG  0.020
 BKN  plan-1  CAJ  0.020
 BKN  plan-1  OAC  0.020
 BKN  plan-1  CAB  0.020
 BKN  plan-2  OAI  0.020
 BKN  plan-2  CAK  0.020
 BKN  plan-2  OAD  0.020
 BKN  plan-2  CAH  0.020

