# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 19:15:47 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: (2~{R})-2-methanoylhept-6-ynoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CCCC#C)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
 DUV  DUV  '(2~{R})-2-methanoylhept-6-ynoic acid'  ligand  20  11  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DUV
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
 DUV  O1   O  O      0  -0.581  -2.4298  -1.8373  -0.1958
 DUV  C2   C  C      0   0.449  -2.4209  -0.6024  -0.0930
 DUV  O3   O  OC    -1  -0.597  -3.3906   0.1488   0.1372
 DUV  C4   C  CH1    0  -0.518  -1.0652   0.1360  -0.2842
 DUV  C5   C  CH2    0  -0.434   0.1401  -0.6784   0.1750
 DUV  C6   C  CH2    0  -0.422   1.4736  -0.0083  -0.1316
 DUV  C7   C  CH2    0  -0.573   2.6547  -0.8987   0.2644
 DUV  C8   C  CSP    0   0.285   3.9442  -0.2771  -0.0083
 DUV  C9   C  CSP1   0  -0.569   4.9996   0.2493  -0.2456
 DUV  C10  C  C1     0   0.201  -1.1736   1.4123   0.4892
 DUV  O11  O  O      0  -0.401  -1.2068   2.5274   0.0246
 DUV  H2   H  HCH1   0   0.256  -0.9616   0.3809  -1.3486
 DUV  H3   H  HCH2   0   0.223   0.0639  -0.8689   1.2513
 DUV  H4   H  HCH2   0   0.238   0.0946  -1.6549  -0.3102
 DUV  H5   H  HCH2   0   0.232   1.5370   0.2214  -1.1985
 DUV  H6   H  HCH2   0   0.232   1.5579   0.9446   0.3979
 DUV  H7   H  HCH2   0   0.266   2.5946  -1.1410   1.3291
 DUV  H8   H  HCH2   0   0.266   2.5962  -1.8503  -0.2708
 DUV  H9   H  H      0   0.277   5.9317   0.7219  -0.4548
 DUV  H10  H  H      0   0.168  -1.2046   1.2631   1.5869

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
 DUV  C9   C8   triple  1.203  0.020  1.203
 DUV  C8   C7   single  1.457  0.020  1.457
 DUV  C7   C6   single  1.531  0.020  1.531
 DUV  O1   C2   deloc   1.239  0.020  1.239
 DUV  C6   C5   single  1.524  0.020  1.524
 DUV  O3   C2   deloc   1.248  0.020  1.248
 DUV  C2   C4   single  1.556  0.020  1.556
 DUV  C5   C4   single  1.525  0.020  1.525
 DUV  C4   C10  single  1.496  0.020  1.496
 DUV  C10  O11  double  1.208  0.020  1.208
 DUV  C4   H2   single  0.939  0.020  1.096
 DUV  C5   H3   single  0.939  0.020  1.096
 DUV  C5   H4   single  0.939  0.020  1.096
 DUV  C6   H5   single  0.939  0.020  1.096
 DUV  C6   H6   single  0.939  0.020  1.096
 DUV  C7   H7   single  0.939  0.020  1.096
 DUV  C7   H8   single  0.939  0.020  1.096
 DUV  C9   H9   single  0.913  0.020  1.066
 DUV  C10  H10  single  0.930  0.020  1.086

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
 DUV  C4   C2   O3   114.46  3.000
 DUV  C4   C2   O1   117.98  3.000
 DUV  O3   C2   O1   127.55  3.000
 DUV  H2   C4   C10  108.54  3.000
 DUV  H2   C4   C5   109.67  3.000
 DUV  C10  C4   C5   110.92  3.000
 DUV  H2   C4   C2   107.91  3.000
 DUV  C10  C4   C2   106.15  3.000
 DUV  C5   C4   C2   113.47  3.000
 DUV  H4   C5   H3   106.16  3.000
 DUV  H4   C5   C6   109.91  3.000
 DUV  H3   C5   C6   109.57  3.000
 DUV  H4   C5   C4   108.11  3.000
 DUV  H3   C5   C4   109.49  3.000
 DUV  C6   C5   C4   113.34  3.000
 DUV  H6   C6   H5   106.56  3.000
 DUV  H6   C6   C7   108.79  3.000
 DUV  H5   C6   C7   109.26  3.000
 DUV  H6   C6   C5   110.69  3.000
 DUV  H5   C6   C5   109.85  3.000
 DUV  C7   C6   C5   111.55  3.000
 DUV  H8   C7   H7   106.31  3.000
 DUV  H8   C7   C8   109.08  3.000
 DUV  H7   C7   C8   108.98  3.000
 DUV  H8   C7   C6   109.77  3.000
 DUV  H7   C7   C6   109.77  3.000
 DUV  C8   C7   C6   112.71  3.000
 DUV  C9   C8   C7   180.00  3.000
 DUV  H9   C9   C8   180.00  3.000
 DUV  H10  C10  O11  120.29  3.000
 DUV  H10  C10  C4   113.52  3.000
 DUV  O11  C10  C4   126.18  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
 DUV  Var_01  C7  C6  C5  C4  -176.36  30.0  1
 DUV  Var_02  C8  C7  C6  C5  -179.54  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DUV  chir_01  C4  C2  C5  C10  positiv

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
 DUV  plan-1  O1   0.020
 DUV  plan-1  C2   0.020
 DUV  plan-1  O3   0.020
 DUV  plan-1  C4   0.020
 DUV  plan-2  C4   0.020
 DUV  plan-2  C10  0.020
 DUV  plan-2  O11  0.020
 DUV  plan-2  H10  0.020

