# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 09:49:57 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{S})-2-methylpentanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CCC(O)=O)C(O)=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
 9ON  9ON  '(2~{S})-2-methylpentanedioic acid'  ligand  18  10  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9ON
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
 9ON  O12  O  O      0  -0.607   2.2622  -1.5555  -0.0704
 9ON  C7   C  C      0   0.423   2.4165  -0.3373   0.1505
 9ON  O10  O  OC    -1  -0.628   3.5139   0.2368   0.3234
 9ON  C4   C  CH1    0  -0.370   1.1571   0.5591   0.2336
 9ON  C5   C  CH3    0  -0.659   1.3229   1.7764  -0.6763
 9ON  C3   C  CH2    0  -0.378  -0.1440  -0.1939  -0.0343
 9ON  C2   C  CH2    0  -0.588  -1.3998   0.6261   0.2196
 9ON  C1   C  C      0   0.411  -2.7367  -0.1258   0.0876
 9ON  O8   O  OC    -1  -0.638  -3.7660   0.5468   0.3173
 9ON  O9   O  O      0  -0.611  -2.7073  -1.3296  -0.2371
 9ON  H2   H  HCH1   0   0.202   1.1199   0.9349   1.2671
 9ON  H3   H  HCH3   0   0.215   0.5027   2.4858  -0.5618
 9ON  H4   H  HCH3   0   0.220   2.2489   2.3045  -0.4565
 9ON  H5   H  HCH3   0   0.203   1.3504   1.4771  -1.7278
 9ON  H6   H  HCH2   0   0.184  -0.1448  -0.5599  -1.0659
 9ON  H7   H  HCH2   0   0.198  -0.1703  -1.0849   0.5947
 9ON  H8   H  HCH2   0   0.208  -1.3570   1.0666   1.2241
 9ON  H9   H  HCH2   0   0.216  -1.4435   1.4858  -0.4572

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
 9ON  O12  C7   deloc   1.248  0.020  1.248
 9ON  C4   C7   single  1.548  0.020  1.548
 9ON  C4   C5   single  1.529  0.020  1.529
 9ON  C4   C3   single  1.527  0.020  1.527
 9ON  C7   O10  deloc   1.251  0.020  1.251
 9ON  C2   C3   single  1.521  0.020  1.521
 9ON  C2   C1   single  1.539  0.020  1.539
 9ON  O9   C1   deloc   1.247  0.020  1.247
 9ON  C1   O8   deloc   1.251  0.020  1.251
 9ON  C4   H2   single  0.970  0.020  1.090
 9ON  C5   H3   single  0.970  0.020  1.090
 9ON  C5   H4   single  0.970  0.020  1.090
 9ON  C5   H5   single  0.970  0.020  1.090
 9ON  C3   H6   single  0.970  0.020  1.090
 9ON  C3   H7   single  0.970  0.020  1.090
 9ON  C2   H8   single  0.970  0.020  1.090
 9ON  C2   H9   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
 9ON  C4   C7  O10  116.15  3.000
 9ON  O10  C7  O12  125.54  3.000
 9ON  C4   C7  O12  118.31  3.000
 9ON  H2   C4  C3   107.73  3.000
 9ON  H2   C4  C5   106.90  3.000
 9ON  C3   C4  C5   112.37  3.000
 9ON  H2   C4  C7   106.00  3.000
 9ON  C3   C4  C7   113.47  3.000
 9ON  C5   C4  C7   109.93  3.000
 9ON  H5   C5  H4   107.79  3.000
 9ON  H5   C5  H3   107.33  3.000
 9ON  H4   C5  H3   107.64  3.000
 9ON  H5   C5  C4   110.92  3.000
 9ON  H4   C5  C4   111.00  3.000
 9ON  H3   C5  C4   111.96  3.000
 9ON  H7   C3  H6   105.68  3.000
 9ON  H7   C3  C2   108.91  3.000
 9ON  H6   C3  C2   109.69  3.000
 9ON  H7   C3  C4   108.80  3.000
 9ON  H6   C3  C4   109.32  3.000
 9ON  C2   C3  C4   114.10  3.000
 9ON  H9   C2  H8   104.60  3.000
 9ON  H9   C2  C1   107.20  3.000
 9ON  H8   C2  C1   107.96  3.000
 9ON  H9   C2  C3   110.67  3.000
 9ON  H8   C2  C3   109.69  3.000
 9ON  C1   C2  C3   116.06  3.000
 9ON  O9   C1  O8   125.89  3.000
 9ON  O8   C1  C2   115.86  3.000
 9ON  O9   C1  C2   118.25  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
 9ON  Var_01  C1  C2  C3  C4  -174.64  30.0  1
 9ON  Var_02  O9  C1  C2  C3    -1.29  30.0  3

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
 9ON  chir_01  C4  C7  C5  C3  negativ

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
 9ON  plan-1  O12  0.020
 9ON  plan-1  C7   0.020
 9ON  plan-1  O10  0.020
 9ON  plan-1  C4   0.020
 9ON  plan-2  C2   0.020
 9ON  plan-2  C1   0.020
 9ON  plan-2  O8   0.020
 9ON  plan-2  O9   0.020

