# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 17:48:04 2020
#   Inital geometry file: a 53 line input string
#   Ligand name: (2~{R})-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
 E5N  E5N  '(2~{R})-2-methylpentanedioic acid'  ligand  20  10  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_E5N
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
 E5N  O42  O  OH1   0  -0.597  -3.7317  -0.5559   0.4120
 E5N  O41  O  O     0  -0.444  -2.7551   1.3428  -0.2269
 E5N  C4   C  C     0   0.557  -2.6711   0.1894   0.1146
 E5N  C41  C  CH2   0  -0.591  -1.3901  -0.5859   0.2530
 E5N  C32  C  CH2   0  -0.411  -0.1525   0.2506  -0.0304
 E5N  C3   C  C     0   0.566   2.3392   0.3822   0.0808
 E5N  O31  O  O     0  -0.441   2.3438   1.4486  -0.4830
 E5N  O32  O  OH1   0  -0.596   3.4279  -0.1441   0.6333
 E5N  C22  C  CH3   0  -0.667   1.3095  -1.7243  -0.7187
 E5N  C31  C  CH1   0  -0.382   1.1384  -0.5248   0.2228
 E5N  H1   H  HOH1  0   0.479  -4.5408  -0.0327   0.3123
 E5N  H2   H  HCH2  0   0.279  -1.3526  -1.0088   1.2621
 E5N  H3   H  HCH2  0   0.283  -1.4555  -1.4446  -0.4209
 E5N  H4   H  HCH2  0   0.237  -0.1726   0.6061  -1.0627
 E5N  H5   H  HCH2  0   0.246  -0.1673   1.1360   0.6081
 E5N  H6   H  HOH1  0   0.479   4.1872   0.4400   0.4875
 E5N  H7   H  HCH3  0   0.249   2.2336  -2.2651  -0.5208
 E5N  H8   H  HCH3  0   0.249   0.4908  -2.4305  -0.5918
 E5N  H9   H  HCH3  0   0.234   1.3160  -1.4029  -1.7615
 E5N  H10  H  HCH1  0   0.271   1.1335  -0.9010   1.2516

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
 E5N  C22  C31  single  1.534  0.020  1.534
 E5N  O31  C3   double  1.206  0.020  1.206
 E5N  C31  C3   single  1.512  0.020  1.512
 E5N  C31  C32  single  1.527  0.020  1.527
 E5N  C3   O32  single  1.329  0.020  1.329
 E5N  O41  C4   double  1.206  0.020  1.206
 E5N  C32  C41  single  1.520  0.020  1.520
 E5N  C4   C41  single  1.504  0.020  1.504
 E5N  C4   O42  single  1.330  0.020  1.330
 E5N  O42  H1   single  0.850  0.020  0.980
 E5N  C41  H2   single  0.970  0.020  1.090
 E5N  C41  H3   single  0.970  0.020  1.090
 E5N  C32  H4   single  0.970  0.020  1.090
 E5N  C32  H5   single  0.970  0.020  1.090
 E5N  O32  H6   single  0.850  0.020  0.980
 E5N  C22  H7   single  0.970  0.020  1.090
 E5N  C22  H8   single  0.970  0.020  1.090
 E5N  C22  H9   single  0.970  0.020  1.090
 E5N  C31  H10  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
 E5N  H1   O42  C4   109.90  3.000
 E5N  C41  C4   O41  125.35  3.000
 E5N  C41  C4   O42  111.71  3.000
 E5N  O41  C4   O42  122.94  3.000
 E5N  H3   C41  H2   105.47  3.000
 E5N  H3   C41  C32  111.46  3.000
 E5N  H2   C41  C32  110.88  3.000
 E5N  H3   C41  C4   107.29  3.000
 E5N  H2   C41  C4   108.25  3.000
 E5N  C32  C41  C4   113.12  3.000
 E5N  H5   C32  H4   106.77  3.000
 E5N  H5   C32  C31  109.05  3.000
 E5N  H4   C32  C31  109.73  3.000
 E5N  H5   C32  C41  109.04  3.000
 E5N  H4   C32  C41  109.90  3.000
 E5N  C31  C32  C41  112.20  3.000
 E5N  C31  C3   O32  111.96  3.000
 E5N  O32  C3   O31  122.76  3.000
 E5N  C31  C3   O31  125.26  3.000
 E5N  H6   O32  C3   109.91  3.000
 E5N  H9   C22  H8   107.87  3.000
 E5N  H9   C22  H7   108.36  3.000
 E5N  H8   C22  H7   107.16  3.000
 E5N  H9   C22  C31  110.90  3.000
 E5N  H8   C22  C31  110.59  3.000
 E5N  H7   C22  C31  111.80  3.000
 E5N  H10  C31  C22  107.96  3.000
 E5N  H10  C31  C3   107.32  3.000
 E5N  C22  C31  C3   108.83  3.000
 E5N  H10  C31  C32  109.05  3.000
 E5N  C3   C31  C32  110.57  3.000
 E5N  C22  C31  C32  112.93  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
 E5N  CONST_01  H1   O42  C4   O41     0.00   0.0  0
 E5N  CONST_02  H6   O32  C3   O31     0.00   0.0  0
 E5N  Var_01    C32  C41  C4   O42  -177.89  30.0  3
 E5N  Var_02    C31  C32  C41  C4    175.48  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
 E5N  chir_01  C31  C22  C3  C32  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
 E5N  plan-1  O42  0.020
 E5N  plan-1  O41  0.020
 E5N  plan-1  C4   0.020
 E5N  plan-1  C41  0.020
 E5N  plan-1  H1   0.020
 E5N  plan-2  C3   0.020
 E5N  plan-2  O31  0.020
 E5N  plan-2  O32  0.020
 E5N  plan-2  C31  0.020
 E5N  plan-2  H6   0.020

