# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:31:06 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  18  10  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  OC    -1  -0.638  -3.7499  -0.5315   0.3009
 E5N  O41  O  O      0  -0.611  -2.6848   1.3507  -0.2203
 E5N  C4   C  C      0   0.411  -2.7180   0.1428   0.0885
 E5N  C41  C  CH2    0  -0.588  -1.3830  -0.6106   0.2280
 E5N  C32  C  CH2    0  -0.378  -0.1243   0.2030  -0.0338
 E5N  C3   C  C      0   0.422   2.4389   0.3289   0.1338
 E5N  O31  O  O      0  -0.606   2.2952   1.5391  -0.1335
 E5N  O32  O  OC    -1  -0.629   3.5304  -0.2457   0.3393
 E5N  C22  C  CH3    0  -0.660   1.3287  -1.7775  -0.6788
 E5N  C31  C  CH1    0  -0.368   1.1735  -0.5572   0.2297
 E5N  H2   H  HCH2   0   0.208  -1.3416  -1.0394   1.2377
 E5N  H3   H  HCH2   0   0.216  -1.4282  -1.4785  -0.4381
 E5N  H4   H  HCH2   0   0.184  -0.1289   0.5662  -1.0662
 E5N  H5   H  HCH2   0   0.197  -0.1434   1.0954   0.5940
 E5N  H7   H  HCH3   0   0.220   2.2525  -2.3107  -0.4613
 E5N  H8   H  HCH3   0   0.216   0.5055  -2.4827  -0.5599
 E5N  H9   H  HCH3   0   0.203   1.3540  -1.4799  -1.7309
 E5N  H10  H  HCH1   0   0.201   1.1399  -0.9311   1.2637

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  1.529  0.020  1.529
 E5N  O31  C3   deloc   1.248  0.020  1.248
 E5N  C31  C3   single  1.548  0.020  1.548
 E5N  C31  C32  single  1.527  0.020  1.527
 E5N  C3   O32  deloc   1.250  0.020  1.250
 E5N  O41  C4   deloc   1.247  0.020  1.247
 E5N  C32  C41  single  1.521  0.020  1.521
 E5N  C4   C41  single  1.539  0.020  1.539
 E5N  C4   O42  deloc   1.251  0.020  1.251
 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  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  C41  C4   O41  118.25  3.000
 E5N  C41  C4   O42  115.86  3.000
 E5N  O41  C4   O42  125.88  3.000
 E5N  H3   C41  H2   104.56  3.000
 E5N  H3   C41  C32  110.69  3.000
 E5N  H2   C41  C32  109.63  3.000
 E5N  H3   C41  C4   107.28  3.000
 E5N  H2   C41  C4   107.90  3.000
 E5N  C32  C41  C4   116.12  3.000
 E5N  H5   C32  H4   105.74  3.000
 E5N  H5   C32  C31  108.83  3.000
 E5N  H4   C32  C31  109.36  3.000
 E5N  H5   C32  C41  108.90  3.000
 E5N  H4   C32  C41  109.65  3.000
 E5N  C31  C32  C41  114.03  3.000
 E5N  C31  C3   O32  116.13  3.000
 E5N  O32  C3   O31  125.55  3.000
 E5N  C31  C3   O31  118.32  3.000
 E5N  H9   C22  H8   107.36  3.000
 E5N  H9   C22  H7   107.81  3.000
 E5N  H8   C22  H7   107.58  3.000
 E5N  H9   C22  C31  110.90  3.000
 E5N  H8   C22  C31  112.00  3.000
 E5N  H7   C22  C31  111.00  3.000
 E5N  H10  C31  C22  106.88  3.000
 E5N  H10  C31  C3   106.13  3.000
 E5N  C22  C31  C3   109.69  3.000
 E5N  H10  C31  C32  107.79  3.000
 E5N  C3   C31  C32  113.52  3.000
 E5N  C22  C31  C32  112.40  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  Var_01  C32  C41  C4   O42  179.80  30.0  3
 E5N  Var_02  C31  C32  C41  C4   175.20  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-2  C3   0.020
 E5N  plan-2  O31  0.020
 E5N  plan-2  O32  0.020
 E5N  plan-2  C31  0.020

