# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 04:25:56 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: (3S)-3-methyl-2-oxopentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](C)C(=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
 1QQ  1QQ  '(3S)-3-methyl-2-oxopentanoic acid'  ligand  19  9  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1QQ
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
 1QQ  C42   C  C     0   0.478   1.7001   0.3072   0.1100
 1QQ  C44   C  C     0   0.312   0.3990  -0.5117  -0.0073
 1QQ  C46   C  CH1   0  -0.365  -0.8853   0.2646   0.0729
 1QQ  C48   C  CH3   0  -0.669  -1.0823   0.9932  -1.2664
 1QQ  C47   C  CH2   0  -0.408  -2.0648  -0.6390   0.4258
 1QQ  C49   C  CH3   0  -0.672  -3.3575   0.1351   0.6463
 1QQ  O45   O  O     0  -0.343   0.4757  -1.7012  -0.1651
 1QQ  O43   O  O     0  -0.404   1.7168   1.4669   0.4263
 1QQ  H46   H  HCH1  0   0.269  -0.7691   1.0254   0.8513
 1QQ  H481  H  HCH3  0   0.235  -1.2321   0.2793  -2.0777
 1QQ  H482  H  HCH3  0   0.256  -1.9573   1.6386  -1.2175
 1QQ  H483  H  HCH3  0   0.247  -0.2318   1.6247  -1.5218
 1QQ  H471  H  HCH2  0   0.225  -2.2093  -1.3823  -0.3621
 1QQ  H472  H  HCH2  0   0.235  -1.8283  -1.1957   1.3361
 1QQ  H491  H  HCH3  0   0.221  -3.2231   0.9239   1.3885
 1QQ  H492  H  HCH3  0   0.226  -3.7221   0.5991  -0.2701
 1QQ  H493  H  HCH3  0   0.236  -4.1426  -0.5285   1.0089
 1QQ  OXT   O  OH1   0  -0.570   2.7570  -0.4265  -0.1601
 1QQ  HXT   H  HOH1  0   0.493   3.5652   0.1026  -0.0723

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
 1QQ  C42  C44   single  1.542  0.020  1.542
 1QQ  C42  O43   double  1.202  0.020  1.202
 1QQ  C44  C46   single  1.503  0.020  1.503
 1QQ  C44  O45   double  1.202  0.020  1.202
 1QQ  C46  C48   single  1.537  0.020  1.537
 1QQ  C46  C47   single  1.527  0.020  1.527
 1QQ  C46  H46   single  0.970  0.020  1.090
 1QQ  C48  H481  single  0.970  0.020  1.090
 1QQ  C48  H482  single  0.970  0.020  1.090
 1QQ  C48  H483  single  0.970  0.020  1.090
 1QQ  C47  C49   single  1.523  0.020  1.523
 1QQ  C47  H471  single  0.970  0.020  1.090
 1QQ  C47  H472  single  0.970  0.020  1.090
 1QQ  C49  H491  single  0.970  0.020  1.090
 1QQ  C49  H492  single  0.970  0.020  1.090
 1QQ  C49  H493  single  0.970  0.020  1.090
 1QQ  C42  OXT   single  1.315  0.020  1.315
 1QQ  OXT  HXT   single  0.850  0.020  0.980

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
 1QQ  OXT   C42  O43   125.54  3.000
 1QQ  OXT   C42  C44   111.49  3.000
 1QQ  O43   C42  C44   122.96  3.000
 1QQ  O45   C44  C46   124.93  3.000
 1QQ  O45   C44  C42   118.79  3.000
 1QQ  C46   C44  C42   116.28  3.000
 1QQ  H46   C46  C47   109.20  3.000
 1QQ  H46   C46  C48   107.68  3.000
 1QQ  C47   C46  C48   112.51  3.000
 1QQ  H46   C46  C44   107.83  3.000
 1QQ  C47   C46  C44   111.51  3.000
 1QQ  C48   C46  C44   107.93  3.000
 1QQ  H483  C48  H482  107.12  3.000
 1QQ  H483  C48  H481  108.19  3.000
 1QQ  H482  C48  H481  108.13  3.000
 1QQ  H483  C48  C46   112.27  3.000
 1QQ  H482  C48  C46   110.17  3.000
 1QQ  H481  C48  C46   110.81  3.000
 1QQ  H472  C47  H471  106.42  3.000
 1QQ  H472  C47  C49   108.79  3.000
 1QQ  H471  C47  C49   109.75  3.000
 1QQ  H472  C47  C46   109.07  3.000
 1QQ  H471  C47  C46   109.75  3.000
 1QQ  C49   C47  C46   112.84  3.000
 1QQ  H493  C49  H492  107.33  3.000
 1QQ  H493  C49  H491  107.60  3.000
 1QQ  H492  C49  H491  107.78  3.000
 1QQ  H493  C49  C47   110.49  3.000
 1QQ  H492  C49  C47   112.25  3.000
 1QQ  H491  C49  C47   111.19  3.000
 1QQ  HXT   OXT  C42   110.29  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
 1QQ  CONST_01  HXT   OXT  C42  C44  180.00   0.0  0
 1QQ  Var_01    O43   C42  C44  C46    9.79  30.0  2
 1QQ  Var_02    H491  C49  C47  C46  -53.94  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
 1QQ  chir_01  C46  C44  C48  C47  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
 1QQ  plan-1  C42  0.020
 1QQ  plan-1  C44  0.020
 1QQ  plan-1  C46  0.020
 1QQ  plan-1  O45  0.020
 1QQ  plan-2  C42  0.020
 1QQ  plan-2  C44  0.020
 1QQ  plan-2  O43  0.020
 1QQ  plan-2  OXT  0.020
 1QQ  plan-2  HXT  0.020

