# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 15:21:44 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: (2-methylpropyl)propanedioic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)CC(C(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
 LML  LML  '(2-methylpropyl)propanedioic acid'  ligand  21  11  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LML
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
 LML  C1    C  C      0   0.415  -0.9922   0.0961  -1.6832
 LML  O1    O  O      0  -0.609  -2.0014   0.8189  -1.5572
 LML  OXT   O  OC    -1  -0.632  -0.5405  -0.3431  -2.7636
 LML  CA    C  CH1    0  -0.486  -0.2155  -0.3198  -0.4156
 LML  CB    C  CH2    0  -0.370  -0.7766   0.2821   0.8666
 LML  CG    C  CH1    0  -0.230   0.0051  -0.0407   2.1423
 LML  CD1   C  CH3    0  -0.648  -0.6993   0.5620   3.3541
 LML  CD2   C  CH3    0  -0.660   0.2262  -1.5371   2.3381
 LML  C     C  C      0   0.410   1.2605   0.0571  -0.6244
 LML  O     O  O      0  -0.630   1.5124   1.2822  -0.6577
 LML  O2    O  OC    -1  -0.627   2.0990  -0.8612  -0.7440
 LML  HA    H  HCH1   0   0.197  -0.2853  -1.4119  -0.3530
 LML  HB1   H  HCH2   0   0.185  -1.8110  -0.0545   1.0005
 LML  HB2   H  HCH2   0   0.194  -0.8287   1.3683   0.7595
 LML  HG    H  HCH1   0   0.204   0.9901   0.4334   2.0609
 LML  HD11  H  HCH3   0   0.217  -0.1166   0.4252   4.2676
 LML  HD12  H  HCH3   0   0.216  -0.8676   1.6336   3.2270
 LML  HD13  H  HCH3   0   0.206  -1.6742   0.0937   3.5134
 LML  HD21  H  HCH3   0   0.203  -0.7215  -2.0834   2.3343
 LML  HD22  H  HCH3   0   0.228   0.8556  -1.9528   1.5512
 LML  HD23  H  HCH3   0   0.214   0.7149  -1.7400   3.2935

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
 LML  C1   O1    deloc   1.248  0.020  1.248
 LML  C1   OXT   deloc   1.251  0.020  1.251
 LML  C1   CA    single  1.544  0.020  1.544
 LML  CA   CB    single  1.524  0.020  1.524
 LML  CA   C     single  1.538  0.020  1.538
 LML  CA   HA    single  0.970  0.020  1.090
 LML  CB   CG    single  1.531  0.020  1.531
 LML  CB   HB1   single  0.970  0.020  1.090
 LML  CB   HB2   single  0.970  0.020  1.090
 LML  CG   CD1   single  1.526  0.020  1.526
 LML  CG   CD2   single  1.525  0.020  1.525
 LML  CG   HG    single  0.970  0.020  1.090
 LML  CD1  HD11  single  0.970  0.020  1.090
 LML  CD1  HD12  single  0.970  0.020  1.090
 LML  CD1  HD13  single  0.970  0.020  1.090
 LML  CD2  HD21  single  0.970  0.020  1.090
 LML  CD2  HD22  single  0.970  0.020  1.090
 LML  CD2  HD23  single  0.970  0.020  1.090
 LML  C    O     deloc   1.251  0.020  1.251
 LML  C    O2    deloc   1.249  0.020  1.249

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
 LML  CA    C1   OXT   115.65  3.000
 LML  CA    C1   O1    118.70  3.000
 LML  OXT   C1   O1    125.65  3.000
 LML  HA    CA   C     108.24  3.000
 LML  HA    CA   CB    108.79  3.000
 LML  C     CA   CB    111.77  3.000
 LML  HA    CA   C1    106.46  3.000
 LML  C     CA   C1    107.79  3.000
 LML  CB    CA   C1    113.53  3.000
 LML  HB2   CB   HB1   105.80  3.000
 LML  HB2   CB   CG    108.40  3.000
 LML  HB1   CB   CG    108.39  3.000
 LML  HB2   CB   CA    109.14  3.000
 LML  HB1   CB   CA    109.21  3.000
 LML  CG    CB   CA    115.47  3.000
 LML  HG    CG   CD2   107.68  3.000
 LML  HG    CG   CD1   107.64  3.000
 LML  CD2   CG   CD1   110.64  3.000
 LML  HG    CG   CB    107.81  3.000
 LML  CD2   CG   CB    112.82  3.000
 LML  CD1   CG   CB    110.05  3.000
 LML  HD13  CD1  HD12  107.45  3.000
 LML  HD13  CD1  HD11  107.48  3.000
 LML  HD12  CD1  HD11  107.61  3.000
 LML  HD13  CD1  CG    110.99  3.000
 LML  HD12  CD1  CG    111.49  3.000
 LML  HD11  CD1  CG    111.62  3.000
 LML  HD23  CD2  HD22  107.59  3.000
 LML  HD23  CD2  HD21  107.33  3.000
 LML  HD22  CD2  HD21  107.90  3.000
 LML  HD23  CD2  CG    111.06  3.000
 LML  HD22  CD2  CG    111.42  3.000
 LML  HD21  CD2  CG    111.35  3.000
 LML  O2    C    O     125.60  3.000
 LML  O2    C    CA    118.49  3.000
 LML  O     C    CA    115.91  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
 LML  Var_01  CG    CB   CA  C1  -176.85  30.0  3
 LML  Var_02  O     C    CA  C1    68.22  30.0  3
 LML  Var_03  CB    CA   C1  O1    -2.52  30.0  3
 LML  Var_04  CD1   CG   CB  CA  -177.20  30.0  3
 LML  Var_05  HD11  CD1  CG  CB  -174.83  30.0  3
 LML  Var_06  HD21  CD2  CG  CB   -55.91  30.0  3

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
 LML  plan-1  C1   0.020
 LML  plan-1  O1   0.020
 LML  plan-1  OXT  0.020
 LML  plan-1  CA   0.020
 LML  plan-2  CA   0.020
 LML  plan-2  C    0.020
 LML  plan-2  O    0.020
 LML  plan-2  O2   0.020

