# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 14 17:28:30 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  23  11  .  2021-08-12  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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   0.592  -1.1278   0.0417  -1.6309
 LML  O1    O  O     0  -0.421  -2.2291   0.5178  -1.5601
 LML  OXT   O  OH1   0  -0.591  -0.5365  -0.2881  -2.7713
 LML  CA    C  CH1   0  -0.523  -0.2416  -0.2901  -0.4453
 LML  CB    C  CH2   0  -0.403  -0.8130   0.2568   0.8639
 LML  CG    C  CH1   0  -0.252   0.0144  -0.0648   2.1106
 LML  CD1   C  CH3   0  -0.647  -0.6310   0.5964   3.3251
 LML  CD2   C  CH3   0  -0.658   0.1676  -1.5653   2.3383
 LML  C     C  C     0   0.552   1.1369   0.2878  -0.6970
 LML  O     O  O     0  -0.432   1.3258   1.4586  -0.9108
 LML  O2    O  OH1   0  -0.578   2.0983  -0.6170  -0.6252
 LML  HXT   H  HOH1  0   0.488  -1.1127  -0.0839  -3.5238
 LML  HA    H  HCH1  0   0.322  -0.1786  -1.3816  -0.4016
 LML  HB1   H  HCH2  0   0.246  -1.8188  -0.1506   0.9961
 LML  HB2   H  HCH2  0   0.244  -0.9251   1.3399   0.7747
 LML  HG    H  HCH1  0   0.225   1.0155   0.3670   1.9948
 LML  HD11  H  HCH3  0   0.229  -0.0449   0.4172   4.2277
 LML  HD12  H  HCH3  0   0.227  -0.7180   1.6766   3.1944
 LML  HD13  H  HCH3  0   0.216  -1.6346   0.2007   3.4977
 LML  HD21  H  HCH3  0   0.218  -0.8086  -2.0466   2.4368
 LML  HD22  H  HCH3  0   0.228   0.7024  -2.0606   1.5270
 LML  HD23  H  HCH3  0   0.232   0.7258  -1.7612   3.2548
 LML  HO2   H  HOH1  0   0.485   2.9638  -0.1978  -0.7534

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    double  1.202  0.020  1.202
 LML  C1   OXT   single  1.326  0.020  1.326
 LML  C1   CA    single  1.517  0.020  1.517
 LML  OXT  HXT   single  0.850  0.020  0.980
 LML  CA   CB    single  1.530  0.020  1.530
 LML  CA   C     single  1.516  0.020  1.516
 LML  CA   HA    single  0.970  0.020  1.090
 LML  CB   CG    single  1.530  0.020  1.530
 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     double  1.205  0.020  1.205
 LML  C    O2    single  1.322  0.020  1.322
 LML  O2   HO2   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
 LML  CA    C1   OXT   110.92  3.000
 LML  CA    C1   O1    125.16  3.000
 LML  OXT   C1   O1    123.90  3.000
 LML  HXT   OXT  C1    110.49  3.000
 LML  HA    CA   C     109.55  3.000
 LML  HA    CA   CB    110.12  3.000
 LML  C     CA   CB    110.22  3.000
 LML  HA    CA   C1    106.44  3.000
 LML  C     CA   C1    108.55  3.000
 LML  CB    CA   C1    111.87  3.000
 LML  HB2   CB   HB1   106.55  3.000
 LML  HB2   CB   CG    109.29  3.000
 LML  HB1   CB   CG    108.70  3.000
 LML  HB2   CB   CA    108.84  3.000
 LML  HB1   CB   CA    108.30  3.000
 LML  CG    CB   CA    114.84  3.000
 LML  HG    CG   CD2   108.15  3.000
 LML  HG    CG   CD1   107.44  3.000
 LML  CD2   CG   CD1   110.48  3.000
 LML  HG    CG   CB    108.96  3.000
 LML  CD2   CG   CB    112.49  3.000
 LML  CD1   CG   CB    109.19  3.000
 LML  HD13  CD1  HD12  107.70  3.000
 LML  HD13  CD1  HD11  107.66  3.000
 LML  HD12  CD1  HD11  107.72  3.000
 LML  HD13  CD1  CG    110.94  3.000
 LML  HD12  CD1  CG    111.54  3.000
 LML  HD11  CD1  CG    111.11  3.000
 LML  HD23  CD2  HD22  107.00  3.000
 LML  HD23  CD2  HD21  107.59  3.000
 LML  HD22  CD2  HD21  107.76  3.000
 LML  HD23  CD2  CG    110.70  3.000
 LML  HD22  CD2  CG    112.65  3.000
 LML  HD21  CD2  CG    110.91  3.000
 LML  O2    C    O     124.09  3.000
 LML  O2    C    CA    113.04  3.000
 LML  O     C    CA    122.85  3.000
 LML  HO2   O2   C     110.24  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  CONST_01  HXT   OXT  C1  O1     0.00   0.0  0
 LML  CONST_02  HO2   O2   C   CA   180.00   0.0  0
 LML  Var_01    CG    CB   CA  C1   178.79  30.0  3
 LML  Var_02    O     C    CA  C1    57.13  30.0  3
 LML  Var_03    CB    CA   C1  O1    -9.20  30.0  3
 LML  Var_04    CD1   CG   CB  CA   177.21  30.0  3
 LML  Var_05    HD11  CD1  CG  CB  -177.92  30.0  3
 LML  Var_06    HD21  CD2  CG  CB   -58.30  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-1  HXT  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
 LML  plan-2  HO2  0.020

