# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:34:06 2022
#   Inital geometry file: a 57 line input string
#   Ligand name: (3R)-3-methyl-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CC(O)=O)[C@H](N)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
 LME  LME  '(3R)-3-methyl-L-glutamic acid'  L-peptide  20  11  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_LME
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
 LME  N    N  NH2    0  -0.794   -7.5519  -17.2389  -4.8311
 LME  CA   C  CH1    0  -0.214   -7.5866  -17.9069  -3.5358
 LME  CB   C  CH1    0  -0.210   -7.2512  -19.4048  -3.6784
 LME  C1   C  CH3    0  -0.667   -5.8281  -19.6228  -4.1882
 LME  CG   C  CH2    0  -0.513   -8.2509  -20.1406  -4.5711
 LME  CD   C  C      0   0.385   -9.7025  -20.1029  -4.0599
 LME  OE1  O  O      0  -0.620   -9.8873  -20.4623  -2.8760
 LME  OE2  O  OC    -1  -0.617  -10.5841  -19.7340  -4.8639
 LME  C    C  C      0   0.385   -6.6868  -17.2667  -2.4455
 LME  O    O  O      0  -0.616   -6.8707  -17.6688  -1.2767
 LME  H2   H  HNH2   0   0.329   -8.0474  -16.3591  -4.7537
 LME  H    H  HNH2   0   0.323   -6.5926  -16.9649  -5.0101
 LME  HA   H  HCH1   0   0.212   -8.6168  -17.8479  -3.1674
 LME  HB   H  HCH1   0   0.197   -7.3234  -19.8374  -2.6779
 LME  H11  H  HCH3   0   0.216   -5.5971  -20.6883  -4.2462
 LME  H12  H  HCH3   0   0.207   -5.6933  -19.2123  -5.1918
 LME  H13  H  HCH3   0   0.220   -5.0794  -19.1636  -3.5405
 LME  HG2  H  HCH2   0   0.183   -8.1956  -19.7430  -5.5866
 LME  HG3  H  HCH2   0   0.201   -7.9409  -21.1919  -4.6308
 LME  OXT  O  OC    -1  -0.606   -5.8472  -16.4203  -2.8160

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
 LME  N   CA   single  1.458  0.019  1.458
 LME  N   H2   single  0.890  0.020  1.040
 LME  N   H    single  0.860  0.020  0.860
 LME  CA  CB   single  1.530  0.020  1.530
 LME  CA  C    single  1.525  0.021  1.525
 LME  CA  HA   single  0.970  0.020  0.970
 LME  CB  C1   single  1.527  0.020  1.527
 LME  CB  CG   single  1.529  0.020  1.529
 LME  CB  HB   single  0.970  0.020  1.090
 LME  C1  H11  single  0.970  0.020  1.090
 LME  C1  H12  single  0.970  0.020  1.090
 LME  C1  H13  single  0.970  0.020  1.090
 LME  CG  CD   single  1.539  0.020  1.539
 LME  CG  HG2  single  0.970  0.020  1.090
 LME  CG  HG3  single  0.970  0.020  1.090
 LME  CD  OE1  deloc   1.251  0.020  1.251
 LME  CD  OE2  deloc   1.249  0.020  1.249
 LME  C   O    deloc   1.231  0.020  1.231
 LME  C   OXT  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
 LME  H    N   H2   103.98  3.000
 LME  H    N   CA   114.00  3.000
 LME  H2   N   CA   108.57  3.000
 LME  HA   CA  C    109.00  3.000
 LME  HA   CA  CB   109.00  3.000
 LME  C    CA  CB   110.10  1.900
 LME  HA   CA  N    110.00  3.000
 LME  C    CA  N    111.00  2.800
 LME  CB   CA  N    110.50  1.700
 LME  HB   CB  CG   107.52  3.000
 LME  HB   CB  C1   108.11  3.000
 LME  CG   CB  C1   110.22  3.000
 LME  HB   CB  CA   106.60  3.000
 LME  CG   CB  CA   112.29  3.000
 LME  C1   CB  CA   111.86  3.000
 LME  H13  C1  H12  107.60  3.000
 LME  H13  C1  H11  107.27  3.000
 LME  H12  C1  H11  106.96  3.000
 LME  H13  C1  CB   112.40  3.000
 LME  H12  C1  CB   111.59  3.000
 LME  H11  C1  CB   110.74  3.000
 LME  HG3  CG  HG2  106.49  3.000
 LME  HG3  CG  CD   107.93  3.000
 LME  HG2  CG  CD   110.34  3.000
 LME  HG3  CG  CB   107.94  3.000
 LME  HG2  CG  CB   109.55  3.000
 LME  CD   CG  CB   114.26  3.000
 LME  OE2  CD  OE1  126.14  3.000
 LME  OE2  CD  CG   117.33  3.000
 LME  OE1  CD  CG   116.52  3.000
 LME  OXT  C   O    126.49  3.000
 LME  OXT  C   CA   117.46  3.000
 LME  O    C   CA   120.80  1.700

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
 LME  Var_01  OE1  CD  CG  CB  -52.09  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
 LME  chir_01  CA  N   CB  C   negativ
 LME  chir_02  CB  CG  C1  CA  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
 LME  plan-1  CG   0.020
 LME  plan-1  CD   0.020
 LME  plan-1  OE1  0.020
 LME  plan-1  OE2  0.020
 LME  plan-2  CA   0.020
 LME  plan-2  C    0.020
 LME  plan-2  O    0.020
 LME  plan-2  OXT  0.020

