# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 17:35:17 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: N-methyl-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[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
 EME  EME  'N-methyl-L-glutamic acid '  L-peptide  20  11  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_EME
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
 EME  C7   C  CH3    0  -0.521  -2.2459   2.3562  -0.1496
 EME  N2   N  NH1    0  -0.596  -1.1498   1.5650   0.3683
 EME  CA   C  CH1    0  -0.161  -0.9581   0.3159  -0.3419
 EME  C    C  C      0   0.394  -2.1143  -0.6850  -0.1122
 EME  O    O  O      0  -0.605  -2.7887  -0.5791   0.9287
 EME  CB   C  CH2    0  -0.419   0.3500  -0.3553   0.0912
 EME  CG   C  CH2    0  -0.599   1.6050   0.4444  -0.2294
 EME  CD   C  C      0   0.416   2.9417  -0.2825   0.0171
 EME  OE2  O  O      0  -0.608   2.9035  -1.4675   0.4018
 EME  OE1  O  OC    -1  -0.634   3.9731   0.3899  -0.1973
 EME  OXT  O  OC    -1  -0.627  -2.2453  -1.5614  -0.9941
 EME  H1   H  HCH3   0   0.220  -2.2434   3.3418   0.3184
 EME  H2   H  HCH3   0   0.179  -2.2120   2.5088  -1.2395
 EME  H3   H  HCH3   0   0.218  -3.1997   1.8851   0.0865
 EME  H4   H  HNH1   0   0.339  -0.3059   2.1161   0.2827
 EME  H6   H  HCH1   0   0.159  -0.8938   0.4849  -1.4333
 EME  H7   H  HCH2   0   0.200   0.3011  -0.5616   1.1652
 EME  H8   H  HCH2   0   0.210   0.4114  -1.3240  -0.4067
 EME  H9   H  HCH2   0   0.218   1.5791   0.7577  -1.2805
 EME  H10  H  HCH2   0   0.214   1.6349   1.3763   0.3458

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
 EME  C7   N2   single  1.448  0.020  1.448
 EME  N2   CA   single  1.450  0.020  1.450
 EME  CB   CA   single  1.530  0.020  1.530
 EME  CB   CG   single  1.522  0.020  1.522
 EME  CA   C    single  1.525  0.021  1.525
 EME  OE2  CD   deloc   1.246  0.020  1.246
 EME  O    C    deloc   1.231  0.020  1.231
 EME  CD   CG   single  1.541  0.020  1.541
 EME  CD   OE1  deloc   1.250  0.020  1.250
 EME  C    OXT  deloc   1.250  0.020  1.250
 EME  C7   H1   single  0.970  0.020  1.090
 EME  C7   H2   single  0.970  0.020  1.090
 EME  C7   H3   single  0.970  0.020  1.090
 EME  N2   H4   single  0.890  0.020  1.040
 EME  CA   H6   single  0.970  0.020  1.090
 EME  CB   H7   single  0.970  0.020  1.090
 EME  CB   H8   single  0.970  0.020  1.090
 EME  CG   H9   single  0.970  0.020  1.090
 EME  CG   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
 EME  H3   C7  H2   107.54  3.000
 EME  H3   C7  H1   107.43  3.000
 EME  H2   C7  H1   107.41  3.000
 EME  H3   C7  N2   110.42  3.000
 EME  H2   C7  N2   113.99  3.000
 EME  H1   C7  N2   109.79  3.000
 EME  H4   N2  CA   108.52  3.000
 EME  H4   N2  C7   107.67  3.000
 EME  CA   N2  C7   113.32  3.000
 EME  H6   CA  CB   107.22  3.000
 EME  H6   CA  C    106.79  3.000
 EME  CB   CA  C    110.10  1.900
 EME  H6   CA  N2   111.06  3.000
 EME  C    CA  N2   112.71  3.000
 EME  CB   CA  N2   110.60  3.000
 EME  OXT  C   O    126.35  3.000
 EME  OXT  C   CA   115.30  3.000
 EME  O    C   CA   120.80  1.700
 EME  H8   CB  H7   106.44  3.000
 EME  H8   CB  CG   108.90  3.000
 EME  H7   CB  CG   110.02  3.000
 EME  H8   CB  CA   107.94  3.000
 EME  H7   CB  CA   108.76  3.000
 EME  CG   CB  CA   114.46  3.000
 EME  H10  CG  H9   105.11  3.000
 EME  H10  CG  CD   107.07  3.000
 EME  H9   CG  CD   107.96  3.000
 EME  H10  CG  CB   111.03  3.000
 EME  H9   CG  CB   109.41  3.000
 EME  CD   CG  CB   115.69  3.000
 EME  OE1  CD  OE2  126.14  3.000
 EME  OE1  CD  CG   115.75  3.000
 EME  OE2  CD  CG   118.10  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
 EME  Var_01  CD   CG  CB  CA  -172.01  30.0  3
 EME  Var_02  OE2  CD  CG  CB     2.80  30.0  2
 EME  Var_03  H1   C7  N2  CA  -171.33  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
 EME  chir_01  CA  N2  CB  C  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
 EME  plan-1  CA   0.020
 EME  plan-1  C    0.020
 EME  plan-1  O    0.020
 EME  plan-1  OXT  0.020
 EME  plan-2  CG   0.020
 EME  plan-2  CD   0.020
 EME  plan-2  OE2  0.020
 EME  plan-2  OE1  0.020

