# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 14:53:43 2022
#   Inital geometry file: a 59 line input string
#   Ligand name: (3S)-3-methyl-L-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CC(N)=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
 LMQ  LMQ  (3S)-3-methyl-L-glutamine  L-peptide  22  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 PERFECT
;

data_comp_LMQ
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
 LMQ  N     N  NH2    0  -0.802  3.3591   0.4874  -2.8515
 LMQ  CA    C  CH1    0  -0.207  2.6277  -0.4688  -3.6729
 LMQ  CB    C  CH1    0  -0.222  2.7353  -0.1076  -5.1680
 LMQ  CB2   C  CH3    0  -0.657  2.0423   1.2163  -5.4685
 LMQ  CG    C  CH2    0  -0.552  4.2052  -0.0859  -5.6160
 LMQ  CD    C  C      0   0.485  4.3683   0.2234  -7.0875
 LMQ  OE1   O  O      0  -0.488  4.7979   1.2934  -7.4972
 LMQ  NE2   N  NH2    0  -0.793  3.9856  -0.7641  -7.9176
 LMQ  C     C  C      0   0.390  3.0345  -1.9516  -3.4539
 LMQ  O     O  O      0  -0.599  4.0891  -2.1686  -2.8226
 LMQ  OXT   O  OC    -1  -0.608  2.2727  -2.8063  -3.9502
 LMQ  H     H  HNH2   0   0.336  2.9024   0.5678  -1.9522
 LMQ  H2    H  HNH2   0   0.328  4.2614   0.0737  -2.6443
 LMQ  HA    H  HCH1   0   0.217  1.5649  -0.3885  -3.4185
 LMQ  HB3   H  HCH1   0   0.219  2.2143  -0.8959  -5.7191
 LMQ  HB21  H  HCH3   0   0.216  2.5509   2.0488  -4.9817
 LMQ  HB22  H  HCH3   0   0.223  2.0058   1.4268  -6.5386
 LMQ  HB23  H  HCH3   0   0.221  1.0118   1.1991  -5.1092
 LMQ  HG2   H  HCH2   0   0.243  4.7447   0.6749  -5.0504
 LMQ  HG3   H  HCH2   0   0.255  4.6718  -1.0510  -5.3994
 LMQ  HE21  H  HNH2   0   0.403  3.6582  -1.6505  -7.5741
 LMQ  HE22  H  HNH2   0   0.394  4.0387  -0.6444  -8.9159

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
 LMQ  N    CA    single  1.458  0.019  1.458
 LMQ  CA   CB    single  1.530  0.020  1.530
 LMQ  CA   C     single  1.525  0.021  1.525
 LMQ  CB   CB2   single  1.524  0.020  1.524
 LMQ  CB   CG    single  1.537  0.020  1.537
 LMQ  CG   CD    single  1.512  0.020  1.512
 LMQ  CD   OE1   double  1.224  0.020  1.224
 LMQ  CD   NE2   single  1.346  0.020  1.346
 LMQ  C    O     deloc   1.231  0.020  1.231
 LMQ  C    OXT   deloc   1.248  0.020  1.248
 LMQ  N    H     single  0.860  0.020  0.860
 LMQ  N    H2    single  0.890  0.020  1.040
 LMQ  CA   HA    single  0.970  0.020  0.970
 LMQ  CB   HB3   single  0.970  0.020  1.090
 LMQ  CB2  HB21  single  0.970  0.020  1.090
 LMQ  CB2  HB22  single  0.970  0.020  1.090
 LMQ  CB2  HB23  single  0.970  0.020  1.090
 LMQ  CG   HG2   single  0.970  0.020  1.090
 LMQ  CG   HG3   single  0.970  0.020  1.090
 LMQ  NE2  HE21  single  0.860  0.020  1.020
 LMQ  NE2  HE22  single  0.860  0.020  1.020

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
 LMQ  H2    N    H     104.62  3.000
 LMQ  H2    N    CA    107.10  3.000
 LMQ  H     N    CA    114.00  3.000
 LMQ  HA    CA   C     109.00  3.000
 LMQ  HA    CA   CB    109.00  3.000
 LMQ  C     CA   CB    110.10  1.900
 LMQ  HA    CA   N     110.00  3.000
 LMQ  C     CA   N     111.00  2.800
 LMQ  CB    CA   N     110.50  1.700
 LMQ  HB3   CB   CG    108.60  3.000
 LMQ  HB3   CB   CB2   108.06  3.000
 LMQ  CG    CB   CB2   111.41  3.000
 LMQ  HB3   CB   CA    106.65  3.000
 LMQ  CG    CB   CA    110.66  3.000
 LMQ  CB2   CB   CA    111.28  3.000
 LMQ  HB23  CB2  HB22  107.12  3.000
 LMQ  HB23  CB2  HB21  107.79  3.000
 LMQ  HB22  CB2  HB21  107.83  3.000
 LMQ  HB23  CB2  CB    110.53  3.000
 LMQ  HB22  CB2  CB    112.09  3.000
 LMQ  HB21  CB2  CB    111.29  3.000
 LMQ  HG3   CG   HG2   107.56  3.000
 LMQ  HG3   CG   CD    109.10  3.000
 LMQ  HG2   CG   CD    107.97  3.000
 LMQ  HG3   CG   CB    109.75  3.000
 LMQ  HG2   CG   CB    109.37  3.000
 LMQ  CD    CG   CB    112.93  3.000
 LMQ  NE2   CD   OE1   122.34  3.000
 LMQ  NE2   CD   CG    114.80  3.000
 LMQ  OE1   CD   CG    122.85  3.000
 LMQ  HE22  NE2  HE21  117.44  3.000
 LMQ  HE22  NE2  CD    120.62  3.000
 LMQ  HE21  NE2  CD    121.92  3.000
 LMQ  OXT   C    O     126.72  3.000
 LMQ  OXT   C    CA    115.97  3.000
 LMQ  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
 LMQ  CONST_01  HE21  NE2  CD  CG    0.00   0.0  0
 LMQ  CONST_02  HE22  NE2  CD  CG  180.00   0.0  0
 LMQ  Var_01    OE1   CD   CG  CB  107.64  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
 LMQ  chir_01  CA  N   CB   C   negativ
 LMQ  chir_02  CB  CG  CB2  CA  positiv

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
 LMQ  plan-1  CG    0.020
 LMQ  plan-1  CD    0.020
 LMQ  plan-1  OE1   0.020
 LMQ  plan-1  NE2   0.020
 LMQ  plan-1  HE21  0.020
 LMQ  plan-1  HE22  0.020
 LMQ  plan-2  CA    0.020
 LMQ  plan-2  C     0.020
 LMQ  plan-2  O     0.020
 LMQ  plan-2  OXT   0.020

