# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 21 03:41:03 2022
#   Inital geometry file: a 65 line input string
#   Ligand name: N,N-dimethyl-L-glutamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)C(=O)CC[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
 QMM  QMM  'N,N-dimethyl-L-glutamine '  L-peptide  25  12  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_QMM
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
 QMM  C     C  C      0   0.411  -4.9752  -1.3169  34.4873
 QMM  CD    C  C      0   0.567  -6.5005  -2.0004  39.2963
 QMM  CG    C  CH2    0  -0.606  -6.7140  -2.3292  37.8306
 QMM  N     N  NH2    0  -0.819  -5.9306  -3.4892  35.2292
 QMM  OXT   O  OC    -1  -0.605  -4.7864  -0.1064  34.7156
 QMM  OE1   O  O      0  -0.500  -5.5458  -1.3282  39.6658
 QMM  NE2   N  NT     0  -0.454  -7.4192  -2.4733  40.1743
 QMM  CH1   C  CH3    0  -0.521  -8.4527  -3.4230  39.8205
 QMM  CH2   C  CH3    0  -0.519  -7.2176  -2.2809  41.5949
 QMM  CA    C  CH1    0  -0.223  -5.9605  -2.0476  35.4398
 QMM  CB    C  CH2    0  -0.379  -5.6765  -1.7140  36.9047
 QMM  O     O  O      0  -0.599  -4.4831  -1.9838  33.5543
 QMM  HG1   H  HCH2   0   0.260  -6.7190  -3.4172  37.7117
 QMM  HG2   H  HCH2   0   0.254  -7.7124  -1.9953  37.5270
 QMM  H     H  HNH2   0   0.331  -6.8566  -3.8802  35.3354
 QMM  H2    H  HNH2   0   0.334  -5.6479  -3.6521  34.2712
 QMM  HH1   H  HCH3   0   0.245  -9.3269  -3.2530  40.4481
 QMM  HH1A  H  HCH3   0   0.259  -8.7698  -3.3109  38.7885
 QMM  HH1B  H  HCH3   0   0.235  -8.1274  -4.4564  39.9700
 QMM  HH2   H  HCH3   0   0.237  -8.1849  -2.1853  42.0875
 QMM  HH2A  H  HCH3   0   0.231  -6.6904  -3.1253  42.0483
 QMM  HH2B  H  HCH3   0   0.251  -6.6462  -1.3777  41.7845
 QMM  HA    H  HCH1   0   0.193  -6.9534  -1.6268  35.2019
 QMM  HB2   H  HCH2   0   0.212  -5.6638  -0.6314  37.0268
 QMM  HB3   H  HCH2   0   0.204  -4.6792  -2.0800  37.1643

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
 QMM  O    C     deloc   1.231  0.020  1.231
 QMM  OXT  C     deloc   1.246  0.020  1.246
 QMM  C    CA    single  1.525  0.021  1.525
 QMM  CG   CD    single  1.517  0.020  1.517
 QMM  CD   OE1   double  1.225  0.020  1.225
 QMM  CD   NE2   single  1.356  0.020  1.356
 QMM  CB   CG    single  1.521  0.020  1.521
 QMM  CG   HG1   single  0.970  0.020  1.090
 QMM  CG   HG2   single  0.970  0.020  1.090
 QMM  N    CA    single  1.458  0.019  1.458
 QMM  N    H     single  0.860  0.020  0.860
 QMM  N    H2    single  0.890  0.020  1.040
 QMM  CH1  NE2   single  1.448  0.020  1.448
 QMM  NE2  CH2   single  1.448  0.020  1.448
 QMM  CH1  HH1   single  0.970  0.020  1.090
 QMM  CH1  HH1A  single  0.970  0.020  1.090
 QMM  CH1  HH1B  single  0.970  0.020  1.090
 QMM  CH2  HH2   single  0.970  0.020  1.090
 QMM  CH2  HH2A  single  0.970  0.020  1.090
 QMM  CH2  HH2B  single  0.970  0.020  1.090
 QMM  CA   CB    single  1.530  0.020  1.530
 QMM  CA   HA    single  0.970  0.020  0.970
 QMM  CB   HB2   single  0.970  0.020  1.090
 QMM  CB   HB3   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
 QMM  O     C    CA    120.80  1.700
 QMM  CA    C    OXT   116.15  3.000
 QMM  O     C    OXT   126.60  3.000
 QMM  NE2   CD   OE1   121.61  3.000
 QMM  NE2   CD   CG    117.05  3.000
 QMM  OE1   CD   CG    121.34  3.000
 QMM  HG2   CG   HG1   105.58  3.000
 QMM  HG2   CG   CB    109.25  3.000
 QMM  HG1   CG   CB    109.83  3.000
 QMM  HG2   CG   CD    109.26  3.000
 QMM  HG1   CG   CD    108.72  3.000
 QMM  CB    CG   CD    113.87  3.000
 QMM  H2    N    H     107.04  3.000
 QMM  H2    N    CA    107.57  3.000
 QMM  H     N    CA    114.00  3.000
 QMM  CH2   NE2  CH1   115.25  3.000
 QMM  CH2   NE2  CD    119.66  3.000
 QMM  CH1   NE2  CD    123.66  3.000
 QMM  HH1B  CH1  HH1A  108.33  3.000
 QMM  HH1B  CH1  HH1   107.90  3.000
 QMM  HH1A  CH1  HH1   107.29  3.000
 QMM  HH1B  CH1  NE2   111.97  3.000
 QMM  HH1A  CH1  NE2   111.92  3.000
 QMM  HH1   CH1  NE2   109.25  3.000
 QMM  HH2B  CH2  HH2A  108.43  3.000
 QMM  HH2B  CH2  HH2   108.38  3.000
 QMM  HH2A  CH2  HH2   107.95  3.000
 QMM  HH2B  CH2  NE2   110.81  3.000
 QMM  HH2A  CH2  NE2   111.80  3.000
 QMM  HH2   CH2  NE2   109.37  3.000
 QMM  HA    CA   CB    109.00  3.000
 QMM  HA    CA   N     110.00  3.000
 QMM  CB    CA   N     110.50  1.700
 QMM  HA    CA   C     109.00  3.000
 QMM  CB    CA   C     110.10  1.900
 QMM  N     CA   C     111.00  2.800
 QMM  HB3   CB   HB2   107.17  3.000
 QMM  HB3   CB   CA    108.90  3.000
 QMM  HB2   CB   CA    109.05  3.000
 QMM  HB3   CB   CG    110.01  3.000
 QMM  HB2   CB   CG    109.98  3.000
 QMM  CA    CB   CG    111.62  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
 QMM  CONST_01  CH1  NE2  CD   CG      0.00   0.0  0
 QMM  CONST_02  CH2  NE2  CD   CG    180.00   0.0  0
 QMM  CONST_03  CH1  NE2  CD   OE1   180.00   0.0  0
 QMM  CONST_04  CH2  NE2  CD   OE1     0.00   0.0  0
 QMM  Var_01    CA   CB   CG   CD   -178.53  30.0  2
 QMM  Var_02    CB   CG   CD   OE1    -1.92  30.0  1
 QMM  Var_03    HH1  CH1  NE2  CD   -149.85  30.0  3
 QMM  Var_04    HH2  CH2  NE2  CD    148.56  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
 QMM  chir_01  CA  C  N  CB  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
 QMM  plan-1  CD   0.020
 QMM  plan-1  CG   0.020
 QMM  plan-1  OE1  0.020
 QMM  plan-1  NE2  0.020
 QMM  plan-1  CH1  0.020
 QMM  plan-1  CH2  0.020
 QMM  plan-2  C    0.020
 QMM  plan-2  OXT  0.020
 QMM  plan-2  CA   0.020
 QMM  plan-2  O    0.020

