# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 10:56:19 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: (4R)-4-(3-methoxy-3-oxopropyl)-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)CC[C@H](C[C@H](N)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
 2QE  2QE  '(4R)-4-(3-methoxy-3-oxopropyl)-L-glutamic acid'  ligand  29  16  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2QE
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
 2QE  O    O  O      0  -0.613  -4.4715  -1.7177   0.5001
 2QE  C    C  C      0   0.403  -3.9703  -0.8249  -0.2123
 2QE  OXT  O  OC    -1  -0.627  -4.2783  -0.5615  -1.3940
 2QE  CA   C  CH1    0  -0.212  -2.8165  -0.0005   0.3898
 2QE  N    N  NH2    0  -0.802  -2.8915   0.0336   1.8421
 2QE  CB   C  CH2    0  -0.420  -1.4978  -0.5588  -0.1765
 2QE  CG   C  CH1    0  -0.339  -0.2229   0.0791   0.3836
 2QE  CD2  C  C      0   0.416  -0.2746   1.6065   0.1975
 2QE  OAG  O  O      0  -0.615  -0.0952   2.0337  -0.9623
 2QE  OAD  O  OC    -1  -0.616  -0.5122   2.3030   1.2079
 2QE  CD1  C  CH2    0  -0.397   1.0036  -0.5451  -0.2774
 2QE  CAH  C  CH2    0  -0.591   2.3034  -0.0049   0.2969
 2QE  CAN  C  C      0   0.601   3.5377  -0.6651  -0.2529
 2QE  OAE  O  O      0  -0.455   3.5551  -1.5294  -1.0940
 2QE  OAK  O  O2     0  -0.458   4.6402  -0.1733   0.3046
 2QE  CAA  C  CH3    0  -0.424   5.8928  -0.7012  -0.1276
 2QE  H2   H  HCH1   0   0.203  -2.9251   1.0308   0.0373
 2QE  H3   H  HNH2   0   0.319  -2.7956  -0.9081   2.2015
 2QE  H4   H  HNH2   0   0.333  -2.1043   0.5653   2.1943
 2QE  H6   H  HCH2   0   0.204  -1.4575  -1.6381   0.0185
 2QE  H7   H  HCH2   0   0.205  -1.5049  -0.4437  -1.2645
 2QE  H8   H  HCH1   0   0.191  -0.1680  -0.1407   1.4563
 2QE  H10  H  HCH2   0   0.217   0.9644  -1.6297  -0.1403
 2QE  H11  H  HCH2   0   0.216   0.9671  -0.3660  -1.3540
 2QE  H12  H  HCH2   0   0.274   2.3898   1.0699   0.1090
 2QE  H13  H  HCH2   0   0.268   2.3163  -0.1138   1.3864
 2QE  H14  H  HCH3   0   0.236   5.9721  -1.7681   0.0809
 2QE  H15  H  HCH3   0   0.236   6.0525  -0.5328  -1.1924
 2QE  H16  H  HCH3   0   0.249   6.6529  -0.1692   0.4374

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
 2QE  O    C    deloc   1.247  0.020  1.247
 2QE  N    CA   single  1.455  0.020  1.455
 2QE  C    CA   single  1.541  0.020  1.541
 2QE  C    OXT  deloc   1.249  0.020  1.249
 2QE  CA   CB   single  1.540  0.020  1.540
 2QE  OAG  CD2  deloc   1.249  0.020  1.249
 2QE  OAD  CD2  deloc   1.250  0.020  1.250
 2QE  CD2  CG   single  1.540  0.020  1.540
 2QE  CB   CG   single  1.532  0.020  1.532
 2QE  CG   CD1  single  1.527  0.020  1.527
 2QE  CAA  OAK  single  1.426  0.020  1.426
 2QE  OAK  CAN  single  1.330  0.020  1.330
 2QE  OAE  CAN  double  1.206  0.020  1.206
 2QE  CAN  CAH  single  1.504  0.020  1.504
 2QE  CD1  CAH  single  1.520  0.020  1.520
 2QE  CA   H2   single  0.970  0.020  1.090
 2QE  N    H3   single  0.890  0.020  1.040
 2QE  N    H4   single  0.890  0.020  1.040
 2QE  CB   H6   single  0.970  0.020  1.090
 2QE  CB   H7   single  0.970  0.020  1.090
 2QE  CG   H8   single  0.970  0.020  1.090
 2QE  CD1  H10  single  0.970  0.020  1.090
 2QE  CD1  H11  single  0.970  0.020  1.090
 2QE  CAH  H12  single  0.970  0.020  1.090
 2QE  CAH  H13  single  0.970  0.020  1.090
 2QE  CAA  H14  single  0.970  0.020  1.090
 2QE  CAA  H15  single  0.970  0.020  1.090
 2QE  CAA  H16  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
 2QE  CA   C    OXT  116.19  3.000
 2QE  OXT  C    O    126.31  3.000
 2QE  CA   C    O    117.44  3.000
 2QE  H2   CA   CB   107.94  3.000
 2QE  H2   CA   N    107.10  3.000
 2QE  CB   CA   N    114.82  3.000
 2QE  H2   CA   C    107.69  3.000
 2QE  CB   CA   C    107.68  3.000
 2QE  N    CA   C    111.35  3.000
 2QE  H4   N    H3   106.93  3.000
 2QE  H4   N    CA   108.62  3.000
 2QE  H3   N    CA   109.13  3.000
 2QE  H7   CB   H6   106.28  3.000
 2QE  H7   CB   CG   108.98  3.000
 2QE  H6   CB   CG   108.30  3.000
 2QE  H7   CB   CA   108.78  3.000
 2QE  H6   CB   CA   108.82  3.000
 2QE  CG   CB   CA   115.30  3.000
 2QE  H8   CG   CD1  107.54  3.000
 2QE  H8   CG   CD2  108.59  3.000
 2QE  CD1  CG   CD2  112.35  3.000
 2QE  H8   CG   CB   108.42  3.000
 2QE  CD1  CG   CB   109.88  3.000
 2QE  CD2  CG   CB   109.94  3.000
 2QE  OAD  CD2  OAG  125.97  3.000
 2QE  OAD  CD2  CG   117.48  3.000
 2QE  OAG  CD2  CG   116.54  3.000
 2QE  H11  CD1  H10  106.56  3.000
 2QE  H11  CD1  CAH  110.05  3.000
 2QE  H10  CD1  CAH  109.61  3.000
 2QE  H11  CD1  CG   109.45  3.000
 2QE  H10  CD1  CG   108.80  3.000
 2QE  CAH  CD1  CG   112.21  3.000
 2QE  H13  CAH  H12  105.52  3.000
 2QE  H13  CAH  CAN  108.09  3.000
 2QE  H12  CAH  CAN  107.67  3.000
 2QE  H13  CAH  CD1  110.52  3.000
 2QE  H12  CAH  CD1  110.58  3.000
 2QE  CAN  CAH  CD1  114.05  3.000
 2QE  OAK  CAN  OAE  123.05  3.000
 2QE  OAE  CAN  CAH  125.55  3.000
 2QE  OAK  CAN  CAH  111.40  3.000
 2QE  CAA  OAK  CAN  117.66  3.000
 2QE  H16  CAA  H15  109.27  3.000
 2QE  H16  CAA  H14  109.21  3.000
 2QE  H15  CAA  H14  109.11  3.000
 2QE  H16  CAA  OAK  106.00  3.000
 2QE  H15  CAA  OAK  111.56  3.000
 2QE  H14  CAA  OAK  111.60  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
 2QE  Var_01  CAN  CAH  CD1  CG    175.72  30.0  3
 2QE  Var_02  OAK  CAN  CAH  CD1  -178.68  30.0  1
 2QE  Var_03  H14  CAA  OAK  CAN   -61.54  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
 2QE  chir_01  CA  N    C   CB   positiv
 2QE  chir_02  CG  CD1  CB  CD2  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
 2QE  plan-1  O    0.020
 2QE  plan-1  C    0.020
 2QE  plan-1  OXT  0.020
 2QE  plan-1  CA   0.020
 2QE  plan-2  CG   0.020
 2QE  plan-2  CD2  0.020
 2QE  plan-2  OAG  0.020
 2QE  plan-2  OAD  0.020
 2QE  plan-3  CAH  0.020
 2QE  plan-3  CAN  0.020
 2QE  plan-3  OAE  0.020
 2QE  plan-3  OAK  0.020

