# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 02:35:26 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  31  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.434  -4.6199  -1.4881   0.4781
 2QE  C    C  C     0   0.552  -3.9472  -0.7114  -0.1492
 2QE  OXT  O  OH1   0  -0.593  -4.1252  -0.4649  -1.4416
 2QE  CA   C  CH1   0  -0.232  -2.7807   0.0760   0.4175
 2QE  N    N  NH2   0  -0.782  -2.8575   0.0698   1.8599
 2QE  CB   C  CH2   0  -0.443  -1.4779  -0.4885  -0.1881
 2QE  CG   C  CH1   0  -0.370  -0.1988   0.1820   0.3296
 2QE  CD2  C  C     0   0.546  -0.2295   1.6534  -0.0203
 2QE  OAG  O  O     0  -0.437  -0.0971   2.0824  -1.1398
 2QE  OAD  O  OH1   0  -0.587  -0.4462   2.4303   1.0344
 2QE  CD1  C  CH2   0  -0.414   1.0283  -0.4945  -0.2833
 2QE  CAH  C  CH2   0  -0.594   2.3334   0.0434   0.2817
 2QE  CAN  C  C     0   0.607   3.5473  -0.6596  -0.2647
 2QE  OAE  O  O     0  -0.451   3.5278  -1.5491  -1.0781
 2QE  OAK  O  O2    0  -0.456   4.6647  -0.1743   0.2610
 2QE  CAA  C  CH3   0  -0.425   5.9008  -0.7405  -0.1745
 2QE  H1   H  HOH1  0   0.483  -4.8476  -1.0094  -1.7890
 2QE  H2   H  HCH1  0   0.279  -2.9091   1.1112   0.0833
 2QE  H3   H  HNH2  0   0.349  -2.6035  -0.8377   2.2313
 2QE  H4   H  HNH2  0   0.357  -2.1984   0.7349   2.2407
 2QE  H6   H  HCH2  0   0.259  -1.4071  -1.5545   0.0481
 2QE  H7   H  HCH2  0   0.253  -1.5036  -0.4083  -1.2772
 2QE  H8   H  HCH1  0   0.264  -0.1510   0.0715   1.4165
 2QE  H9   H  HOH1  0   0.481  -0.4921   3.3601   0.7614
 2QE  H10  H  HCH2  0   0.254   0.9524  -1.5645  -0.0806
 2QE  H11  H  HCH2  0   0.244   1.0052  -0.3794  -1.3687
 2QE  H12  H  HCH2  0   0.281   2.4478   1.1121   0.0733
 2QE  H13  H  HCH2  0   0.282   2.3461  -0.0473   1.3722
 2QE  H14  H  HCH3  0   0.239   5.9591  -1.8030   0.0607
 2QE  H15  H  HCH3  0   0.239   6.0468  -0.6024  -1.2456
 2QE  H16  H  HCH3  0   0.252   6.6791  -0.2102   0.3659

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    double  1.204  0.020  1.204
 2QE  N    CA   single  1.445  0.020  1.445
 2QE  C    CA   single  1.517  0.020  1.517
 2QE  C    OXT  single  1.328  0.020  1.328
 2QE  CA   CB   single  1.544  0.020  1.544
 2QE  OAG  CD2  double  1.206  0.020  1.206
 2QE  OAD  CD2  single  1.328  0.020  1.328
 2QE  CD2  CG   single  1.513  0.020  1.513
 2QE  CB   CG   single  1.534  0.020  1.534
 2QE  CG   CD1  single  1.529  0.020  1.529
 2QE  CAA  OAK  single  1.428  0.020  1.428
 2QE  OAK  CAN  single  1.327  0.020  1.327
 2QE  OAE  CAN  double  1.206  0.020  1.206
 2QE  CAN  CAH  single  1.505  0.020  1.505
 2QE  CD1  CAH  single  1.520  0.020  1.520
 2QE  OXT  H1   single  0.850  0.020  0.980
 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  OAD  H9   single  0.850  0.020  0.980
 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  111.74  3.000
 2QE  OXT  C    O    123.51  3.000
 2QE  CA   C    O    124.74  3.000
 2QE  H1   OXT  C    110.16  3.000
 2QE  H2   CA   CB   108.96  3.000
 2QE  H2   CA   N    107.60  3.000
 2QE  CB   CA   N    115.79  3.000
 2QE  H2   CA   C    106.64  3.000
 2QE  CB   CA   C    108.22  3.000
 2QE  N    CA   C    109.26  3.000
 2QE  H4   N    H3   106.73  3.000
 2QE  H4   N    CA   109.80  3.000
 2QE  H3   N    CA   110.89  3.000
 2QE  H7   CB   H6   106.76  3.000
 2QE  H7   CB   CG   108.91  3.000
 2QE  H6   CB   CG   107.40  3.000
 2QE  H7   CB   CA   110.15  3.000
 2QE  H6   CB   CA   109.04  3.000
 2QE  CG   CB   CA   114.30  3.000
 2QE  H8   CG   CD1  108.58  3.000
 2QE  H8   CG   CD2  109.21  3.000
 2QE  CD1  CG   CD2  110.72  3.000
 2QE  H8   CG   CB   109.13  3.000
 2QE  CD1  CG   CB   109.90  3.000
 2QE  CD2  CG   CB   109.27  3.000
 2QE  OAD  CD2  OAG  123.16  3.000
 2QE  OAD  CD2  CG   112.87  3.000
 2QE  OAG  CD2  CG   123.95  3.000
 2QE  H9   OAD  CD2  110.19  3.000
 2QE  H11  CD1  H10  106.64  3.000
 2QE  H11  CD1  CAH  110.50  3.000
 2QE  H10  CD1  CAH  109.72  3.000
 2QE  H11  CD1  CG   109.57  3.000
 2QE  H10  CD1  CG   107.66  3.000
 2QE  CAH  CD1  CG   112.54  3.000
 2QE  H13  CAH  H12  105.62  3.000
 2QE  H13  CAH  CAN  108.27  3.000
 2QE  H12  CAH  CAN  107.61  3.000
 2QE  H13  CAH  CD1  110.54  3.000
 2QE  H12  CAH  CD1  111.37  3.000
 2QE  CAN  CAH  CD1  113.08  3.000
 2QE  OAK  CAN  OAE  123.43  3.000
 2QE  OAE  CAN  CAH  125.20  3.000
 2QE  OAK  CAN  CAH  111.38  3.000
 2QE  CAA  OAK  CAN  117.59  3.000
 2QE  H16  CAA  H15  109.34  3.000
 2QE  H16  CAA  H14  109.29  3.000
 2QE  H15  CAA  H14  109.18  3.000
 2QE  H16  CAA  OAK  105.97  3.000
 2QE  H15  CAA  OAK  111.45  3.000
 2QE  H14  CAA  OAK  111.54  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  CONST_01  H1   OXT  C    O       0.00   0.0  0
 2QE  CONST_02  H9   OAD  CD2  CG    180.00   0.0  0
 2QE  Var_01    CAN  CAH  CD1  CG    177.24  30.0  3
 2QE  Var_02    OAK  CAN  CAH  CD1  -179.31  30.0  1
 2QE  Var_03    H14  CAA  OAK  CAN   -61.29  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-1  H1   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-2  H9   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

