# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:52:58 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: (4R)-4-[3-(methylamino)-3-oxopropyl]-L-glutamic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=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
 2QD  2QD  '(4R)-4-[3-(methylamino)-3-oxopropyl]-L-glutamic acid'  L-peptide  30  16  .  2016-04-22  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_2QD
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
 2QD  O    O  O      0  -0.618  -1.4432  31.3285  -13.9026
 2QD  C    C  C      0   0.381  -2.6739  31.4723  -13.7442
 2QD  OXT  O  OC    -1  -0.605  -3.2815  32.5489  -13.5735
 2QD  CA   C  CH1    0  -0.217  -3.5259  30.1782  -13.7991
 2QD  N    N  NH2    0  -0.785  -4.8777  30.3160  -13.2693
 2QD  CB   C  CH2    0  -0.416  -3.5840  29.6811  -15.2480
 2QD  CG   C  CH1    0  -0.329  -4.2347  28.3079  -15.4245
 2QD  CD2  C  C      0   0.402  -3.3508  27.2095  -14.7918
 2QD  OAG  O  O      0  -0.614  -2.2267  27.0335  -15.3093
 2QD  OAD  O  OC    -1  -0.612  -3.8212  26.5819  -13.8198
 2QD  CD1  C  CH2    0  -0.423  -4.4936  27.9843  -16.9000
 2QD  CAH  C  CH2    0  -0.567  -5.4949  28.9157  -17.5932
 2QD  CAN  C  C      0   0.522  -6.8321  28.8984  -16.8872
 2QD  OAE  O  O      0  -0.502  -7.5576  27.9108  -16.8948
 2QD  NAK  N  NH1    0  -0.616  -7.1609  30.0210  -16.2274
 2QD  CAA  C  CH3    0  -0.513  -8.3415  30.1229  -15.4052
 2QD  H2   H  HCH1   0   0.204  -3.0119  29.4211  -13.1964
 2QD  H3   H  HNH2   0   0.329  -4.8178  30.5108  -12.2767
 2QD  H4   H  HNH2   0   0.320  -5.2714  31.1636  -13.6640
 2QD  H6   H  HCH2   0   0.208  -2.5734  29.6456  -15.6603
 2QD  H7   H  HCH2   0   0.199  -4.1204  30.4402  -15.8301
 2QD  H8   H  HCH1   0   0.196  -5.1898  28.3128  -14.8928
 2QD  H10  H  HCH2   0   0.219  -4.8664  26.9594  -16.9870
 2QD  H11  H  HCH2   0   0.220  -3.5532  28.0145  -17.4558
 2QD  H12  H  HCH2   0   0.240  -5.0945  29.9287  -17.6618
 2QD  H13  H  HCH2   0   0.261  -5.6493  28.5730  -18.6191
 2QD  H14  H  HNH1   0   0.401  -6.5067  30.7845  -16.2090
 2QD  H15  H  HCH3   0   0.246  -8.3952  31.1303  -15.0020
 2QD  H16  H  HCH3   0   0.235  -9.2480  29.9369  -15.9808
 2QD  H17  H  HCH3   0   0.233  -8.3184  29.4217  -14.5689

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
 2QD  CAH  CD1  single  1.533  0.020  1.533
 2QD  CAH  CAN  single  1.512  0.020  1.512
 2QD  CD1  CG   single  1.533  0.020  1.533
 2QD  CAN  NAK  single  1.343  0.020  1.343
 2QD  CAN  OAE  double  1.225  0.020  1.225
 2QD  NAK  CAA  single  1.442  0.020  1.442
 2QD  CG   CB   single  1.530  0.020  1.530
 2QD  CG   CD2  single  1.545  0.020  1.545
 2QD  CB   CA   single  1.521  0.033  1.521
 2QD  OAG  CD2  deloc   1.250  0.020  1.250
 2QD  CD2  OAD  deloc   1.249  0.020  1.249
 2QD  O    C    deloc   1.231  0.020  1.231
 2QD  CA   C    single  1.525  0.021  1.525
 2QD  CA   N    single  1.458  0.019  1.458
 2QD  C    OXT  deloc   1.248  0.020  1.248
 2QD  CA   H2   single  0.970  0.020  1.090
 2QD  N    H3   single  0.890  0.020  1.040
 2QD  N    H4   single  0.890  0.020  1.040
 2QD  CB   H6   single  0.970  0.020  1.090
 2QD  CB   H7   single  0.970  0.020  1.090
 2QD  CG   H8   single  0.970  0.020  1.090
 2QD  CD1  H10  single  0.970  0.020  1.090
 2QD  CD1  H11  single  0.970  0.020  1.090
 2QD  CAH  H12  single  0.970  0.020  1.090
 2QD  CAH  H13  single  0.970  0.020  1.090
 2QD  NAK  H14  single  0.860  0.020  1.020
 2QD  CAA  H15  single  0.970  0.020  1.090
 2QD  CAA  H16  single  0.970  0.020  1.090
 2QD  CAA  H17  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
 2QD  CA   C    OXT  120.80  1.700
 2QD  OXT  C    O    126.61  3.000
 2QD  CA   C    O    120.80  1.700
 2QD  H2   CA   CB   108.27  3.000
 2QD  H2   CA   N    107.47  3.000
 2QD  CB   CA   N    110.40  1.500
 2QD  H2   CA   C    107.43  3.000
 2QD  N    CA   C    111.00  2.800
 2QD  CB   CA   C    110.50  1.500
 2QD  H4   N    H3   104.08  3.000
 2QD  H4   N    CA   107.29  3.000
 2QD  H3   N    CA   108.62  3.000
 2QD  H7   CB   H6   105.95  3.000
 2QD  H7   CB   CG   110.61  3.000
 2QD  H6   CB   CG   108.71  3.000
 2QD  H7   CB   CA   107.21  3.000
 2QD  H6   CB   CA   109.41  3.000
 2QD  CG   CB   CA   114.60  3.000
 2QD  H8   CG   CD1  108.76  3.000
 2QD  H8   CG   CD2  107.68  3.000
 2QD  CD1  CG   CD2  109.92  3.000
 2QD  H8   CG   CB   108.15  3.000
 2QD  CD2  CG   CB   110.33  3.000
 2QD  CD1  CG   CB   111.87  3.000
 2QD  OAD  CD2  OAG  126.17  3.000
 2QD  OAD  CD2  CG   117.41  3.000
 2QD  OAG  CD2  CG   116.42  3.000
 2QD  H11  CD1  H10  106.18  3.000
 2QD  H11  CD1  CAH  108.38  3.000
 2QD  H10  CD1  CAH  108.10  3.000
 2QD  H11  CD1  CG   109.78  3.000
 2QD  H10  CD1  CG   109.38  3.000
 2QD  CAH  CD1  CG   114.67  3.000
 2QD  H13  CAH  H12  106.50  3.000
 2QD  H13  CAH  CAN  108.04  3.000
 2QD  H12  CAH  CAN  111.37  3.000
 2QD  H13  CAH  CD1  109.04  3.000
 2QD  H12  CAH  CD1  110.65  3.000
 2QD  CAN  CAH  CD1  111.06  3.000
 2QD  NAK  CAN  OAE  122.12  3.000
 2QD  OAE  CAN  CAH  122.00  3.000
 2QD  NAK  CAN  CAH  115.86  3.000
 2QD  H14  NAK  CAA  117.93  3.000
 2QD  H14  NAK  CAN  118.97  3.000
 2QD  CAA  NAK  CAN  122.65  3.000
 2QD  H17  CAA  H16  108.22  3.000
 2QD  H17  CAA  H15  108.20  3.000
 2QD  H16  CAA  H15  108.25  3.000
 2QD  H17  CAA  NAK  111.97  3.000
 2QD  H16  CAA  NAK  111.57  3.000
 2QD  H15  CAA  NAK  108.52  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
 2QD  CONST_01  CAA  NAK  CAN  CAH   180.00   0.0  0
 2QD  CONST_02  CAA  NAK  CAN  OAE     0.00   0.0  0
 2QD  CONST_03  H14  NAK  CAN  CAH     0.00   0.0  0
 2QD  Var_01    CAN  CAH  CD1  CG    -58.14  30.0  1
 2QD  Var_02    NAK  CAN  CAH  CD1   110.11  30.0  3
 2QD  Var_03    H15  CAA  NAK  CAN  -178.72  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
 2QD  chir_01  CA  CB   C   N    negativ
 2QD  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
 2QD  plan-1  CAH  0.020
 2QD  plan-1  CAN  0.020
 2QD  plan-1  OAE  0.020
 2QD  plan-1  NAK  0.020
 2QD  plan-1  CAA  0.020
 2QD  plan-1  H14  0.020
 2QD  plan-2  O    0.020
 2QD  plan-2  C    0.020
 2QD  plan-2  OXT  0.020
 2QD  plan-2  CA   0.020
 2QD  plan-3  CG   0.020
 2QD  plan-3  CD2  0.020
 2QD  plan-3  OAG  0.020
 2QD  plan-3  OAD  0.020

