# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 20:39:36 2022
#   Inital geometry file: a 98 line input string
#   Ligand name: (2S)-2-amino-4-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc2C(=O)N(CC[C@H](N)C(O)=O)C(=O)c2c1
#
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
 4DB  4DB  '(2S)-2-amino-4-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]butanoic acid'  L-peptide  37  21  .  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_4DB
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
 4DB  C     C  C      0   0.417   6.3446  -16.2899  -8.7572
 4DB  N     N  NH2    0  -0.813   8.8022  -16.4800  -8.8420
 4DB  O     O  O      0  -0.604   6.3560  -16.8258  -9.8833
 4DB  CA    C  CH1    0  -0.204   7.6612  -16.3642  -7.9411
 4DB  CB    C  CH2    0  -0.431   7.8797  -15.1537  -7.0307
 4DB  CAD   C  CH3    0  -0.542  11.4941  -18.6889  -0.4353
 4DB  CAE   C  CH3    0  -0.541  10.0696  -20.7044  -0.0393
 4DB  CAF   C  CR16   0  -0.352   8.2304  -19.7283  -1.9372
 4DB  CAG   C  CR16   0  -0.285   7.3020  -19.2788  -2.8597
 4DB  CAH   C  CR16   0  -0.422   9.6273  -17.7740  -2.3178
 4DB  CAI   C  CR6    0   0.424   9.4108  -19.0008  -1.6400
 4DB  CAJ   C  CR5    0   0.562   6.7647  -17.3379  -4.5120
 4DB  CAK   C  CR5    0   0.565   8.6644  -16.1300  -4.0518
 4DB  CAL   C  CR56   0  -0.101   7.5383  -18.0820  -3.5108
 4DB  CAM   C  CR56   0   0.023   8.6870  -17.3634  -3.2245
 4DB  NAN   N  NT     0  -0.501  10.3075  -19.4599  -0.7351
 4DB  NAO   N  NR5    0  -0.594   7.5026  -16.1856  -4.7948
 4DB  CAR   C  CH2    0  -0.323   7.0972  -15.1446  -5.7235
 4DB  OXT   O  OC    -1  -0.596   5.3709  -15.7329  -8.2117
 4DB  HN    H  HNH2   0   0.328   9.5924  -16.8664  -8.3411
 4DB  HNA   H  HNH2   0   0.331   8.5650  -17.1395  -9.5710
 4DB  HA    H  HCH1   0   0.199   7.5611  -17.2605  -7.3031
 4DB  HB    H  HCH2   0   0.223   8.9446  -15.0805  -6.7939
 4DB  HBA   H  HCH2   0   0.225   7.6318  -14.2364  -7.5711
 4DB  HAD   H  HCH3   0   0.242  12.1207  -18.5438  -1.3186
 4DB  HADA  H  HCH3   0   0.242  11.2510  -17.7049  -0.0259
 4DB  HADB  H  HCH3   0   0.265  12.0880  -19.2161   0.3055
 4DB  HAE   H  HCH3   0   0.241   9.1576  -20.6706   0.5624
 4DB  HAEA  H  HCH3   0   0.242   9.9888  -21.5482  -0.7290
 4DB  HAEB  H  HCH3   0   0.263  10.9001  -20.9044   0.6306
 4DB  HAF   H  HCR6   0   0.280   8.0331  -20.6645  -1.4358
 4DB  HAG   H  HCR6   0   0.264   6.4132  -19.8651  -3.0551
 4DB  HAH   H  HCR6   0   0.280  10.5026  -17.1667  -2.1354
 4DB  HAR   H  HCH2   0   0.252   7.2274  -14.1839  -5.2228
 4DB  HARA  H  HCH2   0   0.264   6.0363  -15.2677  -5.9190
 4DB  OAP   O  O      0  -0.412   5.7014  -17.6181  -5.0119
 4DB  OAQ   O  O      0  -0.410   9.4779  -15.2379  -4.0791

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
 4DB  O    C     deloc     1.231  0.020  1.231
 4DB  CA   C     single    1.525  0.021  1.525
 4DB  C    OXT   deloc     1.247  0.020  1.247
 4DB  N    CA    single    1.458  0.019  1.458
 4DB  N    HN    single    0.890  0.020  1.040
 4DB  N    HNA   single    0.890  0.020  1.040
 4DB  CA   CB    single    1.521  0.033  1.521
 4DB  CA   HA    single    0.970  0.020  0.970
 4DB  CB   CAR   single    1.524  0.020  1.524
 4DB  CB   HB    single    0.970  0.020  1.090
 4DB  CB   HBA   single    0.970  0.020  1.090
 4DB  NAN  CAD   single    1.446  0.020  1.446
 4DB  CAD  HAD   single    0.970  0.020  1.090
 4DB  CAD  HADA  single    0.970  0.020  1.090
 4DB  CAD  HADB  single    0.970  0.020  1.090
 4DB  NAN  CAE   single    1.446  0.020  1.446
 4DB  CAE  HAE   single    0.970  0.020  1.090
 4DB  CAE  HAEA  single    0.970  0.020  1.090
 4DB  CAE  HAEB  single    0.970  0.020  1.090
 4DB  CAG  CAF   aromatic  1.384  0.020  1.384
 4DB  CAF  CAI   aromatic  1.418  0.020  1.418
 4DB  CAF  HAF   single    0.930  0.020  1.080
 4DB  CAL  CAG   aromatic  1.383  0.020  1.383
 4DB  CAG  HAG   single    0.930  0.020  1.080
 4DB  CAM  CAH   aromatic  1.369  0.020  1.369
 4DB  CAH  CAI   aromatic  1.418  0.020  1.418
 4DB  CAH  HAH   single    0.930  0.020  1.080
 4DB  CAI  NAN   single    1.354  0.020  1.354
 4DB  OAP  CAJ   double    1.208  0.020  1.208
 4DB  NAO  CAJ   single    1.397  0.020  1.397
 4DB  CAJ  CAL   single    1.468  0.020  1.468
 4DB  NAO  CAK   single    1.380  0.020  1.380
 4DB  CAK  OAQ   double    1.208  0.020  1.208
 4DB  CAK  CAM   single    1.485  0.020  1.485
 4DB  CAL  CAM   aromatic  1.385  0.020  1.385
 4DB  CAR  NAO   single    1.453  0.020  1.453
 4DB  CAR  HAR   single    0.970  0.020  1.090
 4DB  CAR  HARA  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
 4DB  OXT   C    CA    120.80  1.700
 4DB  OXT   C    O     126.43  3.000
 4DB  CA    C    O     120.80  1.700
 4DB  HNA   N    HN    106.91  3.000
 4DB  HNA   N    CA    108.28  3.000
 4DB  HN    N    CA    109.60  3.000
 4DB  HA    CA   CB    109.00  3.000
 4DB  HA    CA   N     110.00  3.000
 4DB  CB    CA   N     110.40  1.500
 4DB  HA    CA   C     110.00  3.000
 4DB  CB    CA   C     110.50  1.500
 4DB  N     CA   C     111.00  2.800
 4DB  HBA   CB   HB    105.77  3.000
 4DB  HBA   CB   CAR   107.62  3.000
 4DB  HB    CB   CAR   108.30  3.000
 4DB  HBA   CB   CA    109.71  3.000
 4DB  HB    CB   CA    108.71  3.000
 4DB  CAR   CB   CA    116.22  3.000
 4DB  HADB  CAD  HADA  107.64  3.000
 4DB  HADB  CAD  HAD   107.59  3.000
 4DB  HADA  CAD  HAD   108.11  3.000
 4DB  HADB  CAD  NAN   109.34  3.000
 4DB  HADA  CAD  NAN   112.02  3.000
 4DB  HAD   CAD  NAN   111.94  3.000
 4DB  HAEB  CAE  HAEA  107.69  3.000
 4DB  HAEB  CAE  HAE   107.71  3.000
 4DB  HAEA  CAE  HAE   108.03  3.000
 4DB  HAEB  CAE  NAN   109.25  3.000
 4DB  HAEA  CAE  NAN   111.91  3.000
 4DB  HAE   CAE  NAN   112.06  3.000
 4DB  HAF   CAF  CAI   119.96  3.000
 4DB  HAF   CAF  CAG   117.93  3.000
 4DB  CAI   CAF  CAG   122.11  3.000
 4DB  HAG   CAG  CAL   121.60  3.000
 4DB  HAG   CAG  CAF   119.69  3.000
 4DB  CAL   CAG  CAF   118.71  3.000
 4DB  HAH   CAH  CAM   119.96  3.000
 4DB  HAH   CAH  CAI   121.94  3.000
 4DB  CAM   CAH  CAI   118.10  3.000
 4DB  NAN   CAI  CAH   120.77  3.000
 4DB  NAN   CAI  CAF   121.16  3.000
 4DB  CAH   CAI  CAF   118.08  3.000
 4DB  OAP   CAJ  NAO   124.92  3.000
 4DB  NAO   CAJ  CAL   106.13  3.000
 4DB  OAP   CAJ  CAL   128.95  3.000
 4DB  OAQ   CAK  NAO   125.78  3.000
 4DB  OAQ   CAK  CAM   128.01  3.000
 4DB  NAO   CAK  CAM   106.21  3.000
 4DB  CAM   CAL  CAJ   108.37  3.000
 4DB  CAM   CAL  CAG   119.57  3.000
 4DB  CAJ   CAL  CAG   132.06  3.000
 4DB  CAL   CAM  CAK   107.64  3.000
 4DB  CAL   CAM  CAH   123.43  3.000
 4DB  CAK   CAM  CAH   128.93  3.000
 4DB  CAI   NAN  CAE   120.30  3.000
 4DB  CAI   NAN  CAD   120.07  3.000
 4DB  CAE   NAN  CAD   119.61  3.000
 4DB  CAR   NAO  CAK   123.38  3.000
 4DB  CAR   NAO  CAJ   124.96  3.000
 4DB  CAK   NAO  CAJ   111.64  3.000
 4DB  HARA  CAR  HAR   107.40  3.000
 4DB  HARA  CAR  NAO   107.85  3.000
 4DB  HAR   CAR  NAO   107.71  3.000
 4DB  HARA  CAR  CB    110.28  3.000
 4DB  HAR   CAR  CB    109.74  3.000
 4DB  NAO   CAR  CB    113.64  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
 4DB  CONST_01  CAM  CAL  CAG  CAF     0.00   0.0  0
 4DB  CONST_02  CAM  CAH  CAI  CAF     0.00   0.0  0
 4DB  CONST_03  CAH  CAI  CAF  CAG     0.00   0.0  0
 4DB  CONST_04  CAH  CAM  CAL  CAG     0.00   0.0  0
 4DB  CONST_05  CAL  CAG  CAF  CAI     0.00   0.0  0
 4DB  CONST_06  CAL  CAM  CAH  CAI     0.00   0.0  0
 4DB  CONST_07  CAL  CAJ  NAO  CAK     0.00   0.0  0
 4DB  CONST_08  NAN  CAI  CAF  CAG   180.00   0.0  0
 4DB  CONST_09  NAN  CAI  CAH  CAM   180.00   0.0  0
 4DB  CONST_10  OAP  CAJ  NAO  CAK   180.00   0.0  0
 4DB  CONST_11  CAR  NAO  CAJ  CAL   180.00   0.0  0
 4DB  CONST_12  HAH  CAH  CAI  CAF   180.00   0.0  0
 4DB  CONST_13  HAF  CAF  CAI  CAH   180.00   0.0  0
 4DB  CONST_14  HAG  CAG  CAF  CAI   180.00   0.0  0
 4DB  CONST_15  CAF  CAI  NAN  CAD   180.00   0.0  0
 4DB  CONST_16  CAH  CAI  NAN  CAD     0.00   0.0  0
 4DB  CONST_17  CAF  CAI  NAN  CAE     0.00   0.0  0
 4DB  CONST_18  CAH  CAI  NAN  CAE   180.00   0.0  0
 4DB  CONST_19  CAR  NAO  CAJ  OAP     0.00   0.0  0
 4DB  Var_01    CAJ  NAO  CAR  CB   -106.26  30.0  3
 4DB  Var_02    NAO  CAR  CB   CA     66.79  30.0  3
 4DB  Var_03    HAD  CAD  NAN  CAI   -60.71  30.0  3
 4DB  Var_04    HAE  CAE  NAN  CAI   -61.27  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
 4DB  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
 4DB  plan-1  CAF  0.020
 4DB  plan-1  CAG  0.020
 4DB  plan-1  CAH  0.020
 4DB  plan-1  CAI  0.020
 4DB  plan-1  CAJ  0.020
 4DB  plan-1  CAK  0.020
 4DB  plan-1  CAL  0.020
 4DB  plan-1  CAM  0.020
 4DB  plan-1  NAN  0.020
 4DB  plan-1  NAO  0.020
 4DB  plan-1  CAR  0.020
 4DB  plan-1  HAF  0.020
 4DB  plan-1  HAG  0.020
 4DB  plan-1  HAH  0.020
 4DB  plan-1  OAP  0.020
 4DB  plan-1  OAQ  0.020
 4DB  plan-2  CAD  0.020
 4DB  plan-2  CAE  0.020
 4DB  plan-2  CAI  0.020
 4DB  plan-2  NAN  0.020
 4DB  plan-3  C    0.020
 4DB  plan-3  O    0.020
 4DB  plan-3  CA   0.020
 4DB  plan-3  OXT  0.020

