# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 18:02:24 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(C)c1ccc2C(=O)N(C[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
 4DP  4DP  3-[5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl]-L-alanine  L-peptide  34  20  .  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_4DP
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
 4DP  OAP   O  O      0  -0.404  -25.5780  64.3311  13.3300
 4DP  CAJ   C  CR5    0   0.552  -26.7404  64.2563  13.6468
 4DP  CAL   C  CR5    0   0.018  -27.7195  65.3634  13.8052
 4DP  CAG   C  C1     0  -0.422  -27.5287  66.7089  13.6406
 4DP  CAH   C  C      0   0.425  -28.6370  67.5714  13.8444
 4DP  NAM   N  NT     0  -0.501  -28.5061  68.9117  13.7038
 4DP  CAD   C  CH3    0  -0.542  -29.6498  69.7777  13.8828
 4DP  CAC   C  CH3    0  -0.542  -27.2350  69.4786  13.3097
 4DP  CAE   C  C1     0  -0.353  -29.8809  66.9894  14.1977
 4DP  CAF   C  C1     0  -0.287  -30.0343  65.6233  14.3550
 4DP  CAK   C  CR5    0  -0.093  -28.9374  64.8047  14.1580
 4DP  CAI   C  CR5    0   0.566  -28.7705  63.3503  14.2384
 4DP  OAO   O  O      0  -0.413  -29.5842  62.4988  14.5079
 4DP  NAN   N  NR5    0  -0.599  -27.4341  63.0939  13.9250
 4DP  CB    C  CH2    0  -0.317  -26.8590  61.7658  13.8885
 4DP  CA    C  CH1    0  -0.221  -26.5081  61.2061  15.2817
 4DP  C     C  C      0   0.404  -25.8485  59.8233  15.0431
 4DP  O     O  O      0  -0.591  -24.6287  59.7222  15.2663
 4DP  N     N  NH2    0  -0.786  -25.6829  62.0730  16.0958
 4DP  OXT   O  OC    -1  -0.610  -26.6127  58.9430  14.5990
 4DP  HAG   H  H      0   0.281  -26.5557  67.0881  13.3620
 4DP  HAD1  H  HCH3   0   0.243  -30.0766  69.6867  14.8844
 4DP  HAD2  H  HCH3   0   0.263  -29.3418  70.8103  13.7500
 4DP  HAD3  H  HCH3   0   0.241  -30.4407  69.5692  13.1571
 4DP  HAC1  H  HCH3   0   0.241  -26.9093  69.1184  12.3303
 4DP  HAC2  H  HCH3   0   0.265  -27.3275  70.5586  13.2506
 4DP  HAC3  H  HCH3   0   0.243  -26.4476  69.2533  14.0330
 4DP  HAE   H  H      0   0.281  -30.7457  67.6183  14.3509
 4DP  HAF   H  H      0   0.264  -31.0016  65.2191  14.6251
 4DP  HB3   H  HCH2   0   0.254  -27.5571  61.0996  13.3830
 4DP  HB2   H  HCH2   0   0.255  -25.9586  61.8229  13.2744
 4DP  HA    H  HCH1   0   0.222  -27.4489  61.0431  15.8166
 4DP  H     H  HNH2   0   0.328  -24.7803  62.2014  15.6572
 4DP  H2    H  HNH2   0   0.335  -26.1042  62.9891  16.1863

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
 4DP  OAP  CAJ   double    1.207  0.020  1.207
 4DP  CAJ  CAL   single    1.486  0.020  1.486
 4DP  CAJ  NAN   single    1.382  0.020  1.382
 4DP  CAL  CAG   aromatic  1.369  0.020  1.369
 4DP  CAL  CAK   aromatic  1.386  0.020  1.386
 4DP  CAG  CAH   aromatic  1.419  0.020  1.419
 4DP  CAG  HAG   single    0.930  0.020  1.080
 4DP  CAH  NAM   single    1.354  0.020  1.354
 4DP  CAH  CAE   aromatic  1.418  0.020  1.418
 4DP  NAM  CAC   single    1.447  0.020  1.447
 4DP  NAM  CAD   single    1.446  0.020  1.446
 4DP  CAD  HAD1  single    0.970  0.020  1.090
 4DP  CAD  HAD2  single    0.970  0.020  1.090
 4DP  CAD  HAD3  single    0.970  0.020  1.090
 4DP  CAC  HAC1  single    0.970  0.020  1.090
 4DP  CAC  HAC2  single    0.970  0.020  1.090
 4DP  CAC  HAC3  single    0.970  0.020  1.090
 4DP  CAE  CAF   aromatic  1.384  0.020  1.384
 4DP  CAE  HAE   single    0.930  0.020  1.080
 4DP  CAF  CAK   aromatic  1.383  0.020  1.383
 4DP  CAF  HAF   single    0.930  0.020  1.080
 4DP  CAK  CAI   single    1.466  0.020  1.466
 4DP  CAI  NAN   single    1.396  0.020  1.396
 4DP  CAI  OAO   double    1.208  0.020  1.208
 4DP  NAN  CB    single    1.448  0.020  1.448
 4DP  CB   CA    single    1.530  0.020  1.530
 4DP  CB   HB3   single    0.970  0.020  1.090
 4DP  CB   HB2   single    0.970  0.020  1.090
 4DP  CA   C     single    1.525  0.021  1.525
 4DP  CA   N     single    1.458  0.019  1.458
 4DP  CA   HA    single    0.970  0.020  0.970
 4DP  C    O     deloc     1.231  0.020  1.231
 4DP  C    OXT   deloc     1.247  0.020  1.247
 4DP  N    H     single    0.860  0.020  0.860
 4DP  N    H2    single    0.890  0.020  1.040

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
 4DP  NAN   CAJ  CAL   105.92  3.000
 4DP  NAN   CAJ  OAP   126.04  3.000
 4DP  CAL   CAJ  OAP   128.03  3.000
 4DP  CAK   CAL  CAG   123.33  3.000
 4DP  CAK   CAL  CAJ   107.81  3.000
 4DP  CAG   CAL  CAJ   128.86  3.000
 4DP  HAG   CAG  CAH   121.79  3.000
 4DP  HAG   CAG  CAL   120.09  3.000
 4DP  CAH   CAG  CAL   118.12  3.000
 4DP  CAE   CAH  NAM   121.12  3.000
 4DP  CAE   CAH  CAG   118.13  3.000
 4DP  NAM   CAH  CAG   120.75  3.000
 4DP  CAC   NAM  CAD   119.61  3.000
 4DP  CAD   NAM  CAH   120.24  3.000
 4DP  CAC   NAM  CAH   120.08  3.000
 4DP  HAD3  CAD  HAD2  107.78  3.000
 4DP  HAD3  CAD  HAD1  108.06  3.000
 4DP  HAD2  CAD  HAD1  107.58  3.000
 4DP  HAD3  CAD  NAM   112.07  3.000
 4DP  HAD2  CAD  NAM   109.28  3.000
 4DP  HAD1  CAD  NAM   111.88  3.000
 4DP  HAC3  CAC  HAC2  107.61  3.000
 4DP  HAC3  CAC  HAC1  108.08  3.000
 4DP  HAC2  CAC  HAC1  107.73  3.000
 4DP  HAC3  CAC  NAM   111.84  3.000
 4DP  HAC2  CAC  NAM   109.26  3.000
 4DP  HAC1  CAC  NAM   112.14  3.000
 4DP  HAE   CAE  CAF   118.03  3.000
 4DP  HAE   CAE  CAH   119.91  3.000
 4DP  CAF   CAE  CAH   122.06  3.000
 4DP  HAF   CAF  CAK   121.56  3.000
 4DP  HAF   CAF  CAE   119.73  3.000
 4DP  CAK   CAF  CAE   118.71  3.000
 4DP  CAI   CAK  CAF   132.05  3.000
 4DP  CAI   CAK  CAL   108.29  3.000
 4DP  CAF   CAK  CAL   119.66  3.000
 4DP  NAN   CAI  OAO   124.41  3.000
 4DP  OAO   CAI  CAK   129.40  3.000
 4DP  NAN   CAI  CAK   106.19  3.000
 4DP  CB    NAN  CAI   123.66  3.000
 4DP  CB    NAN  CAJ   124.55  3.000
 4DP  CAI   NAN  CAJ   111.78  3.000
 4DP  HB2   CB   HB3   107.43  3.000
 4DP  HB2   CB   CA    109.86  3.000
 4DP  HB3   CB   CA    110.07  3.000
 4DP  HB2   CB   NAN   107.09  3.000
 4DP  HB3   CB   NAN   108.55  3.000
 4DP  CA    CB   NAN   113.62  3.000
 4DP  HA    CA   N     110.00  3.000
 4DP  HA    CA   C     109.00  3.000
 4DP  N     CA   C     111.00  2.800
 4DP  HA    CA   CB    109.00  3.000
 4DP  N     CA   CB    110.50  1.700
 4DP  C     CA   CB    110.10  1.900
 4DP  OXT   C    O     127.38  3.000
 4DP  OXT   C    CA    115.06  3.000
 4DP  O     C    CA    120.80  1.700
 4DP  H2    N    H     107.17  3.000
 4DP  H2    N    CA    110.79  3.000
 4DP  H     N    CA    114.00  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
 4DP  CONST_01  CAE   CAH  CAG  CAL    0.00   0.0  0
 4DP  CONST_02  CAE   CAF  CAK  CAL    0.00   0.0  0
 4DP  CONST_03  CAF   CAK  CAL  CAG    0.00   0.0  0
 4DP  CONST_04  CAF   CAE  CAH  CAG    0.00   0.0  0
 4DP  CONST_05  CAK   CAL  CAG  CAH    0.00   0.0  0
 4DP  CONST_06  CAK   CAF  CAE  CAH    0.00   0.0  0
 4DP  CONST_07  CAI   NAN  CAJ  CAL    0.00   0.0  0
 4DP  CONST_08  NAM   CAH  CAG  CAL  180.00   0.0  0
 4DP  CONST_09  CAF   CAE  CAH  NAM  180.00   0.0  0
 4DP  CONST_10  CAI   NAN  CAJ  OAP  180.00   0.0  0
 4DP  CONST_11  CB    NAN  CAJ  CAL  180.00   0.0  0
 4DP  CONST_12  HAG   CAG  CAL  CAJ    0.00   0.0  0
 4DP  CONST_13  HAF   CAF  CAK  CAL  180.00   0.0  0
 4DP  CONST_14  HAE   CAE  CAH  CAG  180.00   0.0  0
 4DP  CONST_15  CAC   NAM  CAH  CAG    0.00   0.0  0
 4DP  CONST_16  CAD   NAM  CAH  CAG  180.00   0.0  0
 4DP  CONST_17  CAE   CAH  NAM  CAD    0.00   0.0  0
 4DP  CONST_18  CAE   CAH  NAM  CAC  180.00   0.0  0
 4DP  CONST_19  CB    NAN  CAJ  OAP    0.00   0.0  0
 4DP  Var_01    CA    CB   NAN  CAJ  101.14  30.0  3
 4DP  Var_02    HAC1  CAC  NAM  CAH   60.62  30.0  3
 4DP  Var_03    HAD1  CAD  NAM  CAH   59.82  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
 4DP  chir_01  CA  CB  C  N  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
 4DP  plan-1  OAP  0.020
 4DP  plan-1  CAJ  0.020
 4DP  plan-1  CAL  0.020
 4DP  plan-1  CAG  0.020
 4DP  plan-1  CAH  0.020
 4DP  plan-1  NAM  0.020
 4DP  plan-1  CAE  0.020
 4DP  plan-1  CAF  0.020
 4DP  plan-1  CAK  0.020
 4DP  plan-1  CAI  0.020
 4DP  plan-1  OAO  0.020
 4DP  plan-1  NAN  0.020
 4DP  plan-1  CB   0.020
 4DP  plan-1  HAG  0.020
 4DP  plan-1  HAE  0.020
 4DP  plan-1  HAF  0.020
 4DP  plan-2  CAH  0.020
 4DP  plan-2  NAM  0.020
 4DP  plan-2  CAD  0.020
 4DP  plan-2  CAC  0.020
 4DP  plan-3  CA   0.020
 4DP  plan-3  C    0.020
 4DP  plan-3  O    0.020
 4DP  plan-3  OXT  0.020

