# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 20 02:22:43 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: 4,4'-(2R)-propane-1,2-diyldipiperazine-2,6-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](CN1CC(=O)NC(=O)C1)N2CC(=O)NC(=O)C2
#
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
 CDX  CDX  4,4'-(2R)-propane-1,2-diyldipiperazine-2,6-dione  ligand  35  19  .  2022-07-24  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_CDX
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
 CDX  OAO   O  O     0  -0.431  -2.2290  -1.3861   2.3759
 CDX  CAP   C  C     0   0.535  -1.1572  -0.8255   2.3774
 CDX  NAI   N  NH1   0  -0.668  -0.0693  -1.3779   3.0116
 CDX  CAC   C  C     0   0.533   1.1551  -0.7774   3.1838
 CDX  OAB   O  O     0  -0.430   2.0224  -1.3015   3.8437
 CDX  CAD   C  CH2   0  -0.402   1.3106   0.5690   2.5306
 CDX  CAQ   C  CH2   0  -0.402  -0.9275   0.5118   1.7260
 CDX  NAJ   N  NT    0  -0.429   0.4577   0.6952   1.3749
 CDX  CAK   C  CH2   0  -0.288   0.7204   1.9225   0.6542
 CDX  CAL   C  CH1   0  -0.128  -0.0605   2.0633  -0.6549
 CDX  CAE   C  CH3   0  -0.678   0.5451   3.2018  -1.4758
 CDX  NAM   N  NT    0  -0.432  -0.1658   0.7890  -1.3478
 CDX  CAR   C  CH2   0  -0.407   1.0757   0.1571  -1.7102
 CDX  CAS   C  C     0   0.542   0.8374  -1.2695  -2.1286
 CDX  OAT   O  O     0  -0.432   1.6782  -2.1358  -2.0529
 CDX  NAN   N  NH1   0  -0.669  -0.4095  -1.5357  -2.6464
 CDX  CAG   C  C     0   0.540  -1.3970  -0.6114  -2.8952
 CDX  CAF   C  CH2   0  -0.406  -1.0949   0.7941  -2.4465
 CDX  OAH   O  O     0  -0.431  -2.4191  -0.9251  -3.4608
 CDX  HAI   H  HNH1  0   0.419  -0.2069  -2.2789   3.4560
 CDX  HAD1  H  HCH2  0   0.290   2.3550   0.6745   2.2344
 CDX  HAD2  H  HCH2  0   0.256   1.1195   1.3358   3.3033
 CDX  HAQ1  H  HCH2  0   0.255  -1.3109   1.2852   2.4162
 CDX  HAQ2  H  HCH2  0   0.294  -1.5477   0.5391   0.8319
 CDX  HAK1  H  HCH2  0   0.246   1.7943   1.9535   0.4446
 CDX  HAK2  H  HCH2  0   0.235   0.5055   2.8160   1.2628
 CDX  HAL   H  HCH1  0   0.255  -1.0895   2.3476  -0.4091
 CDX  HAE1  H  HCH3  0   0.231   1.5685   2.9788  -1.7832
 CDX  HAE2  H  HCH3  0   0.243  -0.0402   3.4107  -2.3718
 CDX  HAE3  H  HCH3  0   0.242   0.5731   4.1193  -0.8864
 CDX  HAR1  H  HCH2  0   0.258   1.6073   0.6536  -2.5410
 CDX  HAR2  H  HCH2  0   0.295   1.7558   0.1323  -0.8608
 CDX  HAN   H  HNH1  0   0.418  -0.5888  -2.4889  -2.9428
 CDX  HAF1  H  HCH2  0   0.289  -2.0353   1.2525  -2.1376
 CDX  HAF2  H  HCH2  0   0.257  -0.7446   1.3503  -3.3343

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
 CDX  OAO  CAP   double  1.210  0.020  1.210
 CDX  CAP  NAI   single  1.375  0.020  1.375
 CDX  CAP  CAQ   single  1.505  0.020  1.505
 CDX  NAI  CAC   single  1.375  0.020  1.375
 CDX  NAI  HAI   single  0.860  0.020  1.020
 CDX  CAC  OAB   double  1.209  0.020  1.209
 CDX  CAC  CAD   single  1.504  0.020  1.504
 CDX  CAD  NAJ   single  1.442  0.020  1.442
 CDX  CAD  HAD1  single  0.970  0.020  1.090
 CDX  CAD  HAD2  single  0.970  0.020  1.090
 CDX  CAQ  NAJ   single  1.441  0.020  1.441
 CDX  CAQ  HAQ1  single  0.970  0.020  1.090
 CDX  CAQ  HAQ2  single  0.970  0.020  1.090
 CDX  NAJ  CAK   single  1.447  0.020  1.447
 CDX  CAK  CAL   single  1.531  0.020  1.531
 CDX  CAK  HAK1  single  0.970  0.020  1.090
 CDX  CAK  HAK2  single  0.970  0.020  1.090
 CDX  CAL  CAE   single  1.529  0.020  1.529
 CDX  CAL  NAM   single  1.454  0.020  1.454
 CDX  CAL  HAL   single  0.970  0.020  1.090
 CDX  CAE  HAE1  single  0.970  0.020  1.090
 CDX  CAE  HAE2  single  0.970  0.020  1.090
 CDX  CAE  HAE3  single  0.970  0.020  1.090
 CDX  NAM  CAR   single  1.439  0.020  1.439
 CDX  NAM  CAF   single  1.439  0.020  1.439
 CDX  CAR  CAS   single  1.506  0.020  1.506
 CDX  CAR  HAR1  single  0.970  0.020  1.090
 CDX  CAR  HAR2  single  0.970  0.020  1.090
 CDX  CAS  OAT   double  1.210  0.020  1.210
 CDX  CAS  NAN   single  1.376  0.020  1.376
 CDX  NAN  CAG   single  1.375  0.020  1.375
 CDX  NAN  HAN   single  0.860  0.020  1.020
 CDX  CAG  CAF   single  1.506  0.020  1.506
 CDX  CAG  OAH   double  1.210  0.020  1.210
 CDX  CAF  HAF1  single  0.970  0.020  1.090
 CDX  CAF  HAF2  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
 CDX  CAQ   CAP  NAI   115.84  3.000
 CDX  CAQ   CAP  OAO   123.13  3.000
 CDX  NAI   CAP  OAO   121.02  3.000
 CDX  HAI   NAI  CAC   117.01  3.000
 CDX  HAI   NAI  CAP   116.85  3.000
 CDX  CAC   NAI  CAP   125.94  3.000
 CDX  CAD   CAC  OAB   123.41  3.000
 CDX  CAD   CAC  NAI   115.38  3.000
 CDX  OAB   CAC  NAI   121.19  3.000
 CDX  HAD2  CAD  HAD1  106.76  3.000
 CDX  HAD2  CAD  NAJ   113.41  3.000
 CDX  HAD1  CAD  NAJ   109.89  3.000
 CDX  HAD2  CAD  CAC   107.43  3.000
 CDX  HAD1  CAD  CAC   107.67  3.000
 CDX  NAJ   CAD  CAC   111.42  3.000
 CDX  HAQ2  CAQ  HAQ1  107.32  3.000
 CDX  HAQ2  CAQ  NAJ   110.15  3.000
 CDX  HAQ1  CAQ  NAJ   113.37  3.000
 CDX  HAQ2  CAQ  CAP   106.90  3.000
 CDX  HAQ1  CAQ  CAP   107.37  3.000
 CDX  NAJ   CAQ  CAP   111.42  3.000
 CDX  CAK   NAJ  CAQ   113.81  3.000
 CDX  CAK   NAJ  CAD   111.47  3.000
 CDX  CAQ   NAJ  CAD   111.24  3.000
 CDX  HAK2  CAK  HAK1  105.91  3.000
 CDX  HAK2  CAK  CAL   107.35  3.000
 CDX  HAK1  CAK  CAL   109.52  3.000
 CDX  HAK2  CAK  NAJ   112.15  3.000
 CDX  HAK1  CAK  NAJ   107.30  3.000
 CDX  CAL   CAK  NAJ   114.28  3.000
 CDX  HAL   CAL  NAM   105.44  3.000
 CDX  HAL   CAL  CAE   107.42  3.000
 CDX  NAM   CAL  CAE   115.18  3.000
 CDX  HAL   CAL  CAK   108.13  3.000
 CDX  NAM   CAL  CAK   111.33  3.000
 CDX  CAE   CAL  CAK   109.00  3.000
 CDX  HAE3  CAE  HAE2  107.26  3.000
 CDX  HAE3  CAE  HAE1  107.46  3.000
 CDX  HAE2  CAE  HAE1  108.12  3.000
 CDX  HAE3  CAE  CAL   110.27  3.000
 CDX  HAE2  CAE  CAL   111.79  3.000
 CDX  HAE1  CAE  CAL   111.74  3.000
 CDX  CAF   NAM  CAR   111.48  3.000
 CDX  CAF   NAM  CAL   114.04  3.000
 CDX  CAR   NAM  CAL   116.24  3.000
 CDX  HAR2  CAR  HAR1  107.26  3.000
 CDX  HAR2  CAR  CAS   107.11  3.000
 CDX  HAR1  CAR  CAS   107.04  3.000
 CDX  HAR2  CAR  NAM   110.64  3.000
 CDX  HAR1  CAR  NAM   114.03  3.000
 CDX  CAS   CAR  NAM   110.45  3.000
 CDX  NAN   CAS  OAT   120.98  3.000
 CDX  NAN   CAS  CAR   115.55  3.000
 CDX  OAT   CAS  CAR   123.45  3.000
 CDX  HAN   NAN  CAG   116.86  3.000
 CDX  HAN   NAN  CAS   116.87  3.000
 CDX  CAG   NAN  CAS   126.06  3.000
 CDX  OAH   CAG  CAF   123.43  3.000
 CDX  OAH   CAG  NAN   121.13  3.000
 CDX  CAF   CAG  NAN   115.42  3.000
 CDX  HAF2  CAF  HAF1  106.82  3.000
 CDX  HAF2  CAF  CAG   107.10  3.000
 CDX  HAF1  CAF  CAG   107.68  3.000
 CDX  HAF2  CAF  NAM   114.25  3.000
 CDX  HAF1  CAF  NAM   109.99  3.000
 CDX  CAG   CAF  NAM   110.72  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
 CDX  CONST_01  CAQ  CAP  NAI  CAC    0.00   0.0  0
 CDX  CONST_02  CAG  NAN  CAS  CAR    0.00   0.0  0
 CDX  CONST_03  CAC  NAI  CAP  OAO  180.00   0.0  0
 CDX  CONST_04  CAG  NAN  CAS  OAT  180.00   0.0  0
 CDX  CONST_05  HAI  NAI  CAP  CAQ  180.00   0.0  0
 CDX  CONST_06  HAN  NAN  CAS  CAR  180.00   0.0  0
 CDX  Var_01    CAD  CAC  NAI  CAP   -4.11  30.0  1
 CDX  Var_02    CAD  NAJ  CAQ  CAP  -57.47  30.0  1
 CDX  Var_03    NAJ  CAQ  CAP  NAI   25.49  30.0  1
 CDX  Var_04    NAJ  CAD  CAC  NAI  -27.57  30.0  1
 CDX  Var_05    CAQ  NAJ  CAD  CAC   58.66  30.0  1
 CDX  Var_06    NAN  CAS  CAR  NAM   27.10  30.0  1
 CDX  Var_07    NAN  CAG  CAF  NAM  -26.50  30.0  1
 CDX  Var_08    CAG  CAF  NAM  CAR   59.54  30.0  1
 CDX  Var_09    CAF  NAM  CAR  CAS  -59.77  30.0  1
 CDX  Var_10    CAF  CAG  NAN  CAS   -5.18  30.0  1
 CDX  Var_11    CAL  CAK  NAJ  CAD  174.75  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
 CDX  chir_01  CAL  CAK  CAE  NAM  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
 CDX  plan-1  NAI  0.020
 CDX  plan-1  CAC  0.020
 CDX  plan-1  OAB  0.020
 CDX  plan-1  CAD  0.020
 CDX  plan-2  NAN  0.020
 CDX  plan-2  CAG  0.020
 CDX  plan-2  CAF  0.020
 CDX  plan-2  OAH  0.020
 CDX  plan-3  OAO  0.020
 CDX  plan-3  CAP  0.020
 CDX  plan-3  NAI  0.020
 CDX  plan-3  CAC  0.020
 CDX  plan-3  CAQ  0.020
 CDX  plan-3  HAI  0.020
 CDX  plan-4  CAR  0.020
 CDX  plan-4  CAS  0.020
 CDX  plan-4  OAT  0.020
 CDX  plan-4  NAN  0.020
 CDX  plan-4  CAG  0.020
 CDX  plan-4  HAN  0.020

