# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 06:18:57 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: (3S,4S)-3-(carboxymethyl)-4-[(1Z,3E,5R)-5-carboxy-1-methylhexa-1,3-dien-1-yl]-L-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](\C=C\C=C(\C)[C@H]1CN[C@@H]([C@H]1CC(O)=O)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
 DOQ  DOQ  (3S,4S)-3-(carboxymethyl)-4-[(1Z,3E,5R)-5-carboxy-1-methylhexa-1,3-dien-1-yl]-L-proline  ligand  40  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DOQ
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
 DOQ  OAD   O  O      0  -0.599  -5.5509  -0.9468   0.3946
 DOQ  CAQ   C  C      0   0.430  -5.3128   0.0724   1.0713
 DOQ  OAG   O  OC    -1  -0.617  -6.0160   0.5309   1.9932
 DOQ  CAS   C  CH1    0  -0.464  -4.0090   0.8486   0.7538
 DOQ  CAB   C  CH3    0  -0.649  -4.3009   2.3374   0.5452
 DOQ  CAK   C  C1     0  -0.146  -3.2900   0.2842  -0.4253
 DOQ  CAI   C  C1     0  -0.272  -2.0561  -0.2324  -0.3985
 DOQ  CAJ   C  C1     0  -0.312  -1.3768  -0.7536  -1.5718
 DOQ  CAP   C  C      0   0.138  -0.1493  -1.2990  -1.6167
 DOQ  CAA   C  CH3    0  -0.744   0.4048  -1.7731  -2.9278
 DOQ  CAT   C  CH1    0  -0.321   0.7053  -1.4456  -0.3862
 DOQ  CAL   C  CH2    0  -0.272   1.7319  -2.5745  -0.4003
 DOQ  N     N  NH1    0  -0.617   2.5323  -2.2409   0.7608
 DOQ  CA    C  CH1    0  -0.141   2.8547  -0.8231   0.6075
 DOQ  C     C  C      0   0.394   3.3009  -0.2056   1.9447
 DOQ  O     O  O     -1  -0.616   2.4748  -0.2287   2.8784
 DOQ  OXT   O  OC     0  -0.626   4.4634   0.2474   1.9983
 DOQ  CB    C  CH1    0  -0.219   1.5679  -0.2057   0.0124
 DOQ  CG    C  CH2    0  -0.574   1.8871   0.7551  -1.1230
 DOQ  CD    C  C      0   0.418   2.6526   2.0102  -0.6696
 DOQ  OE2   O  OC    -1  -0.629   3.6080   2.3853  -1.3824
 DOQ  OE1   O  O      0  -0.615   2.2300   2.5864   0.3536
 DOQ  HAS   H  HCH1   0   0.234  -3.3568   0.7563   1.6322
 DOQ  HAB1  H  HCH3   0   0.212  -4.9611   2.4929  -0.3115
 DOQ  HAB2  H  HCH3   0   0.225  -4.7856   2.7661   1.4212
 DOQ  HAB3  H  HCH3   0   0.218  -3.3824   2.8960   0.3595
 DOQ  HAK   H  H      0   0.218  -3.8135   0.3332  -1.3787
 DOQ  HAI   H  H      0   0.226  -1.5335  -0.2680   0.5537
 DOQ  HAJ   H  H      0   0.216  -1.9350  -0.6776  -2.5029
 DOQ  HAA1  H  HCH3   0   0.239  -0.2782  -1.5569  -3.7492
 DOQ  HAA2  H  HCH3   0   0.238   1.3633  -1.3022  -3.1556
 DOQ  HAA3  H  HCH3   0   0.235   0.5875  -2.8511  -2.9242
 DOQ  HAT   H  HCH1   0   0.235   0.0484  -1.6481   0.4639
 DOQ  HAL1  H  HCH2   0   0.224   1.2766  -3.5639  -0.3051
 DOQ  HAL2  H  HCH2   0   0.190   2.3110  -2.5655  -1.3376
 DOQ  HN    H  HNH1   0   0.335   3.3733  -2.8025   0.8059
 DOQ  HA    H  HCH1   0   0.173   3.6635  -0.6883  -0.1293
 DOQ  HB    H  HCH1   0   0.219   1.0347   0.3552   0.7803
 DOQ  HG1   H  HCH2   0   0.192   2.4493   0.2439  -1.9101
 DOQ  HG2   H  HCH2   0   0.223   0.9491   1.0916  -1.5814

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
 DOQ  OAD  CAQ   deloc   1.246  0.020  1.246
 DOQ  CAQ  OAG   deloc   1.247  0.020  1.247
 DOQ  CAQ  CAS   single  1.550  0.020  1.550
 DOQ  CAS  CAB   single  1.531  0.020  1.531
 DOQ  CAS  CAK   single  1.492  0.020  1.492
 DOQ  CAS  HAS   single  0.970  0.020  1.090
 DOQ  CAB  HAB1  single  0.970  0.020  1.090
 DOQ  CAB  HAB2  single  0.970  0.020  1.090
 DOQ  CAB  HAB3  single  0.970  0.020  1.090
 DOQ  CAK  CAI   double  1.338  0.020  1.338
 DOQ  CAK  HAK   single  0.930  0.020  1.080
 DOQ  CAI  CAJ   single  1.453  0.020  1.453
 DOQ  CAI  HAI   single  0.930  0.020  1.080
 DOQ  CAJ  CAP   double  1.344  0.020  1.344
 DOQ  CAJ  HAJ   single  0.930  0.020  1.080
 DOQ  CAP  CAA   single  1.500  0.020  1.500
 DOQ  CAP  CAT   single  1.505  0.020  1.505
 DOQ  CAA  HAA1  single  0.970  0.020  1.090
 DOQ  CAA  HAA2  single  0.970  0.020  1.090
 DOQ  CAA  HAA3  single  0.970  0.020  1.090
 DOQ  CAT  CAL   single  1.526  0.020  1.526
 DOQ  CAT  CB    single  1.562  0.020  1.562
 DOQ  CAT  HAT   single  0.970  0.020  1.090
 DOQ  CAL  N     single  1.449  0.020  1.449
 DOQ  CAL  HAL1  single  0.970  0.020  1.090
 DOQ  CAL  HAL2  single  0.970  0.020  1.090
 DOQ  N    CA    single  1.462  0.020  1.462
 DOQ  N    HN    single  0.890  0.020  1.040
 DOQ  CA   C     single  1.539  0.020  1.539
 DOQ  CA   CB    single  1.546  0.020  1.546
 DOQ  CA   HA    single  0.970  0.020  1.090
 DOQ  C    O     deloc   1.247  0.020  1.247
 DOQ  C    OXT   deloc   1.249  0.020  1.249
 DOQ  CB   CG    single  1.521  0.020  1.521
 DOQ  CB   HB    single  0.970  0.020  1.090
 DOQ  CG   CD    single  1.538  0.020  1.538
 DOQ  CG   HG1   single  0.970  0.020  1.090
 DOQ  CG   HG2   single  0.970  0.020  1.090
 DOQ  CD   OE2   deloc   1.250  0.020  1.250
 DOQ  CD   OE1   deloc   1.248  0.020  1.248

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
 DOQ  CAS   CAQ  OAG   116.21  3.000
 DOQ  CAS   CAQ  OAD   117.32  3.000
 DOQ  OAG   CAQ  OAD   126.47  3.000
 DOQ  HAS   CAS  CAK   108.31  3.000
 DOQ  HAS   CAS  CAB   107.69  3.000
 DOQ  CAK   CAS  CAB   110.61  3.000
 DOQ  HAS   CAS  CAQ   107.08  3.000
 DOQ  CAK   CAS  CAQ   112.20  3.000
 DOQ  CAB   CAS  CAQ   110.76  3.000
 DOQ  HAB3  CAB  HAB2  108.06  3.000
 DOQ  HAB3  CAB  HAB1  107.60  3.000
 DOQ  HAB2  CAB  HAB1  107.80  3.000
 DOQ  HAB3  CAB  CAS   111.14  3.000
 DOQ  HAB2  CAB  CAS   110.97  3.000
 DOQ  HAB1  CAB  CAS   111.12  3.000
 DOQ  HAK   CAK  CAI   118.58  3.000
 DOQ  HAK   CAK  CAS   116.31  3.000
 DOQ  CAI   CAK  CAS   125.08  3.000
 DOQ  HAI   CAI  CAJ   118.10  3.000
 DOQ  HAI   CAI  CAK   118.28  3.000
 DOQ  CAJ   CAI  CAK   123.62  3.000
 DOQ  HAJ   CAJ  CAP   117.92  3.000
 DOQ  HAJ   CAJ  CAI   115.23  3.000
 DOQ  CAP   CAJ  CAI   126.85  3.000
 DOQ  CAT   CAP  CAA   118.28  3.000
 DOQ  CAT   CAP  CAJ   122.06  3.000
 DOQ  CAA   CAP  CAJ   119.66  3.000
 DOQ  HAA3  CAA  HAA2  106.21  3.000
 DOQ  HAA3  CAA  HAA1  107.63  3.000
 DOQ  HAA2  CAA  HAA1  107.89  3.000
 DOQ  HAA3  CAA  CAP   111.74  3.000
 DOQ  HAA2  CAA  CAP   111.73  3.000
 DOQ  HAA1  CAA  CAP   111.37  3.000
 DOQ  HAT   CAT  CB    106.29  3.000
 DOQ  HAT   CAT  CAL   105.92  3.000
 DOQ  CB    CAT  CAL   102.60  3.000
 DOQ  HAT   CAT  CAP   108.21  3.000
 DOQ  CB    CAT  CAP   116.41  3.000
 DOQ  CAL   CAT  CAP   116.52  3.000
 DOQ  HAL2  CAL  HAL1  107.48  3.000
 DOQ  HAL2  CAL  N     112.91  3.000
 DOQ  HAL1  CAL  N     111.63  3.000
 DOQ  HAL2  CAL  CAT   110.82  3.000
 DOQ  HAL1  CAL  CAT   112.86  3.000
 DOQ  N     CAL  CAT   101.18  3.000
 DOQ  HN    N    CA    111.07  3.000
 DOQ  HN    N    CAL   111.52  3.000
 DOQ  CA    N    CAL   105.13  3.000
 DOQ  HA    CA   CB    107.73  3.000
 DOQ  HA    CA   C     108.60  3.000
 DOQ  CB    CA   C     114.55  3.000
 DOQ  HA    CA   N     110.51  3.000
 DOQ  CB    CA   N     104.12  3.000
 DOQ  C     CA   N     111.21  3.000
 DOQ  OXT   C    O     126.25  3.000
 DOQ  OXT   C    CA    116.91  3.000
 DOQ  O     C    CA    116.82  3.000
 DOQ  HB    CB   CG    107.66  3.000
 DOQ  HB    CB   CA    109.96  3.000
 DOQ  CG    CB   CA    111.39  3.000
 DOQ  HB    CB   CAT   108.54  3.000
 DOQ  CG    CB   CAT   115.26  3.000
 DOQ  CA    CB   CAT   103.94  3.000
 DOQ  HG2   CG   HG1   106.39  3.000
 DOQ  HG2   CG   CD    107.36  3.000
 DOQ  HG1   CG   CD    109.73  3.000
 DOQ  HG2   CG   CB    109.04  3.000
 DOQ  HG1   CG   CB    110.47  3.000
 DOQ  CD    CG   CB    113.56  3.000
 DOQ  OE1   CD   OE2   126.01  3.000
 DOQ  OE1   CD   CG    116.73  3.000
 DOQ  OE2   CD   CG    117.21  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
 DOQ  Var_01  CA    N    CAL  CAT   -49.21  30.0  1
 DOQ  Var_02  CAT   CAP  CAJ  CAI     0.32   0.0  2
 DOQ  Var_03  OE2   CD   CG   CB    136.67  30.0  3
 DOQ  Var_04  HAA1  CAA  CAP  CAT  -176.42  30.0  3
 DOQ  Var_05  CAJ   CAI  CAK  CAS  -178.93   0.0  2
 DOQ  Var_06  CAP   CAJ  CAI  CAK  -179.17  30.0  2

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
 DOQ  chir_01  CAS  CAQ  CAB  CAK  positiv
 DOQ  chir_02  CAT  CB   CAL  CAP  positiv
 DOQ  chir_03  CA   N    CB   C    negativ
 DOQ  chir_04  CB   CG   CA   CAT  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
 DOQ  plan-1  OAD  0.020
 DOQ  plan-1  CAQ  0.020
 DOQ  plan-1  OAG  0.020
 DOQ  plan-1  CAS  0.020
 DOQ  plan-2  CA   0.020
 DOQ  plan-2  C    0.020
 DOQ  plan-2  O    0.020
 DOQ  plan-2  OXT  0.020
 DOQ  plan-3  CG   0.020
 DOQ  plan-3  CD   0.020
 DOQ  plan-3  OE2  0.020
 DOQ  plan-3  OE1  0.020
 DOQ  plan-4  CAS  0.020
 DOQ  plan-4  CAK  0.020
 DOQ  plan-4  CAI  0.020
 DOQ  plan-4  CAJ  0.020
 DOQ  plan-4  HAK  0.020
 DOQ  plan-4  HAI  0.020
 DOQ  plan-5  CAI  0.020
 DOQ  plan-5  CAJ  0.020
 DOQ  plan-5  CAP  0.020
 DOQ  plan-5  CAA  0.020
 DOQ  plan-5  CAT  0.020
 DOQ  plan-5  HAJ  0.020

