# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 16:32:48 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  43  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  -0.437  -5.9566  -0.4689  -0.2193
 DOQ  CAQ   C  C     0   0.572  -5.4518   0.1981   0.6487
 DOQ  OAG   O  OH1   0  -0.594  -6.0672   0.4923   1.7883
 DOQ  CAS   C  CH1   0  -0.472  -4.0714   0.8150   0.5786
 DOQ  CAB   C  CH3   0  -0.648  -4.1885   2.3440   0.4580
 DOQ  CAK   C  C1    0  -0.176  -3.2919   0.2504  -0.5651
 DOQ  CAI   C  C1    0  -0.247  -2.1039  -0.3468  -0.4332
 DOQ  CAJ   C  C1    0  -0.299  -1.3384  -0.8407  -1.5635
 DOQ  CAP   C  C     0   0.126  -0.1056  -1.3747  -1.5377
 DOQ  CAA   C  CH3   0  -0.741   0.5350  -1.8121  -2.8209
 DOQ  CAT   C  CH1   0  -0.335   0.6814  -1.5102  -0.2609
 DOQ  CAL   C  CH2   0  -0.281   1.6290  -2.7110  -0.1841
 DOQ  N     N  NH1   0  -0.609   2.5961  -2.2863   0.8125
 DOQ  CA    C  CH1   0  -0.140   2.9644  -0.9498   0.4075
 DOQ  C     C  C     0   0.527   3.7148  -0.2278   1.5033
 DOQ  O     O  O     0  -0.433   3.4924  -0.3480   2.6804
 DOQ  OXT   O  OH1   0  -0.594   4.6518   0.5726   1.0095
 DOQ  CB    C  CH1   0  -0.256   1.6005  -0.2862   0.0972
 DOQ  CG    C  CH2   0  -0.596   1.6970   0.8104  -0.9508
 DOQ  CD    C  C     0   0.559   2.2784   2.0940  -0.4186
 DOQ  OE2   O  OH1   0  -0.591   2.8617   2.8087  -1.3730
 DOQ  OE1   O  O     0  -0.444   2.1914   2.4680   0.7250
 DOQ  HAG   H  HOH1  0   0.480  -6.9573   0.1095   1.7933
 DOQ  HAS   H  HCH1  0   0.290  -3.5572   0.5856   1.5173
 DOQ  HAB1  H  HCH3  0   0.235  -4.7160   2.6277  -0.4536
 DOQ  HAB2  H  HCH3  0   0.247  -4.7122   2.7785   1.3082
 DOQ  HAB3  H  HCH3  0   0.248  -3.1912   2.7792   0.4182
 DOQ  HAK   H  H     0   0.249  -3.7126   0.3881  -1.5578
 DOQ  HAI   H  H     0   0.245  -1.6928  -0.4635   0.5652
 DOQ  HAJ   H  H     0   0.234  -1.8271  -0.7407  -2.5295
 DOQ  HAA1  H  HCH3  0   0.250  -0.0644  -1.5188  -3.6818
 DOQ  HAA2  H  HCH3  0   0.238   1.5325  -1.3847  -2.9477
 DOQ  HAA3  H  HCH3  0   0.247   0.6612  -2.8970  -2.8605
 DOQ  HAT   H  HCH1  0   0.270  -0.0193  -1.6146   0.5677
 DOQ  HAL1  H  HCH2  0   0.248   1.1144  -3.6197   0.1320
 DOQ  HAL2  H  HCH2  0   0.216   2.0945  -2.9172  -1.1570
 DOQ  HN    H  HNH1  0   0.359   3.3994  -2.9016   0.8380
 DOQ  HA    H  HCH1  0   0.246   3.5757  -0.9347  -0.5082
 DOQ  HO    H  HOH1  0   0.481   5.0789   1.0676   1.7250
 DOQ  HB    H  HCH1  0   0.269   1.2019   0.1542   1.0129
 DOQ  HG1   H  HCH2  0   0.273   2.2574   0.4840  -1.8290
 DOQ  HG2   H  HCH2  0   0.304   0.6950   1.0685  -1.3120
 DOQ  HE2   H  HOH1  0   0.480   3.1791   3.6499  -1.0111

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   double  1.206  0.020  1.206
 DOQ  CAQ  OAG   single  1.328  0.020  1.328
 DOQ  CAQ  CAS   single  1.514  0.020  1.514
 DOQ  OAG  HAG   single  0.850  0.020  0.980
 DOQ  CAS  CAB   single  1.538  0.020  1.538
 DOQ  CAS  CAK   single  1.495  0.020  1.495
 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  1.336  0.020  1.336
 DOQ  CAK  HAK   single  0.930  0.020  1.080
 DOQ  CAI  CAJ   single  1.452  0.020  1.452
 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  1.499  0.020  1.499
 DOQ  CAP  CAT   single  1.506  0.020  1.506
 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  1.532  0.020  1.532
 DOQ  CAT  CB    single  1.572  0.020  1.572
 DOQ  CAT  HAT   single  0.970  0.020  1.090
 DOQ  CAL  N     single  1.452  0.020  1.452
 DOQ  CAL  HAL1  single  0.970  0.020  1.090
 DOQ  CAL  HAL2  single  0.970  0.020  1.090
 DOQ  N    CA    single  1.444  0.020  1.444
 DOQ  N    HN    single  0.890  0.020  1.040
 DOQ  CA   C     single  1.512  0.020  1.512
 DOQ  CA   CB    single  1.548  0.020  1.548
 DOQ  CA   HA    single  0.970  0.020  1.090
 DOQ  C    O     double  1.204  0.020  1.204
 DOQ  C    OXT   single  1.328  0.020  1.328
 DOQ  OXT  HO    single  0.850  0.020  0.980
 DOQ  CB   CG    single  1.520  0.020  1.520
 DOQ  CB   HB    single  0.970  0.020  1.090
 DOQ  CG   CD    single  1.506  0.020  1.506
 DOQ  CG   HG1   single  0.970  0.020  1.090
 DOQ  CG   HG2   single  0.970  0.020  1.090
 DOQ  CD   OE2   single  1.327  0.020  1.327
 DOQ  CD   OE1   double  1.206  0.020  1.206
 DOQ  OE2  HE2   single  0.850  0.020  0.980

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   111.84  3.000
 DOQ  CAS   CAQ  OAD   125.04  3.000
 DOQ  OAG   CAQ  OAD   123.12  3.000
 DOQ  HAG   OAG  CAQ   110.04  3.000
 DOQ  HAS   CAS  CAK   109.39  3.000
 DOQ  HAS   CAS  CAB   108.14  3.000
 DOQ  CAK   CAS  CAB   110.80  3.000
 DOQ  HAS   CAS  CAQ   107.65  3.000
 DOQ  CAK   CAS  CAQ   110.92  3.000
 DOQ  CAB   CAS  CAQ   109.84  3.000
 DOQ  HAB3  CAB  HAB2  108.03  3.000
 DOQ  HAB3  CAB  HAB1  107.97  3.000
 DOQ  HAB2  CAB  HAB1  108.43  3.000
 DOQ  HAB3  CAB  CAS   109.29  3.000
 DOQ  HAB2  CAB  CAS   111.84  3.000
 DOQ  HAB1  CAB  CAS   111.16  3.000
 DOQ  HAK   CAK  CAI   119.40  3.000
 DOQ  HAK   CAK  CAS   116.69  3.000
 DOQ  CAI   CAK  CAS   123.84  3.000
 DOQ  HAI   CAI  CAJ   118.66  3.000
 DOQ  HAI   CAI  CAK   118.39  3.000
 DOQ  CAJ   CAI  CAK   122.95  3.000
 DOQ  HAJ   CAJ  CAP   117.78  3.000
 DOQ  HAJ   CAJ  CAI   115.06  3.000
 DOQ  CAP   CAJ  CAI   127.16  3.000
 DOQ  CAT   CAP  CAA   118.43  3.000
 DOQ  CAT   CAP  CAJ   122.11  3.000
 DOQ  CAA   CAP  CAJ   119.43  3.000
 DOQ  HAA3  CAA  HAA2  106.18  3.000
 DOQ  HAA3  CAA  HAA1  107.59  3.000
 DOQ  HAA2  CAA  HAA1  107.78  3.000
 DOQ  HAA3  CAA  CAP   111.71  3.000
 DOQ  HAA2  CAA  CAP   112.04  3.000
 DOQ  HAA1  CAA  CAP   111.27  3.000
 DOQ  HAT   CAT  CB    106.10  3.000
 DOQ  HAT   CAT  CAL   106.53  3.000
 DOQ  CB    CAT  CAL   103.73  3.000
 DOQ  HAT   CAT  CAP   108.49  3.000
 DOQ  CB    CAT  CAP   115.38  3.000
 DOQ  CAL   CAT  CAP   115.87  3.000
 DOQ  HAL2  CAL  HAL1  107.47  3.000
 DOQ  HAL2  CAL  N     112.37  3.000
 DOQ  HAL1  CAL  N     111.03  3.000
 DOQ  HAL2  CAL  CAT   111.42  3.000
 DOQ  HAL1  CAL  CAT   112.07  3.000
 DOQ  N     CAL  CAT   102.55  3.000
 DOQ  HN    N    CA    111.55  3.000
 DOQ  HN    N    CAL   111.60  3.000
 DOQ  CA    N    CAL   104.36  3.000
 DOQ  HA    CA   CB    108.45  3.000
 DOQ  HA    CA   C     108.71  3.000
 DOQ  CB    CA   C     112.20  3.000
 DOQ  HA    CA   N     112.79  3.000
 DOQ  CB    CA   N     103.19  3.000
 DOQ  C     CA   N     111.43  3.000
 DOQ  OXT   C    O     123.66  3.000
 DOQ  OXT   C    CA    111.64  3.000
 DOQ  O     C    CA    124.70  3.000
 DOQ  HO    OXT  C     110.14  3.000
 DOQ  HB    CB   CG    108.09  3.000
 DOQ  HB    CB   CA    109.06  3.000
 DOQ  CG    CB   CA    113.05  3.000
 DOQ  HB    CB   CAT   106.97  3.000
 DOQ  CG    CB   CAT   116.22  3.000
 DOQ  CA    CB   CAT   103.12  3.000
 DOQ  HG2   CG   HG1   105.94  3.000
 DOQ  HG2   CG   CD    105.59  3.000
 DOQ  HG1   CG   CD    109.93  3.000
 DOQ  HG2   CG   CB    109.82  3.000
 DOQ  HG1   CG   CB    111.81  3.000
 DOQ  CD    CG   CB    113.31  3.000
 DOQ  OE1   CD   OE2   123.12  3.000
 DOQ  OE1   CD   CG    124.84  3.000
 DOQ  OE2   CD   CG    111.99  3.000
 DOQ  HE2   OE2  CD    110.05  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  CONST_01  HO    OXT  C    CA    180.00   0.0  0
 DOQ  CONST_02  HAG   OAG  CAQ  OAD     0.00   0.0  0
 DOQ  CONST_03  HE2   OE2  CD   CG    180.00   0.0  0
 DOQ  Var_01    CA    N    CAL  CAT   -47.76  30.0  1
 DOQ  Var_02    CAT   CAP  CAJ  CAI    -1.10   0.0  2
 DOQ  Var_03    OE2   CD   CG   CB    153.79  30.0  3
 DOQ  Var_04    HAA1  CAA  CAP  CAT  -170.90  30.0  3
 DOQ  Var_05    CAJ   CAI  CAK  CAS  -177.45   0.0  2
 DOQ  Var_06    CAP   CAJ  CAI  CAK   175.45  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-1  HAG  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-2  HO   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-3  HE2  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

