# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:32:20 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: (2~{S})-4-[[(5~{S})-5-azanyl-6-oxidanylidene-hexyl]amino]-2-naphthalen-2-ylsulfanyl-4-oxidanylidene-butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNC(=O)C[C@H](Sc1ccc2ccccc2c1)C(O)=O)C=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
 DQK  DQK  '(2~{S})-4-[[(5~{S})-5-azanyl-6-oxidanylidene-hexyl]amino]-2-naphthalen-2-ylsulfanyl-4-oxidanylidene-butanoic acid'  ligand  50  27  .  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_DQK
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
 DQK  CA   C  CH1    0  -0.210   6.7003   2.2556   0.5360
 DQK  C    C  C1     0   0.186   7.9715   2.1260   1.3287
 DQK  N    N  NH2    0  -0.785   6.9699   2.6904  -0.8145
 DQK  O    O  O      0  -0.377   9.0835   2.2618   0.8860
 DQK  CB   C  CH2    0  -0.442   5.9129   0.9403   0.6882
 DQK  CAD  C  CH2    0  -0.422   4.5195   1.0107   0.0779
 DQK  CAE  C  CH2    0  -0.463   3.7624  -0.3038   0.2081
 DQK  CAF  C  CH2    0  -0.238   2.3796  -0.2212  -0.4196
 DQK  NAG  N  NH1    0  -0.637   1.6945  -1.4920  -0.3346
 DQK  CAJ  C  C      0   0.563   0.6479  -1.8178  -1.1066
 DQK  OAN  O  O      0  -0.509   0.2094  -1.0736  -1.9755
 DQK  CAK  C  CH2    0  -0.543   0.0519  -3.1865  -0.8589
 DQK  CAL  C  CH1    0  -0.509  -1.4441  -3.0958  -0.6034
 DQK  CAM  C  C      0   0.463  -2.1630  -4.4614  -0.4822
 DQK  OAP  O  O      0  -0.591  -3.4059  -4.4155  -0.4232
 DQK  OAO  O  OC    -1  -0.586  -1.4458  -5.4761  -0.4581
 DQK  SAQ  S  S2     0   0.017  -1.7148  -2.1164   0.9259
 DQK  CAR  C  CR6    0  -0.121  -2.7678  -0.8061   0.3921
 DQK  CAS  C  CR16   0  -0.325  -2.4690   0.4801   0.7618
 DQK  CAT  C  CR66   0   0.124  -3.3342   1.5482   0.4282
 DQK  CAX  C  CR16   0  -0.314  -3.0503   2.8824   0.8046
 DQK  CAY  C  CR16   0  -0.257  -3.8991   3.8995   0.4607
 DQK  CAZ  C  CR16   0  -0.260  -5.0710   3.6322  -0.2782
 DQK  CBA  C  CR16   0  -0.310  -5.3680   2.3515  -0.6600
 DQK  CAU  C  CR66   0   0.107  -4.5105   1.2808  -0.3186
 DQK  CAV  C  CR16   0  -0.302  -4.7856  -0.0559  -0.6960
 DQK  CAW  C  CR16   0  -0.252  -3.9498  -1.0759  -0.3411
 DQK  H1   H  HCH1   0   0.264   6.1218   3.0394   1.0442
 DQK  H2   H  H      0   0.189   7.8101   1.8698   2.3923
 DQK  H3   H  HNH2   0   0.344   7.3943   1.9385  -1.3443
 DQK  H4   H  HNH2   0   0.356   6.1030   2.9136  -1.2843
 DQK  H6   H  HCH2   0   0.233   6.4809   0.1290   0.2194
 DQK  H7   H  HCH2   0   0.230   5.8279   0.6869   1.7499
 DQK  H8   H  HCH2   0   0.225   3.9531   1.8139   0.5608
 DQK  H9   H  HCH2   0   0.217   4.5917   1.2738  -0.9814
 DQK  H10  H  HCH2   0   0.231   4.3303  -1.1037  -0.2762
 DQK  H11  H  HCH2   0   0.229   3.6743  -0.5752   1.2651
 DQK  H12  H  HCH2   0   0.226   1.7949   0.5648   0.0712
 DQK  H13  H  HCH2   0   0.233   2.4686   0.0607  -1.4701
 DQK  H14  H  HNH1   0   0.394   1.9522  -2.1151   0.4134
 DQK  H15  H  HCH2   0   0.272   0.2205  -3.7933  -1.7529
 DQK  H16  H  HCH2   0   0.248   0.5497  -3.7035  -0.0371
 DQK  H17  H  HCH1   0   0.288  -1.9139  -2.5273  -1.4086
 DQK  H19  H  HCR6   0   0.257  -1.5585   0.6944   1.3090
 DQK  H20  H  HCR6   0   0.255  -2.1504   3.0892   1.3713
 DQK  H21  H  HCR6   0   0.258  -3.6730   4.9161   0.7549
 DQK  H22  H  HCR6   0   0.258  -5.7339   4.4457  -0.5429
 DQK  H23  H  HCR6   0   0.255  -6.2655   2.1432  -1.2302
 DQK  H24  H  HCR6   0   0.255  -5.6856  -0.2678  -1.2613
 DQK  H25  H  HCR6   0   0.276  -4.1763  -2.1002  -0.6103

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
 DQK  CAY  CAZ  aromatic  1.411  0.020  1.411
 DQK  CAY  CAX  aromatic  1.369  0.020  1.369
 DQK  CAZ  CBA  aromatic  1.369  0.020  1.369
 DQK  CAX  CAT  aromatic  1.415  0.020  1.415
 DQK  CBA  CAU  aromatic  1.414  0.020  1.414
 DQK  OAP  CAM  deloc     1.245  0.020  1.245
 DQK  CAT  CAU  aromatic  1.419  0.020  1.419
 DQK  CAT  CAS  aromatic  1.414  0.020  1.414
 DQK  OAO  CAM  deloc     1.243  0.020  1.243
 DQK  CAU  CAV  aromatic  1.416  0.020  1.416
 DQK  CAM  CAL  single    1.548  0.020  1.548
 DQK  CAS  CAR  aromatic  1.371  0.020  1.371
 DQK  CAV  CAW  aromatic  1.366  0.020  1.366
 DQK  CAR  CAW  aromatic  1.417  0.020  1.417
 DQK  CAR  SAQ  single    1.764  0.020  1.764
 DQK  CAL  CAK  single    1.520  0.020  1.520
 DQK  CAL  SAQ  single    1.836  0.020  1.836
 DQK  CAK  CAJ  single    1.513  0.020  1.513
 DQK  OAN  CAJ  double    1.225  0.020  1.225
 DQK  CAJ  NAG  single    1.341  0.020  1.341
 DQK  NAG  CAF  single    1.446  0.020  1.446
 DQK  CAF  CAE  single    1.521  0.020  1.521
 DQK  CAE  CAD  single    1.522  0.020  1.522
 DQK  CAD  CB   single    1.523  0.020  1.523
 DQK  CB   CA   single    1.541  0.020  1.541
 DQK  C    O    double    1.205  0.020  1.205
 DQK  C    CA   single    1.504  0.020  1.504
 DQK  CA   N    single    1.444  0.020  1.444
 DQK  CA   H1   single    0.970  0.020  1.090
 DQK  C    H2   single    0.930  0.020  1.080
 DQK  N    H3   single    0.890  0.020  1.040
 DQK  N    H4   single    0.890  0.020  1.040
 DQK  CB   H6   single    0.970  0.020  1.090
 DQK  CB   H7   single    0.970  0.020  1.090
 DQK  CAD  H8   single    0.970  0.020  1.090
 DQK  CAD  H9   single    0.970  0.020  1.090
 DQK  CAE  H10  single    0.970  0.020  1.090
 DQK  CAE  H11  single    0.970  0.020  1.090
 DQK  CAF  H12  single    0.970  0.020  1.090
 DQK  CAF  H13  single    0.970  0.020  1.090
 DQK  NAG  H14  single    0.860  0.020  1.020
 DQK  CAK  H15  single    0.970  0.020  1.090
 DQK  CAK  H16  single    0.970  0.020  1.090
 DQK  CAL  H17  single    0.970  0.020  1.090
 DQK  CAS  H19  single    0.930  0.020  1.080
 DQK  CAX  H20  single    0.930  0.020  1.080
 DQK  CAY  H21  single    0.930  0.020  1.080
 DQK  CAZ  H22  single    0.930  0.020  1.080
 DQK  CBA  H23  single    0.930  0.020  1.080
 DQK  CAV  H24  single    0.930  0.020  1.080
 DQK  CAW  H25  single    0.930  0.020  1.080

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
 DQK  H1   CA   CB   107.12  3.000
 DQK  H1   CA   N    108.42  3.000
 DQK  CB   CA   N    116.41  3.000
 DQK  H1   CA   C    105.23  3.000
 DQK  N    CA   C    111.17  3.000
 DQK  CB   CA   C    107.85  3.000
 DQK  H2   C    O    120.95  3.000
 DQK  H2   C    CA   113.81  3.000
 DQK  O    C    CA   125.24  3.000
 DQK  H4   N    H3   106.27  3.000
 DQK  H4   N    CA   109.93  3.000
 DQK  H3   N    CA   110.11  3.000
 DQK  H7   CB   H6   106.49  3.000
 DQK  H7   CB   CAD  109.16  3.000
 DQK  H6   CB   CAD  109.70  3.000
 DQK  H7   CB   CA   109.45  3.000
 DQK  H6   CB   CA   108.96  3.000
 DQK  CAD  CB   CA   112.87  3.000
 DQK  H9   CAD  H8   106.55  3.000
 DQK  H9   CAD  CAE  108.86  3.000
 DQK  H8   CAD  CAE  109.78  3.000
 DQK  H9   CAD  CB   109.80  3.000
 DQK  H8   CAD  CB   109.30  3.000
 DQK  CAE  CAD  CB   112.39  3.000
 DQK  H11  CAE  H10  106.73  3.000
 DQK  H11  CAE  CAF  109.81  3.000
 DQK  H10  CAE  CAF  109.21  3.000
 DQK  H11  CAE  CAD  109.67  3.000
 DQK  H10  CAE  CAD  109.59  3.000
 DQK  CAF  CAE  CAD  111.71  3.000
 DQK  H13  CAF  H12  106.82  3.000
 DQK  H13  CAF  NAG  108.80  3.000
 DQK  H12  CAF  NAG  110.56  3.000
 DQK  H13  CAF  CAE  109.71  3.000
 DQK  H12  CAF  CAE  109.83  3.000
 DQK  NAG  CAF  CAE  111.02  3.000
 DQK  H14  NAG  CAJ  118.50  3.000
 DQK  H14  NAG  CAF  117.78  3.000
 DQK  CAJ  NAG  CAF  123.33  3.000
 DQK  CAK  CAJ  OAN  121.64  3.000
 DQK  OAN  CAJ  NAG  122.69  3.000
 DQK  CAK  CAJ  NAG  115.66  3.000
 DQK  H16  CAK  H15  106.41  3.000
 DQK  H16  CAK  CAL  110.52  3.000
 DQK  H15  CAK  CAL  108.80  3.000
 DQK  H16  CAK  CAJ  111.85  3.000
 DQK  H15  CAK  CAJ  107.90  3.000
 DQK  CAL  CAK  CAJ  111.17  3.000
 DQK  H17  CAL  SAQ  105.85  3.000
 DQK  H17  CAL  CAM  108.49  3.000
 DQK  SAQ  CAL  CAM  109.68  3.000
 DQK  H17  CAL  CAK  109.30  3.000
 DQK  SAQ  CAL  CAK  108.47  3.000
 DQK  CAM  CAL  CAK  114.68  3.000
 DQK  OAO  CAM  OAP  127.24  3.000
 DQK  OAO  CAM  CAL  116.98  3.000
 DQK  OAP  CAM  CAL  115.77  3.000
 DQK  CAR  SAQ  CAL  103.43  3.000
 DQK  CAW  CAR  CAS  120.00  3.000
 DQK  CAW  CAR  SAQ  120.87  3.000
 DQK  CAS  CAR  SAQ  119.03  3.000
 DQK  H19  CAS  CAT  118.92  3.000
 DQK  H19  CAS  CAR  120.31  3.000
 DQK  CAT  CAS  CAR  120.76  3.000
 DQK  CAU  CAT  CAX  118.95  3.000
 DQK  CAU  CAT  CAS  119.27  3.000
 DQK  CAX  CAT  CAS  121.77  3.000
 DQK  H20  CAX  CAY  120.31  3.000
 DQK  H20  CAX  CAT  119.06  3.000
 DQK  CAY  CAX  CAT  120.63  3.000
 DQK  H21  CAY  CAZ  119.59  3.000
 DQK  H21  CAY  CAX  120.01  3.000
 DQK  CAZ  CAY  CAX  120.39  3.000
 DQK  H22  CAZ  CBA  120.14  3.000
 DQK  H22  CAZ  CAY  119.63  3.000
 DQK  CBA  CAZ  CAY  120.22  3.000
 DQK  H23  CBA  CAU  118.95  3.000
 DQK  H23  CBA  CAZ  120.41  3.000
 DQK  CAU  CBA  CAZ  120.64  3.000
 DQK  CAV  CAU  CBA  122.19  3.000
 DQK  CAV  CAU  CAT  118.64  3.000
 DQK  CBA  CAU  CAT  119.16  3.000
 DQK  H24  CAV  CAW  119.85  3.000
 DQK  H24  CAV  CAU  119.02  3.000
 DQK  CAW  CAV  CAU  121.13  3.000
 DQK  H25  CAW  CAV  120.92  3.000
 DQK  H25  CAW  CAR  118.90  3.000
 DQK  CAV  CAW  CAR  120.18  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
 DQK  CONST_01  CAX  CAT  CAS  CAR   180.00   0.0  0
 DQK  CONST_02  CAU  CAT  CAS  CAR     0.00   0.0  0
 DQK  CONST_03  CAU  CAV  CAW  CAR     0.00   0.0  0
 DQK  CONST_04  CAY  CAX  CAT  CAS   180.00   0.0  0
 DQK  CONST_05  CBA  CAU  CAT  CAS   180.00   0.0  0
 DQK  CONST_06  CAV  CAU  CAT  CAS     0.00   0.0  0
 DQK  CONST_07  CAV  CAW  CAR  CAS     0.00   0.0  0
 DQK  CONST_08  CAZ  CAY  CAX  CAT     0.00   0.0  0
 DQK  CONST_09  CAZ  CBA  CAU  CAT     0.00   0.0  0
 DQK  CONST_10  CAW  CAV  CAU  CAT     0.00   0.0  0
 DQK  CONST_11  CAW  CAR  CAS  CAT     0.00   0.0  0
 DQK  CONST_12  CBA  CAZ  CAY  CAX     0.00   0.0  0
 DQK  CONST_13  CBA  CAU  CAT  CAX     0.00   0.0  0
 DQK  CONST_14  CAV  CAU  CAT  CAX   180.00   0.0  0
 DQK  CONST_15  CAU  CBA  CAZ  CAY     0.00   0.0  0
 DQK  CONST_16  CAU  CAT  CAX  CAY     0.00   0.0  0
 DQK  CONST_17  CAV  CAU  CBA  CAZ   180.00   0.0  0
 DQK  CONST_18  CAW  CAV  CAU  CBA   180.00   0.0  0
 DQK  CONST_19  CAT  CAS  CAR  SAQ   180.00   0.0  0
 DQK  CONST_20  CAV  CAW  CAR  SAQ   180.00   0.0  0
 DQK  CONST_21  H24  CAV  CAW  CAR   180.00   0.0  0
 DQK  CONST_22  H20  CAX  CAT  CAS     0.00   0.0  0
 DQK  CONST_23  H25  CAW  CAR  CAS   180.00   0.0  0
 DQK  CONST_24  H21  CAY  CAX  CAT   180.00   0.0  0
 DQK  CONST_25  H23  CBA  CAU  CAT   180.00   0.0  0
 DQK  CONST_26  H22  CAZ  CAY  CAX   180.00   0.0  0
 DQK  CONST_27  H19  CAS  CAT  CAX     0.00   0.0  0
 DQK  CONST_28  CAK  CAJ  NAG  CAF   180.00   0.0  0
 DQK  CONST_29  OAN  CAJ  NAG  CAF     0.00   0.0  0
 DQK  CONST_30  H14  NAG  CAJ  OAN   180.00   0.0  0
 DQK  Var_01    CAS  CAR  SAQ  CAL  -133.00  30.0  2
 DQK  Var_02    CAE  CAD  CB   CA    178.78  30.0  1
 DQK  Var_03    CAF  CAE  CAD  CB   -179.36  30.0  1
 DQK  Var_04    NAG  CAF  CAE  CAD   177.73  30.0  1
 DQK  Var_05    CAJ  NAG  CAF  CAE  -160.94  30.0  1
 DQK  Var_06    CAL  CAK  CAJ  NAG   126.54  30.0  1

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
 DQK  chir_01  CA   CB   C    N    negativ
 DQK  chir_02  CAL  CAM  CAK  SAQ  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
 DQK  plan-1  SAQ  0.020
 DQK  plan-1  CAR  0.020
 DQK  plan-1  CAS  0.020
 DQK  plan-1  CAT  0.020
 DQK  plan-1  CAX  0.020
 DQK  plan-1  CAY  0.020
 DQK  plan-1  CAZ  0.020
 DQK  plan-1  CBA  0.020
 DQK  plan-1  CAU  0.020
 DQK  plan-1  CAV  0.020
 DQK  plan-1  CAW  0.020
 DQK  plan-1  H19  0.020
 DQK  plan-1  H20  0.020
 DQK  plan-1  H21  0.020
 DQK  plan-1  H22  0.020
 DQK  plan-1  H23  0.020
 DQK  plan-1  H24  0.020
 DQK  plan-1  H25  0.020
 DQK  plan-2  CAF  0.020
 DQK  plan-2  NAG  0.020
 DQK  plan-2  CAJ  0.020
 DQK  plan-2  OAN  0.020
 DQK  plan-2  CAK  0.020
 DQK  plan-2  H14  0.020
 DQK  plan-3  CAL  0.020
 DQK  plan-3  CAM  0.020
 DQK  plan-3  OAP  0.020
 DQK  plan-3  OAO  0.020
 DQK  plan-4  CA   0.020
 DQK  plan-4  C    0.020
 DQK  plan-4  O    0.020
 DQK  plan-4  H2   0.020

