# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 11:55:22 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: N~2~-{[(1S)-1-carboxybut-3-yn-1-yl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](CCCCNC(=O)c1ccc(I)cc1)NC(=O)N[C@@H](CC#C)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
 2QQ  2QQ  N~2~-{[(1S)-1-carboxybut-3-yn-1-yl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine  ligand  51  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2QQ
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
 2QQ  CAL  C  CR16  0  -0.283  -4.2318   0.7507  -0.6007
 2QQ  CAJ  C  CR16  0  -0.210  -5.6009   0.9354  -0.4712
 2QQ  CAZ  C  CR6   0  -0.223  -6.3521  -0.0217   0.1942
 2QQ  IAH  I  I     0   0.068  -8.4279   0.2423   0.3854
 2QQ  CAK  C  CR16  0  -0.212  -5.7528  -1.1482   0.7412
 2QQ  CAM  C  CR16  0  -0.261  -4.3822  -1.3107   0.6172
 2QQ  CBA  C  CR6   0  -0.027  -3.6111  -0.3748  -0.0663
 2QQ  CAY  C  C     0   0.527  -2.1347  -0.6048  -0.1585
 2QQ  OAE  O  O     0  -0.489  -1.5459  -1.2415   0.7055
 2QQ  NAS  N  NH1   0  -0.645  -1.5254  -0.0943  -1.2378
 2QQ  CAP  C  CH2   0  -0.281  -0.0957  -0.1731  -1.4483
 2QQ  CAN  C  CH2   0  -0.431   0.6753   0.9485  -0.7616
 2QQ  CAO  C  CH2   0  -0.423   2.1737   0.8322  -1.0092
 2QQ  CAR  C  CH2   0  -0.467   2.9486   1.9752  -0.3648
 2QQ  CBC  C  CH1   0  -0.175   4.4591   1.8786  -0.6063
 2QQ  CAW  C  C     0   0.539   5.1459   3.1304  -0.0803
 2QQ  OAG  O  O     0  -0.436   5.7047   3.2063   0.9828
 2QQ  OAC  O  OH1   0  -0.592   5.0192   4.1445  -0.9251
 2QQ  NAU  N  NH1   0  -0.682   4.9856   0.6995   0.0217
 2QQ  CAX  C  C     0   0.768   6.2851   0.3515  -0.1739
 2QQ  OAD  O  O     0  -0.535   7.0010   0.9188  -0.9892
 2QQ  N    N  NH1   0  -0.676   6.7336  -0.6732   0.6034
 2QQ  CA   C  CH1   0  -0.187   8.0154  -1.2529   0.3408
 2QQ  C    C  C     0   0.543   8.0188  -2.0228  -0.9762
 2QQ  O    O  O     0  -0.425   7.0298  -2.3274  -1.5874
 2QQ  OXT  O  OH1   0  -0.590   9.2523  -2.3288  -1.3492
 2QQ  CB   C  CH2   0  -0.609   8.4169  -2.1923   1.4900
 2QQ  CAI  C  CSP   0   0.305   8.4810  -1.4943   2.7658
 2QQ  CAA  C  CSP1  0  -0.554   8.5322  -0.9219   3.8209
 2QQ  H1   H  HCR6  0   0.271  -3.6596   1.5188  -1.1057
 2QQ  H2   H  HCR6  0   0.286  -6.0603   1.8219  -0.8855
 2QQ  H3   H  HCR6  0   0.285  -6.3345  -1.8962   1.2619
 2QQ  H4   H  HCR6  0   0.271  -3.9143  -2.1842   1.0509
 2QQ  H5   H  HNH1  0   0.410  -2.0729   0.3708  -1.9427
 2QQ  H6   H  HCH2  0   0.241   0.2628  -1.1432  -1.1005
 2QQ  H7   H  HCH2  0   0.250   0.0763  -0.1383  -2.5245
 2QQ  H8   H  HCH2  0   0.226   0.3099   1.9128  -1.1266
 2QQ  H9   H  HCH2  0   0.230   0.4766   0.9204   0.3133
 2QQ  H10  H  HCH2  0   0.231   2.5300  -0.1283  -0.6272
 2QQ  H11  H  HCH2  0   0.226   2.3716   0.8293  -2.0861
 2QQ  H12  H  HCH2  0   0.260   2.5899   2.9239  -0.7694
 2QQ  H13  H  HCH2  0   0.244   2.7550   2.0030   0.7126
 2QQ  H14  H  HCH1  0   0.282   4.6292   1.8233  -1.6849
 2QQ  H15  H  HOH1  0   0.483   5.4241   4.9438  -0.5554
 2QQ  H16  H  HNH1  0   0.398   4.5143   0.3704   0.8504
 2QQ  H17  H  HNH1  0   0.399   6.0582  -1.2428   1.0900
 2QQ  H18  H  HCH1  0   0.304   8.7645  -0.4610   0.2704
 2QQ  H19  H  HOH1  0   0.487   9.2411  -2.8430  -2.1708
 2QQ  H20  H  HCH2  0   0.294   7.7043  -3.0192   1.5615
 2QQ  H21  H  HCH2  0   0.307   9.3890  -2.6370   1.2724
 2QQ  H22  H  H     0   0.280   8.5839  -0.4134   4.7562

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
 2QQ  O    C    double    1.202  0.020  1.202
 2QQ  C    OXT  single    1.324  0.020  1.324
 2QQ  C    CA   single    1.525  0.020  1.525
 2QQ  CAA  CAI  triple    1.202  0.020  1.202
 2QQ  CAI  CB   single    1.456  0.020  1.456
 2QQ  CB   CA   single    1.538  0.020  1.538
 2QQ  CA   N    single    1.431  0.020  1.431
 2QQ  OAD  CAX  double    1.224  0.020  1.224
 2QQ  CAN  CAP  single    1.524  0.020  1.524
 2QQ  CAN  CAO  single    1.523  0.020  1.523
 2QQ  CAP  NAS  single    1.447  0.020  1.447
 2QQ  N    CAX  single    1.362  0.020  1.362
 2QQ  CAX  NAU  single    1.359  0.020  1.359
 2QQ  CAR  CAO  single    1.524  0.020  1.524
 2QQ  CAR  CBC  single    1.533  0.020  1.533
 2QQ  NAU  CBC  single    1.436  0.020  1.436
 2QQ  OAE  CAY  double    1.224  0.020  1.224
 2QQ  NAS  CAY  single    1.340  0.020  1.340
 2QQ  CBC  CAW  single    1.522  0.020  1.522
 2QQ  CAY  CBA  single    1.497  0.020  1.497
 2QQ  CAW  OAG  double    1.203  0.020  1.203
 2QQ  CAW  OAC  single    1.326  0.020  1.326
 2QQ  CBA  CAM  aromatic  1.392  0.020  1.392
 2QQ  CBA  CAL  aromatic  1.392  0.020  1.392
 2QQ  CAM  CAK  aromatic  1.386  0.020  1.386
 2QQ  CAL  CAJ  aromatic  1.388  0.020  1.388
 2QQ  CAK  CAZ  aromatic  1.388  0.020  1.388
 2QQ  CAJ  CAZ  aromatic  1.387  0.020  1.387
 2QQ  CAZ  IAH  single    2.101  0.020  2.101
 2QQ  CAL  H1   single    0.929  0.020  1.085
 2QQ  CAJ  H2   single    0.929  0.020  1.085
 2QQ  CAK  H3   single    0.929  0.020  1.085
 2QQ  CAM  H4   single    0.929  0.020  1.085
 2QQ  NAS  H5   single    0.868  0.020  1.013
 2QQ  CAP  H6   single    0.939  0.020  1.096
 2QQ  CAP  H7   single    0.939  0.020  1.096
 2QQ  CAN  H8   single    0.939  0.020  1.096
 2QQ  CAN  H9   single    0.939  0.020  1.096
 2QQ  CAO  H10  single    0.939  0.020  1.096
 2QQ  CAO  H11  single    0.939  0.020  1.096
 2QQ  CAR  H12  single    0.939  0.020  1.096
 2QQ  CAR  H13  single    0.939  0.020  1.096
 2QQ  CBC  H14  single    0.939  0.020  1.096
 2QQ  OAC  H15  single    0.832  0.020  0.971
 2QQ  NAU  H16  single    0.868  0.020  1.013
 2QQ  N    H17  single    0.868  0.020  1.013
 2QQ  CA   H18  single    0.939  0.020  1.096
 2QQ  OXT  H19  single    0.832  0.020  0.971
 2QQ  CB   H20  single    0.939  0.020  1.096
 2QQ  CB   H21  single    0.939  0.020  1.096
 2QQ  CAA  H22  single    0.913  0.020  1.066

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
 2QQ  H1   CAL  CBA  121.13  3.000
 2QQ  H1   CAL  CAJ  118.07  3.000
 2QQ  CBA  CAL  CAJ  120.78  3.000
 2QQ  H2   CAJ  CAZ  121.31  3.000
 2QQ  H2   CAJ  CAL  119.52  3.000
 2QQ  CAZ  CAJ  CAL  119.17  3.000
 2QQ  CAK  CAZ  IAH  119.51  3.000
 2QQ  IAH  CAZ  CAJ  119.48  3.000
 2QQ  CAK  CAZ  CAJ  121.01  3.000
 2QQ  H3   CAK  CAM  119.61  3.000
 2QQ  H3   CAK  CAZ  121.26  3.000
 2QQ  CAM  CAK  CAZ  119.14  3.000
 2QQ  H4   CAM  CBA  120.01  3.000
 2QQ  H4   CAM  CAK  119.12  3.000
 2QQ  CBA  CAM  CAK  120.86  3.000
 2QQ  CAY  CBA  CAM  118.25  3.000
 2QQ  CAM  CBA  CAL  119.02  3.000
 2QQ  CAY  CBA  CAL  122.70  3.000
 2QQ  NAS  CAY  OAE  123.21  3.000
 2QQ  NAS  CAY  CBA  116.07  3.000
 2QQ  OAE  CAY  CBA  120.71  3.000
 2QQ  H5   NAS  CAP  117.43  3.000
 2QQ  H5   NAS  CAY  119.52  3.000
 2QQ  CAP  NAS  CAY  123.06  3.000
 2QQ  H7   CAP  H6   106.92  3.000
 2QQ  H7   CAP  CAN  109.96  3.000
 2QQ  H6   CAP  CAN  110.15  3.000
 2QQ  H7   CAP  NAS  107.31  3.000
 2QQ  H6   CAP  NAS  109.06  3.000
 2QQ  CAN  CAP  NAS  113.21  3.000
 2QQ  H9   CAN  H8   106.86  3.000
 2QQ  H9   CAN  CAO  109.66  3.000
 2QQ  H8   CAN  CAO  109.98  3.000
 2QQ  H9   CAN  CAP  109.39  3.000
 2QQ  H8   CAN  CAP  109.23  3.000
 2QQ  CAO  CAN  CAP  111.60  3.000
 2QQ  H11  CAO  H10  106.40  3.000
 2QQ  H11  CAO  CAR  109.03  3.000
 2QQ  H10  CAO  CAR  110.21  3.000
 2QQ  H11  CAO  CAN  109.75  3.000
 2QQ  H10  CAO  CAN  109.32  3.000
 2QQ  CAR  CAO  CAN  111.98  3.000
 2QQ  H13  CAR  H12  106.52  3.000
 2QQ  H13  CAR  CBC  109.32  3.000
 2QQ  H12  CAR  CBC  108.67  3.000
 2QQ  H13  CAR  CAO  110.19  3.000
 2QQ  H12  CAR  CAO  109.14  3.000
 2QQ  CBC  CAR  CAO  112.78  3.000
 2QQ  H14  CBC  NAU  109.45  3.000
 2QQ  H14  CBC  CAW  108.20  3.000
 2QQ  NAU  CBC  CAW  111.03  3.000
 2QQ  H14  CBC  CAR  108.17  3.000
 2QQ  CAW  CBC  CAR  109.78  3.000
 2QQ  NAU  CBC  CAR  110.13  3.000
 2QQ  OAC  CAW  OAG  123.99  3.000
 2QQ  OAC  CAW  CBC  111.46  3.000
 2QQ  OAG  CAW  CBC  124.53  3.000
 2QQ  H15  OAC  CAW  110.35  3.000
 2QQ  H16  NAU  CAX  118.77  3.000
 2QQ  H16  NAU  CBC  117.13  3.000
 2QQ  CAX  NAU  CBC  119.86  3.000
 2QQ  N    CAX  OAD  122.42  3.000
 2QQ  N    CAX  NAU  115.17  3.000
 2QQ  OAD  CAX  NAU  122.41  3.000
 2QQ  H17  N    CA   117.36  3.000
 2QQ  H17  N    CAX  118.66  3.000
 2QQ  CA   N    CAX  119.66  3.000
 2QQ  H18  CA   CB   108.18  3.000
 2QQ  H18  CA   C    107.98  3.000
 2QQ  CB   CA   C    109.65  3.000
 2QQ  H18  CA   N    109.41  3.000
 2QQ  CB   CA   N    110.13  3.000
 2QQ  C    CA   N    111.40  3.000
 2QQ  OXT  C    O    124.37  3.000
 2QQ  OXT  C    CA   111.21  3.000
 2QQ  O    C    CA   124.41  3.000
 2QQ  H19  OXT  C    110.51  3.000
 2QQ  H21  CB   H20  106.58  3.000
 2QQ  H21  CB   CAI  109.33  3.000
 2QQ  H20  CB   CAI  109.50  3.000
 2QQ  H21  CB   CA   109.43  3.000
 2QQ  H20  CB   CA   109.91  3.000
 2QQ  CAI  CB   CA   111.94  3.000
 2QQ  CAA  CAI  CB   180.00  3.000
 2QQ  H22  CAA  CAI  180.00  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
 2QQ  CONST_01  CAK  CAM  CBA  CAL     0.00   0.0  0
 2QQ  CONST_02  CAK  CAZ  CAJ  CAL     0.00   0.0  0
 2QQ  CONST_03  CAM  CBA  CAL  CAJ     0.00   0.0  0
 2QQ  CONST_04  CAM  CAK  CAZ  CAJ     0.00   0.0  0
 2QQ  CONST_05  CBA  CAM  CAK  CAZ     0.00   0.0  0
 2QQ  CONST_06  CBA  CAL  CAJ  CAZ     0.00   0.0  0
 2QQ  CONST_07  IAH  CAZ  CAJ  CAL   180.00   0.0  0
 2QQ  CONST_08  CAY  CBA  CAL  CAJ   180.00   0.0  0
 2QQ  CONST_09  CAM  CAK  CAZ  IAH   180.00   0.0  0
 2QQ  CONST_10  CAY  CBA  CAM  CAK   180.00   0.0  0
 2QQ  CONST_11  H4   CAM  CBA  CAL   180.00   0.0  0
 2QQ  CONST_12  H3   CAK  CAZ  CAJ   180.00   0.0  0
 2QQ  CONST_13  H1   CAL  CAJ  CAZ   180.00   0.0  0
 2QQ  CONST_14  H2   CAJ  CAZ  CAK   180.00   0.0  0
 2QQ  CONST_15  CAP  NAS  CAY  CBA   180.00   0.0  0
 2QQ  CONST_16  H5   NAS  CAY  CBA     0.00   0.0  0
 2QQ  CONST_17  CAP  NAS  CAY  OAE     0.00   0.0  0
 2QQ  CONST_18  OAD  CAX  NAU  CBC     0.00   0.0  0
 2QQ  CONST_19  CA   N    CAX  OAD     0.00   0.0  0
 2QQ  CONST_20  N    CAX  NAU  CBC   180.00   0.0  0
 2QQ  CONST_21  CA   N    CAX  NAU   180.00   0.0  0
 2QQ  CONST_22  H17  N    CAX  OAD   180.00   0.0  0
 2QQ  CONST_24  H15  OAC  CAW  CBC   180.00   0.0  0
 2QQ  CONST_25  H19  OXT  C    CA    180.00   0.0  0
 2QQ  Var_01    OAE  CAY  CBA  CAL   150.57  30.0  2
 2QQ  Var_02    CAN  CAP  NAS  CAY   -84.97  30.0  2
 2QQ  Var_03    CAO  CAN  CAP  NAS  -179.88  30.0  1
 2QQ  Var_04    CAR  CAO  CAN  CAP   178.12  30.0  3
 2QQ  Var_05    CBC  CAR  CAO  CAN  -179.83  30.0  1
 2QQ  Var_06    H20  CB   CAI  CAA    20.86  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
 2QQ  chir_01  CBC  CAR  NAU  CAW  positiv
 2QQ  chir_02  CA   N    C    CB   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
 2QQ  plan-1  CAL  0.020
 2QQ  plan-1  CAJ  0.020
 2QQ  plan-1  CAZ  0.020
 2QQ  plan-1  IAH  0.020
 2QQ  plan-1  CAK  0.020
 2QQ  plan-1  CAM  0.020
 2QQ  plan-1  CBA  0.020
 2QQ  plan-1  CAY  0.020
 2QQ  plan-1  H1   0.020
 2QQ  plan-1  H2   0.020
 2QQ  plan-1  H3   0.020
 2QQ  plan-1  H4   0.020
 2QQ  plan-2  CBA  0.020
 2QQ  plan-2  CAY  0.020
 2QQ  plan-2  OAE  0.020
 2QQ  plan-2  NAS  0.020
 2QQ  plan-2  CAP  0.020
 2QQ  plan-2  H5   0.020
 2QQ  plan-3  CBC  0.020
 2QQ  plan-3  NAU  0.020
 2QQ  plan-3  CAX  0.020
 2QQ  plan-3  OAD  0.020
 2QQ  plan-3  N    0.020
 2QQ  plan-3  CA   0.020
 2QQ  plan-3  H16  0.020
 2QQ  plan-3  H17  0.020
 2QQ  plan-4  CBC  0.020
 2QQ  plan-4  CAW  0.020
 2QQ  plan-4  OAG  0.020
 2QQ  plan-4  OAC  0.020
 2QQ  plan-4  H15  0.020
 2QQ  plan-5  CA   0.020
 2QQ  plan-5  C    0.020
 2QQ  plan-5  O    0.020
 2QQ  plan-5  OXT  0.020
 2QQ  plan-5  H19  0.020

