# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:15:33 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  49  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  C1     0  -0.280  -4.0861   0.6119   0.2447
 2QQ  CAJ  C  C1     0  -0.210  -5.4061   0.9218   0.5402
 2QQ  CAZ  C  C      0  -0.223  -6.3987  -0.0006   0.2450
 2QQ  IAH  I  I      0   0.068  -8.4025   0.4623   0.6780
 2QQ  CAK  C  C1     0  -0.213  -6.0895  -1.2271  -0.3272
 2QQ  CAM  C  C1     0  -0.259  -4.7651  -1.5279  -0.6029
 2QQ  CBA  C  C      0  -0.034  -3.7540  -0.6096  -0.3349
 2QQ  CAY  C  C      0   0.526  -2.3411  -1.0012  -0.6384
 2QQ  OAE  O  O      0  -0.489  -2.0023  -2.1774  -0.6200
 2QQ  NAS  N  NH1    0  -0.649  -1.5040   0.0079  -0.9199
 2QQ  CAP  C  CH2    0  -0.251  -0.0932  -0.1653  -1.1963
 2QQ  CAN  C  CH2    0  -0.452   0.7215   0.9926  -0.6401
 2QQ  CAO  C  CH2    0  -0.414   2.2086   0.8347  -0.9315
 2QQ  CAR  C  CH2    0  -0.459   3.0304   1.9860  -0.3654
 2QQ  CBC  C  CH1    0  -0.179   4.5304   1.8822  -0.6430
 2QQ  CAW  C  C      0   0.401   5.2454   3.1652  -0.1468
 2QQ  OAG  O  O      0  -0.599   5.9312   3.0817   0.8869
 2QQ  OAC  O  OC    -1  -0.622   5.0330   4.1888  -0.8297
 2QQ  NAU  N  NH1    0  -0.672   5.0426   0.6677  -0.0489
 2QQ  CAX  C  C      0   0.737   6.3377   0.3028  -0.2640
 2QQ  OAD  O  O      0  -0.559   7.0019   0.7524  -1.1928
 2QQ  N    N  NH1    0  -0.659   6.8350  -0.5964   0.6320
 2QQ  CA   C  CH1    0  -0.212   8.0284  -1.3436   0.3345
 2QQ  C    C  C      0   0.414   7.7985  -2.5392  -0.6309
 2QQ  O    O  O     -1  -0.588   6.6601  -2.6805  -1.1063
 2QQ  OXT  O  OC     0  -0.614   8.8038  -3.2453  -0.8478
 2QQ  CB   C  CH2    0  -0.605   8.6737  -1.8287   1.6391
 2QQ  CAI  C  CSP    0   0.305   9.0338  -0.7391   2.5362
 2QQ  CAA  C  CSP1   0  -0.574   9.3457   0.1595   3.2728
 2QQ  H1   H  H      0   0.270  -3.3215   1.3344   0.5008
 2QQ  H2   H  H      0   0.286  -5.6410   1.8713   1.0006
 2QQ  H3   H  H      0   0.284  -6.8611  -1.9489  -0.5569
 2QQ  H4   H  H      0   0.272  -4.5219  -2.4866  -1.0409
 2QQ  H5   H  HNH1   0   0.405  -1.8875   0.9265  -1.0773
 2QQ  H6   H  HCH2   0   0.243   0.2321  -1.1015  -0.7440
 2QQ  H7   H  HCH2   0   0.234   0.0729  -0.2565  -2.2749
 2QQ  H8   H  HCH2   0   0.225   0.3628   1.9349  -1.0678
 2QQ  H9   H  HCH2   0   0.227   0.5611   1.0580   0.4402
 2QQ  H10  H  HCH2   0   0.222   2.5595  -0.1150  -0.5183
 2QQ  H11  H  HCH2   0   0.216   2.3674   0.7749  -2.0136
 2QQ  H12  H  HCH2   0   0.234   2.6745   2.9271  -0.7900
 2QQ  H13  H  HCH2   0   0.216   2.8651   2.0566   0.7170
 2QQ  H14  H  HCH1   0   0.222   4.6635   1.8168  -1.7266
 2QQ  H16  H  HNH1   0   0.368   4.6663   0.4506   0.8620
 2QQ  H17  H  HNH1   0   0.370   6.1556  -1.0905   1.1915
 2QQ  H18  H  HCH1   0   0.253   8.7317  -0.6640  -0.1518
 2QQ  H20  H  HCH2   0   0.265   7.9965  -2.5136   2.1605
 2QQ  H21  H  HCH2   0   0.279   9.5647  -2.4057   1.3920
 2QQ  H22  H  H      0   0.276   9.6166   0.9594   3.9225

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    deloc     1.242  0.020  1.242
 2QQ  C    OXT  deloc     1.248  0.020  1.248
 2QQ  C    CA   single    1.554  0.020  1.554
 2QQ  CAA  CAI  triple    1.203  0.020  1.203
 2QQ  CAI  CB   single    1.457  0.020  1.457
 2QQ  CB   CA   single    1.534  0.020  1.534
 2QQ  CA   N    single    1.439  0.020  1.439
 2QQ  OAD  CAX  double    1.227  0.020  1.227
 2QQ  CAN  CAP  single    1.521  0.020  1.521
 2QQ  CAN  CAO  single    1.524  0.020  1.524
 2QQ  CAP  NAS  single    1.448  0.020  1.448
 2QQ  N    CAX  single    1.363  0.020  1.363
 2QQ  CAX  NAU  single    1.363  0.020  1.363
 2QQ  CAR  CAO  single    1.524  0.020  1.524
 2QQ  CAR  CBC  single    1.529  0.020  1.529
 2QQ  NAU  CBC  single    1.446  0.020  1.446
 2QQ  OAE  CAY  double    1.224  0.020  1.224
 2QQ  NAS  CAY  single    1.341  0.020  1.341
 2QQ  CBC  CAW  single    1.550  0.020  1.550
 2QQ  CAY  CBA  single    1.497  0.020  1.497
 2QQ  CAW  OAG  deloc     1.243  0.020  1.243
 2QQ  CAW  OAC  deloc     1.249  0.020  1.249
 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    2.102  0.020  2.102
 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  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  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  121.03  3.000
 2QQ  H1   CAL  CAJ  118.19  3.000
 2QQ  CBA  CAL  CAJ  120.76  3.000
 2QQ  H2   CAJ  CAZ  121.28  3.000
 2QQ  H2   CAJ  CAL  119.58  3.000
 2QQ  CAZ  CAJ  CAL  119.14  3.000
 2QQ  CAK  CAZ  IAH  119.47  3.000
 2QQ  IAH  CAZ  CAJ  119.47  3.000
 2QQ  CAK  CAZ  CAJ  121.06  3.000
 2QQ  H3   CAK  CAM  119.66  3.000
 2QQ  H3   CAK  CAZ  121.22  3.000
 2QQ  CAM  CAK  CAZ  119.12  3.000
 2QQ  H4   CAM  CBA  119.96  3.000
 2QQ  H4   CAM  CAK  119.19  3.000
 2QQ  CBA  CAM  CAK  120.84  3.000
 2QQ  CAY  CBA  CAM  118.28  3.000
 2QQ  CAM  CBA  CAL  119.07  3.000
 2QQ  CAY  CBA  CAL  122.61  3.000
 2QQ  NAS  CAY  OAE  123.60  3.000
 2QQ  NAS  CAY  CBA  115.77  3.000
 2QQ  OAE  CAY  CBA  120.63  3.000
 2QQ  H5   NAS  CAP  116.74  3.000
 2QQ  H5   NAS  CAY  118.75  3.000
 2QQ  CAP  NAS  CAY  123.94  3.000
 2QQ  H7   CAP  H6   106.98  3.000
 2QQ  H7   CAP  CAN  110.02  3.000
 2QQ  H6   CAP  CAN  110.03  3.000
 2QQ  H7   CAP  NAS  110.22  3.000
 2QQ  H6   CAP  NAS  108.33  3.000
 2QQ  CAN  CAP  NAS  111.16  3.000
 2QQ  H9   CAN  H8   106.63  3.000
 2QQ  H9   CAN  CAO  109.76  3.000
 2QQ  H8   CAN  CAO  109.52  3.000
 2QQ  H9   CAN  CAP  109.15  3.000
 2QQ  H8   CAN  CAP  109.68  3.000
 2QQ  CAO  CAN  CAP  111.96  3.000
 2QQ  H11  CAO  H10  106.22  3.000
 2QQ  H11  CAO  CAR  109.28  3.000
 2QQ  H10  CAO  CAR  110.04  3.000
 2QQ  H11  CAO  CAN  109.64  3.000
 2QQ  H10  CAO  CAN  109.32  3.000
 2QQ  CAR  CAO  CAN  112.15  3.000
 2QQ  H13  CAR  H12  106.20  3.000
 2QQ  H13  CAR  CBC  109.35  3.000
 2QQ  H12  CAR  CBC  107.92  3.000
 2QQ  H13  CAR  CAO  109.50  3.000
 2QQ  H12  CAR  CAO  109.32  3.000
 2QQ  CBC  CAR  CAO  114.23  3.000
 2QQ  H14  CBC  NAU  108.29  3.000
 2QQ  H14  CBC  CAW  108.09  3.000
 2QQ  NAU  CBC  CAW  113.59  3.000
 2QQ  H14  CBC  CAR  107.66  3.000
 2QQ  CAW  CBC  CAR  109.76  3.000
 2QQ  NAU  CBC  CAR  109.27  3.000
 2QQ  OAC  CAW  OAG  127.13  3.000
 2QQ  OAC  CAW  CBC  115.14  3.000
 2QQ  OAG  CAW  CBC  117.71  3.000
 2QQ  H16  NAU  CAX  116.06  3.000
 2QQ  H16  NAU  CBC  114.80  3.000
 2QQ  CAX  NAU  CBC  119.79  3.000
 2QQ  N    CAX  OAD  122.80  3.000
 2QQ  N    CAX  NAU  114.81  3.000
 2QQ  OAD  CAX  NAU  122.40  3.000
 2QQ  H17  N    CA   114.75  3.000
 2QQ  H17  N    CAX  116.21  3.000
 2QQ  CA   N    CAX  120.60  3.000
 2QQ  H18  CA   CB   107.73  3.000
 2QQ  H18  CA   C    107.30  3.000
 2QQ  CB   CA   C    110.32  3.000
 2QQ  H18  CA   N    107.64  3.000
 2QQ  CB   CA   N    109.70  3.000
 2QQ  C    CA   N    113.91  3.000
 2QQ  OXT  C    O    127.43  3.000
 2QQ  OXT  C    CA   115.11  3.000
 2QQ  O    C    CA   117.46  3.000
 2QQ  H21  CB   H20  106.40  3.000
 2QQ  H21  CB   CAI  109.48  3.000
 2QQ  H20  CB   CAI  109.11  3.000
 2QQ  H21  CB   CA   108.57  3.000
 2QQ  H20  CB   CA   110.03  3.000
 2QQ  CAI  CB   CA   113.03  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  Var_01    OAE  CAY  CBA  CAL   150.08  30.0  2
 2QQ  Var_02    CAN  CAP  NAS  CAY  -144.37  30.0  2
 2QQ  Var_03    CAO  CAN  CAP  NAS  -179.50  30.0  2
 2QQ  Var_04    CAR  CAO  CAN  CAP  -179.49  30.0  3
 2QQ  Var_05    CBC  CAR  CAO  CAN  -179.43  30.0  2
 2QQ  Var_06    H20  CB   CAI  CAA   135.26  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-5  CA   0.020
 2QQ  plan-5  C    0.020
 2QQ  plan-5  O    0.020
 2QQ  plan-5  OXT  0.020

