# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 04:31:24 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: N~2~-{[(1S)-1-carboxy-2-(pyridin-4-yl)ethyl]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](Cc2ccncc2)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
 2QN  2QN  N~2~-{[(1S)-1-carboxy-2-(pyridin-4-yl)ethyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine  ligand  58  33  .  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_2QN
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
 2QN  CAN  C  CR16  0  -0.259  -5.7490   1.5643   0.5197
 2QN  CAL  C  CR16  0  -0.213  -7.0613   1.2230   0.2335
 2QN  CBC  C  CR6   0  -0.223  -7.3309  -0.0229  -0.3163
 2QN  IAG  I  I     0   0.069  -9.3156  -0.5478  -0.7650
 2QN  CAM  C  CR16  0  -0.210  -6.3104  -0.9244  -0.5794
 2QN  CAO  C  CR16  0  -0.280  -5.0031  -0.5736  -0.2744
 2QN  CBE  C  CR6   0  -0.034  -4.7108   0.6679   0.2832
 2QN  CBB  C  C     0   0.530  -3.3137   1.1021   0.5985
 2QN  OAD  O  O     0  -0.488  -3.0046   2.2862   0.5734
 2QN  NAV  N  NH1   0  -0.652  -2.4482   0.1223   0.8981
 2QN  CAR  C  CH2   0  -0.243  -1.0571   0.3644   1.2183
 2QN  CAP  C  CH2   0  -0.465  -0.2147  -0.8728   0.9503
 2QN  CAQ  C  CH2   0  -0.418   1.2488  -0.6356   1.2960
 2QN  CB   C  CH2   0  -0.459   2.1014  -1.8778   1.0701
 2QN  CA   C  CH1   0  -0.190   3.5691  -1.6529   1.4498
 2QN  C    C  C     0   0.544   4.3503  -2.9585   1.3922
 2QN  OXT  O  OH1   0  -0.593   3.9990  -3.7768   2.3749
 2QN  O    O  O     0  -0.432   5.1727  -3.2273   0.5561
 2QN  N    N  NH1   0  -0.676   4.1564  -0.6634   0.5935
 2QN  CBA  C  C     0   0.762   5.3467  -0.0893   0.9128
 2QN  OAC  O  O     0  -0.536   5.8887  -0.2505   1.9986
 2QN  NAX  N  NH1   0  -0.671   5.8913   0.6816  -0.0710
 2QN  CBG  C  CH1   0  -0.189   7.0097   1.5294   0.2109
 2QN  CAZ  C  C     0   0.544   6.5897   2.7501   1.0217
 2QN  OAF  O  O     0  -0.427   5.4487   3.0643   1.2350
 2QN  OAB  O  OH1   0  -0.591   7.6423   3.4250   1.4592
 2QN  CAT  C  CH2   0  -0.562   7.6901   1.9524  -1.1011
 2QN  CBD  C  CR6   0   0.242   8.2742   0.7652  -1.8094
 2QN  CAJ  C  CR16  0  -0.368   9.4814   0.2133  -1.3935
 2QN  CAH  C  CR16  0  -0.058   9.9799  -0.8983  -2.0531
 2QN  NAU  N  N     0  -0.410   9.3665  -1.4802  -3.0784
 2QN  CAI  C  CR16  0  -0.059   8.2154  -0.9522  -3.4766
 2QN  CAK  C  CR16  0  -0.382   7.6336   0.1574  -2.8812
 2QN  H1   H  HCR6  0   0.272  -5.5372   2.5383   0.9403
 2QN  H2   H  HCR6  0   0.284  -7.8543   1.9290   0.4383
 2QN  H3   H  HCR6  0   0.286  -6.5142  -1.8890  -1.0231
 2QN  H4   H  HCR6  0   0.270  -4.2168  -1.2804  -0.5070
 2QN  H5   H  HNH1  0   0.405  -2.8045  -0.8033   1.0772
 2QN  H6   H  HCH2  0   0.242  -0.6995   1.1970   0.6118
 2QN  H7   H  HCH2  0   0.234  -0.9516   0.6657   2.2660
 2QN  H8   H  HCH2  0   0.231  -0.5980  -1.7146   1.5366
 2QN  H9   H  HCH2  0   0.234  -0.3081  -1.1540  -0.1025
 2QN  H10  H  HCH2  0   0.233   1.6322   0.1982   0.7020
 2QN  H11  H  HCH2  0   0.227   1.3337  -0.3319   2.3444
 2QN  H12  H  HCH2  0   0.258   1.7034  -2.7000   1.6675
 2QN  H13  H  HCH2  0   0.243   2.0376  -2.1956   0.0243
 2QN  H14  H  HCH1  0   0.286   3.5985  -1.2957   2.4826
 2QN  H15  H  HOH1  0   0.484   4.4864  -4.6116   2.3072
 2QN  H16  H  HNH1  0   0.396   3.8728  -0.6756  -0.3746
 2QN  H17  H  HNH1  0   0.393   5.3034   0.9531  -0.8443
 2QN  H18  H  HCH1  0   0.304   7.7347   0.9727   0.8101
 2QN  H19  H  HOH1  0   0.487   7.3601   4.2120   1.9495
 2QN  H20  H  HCH2  0   0.279   6.9658   2.4609  -1.7426
 2QN  H21  H  HCH2  0   0.292   8.4797   2.6711  -0.8813
 2QN  H22  H  HCR6  0   0.266  10.0358   0.6418  -0.5674
 2QN  H23  H  HCR6  0   0.263  10.9214  -1.3356  -1.7397
 2QN  H24  H  HCR6  0   0.263   7.7247  -1.4339  -4.3151
 2QN  H25  H  HCR6  0   0.264   6.6932   0.5396  -3.2576

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
 2QN  OAF  CAZ  double    1.203  0.020  1.203
 2QN  CAH  CAJ  aromatic  1.385  0.020  1.385
 2QN  CAH  NAU  aromatic  1.329  0.020  1.329
 2QN  CAJ  CBD  aromatic  1.391  0.020  1.391
 2QN  NAU  CAI  aromatic  1.328  0.020  1.328
 2QN  CAZ  OAB  single    1.325  0.020  1.325
 2QN  CAZ  CBG  single    1.524  0.020  1.524
 2QN  CBD  CAT  single    1.501  0.020  1.501
 2QN  CBD  CAK  aromatic  1.389  0.020  1.389
 2QN  CAT  CBG  single    1.537  0.020  1.537
 2QN  CAI  CAK  aromatic  1.387  0.020  1.387
 2QN  CBG  NAX  single    1.431  0.020  1.431
 2QN  CAP  CAR  single    1.521  0.020  1.521
 2QN  CAP  CAQ  single    1.522  0.020  1.522
 2QN  OAC  CBA  double    1.224  0.020  1.224
 2QN  NAX  CBA  single    1.363  0.020  1.363
 2QN  CAR  NAV  single    1.448  0.020  1.448
 2QN  CBA  N    single    1.360  0.020  1.360
 2QN  CB   CAQ  single    1.524  0.020  1.524
 2QN  CB   CA   single    1.533  0.020  1.533
 2QN  N    CA   single    1.434  0.020  1.434
 2QN  OAD  CBB  double    1.224  0.020  1.224
 2QN  NAV  CBB  single    1.341  0.020  1.341
 2QN  CA   C    single    1.523  0.020  1.523
 2QN  CBB  CBE  single    1.497  0.020  1.497
 2QN  C    O    double    1.203  0.020  1.203
 2QN  C    OXT  single    1.326  0.020  1.326
 2QN  CBE  CAN  aromatic  1.392  0.020  1.392
 2QN  CBE  CAO  aromatic  1.392  0.020  1.392
 2QN  CAN  CAL  aromatic  1.386  0.020  1.386
 2QN  CAO  CAM  aromatic  1.388  0.020  1.388
 2QN  CAL  CBC  aromatic  1.388  0.020  1.388
 2QN  CAM  CBC  aromatic  1.387  0.020  1.387
 2QN  CBC  IAG  single    2.101  0.020  2.101
 2QN  CAN  H1   single    0.930  0.020  1.080
 2QN  CAL  H2   single    0.930  0.020  1.080
 2QN  CAM  H3   single    0.930  0.020  1.080
 2QN  CAO  H4   single    0.930  0.020  1.080
 2QN  NAV  H5   single    0.860  0.020  1.020
 2QN  CAR  H6   single    0.970  0.020  1.090
 2QN  CAR  H7   single    0.970  0.020  1.090
 2QN  CAP  H8   single    0.970  0.020  1.090
 2QN  CAP  H9   single    0.970  0.020  1.090
 2QN  CAQ  H10  single    0.970  0.020  1.090
 2QN  CAQ  H11  single    0.970  0.020  1.090
 2QN  CB   H12  single    0.970  0.020  1.090
 2QN  CB   H13  single    0.970  0.020  1.090
 2QN  CA   H14  single    0.970  0.020  1.090
 2QN  OXT  H15  single    0.850  0.020  0.980
 2QN  N    H16  single    0.890  0.020  1.040
 2QN  NAX  H17  single    0.890  0.020  1.040
 2QN  CBG  H18  single    0.970  0.020  1.090
 2QN  OAB  H19  single    0.850  0.020  0.980
 2QN  CAT  H20  single    0.970  0.020  1.090
 2QN  CAT  H21  single    0.970  0.020  1.090
 2QN  CAJ  H22  single    0.930  0.020  1.080
 2QN  CAH  H23  single    0.930  0.020  1.080
 2QN  CAI  H24  single    0.930  0.020  1.080
 2QN  CAK  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
 2QN  H1   CAN  CBE  119.99  3.000
 2QN  H1   CAN  CAL  119.17  3.000
 2QN  CBE  CAN  CAL  120.84  3.000
 2QN  H2   CAL  CBC  121.23  3.000
 2QN  H2   CAL  CAN  119.64  3.000
 2QN  CBC  CAL  CAN  119.13  3.000
 2QN  CAM  CBC  IAG  119.48  3.000
 2QN  IAG  CBC  CAL  119.48  3.000
 2QN  CAM  CBC  CAL  121.04  3.000
 2QN  H3   CAM  CAO  119.56  3.000
 2QN  H3   CAM  CBC  121.27  3.000
 2QN  CAO  CAM  CBC  119.16  3.000
 2QN  H4   CAO  CBE  121.05  3.000
 2QN  H4   CAO  CAM  118.17  3.000
 2QN  CBE  CAO  CAM  120.76  3.000
 2QN  CBB  CBE  CAO  122.63  3.000
 2QN  CAO  CBE  CAN  119.06  3.000
 2QN  CBB  CBE  CAN  118.27  3.000
 2QN  NAV  CBB  OAD  123.26  3.000
 2QN  NAV  CBB  CBE  115.94  3.000
 2QN  OAD  CBB  CBE  120.80  3.000
 2QN  H5   NAV  CAR  116.99  3.000
 2QN  H5   NAV  CBB  118.85  3.000
 2QN  CAR  NAV  CBB  123.18  3.000
 2QN  H7   CAR  H6   106.88  3.000
 2QN  H7   CAR  CAP  109.82  3.000
 2QN  H6   CAR  CAP  109.97  3.000
 2QN  H7   CAR  NAV  110.50  3.000
 2QN  H6   CAR  NAV  108.65  3.000
 2QN  CAP  CAR  NAV  110.93  3.000
 2QN  H9   CAP  H8   106.73  3.000
 2QN  H9   CAP  CAQ  109.92  3.000
 2QN  H8   CAP  CAQ  109.55  3.000
 2QN  H9   CAP  CAR  109.36  3.000
 2QN  H8   CAP  CAR  109.71  3.000
 2QN  CAQ  CAP  CAR  111.46  3.000
 2QN  H11  CAQ  H10  106.36  3.000
 2QN  H11  CAQ  CB   108.95  3.000
 2QN  H10  CAQ  CB   110.18  3.000
 2QN  H11  CAQ  CAP  109.58  3.000
 2QN  H10  CAQ  CAP  109.43  3.000
 2QN  CB   CAQ  CAP  112.17  3.000
 2QN  H13  CB   H12  106.43  3.000
 2QN  H13  CB   CA   109.57  3.000
 2QN  H12  CB   CA   108.92  3.000
 2QN  H13  CB   CAQ  110.23  3.000
 2QN  H12  CB   CAQ  109.21  3.000
 2QN  CA   CB   CAQ  112.31  3.000
 2QN  H14  CA   N    109.12  3.000
 2QN  H14  CA   C    107.58  3.000
 2QN  N    CA   C    111.03  3.000
 2QN  H14  CA   CB   107.92  3.000
 2QN  C    CA   CB   110.87  3.000
 2QN  N    CA   CB   110.21  3.000
 2QN  O    C    OXT  123.92  3.000
 2QN  OXT  C    CA   111.42  3.000
 2QN  O    C    CA   124.65  3.000
 2QN  H15  OXT  C    110.28  3.000
 2QN  H16  N    CBA  118.46  3.000
 2QN  H16  N    CA   116.71  3.000
 2QN  CBA  N    CA   120.64  3.000
 2QN  NAX  CBA  OAC  122.52  3.000
 2QN  NAX  CBA  N    114.78  3.000
 2QN  OAC  CBA  N    122.71  3.000
 2QN  H17  NAX  CBG  116.55  3.000
 2QN  H17  NAX  CBA  118.20  3.000
 2QN  CBG  NAX  CBA  120.33  3.000
 2QN  H18  CBG  CAT  108.33  3.000
 2QN  H18  CBG  CAZ  107.40  3.000
 2QN  CAT  CBG  CAZ  110.83  3.000
 2QN  H18  CBG  NAX  108.94  3.000
 2QN  CAT  CBG  NAX  109.92  3.000
 2QN  CAZ  CBG  NAX  111.33  3.000
 2QN  OAB  CAZ  OAF  124.21  3.000
 2QN  OAB  CAZ  CBG  111.38  3.000
 2QN  OAF  CAZ  CBG  124.41  3.000
 2QN  H19  OAB  CAZ  110.45  3.000
 2QN  H21  CAT  H20  106.95  3.000
 2QN  H21  CAT  CBD  109.56  3.000
 2QN  H20  CAT  CBD  110.43  3.000
 2QN  H21  CAT  CBG  109.26  3.000
 2QN  H20  CAT  CBG  109.62  3.000
 2QN  CBD  CAT  CBG  110.94  3.000
 2QN  CAK  CBD  CAJ  117.22  3.000
 2QN  CAK  CBD  CAT  122.06  3.000
 2QN  CAJ  CBD  CAT  120.70  3.000
 2QN  H22  CAJ  CAH  119.76  3.000
 2QN  H22  CAJ  CBD  121.01  3.000
 2QN  CAH  CAJ  CBD  119.23  3.000
 2QN  H23  CAH  NAU  116.56  3.000
 2QN  H23  CAH  CAJ  119.89  3.000
 2QN  NAU  CAH  CAJ  123.55  3.000
 2QN  CAI  NAU  CAH  117.22  3.000
 2QN  H24  CAI  CAK  119.83  3.000
 2QN  H24  CAI  NAU  116.59  3.000
 2QN  CAK  CAI  NAU  123.58  3.000
 2QN  H25  CAK  CAI  119.83  3.000
 2QN  H25  CAK  CBD  120.97  3.000
 2QN  CAI  CAK  CBD  119.20  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
 2QN  CONST_01  CAM  CAO  CBE  CAN     0.00   0.0  0
 2QN  CONST_02  CAM  CBC  CAL  CAN     0.00   0.0  0
 2QN  CONST_03  CAO  CBE  CAN  CAL     0.00   0.0  0
 2QN  CONST_04  CAO  CAM  CBC  CAL     0.00   0.0  0
 2QN  CONST_05  CBE  CAN  CAL  CBC     0.00   0.0  0
 2QN  CONST_06  CBE  CAO  CAM  CBC     0.00   0.0  0
 2QN  CONST_07  NAU  CAH  CAJ  CBD     0.00   0.0  0
 2QN  CONST_08  NAU  CAI  CAK  CBD     0.00   0.0  0
 2QN  CONST_09  CAI  NAU  CAH  CAJ     0.00   0.0  0
 2QN  CONST_10  CAI  CAK  CBD  CAJ     0.00   0.0  0
 2QN  CONST_11  CAK  CBD  CAJ  CAH     0.00   0.0  0
 2QN  CONST_12  CAK  CAI  NAU  CAH     0.00   0.0  0
 2QN  CONST_13  IAG  CBC  CAL  CAN   180.00   0.0  0
 2QN  CONST_14  CBB  CBE  CAN  CAL   180.00   0.0  0
 2QN  CONST_15  CAO  CAM  CBC  IAG   180.00   0.0  0
 2QN  CONST_16  CBB  CBE  CAO  CAM   180.00   0.0  0
 2QN  CONST_17  CAH  CAJ  CBD  CAT   180.00   0.0  0
 2QN  CONST_18  CAI  CAK  CBD  CAT   180.00   0.0  0
 2QN  CONST_19  H4   CAO  CBE  CAN   180.00   0.0  0
 2QN  CONST_20  H3   CAM  CBC  CAL   180.00   0.0  0
 2QN  CONST_21  H1   CAN  CAL  CBC   180.00   0.0  0
 2QN  CONST_22  H2   CAL  CBC  CAM   180.00   0.0  0
 2QN  CONST_23  H23  CAH  CAJ  CBD   180.00   0.0  0
 2QN  CONST_24  H24  CAI  CAK  CBD   180.00   0.0  0
 2QN  CONST_25  H25  CAK  CBD  CAJ   180.00   0.0  0
 2QN  CONST_26  H22  CAJ  CAH  NAU   180.00   0.0  0
 2QN  CONST_27  CAR  NAV  CBB  CBE   180.00   0.0  0
 2QN  CONST_28  H5   NAV  CBB  CBE     0.00   0.0  0
 2QN  CONST_29  CAR  NAV  CBB  OAD     0.00   0.0  0
 2QN  CONST_30  OAC  CBA  N    CA      0.00   0.0  0
 2QN  CONST_31  CBG  NAX  CBA  OAC     0.00   0.0  0
 2QN  CONST_32  NAX  CBA  N    CA    180.00   0.0  0
 2QN  CONST_33  CBG  NAX  CBA  N     180.00   0.0  0
 2QN  CONST_34  H17  NAX  CBA  OAC   180.00   0.0  0
 2QN  CONST_35  H16  N    CBA  OAC   180.00   0.0  0
 2QN  CONST_36  H15  OXT  C    CA    180.00   0.0  0
 2QN  CONST_37  H19  OAB  CAZ  CBG   180.00   0.0  0
 2QN  Var_01    OAD  CBB  CBE  CAN   -27.05  30.0  2
 2QN  Var_02    CAJ  CBD  CAT  CBG   -78.31  30.0  3
 2QN  Var_03    CAP  CAR  NAV  CBB  -156.52  30.0  2
 2QN  Var_04    CAQ  CAP  CAR  NAV  -179.45  30.0  1
 2QN  Var_05    CB   CAQ  CAP  CAR   178.41  30.0  3
 2QN  Var_06    CA   CB   CAQ  CAP  -178.59  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
 2QN  chir_01  CA   CB   N    C    positiv
 2QN  chir_02  CBG  NAX  CAZ  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
 2QN  plan-1  CAN  0.020
 2QN  plan-1  CAL  0.020
 2QN  plan-1  CBC  0.020
 2QN  plan-1  IAG  0.020
 2QN  plan-1  CAM  0.020
 2QN  plan-1  CAO  0.020
 2QN  plan-1  CBE  0.020
 2QN  plan-1  CBB  0.020
 2QN  plan-1  H1   0.020
 2QN  plan-1  H2   0.020
 2QN  plan-1  H3   0.020
 2QN  plan-1  H4   0.020
 2QN  plan-2  CBG  0.020
 2QN  plan-2  CAZ  0.020
 2QN  plan-2  OAF  0.020
 2QN  plan-2  OAB  0.020
 2QN  plan-2  H19  0.020
 2QN  plan-3  CAT  0.020
 2QN  plan-3  CBD  0.020
 2QN  plan-3  CAJ  0.020
 2QN  plan-3  CAH  0.020
 2QN  plan-3  NAU  0.020
 2QN  plan-3  CAI  0.020
 2QN  plan-3  CAK  0.020
 2QN  plan-3  H22  0.020
 2QN  plan-3  H23  0.020
 2QN  plan-3  H24  0.020
 2QN  plan-3  H25  0.020
 2QN  plan-4  CBE  0.020
 2QN  plan-4  CBB  0.020
 2QN  plan-4  OAD  0.020
 2QN  plan-4  NAV  0.020
 2QN  plan-4  CAR  0.020
 2QN  plan-4  H5   0.020
 2QN  plan-5  CA   0.020
 2QN  plan-5  N    0.020
 2QN  plan-5  CBA  0.020
 2QN  plan-5  OAC  0.020
 2QN  plan-5  NAX  0.020
 2QN  plan-5  CBG  0.020
 2QN  plan-5  H16  0.020
 2QN  plan-5  H17  0.020
 2QN  plan-6  CA   0.020
 2QN  plan-6  C    0.020
 2QN  plan-6  OXT  0.020
 2QN  plan-6  O    0.020
 2QN  plan-6  H15  0.020

