# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 12:37:32 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  56  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 GRAND
;

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  -0.260  -5.7613   1.6096   0.5385
 2QN  CAL  C  CR16   0  -0.213  -7.0731   1.2639   0.2553
 2QN  CBC  C  CR6    0  -0.223  -7.3418   0.0102  -0.2768
 2QN  IAG  I  I      0   0.068  -9.3258  -0.5216  -0.7209
 2QN  CAM  C  CR16   0  -0.210  -6.3207  -0.8948  -0.5253
 2QN  CAO  C  CR16   0  -0.280  -5.0139  -0.5393  -0.2234
 2QN  CBE  C  CR6    0  -0.034  -4.7224   0.7102   0.3168
 2QN  CBB  C  C      0   0.529  -3.3255   1.1492   0.6281
 2QN  OAD  O  O      0  -0.489  -3.0167   2.3329   0.5837
 2QN  NAV  N  NH1    0  -0.651  -2.4627   0.1737   0.9464
 2QN  CAR  C  CH2    0  -0.244  -1.0679   0.4102   1.2569
 2QN  CAP  C  CH2    0  -0.460  -0.2297  -0.8237   0.9622
 2QN  CAQ  C  CH2    0  -0.411   1.2403  -0.6051   1.2941
 2QN  CB   C  CH2    0  -0.448   2.0874  -1.8397   1.0146
 2QN  CA   C  CH1    0  -0.195   3.5647  -1.6673   1.3649
 2QN  C    C  C      0   0.404   4.3240  -3.0115   1.2190
 2QN  OXT  O  OC    -1  -0.622   3.9536  -3.9176   1.9946
 2QN  O    O  O      0  -0.595   5.2132  -3.0817   0.3532
 2QN  N    N  NH1    0  -0.664   4.1281  -0.6001   0.5709
 2QN  CBA  C  C      0   0.740   5.3383  -0.0672   0.8934
 2QN  OAC  O  O      0  -0.564   5.8505  -0.2069   2.0007
 2QN  NAX  N  NH1    0  -0.660   5.9393   0.6407  -0.1052
 2QN  CBG  C  CH1    0  -0.189   6.9930   1.5728   0.2066
 2QN  CAZ  C  C      0   0.407   6.5002   2.8578   0.9253
 2QN  OAF  O  O      0  -0.591   5.2750   2.9964   1.0771
 2QN  OAB  O  OC    -1  -0.617   7.4001   3.6425   1.2854
 2QN  CAT  C  CH2    0  -0.554   7.7485   1.9346  -1.0781
 2QN  CBD  C  C      0   0.253   8.3698   0.7340  -1.7247
 2QN  CAJ  C  C1     0  -0.376   9.5657   0.2024  -1.2503
 2QN  CAH  C  C1     0  -0.063  10.0957  -0.9267  -1.8531
 2QN  NAU  N  N      0  -0.415   9.5254  -1.5493  -2.8799
 2QN  CAI  C  C1     0  -0.064   8.3852  -1.0425  -3.3351
 2QN  CAK  C  C1     0  -0.382   7.7755   0.0812  -2.7984
 2QN  H1   H  HCR6   0   0.271  -5.5505   2.5898   0.9449
 2QN  H2   H  HCR6   0   0.284  -7.8665   1.9727   0.4484
 2QN  H3   H  HCR6   0   0.286  -6.5235  -1.8658  -0.9552
 2QN  H4   H  HCR6   0   0.270  -4.2275  -1.2496  -0.4449
 2QN  H5   H  HNH1   0   0.405  -2.8208  -0.7494   1.1340
 2QN  H6   H  HCH2   0   0.241  -0.7162   1.2517   0.6593
 2QN  H7   H  HCH2   0   0.232  -0.9533   0.6965   2.3079
 2QN  H8   H  HCH2   0   0.225  -0.6116  -1.6744   1.5371
 2QN  H9   H  HCH2   0   0.228  -0.3359  -1.0878  -0.0942
 2QN  H10  H  HCH2   0   0.222   1.6205   0.2464   0.7227
 2QN  H11  H  HCH2   0   0.214   1.3401  -0.3324   2.3504
 2QN  H12  H  HCH2   0   0.230   1.7015  -2.6836   1.5894
 2QN  H13  H  HCH2   0   0.214   1.9897  -2.1198  -0.0417
 2QN  H14  H  HCH1   0   0.227   3.6213  -1.3694   2.4157
 2QN  H16  H  HNH1   0   0.366   3.9187  -0.6562  -0.4146
 2QN  H17  H  HNH1   0   0.366   5.3448   0.9161  -0.8724
 2QN  H18  H  HCH1   0   0.244   7.6971   1.0704   0.8748
 2QN  H20  H  HCH2   0   0.250   7.0685   2.4270  -1.7800
 2QN  H21  H  HCH2   0   0.264   8.5223   2.6588  -0.8237
 2QN  H22  H  H      0   0.259  10.0874   0.6626  -0.4197
 2QN  H23  H  H      0   0.258  11.0286  -1.3452  -1.4909
 2QN  H24  H  H      0   0.258   7.9275  -1.5563  -4.1738
 2QN  H25  H  H      0   0.256   6.8458   0.4407  -3.2218

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  deloc     1.242  0.020  1.242
 2QN  CAH  CAJ  aromatic  1.385  0.020  1.385
 2QN  CAH  NAU  aromatic  1.329  0.020  1.329
 2QN  CAJ  CBD  aromatic  1.392  0.020  1.392
 2QN  NAU  CAI  aromatic  1.328  0.020  1.328
 2QN  CAZ  OAB  deloc     1.247  0.020  1.247
 2QN  CAZ  CBG  single    1.553  0.020  1.553
 2QN  CBD  CAT  single    1.499  0.020  1.499
 2QN  CBD  CAK  aromatic  1.390  0.020  1.390
 2QN  CAT  CBG  single    1.534  0.020  1.534
 2QN  CAI  CAK  aromatic  1.387  0.020  1.387
 2QN  CBG  NAX  single    1.441  0.020  1.441
 2QN  CAP  CAR  single    1.520  0.020  1.520
 2QN  CAP  CAQ  single    1.523  0.020  1.523
 2QN  OAC  CBA  double    1.228  0.020  1.228
 2QN  NAX  CBA  single    1.364  0.020  1.364
 2QN  CAR  NAV  single    1.448  0.020  1.448
 2QN  CBA  N    single    1.361  0.020  1.361
 2QN  CB   CAQ  single    1.523  0.020  1.523
 2QN  CB   CA   single    1.528  0.020  1.528
 2QN  N    CA   single    1.445  0.020  1.445
 2QN  OAD  CBB  double    1.224  0.020  1.224
 2QN  NAV  CBB  single    1.341  0.020  1.341
 2QN  CA   C    single    1.551  0.020  1.551
 2QN  CBB  CBE  single    1.497  0.020  1.497
 2QN  C    O    deloc     1.243  0.020  1.243
 2QN  C    OXT  deloc     1.249  0.020  1.249
 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    2.102  0.020  2.102
 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  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  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  119.16  3.000
 2QN  CBE  CAN  CAL  120.85  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  119.49  3.000
 2QN  CAM  CBC  CAL  121.03  3.000
 2QN  H3   CAM  CAO  119.55  3.000
 2QN  H3   CAM  CBC  121.29  3.000
 2QN  CAO  CAM  CBC  119.16  3.000
 2QN  H4   CAO  CBE  121.07  3.000
 2QN  H4   CAO  CAM  118.13  3.000
 2QN  CBE  CAO  CAM  120.77  3.000
 2QN  CBB  CBE  CAO  122.64  3.000
 2QN  CAO  CBE  CAN  119.05  3.000
 2QN  CBB  CBE  CAN  118.28  3.000
 2QN  NAV  CBB  OAD  123.36  3.000
 2QN  NAV  CBB  CBE  115.88  3.000
 2QN  OAD  CBB  CBE  120.76  3.000
 2QN  H5   NAV  CAR  116.86  3.000
 2QN  H5   NAV  CBB  118.82  3.000
 2QN  CAR  NAV  CBB  123.50  3.000
 2QN  H7   CAR  H6   106.88  3.000
 2QN  H7   CAR  CAP  109.90  3.000
 2QN  H6   CAR  CAP  110.02  3.000
 2QN  H7   CAR  NAV  110.43  3.000
 2QN  H6   CAR  NAV  108.61  3.000
 2QN  CAP  CAR  NAV  110.91  3.000
 2QN  H9   CAP  H8   106.58  3.000
 2QN  H9   CAP  CAQ  109.81  3.000
 2QN  H8   CAP  CAQ  109.49  3.000
 2QN  H9   CAP  CAR  109.24  3.000
 2QN  H8   CAP  CAR  109.65  3.000
 2QN  CAQ  CAP  CAR  111.93  3.000
 2QN  H11  CAQ  H10  106.16  3.000
 2QN  H11  CAQ  CB   109.15  3.000
 2QN  H10  CAQ  CB   109.99  3.000
 2QN  H11  CAQ  CAP  109.51  3.000
 2QN  H10  CAQ  CAP  109.48  3.000
 2QN  CB   CAQ  CAP  112.37  3.000
 2QN  H13  CB   H12  106.15  3.000
 2QN  H13  CB   CA   109.61  3.000
 2QN  H12  CB   CA   107.96  3.000
 2QN  H13  CB   CAQ  109.51  3.000
 2QN  H12  CB   CAQ  109.47  3.000
 2QN  CA   CB   CAQ  113.84  3.000
 2QN  H14  CA   N    107.85  3.000
 2QN  H14  CA   C    107.53  3.000
 2QN  N    CA   C    113.44  3.000
 2QN  H14  CA   CB   107.52  3.000
 2QN  C    CA   CB   110.73  3.000
 2QN  N    CA   CB   109.54  3.000
 2QN  O    C    OXT  127.14  3.000
 2QN  OXT  C    CA   115.17  3.000
 2QN  O    C    CA   117.69  3.000
 2QN  H16  N    CBA  115.95  3.000
 2QN  H16  N    CA   114.51  3.000
 2QN  CBA  N    CA   120.39  3.000
 2QN  NAX  CBA  OAC  122.39  3.000
 2QN  NAX  CBA  N    114.94  3.000
 2QN  OAC  CBA  N    122.68  3.000
 2QN  H17  NAX  CBG  114.76  3.000
 2QN  H17  NAX  CBA  116.04  3.000
 2QN  CBG  NAX  CBA  119.97  3.000
 2QN  H18  CBG  CAT  107.65  3.000
 2QN  H18  CBG  CAZ  107.57  3.000
 2QN  CAT  CBG  CAZ  110.42  3.000
 2QN  H18  CBG  NAX  107.82  3.000
 2QN  CAT  CBG  NAX  109.36  3.000
 2QN  CAZ  CBG  NAX  113.79  3.000
 2QN  OAB  CAZ  OAF  127.31  3.000
 2QN  OAB  CAZ  CBG  115.18  3.000
 2QN  OAF  CAZ  CBG  117.51  3.000
 2QN  H21  CAT  H20  106.97  3.000
 2QN  H21  CAT  CBD  109.80  3.000
 2QN  H20  CAT  CBD  109.96  3.000
 2QN  H21  CAT  CBG  108.12  3.000
 2QN  H20  CAT  CBG  109.72  3.000
 2QN  CBD  CAT  CBG  112.13  3.000
 2QN  CAK  CBD  CAJ  116.82  3.000
 2QN  CAK  CBD  CAT  122.16  3.000
 2QN  CAJ  CBD  CAT  121.01  3.000
 2QN  H22  CAJ  CAH  119.70  3.000
 2QN  H22  CAJ  CBD  120.84  3.000
 2QN  CAH  CAJ  CBD  119.45  3.000
 2QN  H23  CAH  NAU  116.50  3.000
 2QN  H23  CAH  CAJ  119.89  3.000
 2QN  NAU  CAH  CAJ  123.62  3.000
 2QN  CAI  NAU  CAH  117.02  3.000
 2QN  H24  CAI  CAK  119.84  3.000
 2QN  H24  CAI  NAU  116.51  3.000
 2QN  CAK  CAI  NAU  123.64  3.000
 2QN  H25  CAK  CAI  119.69  3.000
 2QN  H25  CAK  CBD  120.87  3.000
 2QN  CAI  CAK  CBD  119.45  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  Var_01    OAD  CBB  CBE  CAN   -27.19  30.0  2
 2QN  Var_02    CAJ  CBD  CAT  CBG   -79.38  30.0  3
 2QN  Var_03    CAP  CAR  NAV  CBB  -154.36  30.0  1
 2QN  Var_04    CAQ  CAP  CAR  NAV  -179.42  30.0  2
 2QN  Var_05    CB   CAQ  CAP  CAR   179.48  30.0  3
 2QN  Var_06    CA   CB   CAQ  CAP  -178.73  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
 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-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

