# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 13:25:32 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: N~2~-{[(S)-carboxy(4-hydroxyphenyl)methyl]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](C(O)=O)c2ccc(O)cc2
#
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
 2QM  2QM  N~2~-{[(S)-carboxy(4-hydroxyphenyl)methyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine  ligand  57  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_2QM
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
 2QM  CAO  C  CR16  0  -0.265   7.2102   2.3709   0.0567
 2QM  CAI  C  CR16  0  -0.368   7.7108   3.5720  -0.4180
 2QM  CBB  C  CR6   0   0.352   8.8688   3.5872  -1.1932
 2QM  OAG  O  OH1   0  -0.627   9.4019   4.7220  -1.6810
 2QM  CAJ  C  CR16  0  -0.324   9.5133   2.3874  -1.4861
 2QM  CAP  C  CR16  0  -0.299   8.9982   1.1937  -1.0096
 2QM  CBE  C  CR6   0   0.051   7.8428   1.1659  -0.2365
 2QM  CBG  C  CH1   0  -0.200   7.3009  -0.1453   0.2836
 2QM  CAY  C  C     0   0.543   7.4095  -0.1271   1.8042
 2QM  OAF  O  O     0  -0.437   6.5357   0.2358   2.5466
 2QM  OAB  O  OH1   0  -0.587   8.6177  -0.4992   2.1982
 2QM  NAW  N  NH1   0  -0.692   5.9402  -0.3369  -0.1300
 2QM  CAZ  C  C     0   0.781   5.2806  -1.4687   0.2194
 2QM  OAC  O  O     0  -0.543   5.8212  -2.3552   0.8729
 2QM  N    N  NH1   0  -0.685   3.9843  -1.5452  -0.1819
 2QM  CA   C  CH1   0  -0.180   3.2464  -2.7610   0.0058
 2QM  C    C  C     0   0.541   3.7987  -3.8768  -0.8703
 2QM  O    O  O     0  -0.436   4.4992  -3.7061  -1.8339
 2QM  OXT  O  OH1   0  -0.592   3.3832  -5.0668  -0.4588
 2QM  CB   C  CH2   0  -0.465   1.7621  -2.5406  -0.3037
 2QM  CAR  C  CH2   0  -0.422   1.1227  -1.4753   0.5799
 2QM  CAQ  C  CH2   0  -0.431  -0.3851  -1.4039   0.3757
 2QM  CAS  C  CH2   0  -0.282  -1.0222  -0.3150   1.2312
 2QM  NAU  N  NH1   0  -0.646  -2.4610  -0.2494   1.0862
 2QM  CBA  C  C     0   0.529  -3.0666   0.4255   0.0990
 2QM  OAD  O  O     0  -0.489  -2.4595   1.1069  -0.7170
 2QM  CBD  C  CR6   0  -0.027  -4.5594   0.3226   0.0486
 2QM  CAM  C  CR16  0  -0.261  -5.2740   1.3792  -0.5088
 2QM  CAK  C  CR16  0  -0.212  -6.6564   1.3359  -0.5947
 2QM  CBC  C  CR6   0  -0.223  -7.3275   0.2101  -0.1373
 2QM  IAH  I  I     0   0.068  -9.4227   0.1275  -0.2734
 2QM  CAL  C  CR16  0  -0.210  -6.6354  -0.8636   0.4022
 2QM  CAN  C  CR16  0  -0.284  -5.2524  -0.7990   0.4948
 2QM  H1   H  HCR6  0   0.266   6.3146   2.3861   0.6665
 2QM  H2   H  HCR6  0   0.276   7.2000   4.4984  -0.1805
 2QM  H3   H  HOH1  0   0.476   8.8687   5.4830  -1.4256
 2QM  H4   H  HCR6  0   0.268  10.4121   2.3920  -2.0897
 2QM  H5   H  HCR6  0   0.261   9.5066   0.2676  -1.2484
 2QM  H6   H  HCH1  0   0.295   7.9338  -0.9534  -0.0945
 2QM  H7   H  HOH1  0   0.483   8.6982  -0.4149   3.1603
 2QM  H8   H  HNH1  0   0.406   5.4798   0.3936  -0.6481
 2QM  H9   H  HNH1  0   0.398   3.6485  -0.9004  -0.8804
 2QM  H10  H  HCH1  0   0.284   3.3316  -3.0761   1.0493
 2QM  H11  H  HOH1  0   0.484   3.6995  -5.7595  -1.0581
 2QM  H12  H  HCH2  0   0.245   1.6414  -2.2727  -1.3585
 2QM  H13  H  HCH2  0   0.258   1.2376  -3.4872  -0.1607
 2QM  H14  H  HCH2  0   0.226   1.3428  -1.6957   1.6295
 2QM  H15  H  HCH2  0   0.229   1.5640  -0.4971   0.3706
 2QM  H16  H  HCH2  0   0.230  -0.6086  -1.2113  -0.6774
 2QM  H17  H  HCH2  0   0.226  -0.8376  -2.3683   0.6240
 2QM  H18  H  HCH2  0   0.251  -0.8101  -0.4955   2.2855
 2QM  H19  H  HCH2  0   0.241  -0.5943   0.6571   0.9813
 2QM  H20  H  HNH1  0   0.410  -3.0176  -0.7440   1.7632
 2QM  H21  H  HCR6  0   0.271  -4.7517   2.2526  -0.8752
 2QM  H22  H  HCR6  0   0.285  -7.1913   2.1747  -1.0180
 2QM  H23  H  HCR6  0   0.286  -7.1509  -1.7491   0.7471
 2QM  H24  H  HCR6  0   0.270  -4.7296  -1.6562   0.8999

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
 2QM  OAF  CAY  double    1.203  0.020  1.203
 2QM  CAJ  CBB  aromatic  1.393  0.020  1.393
 2QM  CAJ  CAP  aromatic  1.385  0.020  1.385
 2QM  OAG  CBB  single    1.345  0.020  1.345
 2QM  CBB  CAI  aromatic  1.394  0.020  1.394
 2QM  CAP  CBE  aromatic  1.390  0.020  1.390
 2QM  CAY  OAB  single    1.324  0.020  1.324
 2QM  CAY  CBG  single    1.525  0.020  1.525
 2QM  CAI  CAO  aromatic  1.385  0.020  1.385
 2QM  CBE  CAO  aromatic  1.392  0.020  1.392
 2QM  CBE  CBG  single    1.511  0.020  1.511
 2QM  CBG  NAW  single    1.435  0.020  1.435
 2QM  OAC  CAZ  double    1.227  0.020  1.227
 2QM  NAW  CAZ  single    1.356  0.020  1.356
 2QM  CAQ  CAS  single    1.524  0.020  1.524
 2QM  CAQ  CAR  single    1.523  0.020  1.523
 2QM  CAS  NAU  single    1.448  0.020  1.448
 2QM  CAZ  N    single    1.359  0.020  1.359
 2QM  CAR  CB   single    1.525  0.020  1.525
 2QM  CB   CA   single    1.532  0.020  1.532
 2QM  N    CA   single    1.435  0.020  1.435
 2QM  OAD  CBA  double    1.224  0.020  1.224
 2QM  NAU  CBA  single    1.340  0.020  1.340
 2QM  CA   C    single    1.522  0.020  1.522
 2QM  CBA  CBD  single    1.497  0.020  1.497
 2QM  C    O    double    1.204  0.020  1.204
 2QM  C    OXT  single    1.326  0.020  1.326
 2QM  CBD  CAM  aromatic  1.392  0.020  1.392
 2QM  CBD  CAN  aromatic  1.392  0.020  1.392
 2QM  CAM  CAK  aromatic  1.386  0.020  1.386
 2QM  CAN  CAL  aromatic  1.388  0.020  1.388
 2QM  CAK  CBC  aromatic  1.388  0.020  1.388
 2QM  CAL  CBC  aromatic  1.387  0.020  1.387
 2QM  CBC  IAH  single    2.101  0.020  2.101
 2QM  CAO  H1   single    0.930  0.020  1.080
 2QM  CAI  H2   single    0.930  0.020  1.080
 2QM  OAG  H3   single    0.850  0.020  0.980
 2QM  CAJ  H4   single    0.930  0.020  1.080
 2QM  CAP  H5   single    0.930  0.020  1.080
 2QM  CBG  H6   single    0.970  0.020  1.090
 2QM  OAB  H7   single    0.850  0.020  0.980
 2QM  NAW  H8   single    0.860  0.020  1.020
 2QM  N    H9   single    0.890  0.020  1.040
 2QM  CA   H10  single    0.970  0.020  1.090
 2QM  OXT  H11  single    0.850  0.020  0.980
 2QM  CB   H12  single    0.970  0.020  1.090
 2QM  CB   H13  single    0.970  0.020  1.090
 2QM  CAR  H14  single    0.970  0.020  1.090
 2QM  CAR  H15  single    0.970  0.020  1.090
 2QM  CAQ  H16  single    0.970  0.020  1.090
 2QM  CAQ  H17  single    0.970  0.020  1.090
 2QM  CAS  H18  single    0.970  0.020  1.090
 2QM  CAS  H19  single    0.970  0.020  1.090
 2QM  NAU  H20  single    0.860  0.020  1.020
 2QM  CAM  H21  single    0.930  0.020  1.080
 2QM  CAK  H22  single    0.930  0.020  1.080
 2QM  CAL  H23  single    0.930  0.020  1.080
 2QM  CAN  H24  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
 2QM  H1   CAO  CBE  120.41  3.000
 2QM  H1   CAO  CAI  118.64  3.000
 2QM  CBE  CAO  CAI  120.94  3.000
 2QM  H2   CAI  CBB  120.27  3.000
 2QM  H2   CAI  CAO  119.71  3.000
 2QM  CBB  CAI  CAO  120.02  3.000
 2QM  CAJ  CBB  OAG  117.84  3.000
 2QM  OAG  CBB  CAI  122.69  3.000
 2QM  CAJ  CBB  CAI  119.47  3.000
 2QM  H3   OAG  CBB  110.54  3.000
 2QM  H4   CAJ  CAP  120.29  3.000
 2QM  H4   CAJ  CBB  119.84  3.000
 2QM  CAP  CAJ  CBB  119.87  3.000
 2QM  H5   CAP  CBE  119.70  3.000
 2QM  H5   CAP  CAJ  119.12  3.000
 2QM  CBE  CAP  CAJ  121.18  3.000
 2QM  CBG  CBE  CAP  120.45  3.000
 2QM  CBG  CBE  CAO  121.04  3.000
 2QM  CAP  CBE  CAO  118.51  3.000
 2QM  H6   CBG  NAW  110.51  3.000
 2QM  H6   CBG  CAY  108.20  3.000
 2QM  NAW  CBG  CAY  110.89  3.000
 2QM  H6   CBG  CBE  108.34  3.000
 2QM  NAW  CBG  CBE  110.90  3.000
 2QM  CAY  CBG  CBE  107.90  3.000
 2QM  OAB  CAY  OAF  124.33  3.000
 2QM  OAB  CAY  CBG  111.00  3.000
 2QM  OAF  CAY  CBG  124.58  3.000
 2QM  H7   OAB  CAY  110.28  3.000
 2QM  H8   NAW  CAZ  121.04  3.000
 2QM  H8   NAW  CBG  119.01  3.000
 2QM  CAZ  NAW  CBG  119.90  3.000
 2QM  N    CAZ  OAC  122.47  3.000
 2QM  N    CAZ  NAW  115.79  3.000
 2QM  OAC  CAZ  NAW  121.74  3.000
 2QM  H9   N    CA   117.47  3.000
 2QM  H9   N    CAZ  119.09  3.000
 2QM  CA   N    CAZ  119.98  3.000
 2QM  H10  CA   CB   108.04  3.000
 2QM  H10  CA   C    108.04  3.000
 2QM  CB   CA   C    109.92  3.000
 2QM  H10  CA   N    109.21  3.000
 2QM  C    CA   N    111.05  3.000
 2QM  CB   CA   N    110.49  3.000
 2QM  OXT  C    O    123.93  3.000
 2QM  OXT  C    CA   111.44  3.000
 2QM  O    C    CA   124.61  3.000
 2QM  H11  OXT  C    110.33  3.000
 2QM  H13  CB   H12  106.58  3.000
 2QM  H13  CB   CAR  109.18  3.000
 2QM  H12  CB   CAR  109.95  3.000
 2QM  H13  CB   CA   108.32  3.000
 2QM  H12  CB   CA   109.67  3.000
 2QM  CAR  CB   CA   112.94  3.000
 2QM  H15  CAR  H14  106.40  3.000
 2QM  H15  CAR  CAQ  109.39  3.000
 2QM  H14  CAR  CAQ  109.69  3.000
 2QM  H15  CAR  CB   110.18  3.000
 2QM  H14  CAR  CB   109.31  3.000
 2QM  CAQ  CAR  CB   111.73  3.000
 2QM  H17  CAQ  H16  106.82  3.000
 2QM  H17  CAQ  CAS  109.24  3.000
 2QM  H16  CAQ  CAS  109.22  3.000
 2QM  H17  CAQ  CAR  109.73  3.000
 2QM  H16  CAQ  CAR  109.85  3.000
 2QM  CAS  CAQ  CAR  111.84  3.000
 2QM  H19  CAS  H18  107.02  3.000
 2QM  H19  CAS  NAU  109.06  3.000
 2QM  H18  CAS  NAU  107.32  3.000
 2QM  H19  CAS  CAQ  110.12  3.000
 2QM  H18  CAS  CAQ  110.06  3.000
 2QM  NAU  CAS  CAQ  113.05  3.000
 2QM  H20  NAU  CBA  119.54  3.000
 2QM  H20  NAU  CAS  117.39  3.000
 2QM  CBA  NAU  CAS  123.07  3.000
 2QM  CBD  CBA  OAD  120.68  3.000
 2QM  CBD  CBA  NAU  116.14  3.000
 2QM  OAD  CBA  NAU  123.17  3.000
 2QM  CAN  CBD  CAM  118.98  3.000
 2QM  CAN  CBD  CBA  122.75  3.000
 2QM  CAM  CBD  CBA  118.24  3.000
 2QM  H21  CAM  CAK  119.07  3.000
 2QM  H21  CAM  CBD  120.05  3.000
 2QM  CAK  CAM  CBD  120.88  3.000
 2QM  H22  CAK  CBC  121.27  3.000
 2QM  H22  CAK  CAM  119.58  3.000
 2QM  CBC  CAK  CAM  119.16  3.000
 2QM  CAL  CBC  IAH  119.50  3.000
 2QM  IAH  CBC  CAK  119.51  3.000
 2QM  CAL  CBC  CAK  120.98  3.000
 2QM  H23  CAL  CAN  119.48  3.000
 2QM  H23  CAL  CBC  121.35  3.000
 2QM  CAN  CAL  CBC  119.17  3.000
 2QM  H24  CAN  CAL  117.99  3.000
 2QM  H24  CAN  CBD  121.17  3.000
 2QM  CAL  CAN  CBD  120.82  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
 2QM  CONST_01  CAJ  CBB  CAI  CAO     0.00   0.0  0
 2QM  CONST_02  CAJ  CAP  CBE  CAO     0.00   0.0  0
 2QM  CONST_03  CAP  CAJ  CBB  CAI     0.00   0.0  0
 2QM  CONST_04  CAP  CBE  CAO  CAI     0.00   0.0  0
 2QM  CONST_05  CBE  CAP  CAJ  CBB     0.00   0.0  0
 2QM  CONST_06  CBE  CAO  CAI  CBB     0.00   0.0  0
 2QM  CONST_07  CBC  CAK  CAM  CBD     0.00   0.0  0
 2QM  CONST_08  CBC  CAL  CAN  CBD     0.00   0.0  0
 2QM  CONST_09  CAL  CAN  CBD  CAM     0.00   0.0  0
 2QM  CONST_10  CAL  CBC  CAK  CAM     0.00   0.0  0
 2QM  CONST_11  CAN  CBD  CAM  CAK     0.00   0.0  0
 2QM  CONST_12  CAN  CAL  CBC  CAK     0.00   0.0  0
 2QM  CONST_13  OAG  CBB  CAI  CAO   180.00   0.0  0
 2QM  CONST_14  CBG  CBE  CAO  CAI   180.00   0.0  0
 2QM  CONST_15  CAP  CAJ  CBB  OAG   180.00   0.0  0
 2QM  CONST_16  CBG  CBE  CAP  CAJ   180.00   0.0  0
 2QM  CONST_17  CAK  CAM  CBD  CBA   180.00   0.0  0
 2QM  CONST_18  CAL  CAN  CBD  CBA   180.00   0.0  0
 2QM  CONST_19  IAH  CBC  CAK  CAM   180.00   0.0  0
 2QM  CONST_20  CAN  CAL  CBC  IAH   180.00   0.0  0
 2QM  CONST_21  H5   CAP  CBE  CAO   180.00   0.0  0
 2QM  CONST_22  H4   CAJ  CBB  CAI   180.00   0.0  0
 2QM  CONST_23  H1   CAO  CAI  CBB   180.00   0.0  0
 2QM  CONST_24  H2   CAI  CBB  CAJ   180.00   0.0  0
 2QM  CONST_25  H22  CAK  CAM  CBD   180.00   0.0  0
 2QM  CONST_26  H23  CAL  CAN  CBD   180.00   0.0  0
 2QM  CONST_27  H24  CAN  CBD  CAM   180.00   0.0  0
 2QM  CONST_28  H21  CAM  CAK  CBC   180.00   0.0  0
 2QM  CONST_29  CBD  CBA  NAU  CAS   180.00   0.0  0
 2QM  CONST_30  H20  NAU  CBA  CBD     0.00   0.0  0
 2QM  CONST_31  OAC  CAZ  NAW  CBG     0.00   0.0  0
 2QM  CONST_32  CA   N    CAZ  OAC     0.00   0.0  0
 2QM  CONST_33  OAD  CBA  NAU  CAS     0.00   0.0  0
 2QM  CONST_34  N    CAZ  NAW  CBG   180.00   0.0  0
 2QM  CONST_35  CA   N    CAZ  NAW   180.00   0.0  0
 2QM  CONST_36  H8   NAW  CAZ  OAC   180.00   0.0  0
 2QM  CONST_37  H9   N    CAZ  OAC   180.00   0.0  0
 2QM  CONST_38  H7   OAB  CAY  CBG   180.00   0.0  0
 2QM  CONST_39  H11  OXT  C    CA    180.00   0.0  0
 2QM  Var_01    CAM  CBD  CBA  NAU   152.35  30.0  2
 2QM  Var_02    CAQ  CAR  CB   CA   -172.66  30.0  2
 2QM  Var_03    CAS  CAQ  CAR  CB   -178.52  30.0  1
 2QM  Var_04    NAU  CAS  CAQ  CAR  -178.34  30.0  3
 2QM  Var_05    CBA  NAU  CAS  CAQ   -84.16  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
 2QM  chir_01  CBG  CAY  CBE  NAW  positiv
 2QM  chir_02  CA   N    CB   C    negativ

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
 2QM  plan-1  CAO  0.020
 2QM  plan-1  CAI  0.020
 2QM  plan-1  CBB  0.020
 2QM  plan-1  OAG  0.020
 2QM  plan-1  CAJ  0.020
 2QM  plan-1  CAP  0.020
 2QM  plan-1  CBE  0.020
 2QM  plan-1  CBG  0.020
 2QM  plan-1  H1   0.020
 2QM  plan-1  H2   0.020
 2QM  plan-1  H4   0.020
 2QM  plan-1  H5   0.020
 2QM  plan-2  CA   0.020
 2QM  plan-2  C    0.020
 2QM  plan-2  O    0.020
 2QM  plan-2  OXT  0.020
 2QM  plan-2  H11  0.020
 2QM  plan-3  CBA  0.020
 2QM  plan-3  CBD  0.020
 2QM  plan-3  CAM  0.020
 2QM  plan-3  CAK  0.020
 2QM  plan-3  CBC  0.020
 2QM  plan-3  IAH  0.020
 2QM  plan-3  CAL  0.020
 2QM  plan-3  CAN  0.020
 2QM  plan-3  H21  0.020
 2QM  plan-3  H22  0.020
 2QM  plan-3  H23  0.020
 2QM  plan-3  H24  0.020
 2QM  plan-4  CBG  0.020
 2QM  plan-4  NAW  0.020
 2QM  plan-4  CAZ  0.020
 2QM  plan-4  OAC  0.020
 2QM  plan-4  N    0.020
 2QM  plan-4  CA   0.020
 2QM  plan-4  H8   0.020
 2QM  plan-4  H9   0.020
 2QM  plan-5  CAS  0.020
 2QM  plan-5  NAU  0.020
 2QM  plan-5  CBA  0.020
 2QM  plan-5  OAD  0.020
 2QM  plan-5  CBD  0.020
 2QM  plan-5  H20  0.020
 2QM  plan-6  CBG  0.020
 2QM  plan-6  CAY  0.020
 2QM  plan-6  OAF  0.020
 2QM  plan-6  OAB  0.020
 2QM  plan-6  H7   0.020

