# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 05:51:22 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: (2S)-2-[({(1S)-1-carboxy-2-[(2S)-oxiran-2-yl]ethyl}carbamoyl)amino]-6-[(4-iodobenzoyl)amino]hexanoic acid (non-preferred name)
#   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[C@H]2CO2)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
 2QS  2QS  '(2S)-2-[({(1S)-1-carboxy-2-[(2S)-oxiran-2-yl]ethyl}carbamoyl)amino]-6-[(4-iodobenzoyl)amino]hexanoic acid (non-preferred name)'  ligand  52  30  .  2022-09-22  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2QS
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
 2QS  CAP  C  CH2    0  -0.252   -9.9363  -1.0495  -3.1193
 2QS  OAU  O  O2     0  -0.495   -9.9035  -0.0884  -2.0739
 2QS  CBB  C  CH1    0   0.025   -8.7370  -0.8659  -2.3099
 2QS  CAQ  C  CH2    0  -0.503   -8.3565  -1.8470  -1.2385
 2QS  CBD  C  CH1    0  -0.190   -7.7242  -1.1874  -0.0122
 2QS  CAW  C  C      0   0.406   -7.4844  -2.2395   1.1007
 2QS  OAF  O  OC    -1  -0.621   -8.5183  -2.7470   1.5817
 2QS  OAB  O  O      0  -0.596   -6.3078  -2.4991   1.4059
 2QS  NAT  N  NH1    0  -0.670   -6.5305  -0.4786  -0.4085
 2QS  CAX  C  C      0   0.750   -5.9601   0.4180   0.4464
 2QS  OAC  O  O      0  -0.562   -6.5583   0.8826   1.4118
 2QS  N    N  NH1    0  -0.672   -4.6746   0.7613   0.1502
 2QS  CA   C  CH1    0  -0.178   -4.1151   1.9667   0.7196
 2QS  C    C  C      0   0.402   -4.8429   3.2576   0.2678
 2QS  OXT  O  OC    -1  -0.624   -4.5813   4.2781   0.9381
 2QS  O    O  O      0  -0.598   -5.5902   3.1827  -0.7230
 2QS  CB   C  CH2    0  -0.456   -2.6304   2.0573   0.3690
 2QS  CAM  C  CH2    0  -0.410   -1.7938   0.8950   0.8884
 2QS  CAL  C  CH2    0  -0.465   -0.3138   1.0644   0.5691
 2QS  CAN  C  CH2    0  -0.242    0.5134  -0.1049   1.0775
 2QS  NAR  N  NH1    0  -0.659    1.9178   0.0900   0.7800
 2QS  CAY  C  C      0   0.531    2.8086  -0.9113   0.7773
 2QS  OAD  O  O      0  -0.492    2.5091  -2.0721   1.0261
 2QS  CBA  C  CR6    0  -0.035    4.2202  -0.5386   0.4460
 2QS  CAJ  C  CR16   0  -0.300    4.5443   0.5607  -0.3446
 2QS  CAH  C  CR16   0  -0.231    5.8667   0.8530  -0.6471
 2QS  CAZ  C  CR6    0  -0.223    6.8701   0.0366  -0.1469
 2QS  IAG  I  I      0   0.059    8.8772   0.4745  -0.5911
 2QS  CAI  C  CR16   0  -0.228    6.5699  -1.0687   0.6374
 2QS  CAK  C  CR16   0  -0.270    5.2437  -1.3543   0.9206
 2QS  H1   H  HCH2   0   0.233  -10.5710  -1.9154  -2.9465
 2QS  H2   H  HCH2   0   0.235   -9.9755  -0.6525  -4.1302
 2QS  H3   H  HCH1   0   0.250   -7.9137  -0.3049  -2.7492
 2QS  H4   H  HCH2   0   0.247   -9.2375  -2.4061  -0.9186
 2QS  H5   H  HCH2   0   0.232   -7.6622  -2.5769  -1.6702
 2QS  H6   H  HCH1   0   0.237   -8.4356  -0.4548   0.3761
 2QS  H8   H  HNH1   0   0.366   -5.8917  -1.0120  -0.9798
 2QS  H9   H  HNH1   0   0.365   -4.3659   0.5539  -0.7881
 2QS  H10  H  HCH1   0   0.221   -4.1950   1.8984   1.8082
 2QS  H12  H  HCH2   0   0.214   -2.5151   2.1346  -0.7192
 2QS  H13  H  HCH2   0   0.232   -2.2463   2.9923   0.7830
 2QS  H14  H  HCH2   0   0.214   -1.9269   0.8091   1.9722
 2QS  H15  H  HCH2   0   0.221   -2.1523  -0.0456   0.4610
 2QS  H16  H  HCH2   0   0.228   -0.1779   1.1614  -0.5123
 2QS  H17  H  HCH2   0   0.225    0.0507   1.9956   1.0158
 2QS  H18  H  HCH2   0   0.228    0.3647  -0.2271   2.1559
 2QS  H19  H  HCH2   0   0.245    0.1786  -1.0292   0.6043
 2QS  H20  H  HNH1   0   0.417    2.2499   1.0402   0.7351
 2QS  H21  H  HCR6   0   0.294    3.7745   1.1980  -0.7612
 2QS  H22  H  HCR6   0   0.311    6.0943   1.7063  -1.2708
 2QS  H23  H  HCR6   0   0.302    7.3496  -1.7095   1.0253
 2QS  H24  H  HCR6   0   0.284    5.0095  -2.2207   1.5246

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
 2QS  OAB  CAW  deloc     1.243  0.020  1.243
 2QS  OAU  CBB  single    1.422  0.020  1.422
 2QS  OAU  CAP  single    1.420  0.020  1.420
 2QS  OAF  CAW  deloc     1.248  0.020  1.248
 2QS  CAW  CBD  single    1.550  0.020  1.550
 2QS  CBB  CAP  single    1.458  0.020  1.458
 2QS  CBB  CAQ  single    1.502  0.020  1.502
 2QS  CBD  CAQ  single    1.529  0.020  1.529
 2QS  CBD  NAT  single    1.444  0.020  1.444
 2QS  OAC  CAX  double    1.227  0.020  1.227
 2QS  NAT  CAX  single    1.364  0.020  1.364
 2QS  CAX  N    single    1.363  0.020  1.363
 2QS  CAL  CAN  single    1.520  0.020  1.520
 2QS  CAL  CAM  single    1.523  0.020  1.523
 2QS  CB   CAM  single    1.523  0.020  1.523
 2QS  CB   CA   single    1.528  0.020  1.528
 2QS  CAN  NAR  single    1.449  0.020  1.449
 2QS  N    CA   single    1.446  0.020  1.446
 2QS  CA   C    single    1.549  0.020  1.549
 2QS  OAD  CAY  double    1.224  0.020  1.224
 2QS  NAR  CAY  single    1.340  0.020  1.340
 2QS  CAY  CBA  single    1.497  0.020  1.497
 2QS  C    O    deloc     1.243  0.020  1.243
 2QS  C    OXT  deloc     1.249  0.020  1.249
 2QS  CBA  CAK  aromatic  1.392  0.020  1.392
 2QS  CBA  CAJ  aromatic  1.392  0.020  1.392
 2QS  CAK  CAI  aromatic  1.386  0.020  1.386
 2QS  CAJ  CAH  aromatic  1.388  0.020  1.388
 2QS  CAI  CAZ  aromatic  1.388  0.020  1.388
 2QS  CAH  CAZ  aromatic  1.387  0.020  1.387
 2QS  CAZ  IAG  single    2.102  0.020  2.102
 2QS  CAP  H1   single    0.970  0.020  1.090
 2QS  CAP  H2   single    0.970  0.020  1.090
 2QS  CBB  H3   single    0.970  0.020  1.090
 2QS  CAQ  H4   single    0.970  0.020  1.090
 2QS  CAQ  H5   single    0.970  0.020  1.090
 2QS  CBD  H6   single    0.970  0.020  1.090
 2QS  NAT  H8   single    0.890  0.020  1.040
 2QS  N    H9   single    0.890  0.020  1.040
 2QS  CA   H10  single    0.970  0.020  1.090
 2QS  CB   H12  single    0.970  0.020  1.090
 2QS  CB   H13  single    0.970  0.020  1.090
 2QS  CAM  H14  single    0.970  0.020  1.090
 2QS  CAM  H15  single    0.970  0.020  1.090
 2QS  CAL  H16  single    0.970  0.020  1.090
 2QS  CAL  H17  single    0.970  0.020  1.090
 2QS  CAN  H18  single    0.970  0.020  1.090
 2QS  CAN  H19  single    0.970  0.020  1.090
 2QS  NAR  H20  single    0.860  0.020  1.020
 2QS  CAJ  H21  single    0.930  0.020  1.080
 2QS  CAH  H22  single    0.930  0.020  1.080
 2QS  CAI  H23  single    0.930  0.020  1.080
 2QS  CAK  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
 2QS  H2   CAP  H1   114.69  3.000
 2QS  H2   CAP  CBB  119.99  3.000
 2QS  H1   CAP  CBB  119.48  3.000
 2QS  H2   CAP  OAU  115.99  3.000
 2QS  H1   CAP  OAU  115.80  3.000
 2QS  CBB  CAP  OAU   59.17  3.000
 2QS  CBB  OAU  CAP   61.75  3.000
 2QS  H3   CBB  CAQ  115.65  3.000
 2QS  H3   CBB  OAU  113.93  3.000
 2QS  CAQ  CBB  OAU  116.54  3.000
 2QS  H3   CBB  CAP  117.56  3.000
 2QS  CAQ  CBB  CAP  121.47  3.000
 2QS  OAU  CBB  CAP   59.09  3.000
 2QS  H5   CAQ  H4   106.60  3.000
 2QS  H5   CAQ  CBD  109.95  3.000
 2QS  H4   CAQ  CBD  108.65  3.000
 2QS  H5   CAQ  CBB  108.33  3.000
 2QS  H4   CAQ  CBB  109.83  3.000
 2QS  CBD  CAQ  CBB  113.27  3.000
 2QS  H6   CBD  NAT  107.86  3.000
 2QS  H6   CBD  CAW  107.50  3.000
 2QS  NAT  CBD  CAW  113.73  3.000
 2QS  H6   CBD  CAQ  107.75  3.000
 2QS  NAT  CBD  CAQ  109.48  3.000
 2QS  CAW  CBD  CAQ  110.30  3.000
 2QS  OAB  CAW  OAF  127.20  3.000
 2QS  OAF  CAW  CBD  115.12  3.000
 2QS  OAB  CAW  CBD  117.68  3.000
 2QS  H8   NAT  CAX  115.94  3.000
 2QS  H8   NAT  CBD  114.78  3.000
 2QS  CAX  NAT  CBD  119.77  3.000
 2QS  N    CAX  OAC  122.37  3.000
 2QS  N    CAX  NAT  115.07  3.000
 2QS  OAC  CAX  NAT  122.56  3.000
 2QS  H9   N    CA   114.78  3.000
 2QS  H9   N    CAX  116.02  3.000
 2QS  CA   N    CAX  119.30  3.000
 2QS  H10  CA   CB   107.64  3.000
 2QS  H10  CA   C    107.94  3.000
 2QS  CB   CA   C    109.88  3.000
 2QS  H10  CA   N    108.16  3.000
 2QS  C    CA   N    113.45  3.000
 2QS  CB   CA   N    109.58  3.000
 2QS  O    C    OXT  127.08  3.000
 2QS  OXT  C    CA   115.21  3.000
 2QS  O    C    CA   117.68  3.000
 2QS  H13  CB   H12  106.18  3.000
 2QS  H13  CB   CAM  109.32  3.000
 2QS  H12  CB   CAM  109.53  3.000
 2QS  H13  CB   CA   107.78  3.000
 2QS  H12  CB   CA   109.50  3.000
 2QS  CAM  CB   CA   114.21  3.000
 2QS  H15  CAM  H14  106.23  3.000
 2QS  H15  CAM  CAL  109.40  3.000
 2QS  H14  CAM  CAL  109.52  3.000
 2QS  H15  CAM  CB   110.06  3.000
 2QS  H14  CAM  CB   109.30  3.000
 2QS  CAL  CAM  CB   112.16  3.000
 2QS  H17  CAL  H16  106.64  3.000
 2QS  H17  CAL  CAN  109.67  3.000
 2QS  H16  CAL  CAN  109.34  3.000
 2QS  H17  CAL  CAM  109.42  3.000
 2QS  H16  CAL  CAM  109.74  3.000
 2QS  CAN  CAL  CAM  111.90  3.000
 2QS  H19  CAN  H18  106.91  3.000
 2QS  H19  CAN  NAR  108.81  3.000
 2QS  H18  CAN  NAR  110.41  3.000
 2QS  H19  CAN  CAL  109.86  3.000
 2QS  H18  CAN  CAL  109.95  3.000
 2QS  NAR  CAN  CAL  110.82  3.000
 2QS  H20  NAR  CAY  119.04  3.000
 2QS  H20  NAR  CAN  117.10  3.000
 2QS  CAY  NAR  CAN  122.97  3.000
 2QS  CBA  CAY  OAD  120.78  3.000
 2QS  CBA  CAY  NAR  116.18  3.000
 2QS  OAD  CAY  NAR  123.05  3.000
 2QS  CAK  CBA  CAJ  119.02  3.000
 2QS  CAJ  CBA  CAY  122.80  3.000
 2QS  CAK  CBA  CAY  118.15  3.000
 2QS  H21  CAJ  CAH  118.02  3.000
 2QS  H21  CAJ  CBA  121.18  3.000
 2QS  CAH  CAJ  CBA  120.79  3.000
 2QS  H22  CAH  CAZ  121.36  3.000
 2QS  H22  CAH  CAJ  119.51  3.000
 2QS  CAZ  CAH  CAJ  119.14  3.000
 2QS  CAI  CAZ  IAG  119.46  3.000
 2QS  IAG  CAZ  CAH  119.47  3.000
 2QS  CAI  CAZ  CAH  121.07  3.000
 2QS  H23  CAI  CAK  119.65  3.000
 2QS  H23  CAI  CAZ  121.24  3.000
 2QS  CAK  CAI  CAZ  119.11  3.000
 2QS  H24  CAK  CAI  119.10  3.000
 2QS  H24  CAK  CBA  120.03  3.000
 2QS  CAI  CAK  CBA  120.87  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
 2QS  CONST_01  CAZ  CAI  CAK  CBA     0.00   0.0  0
 2QS  CONST_02  CAZ  CAH  CAJ  CBA     0.00   0.0  0
 2QS  CONST_03  CAI  CAK  CBA  CAJ     0.00   0.0  0
 2QS  CONST_04  CAI  CAZ  CAH  CAJ     0.00   0.0  0
 2QS  CONST_05  CAK  CBA  CAJ  CAH     0.00   0.0  0
 2QS  CONST_06  CAK  CAI  CAZ  CAH     0.00   0.0  0
 2QS  CONST_07  CAI  CAK  CBA  CAY   180.00   0.0  0
 2QS  CONST_08  CAH  CAJ  CBA  CAY   180.00   0.0  0
 2QS  CONST_09  IAG  CAZ  CAH  CAJ   180.00   0.0  0
 2QS  CONST_10  CAK  CAI  CAZ  IAG   180.00   0.0  0
 2QS  CONST_11  H23  CAI  CAK  CBA   180.00   0.0  0
 2QS  CONST_12  H22  CAH  CAJ  CBA   180.00   0.0  0
 2QS  CONST_13  H24  CAK  CBA  CAJ   180.00   0.0  0
 2QS  CONST_14  H21  CAJ  CAH  CAZ   180.00   0.0  0
 2QS  CONST_15  CBA  CAY  NAR  CAN   180.00   0.0  0
 2QS  CONST_16  H20  NAR  CAY  CBA     0.00   0.0  0
 2QS  CONST_19  OAD  CAY  NAR  CAN     0.00   0.0  0
 2QS  Var_01    CAQ  CBB  OAU  CAP  -112.40  30.0  1
 2QS  Var_02    CBD  CAQ  CBB  CAP  -143.90  30.0  3
 2QS  Var_03    CAK  CBA  CAY  NAR   155.08  30.0  2
 2QS  Var_04    CAL  CAM  CB   CA   -177.35  30.0  3
 2QS  Var_05    CAN  CAL  CAM  CB   -179.43  30.0  1
 2QS  Var_06    NAR  CAN  CAL  CAM  -179.11  30.0  3
 2QS  Var_07    CAY  NAR  CAN  CAL  -161.23  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
 2QS  chir_02  CBD  CAW  CAQ  NAT  positiv
 2QS  chir_03  CA   N    CB   C    negativ
 2QS  chir_04  CBB  OAU  CAP  CAQ  both

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
 2QS  plan-1  CAY  0.020
 2QS  plan-1  CBA  0.020
 2QS  plan-1  CAJ  0.020
 2QS  plan-1  CAH  0.020
 2QS  plan-1  CAZ  0.020
 2QS  plan-1  IAG  0.020
 2QS  plan-1  CAI  0.020
 2QS  plan-1  CAK  0.020
 2QS  plan-1  H21  0.020
 2QS  plan-1  H22  0.020
 2QS  plan-1  H23  0.020
 2QS  plan-1  H24  0.020
 2QS  plan-2  CBD  0.020
 2QS  plan-2  NAT  0.020
 2QS  plan-2  CAX  0.020
 2QS  plan-2  OAC  0.020
 2QS  plan-2  N    0.020
 2QS  plan-2  CA   0.020
 2QS  plan-2  H8   0.020
 2QS  plan-2  H9   0.020
 2QS  plan-3  CAN  0.020
 2QS  plan-3  NAR  0.020
 2QS  plan-3  CAY  0.020
 2QS  plan-3  OAD  0.020
 2QS  plan-3  CBA  0.020
 2QS  plan-3  H20  0.020
 2QS  plan-4  CBD  0.020
 2QS  plan-4  CAW  0.020
 2QS  plan-4  OAF  0.020
 2QS  plan-4  OAB  0.020
 2QS  plan-5  CA   0.020
 2QS  plan-5  C    0.020
 2QS  plan-5  OXT  0.020
 2QS  plan-5  O    0.020

