# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 14:06:42 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  54  30  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.248   -9.4815  -1.5095  -3.3816
 2QS  OAU  O  O2    0  -0.486   -9.3918  -0.3391  -2.5812
 2QS  CBB  C  CH1   0   0.015   -8.3361  -1.2820  -2.5080
 2QS  CAQ  C  CH2   0  -0.521   -8.1945  -2.0188  -1.2043
 2QS  CBD  C  CH1   0  -0.177   -7.7477  -1.0927  -0.0659
 2QS  CAW  C  C     0   0.541   -7.6970  -1.8702   1.2424
 2QS  OAF  O  OH1   0  -0.591   -8.9138  -2.1084   1.7105
 2QS  OAB  O  O     0  -0.433   -6.6845  -2.2471   1.7715
 2QS  NAT  N  NH1   0  -0.685   -6.4749  -0.5052  -0.3696
 2QS  CAX  C  C     0   0.767   -5.9828   0.4805   0.4317
 2QS  OAC  O  O     0  -0.536   -6.6535   1.0074   1.3109
 2QS  N    N  NH1   0  -0.684   -4.6960   0.8418   0.1853
 2QS  CA   C  CH1   0  -0.172   -4.1364   1.9851   0.8495
 2QS  C    C  C     0   0.539   -4.8652   3.2590   0.4473
 2QS  OXT  O  OH1   0  -0.592   -4.7052   4.2165   1.3504
 2QS  O    O  O     0  -0.437   -5.4787   3.3981  -0.5788
 2QS  CB   C  CH2   0  -0.469   -2.6472   2.1175   0.5145
 2QS  CAM  C  CH2   0  -0.421   -1.8240   0.9273   0.9915
 2QS  CAL  C  CH2   0  -0.458   -0.3434   1.1001   0.6783
 2QS  CAN  C  CH2   0  -0.248    0.4682  -0.1008   1.1386
 2QS  NAR  N  NH1   0  -0.651    1.8740   0.0752   0.8410
 2QS  CAY  C  C     0   0.528    2.7064  -0.9416   0.5704
 2QS  OAD  O  O     0  -0.488    2.3587  -2.1151   0.5668
 2QS  CBA  C  CR6   0  -0.034    4.1205  -0.5625   0.2591
 2QS  CAJ  C  CR16  0  -0.279    4.4586   0.6525  -0.3300
 2QS  CAH  C  CR16  0  -0.210    5.7797   0.9518  -0.6310
 2QS  CAZ  C  CR6   0  -0.223    6.7672   0.0252  -0.3320
 2QS  IAG  I  I     0   0.069    8.7727   0.4723  -0.7726
 2QS  CAI  C  CR16  0  -0.213    6.4514  -1.1954   0.2494
 2QS  CAK  C  CR16  0  -0.259    5.1260  -1.4856   0.5312
 2QS  H1   H  HCH2  0   0.241  -10.2447  -2.2255  -3.0875
 2QS  H2   H  HCH2  0   0.243   -9.3807  -1.3618  -4.4531
 2QS  H3   H  HCH1  0   0.263   -7.4069  -0.9495  -2.9676
 2QS  H4   H  HCH2  0   0.278   -9.1451  -2.4808  -0.9326
 2QS  H5   H  HCH2  0   0.264   -7.4720  -2.8298  -1.3311
 2QS  H6   H  HCH1  0   0.295   -8.4954  -0.3028   0.0401
 2QS  H7   H  HOH1  0   0.485   -8.8661  -2.6394   2.5200
 2QS  H8   H  HNH1  0   0.398   -5.8216  -1.0667  -0.8946
 2QS  H9   H  HNH1  0   0.398   -4.2662   0.5523  -0.6800
 2QS  H10  H  HCH1  0   0.282   -4.2341   1.8623   1.9315
 2QS  H11  H  HOH1  0   0.483   -5.1336   5.0335   1.0530
 2QS  H12  H  HCH2  0   0.245   -2.5283   2.2481  -0.5662
 2QS  H13  H  HCH2  0   0.260   -2.2658   3.0286   0.9806
 2QS  H14  H  HCH2  0   0.230   -1.9609   0.8010   2.0700
 2QS  H15  H  HCH2  0   0.231   -2.1857   0.0070   0.5250
 2QS  H16  H  HCH2  0   0.233   -0.2062   1.2386  -0.3979
 2QS  H17  H  HCH2  0   0.231    0.0302   2.0080   1.1632
 2QS  H18  H  HCH2  0   0.235    0.3228  -0.2611   2.2122
 2QS  H19  H  HCH2  0   0.244    0.1191  -1.0008   0.6327
 2QS  H20  H  HNH1  0   0.405    2.2629   0.9914   1.0006
 2QS  H21  H  HCR6  0   0.270    3.6975   1.3773  -0.5893
 2QS  H22  H  HCR6  0   0.286    6.0194   1.8966  -1.0987
 2QS  H23  H  HCR6  0   0.284    7.2190  -1.9205   0.4825
 2QS  H24  H  HCR6  0   0.272    4.8779  -2.4395   0.9770

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  double    1.203  0.020  1.203
 2QS  OAU  CBB  single    1.417  0.020  1.417
 2QS  OAU  CAP  single    1.421  0.020  1.421
 2QS  OAF  CAW  single    1.325  0.020  1.325
 2QS  CAW  CBD  single    1.523  0.020  1.523
 2QS  CBB  CAP  single    1.458  0.020  1.458
 2QS  CBB  CAQ  single    1.504  0.020  1.504
 2QS  CBD  CAQ  single    1.534  0.020  1.534
 2QS  CBD  NAT  single    1.434  0.020  1.434
 2QS  OAC  CAX  double    1.225  0.020  1.225
 2QS  NAT  CAX  single    1.362  0.020  1.362
 2QS  CAX  N    single    1.359  0.020  1.359
 2QS  CAL  CAN  single    1.521  0.020  1.521
 2QS  CAL  CAM  single    1.523  0.020  1.523
 2QS  CB   CAM  single    1.524  0.020  1.524
 2QS  CB   CA   single    1.532  0.020  1.532
 2QS  CAN  NAR  single    1.448  0.020  1.448
 2QS  N    CA   single    1.436  0.020  1.436
 2QS  CA   C    single    1.522  0.020  1.522
 2QS  OAD  CAY  double    1.224  0.020  1.224
 2QS  NAR  CAY  single    1.342  0.020  1.342
 2QS  CAY  CBA  single    1.497  0.020  1.497
 2QS  C    O    double    1.204  0.020  1.204
 2QS  C    OXT  single    1.326  0.020  1.326
 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    2.101  0.020  2.101
 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  OAF  H7   single    0.850  0.020  0.980
 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  OXT  H11  single    0.850  0.020  0.980
 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   114.93  3.000
 2QS  H2   CAP  CBB  119.79  3.000
 2QS  H1   CAP  CBB  119.48  3.000
 2QS  H2   CAP  OAU  115.96  3.000
 2QS  H1   CAP  OAU  115.75  3.000
 2QS  CBB  CAP  OAU   58.97  3.000
 2QS  CBB  OAU  CAP   61.84  3.000
 2QS  H3   CBB  CAQ  115.80  3.000
 2QS  H3   CBB  OAU  114.25  3.000
 2QS  CAQ  CBB  OAU  116.15  3.000
 2QS  H3   CBB  CAP  117.72  3.000
 2QS  CAQ  CBB  CAP  121.11  3.000
 2QS  OAU  CBB  CAP   59.19  3.000
 2QS  H5   CAQ  H4   106.88  3.000
 2QS  H5   CAQ  CBD  109.96  3.000
 2QS  H4   CAQ  CBD  108.94  3.000
 2QS  H5   CAQ  CBB  108.96  3.000
 2QS  H4   CAQ  CBB  109.95  3.000
 2QS  CBD  CAQ  CBB  112.02  3.000
 2QS  H6   CBD  NAT  109.37  3.000
 2QS  H6   CBD  CAW  107.97  3.000
 2QS  NAT  CBD  CAW  111.19  3.000
 2QS  H6   CBD  CAQ  108.01  3.000
 2QS  NAT  CBD  CAQ  110.40  3.000
 2QS  CAW  CBD  CAQ  109.82  3.000
 2QS  OAB  CAW  OAF  124.13  3.000
 2QS  OAF  CAW  CBD  111.39  3.000
 2QS  OAB  CAW  CBD  124.47  3.000
 2QS  H7   OAF  CAW  110.39  3.000
 2QS  H8   NAT  CAX  118.35  3.000
 2QS  H8   NAT  CBD  117.18  3.000
 2QS  CAX  NAT  CBD  119.50  3.000
 2QS  N    CAX  OAC  122.29  3.000
 2QS  N    CAX  NAT  115.32  3.000
 2QS  OAC  CAX  NAT  122.39  3.000
 2QS  H9   N    CA   117.34  3.000
 2QS  H9   N    CAX  118.87  3.000
 2QS  CA   N    CAX  119.79  3.000
 2QS  H10  CA   CB   108.24  3.000
 2QS  H10  CA   C    108.23  3.000
 2QS  CB   CA   C    109.60  3.000
 2QS  H10  CA   N    109.48  3.000
 2QS  C    CA   N    110.96  3.000
 2QS  CB   CA   N    110.27  3.000
 2QS  O    C    OXT  123.97  3.000
 2QS  OXT  C    CA   111.52  3.000
 2QS  O    C    CA   124.48  3.000
 2QS  H11  OXT  C    110.26  3.000
 2QS  H13  CB   H12  106.49  3.000
 2QS  H13  CB   CAM  109.23  3.000
 2QS  H12  CB   CAM  110.08  3.000
 2QS  H13  CB   CA   108.56  3.000
 2QS  H12  CB   CA   109.37  3.000
 2QS  CAM  CB   CA   112.90  3.000
 2QS  H15  CAM  H14  106.38  3.000
 2QS  H15  CAM  CAL  109.23  3.000
 2QS  H14  CAM  CAL  109.71  3.000
 2QS  H15  CAM  CB   110.20  3.000
 2QS  H14  CAM  CB   109.33  3.000
 2QS  CAL  CAM  CB   111.85  3.000
 2QS  H17  CAL  H16  106.73  3.000
 2QS  H17  CAL  CAN  109.80  3.000
 2QS  H16  CAL  CAN  109.32  3.000
 2QS  H17  CAL  CAM  109.55  3.000
 2QS  H16  CAL  CAM  109.79  3.000
 2QS  CAN  CAL  CAM  111.53  3.000
 2QS  H19  CAN  H18  106.95  3.000
 2QS  H19  CAN  NAR  108.43  3.000
 2QS  H18  CAN  NAR  110.38  3.000
 2QS  H19  CAN  CAL  109.92  3.000
 2QS  H18  CAN  CAL  109.96  3.000
 2QS  NAR  CAN  CAL  111.10  3.000
 2QS  H20  NAR  CAY  118.78  3.000
 2QS  H20  NAR  CAN  116.90  3.000
 2QS  CAY  NAR  CAN  123.49  3.000
 2QS  CBA  CAY  OAD  120.70  3.000
 2QS  CBA  CAY  NAR  115.86  3.000
 2QS  OAD  CAY  NAR  123.44  3.000
 2QS  CAK  CBA  CAJ  119.08  3.000
 2QS  CAJ  CBA  CAY  122.59  3.000
 2QS  CAK  CBA  CAY  118.29  3.000
 2QS  H21  CAJ  CAH  118.23  3.000
 2QS  H21  CAJ  CBA  121.00  3.000
 2QS  CAH  CAJ  CBA  120.76  3.000
 2QS  H22  CAH  CAZ  121.29  3.000
 2QS  H22  CAH  CAJ  119.57  3.000
 2QS  CAZ  CAH  CAJ  119.14  3.000
 2QS  CAI  CAZ  IAG  119.47  3.000
 2QS  IAG  CAZ  CAH  119.48  3.000
 2QS  CAI  CAZ  CAH  121.05  3.000
 2QS  H23  CAI  CAK  119.65  3.000
 2QS  H23  CAI  CAZ  121.22  3.000
 2QS  CAK  CAI  CAZ  119.13  3.000
 2QS  H24  CAK  CAI  119.20  3.000
 2QS  H24  CAK  CBA  119.97  3.000
 2QS  CAI  CAK  CBA  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
 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_17  OAC  CAX  NAT  CBD     0.00   0.0  0
 2QS  CONST_18  CA   N    CAX  OAC     0.00   0.0  0
 2QS  CONST_19  OAD  CAY  NAR  CAN     0.00   0.0  0
 2QS  CONST_20  N    CAX  NAT  CBD   180.00   0.0  0
 2QS  CONST_21  CA   N    CAX  NAT   180.00   0.0  0
 2QS  CONST_24  H7   OAF  CAW  CBD   180.00   0.0  0
 2QS  CONST_25  H11  OXT  C    CA    180.00   0.0  0
 2QS  Var_01    CAQ  CBB  OAU  CAP  -112.18  30.0  1
 2QS  Var_02    CBD  CAQ  CBB  CAP  -136.29  30.0  3
 2QS  Var_03    CAK  CBA  CAY  NAR   152.80  30.0  2
 2QS  Var_04    CAL  CAM  CB   CA   -178.53  30.0  3
 2QS  Var_05    CAN  CAL  CAM  CB   -179.14  30.0  1
 2QS  Var_06    NAR  CAN  CAL  CAM  -179.79  30.0  3
 2QS  Var_07    CAY  NAR  CAN  CAL  -149.43  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-4  H7   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
 2QS  plan-5  H11  0.020

