# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 13:32:25 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1ccccc1CN(CCN(CC(O)=O)Cc2cccc(O)c2O)CC(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
 9YK  9YK  '2-[2-[[2,3-bis(oxidanyl)phenyl]methyl-(2-hydroxy-2-oxoethyl)amino]ethyl-[(2-methylsulfanylphenyl)methyl]amino]ethanoic acid'  ligand  56  30  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9YK
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
 9YK  OAX  O  OH1   0  -0.649  -6.8565   0.7561   0.5259
 9YK  CAR  C  CR6   0   0.266  -5.6168   1.2902   0.6353
 9YK  CAS  C  CR6   0   0.260  -4.5801   0.3774   0.8839
 9YK  OAY  O  OH1   0  -0.629  -4.8375  -0.9461   0.9839
 9YK  CAQ  C  CR16  0  -0.385  -5.3413   2.6403   0.5118
 9YK  CAE  C  CR16  0  -0.264  -4.0315   3.0940   0.6333
 9YK  CAF  C  CR16  0  -0.310  -3.0126   2.1937   0.8813
 9YK  CAG  C  CR6   0  -0.001  -3.2724   0.8291   1.0180
 9YK  CAH  C  CH2   0  -0.340  -2.1267  -0.1151   1.2779
 9YK  N    N  NT    0  -0.413  -1.3717  -0.3883   0.0628
 9YK  CA   C  CH2   0  -0.449  -2.1317  -1.0198  -0.9777
 9YK  C    C  C     0   0.537  -2.6322  -2.4283  -0.7127
 9YK  OXT  O  OH1   0  -0.599  -3.4745  -2.8180  -1.6660
 9YK  O    O  O     0  -0.443  -2.3090  -3.1352   0.2080
 9YK  CAJ  C  CH2   0  -0.268  -0.0435  -0.9202   0.3130
 9YK  CAK  C  CH2   0  -0.306   0.8883  -0.7430  -0.8812
 9YK  NAL  N  NT    0  -0.406   2.2432  -1.1504  -0.5366
 9YK  CAT  C  CH2   0  -0.416   2.4005  -2.5789  -0.6410
 9YK  CAZ  C  C     0   0.522   3.5273  -3.1390   0.1962
 9YK  OBD  O  OH1   0  -0.599   3.7940  -4.3923  -0.1658
 9YK  OBA  O  O     0  -0.419   4.0964  -2.5715   1.0898
 9YK  CAM  C  CH2   0  -0.341   3.2714  -0.4634  -1.3016
 9YK  CAN  C  CR6   0   0.087   3.1986   1.0350  -1.1951
 9YK  CAO  C  CR16  0  -0.298   3.0717   1.7879  -2.3568
 9YK  CAP  C  CR16  0  -0.259   3.0280   3.1749  -2.3299
 9YK  CAW  C  CR16  0  -0.255   3.0990   3.8250  -1.1089
 9YK  CAV  C  CR16  0  -0.249   3.2146   3.0947   0.0658
 9YK  CAU  C  CR6   0  -0.161   3.2721   1.7020   0.0394
 9YK  SBB  S  S2    0   0.078   3.4401   0.7374   1.5086
 9YK  CBE  C  CH3   0  -0.804   3.9896   1.9651   2.7145
 9YK  H1   H  HOH1  0   0.482  -7.5076   1.4388   0.3304
 9YK  H2   H  HOH1  0   0.472  -5.7687  -1.1206   0.8034
 9YK  H3   H  HCR6  0   0.271  -6.1483   3.3390   0.3219
 9YK  H4   H  HCR6  0   0.252  -3.8202   4.1505   0.5362
 9YK  H5   H  HCR6  0   0.244  -1.9911   2.5416   0.9775
 9YK  H6   H  HCH2  0   0.248  -1.4434   0.3766   1.9739
 9YK  H7   H  HCH2  0   0.230  -2.4729  -1.0232   1.7840
 9YK  H9   H  HCH2  0   0.289  -2.9950  -0.3969  -1.2300
 9YK  H10  H  HCH2  0   0.293  -1.5452  -1.0587  -1.9006
 9YK  H11  H  HOH1  0   0.477  -3.7665  -3.7262  -1.4972
 9YK  H12  H  HCH2  0   0.235   0.3941  -0.3432   1.1307
 9YK  H13  H  HCH2  0   0.206  -0.0573  -1.9654   0.6489
 9YK  H14  H  HCH2  0   0.212   0.5292  -1.2816  -1.7715
 9YK  H15  H  HCH2  0   0.249   0.8858   0.3158  -1.1404
 9YK  H17  H  HCH2  0   0.295   1.4925  -3.0768  -0.2863
 9YK  H18  H  HCH2  0   0.248   2.5294  -2.9170  -1.6823
 9YK  H19  H  HOH1  0   0.481   4.4848  -4.7614   0.4043
 9YK  H20  H  HCH2  0   0.259   4.2450  -0.7953  -0.9281
 9YK  H21  H  HCH2  0   0.226   3.2358  -0.7401  -2.3678
 9YK  H22  H  HCR6  0   0.251   3.0066   1.2685  -3.3060
 9YK  H23  H  HCR6  0   0.254   2.9342   3.7368  -3.2497
 9YK  H24  H  HCR6  0   0.257   3.0604   4.9055  -1.0591
 9YK  H25  H  HCR6  0   0.262   3.2605   3.6318   1.0027
 9YK  H26  H  HCH3  0   0.268   4.8799   2.4954   2.3790
 9YK  H27  H  HCH3  0   0.265   3.2094   2.6802   2.9693
 9YK  H28  H  HCH3  0   0.286   4.2385   1.4024   3.6129

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
 9YK  OBA  CAZ  double    1.202  0.020  1.202
 9YK  CAF  CAE  aromatic  1.382  0.020  1.382
 9YK  CAF  CAG  aromatic  1.396  0.020  1.396
 9YK  CAH  CAG  single    1.507  0.020  1.507
 9YK  CAH  N    single    1.456  0.020  1.456
 9YK  CAE  CAQ  aromatic  1.392  0.020  1.392
 9YK  CAG  CAS  aromatic  1.390  0.020  1.390
 9YK  CAJ  N    single    1.452  0.020  1.452
 9YK  CAJ  CAK  single    1.525  0.020  1.525
 9YK  CAZ  OBD  single    1.332  0.020  1.332
 9YK  CAZ  CAT  single    1.511  0.020  1.511
 9YK  N    CA   single    1.435  0.020  1.435
 9YK  CAQ  CAR  aromatic  1.383  0.020  1.383
 9YK  CAS  CAR  aromatic  1.404  0.020  1.404
 9YK  CAS  OAY  single    1.352  0.020  1.352
 9YK  CAT  NAL  single    1.441  0.020  1.441
 9YK  CAK  NAL  single    1.456  0.020  1.456
 9YK  CA   C    single    1.518  0.020  1.518
 9YK  CAR  OAX  single    1.354  0.020  1.354
 9YK  NAL  CAM  single    1.454  0.020  1.454
 9YK  C    O    double    1.205  0.020  1.205
 9YK  C    OXT  single    1.331  0.020  1.331
 9YK  CAO  CAP  aromatic  1.388  0.020  1.388
 9YK  CAO  CAN  aromatic  1.390  0.020  1.390
 9YK  CAP  CAW  aromatic  1.385  0.020  1.385
 9YK  CBE  SBB  single    1.806  0.020  1.806
 9YK  CAM  CAN  single    1.504  0.020  1.504
 9YK  CAN  CAU  aromatic  1.405  0.020  1.405
 9YK  CAW  CAV  aromatic  1.388  0.020  1.388
 9YK  CAU  CAV  aromatic  1.394  0.020  1.394
 9YK  CAU  SBB  single    1.766  0.020  1.766
 9YK  OAX  H1   single    0.850  0.020  0.980
 9YK  OAY  H2   single    0.850  0.020  0.980
 9YK  CAQ  H3   single    0.930  0.020  1.080
 9YK  CAE  H4   single    0.930  0.020  1.080
 9YK  CAF  H5   single    0.930  0.020  1.080
 9YK  CAH  H6   single    0.970  0.020  1.090
 9YK  CAH  H7   single    0.970  0.020  1.090
 9YK  CA   H9   single    0.970  0.020  1.090
 9YK  CA   H10  single    0.970  0.020  1.090
 9YK  OXT  H11  single    0.850  0.020  0.980
 9YK  CAJ  H12  single    0.970  0.020  1.090
 9YK  CAJ  H13  single    0.970  0.020  1.090
 9YK  CAK  H14  single    0.970  0.020  1.090
 9YK  CAK  H15  single    0.970  0.020  1.090
 9YK  CAT  H17  single    0.970  0.020  1.090
 9YK  CAT  H18  single    0.970  0.020  1.090
 9YK  OBD  H19  single    0.850  0.020  0.980
 9YK  CAM  H20  single    0.970  0.020  1.090
 9YK  CAM  H21  single    0.970  0.020  1.090
 9YK  CAO  H22  single    0.930  0.020  1.080
 9YK  CAP  H23  single    0.930  0.020  1.080
 9YK  CAW  H24  single    0.930  0.020  1.080
 9YK  CAV  H25  single    0.930  0.020  1.080
 9YK  CBE  H26  single    0.970  0.020  1.090
 9YK  CBE  H27  single    0.970  0.020  1.090
 9YK  CBE  H28  single    0.970  0.020  1.090

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
 9YK  H1   OAX  CAR  110.83  3.000
 9YK  CAQ  CAR  CAS  120.23  3.000
 9YK  CAS  CAR  OAX  115.72  3.000
 9YK  CAQ  CAR  OAX  124.05  3.000
 9YK  CAG  CAS  OAY  119.35  3.000
 9YK  OAY  CAS  CAR  120.61  3.000
 9YK  CAG  CAS  CAR  120.04  3.000
 9YK  H2   OAY  CAS  110.31  3.000
 9YK  H3   CAQ  CAE  120.38  3.000
 9YK  H3   CAQ  CAR  119.76  3.000
 9YK  CAE  CAQ  CAR  119.86  3.000
 9YK  H4   CAE  CAF  120.55  3.000
 9YK  H4   CAE  CAQ  119.64  3.000
 9YK  CAF  CAE  CAQ  119.82  3.000
 9YK  H5   CAF  CAG  118.73  3.000
 9YK  H5   CAF  CAE  120.13  3.000
 9YK  CAG  CAF  CAE  121.15  3.000
 9YK  CAH  CAG  CAF  119.21  3.000
 9YK  CAH  CAG  CAS  121.88  3.000
 9YK  CAF  CAG  CAS  118.90  3.000
 9YK  H7   CAH  H6   106.05  3.000
 9YK  H7   CAH  N    113.18  3.000
 9YK  H6   CAH  N    106.96  3.000
 9YK  H7   CAH  CAG  111.02  3.000
 9YK  H6   CAH  CAG  107.66  3.000
 9YK  N    CAH  CAG  111.57  3.000
 9YK  CAJ  N    CA   116.62  3.000
 9YK  CA   N    CAH  114.39  3.000
 9YK  CAJ  N    CAH  113.52  3.000
 9YK  H10  CA   H9   104.39  3.000
 9YK  H10  CA   C    106.92  3.000
 9YK  H9   CA   C    107.96  3.000
 9YK  H10  CA   N    110.08  3.000
 9YK  H9   CA   N    109.55  3.000
 9YK  C    CA   N    117.15  3.000
 9YK  O    C    OXT  123.06  3.000
 9YK  OXT  C    CA   110.82  3.000
 9YK  O    C    CA   126.11  3.000
 9YK  H11  OXT  C    109.91  3.000
 9YK  H13  CAJ  H12  106.19  3.000
 9YK  H13  CAJ  CAK  110.96  3.000
 9YK  H12  CAJ  CAK  106.27  3.000
 9YK  H13  CAJ  N    112.94  3.000
 9YK  H12  CAJ  N    107.57  3.000
 9YK  CAK  CAJ  N    112.41  3.000
 9YK  H15  CAK  H14  106.40  3.000
 9YK  H15  CAK  NAL  109.28  3.000
 9YK  H14  CAK  NAL  110.98  3.000
 9YK  H15  CAK  CAJ  107.31  3.000
 9YK  H14  CAK  CAJ  112.16  3.000
 9YK  NAL  CAK  CAJ  110.53  3.000
 9YK  CAM  NAL  CAT  110.68  3.000
 9YK  CAM  NAL  CAK  113.65  3.000
 9YK  CAT  NAL  CAK  111.21  3.000
 9YK  H18  CAT  H17  105.28  3.000
 9YK  H18  CAT  CAZ  108.80  3.000
 9YK  H17  CAT  CAZ  105.69  3.000
 9YK  H18  CAT  NAL  112.66  3.000
 9YK  H17  CAT  NAL  109.69  3.000
 9YK  CAZ  CAT  NAL  114.12  3.000
 9YK  OBA  CAZ  OBD  123.48  3.000
 9YK  OBD  CAZ  CAT  110.34  3.000
 9YK  OBA  CAZ  CAT  126.15  3.000
 9YK  H19  OBD  CAZ  109.97  3.000
 9YK  H21  CAM  H20  106.42  3.000
 9YK  H21  CAM  CAN  108.49  3.000
 9YK  H20  CAM  CAN  108.72  3.000
 9YK  H21  CAM  NAL  111.56  3.000
 9YK  H20  CAM  NAL  107.83  3.000
 9YK  CAN  CAM  NAL  113.53  3.000
 9YK  CAU  CAN  CAO  118.81  3.000
 9YK  CAU  CAN  CAM  122.18  3.000
 9YK  CAO  CAN  CAM  119.00  3.000
 9YK  H22  CAO  CAP  119.60  3.000
 9YK  H22  CAO  CAN  118.54  3.000
 9YK  CAP  CAO  CAN  121.86  3.000
 9YK  H23  CAP  CAW  120.67  3.000
 9YK  H23  CAP  CAO  120.35  3.000
 9YK  CAW  CAP  CAO  118.98  3.000
 9YK  H24  CAW  CAV  119.29  3.000
 9YK  H24  CAW  CAP  120.49  3.000
 9YK  CAV  CAW  CAP  120.22  3.000
 9YK  H25  CAV  CAU  120.73  3.000
 9YK  H25  CAV  CAW  118.40  3.000
 9YK  CAU  CAV  CAW  120.87  3.000
 9YK  SBB  CAU  CAV  122.27  3.000
 9YK  SBB  CAU  CAN  118.48  3.000
 9YK  CAV  CAU  CAN  119.25  3.000
 9YK  CBE  SBB  CAU  102.31  3.000
 9YK  H28  CBE  H27  108.07  3.000
 9YK  H28  CBE  H26  108.59  3.000
 9YK  H27  CBE  H26  109.76  3.000
 9YK  H28  CBE  SBB  105.61  3.000
 9YK  H27  CBE  SBB  112.62  3.000
 9YK  H26  CBE  SBB  111.95  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
 9YK  CONST_01  CAF  CAE  CAQ  CAR     0.00   0.0  0
 9YK  CONST_02  CAF  CAG  CAS  CAR     0.00   0.0  0
 9YK  CONST_03  CAE  CAF  CAG  CAS     0.00   0.0  0
 9YK  CONST_04  CAE  CAQ  CAR  CAS     0.00   0.0  0
 9YK  CONST_05  CAG  CAF  CAE  CAQ     0.00   0.0  0
 9YK  CONST_06  CAG  CAS  CAR  CAQ     0.00   0.0  0
 9YK  CONST_07  CAW  CAP  CAO  CAN     0.00   0.0  0
 9YK  CONST_08  CAW  CAV  CAU  CAN     0.00   0.0  0
 9YK  CONST_09  CAV  CAW  CAP  CAO     0.00   0.0  0
 9YK  CONST_10  CAV  CAU  CAN  CAO     0.00   0.0  0
 9YK  CONST_11  CAU  CAN  CAO  CAP     0.00   0.0  0
 9YK  CONST_12  CAU  CAV  CAW  CAP     0.00   0.0  0
 9YK  CONST_13  CAE  CAQ  CAR  OAX   180.00   0.0  0
 9YK  CONST_14  CAG  CAS  CAR  OAX   180.00   0.0  0
 9YK  CONST_15  CAH  CAG  CAS  CAR   180.00   0.0  0
 9YK  CONST_16  CAF  CAG  CAS  OAY   180.00   0.0  0
 9YK  CONST_17  CAQ  CAR  CAS  OAY   180.00   0.0  0
 9YK  CONST_18  CAH  CAG  CAF  CAE   180.00   0.0  0
 9YK  CONST_19  CAP  CAO  CAN  CAM   180.00   0.0  0
 9YK  CONST_20  CAV  CAU  CAN  CAM   180.00   0.0  0
 9YK  CONST_21  SBB  CAU  CAN  CAO   180.00   0.0  0
 9YK  CONST_22  SBB  CAU  CAV  CAW   180.00   0.0  0
 9YK  CONST_23  H4   CAE  CAQ  CAR   180.00   0.0  0
 9YK  CONST_24  H5   CAF  CAG  CAS   180.00   0.0  0
 9YK  CONST_25  H3   CAQ  CAR  CAS   180.00   0.0  0
 9YK  CONST_26  H23  CAP  CAO  CAN   180.00   0.0  0
 9YK  CONST_27  H25  CAV  CAU  CAN   180.00   0.0  0
 9YK  CONST_28  H24  CAW  CAP  CAO   180.00   0.0  0
 9YK  CONST_29  H22  CAO  CAP  CAW   180.00   0.0  0
 9YK  CONST_30  H11  OXT  C    CA    180.00   0.0  0
 9YK  CONST_31  H19  OBD  CAZ  CAT   180.00   0.0  0
 9YK  Var_01    N    CAH  CAG  CAS   101.10  30.0  2
 9YK  Var_02    CAO  CAN  CAM  NAL  -123.06  30.0  2
 9YK  Var_03    CAJ  N    CAH  CAG   161.26  30.0  3
 9YK  Var_04    CAN  CAM  NAL  CAK    56.20  30.0  3
 9YK  Var_05    H26  CBE  SBB  CAU   -54.66  30.0  3
 9YK  Var_06    CAK  CAJ  N    CAH  -159.92  30.0  1
 9YK  Var_07    C    CA   N    CAH   -65.89  30.0  3
 9YK  Var_08    NAL  CAK  CAJ  N     173.60  30.0  3
 9YK  Var_09    O    C    CA   N     -10.50  30.0  3
 9YK  Var_10    CAT  NAL  CAK  CAJ    82.19  30.0  3
 9YK  Var_11    CAZ  CAT  NAL  CAK  -156.56  30.0  2
 9YK  Var_12    OBA  CAZ  CAT  NAL    15.16  30.0  2

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
 9YK  plan-1  OAX  0.020
 9YK  plan-1  CAR  0.020
 9YK  plan-1  CAS  0.020
 9YK  plan-1  OAY  0.020
 9YK  plan-1  CAQ  0.020
 9YK  plan-1  CAE  0.020
 9YK  plan-1  CAF  0.020
 9YK  plan-1  CAG  0.020
 9YK  plan-1  CAH  0.020
 9YK  plan-1  H3   0.020
 9YK  plan-1  H4   0.020
 9YK  plan-1  H5   0.020
 9YK  plan-2  CAM  0.020
 9YK  plan-2  CAN  0.020
 9YK  plan-2  CAO  0.020
 9YK  plan-2  CAP  0.020
 9YK  plan-2  CAW  0.020
 9YK  plan-2  CAV  0.020
 9YK  plan-2  CAU  0.020
 9YK  plan-2  SBB  0.020
 9YK  plan-2  H22  0.020
 9YK  plan-2  H23  0.020
 9YK  plan-2  H24  0.020
 9YK  plan-2  H25  0.020
 9YK  plan-3  CA   0.020
 9YK  plan-3  C    0.020
 9YK  plan-3  OXT  0.020
 9YK  plan-3  O    0.020
 9YK  plan-3  H11  0.020
 9YK  plan-4  CAT  0.020
 9YK  plan-4  CAZ  0.020
 9YK  plan-4  OBD  0.020
 9YK  plan-4  OBA  0.020
 9YK  plan-4  H19  0.020

