# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 03:30:57 2020
#   Inital geometry file: a 155 line input string
#   Ligand name: N-acetyl-L-phenylalanyl-4-[(5S)-1,1-dioxido-3-oxoisothiazolidin-5-yl]-L-phenylalaninamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H](Cc1ccccc1)C(=O)N[C@@H](Cc2ccc(cc2)[C@@H]3CC(=O)N[S]3(=O)=O)C(N)=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
 IZD  IZD  N-acetyl-L-phenylalanyl-4-[(5S)-1,1-dioxido-3-oxoisothiazolidin-5-yl]-L-phenylalaninamide  ligand  60  34  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IZD
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
 IZD  C1    C  CH1   0  -0.599   -3.8972   1.6957  -3.2170
 IZD  C2    C  CH2   0  -0.573   -4.5256   1.8161  -4.5998
 IZD  C3    C  C     0   0.580   -5.4590   0.6408  -4.7977
 IZD  N4    N  NC1   0  -0.790   -5.8138   0.1146  -3.5833
 IZD  S5    S  S     0   1.421   -5.2267   0.9401  -2.2415
 IZD  O6    O  OS    0  -0.635   -4.7438  -0.0157  -1.2635
 IZD  O7    O  OS    0  -0.612   -6.1797   1.9446  -1.8137
 IZD  O9    O  O     0  -0.420   -5.8564   0.2258  -5.8577
 IZD  C11   C  CR6   0   0.173   -3.3982   2.9272  -2.5269
 IZD  C12   C  CR16  0  -0.270   -2.4590   2.7811  -1.5084
 IZD  C13   C  CR16  0  -0.285   -2.0147   3.8817  -0.7963
 IZD  C14   C  CR6   0   0.134   -2.4850   5.1579  -1.0914
 IZD  C15   C  CR16  0  -0.277   -3.4010   5.3026  -2.1283
 IZD  C16   C  CR16  0  -0.282   -3.8634   4.2008  -2.8292
 IZD  C21   C  CH2   0  -0.521   -2.0734   6.3363  -0.2620
 IZD  C22   C  CH1   0  -0.203   -3.0649   6.5554   0.9025
 IZD  C25   C  C     0   0.527   -2.6089   7.7615   1.7186
 IZD  O26   O  O     0  -0.484   -2.9085   8.8962   1.3787
 IZD  N27   N  NH2   0  -0.795   -1.8332   7.4732   2.7667
 IZD  N45   N  NH1   0  -0.636   -4.3939   6.7969   0.4087
 IZD  C47   C  C     0   0.589   -5.3796   5.8828   0.4021
 IZD  C48   C  CH1   0  -0.222   -6.6782   6.3702  -0.2372
 IZD  O49   O  O     0  -0.473   -5.2943   4.7717   0.8934
 IZD  N51   N  NH1   0  -0.607   -7.1899   5.3861  -1.1526
 IZD  C4    C  CH2   0  -0.536   -7.7063   6.6678   0.8660
 IZD  C5    C  CR6   0   0.154   -8.9543   7.2818   0.3005
 IZD  C30   C  CR16  0  -0.306   -9.0285   8.6568   0.0888
 IZD  C31   C  CR16  0  -0.241  -10.1624   9.2305  -0.4694
 IZD  C6    C  CR16  0  -0.272  -11.2417   8.4323  -0.8275
 IZD  C33   C  CR16  0  -0.241  -11.1785   7.0607  -0.6211
 IZD  C34   C  CR16  0  -0.308  -10.0419   6.4917  -0.0616
 IZD  C67   C  C     0   0.539   -7.1664   5.5218  -2.4914
 IZD  O70   O  O     0  -0.504   -6.6537   6.4778  -3.0581
 IZD  C71   C  CH3   0  -0.768   -7.8474   4.4204  -3.2636
 IZD  H1    H  HCH1  0   0.365   -3.1159   0.9313  -3.2457
 IZD  H2C1  H  HCH2  0   0.333   -3.7639   1.8310  -5.3773
 IZD  H2C2  H  HCH2  0   0.306   -5.1198   2.7262  -4.7049
 IZD  H4    H  HNC1  0   0.450   -6.5044  -0.6232  -3.4879
 IZD  H12   H  HCR6  0   0.260   -2.0703   1.7984  -1.2691
 IZD  H13   H  HCR6  0   0.253   -1.2919   3.7456  -0.0006
 IZD  H15   H  HCR6  0   0.253   -3.7745   6.2849  -2.3878
 IZD  H16   H  HCR6  0   0.238   -4.5827   4.3616  -3.6208
 IZD  H211  H  HCH2  0   0.271   -1.0726   6.1874   0.1487
 IZD  H212  H  HCH2  0   0.267   -2.0436   7.2424  -0.8719
 IZD  H22   H  HCH1  0   0.293   -3.0906   5.6586   1.5228
 IZD  H271  H  HNH2  0   0.407   -1.4530   8.2087   3.3409
 IZD  H272  H  HNH2  0   0.414   -1.6600   6.5261   3.0562
 IZD  H45   H  HNH1  0   0.400   -4.5544   7.6877  -0.0362
 IZD  H48   H  HCH1  0   0.283   -6.4984   7.2815  -0.8096
 IZD  H51   H  HNH1  0   0.397   -7.5465   4.5299  -0.7595
 IZD  H4C1  H  HCH2  0   0.272   -7.2494   7.3425   1.5935
 IZD  H4C2  H  HCH2  0   0.264   -7.9407   5.7402   1.3947
 IZD  H30   H  HCR6  0   0.246   -8.1907   9.2862   0.3682
 IZD  H31   H  HCR6  0   0.254  -10.2046  10.3014  -0.6222
 IZD  H6    H  HCR6  0   0.254  -12.1280   8.8774  -1.2606
 IZD  H33   H  HCR6  0   0.253  -12.0161   6.4317  -0.8946
 IZD  H34   H  HCR6  0   0.245  -10.0041   5.4213   0.1030
 IZD  H711  H  HCH3  0   0.266   -8.6281   4.8598  -3.8843
 IZD  H712  H  HCH3  0   0.252   -7.1344   3.9426  -3.9348
 IZD  H713  H  HCH3  0   0.249   -8.2933   3.6510  -2.6387

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
 IZD  C1   C2    single    1.524  0.020  1.524
 IZD  C1   S5    single    1.814  0.020  1.814
 IZD  C1   C11   single    1.497  0.020  1.497
 IZD  C1   H1    single    0.970  0.020  1.090
 IZD  C2   C3    single    1.514  0.020  1.514
 IZD  C2   H2C1  single    0.970  0.020  1.090
 IZD  C2   H2C2  single    0.970  0.020  1.090
 IZD  C3   N4    single    1.370  0.020  1.370
 IZD  C3   O9    double    1.206  0.020  1.206
 IZD  N4   S5    single    1.681  0.020  1.681
 IZD  N4   H4    single    0.860  0.020  1.020
 IZD  S5   O6    double    1.450  0.020  1.450
 IZD  S5   O7    double    1.449  0.020  1.449
 IZD  C11  C12   aromatic  1.393  0.020  1.393
 IZD  C11  C16   aromatic  1.389  0.020  1.389
 IZD  C12  C13   aromatic  1.384  0.020  1.384
 IZD  C12  H12   single    0.930  0.020  1.080
 IZD  C13  C14   aromatic  1.392  0.020  1.392
 IZD  C13  H13   single    0.930  0.020  1.080
 IZD  C14  C15   aromatic  1.391  0.020  1.391
 IZD  C14  C21   single    1.499  0.020  1.499
 IZD  C15  C16   aromatic  1.385  0.020  1.385
 IZD  C15  H15   single    0.930  0.020  1.080
 IZD  C16  H16   single    0.930  0.020  1.080
 IZD  C21  C22   single    1.545  0.020  1.545
 IZD  C21  H211  single    0.970  0.020  1.090
 IZD  C21  H212  single    0.970  0.020  1.090
 IZD  C22  C25   single    1.526  0.020  1.526
 IZD  C22  N45   single    1.438  0.020  1.438
 IZD  C22  H22   single    0.970  0.020  1.090
 IZD  C25  O26   double    1.222  0.020  1.222
 IZD  C25  N27   single    1.335  0.020  1.335
 IZD  N27  H271  single    0.860  0.020  1.020
 IZD  N27  H272  single    0.860  0.020  1.020
 IZD  N45  C47   single    1.344  0.020  1.344
 IZD  N45  H45   single    0.860  0.020  1.020
 IZD  C47  C48   single    1.527  0.020  1.527
 IZD  C47  O49   double    1.218  0.020  1.218
 IZD  C48  N51   single    1.438  0.020  1.438
 IZD  C48  C4    single    1.537  0.020  1.537
 IZD  C48  H48   single    0.970  0.020  1.090
 IZD  N51  C67   single    1.346  0.020  1.346
 IZD  N51  H51   single    0.860  0.020  1.020
 IZD  C4   C5    single    1.501  0.020  1.501
 IZD  C4   H4C1  single    0.970  0.020  1.090
 IZD  C4   H4C2  single    0.970  0.020  1.090
 IZD  C5   C30   aromatic  1.393  0.020  1.393
 IZD  C5   C34   aromatic  1.392  0.020  1.392
 IZD  C30  C31   aromatic  1.388  0.020  1.388
 IZD  C30  H30   single    0.930  0.020  1.080
 IZD  C31  C6    aromatic  1.389  0.020  1.389
 IZD  C31  H31   single    0.930  0.020  1.080
 IZD  C6   C33   aromatic  1.388  0.020  1.388
 IZD  C6   H6    single    0.930  0.020  1.080
 IZD  C33  C34   aromatic  1.389  0.020  1.389
 IZD  C33  H33   single    0.930  0.020  1.080
 IZD  C34  H34   single    0.930  0.020  1.080
 IZD  C67  O70   double    1.224  0.020  1.224
 IZD  C67  C71   single    1.508  0.020  1.508
 IZD  C71  H711  single    0.970  0.020  1.090
 IZD  C71  H712  single    0.970  0.020  1.090
 IZD  C71  H713  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
 IZD  H1    C1   C11   110.42  3.000
 IZD  H1    C1   S5    104.28  3.000
 IZD  C11   C1   S5    109.82  3.000
 IZD  H1    C1   C2    109.03  3.000
 IZD  C11   C1   C2    119.39  3.000
 IZD  S5    C1   C2    102.63  3.000
 IZD  H2C2  C2   H2C1  107.50  3.000
 IZD  H2C2  C2   C3    107.39  3.000
 IZD  H2C1  C2   C3    110.41  3.000
 IZD  H2C2  C2   C1    112.19  3.000
 IZD  H2C1  C2   C1    111.14  3.000
 IZD  C3    C2   C1    108.16  3.000
 IZD  O9    C3   N4    124.17  3.000
 IZD  O9    C3   C2    125.83  3.000
 IZD  N4    C3   C2    110.00  3.000
 IZD  H4    N4   S5    121.29  3.000
 IZD  H4    N4   C3    122.59  3.000
 IZD  S5    N4   C3    115.36  3.000
 IZD  O7    S5   O6    118.47  3.000
 IZD  O7    S5   N4    110.26  3.000
 IZD  O6    S5   N4    109.32  3.000
 IZD  O7    S5   C1    110.61  3.000
 IZD  O6    S5   C1    113.15  3.000
 IZD  N4    S5   C1     91.79  3.000
 IZD  C16   C11  C12   118.75  3.000
 IZD  C16   C11  C1    122.83  3.000
 IZD  C12   C11  C1    118.39  3.000
 IZD  H12   C12  C13   119.50  3.000
 IZD  H12   C12  C11   119.90  3.000
 IZD  C13   C12  C11   120.60  3.000
 IZD  H13   C13  C14   119.75  3.000
 IZD  H13   C13  C12   119.48  3.000
 IZD  C14   C13  C12   120.77  3.000
 IZD  C21   C14  C15   120.77  3.000
 IZD  C21   C14  C13   120.72  3.000
 IZD  C15   C14  C13   118.42  3.000
 IZD  H15   C15  C16   119.03  3.000
 IZD  H15   C15  C14   120.02  3.000
 IZD  C16   C15  C14   120.94  3.000
 IZD  H16   C16  C15   118.29  3.000
 IZD  H16   C16  C11   121.22  3.000
 IZD  C15   C16  C11   120.48  3.000
 IZD  H212  C21  H211  107.33  3.000
 IZD  H212  C21  C22   108.69  3.000
 IZD  H211  C21  C22   108.91  3.000
 IZD  H212  C21  C14   110.53  3.000
 IZD  H211  C21  C14   110.66  3.000
 IZD  C22   C21  C14   110.63  3.000
 IZD  H22   C22  N45   108.15  3.000
 IZD  H22   C22  C25   110.65  3.000
 IZD  N45   C22  C25   109.09  3.000
 IZD  H22   C22  C21   109.09  3.000
 IZD  N45   C22  C21   110.98  3.000
 IZD  C25   C22  C21   108.87  3.000
 IZD  N27   C25  O26   124.15  3.000
 IZD  N27   C25  C22   115.00  3.000
 IZD  O26   C25  C22   120.79  3.000
 IZD  H272  N27  H271  117.29  3.000
 IZD  H272  N27  C25   121.97  3.000
 IZD  H271  N27  C25   120.59  3.000
 IZD  H45   N45  C47   118.80  3.000
 IZD  H45   N45  C22   116.53  3.000
 IZD  C47   N45  C22   124.41  3.000
 IZD  O49   C47  C48   121.30  3.000
 IZD  O49   C47  N45   124.54  3.000
 IZD  C48   C47  N45   114.11  3.000
 IZD  H48   C48  C4    108.97  3.000
 IZD  H48   C48  N51   107.24  3.000
 IZD  C4    C48  N51   110.57  3.000
 IZD  H48   C48  C47   110.24  3.000
 IZD  C4    C48  C47   109.27  3.000
 IZD  N51   C48  C47   110.52  3.000
 IZD  H51   N51  C67   118.69  3.000
 IZD  H51   N51  C48   117.33  3.000
 IZD  C67   N51  C48   123.92  3.000
 IZD  H4C2  C4   H4C1  106.96  3.000
 IZD  H4C2  C4   C5    110.55  3.000
 IZD  H4C1  C4   C5    110.24  3.000
 IZD  H4C2  C4   C48   109.04  3.000
 IZD  H4C1  C4   C48   108.53  3.000
 IZD  C5    C4   C48   111.40  3.000
 IZD  C34   C5   C30   118.62  3.000
 IZD  C34   C5   C4    121.01  3.000
 IZD  C30   C5   C4    120.34  3.000
 IZD  H30   C30  C31   119.66  3.000
 IZD  H30   C30  C5    119.51  3.000
 IZD  C31   C30  C5    120.84  3.000
 IZD  H31   C31  C6    120.11  3.000
 IZD  H31   C31  C30   119.84  3.000
 IZD  C6    C31  C30   120.06  3.000
 IZD  H6    C6   C33   120.20  3.000
 IZD  H6    C6   C31   120.21  3.000
 IZD  C33   C6   C31   119.59  3.000
 IZD  H33   C33  C34   119.79  3.000
 IZD  H33   C33  C6    120.08  3.000
 IZD  C34   C33  C6    120.13  3.000
 IZD  H34   C34  C33   119.64  3.000
 IZD  H34   C34  C5    119.59  3.000
 IZD  C33   C34  C5    120.77  3.000
 IZD  C71   C67  O70   121.51  3.000
 IZD  C71   C67  N51   115.34  3.000
 IZD  O70   C67  N51   123.14  3.000
 IZD  H713  C71  H712  108.19  3.000
 IZD  H713  C71  H711  108.61  3.000
 IZD  H712  C71  H711  107.14  3.000
 IZD  H713  C71  C67   114.08  3.000
 IZD  H712  C71  C67   109.89  3.000
 IZD  H711  C71  C67   108.71  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
 IZD  CONST_01  C14   C13  C12  C11    0.00   0.0  0
 IZD  CONST_02  C14   C15  C16  C11    0.00   0.0  0
 IZD  CONST_03  C15   C16  C11  C12    0.00   0.0  0
 IZD  CONST_04  C15   C14  C13  C12    0.00   0.0  0
 IZD  CONST_05  C16   C11  C12  C13    0.00   0.0  0
 IZD  CONST_06  C16   C15  C14  C13    0.00   0.0  0
 IZD  CONST_07  C6    C31  C30  C5     0.00   0.0  0
 IZD  CONST_08  C6    C33  C34  C5     0.00   0.0  0
 IZD  CONST_09  C33   C34  C5   C30    0.00   0.0  0
 IZD  CONST_10  C33   C6   C31  C30    0.00   0.0  0
 IZD  CONST_11  C34   C5   C30  C31    0.00   0.0  0
 IZD  CONST_12  C34   C33  C6   C31    0.00   0.0  0
 IZD  CONST_13  C13   C12  C11  C1   180.00   0.0  0
 IZD  CONST_14  C15   C16  C11  C1   180.00   0.0  0
 IZD  CONST_15  S5    N4   C3   C2     0.00   0.0  0
 IZD  CONST_16  C21   C14  C13  C12  180.00   0.0  0
 IZD  CONST_17  C21   C14  C15  C16  180.00   0.0  0
 IZD  CONST_18  C31   C30  C5   C4   180.00   0.0  0
 IZD  CONST_19  C33   C34  C5   C4   180.00   0.0  0
 IZD  CONST_20  O9    C3   N4   S5   180.00   0.0  0
 IZD  CONST_21  H12   C12  C11  C1     0.00   0.0  0
 IZD  CONST_22  H16   C16  C11  C1     0.00   0.0  0
 IZD  CONST_23  H13   C13  C12  C11  180.00   0.0  0
 IZD  CONST_24  H15   C15  C16  C11  180.00   0.0  0
 IZD  CONST_25  H31   C31  C30  C5   180.00   0.0  0
 IZD  CONST_26  H33   C33  C34  C5   180.00   0.0  0
 IZD  CONST_27  H34   C34  C5   C30  180.00   0.0  0
 IZD  CONST_28  H6    C6   C31  C30  180.00   0.0  0
 IZD  CONST_29  H30   C30  C31  C6   180.00   0.0  0
 IZD  CONST_30  H4    N4   C3   C2   180.00   0.0  0
 IZD  CONST_31  C48   C47  N45  C22  180.00   0.0  0
 IZD  CONST_32  O49   C47  N45  C22    0.00   0.0  0
 IZD  CONST_33  O70   C67  N51  C48    0.00   0.0  0
 IZD  CONST_34  C71   C67  N51  C48  180.00   0.0  0
 IZD  CONST_35  H271  N27  C25  C22  180.00   0.0  0
 IZD  CONST_36  H272  N27  C25  C22    0.00   0.0  0
 IZD  CONST_37  H45   N45  C47  C48    0.00   0.0  0
 IZD  CONST_38  H51   N51  C67  O70  180.00   0.0  0
 IZD  Var_01    N4    C3   C2   C1    20.85  30.0  1
 IZD  Var_02    C3    N4   S5   C1   -21.59  30.0  1
 IZD  Var_03    C22   C21  C14  C13  -90.51  30.0  2
 IZD  Var_04    C30   C5   C4   C48  -85.24  30.0  2
 IZD  Var_05    H711  C71  C67  N51  122.30  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
 IZD  chir_01  C1   C2   S5   C11  positiv
 IZD  chir_02  C22  N45  C21  C25  negativ
 IZD  chir_03  C48  N51  C47  C4   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
 IZD  plan-1  C1    0.020
 IZD  plan-1  C11   0.020
 IZD  plan-1  C12   0.020
 IZD  plan-1  C13   0.020
 IZD  plan-1  C14   0.020
 IZD  plan-1  C15   0.020
 IZD  plan-1  C16   0.020
 IZD  plan-1  C21   0.020
 IZD  plan-1  H12   0.020
 IZD  plan-1  H13   0.020
 IZD  plan-1  H15   0.020
 IZD  plan-1  H16   0.020
 IZD  plan-2  C4    0.020
 IZD  plan-2  C5    0.020
 IZD  plan-2  C30   0.020
 IZD  plan-2  C31   0.020
 IZD  plan-2  C6    0.020
 IZD  plan-2  C33   0.020
 IZD  plan-2  C34   0.020
 IZD  plan-2  H30   0.020
 IZD  plan-2  H31   0.020
 IZD  plan-2  H6    0.020
 IZD  plan-2  H33   0.020
 IZD  plan-2  H34   0.020
 IZD  plan-3  C22   0.020
 IZD  plan-3  N45   0.020
 IZD  plan-3  C47   0.020
 IZD  plan-3  C48   0.020
 IZD  plan-3  O49   0.020
 IZD  plan-3  H45   0.020
 IZD  plan-4  C48   0.020
 IZD  plan-4  N51   0.020
 IZD  plan-4  C67   0.020
 IZD  plan-4  O70   0.020
 IZD  plan-4  C71   0.020
 IZD  plan-4  H51   0.020
 IZD  plan-5  C22   0.020
 IZD  plan-5  C25   0.020
 IZD  plan-5  O26   0.020
 IZD  plan-5  N27   0.020
 IZD  plan-5  H271  0.020
 IZD  plan-5  H272  0.020
 IZD  plan-6  C2    0.020
 IZD  plan-6  C3    0.020
 IZD  plan-6  N4    0.020
 IZD  plan-6  S5    0.020
 IZD  plan-6  O9    0.020
 IZD  plan-6  H4    0.020

