# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 14:22:33 2020
#   Inital geometry file: a 181 line input string
#   Ligand name: (2S)-2-({(2S)-3-[(R)-[(1R)-1-({(4S)-4-amino-5-[(2S)-2-cyanopyrrolidin-1-yl]-5-oxopentanoyl}amino)ethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}amino)propanoic acid (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](NC(=O)[C@H](Cc1ccccc1)C[P@](O)(=O)[C@H](C)NC(=O)CC[C@H](N)C(=O)N2CCC[C@H]2C#N)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
 I20  I20  '(2S)-2-({(2S)-3-[(R)-[(1R)-1-({(4S)-4-amino-5-[(2S)-2-cyanopyrrolidin-1-yl]-5-oxopentanoyl}amino)ethyl](hydroxy)phosphoryl]-2-benzylpropanoyl}amino)propanoic acid (non-preferred name)'  ligand  72  38  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_I20
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
 I20  C1    C  CH3    0  -0.670   -0.0889   2.8464  -0.1201
 I20  C2    C  CH1    0  -0.318   -0.4195   1.3942  -0.4289
 I20  O5    O  O      0  -0.802    0.3295  -1.2106  -0.0948
 I20  C7    C  CH2    0  -0.716    2.3352   0.5408  -0.8202
 I20  C8    C  CH1    0  -0.363    3.6124  -0.0762  -0.2412
 I20  C9    C  CH2    0  -0.502    3.6210  -1.6104  -0.3098
 I20  C10   C  C      0   0.585    4.8273   0.4603  -0.9822
 I20  C11   C  C      0   0.130    4.8653  -2.1890   0.3031
 I20  C12   C  C1     0  -0.310    4.9891  -2.2721   1.6891
 I20  C13   C  C1     0  -0.238    6.1482  -2.7594   2.2751
 I20  C14   C  C1     0  -0.274    7.2085  -3.1751   1.4790
 I20  C15   C  C1     0  -0.239    7.0978  -3.0977   0.0976
 I20  C16   C  C1     0  -0.295    5.9354  -2.6070  -0.4835
 I20  C27   C  CH2    0  -0.429   -5.0542  -0.3475  -0.1431
 I20  N29   N  NH2    0  -0.771   -5.7525  -2.2804   1.1819
 I20  C30   C  C      0   0.561   -2.6081   0.2436  -0.3976
 I20  C32   C  CH2    0  -0.581   -3.6986  -0.2373   0.5362
 I20  C35   C  CH1    0  -0.198    6.9398   1.6989  -0.6971
 I20  NZ    N  NS     0  -0.267   -9.2675  -0.2397  -3.1767
 I20  CD    C  CH1    0  -0.129   -9.3684   0.4530  -0.6583
 I20  CG    C  CH2    0  -0.480   -9.7320   1.9408  -0.5226
 I20  CB    C  CH2    0  -0.473   -9.0008   2.3518   0.7483
 I20  CA    C  CH2    0  -0.281   -7.6866   1.5925   0.6460
 I20  N     N  NT     0  -0.489   -8.0847   0.3360   0.0165
 I20  C     C  C      0   0.550   -7.4774  -0.8664   0.0907
 I20  O     O  O      0  -0.484   -7.9868  -1.8512  -0.4258
 I20  C28   C  CH1    0  -0.226   -6.1173  -0.9399   0.7917
 I20  O31   O  O      0  -0.510   -2.5880  -0.0624  -1.5831
 I20  N3    N  NH1    0  -0.628   -1.6839   1.0278   0.1813
 I20  P4    P  P      0   1.186    0.8463   0.1813   0.2073
 I20  O6    O  OP    -1  -0.815    1.1508   0.5571   1.6447
 I20  N34   N  NH1    0  -0.626    5.6726   1.1780  -0.2399
 I20  C37   C  C      0   0.417    7.8137   2.0546   0.5302
 I20  O39   O  OC    -1  -0.608    8.9876   2.3770   0.2757
 I20  O38   O  O      0  -0.597    7.2711   2.0093   1.6518
 I20  C36   C  CH3    0  -0.657    6.7697   2.9234  -1.5952
 I20  O33   O  O      0  -0.522    4.9954   0.2390  -2.1789
 I20  H11   H  HCH3   0   0.224    0.0385   2.9989   0.9525
 I20  H12A  H  HCH3   0   0.232    0.8366   3.1516  -0.6082
 I20  H13A  H  HCH3   0   0.233   -0.8804   3.5110  -0.4703
 I20  H2    H  HCH1   0   0.250   -0.5271   1.2607  -1.5066
 I20  H71   H  HCH2   0   0.249    2.4660   1.6262  -0.8675
 I20  H72   H  HCH2   0   0.240    2.1728   0.1995  -1.8458
 I20  H8    H  HCH1   0   0.244    3.6748   0.2187   0.8112
 I20  H91   H  HCH2   0   0.259    2.7366  -1.9881   0.2044
 I20  H92   H  HCH2   0   0.234    3.5308  -1.9231  -1.3529
 I20  H12   H  H      0   0.240    4.1642  -1.9490   2.3149
 I20  H13   H  H      0   0.248    6.2239  -2.8183   3.3537
 I20  H14   H  H      0   0.249    8.1132  -3.5591   1.9326
 I20  H15   H  H      0   0.247    7.9184  -3.4218  -0.5303
 I20  H16   H  H      0   0.239    5.8595  -2.5421  -1.5623
 I20  H271  H  HCH2   0   0.250   -5.3691   0.6407  -0.4863
 I20  H272  H  HCH2   0   0.243   -4.9777  -0.9716  -1.0380
 I20  H291  H  HNH2   0   0.353   -6.3899  -2.6256   1.8880
 I20  H292  H  HNH2   0   0.342   -5.8451  -2.9045   0.3895
 I20  H321  H  HCH2   0   0.247   -3.7694   0.4168   1.4092
 I20  H322  H  HCH2   0   0.274   -3.3997  -1.2188   0.9143
 I20  H35   H  HCH1   0   0.230    7.4585   0.9212  -1.2679
 I20  HG2   H  HCH2   0   0.281  -10.8098   2.0789  -0.4752
 I20  HB1   H  HCH2   0   0.268   -8.8519   3.4279   0.8165
 I20  HB2   H  HCH2   0   0.253   -9.5537   2.0275   1.6316
 I20  HA1   H  HCH2   0   0.253   -6.9692   2.1324   0.0221
 I20  HA2   H  HCH2   0   0.269   -7.2310   1.4209   1.6192
 I20  H28   H  HCH1   0   0.256   -6.1523  -0.3323   1.7012
 I20  HN3   H  HNH1   0   0.388   -1.7518   1.1671   1.1781
 I20  HN34  H  HNH1   0   0.381    5.5346   1.2443   0.7587
 I20  H361  H  HCH3   0   0.225    7.7399   3.2806  -1.9368
 I20  H362  H  HCH3   0   0.229    6.1699   2.6839  -2.4721
 I20  H363  H  HCH3   0   0.216    6.2763   3.7347  -1.0571
 I20  HD    H  HCH1   0   0.327  -10.1230  -0.1748  -0.1756
 I20  CE    C  CSP    0   0.133   -9.2912   0.0401  -2.0615
 I20  HG1   H  HCH2   0   0.265   -9.3533   2.5043  -1.3767

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
 I20  CB   CG    single    1.523  0.020  1.523
 I20  CB   CA    single    1.521  0.020  1.521
 I20  CG   CD    single    1.538  0.020  1.538
 I20  CA   N     single    1.461  0.020  1.461
 I20  CD   CE    single    1.465  0.020  1.465
 I20  CD   N     single    1.455  0.020  1.455
 I20  CE   NZ    triple    1.150  0.020  1.150
 I20  N    C     single    1.349  0.020  1.349
 I20  C    C28   single    1.532  0.020  1.532
 I20  C    O     double    1.223  0.020  1.223
 I20  N29  C28   single    1.443  0.020  1.443
 I20  C28  C27   single    1.535  0.020  1.535
 I20  C27  C32   single    1.520  0.020  1.520
 I20  C32  C30   single    1.514  0.020  1.514
 I20  O31  C30   double    1.225  0.020  1.225
 I20  C30  N3    single    1.343  0.020  1.343
 I20  N3   C2    single    1.451  0.020  1.451
 I20  O5   P4    deloc     1.515  0.020  1.515
 I20  C2   P4    single    1.865  0.020  1.865
 I20  C2   C1    single    1.521  0.020  1.521
 I20  P4   O6    deloc     1.517  0.020  1.517
 I20  P4   C7    single    1.844  0.020  1.844
 I20  C7   C8    single    1.532  0.020  1.532
 I20  C8   C9    single    1.536  0.020  1.536
 I20  C8   C10   single    1.521  0.020  1.521
 I20  C9   C11   single    1.503  0.020  1.503
 I20  C10  O33   double    1.229  0.020  1.229
 I20  C10  N34   single    1.334  0.020  1.334
 I20  C16  C11   aromatic  1.392  0.020  1.392
 I20  C16  C15   aromatic  1.389  0.020  1.389
 I20  N34  C35   single    1.444  0.020  1.444
 I20  O38  C37   deloc     1.247  0.020  1.247
 I20  C11  C12   aromatic  1.394  0.020  1.394
 I20  C15  C14   aromatic  1.388  0.020  1.388
 I20  C37  C35   single    1.548  0.020  1.548
 I20  C37  O39   deloc     1.244  0.020  1.244
 I20  C35  C36   single    1.528  0.020  1.528
 I20  C12  C13   aromatic  1.387  0.020  1.387
 I20  C14  C13   aromatic  1.390  0.020  1.390
 I20  C1   H11   single    0.970  0.020  1.090
 I20  C1   H12A  single    0.970  0.020  1.090
 I20  C1   H13A  single    0.970  0.020  1.090
 I20  C2   H2    single    0.970  0.020  1.090
 I20  C7   H71   single    0.970  0.020  1.090
 I20  C7   H72   single    0.970  0.020  1.090
 I20  C8   H8    single    0.970  0.020  1.090
 I20  C9   H91   single    0.970  0.020  1.090
 I20  C9   H92   single    0.970  0.020  1.090
 I20  C12  H12   single    0.930  0.020  1.080
 I20  C13  H13   single    0.930  0.020  1.080
 I20  C14  H14   single    0.930  0.020  1.080
 I20  C15  H15   single    0.930  0.020  1.080
 I20  C16  H16   single    0.930  0.020  1.080
 I20  C27  H271  single    0.970  0.020  1.090
 I20  C27  H272  single    0.970  0.020  1.090
 I20  N29  H291  single    0.890  0.020  1.040
 I20  N29  H292  single    0.890  0.020  1.040
 I20  C32  H321  single    0.970  0.020  1.090
 I20  C32  H322  single    0.970  0.020  1.090
 I20  C35  H35   single    0.970  0.020  1.090
 I20  CD   HD    single    0.970  0.020  1.090
 I20  CG   HG1   single    0.970  0.020  1.090
 I20  CG   HG2   single    0.970  0.020  1.090
 I20  CB   HB1   single    0.970  0.020  1.090
 I20  CB   HB2   single    0.970  0.020  1.090
 I20  CA   HA1   single    0.970  0.020  1.090
 I20  CA   HA2   single    0.970  0.020  1.090
 I20  C28  H28   single    0.970  0.020  1.090
 I20  N3   HN3   single    0.860  0.020  1.020
 I20  N34  HN34  single    0.860  0.020  1.020
 I20  C36  H361  single    0.970  0.020  1.090
 I20  C36  H362  single    0.970  0.020  1.090
 I20  C36  H363  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
 I20  H13A  C1   H12A  107.55  3.000
 I20  H13A  C1   H11   108.37  3.000
 I20  H12A  C1   H11   107.58  3.000
 I20  H13A  C1   C2    111.01  3.000
 I20  H12A  C1   C2    111.16  3.000
 I20  H11   C1   C2    111.01  3.000
 I20  H2    C2   P4    108.92  3.000
 I20  H2    C2   N3    107.37  3.000
 I20  P4    C2   N3    106.48  3.000
 I20  H2    C2   C1    109.80  3.000
 I20  P4    C2   C1    113.84  3.000
 I20  N3    C2   C1    110.19  3.000
 I20  H72   C7   H71   106.68  3.000
 I20  H72   C7   P4    110.00  3.000
 I20  H71   C7   P4    108.29  3.000
 I20  H72   C7   C8    110.65  3.000
 I20  H71   C7   C8    108.43  3.000
 I20  P4    C7   C8    112.58  3.000
 I20  H8    C8   C10   109.13  3.000
 I20  H8    C8   C9    108.16  3.000
 I20  C10   C8   C9    109.04  3.000
 I20  H8    C8   C7    107.60  3.000
 I20  C10   C8   C7    109.87  3.000
 I20  C9    C8   C7    112.97  3.000
 I20  H92   C9   H91   106.50  3.000
 I20  H92   C9   C11   110.33  3.000
 I20  H91   C9   C11   110.23  3.000
 I20  H92   C9   C8    109.15  3.000
 I20  H91   C9   C8    108.68  3.000
 I20  C11   C9   C8    111.78  3.000
 I20  O33   C10  N34   123.51  3.000
 I20  N34   C10  C8    115.14  3.000
 I20  O33   C10  C8    121.35  3.000
 I20  C16   C11  C12   118.40  3.000
 I20  C12   C11  C9    120.13  3.000
 I20  C16   C11  C9    121.44  3.000
 I20  H12   C12  C13   119.76  3.000
 I20  H12   C12  C11   119.23  3.000
 I20  C13   C12  C11   121.01  3.000
 I20  H13   C13  C14   120.07  3.000
 I20  H13   C13  C12   119.89  3.000
 I20  C14   C13  C12   120.04  3.000
 I20  H14   C14  C15   120.23  3.000
 I20  H14   C14  C13   120.25  3.000
 I20  C15   C14  C13   119.52  3.000
 I20  H15   C15  C16   119.82  3.000
 I20  H15   C15  C14   119.99  3.000
 I20  C16   C15  C14   120.18  3.000
 I20  H16   C16  C15   119.75  3.000
 I20  H16   C16  C11   119.39  3.000
 I20  C15   C16  C11   120.86  3.000
 I20  H272  C27  H271  106.22  3.000
 I20  H272  C27  C28   109.06  3.000
 I20  H271  C27  C28   109.93  3.000
 I20  H272  C27  C32   110.16  3.000
 I20  H271  C27  C32   109.38  3.000
 I20  C28   C27  C32   111.94  3.000
 I20  H292  N29  H291  106.15  3.000
 I20  H292  N29  C28   109.73  3.000
 I20  H291  N29  C28   110.26  3.000
 I20  N3    C30  O31   123.49  3.000
 I20  N3    C30  C32   114.53  3.000
 I20  O31   C30  C32   121.98  3.000
 I20  H322  C32  H321  106.18  3.000
 I20  H322  C32  C30   107.55  3.000
 I20  H321  C32  C30   110.44  3.000
 I20  H322  C32  C27   109.46  3.000
 I20  H321  C32  C27   110.03  3.000
 I20  C30   C32  C27   112.94  3.000
 I20  H35   C35  C36   108.39  3.000
 I20  H35   C35  C37   108.00  3.000
 I20  C36   C35  C37   110.16  3.000
 I20  H35   C35  N34   108.93  3.000
 I20  C36   C35  N34   112.17  3.000
 I20  C37   C35  N34   109.10  3.000
 I20  HD    CD   N     110.96  3.000
 I20  HD    CD   CG    110.69  3.000
 I20  N     CD   CG    104.21  3.000
 I20  HD    CD   CE    107.30  3.000
 I20  N     CD   CE    112.03  3.000
 I20  CG    CD   CE    111.70  3.000
 I20  HG2   CG   HG1   108.21  3.000
 I20  HG2   CG   CB    113.90  3.000
 I20  HG1   CG   CB    110.32  3.000
 I20  HG2   CG   CD    111.16  3.000
 I20  HG1   CG   CD    110.40  3.000
 I20  CB    CG   CD    102.78  3.000
 I20  HB2   CB   HB1   108.20  3.000
 I20  HB2   CB   CA    110.11  3.000
 I20  HB1   CB   CA    112.30  3.000
 I20  HB2   CB   CG    110.61  3.000
 I20  HB1   CB   CG    112.63  3.000
 I20  CA    CB   CG    102.94  3.000
 I20  HA2   CA   HA1   108.27  3.000
 I20  HA2   CA   N     111.34  3.000
 I20  HA1   CA   N     110.96  3.000
 I20  HA2   CA   CB    112.35  3.000
 I20  HA1   CA   CB    111.03  3.000
 I20  N     CA   CB    102.88  3.000
 I20  C     N    CA    128.34  3.000
 I20  C     N    CD    119.63  3.000
 I20  CA    N    CD    111.79  3.000
 I20  C28   C    O     121.62  3.000
 I20  O     C    N     120.46  3.000
 I20  C28   C    N     117.88  3.000
 I20  H28   C28  C     108.98  3.000
 I20  H28   C28  N29   107.40  3.000
 I20  C     C28  N29   113.13  3.000
 I20  H28   C28  C27   108.30  3.000
 I20  N29   C28  C27   110.37  3.000
 I20  C     C28  C27   108.53  3.000
 I20  HN3   N3   C30   117.40  3.000
 I20  HN3   N3   C2    116.06  3.000
 I20  C30   N3   C2    124.45  3.000
 I20  O6    P4   C7    108.52  3.000
 I20  C7    P4   O5    110.08  3.000
 I20  O6    P4   O5    119.02  3.000
 I20  C7    P4   C2    103.36  3.000
 I20  O6    P4   C2    107.36  3.000
 I20  O5    P4   C2    107.33  3.000
 I20  HN34  N34  C35   114.15  3.000
 I20  HN34  N34  C10   119.90  3.000
 I20  C35   N34  C10   125.01  3.000
 I20  O38   C37  O39   127.18  3.000
 I20  O39   C37  C35   115.47  3.000
 I20  O38   C37  C35   117.34  3.000
 I20  H363  C36  H362  108.15  3.000
 I20  H363  C36  H361  108.28  3.000
 I20  H362  C36  H361  108.07  3.000
 I20  H363  C36  C35   110.87  3.000
 I20  H362  C36  C35   110.99  3.000
 I20  H361  C36  C35   110.37  3.000
 I20  CD    CE   NZ    180.00  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
 I20  CONST_01  C14   C15  C16  C11    0.00   0.0  0
 I20  CONST_02  C14   C13  C12  C11    0.00   0.0  0
 I20  CONST_03  C15   C16  C11  C12    0.00   0.0  0
 I20  CONST_04  C15   C14  C13  C12    0.00   0.0  0
 I20  CONST_05  C16   C11  C12  C13    0.00   0.0  0
 I20  CONST_06  C16   C15  C14  C13    0.00   0.0  0
 I20  CONST_07  C15   C16  C11  C9   180.00   0.0  0
 I20  CONST_08  C13   C12  C11  C9   180.00   0.0  0
 I20  CONST_09  H15   C15  C16  C11  180.00   0.0  0
 I20  CONST_10  H13   C13  C12  C11  180.00   0.0  0
 I20  CONST_11  H16   C16  C11  C12  180.00   0.0  0
 I20  CONST_12  H14   C14  C13  C12  180.00   0.0  0
 I20  CONST_13  H12   C12  C13  C14  180.00   0.0  0
 I20  CONST_14  C28   C    N    CD   180.00   0.0  0
 I20  CONST_15  O     C    N    CD     0.00   0.0  0
 I20  CONST_16  C28   C    N    CA     0.00   0.0  0
 I20  CONST_17  O     C    N    CA   180.00   0.0  0
 I20  CONST_18  C32   C30  N3   C2   180.00   0.0  0
 I20  CONST_19  O31   C30  N3   C2     0.00   0.0  0
 I20  CONST_20  C35   N34  C10  C8   180.00   0.0  0
 I20  CONST_21  O33   C10  N34  C35    0.00   0.0  0
 I20  CONST_22  HN34  N34  C10  C8     0.00   0.0  0
 I20  CONST_23  HN3   N3   C30  C32    0.00   0.0  0
 I20  Var_01    CA    CB   CG   CD    38.60  30.0  1
 I20  Var_02    CB    CA   N    CD    19.39  30.0  1
 I20  Var_03    N     CA   CB   CG   -35.59  30.0  1
 I20  Var_04    C16   C11  C9   C8   -99.88  30.0  2
 I20  Var_05    C8    C7   P4   C2   165.05  30.0  3
 I20  Var_06    O31   C30  C32  C27  -34.69  30.0  3
 I20  Var_07    C28   C27  C32  C30  175.53  30.0  1

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
 I20  chir_01  C2   N3   P4   C1   positiv
 I20  chir_02  C8   C10  C9   C7   positiv
 I20  chir_03  C35  N34  C37  C36  positiv
 I20  chir_04  CD   CG   CE   N    negativ
 I20  chir_05  C28  N29  C27  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
 I20  plan-1  C9    0.020
 I20  plan-1  C11   0.020
 I20  plan-1  C12   0.020
 I20  plan-1  C13   0.020
 I20  plan-1  C14   0.020
 I20  plan-1  C15   0.020
 I20  plan-1  C16   0.020
 I20  plan-1  H12   0.020
 I20  plan-1  H13   0.020
 I20  plan-1  H14   0.020
 I20  plan-1  H15   0.020
 I20  plan-1  H16   0.020
 I20  plan-2  C2    0.020
 I20  plan-2  C30   0.020
 I20  plan-2  C32   0.020
 I20  plan-2  O31   0.020
 I20  plan-2  N3    0.020
 I20  plan-2  HN3   0.020
 I20  plan-3  CD    0.020
 I20  plan-3  CA    0.020
 I20  plan-3  N     0.020
 I20  plan-3  C     0.020
 I20  plan-3  O     0.020
 I20  plan-3  C28   0.020
 I20  plan-4  C8    0.020
 I20  plan-4  C10   0.020
 I20  plan-4  C35   0.020
 I20  plan-4  N34   0.020
 I20  plan-4  O33   0.020
 I20  plan-4  HN34  0.020
 I20  plan-5  C35   0.020
 I20  plan-5  C37   0.020
 I20  plan-5  O39   0.020
 I20  plan-5  O38   0.020

