# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 12:40:05 2020
#   Inital geometry file: a 146 line input string
#   Ligand name: 5-{[{[(1R)-2-(tert-butylamino)-2-oxo-1-phenylethyl]carbamoyl}(methyl)amino]methyl}-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccc2OCOc2c1C(O)=O)C(=O)N[C@@H](C(=O)NC(C)(C)C)c3ccccc3
#
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
 S8Y  S8Y  '5-{[{[(1R)-2-(tert-butylamino)-2-oxo-1-phenylethyl]carbamoyl}(methyl)amino]methyl}-1,3-benzodioxole-4-carboxylic acid'  ligand  59  32  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_S8Y
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
 S8Y  C1    C  CR16  0  -0.266   1.6697  -3.6114  -0.3465
 S8Y  C2    C  CR16  0  -0.243   2.1968  -3.0783  -1.5147
 S8Y  C3    C  CR16  0  -0.239   1.4494  -2.7838   0.7477
 S8Y  C4    C  CR16  0  -0.318   2.4949  -1.7236  -1.5892
 S8Y  C5    C  CR16  0  -0.291   1.7560  -1.4331   0.6730
 S8Y  C6    C  CR16  0  -0.319  -2.0360  -0.3272   0.5991
 S8Y  C7    C  CR16  0  -0.322  -2.6557  -1.5146   1.0073
 S8Y  C8    C  CR6   0  -0.205  -4.1390   0.6307  -0.1155
 S8Y  C9    C  CR6   0   0.166   2.2748  -0.8916  -0.4996
 S8Y  C10   C  CR6   0   0.079  -2.7290   0.7322   0.0406
 S8Y  C11   C  CR56  0   0.301  -4.0098  -1.5935   0.8474
 S8Y  C12   C  CR56  0   0.340  -4.7392  -0.5413   0.3114
 S8Y  C14   C  C     0   0.568   3.9014   0.8049   0.2459
 S8Y  C16   C  CH2   0   0.069  -6.1559  -2.1529   0.9063
 S8Y  C17   C  CH3   0  -0.642   6.4359  -0.5950   1.3002
 S8Y  C18   C  CH3   0  -0.642   6.8328   1.8023   0.6425
 S8Y  C19   C  CH3   0  -0.681   7.2879  -0.0382  -0.9756
 S8Y  C20   C  CH3   0  -0.568  -0.4227   2.5186   1.4742
 S8Y  C21   C  CH2   0  -0.345  -1.9778   1.9853  -0.3836
 S8Y  C22   C  CH1   0  -0.267   2.6227   0.5845  -0.5721
 S8Y  C23   C  CT    0   0.094   6.3791   0.4240   0.1616
 S8Y  N24   N  NH1   0  -0.642   5.0234   0.4887  -0.4029
 S8Y  N25   N  NH1   0  -0.704   1.5976   1.4298  -0.0248
 S8Y  N26   N  NT    0  -0.495  -0.6255   2.0569   0.1165
 S8Y  O27   O  OH1   0  -0.585  -6.1973   1.7190  -0.3224
 S8Y  O28   O  O     0  -0.434  -4.5101   2.5019  -1.5436
 S8Y  O29   O  O     0  -0.488   3.8383   1.1934   1.4039
 S8Y  O30   O  O     0  -0.530   0.1797   0.9941  -1.7250
 S8Y  O31   O  O     0  -0.482  -4.8374  -2.6261   1.1278
 S8Y  O32   O  O     0  -0.467  -6.0363  -0.8982   0.2450
 S8Y  H1    H  HCR6  0   0.256   1.4289  -4.6650  -0.2889
 S8Y  H2    H  HCR6  0   0.256   2.3673  -3.7152  -2.3731
 S8Y  H3    H  HCR6  0   0.255   1.0397  -3.1905   1.6633
 S8Y  H4    H  HCR6  0   0.253   2.8926  -1.3097  -2.5088
 S8Y  H5    H  HCR6  0   0.246   1.5871  -0.8012   1.5369
 S8Y  H6    H  HCR6  0   0.250  -0.9685  -0.2574   0.7437
 S8Y  H7    H  HCR6  0   0.276  -2.0810  -2.3298   1.4257
 S8Y  H22   H  HCH1  0   0.295   2.8084   0.8514  -1.6157
 S8Y  H211  H  HCH2  0   0.276  -1.9588   2.0525  -1.4690
 S8Y  H212  H  HCH2  0   0.261  -2.5046   2.8723  -0.0324
 S8Y  H27   H  HOH1  0   0.487  -6.6868   2.4196  -0.7795
 S8Y  H24   H  HNH1  0   0.404   4.9281   0.2035  -1.3655
 S8Y  H25   H  HNH1  0   0.405   1.7425   1.7268   0.9277
 S8Y  H161  H  HCH2  0   0.250  -6.7017  -2.8509   0.2716
 S8Y  H162  H  HCH2  0   0.240  -6.6720  -2.0162   1.8615
 S8Y  H171  H  HCH3  0   0.239   5.8343  -0.2856   2.1530
 S8Y  H172  H  HCH3  0   0.229   6.0823  -1.5708   0.9641
 S8Y  H173  H  HCH3  0   0.229   7.4647  -0.7090   1.6442
 S8Y  H181  H  HCH3  0   0.228   7.8711   1.7537   0.9738
 S8Y  H182  H  HCH3  0   0.229   6.7700   2.5339  -0.1639
 S8Y  H183  H  HCH3  0   0.240   6.2325   2.1568   1.4781
 S8Y  H191  H  HCH3  0   0.238   6.9857  -1.0167  -1.3557
 S8Y  H192  H  HCH3  0   0.241   7.2790   0.6703  -1.8064
 S8Y  H193  H  HCH3  0   0.244   8.3148  -0.1223  -0.6210
 S8Y  H201  H  HCH3  0   0.256   0.4007   3.2316   1.5374
 S8Y  H202  H  HCH3  0   0.272  -1.3165   3.0409   1.8055
 S8Y  H203  H  HCH3  0   0.240  -0.2374   1.7064   2.1834
 S8Y  C15   C  C     0   0.746   0.3685   1.4643  -0.6086
 S8Y  C13   C  C     0   0.518  -4.9401   1.7095  -0.7397

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
 S8Y  C1   C2    aromatic  1.388  0.020  1.388
 S8Y  C1   C3    aromatic  1.389  0.020  1.389
 S8Y  C2   C4    aromatic  1.389  0.020  1.389
 S8Y  C3   C5    aromatic  1.387  0.020  1.387
 S8Y  C4   C9    aromatic  1.388  0.020  1.388
 S8Y  C5   C9    aromatic  1.392  0.020  1.392
 S8Y  C6   C7    aromatic  1.400  0.020  1.400
 S8Y  C6   C10   aromatic  1.384  0.020  1.384
 S8Y  C7   C11   aromatic  1.366  0.020  1.366
 S8Y  C8   C10   aromatic  1.422  0.020  1.422
 S8Y  C8   C12   aromatic  1.384  0.020  1.384
 S8Y  C8   C13   single    1.482  0.020  1.482
 S8Y  C9   C22   single    1.518  0.020  1.518
 S8Y  C10  C21   single    1.521  0.020  1.521
 S8Y  C11  C12   aromatic  1.388  0.020  1.388
 S8Y  C11  O31   single    1.353  0.020  1.353
 S8Y  C12  O32   single    1.347  0.020  1.347
 S8Y  C13  O27   single    1.325  0.020  1.325
 S8Y  C13  O28   double    1.208  0.020  1.208
 S8Y  C14  C22   single    1.534  0.020  1.534
 S8Y  C14  N24   single    1.334  0.020  1.334
 S8Y  C14  O29   double    1.223  0.020  1.223
 S8Y  C15  N25   single    1.361  0.020  1.361
 S8Y  C15  N26   single    1.366  0.020  1.366
 S8Y  C15  O30   double    1.226  0.020  1.226
 S8Y  C16  O31   single    1.418  0.020  1.418
 S8Y  C16  O32   single    1.423  0.020  1.423
 S8Y  C17  C23   single    1.529  0.020  1.529
 S8Y  C18  C23   single    1.529  0.020  1.529
 S8Y  C19  C23   single    1.527  0.020  1.527
 S8Y  C20  N26   single    1.448  0.020  1.448
 S8Y  C21  N26   single    1.444  0.020  1.444
 S8Y  C22  N25   single    1.437  0.020  1.437
 S8Y  C23  N24   single    1.470  0.020  1.470
 S8Y  C1   H1    single    0.930  0.020  1.080
 S8Y  C2   H2    single    0.930  0.020  1.080
 S8Y  C3   H3    single    0.930  0.020  1.080
 S8Y  C4   H4    single    0.930  0.020  1.080
 S8Y  C5   H5    single    0.930  0.020  1.080
 S8Y  C6   H6    single    0.930  0.020  1.080
 S8Y  C7   H7    single    0.930  0.020  1.080
 S8Y  C22  H22   single    0.970  0.020  1.090
 S8Y  C21  H211  single    0.970  0.020  1.090
 S8Y  C21  H212  single    0.970  0.020  1.090
 S8Y  O27  H27   single    0.850  0.020  0.980
 S8Y  N24  H24   single    0.860  0.020  1.020
 S8Y  N25  H25   single    0.860  0.020  1.020
 S8Y  C16  H161  single    0.970  0.020  1.090
 S8Y  C16  H162  single    0.970  0.020  1.090
 S8Y  C17  H171  single    0.970  0.020  1.090
 S8Y  C17  H172  single    0.970  0.020  1.090
 S8Y  C17  H173  single    0.970  0.020  1.090
 S8Y  C18  H181  single    0.970  0.020  1.090
 S8Y  C18  H182  single    0.970  0.020  1.090
 S8Y  C18  H183  single    0.970  0.020  1.090
 S8Y  C19  H191  single    0.970  0.020  1.090
 S8Y  C19  H192  single    0.970  0.020  1.090
 S8Y  C19  H193  single    0.970  0.020  1.090
 S8Y  C20  H201  single    0.970  0.020  1.090
 S8Y  C20  H202  single    0.970  0.020  1.090
 S8Y  C20  H203  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
 S8Y  H1    C1   C3    120.17  3.000
 S8Y  H1    C1   C2    120.21  3.000
 S8Y  C3    C1   C2    119.62  3.000
 S8Y  H2    C2   C4    119.84  3.000
 S8Y  H2    C2   C1    120.08  3.000
 S8Y  C4    C2   C1    120.08  3.000
 S8Y  H3    C3   C5    119.68  3.000
 S8Y  H3    C3   C1    120.16  3.000
 S8Y  C5    C3   C1    120.17  3.000
 S8Y  H4    C4   C9    119.67  3.000
 S8Y  H4    C4   C2    119.77  3.000
 S8Y  C9    C4   C2    120.55  3.000
 S8Y  H5    C5   C9    120.19  3.000
 S8Y  H5    C5   C3    119.37  3.000
 S8Y  C9    C5   C3    120.44  3.000
 S8Y  H6    C6   C10   120.00  3.000
 S8Y  H6    C6   C7    116.96  3.000
 S8Y  C10   C6   C7    123.05  3.000
 S8Y  H7    C7   C11   121.90  3.000
 S8Y  H7    C7   C6    121.12  3.000
 S8Y  C11   C7   C6    116.98  3.000
 S8Y  C13   C8   C12   120.80  3.000
 S8Y  C13   C8   C10   122.03  3.000
 S8Y  C12   C8   C10   117.16  3.000
 S8Y  C22   C9   C5    120.26  3.000
 S8Y  C22   C9   C4    120.58  3.000
 S8Y  C5    C9   C4    119.15  3.000
 S8Y  C21   C10  C8    121.18  3.000
 S8Y  C21   C10  C6    119.73  3.000
 S8Y  C8    C10  C6    119.09  3.000
 S8Y  O31   C11  C12   109.70  3.000
 S8Y  O31   C11  C7    128.79  3.000
 S8Y  C12   C11  C7    121.50  3.000
 S8Y  O32   C12  C11   108.92  3.000
 S8Y  O32   C12  C8    128.81  3.000
 S8Y  C11   C12  C8    122.21  3.000
 S8Y  O29   C14  N24   125.39  3.000
 S8Y  O29   C14  C22   120.50  3.000
 S8Y  N24   C14  C22   114.06  3.000
 S8Y  H162  C16  H161  110.62  3.000
 S8Y  H162  C16  O32   109.57  3.000
 S8Y  H161  C16  O32   109.63  3.000
 S8Y  H162  C16  O31   110.11  3.000
 S8Y  H161  C16  O31   110.05  3.000
 S8Y  O32   C16  O31   106.77  3.000
 S8Y  H173  C17  H172  108.02  3.000
 S8Y  H173  C17  H171  107.69  3.000
 S8Y  H172  C17  H171  108.45  3.000
 S8Y  H173  C17  C23   109.85  3.000
 S8Y  H172  C17  C23   110.78  3.000
 S8Y  H171  C17  C23   111.93  3.000
 S8Y  H183  C18  H182  108.51  3.000
 S8Y  H183  C18  H181  107.84  3.000
 S8Y  H182  C18  H181  108.01  3.000
 S8Y  H183  C18  C23   111.81  3.000
 S8Y  H182  C18  C23   110.80  3.000
 S8Y  H181  C18  C23   109.74  3.000
 S8Y  H193  C19  H192  107.78  3.000
 S8Y  H193  C19  H191  107.75  3.000
 S8Y  H192  C19  H191  108.31  3.000
 S8Y  H193  C19  C23   109.99  3.000
 S8Y  H192  C19  C23   111.43  3.000
 S8Y  H191  C19  C23   111.44  3.000
 S8Y  H203  C20  H202  107.36  3.000
 S8Y  H203  C20  H201  108.65  3.000
 S8Y  H202  C20  H201  106.79  3.000
 S8Y  H203  C20  N26   113.25  3.000
 S8Y  H202  C20  N26   108.89  3.000
 S8Y  H201  C20  N26   111.61  3.000
 S8Y  H212  C21  H211  106.24  3.000
 S8Y  H212  C21  N26   107.51  3.000
 S8Y  H211  C21  N26   109.04  3.000
 S8Y  H212  C21  C10   109.99  3.000
 S8Y  H211  C21  C10   109.74  3.000
 S8Y  N26   C21  C10   114.01  3.000
 S8Y  H22   C22  N25   109.95  3.000
 S8Y  H22   C22  C14   109.42  3.000
 S8Y  N25   C22  C14   107.88  3.000
 S8Y  H22   C22  C9    108.78  3.000
 S8Y  N25   C22  C9    112.97  3.000
 S8Y  C14   C22  C9    107.77  3.000
 S8Y  N24   C23  C19   106.03  3.000
 S8Y  N24   C23  C18   110.78  3.000
 S8Y  C19   C23  C18   109.30  3.000
 S8Y  N24   C23  C17   110.46  3.000
 S8Y  C19   C23  C17   109.31  3.000
 S8Y  C18   C23  C17   110.83  3.000
 S8Y  H24   N24  C23   116.19  3.000
 S8Y  H24   N24  C14   116.86  3.000
 S8Y  C23   N24  C14   126.82  3.000
 S8Y  H25   N25  C22   115.51  3.000
 S8Y  H25   N25  C15   121.84  3.000
 S8Y  C22   N25  C15   119.72  3.000
 S8Y  C21   N26  C20   118.15  3.000
 S8Y  C21   N26  C15   118.45  3.000
 S8Y  C20   N26  C15   122.29  3.000
 S8Y  H27   O27  C13   109.63  3.000
 S8Y  C16   O31  C11   106.37  3.000
 S8Y  C16   O32  C12   106.95  3.000
 S8Y  O30   C15  N26   122.54  3.000
 S8Y  O30   C15  N25   121.33  3.000
 S8Y  N26   C15  N25   116.14  3.000
 S8Y  O28   C13  O27   122.87  3.000
 S8Y  O28   C13  C8    124.44  3.000
 S8Y  O27   C13  C8    112.68  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
 S8Y  CONST_01  C9    C4   C2   C1      0.00   0.0  0
 S8Y  CONST_02  C9    C5   C3   C1      0.00   0.0  0
 S8Y  CONST_03  C5    C3   C1   C2      0.00   0.0  0
 S8Y  CONST_04  C5    C9   C4   C2      0.00   0.0  0
 S8Y  CONST_05  C4    C2   C1   C3      0.00   0.0  0
 S8Y  CONST_06  C4    C9   C5   C3      0.00   0.0  0
 S8Y  CONST_07  C12   C11  C7   C6      0.00   0.0  0
 S8Y  CONST_08  C12   C8   C10  C6      0.00   0.0  0
 S8Y  CONST_09  C8    C10  C6   C7      0.00   0.0  0
 S8Y  CONST_10  C8    C12  C11  C7      0.00   0.0  0
 S8Y  CONST_11  C11   C7   C6   C10     0.00   0.0  0
 S8Y  CONST_12  C11   C12  C8   C10     0.00   0.0  0
 S8Y  CONST_13  C22   C9   C4   C2    180.00   0.0  0
 S8Y  CONST_14  C22   C9   C5   C3    180.00   0.0  0
 S8Y  CONST_15  C13   C8   C10  C6    180.00   0.0  0
 S8Y  CONST_16  C21   C10  C6   C7    180.00   0.0  0
 S8Y  CONST_17  C13   C8   C12  C11   180.00   0.0  0
 S8Y  CONST_18  C21   C10  C8   C12   180.00   0.0  0
 S8Y  CONST_19  O32   C12  C8   C13     0.00   0.0  0
 S8Y  CONST_20  H4    C4   C2   C1    180.00   0.0  0
 S8Y  CONST_21  H5    C5   C3   C1    180.00   0.0  0
 S8Y  CONST_22  H3    C3   C1   C2    180.00   0.0  0
 S8Y  CONST_23  H2    C2   C1   C3    180.00   0.0  0
 S8Y  CONST_24  H1    C1   C2   C4    180.00   0.0  0
 S8Y  CONST_25  H6    C6   C10  C8    180.00   0.0  0
 S8Y  CONST_26  H7    C7   C6   C10   180.00   0.0  0
 S8Y  CONST_27  H27   O27  C13  C8    180.00   0.0  0
 S8Y  CONST_28  O30   C15  N26  C20   180.00   0.0  0
 S8Y  CONST_29  O30   C15  N26  C21     0.00   0.0  0
 S8Y  CONST_30  C23   N24  C14  C22   180.00   0.0  0
 S8Y  CONST_31  O30   C15  N25  C22     0.00   0.0  0
 S8Y  CONST_32  O29   C14  N24  C23     0.00   0.0  0
 S8Y  CONST_33  N25   C15  N26  C20     0.00   0.0  0
 S8Y  CONST_34  N25   C15  N26  C21   180.00   0.0  0
 S8Y  CONST_35  N26   C15  N25  C22   180.00   0.0  0
 S8Y  CONST_36  H24   N24  C14  C22     0.00   0.0  0
 S8Y  CONST_37  H25   N25  C15  O30   180.00   0.0  0
 S8Y  Var_01    O32   C16  O31  C11    10.96  30.0  1
 S8Y  Var_02    O31   C16  O32  C12   -11.11  30.0  1
 S8Y  Var_03    N26   C21  C10  C6    -13.06  30.0  2
 S8Y  Var_04    O27   C13  C8   C10  -153.70  30.0  2
 S8Y  Var_05    C15   N26  C21  C10    86.88  30.0  3
 S8Y  Var_06    C17   C23  N24  C14    59.34  30.0  3
 S8Y  Var_07    H201  C20  N26  C15    56.68  30.0  3
 S8Y  Var_08    H181  C18  C23  C17    62.13  30.0  3
 S8Y  Var_09    H191  C19  C23  C17    59.30  30.0  3
 S8Y  Var_10    H171  C17  C23  C18    57.05  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
 S8Y  chir_01  C22  C9  C14  N25  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
 S8Y  plan-1  C1   0.020
 S8Y  plan-1  C2   0.020
 S8Y  plan-1  C3   0.020
 S8Y  plan-1  C4   0.020
 S8Y  plan-1  C5   0.020
 S8Y  plan-1  C9   0.020
 S8Y  plan-1  C22  0.020
 S8Y  plan-1  H1   0.020
 S8Y  plan-1  H2   0.020
 S8Y  plan-1  H3   0.020
 S8Y  plan-1  H4   0.020
 S8Y  plan-1  H5   0.020
 S8Y  plan-2  C6   0.020
 S8Y  plan-2  C7   0.020
 S8Y  plan-2  C8   0.020
 S8Y  plan-2  C10  0.020
 S8Y  plan-2  C11  0.020
 S8Y  plan-2  C12  0.020
 S8Y  plan-2  C21  0.020
 S8Y  plan-2  O31  0.020
 S8Y  plan-2  O32  0.020
 S8Y  plan-2  H6   0.020
 S8Y  plan-2  H7   0.020
 S8Y  plan-2  C13  0.020
 S8Y  plan-3  C14  0.020
 S8Y  plan-3  C22  0.020
 S8Y  plan-3  C23  0.020
 S8Y  plan-3  N24  0.020
 S8Y  plan-3  O29  0.020
 S8Y  plan-3  H24  0.020
 S8Y  plan-4  C20  0.020
 S8Y  plan-4  C21  0.020
 S8Y  plan-4  C22  0.020
 S8Y  plan-4  N25  0.020
 S8Y  plan-4  N26  0.020
 S8Y  plan-4  O30  0.020
 S8Y  plan-4  H25  0.020
 S8Y  plan-4  C15  0.020
 S8Y  plan-5  C8   0.020
 S8Y  plan-5  O27  0.020
 S8Y  plan-5  O28  0.020
 S8Y  plan-5  H27  0.020
 S8Y  plan-5  C13  0.020

