# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 03:03:20 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 5-({(1R,2S)-2-[(5-aminopentanoyl)amino]-2,3-dihydro-1H-inden-1-yl}methyl)-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCCC(=O)N[C@H]1Cc2ccccc2[C@H]1Cc3ccc4OCOc4c3C(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
 E4F  E4F  '5-({(1R,2S)-2-[(5-aminopentanoyl)amino]-2,3-dihydro-1H-inden-1-yl}methyl)-1,3-benzodioxole-4-carboxylic acid'  ligand  56  30  .  2021-08-09  2021-08-09  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_E4F
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
 E4F  C1   C  CR16  0  -0.261   2.0220   4.8807  -0.1530
 E4F  C2   C  CR16  0  -0.260   2.7982   3.8145  -0.5947
 E4F  C3   C  CR16  0  -0.326   0.6919   4.6848   0.2060
 E4F  C4   C  CR16  0  -0.311   2.2564   2.5356  -0.6797
 E4F  C5   C  CR16  0  -0.329   2.8344   0.1358   1.7047
 E4F  C6   C  CR16  0  -0.325   4.1607  -0.3122   1.6618
 E4F  C7   C  CR6   0  -0.191   2.1560  -1.4078  -0.0272
 E4F  C8   C  CR56  0   0.090   0.1538   3.4109   0.1190
 E4F  C9   C  CR56  0   0.153   0.9320   2.3411  -0.3201
 E4F  C10  C  CR6   0   0.142   1.8320  -0.3831   0.9006
 E4F  C11  C  CR56  0   0.292   4.4495  -1.2933   0.7538
 E4F  C12  C  CR56  0   0.326   3.4738  -1.8153  -0.0820
 E4F  C15  C  CH2   0  -0.524  -1.2400   2.9513   0.4381
 E4F  C16  C  CH2   0   0.068   5.3467  -2.9674  -0.3899
 E4F  C17  C  CR15  0  -0.355   0.1380   1.0640  -0.2893
 E4F  C18  C  CR15  0  -0.048  -1.3132   1.6105  -0.3043
 E4F  C19  C  CH2   0  -0.516   0.4624   0.2361   0.9672
 E4F  C20  C  CH2   0  -0.560  -3.8973  -1.0933   0.2810
 E4F  C21  C  CH2   0  -0.425  -5.2917  -0.6892  -0.2022
 E4F  C22  C  CH2   0  -0.429  -6.3924  -1.4769   0.4945
 E4F  C23  C  CH2   0  -0.272  -7.7831  -1.0610   0.0401
 E4F  N25  N  NH1   0  -0.646  -2.3206   0.7338   0.2315
 E4F  N24  N  NH2   0  -0.801  -8.8071  -1.8402   0.7211
 E4F  O30  O  OH1   0  -0.582   0.0203  -2.2974  -0.4305
 E4F  O26  O  O     0  -0.425   1.4812  -2.3130  -2.1132
 E4F  O27  O  O     0  -0.502  -2.4855  -0.5869  -1.5896
 E4F  O28  O  O     0  -0.483   5.6353  -1.8933   0.4911
 E4F  O29  O  O     0  -0.470   4.0248  -2.7562  -0.8750
 E4F  H1   H  HCR6  0   0.252   2.4528   5.8724  -0.0971
 E4F  H2   H  HCR6  0   0.251   3.8293   3.9828  -0.8783
 E4F  H3   H  HCR6  0   0.246   0.0886   5.5206   0.5397
 E4F  H4   H  HCR6  0   0.242   2.8631   1.7083  -1.0277
 E4F  H5   H  HCR6  0   0.257   2.5859   0.9301   2.3962
 E4F  H6   H  HCR6  0   0.279   4.9149   0.1089   2.3124
 E4F  H7   H  HCH2  0   0.254  -1.3637   2.8122   1.5185
 E4F  H8   H  HCH2  0   0.267  -2.0139   3.6495   0.1167
 E4F  H9   H  HCH2  0   0.251   6.0472  -2.9638  -1.2239
 E4F  H10  H  HCH2  0   0.238   5.3931  -3.9191   0.1497
 E4F  H11  H  HCR5  0   0.264   0.3090   0.4588  -1.1821
 E4F  H12  H  HCR5  0   0.276  -1.5617   1.8161  -1.3485
 E4F  H13  H  HCH2  0   0.267  -0.3023  -0.5248   1.1091
 E4F  H14  H  HCH2  0   0.256   0.4177   0.8831   1.8472
 E4F  H15  H  HCH2  0   0.256  -3.7372  -2.1565   0.0902
 E4F  H16  H  HCH2  0   0.247  -3.8277  -0.9441   1.3613
 E4F  H17  H  HCH2  0   0.227  -5.4378   0.3810  -0.0260
 E4F  H18  H  HCH2  0   0.230  -5.3599  -0.8399  -1.2831
 E4F  H19  H  HCH2  0   0.218  -6.2586  -2.5472   0.3099
 E4F  H20  H  HCH2  0   0.216  -6.3088  -1.3352   1.5779
 E4F  H21  H  HCH2  0   0.188  -7.8902   0.0247   0.1805
 E4F  H22  H  HCH2  0   0.212  -7.8756  -1.2395  -1.0349
 E4F  H23  H  HNH1  0   0.400  -2.6058   0.8695   1.1880
 E4F  H24  H  HNH2  0   0.337  -8.7990  -1.6097   1.7074
 E4F  H25  H  HNH2  0   0.346  -9.7212  -1.5638   0.3864
 E4F  H27  H  HOH1  0   0.484  -0.5928  -2.6241  -1.1067
 E4F  C13  C  C     0   0.475   1.2005  -2.0382  -0.9723
 E4F  C14  C  C     0   0.535  -2.8273  -0.3128  -0.4462

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
 E4F  N24  C23  single    1.456  0.020  1.456
 E4F  C23  C22  single    1.521  0.020  1.521
 E4F  C22  C21  single    1.522  0.020  1.522
 E4F  C21  C20  single    1.530  0.020  1.530
 E4F  C15  C8   single    1.502  0.020  1.502
 E4F  C15  C18  single    1.534  0.020  1.534
 E4F  C20  C14  single    1.511  0.020  1.511
 E4F  O26  C13  double    1.207  0.020  1.207
 E4F  O30  C13  single    1.324  0.020  1.324
 E4F  N25  C14  single    1.346  0.020  1.346
 E4F  N25  C18  single    1.439  0.020  1.439
 E4F  C3   C8   aromatic  1.386  0.020  1.386
 E4F  C3   C1   aromatic  1.392  0.020  1.392
 E4F  C13  C7   single    1.484  0.020  1.484
 E4F  C8   C9   aromatic  1.394  0.020  1.394
 E4F  C14  O27  double    1.224  0.020  1.224
 E4F  C18  C17  single    1.551  0.020  1.551
 E4F  C1   C2   aromatic  1.391  0.020  1.391
 E4F  C19  C17  single    1.539  0.020  1.539
 E4F  C19  C10  single    1.505  0.020  1.505
 E4F  C9   C17  single    1.504  0.020  1.504
 E4F  C9   C4   aromatic  1.386  0.020  1.386
 E4F  C7   C10  aromatic  1.420  0.020  1.420
 E4F  C7   C12  aromatic  1.380  0.020  1.380
 E4F  C2   C4   aromatic  1.392  0.020  1.392
 E4F  C10  C5   aromatic  1.386  0.020  1.386
 E4F  O29  C12  single    1.348  0.020  1.348
 E4F  O29  C16  single    1.424  0.020  1.424
 E4F  C12  C11  aromatic  1.387  0.020  1.387
 E4F  C5   C6   aromatic  1.401  0.020  1.401
 E4F  C16  O28  single    1.419  0.020  1.419
 E4F  C11  C6   aromatic  1.368  0.020  1.368
 E4F  C11  O28  single    1.355  0.020  1.355
 E4F  C1   H1   single    0.930  0.020  1.080
 E4F  C2   H2   single    0.930  0.020  1.080
 E4F  C3   H3   single    0.930  0.020  1.080
 E4F  C4   H4   single    0.930  0.020  1.080
 E4F  C5   H5   single    0.930  0.020  1.080
 E4F  C6   H6   single    0.930  0.020  1.080
 E4F  C15  H7   single    0.970  0.020  1.090
 E4F  C15  H8   single    0.970  0.020  1.090
 E4F  C16  H9   single    0.970  0.020  1.090
 E4F  C16  H10  single    0.970  0.020  1.090
 E4F  C17  H11  single    0.970  0.020  1.090
 E4F  C18  H12  single    0.970  0.020  1.090
 E4F  C19  H13  single    0.970  0.020  1.090
 E4F  C19  H14  single    0.970  0.020  1.090
 E4F  C20  H15  single    0.970  0.020  1.090
 E4F  C20  H16  single    0.970  0.020  1.090
 E4F  C21  H17  single    0.970  0.020  1.090
 E4F  C21  H18  single    0.970  0.020  1.090
 E4F  C22  H19  single    0.970  0.020  1.090
 E4F  C22  H20  single    0.970  0.020  1.090
 E4F  C23  H21  single    0.970  0.020  1.090
 E4F  C23  H22  single    0.970  0.020  1.090
 E4F  N25  H23  single    0.860  0.020  1.020
 E4F  N24  H24  single    0.890  0.020  1.040
 E4F  N24  H25  single    0.890  0.020  1.040
 E4F  O30  H27  single    0.850  0.020  0.980

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
 E4F  H1   C1   C3   119.73  3.000
 E4F  H1   C1   C2   119.77  3.000
 E4F  C3   C1   C2   120.49  3.000
 E4F  H2   C2   C4   119.85  3.000
 E4F  H2   C2   C1   119.70  3.000
 E4F  C4   C2   C1   120.44  3.000
 E4F  H3   C3   C8   120.82  3.000
 E4F  H3   C3   C1   120.20  3.000
 E4F  C8   C3   C1   118.97  3.000
 E4F  H4   C4   C9   120.75  3.000
 E4F  H4   C4   C2   120.23  3.000
 E4F  C9   C4   C2   119.02  3.000
 E4F  H5   C5   C10  118.66  3.000
 E4F  H5   C5   C6   118.15  3.000
 E4F  C10  C5   C6   123.19  3.000
 E4F  H6   C6   C11  122.11  3.000
 E4F  H6   C6   C5   121.16  3.000
 E4F  C11  C6   C5   116.73  3.000
 E4F  C13  C7   C12  117.63  3.000
 E4F  C12  C7   C10  117.19  3.000
 E4F  C13  C7   C10  125.14  3.000
 E4F  C15  C8   C9   110.50  3.000
 E4F  C9   C8   C3   120.56  3.000
 E4F  C15  C8   C3   128.93  3.000
 E4F  C17  C9   C8   110.51  3.000
 E4F  C17  C9   C4   128.96  3.000
 E4F  C8   C9   C4   120.50  3.000
 E4F  C19  C10  C7   122.26  3.000
 E4F  C7   C10  C5   118.96  3.000
 E4F  C19  C10  C5   118.60  3.000
 E4F  O28  C11  C12  109.40  3.000
 E4F  O28  C11  C6   129.15  3.000
 E4F  C12  C11  C6   121.44  3.000
 E4F  O29  C12  C11  109.25  3.000
 E4F  C11  C12  C7   122.45  3.000
 E4F  O29  C12  C7   128.28  3.000
 E4F  H8   C15  H7   106.95  3.000
 E4F  H8   C15  C18  112.52  3.000
 E4F  H7   C15  C18  111.14  3.000
 E4F  H8   C15  C8   113.58  3.000
 E4F  H7   C15  C8   110.66  3.000
 E4F  C18  C15  C8   102.06  3.000
 E4F  H10  C16  H9   110.67  3.000
 E4F  H10  C16  O29  109.64  3.000
 E4F  H9   C16  O29  109.62  3.000
 E4F  H10  C16  O28  110.09  3.000
 E4F  H9   C16  O28  110.01  3.000
 E4F  O29  C16  O28  106.74  3.000
 E4F  H11  C17  C19  109.65  3.000
 E4F  H11  C17  C18  109.51  3.000
 E4F  C19  C17  C18  113.24  3.000
 E4F  H11  C17  C9   111.79  3.000
 E4F  C19  C17  C9   111.23  3.000
 E4F  C18  C17  C9   101.22  3.000
 E4F  H12  C18  N25  108.13  3.000
 E4F  H12  C18  C17  106.76  3.000
 E4F  N25  C18  C17  115.90  3.000
 E4F  H12  C18  C15  107.99  3.000
 E4F  C17  C18  C15  104.99  3.000
 E4F  N25  C18  C15  112.68  3.000
 E4F  H14  C19  H13  106.27  3.000
 E4F  H14  C19  C17  109.28  3.000
 E4F  H13  C19  C17  109.54  3.000
 E4F  H14  C19  C10  108.45  3.000
 E4F  H13  C19  C10  110.96  3.000
 E4F  C17  C19  C10  112.15  3.000
 E4F  H16  C20  H15  107.24  3.000
 E4F  H16  C20  C21  109.52  3.000
 E4F  H15  C20  C21  109.61  3.000
 E4F  H16  C20  C14  111.11  3.000
 E4F  H15  C20  C14  108.36  3.000
 E4F  C21  C20  C14  110.91  3.000
 E4F  H18  C21  H17  106.60  3.000
 E4F  H18  C21  C22  109.63  3.000
 E4F  H17  C21  C22  109.62  3.000
 E4F  H18  C21  C20  109.43  3.000
 E4F  H17  C21  C20  109.22  3.000
 E4F  C22  C21  C20  112.19  3.000
 E4F  H20  C22  H19  106.49  3.000
 E4F  H20  C22  C23  109.25  3.000
 E4F  H19  C22  C23  109.20  3.000
 E4F  H20  C22  C21  109.30  3.000
 E4F  H19  C22  C21  109.91  3.000
 E4F  C23  C22  C21  112.51  3.000
 E4F  H22  C23  H21  106.16  3.000
 E4F  H22  C23  N24  108.24  3.000
 E4F  H21  C23  N24  113.58  3.000
 E4F  H22  C23  C22  109.05  3.000
 E4F  H21  C23  C22  108.71  3.000
 E4F  N24  C23  C22  110.92  3.000
 E4F  H23  N25  C18  118.02  3.000
 E4F  H23  N25  C14  118.44  3.000
 E4F  C18  N25  C14  123.36  3.000
 E4F  H25  N24  H24  105.50  3.000
 E4F  H25  N24  C23  109.54  3.000
 E4F  H24  N24  C23  109.15  3.000
 E4F  H27  O30  C13  110.13  3.000
 E4F  C16  O28  C11  106.12  3.000
 E4F  C16  O29  C12  106.41  3.000
 E4F  O26  C13  O30  123.34  3.000
 E4F  O30  C13  C7   113.35  3.000
 E4F  O26  C13  C7   123.30  3.000
 E4F  O27  C14  N25  122.63  3.000
 E4F  O27  C14  C20  122.10  3.000
 E4F  N25  C14  C20  115.21  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
 E4F  CONST_01  C9   C8   C3   C1     0.00   0.0  0
 E4F  CONST_02  C9   C4   C2   C1     0.00   0.0  0
 E4F  CONST_03  C8   C3   C1   C2     0.00   0.0  0
 E4F  CONST_04  C8   C9   C4   C2     0.00   0.0  0
 E4F  CONST_05  C4   C9   C8   C3     0.00   0.0  0
 E4F  CONST_06  C4   C2   C1   C3     0.00   0.0  0
 E4F  CONST_07  C12  C7   C10  C5     0.00   0.0  0
 E4F  CONST_08  C12  C11  C6   C5     0.00   0.0  0
 E4F  CONST_09  C7   C10  C5   C6     0.00   0.0  0
 E4F  CONST_10  C7   C12  C11  C6     0.00   0.0  0
 E4F  CONST_11  C11  C12  C7   C10    0.00   0.0  0
 E4F  CONST_12  C11  C6   C5   C10    0.00   0.0  0
 E4F  CONST_13  C13  C7   C10  C5   180.00   0.0  0
 E4F  CONST_14  C19  C10  C5   C6   180.00   0.0  0
 E4F  CONST_15  C13  C7   C12  C11  180.00   0.0  0
 E4F  CONST_16  C19  C10  C7   C12  180.00   0.0  0
 E4F  CONST_17  O29  C12  C7   C13    0.00   0.0  0
 E4F  CONST_18  H4   C4   C2   C1   180.00   0.0  0
 E4F  CONST_19  H3   C3   C1   C2   180.00   0.0  0
 E4F  CONST_20  H2   C2   C1   C3   180.00   0.0  0
 E4F  CONST_21  H1   C1   C2   C4   180.00   0.0  0
 E4F  CONST_22  H5   C5   C10  C7   180.00   0.0  0
 E4F  CONST_23  H6   C6   C5   C10  180.00   0.0  0
 E4F  CONST_24  C20  C14  N25  C18  180.00   0.0  0
 E4F  CONST_25  O27  C14  N25  C18    0.00   0.0  0
 E4F  CONST_26  H27  O30  C13  C7   180.00   0.0  0
 E4F  CONST_27  H23  N25  C14  C20    0.00   0.0  0
 E4F  Var_01    C18  C15  C8   C3   161.41  30.0  1
 E4F  Var_02    O29  C16  O28  C11   14.09  30.0  1
 E4F  Var_03    O28  C16  O29  C12  -13.87  30.0  1
 E4F  Var_04    C17  C19  C10  C5   107.48  30.0  2
 E4F  Var_05    O26  C13  C7   C10  139.45  30.0  2
 E4F  Var_06    C22  C21  C20  C14  178.97  30.0  1
 E4F  Var_07    C23  C22  C21  C20  178.83  30.0  1
 E4F  Var_08    N24  C23  C22  C21  179.66  30.0  1
 E4F  Var_09    N25  C14  C20  C21   99.86  30.0  3
 E4F  Var_10    H24  N24  C23  C22   66.41  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
 E4F  chir_01  C17  C18  C19  C9   positiv
 E4F  chir_02  C18  N25  C17  C15  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
 E4F  plan-1  C1   0.020
 E4F  plan-1  C2   0.020
 E4F  plan-1  C3   0.020
 E4F  plan-1  C4   0.020
 E4F  plan-1  C8   0.020
 E4F  plan-1  C9   0.020
 E4F  plan-1  C15  0.020
 E4F  plan-1  C17  0.020
 E4F  plan-1  H1   0.020
 E4F  plan-1  H2   0.020
 E4F  plan-1  H3   0.020
 E4F  plan-1  H4   0.020
 E4F  plan-2  C5   0.020
 E4F  plan-2  C6   0.020
 E4F  plan-2  C7   0.020
 E4F  plan-2  C10  0.020
 E4F  plan-2  C11  0.020
 E4F  plan-2  C12  0.020
 E4F  plan-2  C19  0.020
 E4F  plan-2  O28  0.020
 E4F  plan-2  O29  0.020
 E4F  plan-2  H5   0.020
 E4F  plan-2  H6   0.020
 E4F  plan-2  C13  0.020
 E4F  plan-3  C18  0.020
 E4F  plan-3  C20  0.020
 E4F  plan-3  N25  0.020
 E4F  plan-3  O27  0.020
 E4F  plan-3  H23  0.020
 E4F  plan-3  C14  0.020
 E4F  plan-4  C7   0.020
 E4F  plan-4  O30  0.020
 E4F  plan-4  O26  0.020
 E4F  plan-4  H27  0.020
 E4F  plan-4  C13  0.020

