# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 01:35:21 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 5-[(2S)-2-{[(5-aminopentanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)C[C@H](CNC(=O)CCCCN)Cc1ccc2OCOc2c1C(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
 9PA  9PA  '5-[(2S)-2-{[(5-aminopentanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  57  27  .  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_9PA
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
 9PA  O1    O  OH1   0  -0.584   3.1163  -1.9768   1.1406
 9PA  C2    C  C     0   0.472   2.8749  -0.7086   1.4367
 9PA  O3    O  O     0  -0.425   2.6201  -0.3258   2.5520
 9PA  C4    C  CR6   0  -0.191   2.9951   0.2010   0.2696
 9PA  C5    C  CR56  0   0.326   3.5809   1.4331   0.4851
 9PA  O6    O  O     0  -0.469   4.0755   1.9327   1.6349
 9PA  C7    C  CH2   0   0.069   4.7555   3.1370   1.2962
 9PA  O8    O  O     0  -0.483   4.3884   3.4538  -0.0375
 9PA  C9    C  CR56  0   0.294   3.7759   2.3531  -0.5342
 9PA  C10   C  CR16  0  -0.324   3.3630   2.0992  -1.8129
 9PA  C11   C  CR16  0  -0.344   2.7328   0.8685  -2.0380
 9PA  C12   C  CR6   0   0.137   2.5412  -0.0813  -1.0458
 9PA  C13   C  CH2   0  -0.515   1.7897  -1.3415  -1.3919
 9PA  C14   C  CH1   0  -0.269   0.4147  -1.4723  -0.7105
 9PA  C15   C  CH2   0  -0.260  -0.5268  -0.3960  -1.2634
 9PA  N16   N  NH1   0  -0.633  -1.6476  -0.1055  -0.3978
 9PA  C17   C  C     0   0.558  -2.9409  -0.1657  -0.7548
 9PA  O18   O  O     0  -0.508  -3.3127  -0.4602  -1.8844
 9PA  C19   C  CH2   0  -0.574  -3.9281   0.1147   0.3582
 9PA  C20   C  CH2   0  -0.421  -5.0888   0.9948  -0.0893
 9PA  C21   C  CH2   0  -0.427  -6.1408   1.1640   0.9980
 9PA  C22   C  CH2   0  -0.272  -7.2921   2.0557   0.5587
 9PA  N23   N  NH2   0  -0.801  -8.2891   2.1795   1.6130
 9PA  C24   C  CH2   0  -0.392  -0.0950  -2.9020  -0.9123
 9PA  C25   C  CH1   0  -0.252  -1.3907  -3.3177  -0.2121
 9PA  C26   C  CH3   0  -0.646  -1.7124  -4.7684  -0.5650
 9PA  C27   C  CH3   0  -0.654  -1.3114  -3.1509   1.3012
 9PA  HO1   H  HOH1  0   0.487   3.0152  -2.5274   1.9322
 9PA  H7    H  HCH2  0   0.250   4.4415   3.9352   1.9684
 9PA  H7A   H  HCH2  0   0.239   5.8369   2.9799   1.3615
 9PA  H10   H  HCR6  0   0.280   3.5049   2.8114  -2.6141
 9PA  H11   H  HCR6  0   0.262   2.3777   0.6509  -3.0371
 9PA  H13   H  HCH2  0   0.249   1.6393  -1.3631  -2.4750
 9PA  H13A  H  HCH2  0   0.262   2.3878  -2.2214  -1.1566
 9PA  H14   H  HCH1  0   0.225   0.5399  -1.2930   0.3634
 9PA  H15   H  HCH2  0   0.250   0.0314   0.5305  -1.4239
 9PA  H15A  H  HCH2  0   0.247  -0.9134  -0.7045  -2.2352
 9PA  HN16  H  HNH1  0   0.392  -1.4301   0.2090   0.5335
 9PA  H19   H  HCH2  0   0.261  -4.3126  -0.8555   0.6927
 9PA  H19A  H  HCH2  0   0.245  -3.4301   0.5579   1.2242
 9PA  H20   H  HCH2  0   0.224  -4.7068   1.9766  -0.3857
 9PA  H20A  H  HCH2  0   0.225  -5.5513   0.5606  -0.9787
 9PA  H21   H  HCH2  0   0.215  -6.5352   0.1848   1.2870
 9PA  H21A  H  HCH2  0   0.213  -5.6775   1.5890   1.8957
 9PA  H22   H  HCH2  0   0.187  -6.8853   3.0217   0.2245
 9PA  H22A  H  HCH2  0   0.212  -7.7747   1.6105  -0.3161
 9PA  HN23  H  HNH2  0   0.337  -7.8918   2.6994   2.3862
 9PA  HN2A  H  HNH2  0   0.345  -9.0620   2.7421   1.2810
 9PA  H24   H  HCH2  0   0.219  -0.2080  -3.0726  -1.9897
 9PA  H24A  H  HCH2  0   0.215   0.6952  -3.5869  -0.5811
 9PA  H25   H  HCH1  0   0.228  -2.2147  -2.7065  -0.5886
 9PA  H26   H  HCH3  0   0.211  -0.9238  -5.4409  -0.2177
 9PA  H26A  H  HCH3  0   0.225  -2.6468  -5.0884  -0.1011
 9PA  H26B  H  HCH3  0   0.223  -1.8128  -4.9044  -1.6433
 9PA  H27   H  HCH3  0   0.226  -2.2358  -3.4799   1.7799
 9PA  H27A  H  HCH3  0   0.212  -0.4943  -3.7492   1.7132
 9PA  H27B  H  HCH3  0   0.219  -1.1444  -2.1160   1.6007

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
 9PA  C2   O1    single    1.325  0.020  1.325
 9PA  O1   HO1   single    0.850  0.020  0.980
 9PA  C4   C2    single    1.485  0.020  1.485
 9PA  C2   O3    double    1.206  0.020  1.206
 9PA  C5   C4    aromatic  1.381  0.020  1.381
 9PA  C12  C4    aromatic  1.420  0.020  1.420
 9PA  C9   C5    aromatic  1.387  0.020  1.387
 9PA  C5   O6    single    1.348  0.020  1.348
 9PA  C7   O6    single    1.424  0.020  1.424
 9PA  O8   C7    single    1.419  0.020  1.419
 9PA  C7   H7    single    0.970  0.020  1.090
 9PA  C7   H7A   single    0.970  0.020  1.090
 9PA  O8   C9    single    1.354  0.020  1.354
 9PA  C10  C9    aromatic  1.367  0.020  1.367
 9PA  C10  C11   aromatic  1.401  0.020  1.401
 9PA  C10  H10   single    0.930  0.020  1.080
 9PA  C11  C12   aromatic  1.387  0.020  1.387
 9PA  C11  H11   single    0.930  0.020  1.080
 9PA  C12  C13   single    1.508  0.020  1.508
 9PA  C14  C13   single    1.540  0.020  1.540
 9PA  C13  H13   single    0.970  0.020  1.090
 9PA  C13  H13A  single    0.970  0.020  1.090
 9PA  C15  C14   single    1.533  0.020  1.533
 9PA  C14  C24   single    1.531  0.020  1.531
 9PA  C14  H14   single    0.970  0.020  1.090
 9PA  C15  N16   single    1.446  0.020  1.446
 9PA  C15  H15   single    0.970  0.020  1.090
 9PA  C15  H15A  single    0.970  0.020  1.090
 9PA  N16  C17   single    1.343  0.020  1.343
 9PA  N16  HN16  single    0.860  0.020  1.020
 9PA  O18  C17   double    1.225  0.020  1.225
 9PA  C17  C19   single    1.514  0.020  1.514
 9PA  C19  C20   single    1.524  0.020  1.524
 9PA  C19  H19   single    0.970  0.020  1.090
 9PA  C19  H19A  single    0.970  0.020  1.090
 9PA  C20  C21   single    1.522  0.020  1.522
 9PA  C20  H20   single    0.970  0.020  1.090
 9PA  C20  H20A  single    0.970  0.020  1.090
 9PA  C21  C22   single    1.521  0.020  1.521
 9PA  C21  H21   single    0.970  0.020  1.090
 9PA  C21  H21A  single    0.970  0.020  1.090
 9PA  C22  N23   single    1.456  0.020  1.456
 9PA  C22  H22   single    0.970  0.020  1.090
 9PA  C22  H22A  single    0.970  0.020  1.090
 9PA  N23  HN23  single    0.890  0.020  1.040
 9PA  N23  HN2A  single    0.890  0.020  1.040
 9PA  C24  C25   single    1.530  0.020  1.530
 9PA  C24  H24   single    0.970  0.020  1.090
 9PA  C24  H24A  single    0.970  0.020  1.090
 9PA  C26  C25   single    1.527  0.020  1.527
 9PA  C25  C27   single    1.525  0.020  1.525
 9PA  C25  H25   single    0.970  0.020  1.090
 9PA  C26  H26   single    0.970  0.020  1.090
 9PA  C26  H26A  single    0.970  0.020  1.090
 9PA  C26  H26B  single    0.970  0.020  1.090
 9PA  C27  H27   single    0.970  0.020  1.090
 9PA  C27  H27A  single    0.970  0.020  1.090
 9PA  C27  H27B  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
 9PA  HO1   O1   C2    110.01  3.000
 9PA  C4    C2   O3    123.33  3.000
 9PA  O3    C2   O1    123.30  3.000
 9PA  C4    C2   O1    113.34  3.000
 9PA  C12   C4   C5    117.23  3.000
 9PA  C12   C4   C2    125.50  3.000
 9PA  C5    C4   C2    117.27  3.000
 9PA  C9    C5   O6    109.24  3.000
 9PA  O6    C5   C4    128.28  3.000
 9PA  C9    C5   C4    122.46  3.000
 9PA  C7    O6   C5    106.61  3.000
 9PA  H7A   C7   H7    110.67  3.000
 9PA  H7A   C7   O8    110.10  3.000
 9PA  H7    C7   O8    109.98  3.000
 9PA  H7A   C7   O6    109.64  3.000
 9PA  H7    C7   O6    109.58  3.000
 9PA  O8    C7   O6    106.79  3.000
 9PA  C9    O8   C7    106.28  3.000
 9PA  C10   C9   O8    129.09  3.000
 9PA  C10   C9   C5    121.44  3.000
 9PA  O8    C9   C5    109.46  3.000
 9PA  H10   C10  C11   121.24  3.000
 9PA  H10   C10  C9    122.07  3.000
 9PA  C11   C10  C9    116.69  3.000
 9PA  H11   C11  C12   118.51  3.000
 9PA  H11   C11  C10   118.20  3.000
 9PA  C12   C11  C10   123.29  3.000
 9PA  C13   C12  C11   118.50  3.000
 9PA  C13   C12  C4    122.56  3.000
 9PA  C11   C12  C4    118.85  3.000
 9PA  H13A  C13  H13   105.87  3.000
 9PA  H13A  C13  C14   109.02  3.000
 9PA  H13   C13  C14   108.28  3.000
 9PA  H13A  C13  C12   110.60  3.000
 9PA  H13   C13  C12   108.21  3.000
 9PA  C14   C13  C12   114.49  3.000
 9PA  H14   C14  C24   108.66  3.000
 9PA  H14   C14  C15   107.98  3.000
 9PA  C24   C14  C15   113.80  3.000
 9PA  H14   C14  C13   108.52  3.000
 9PA  C24   C14  C13   108.55  3.000
 9PA  C15   C14  C13   109.21  3.000
 9PA  H15A  C15  H15   106.85  3.000
 9PA  H15A  C15  N16   108.39  3.000
 9PA  H15   C15  N16   108.26  3.000
 9PA  H15A  C15  C14   109.91  3.000
 9PA  H15   C15  C14   109.53  3.000
 9PA  N16   C15  C14   113.66  3.000
 9PA  HN16  N16  C17   117.90  3.000
 9PA  HN16  N16  C15   116.69  3.000
 9PA  C17   N16  C15   125.34  3.000
 9PA  C19   C17  O18   121.63  3.000
 9PA  C19   C17  N16   115.10  3.000
 9PA  O18   C17  N16   123.24  3.000
 9PA  H19A  C19  H19   106.08  3.000
 9PA  H19A  C19  C20   110.21  3.000
 9PA  H19   C19  C20   109.50  3.000
 9PA  H19A  C19  C17   111.14  3.000
 9PA  H19   C19  C17   106.81  3.000
 9PA  C20   C19  C17   112.82  3.000
 9PA  H20A  C20  H20   106.49  3.000
 9PA  H20A  C20  C21   109.46  3.000
 9PA  H20   C20  C21   109.57  3.000
 9PA  H20A  C20  C19   109.39  3.000
 9PA  H20   C20  C19   109.38  3.000
 9PA  C21   C20  C19   112.39  3.000
 9PA  H21A  C21  H21   106.43  3.000
 9PA  H21A  C21  C22   109.22  3.000
 9PA  H21   C21  C22   109.15  3.000
 9PA  H21A  C21  C20   109.64  3.000
 9PA  H21   C21  C20   109.77  3.000
 9PA  C22   C21  C20   112.46  3.000
 9PA  H22A  C22  H22   106.12  3.000
 9PA  H22A  C22  N23   108.15  3.000
 9PA  H22   C22  N23   113.48  3.000
 9PA  H22A  C22  C21   109.05  3.000
 9PA  H22   C22  C21   108.82  3.000
 9PA  N23   C22  C21   111.03  3.000
 9PA  HN2A  N23  HN23  105.34  3.000
 9PA  HN2A  N23  C22   109.43  3.000
 9PA  HN23  N23  C22   109.14  3.000
 9PA  H24A  C24  H24   105.89  3.000
 9PA  H24A  C24  C25   107.59  3.000
 9PA  H24   C24  C25   108.66  3.000
 9PA  H24A  C24  C14   107.66  3.000
 9PA  H24   C24  C14   108.00  3.000
 9PA  C25   C24  C14   118.37  3.000
 9PA  H25   C25  C27   108.66  3.000
 9PA  H25   C25  C26   107.03  3.000
 9PA  C27   C25  C26   110.13  3.000
 9PA  H25   C25  C24   109.20  3.000
 9PA  C27   C25  C24   112.36  3.000
 9PA  C26   C25  C24   109.31  3.000
 9PA  H26B  C26  H26A  107.74  3.000
 9PA  H26B  C26  H26   107.67  3.000
 9PA  H26A  C26  H26   107.60  3.000
 9PA  H26B  C26  C25   111.47  3.000
 9PA  H26A  C26  C25   111.15  3.000
 9PA  H26   C26  C25   111.04  3.000
 9PA  H27B  C27  H27A  107.54  3.000
 9PA  H27B  C27  H27   107.18  3.000
 9PA  H27A  C27  H27   107.62  3.000
 9PA  H27B  C27  C25   112.61  3.000
 9PA  H27A  C27  C25   110.67  3.000
 9PA  H27   C27  C25   110.99  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
 9PA  CONST_01  C10   C9   C5   C4      0.00   0.0  0
 9PA  CONST_02  C10   C11  C12  C4      0.00   0.0  0
 9PA  CONST_03  C11   C12  C4   C5      0.00   0.0  0
 9PA  CONST_04  C11   C10  C9   C5      0.00   0.0  0
 9PA  CONST_05  C12   C4   C5   C9      0.00   0.0  0
 9PA  CONST_06  C12   C11  C10  C9      0.00   0.0  0
 9PA  CONST_07  C9    C5   C4   C2    180.00   0.0  0
 9PA  CONST_08  O6    C5   C4   C2      0.00   0.0  0
 9PA  CONST_09  C11   C12  C4   C2    180.00   0.0  0
 9PA  CONST_10  C13   C12  C4   C5    180.00   0.0  0
 9PA  CONST_11  C13   C12  C11  C10   180.00   0.0  0
 9PA  CONST_12  H11   C11  C12  C4    180.00   0.0  0
 9PA  CONST_13  H10   C10  C9   C5    180.00   0.0  0
 9PA  CONST_14  HO1   O1   C2   C4    180.00   0.0  0
 9PA  CONST_15  O18   C17  N16  C15     0.00   0.0  0
 9PA  CONST_16  C19   C17  N16  C15   180.00   0.0  0
 9PA  CONST_17  HN16  N16  C17  O18   180.00   0.0  0
 9PA  Var_01    O8    C7   O6   C5     12.24  30.0  1
 9PA  Var_02    C9    C5   O6   C7     -7.38  30.0  1
 9PA  Var_03    C10   C9   O8   C7   -172.52  30.0  1
 9PA  Var_04    C5    C4   C2   O1   -140.55  30.0  2
 9PA  Var_05    C14   C13  C12  C4     64.46  30.0  2
 9PA  Var_06    C17   N16  C15  C14  -124.54  30.0  3
 9PA  Var_07    C26   C25  C24  C14   179.41  30.0  3
 9PA  Var_08    C20   C19  C17  N16   138.09  30.0  3
 9PA  Var_09    C21   C20  C19  C17   174.66  30.0  3
 9PA  Var_10    C22   C21  C20  C19   179.32  30.0  3
 9PA  Var_11    N23   C22  C21  C20   179.11  30.0  3
 9PA  Var_12    HN23  N23  C22  C21    67.74  30.0  3
 9PA  Var_13    H26   C26  C25  C24    61.74  30.0  3
 9PA  Var_14    H27   C27  C25  C24  -178.39  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
 9PA  chir_01  C14  C13  C15  C24  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
 9PA  plan-1  C15   0.020
 9PA  plan-1  N16   0.020
 9PA  plan-1  C17   0.020
 9PA  plan-1  O18   0.020
 9PA  plan-1  C19   0.020
 9PA  plan-1  HN16  0.020
 9PA  plan-2  C2    0.020
 9PA  plan-2  C4    0.020
 9PA  plan-2  C5    0.020
 9PA  plan-2  O6    0.020
 9PA  plan-2  O8    0.020
 9PA  plan-2  C9    0.020
 9PA  plan-2  C10   0.020
 9PA  plan-2  C11   0.020
 9PA  plan-2  C12   0.020
 9PA  plan-2  C13   0.020
 9PA  plan-2  H10   0.020
 9PA  plan-2  H11   0.020
 9PA  plan-3  O1    0.020
 9PA  plan-3  C2    0.020
 9PA  plan-3  O3    0.020
 9PA  plan-3  C4    0.020
 9PA  plan-3  HO1   0.020

