# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 20:26:51 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  56  27  .  2021-08-06  2022-09-22
;
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  OC    -1  -0.585   3.3723  -1.8823   1.2857
 9PA  C2    C  C      0   0.363   2.8422  -0.7711   1.4600
 9PA  O3    O  O      0  -0.592   2.2659  -0.3555   2.4800
 9PA  C4    C  C      0  -0.182   2.9375   0.2147   0.3030
 9PA  C5    C  CR5    0   0.286   3.4976   1.4545   0.5081
 9PA  O6    O  O      0  -0.482   3.9844   1.9688   1.6718
 9PA  C7    C  CH2    0   0.067   4.6910   3.1432   1.3119
 9PA  O8    O  O      0  -0.491   4.2598   3.5029   0.0074
 9PA  C9    C  CR5    0   0.280   3.6698   2.3884  -0.5004
 9PA  C10   C  C1     0  -0.350   3.2534   2.1426  -1.7831
 9PA  C11   C  C1     0  -0.340   2.6509   0.8990  -2.0097
 9PA  C12   C  C      0   0.086   2.4923  -0.0554  -1.0113
 9PA  C13   C  CH2    0  -0.501   1.7954  -1.3518  -1.3294
 9PA  C14   C  CH1    0  -0.270   0.4080  -1.4952  -0.6767
 9PA  C15   C  CH2    0  -0.263  -0.5522  -0.4624  -1.2762
 9PA  N16   N  NH1    0  -0.632  -1.6709  -0.1507  -0.4134
 9PA  C17   C  C      0   0.557  -2.9647  -0.2017  -0.7655
 9PA  O18   O  O      0  -0.511  -3.3440  -0.4993  -1.8924
 9PA  C19   C  CH2    0  -0.574  -3.9455   0.0935   0.3497
 9PA  C20   C  CH2    0  -0.421  -5.1012   0.9798  -0.0981
 9PA  C21   C  CH2    0  -0.427  -6.1463   1.1650   0.9932
 9PA  C22   C  CH2    0  -0.272  -7.2910   2.0658   0.5559
 9PA  N23   N  NH2    0  -0.801  -8.2812   2.2040   1.6149
 9PA  C24   C  CH2    0  -0.389  -0.0663  -2.9404  -0.8527
 9PA  C25   C  CH1    0  -0.252  -1.3835  -3.3590  -0.1962
 9PA  C26   C  CH3    0  -0.646  -1.6864  -4.8144  -0.5463
 9PA  C27   C  CH3    0  -0.651  -1.3578  -3.1780   1.3174
 9PA  H7    H  HCH2   0   0.241   4.4585   3.9452   2.0122
 9PA  H7A   H  HCH2   0   0.224   5.7697   2.9440   1.3043
 9PA  H10   H  H      0   0.264   3.3772   2.8650  -2.5784
 9PA  H11   H  H      0   0.246   2.2997   0.6701  -3.0087
 9PA  H13   H  HCH2   0   0.231   1.6837  -1.4459  -2.4140
 9PA  H13A  H  HCH2   0   0.247   2.4134  -2.1890  -1.0034
 9PA  H14   H  HCH1   0   0.239   0.5185  -1.2836   0.3926
 9PA  H15   H  HCH2   0   0.248  -0.0102   0.4640  -1.4856
 9PA  H15A  H  HCH2   0   0.242  -0.9426  -0.8216  -2.2293
 9PA  HN16  H  HNH1   0   0.391  -1.4483   0.1616   0.5174
 9PA  H19   H  HCH2   0   0.260  -4.3355  -0.8715   0.6928
 9PA  H19A  H  HCH2   0   0.245  -3.4396   0.5386   1.2103
 9PA  H20   H  HCH2   0   0.223  -4.7129   1.9565  -0.4033
 9PA  H20A  H  HCH2   0   0.224  -5.5715   0.5435  -0.9823
 9PA  H21   H  HCH2   0   0.215  -6.5489   0.1911   1.2890
 9PA  H21A  H  HCH2   0   0.213  -5.6739   1.5892   1.8866
 9PA  H22   H  HCH2   0   0.187  -6.8771   3.0263   0.2150
 9PA  H22A  H  HCH2   0   0.211  -7.7827   1.6212  -0.3143
 9PA  HN23  H  HNH2   0   0.337  -7.8746   2.7235   2.3835
 9PA  HN2A  H  HNH2   0   0.345  -9.0507   2.7723   1.2845
 9PA  H24   H  HCH2   0   0.212  -0.1312  -3.1465  -1.9283
 9PA  H24A  H  HCH2   0   0.211   0.7218  -3.5992  -0.4677
 9PA  H25   H  HCH1   0   0.226  -2.1975  -2.7555  -0.6062
 9PA  H26   H  HCH3   0   0.210  -0.9025  -5.4789  -0.1736
 9PA  H26A  H  HCH3   0   0.223  -2.6308  -5.1383  -0.1055
 9PA  H26B  H  HCH3   0   0.222  -1.7569  -4.9588  -1.6260
 9PA  H27   H  HCH3   0   0.223  -2.3054  -3.4841   1.7652
 9PA  H27A  H  HCH3   0   0.211  -0.5677  -3.7872   1.7642
 9PA  H27B  H  HCH3   0   0.219  -1.1789  -2.1438   1.6121

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    deloc     1.243  0.020  1.243
 9PA  C4   C2    single    1.523  0.020  1.523
 9PA  C2   O3    deloc     1.243  0.020  1.243
 9PA  C5   C4    aromatic  1.376  0.020  1.376
 9PA  C12  C4    aromatic  1.414  0.020  1.414
 9PA  C9   C5    aromatic  1.385  0.020  1.385
 9PA  C5   O6    single    1.362  0.020  1.362
 9PA  C7   O6    single    1.417  0.020  1.417
 9PA  O8   C7    single    1.420  0.020  1.420
 9PA  C7   H7    single    0.970  0.020  1.090
 9PA  C7   H7A   single    0.970  0.020  1.090
 9PA  O8   C9    single    1.360  0.020  1.360
 9PA  C10  C9    aromatic  1.371  0.020  1.371
 9PA  C10  C11   aromatic  1.400  0.020  1.400
 9PA  C10  H10   single    0.930  0.020  1.080
 9PA  C11  C12   aromatic  1.390  0.020  1.390
 9PA  C11  H11   single    0.930  0.020  1.080
 9PA  C12  C13   single    1.506  0.020  1.506
 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    1.532  0.020  1.532
 9PA  C14  C24   single    1.531  0.020  1.531
 9PA  C14  H14   single    0.970  0.020  1.090
 9PA  C15  N16   single    1.447  0.020  1.447
 9PA  C15  H15   single    0.970  0.020  1.090
 9PA  C15  H15A  single    0.970  0.020  1.090
 9PA  N16  C17   single    1.342  0.020  1.342
 9PA  N16  HN16  single    0.860  0.020  1.020
 9PA  O18  C17   double    1.226  0.020  1.226
 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  C4    C2   O3    115.85  3.000
 9PA  O3    C2   O1    127.69  3.000
 9PA  C4    C2   O1    116.44  3.000
 9PA  C12   C4   C5    116.04  3.000
 9PA  C12   C4   C2    124.26  3.000
 9PA  C5    C4   C2    119.70  3.000
 9PA  C9    C5   O6    108.85  3.000
 9PA  O6    C5   C4    127.81  3.000
 9PA  C9    C5   C4    123.34  3.000
 9PA  C7    O6   C5    105.91  3.000
 9PA  H7A   C7   H7    110.36  3.000
 9PA  H7A   C7   O8    109.76  3.000
 9PA  H7    C7   O8    109.82  3.000
 9PA  H7A   C7   O6    109.98  3.000
 9PA  H7    C7   O6    109.90  3.000
 9PA  O8    C7   O6    106.97  3.000
 9PA  C9    O8   C7    105.50  3.000
 9PA  C10   C9   O8    128.92  3.000
 9PA  C10   C9   C5    121.51  3.000
 9PA  O8    C9   C5    109.55  3.000
 9PA  H10   C10  C11   121.56  3.000
 9PA  H10   C10  C9    122.25  3.000
 9PA  C11   C10  C9    116.18  3.000
 9PA  H11   C11  C12   118.69  3.000
 9PA  H11   C11  C10   118.45  3.000
 9PA  C12   C11  C10   122.86  3.000
 9PA  C13   C12  C11   119.48  3.000
 9PA  C13   C12  C4    120.44  3.000
 9PA  C11   C12  C4    120.03  3.000
 9PA  H13A  C13  H13   106.74  3.000
 9PA  H13A  C13  C14   108.20  3.000
 9PA  H13   C13  C14   108.67  3.000
 9PA  H13A  C13  C12   109.61  3.000
 9PA  H13   C13  C12   109.31  3.000
 9PA  C14   C13  C12   114.05  3.000
 9PA  H14   C14  C24   109.00  3.000
 9PA  H14   C14  C15   108.35  3.000
 9PA  C24   C14  C15   113.39  3.000
 9PA  H14   C14  C13   107.75  3.000
 9PA  C24   C14  C13   108.56  3.000
 9PA  C15   C14  C13   109.64  3.000
 9PA  H15A  C15  H15   106.80  3.000
 9PA  H15A  C15  N16   108.38  3.000
 9PA  H15   C15  N16   108.36  3.000
 9PA  H15A  C15  C14   110.13  3.000
 9PA  H15   C15  C14   109.59  3.000
 9PA  N16   C15  C14   113.36  3.000
 9PA  HN16  N16  C17   117.88  3.000
 9PA  HN16  N16  C15   116.57  3.000
 9PA  C17   N16  C15   125.52  3.000
 9PA  C19   C17  O18   121.60  3.000
 9PA  C19   C17  N16   115.08  3.000
 9PA  O18   C17  N16   123.29  3.000
 9PA  H19A  C19  H19   106.07  3.000
 9PA  H19A  C19  C20   110.22  3.000
 9PA  H19   C19  C20   109.53  3.000
 9PA  H19A  C19  C17   111.07  3.000
 9PA  H19   C19  C17   106.82  3.000
 9PA  C20   C19  C17   112.85  3.000
 9PA  H20A  C20  H20   106.47  3.000
 9PA  H20A  C20  C21   109.47  3.000
 9PA  H20   C20  C21   109.56  3.000
 9PA  H20A  C20  C19   109.40  3.000
 9PA  H20   C20  C19   109.39  3.000
 9PA  C21   C20  C19   112.38  3.000
 9PA  H21A  C21  H21   106.42  3.000
 9PA  H21A  C21  C22   109.24  3.000
 9PA  H21   C21  C22   109.14  3.000
 9PA  H21A  C21  C20   109.61  3.000
 9PA  H21   C21  C20   109.75  3.000
 9PA  C22   C21  C20   112.50  3.000
 9PA  H22A  C22  H22   106.11  3.000
 9PA  H22A  C22  N23   108.15  3.000
 9PA  H22   C22  N23   113.47  3.000
 9PA  H22A  C22  C21   109.05  3.000
 9PA  H22   C22  C21   108.85  3.000
 9PA  N23   C22  C21   111.03  3.000
 9PA  HN2A  N23  HN23  105.36  3.000
 9PA  HN2A  N23  C22   109.44  3.000
 9PA  HN23  N23  C22   109.12  3.000
 9PA  H24A  C24  H24   105.89  3.000
 9PA  H24A  C24  C25   107.67  3.000
 9PA  H24   C24  C25   108.56  3.000
 9PA  H24A  C24  C14   107.69  3.000
 9PA  H24   C24  C14   107.96  3.000
 9PA  C25   C24  C14   118.40  3.000
 9PA  H25   C25  C27   108.62  3.000
 9PA  H25   C25  C26   107.01  3.000
 9PA  C27   C25  C26   110.12  3.000
 9PA  H25   C25  C24   109.21  3.000
 9PA  C27   C25  C24   112.27  3.000
 9PA  C26   C25  C24   109.46  3.000
 9PA  H26B  C26  H26A  107.72  3.000
 9PA  H26B  C26  H26   107.65  3.000
 9PA  H26A  C26  H26   107.61  3.000
 9PA  H26B  C26  C25   111.44  3.000
 9PA  H26A  C26  C25   111.21  3.000
 9PA  H26   C26  C25   111.03  3.000
 9PA  H27B  C27  H27A  107.43  3.000
 9PA  H27B  C27  H27   107.31  3.000
 9PA  H27A  C27  H27   107.66  3.000
 9PA  H27B  C27  C25   112.57  3.000
 9PA  H27A  C27  C25   110.60  3.000
 9PA  H27   C27  C25   111.05  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  O18   C17  N16  C15     0.00   0.0  0
 9PA  CONST_15  C19   C17  N16  C15   180.00   0.0  0
 9PA  CONST_16  HN16  N16  C17  O18   180.00   0.0  0
 9PA  Var_01    O8    C7   O6   C5     17.45  30.0  1
 9PA  Var_02    C9    C5   O6   C7    -10.76  30.0  1
 9PA  Var_03    C10   C9   O8   C7   -170.06  30.0  1
 9PA  Var_04    C5    C4   C2   O1   -123.75  30.0  2
 9PA  Var_05    C14   C13  C12  C4     67.68  30.0  2
 9PA  Var_06    C17   N16  C15  C14  -127.12  30.0  3
 9PA  Var_07    C26   C25  C24  C14   177.76  30.0  3
 9PA  Var_08    C20   C19  C17  N16   138.15  30.0  3
 9PA  Var_09    C21   C20  C19  C17   174.73  30.0  3
 9PA  Var_10    C22   C21  C20  C19   179.16  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    61.18  30.0  3
 9PA  Var_14    H27   C27  C25  C24  -179.88  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

