# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 16:39:57 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 5-[(2S)-2-{[(4-aminobutanoyl)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)CCCN)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
 K1T  K1T  '5-[(2S)-2-{[(4-aminobutanoyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  54  26  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_K1T
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
 K1T  C1    C  CH3   0  -0.656  -0.1349  -3.8809   1.3000
 K1T  C2    C  CH1   0  -0.238  -0.0209  -3.9112  -0.2211
 K1T  C3    C  CH3   0  -0.651  -0.6427  -5.1904  -0.7740
 K1T  C4    C  CH2   0  -0.398  -0.6787  -2.6935  -0.8739
 K1T  C5    C  CH1   0  -0.274  -0.0322  -1.3359  -0.5908
 K1T  C7    C  CH2   0  -0.524   1.3116  -1.2124  -1.3266
 K1T  C8    C  CR6   0   0.122   2.0523   0.0757  -1.0734
 K1T  C9    C  CR6   0  -0.191   2.5978   0.3960   0.1958
 K1T  C10   C  CR6   0   0.337   3.1728   1.6425   0.3419
 K1T  C11   C  CR6   0   0.296   3.2606   2.5455  -0.7072
 K1T  C12   C  CR16  0  -0.324   2.7545   2.2561  -1.9445
 K1T  C13   C  CR16  0  -0.338   2.1400   1.0067  -2.0970
 K1T  O14   O  O2    0  -0.483   3.9239   3.6523  -0.2977
 K1T  C15   C  CH2   0   0.070   4.1512   3.4959   1.0946
 K1T  O16   O  O2    0  -0.472   3.7843   2.1606   1.4263
 K1T  C17   C  C     0   0.481   2.6328  -0.5735   1.3198
 K1T  O18   O  OH1   0  -0.582   2.3569  -0.0017   2.4829
 K1T  O19   O  O     0  -0.423   2.8964  -1.7444   1.2014
 K1T  C20   C  CH2   0  -0.252  -0.9686  -0.1958  -0.9991
 K1T  N21   N  NH1   0  -0.630  -2.1605  -0.1588  -0.1838
 K1T  C22   C  C     0   0.544  -3.4212  -0.2025  -0.6439
 K1T  O23   O  O     0  -0.508  -3.7047  -0.2560  -1.8347
 K1T  C24   C  CH2   0  -0.572  -4.4926  -0.1768   0.4242
 K1T  C25   C  CH2   0  -0.429  -5.4577   0.9913   0.2430
 K1T  C26   C  CH2   0  -0.272  -6.5436   0.9958   1.3070
 K1T  N27   N  NH2   0  -0.800  -7.4280   2.1388   1.1397
 K1T  H1    H  HCH3  0   0.228   0.3693  -3.0188   1.7369
 K1T  H1A   H  HCH3  0   0.210  -1.1825  -3.8498   1.6111
 K1T  H1B   H  HCH3  0   0.224   0.3124  -4.7739   1.7405
 K1T  H2    H  HCH1  0   0.218   1.0434  -3.9252  -0.4806
 K1T  H3    H  HCH3  0   0.212  -1.7130  -5.2318  -0.5562
 K1T  H3A   H  HCH3  0   0.224  -0.5245  -5.2548  -1.8573
 K1T  H3B   H  HCH3  0   0.224  -0.1824  -6.0770  -0.3346
 K1T  H4    H  HCH2  0   0.217  -0.6999  -2.8371  -1.9611
 K1T  H4A   H  HCH2  0   0.224  -1.7260  -2.6663  -0.5550
 K1T  H5    H  HCH1  0   0.228   0.1420  -1.2402   0.4874
 K1T  H7    H  HCH2  0   0.267   1.9398  -2.0651  -1.0722
 K1T  H7A   H  HCH2  0   0.246   1.1187  -1.2901  -2.4006
 K1T  H12   H  HCR6  0   0.280   2.8236   2.9524  -2.7690
 K1T  H13   H  HCR6  0   0.260   1.7099   0.7594  -3.0590
 K1T  H15   H  HCH2  0   0.248   5.2063   3.6525   1.3202
 K1T  H15A  H  HCH2  0   0.240   3.5294   4.1982   1.6574
 K1T  HO18  H  HOH1  0   0.487   2.4485  -0.6482   3.1999
 K1T  H20   H  HCH2  0   0.251  -0.4504   0.7635  -0.9205
 K1T  H20A  H  HCH2  0   0.240  -1.2678  -0.3104  -2.0415
 K1T  HN21  H  HNH1  0   0.396  -2.0264  -0.0866   0.8119
 K1T  H24   H  HCH2  0   0.259  -5.0438  -1.1201   0.3626
 K1T  H24A  H  HCH2  0   0.244  -4.0518  -0.1414   1.4235
 K1T  H25   H  HCH2  0   0.227  -4.9097   1.9367   0.2873
 K1T  H25A  H  HCH2  0   0.227  -5.9162   0.9372  -0.7482
 K1T  H26   H  HCH2  0   0.191  -7.0649   0.0270   1.2870
 K1T  H26A  H  HCH2  0   0.215  -6.0766   1.0682   2.2932
 K1T  HN27  H  HNH2  0   0.338  -7.9661   2.0260   0.2891
 K1T  HN2A  H  HNH2  0   0.347  -8.1059   2.1541   1.8907

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
 K1T  C1   C2    single    1.526  0.020  1.526
 K1T  C1   H1    single    0.970  0.020  1.090
 K1T  C1   H1A   single    0.970  0.020  1.090
 K1T  C1   H1B   single    0.970  0.020  1.090
 K1T  C4   C2    single    1.530  0.020  1.530
 K1T  C2   C3    single    1.526  0.020  1.526
 K1T  C2   H2    single    0.970  0.020  1.090
 K1T  C3   H3    single    0.970  0.020  1.090
 K1T  C3   H3A   single    0.970  0.020  1.090
 K1T  C3   H3B   single    0.970  0.020  1.090
 K1T  C5   C4    single    1.530  0.020  1.530
 K1T  C4   H4    single    0.970  0.020  1.090
 K1T  C4   H4A   single    0.970  0.020  1.090
 K1T  C20  C5    single    1.531  0.020  1.531
 K1T  C5   C7    single    1.537  0.020  1.537
 K1T  C5   H5    single    0.970  0.020  1.090
 K1T  C8   C7    single    1.507  0.020  1.507
 K1T  C7   H7    single    0.970  0.020  1.090
 K1T  C7   H7A   single    0.970  0.020  1.090
 K1T  C13  C8    aromatic  1.386  0.020  1.386
 K1T  C8   C9    aromatic  1.418  0.020  1.418
 K1T  C10  C9    aromatic  1.380  0.020  1.380
 K1T  C9   C17   single    1.485  0.020  1.485
 K1T  C11  C10   aromatic  1.387  0.020  1.387
 K1T  C10  O16   single    1.348  0.020  1.348
 K1T  O14  C11   single    1.354  0.020  1.354
 K1T  C12  C11   aromatic  1.368  0.020  1.368
 K1T  C12  C13   aromatic  1.401  0.020  1.401
 K1T  C12  H12   single    0.930  0.020  1.080
 K1T  C13  H13   single    0.930  0.020  1.080
 K1T  O14  C15   single    1.419  0.020  1.419
 K1T  C15  O16   single    1.424  0.020  1.424
 K1T  C15  H15   single    0.970  0.020  1.090
 K1T  C15  H15A  single    0.970  0.020  1.090
 K1T  C17  O19   double    1.206  0.020  1.206
 K1T  C17  O18   single    1.325  0.020  1.325
 K1T  O18  HO18  single    0.850  0.020  0.980
 K1T  C20  N21   single    1.444  0.020  1.444
 K1T  C20  H20   single    0.970  0.020  1.090
 K1T  C20  H20A  single    0.970  0.020  1.090
 K1T  N21  C22   single    1.343  0.020  1.343
 K1T  N21  HN21  single    0.860  0.020  1.020
 K1T  O23  C22   double    1.225  0.020  1.225
 K1T  C22  C24   single    1.513  0.020  1.513
 K1T  C24  C25   single    1.526  0.020  1.526
 K1T  C24  H24   single    0.970  0.020  1.090
 K1T  C24  H24A  single    0.970  0.020  1.090
 K1T  C25  C26   single    1.520  0.020  1.520
 K1T  C25  H25   single    0.970  0.020  1.090
 K1T  C25  H25A  single    0.970  0.020  1.090
 K1T  C26  N27   single    1.455  0.020  1.455
 K1T  C26  H26   single    0.970  0.020  1.090
 K1T  C26  H26A  single    0.970  0.020  1.090
 K1T  N27  HN27  single    0.890  0.020  1.040
 K1T  N27  HN2A  single    0.890  0.020  1.040

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
 K1T  H1B   C1   H1A   107.52  3.000
 K1T  H1B   C1   H1    107.20  3.000
 K1T  H1A   C1   H1    107.86  3.000
 K1T  H1B   C1   C2    110.82  3.000
 K1T  H1A   C1   C2    110.85  3.000
 K1T  H1    C1   C2    112.38  3.000
 K1T  H2    C2   C4    109.07  3.000
 K1T  H2    C2   C3    107.42  3.000
 K1T  C4    C2   C3    109.71  3.000
 K1T  H2    C2   C1    108.00  3.000
 K1T  C3    C2   C1    110.33  3.000
 K1T  C4    C2   C1    112.17  3.000
 K1T  H3B   C3   H3A   107.81  3.000
 K1T  H3B   C3   H3    107.57  3.000
 K1T  H3A   C3   H3    107.55  3.000
 K1T  H3B   C3   C2    111.30  3.000
 K1T  H3A   C3   C2    111.40  3.000
 K1T  H3    C3   C2    111.01  3.000
 K1T  H4A   C4   H4    105.87  3.000
 K1T  H4A   C4   C5    109.16  3.000
 K1T  H4    C4   C5    107.93  3.000
 K1T  H4A   C4   C2    107.85  3.000
 K1T  H4    C4   C2    109.08  3.000
 K1T  C5    C4   C2    116.45  3.000
 K1T  H5    C5   C20   107.12  3.000
 K1T  H5    C5   C7    108.96  3.000
 K1T  C20   C5   C7    110.32  3.000
 K1T  H5    C5   C4    109.06  3.000
 K1T  C7    C5   C4    110.62  3.000
 K1T  C20   C5   C4    110.67  3.000
 K1T  H7A   C7   H7    105.98  3.000
 K1T  H7A   C7   C8    108.20  3.000
 K1T  H7    C7   C8    110.26  3.000
 K1T  H7A   C7   C5    108.07  3.000
 K1T  H7    C7   C5    109.24  3.000
 K1T  C8    C7   C5    114.70  3.000
 K1T  C13   C8   C9    119.00  3.000
 K1T  C9    C8   C7    122.17  3.000
 K1T  C13   C8   C7    118.74  3.000
 K1T  C17   C9   C10   119.98  3.000
 K1T  C17   C9   C8    122.62  3.000
 K1T  C10   C9   C8    117.31  3.000
 K1T  O16   C10  C11   109.23  3.000
 K1T  O16   C10  C9    128.38  3.000
 K1T  C11   C10  C9    122.29  3.000
 K1T  O14   C11  C12   128.90  3.000
 K1T  C12   C11  C10   121.53  3.000
 K1T  O14   C11  C10   109.54  3.000
 K1T  H12   C12  C13   121.29  3.000
 K1T  H12   C12  C11   121.99  3.000
 K1T  C13   C12  C11   116.72  3.000
 K1T  H13   C13  C12   118.35  3.000
 K1T  H13   C13  C8    118.54  3.000
 K1T  C12   C13  C8    123.11  3.000
 K1T  C15   O14  C11   106.57  3.000
 K1T  H15A  C15  H15   110.57  3.000
 K1T  H15A  C15  O16   109.62  3.000
 K1T  H15   C15  O16   109.63  3.000
 K1T  H15A  C15  O14   110.05  3.000
 K1T  H15   C15  O14   110.01  3.000
 K1T  O16   C15  O14   106.89  3.000
 K1T  C15   O16  C10   106.85  3.000
 K1T  O19   C17  O18   123.41  3.000
 K1T  O18   C17  C9    112.20  3.000
 K1T  O19   C17  C9    124.39  3.000
 K1T  HO18  O18  C17   109.98  3.000
 K1T  H20A  C20  H20   106.91  3.000
 K1T  H20A  C20  N21   108.41  3.000
 K1T  H20   C20  N21   109.16  3.000
 K1T  H20A  C20  C5    110.15  3.000
 K1T  H20   C20  C5    110.14  3.000
 K1T  N21   C20  C5    111.92  3.000
 K1T  HN21  N21  C22   117.77  3.000
 K1T  HN21  N21  C20   116.74  3.000
 K1T  C22   N21  C20   125.48  3.000
 K1T  C24   C22  O23   121.53  3.000
 K1T  C24   C22  N21   114.99  3.000
 K1T  O23   C22  N21   123.48  3.000
 K1T  H24A  C24  H24   106.41  3.000
 K1T  H24A  C24  C25   109.81  3.000
 K1T  H24   C24  C25   109.55  3.000
 K1T  H24A  C24  C22   111.13  3.000
 K1T  H24   C24  C22   107.60  3.000
 K1T  C25   C24  C22   112.15  3.000
 K1T  H25A  C25  H25   106.84  3.000
 K1T  H25A  C25  C26   109.58  3.000
 K1T  H25   C25  C26   109.09  3.000
 K1T  H25A  C25  C24   109.57  3.000
 K1T  H25   C25  C24   109.87  3.000
 K1T  C26   C25  C24   111.77  3.000
 K1T  H26A  C26  H26   106.09  3.000
 K1T  H26A  C26  N27   108.14  3.000
 K1T  H26   C26  N27   113.68  3.000
 K1T  H26A  C26  C25   109.05  3.000
 K1T  H26   C26  C25   108.85  3.000
 K1T  N27   C26  C25   110.85  3.000
 K1T  HN2A  N27  HN27  105.61  3.000
 K1T  HN2A  N27  C26   109.50  3.000
 K1T  HN27  N27  C26   109.39  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
 K1T  CONST_01  C11   C12  C13  C8      0.00   0.0  0
 K1T  CONST_02  C11   C10  C9   C8      0.00   0.0  0
 K1T  CONST_03  C12   C13  C8   C9      0.00   0.0  0
 K1T  CONST_04  C12   C11  C10  C9      0.00   0.0  0
 K1T  CONST_05  C13   C8   C9   C10     0.00   0.0  0
 K1T  CONST_06  C13   C12  C11  C10     0.00   0.0  0
 K1T  CONST_07  C12   C13  C8   C7    180.00   0.0  0
 K1T  CONST_08  C10   C9   C8   C7    180.00   0.0  0
 K1T  CONST_09  C17   C9   C10  C11   180.00   0.0  0
 K1T  CONST_10  C17   C9   C8   C13   180.00   0.0  0
 K1T  CONST_11  C17   C9   C10  O16     0.00   0.0  0
 K1T  CONST_12  H12   C12  C13  C8    180.00   0.0  0
 K1T  CONST_13  H13   C13  C8   C9    180.00   0.0  0
 K1T  CONST_14  HO18  O18  C17  C9    180.00   0.0  0
 K1T  CONST_15  O23   C22  N21  C20     0.00   0.0  0
 K1T  CONST_16  C24   C22  N21  C20   180.00   0.0  0
 K1T  CONST_17  HN21  N21  C22  O23   180.00   0.0  0
 K1T  Var_01    O14   C15  O16  C10    -9.45  30.0  1
 K1T  Var_02    O16   C15  O14  C11     9.22  30.0  1
 K1T  Var_03    C13   C8   C7   C5   -109.19  30.0  2
 K1T  Var_04    O19   C17  C9   C8     40.62  30.0  2
 K1T  Var_05    C5    C4   C2   C1     65.89  30.0  2
 K1T  Var_06    C22   N21  C20  C5   -124.22  30.0  3
 K1T  Var_07    C25   C24  C22  N21   122.44  30.0  3
 K1T  Var_08    C26   C25  C24  C22   179.07  30.0  3
 K1T  Var_09    N27   C26  C25  C24   178.29  30.0  3
 K1T  Var_10    H3    C3   C2   C1     63.12  30.0  3
 K1T  Var_11    H1    C1   C2   C3    175.45  30.0  3
 K1T  Var_12    HN27  N27  C26  C25    68.24  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
 K1T  chir_01  C5  C4  C20  C7  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
 K1T  plan-1  C20   0.020
 K1T  plan-1  N21   0.020
 K1T  plan-1  C22   0.020
 K1T  plan-1  O23   0.020
 K1T  plan-1  C24   0.020
 K1T  plan-1  HN21  0.020
 K1T  plan-2  C7    0.020
 K1T  plan-2  C8    0.020
 K1T  plan-2  C9    0.020
 K1T  plan-2  C10   0.020
 K1T  plan-2  C11   0.020
 K1T  plan-2  C12   0.020
 K1T  plan-2  C13   0.020
 K1T  plan-2  O14   0.020
 K1T  plan-2  O16   0.020
 K1T  plan-2  C17   0.020
 K1T  plan-2  H12   0.020
 K1T  plan-2  H13   0.020
 K1T  plan-3  C9    0.020
 K1T  plan-3  C17   0.020
 K1T  plan-3  O18   0.020
 K1T  plan-3  O19   0.020
 K1T  plan-3  HO18  0.020

