# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 10 06:40:06 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  53  26  .  2022-03-22  2022-03-22
;
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  -0.663  -0.2256  -3.4241   1.4661
 K1T  C2    C  CH1    0  -0.234  -0.1195  -3.5880  -0.0473
 K1T  C3    C  CH3    0  -0.651  -0.7502  -4.9073  -0.4841
 K1T  C4    C  CH2    0  -0.401  -0.7783  -2.4278  -0.7985
 K1T  C5    C  CH1    0  -0.257  -0.0965  -1.0667  -0.6612
 K1T  C7    C  CH2    0  -0.522   1.1953  -1.0057  -1.4927
 K1T  C8    C  CR6    0   0.093   2.0653   0.1812  -1.1761
 K1T  C9    C  CR6    0  -0.178   2.7720   0.2364   0.0460
 K1T  C10   C  CR6    0   0.286   3.4853   1.3882   0.2792
 K1T  C11   C  CR6    0   0.280   3.5603   2.4342  -0.6251
 K1T  C12   C  CR16   0  -0.349   2.8885   2.3978  -1.8197
 K1T  C13   C  CR16   0  -0.340   2.1318   1.2460  -2.0677
 K1T  O14   O  O2     0  -0.491   4.3900   3.3961  -0.1405
 K1T  C15   C  CH2    0   0.067   4.6433   3.0360   1.2100
 K1T  O16   O  O2     0  -0.485   4.2773   1.6739   1.3508
 K1T  C17   C  C      0   0.377   2.7941  -0.8948   1.0665
 K1T  O18   O  OC    -1  -0.596   2.3563  -0.6162   2.1966
 K1T  O19   O  O      0  -0.585   3.2703  -1.9747   0.6761
 K1T  C20   C  CH2    0  -0.263  -1.0309   0.0660  -1.0945
 K1T  N21   N  NH1    0  -0.633  -2.1681   0.2294  -0.2175
 K1T  C22   C  C      0   0.556  -3.4448  -0.0232  -0.5494
 K1T  O23   O  O      0  -0.508  -3.7932  -0.3664  -1.6727
 K1T  C24   C  CH2    0  -0.583  -4.4392   0.1207   0.5843
 K1T  C25   C  CH2    0  -0.427  -5.7717   0.7049   0.1357
 K1T  C26   C  CH2    0  -0.271  -6.7831   0.7514   1.2704
 K1T  N27   N  NH2    0  -0.800  -8.0418   1.3231   0.8157
 K1T  H1    H  HCH3   0   0.239   0.3062  -2.5438   1.8273
 K1T  H1A   H  HCH3   0   0.204  -1.2710  -3.3402   1.7764
 K1T  H1B   H  HCH3   0   0.218   0.1989  -4.2890   1.9803
 K1T  H2    H  HCH1   0   0.217   0.9447  -3.6265  -0.3038
 K1T  H3    H  HCH3   0   0.210  -1.8177  -4.9276  -0.2492
 K1T  H3A   H  HCH3   0   0.221  -0.6476  -5.0594  -1.5603
 K1T  H3B   H  HCH3   0   0.222  -0.2863  -5.7578   0.0187
 K1T  H4    H  HCH2   0   0.211  -0.8366  -2.6735  -1.8663
 K1T  H4A   H  HCH2   0   0.219  -1.8145  -2.3532  -0.4520
 K1T  H5    H  HCH1   0   0.234   0.1587  -0.8917   0.3896
 K1T  H7    H  HCH2   0   0.255   1.7666  -1.9203  -1.3372
 K1T  H7A   H  HCH2   0   0.232   0.9233  -0.9851  -2.5531
 K1T  H12   H  HCR6   0   0.264   2.9386   3.2072  -2.5351
 K1T  H13   H  HCR6   0   0.244   1.5721   1.1867  -2.9936
 K1T  H15   H  HCH2   0   0.241   5.7027   3.1605   1.4332
 K1T  H15A  H  HCH2   0   0.224   4.0364   3.6572   1.8797
 K1T  H20   H  HCH2   0   0.249  -0.4782   1.0080  -1.1242
 K1T  H20A  H  HCH2   0   0.237  -1.4005  -0.1182  -2.1037
 K1T  HN21  H  HNH1   0   0.394  -1.9737   0.5127   0.7291
 K1T  H24   H  HCH2   0   0.263  -4.5979  -0.8816   0.9982
 K1T  H24A  H  HCH2   0   0.247  -4.0188   0.7192   1.3966
 K1T  H25   H  HCH2   0   0.225  -5.6254   1.7158  -0.2549
 K1T  H25A  H  HCH2   0   0.224  -6.1737   0.1050  -0.6847
 K1T  H26   H  HCH2   0   0.189  -6.8859  -0.2583   1.6953
 K1T  H26A  H  HCH2   0   0.214  -6.3943   1.3810   2.0758
 K1T  HN27  H  HNH2   0   0.337  -8.4737   0.6929   0.1509
 K1T  HN2A  H  HNH2   0   0.346  -8.6870   1.3821   1.5930

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    1.531  0.020  1.531
 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    1.529  0.020  1.529
 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    1.505  0.020  1.505
 K1T  C7   H7    single    0.970  0.020  1.090
 K1T  C7   H7A   single    0.970  0.020  1.090
 K1T  C13  C8    aromatic  1.390  0.020  1.390
 K1T  C8   C9    aromatic  1.413  0.020  1.413
 K1T  C10  C9    aromatic  1.375  0.020  1.375
 K1T  C9   C17   single    1.524  0.020  1.524
 K1T  C11  C10   aromatic  1.385  0.020  1.385
 K1T  C10  O16   single    1.363  0.020  1.363
 K1T  O14  C11   single    1.360  0.020  1.360
 K1T  C12  C11   aromatic  1.371  0.020  1.371
 K1T  C12  C13   aromatic  1.400  0.020  1.400
 K1T  C12  H12   single    0.930  0.020  1.080
 K1T  C13  H13   single    0.930  0.020  1.080
 K1T  O14  C15   single    1.420  0.020  1.420
 K1T  C15  O16   single    1.417  0.020  1.417
 K1T  C15  H15   single    0.970  0.020  1.090
 K1T  C15  H15A  single    0.970  0.020  1.090
 K1T  C17  O19   deloc     1.243  0.020  1.243
 K1T  C17  O18   deloc     1.243  0.020  1.243
 K1T  C20  N21   single    1.445  0.020  1.445
 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    1.515  0.020  1.515
 K1T  C24  C25   single    1.522  0.020  1.522
 K1T  C24  H24   single    0.970  0.020  1.090
 K1T  C24  H24A  single    0.970  0.020  1.090
 K1T  C25  C26   single    1.521  0.020  1.521
 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   107.38  3.000
 K1T  H1B   C1   H1    107.09  3.000
 K1T  H1A   C1   H1    108.08  3.000
 K1T  H1B   C1   C2    110.79  3.000
 K1T  H1A   C1   C2    110.86  3.000
 K1T  H1    C1   C2    112.42  3.000
 K1T  H2    C2   C4    109.25  3.000
 K1T  H2    C2   C3    107.70  3.000
 K1T  C4    C2   C3    109.68  3.000
 K1T  H2    C2   C1    107.67  3.000
 K1T  C3    C2   C1    110.37  3.000
 K1T  C4    C2   C1    112.04  3.000
 K1T  H3B   C3   H3A   107.80  3.000
 K1T  H3B   C3   H3    107.55  3.000
 K1T  H3A   C3   H3    107.51  3.000
 K1T  H3B   C3   C2    111.47  3.000
 K1T  H3A   C3   C2    111.33  3.000
 K1T  H3    C3   C2    110.98  3.000
 K1T  H4A   C4   H4    105.84  3.000
 K1T  H4A   C4   C5    109.45  3.000
 K1T  H4    C4   C5    108.09  3.000
 K1T  H4A   C4   C2    107.66  3.000
 K1T  H4    C4   C2    109.31  3.000
 K1T  C5    C4   C2    116.03  3.000
 K1T  H5    C5   C20   107.19  3.000
 K1T  H5    C5   C7    108.46  3.000
 K1T  C20   C5   C7    109.29  3.000
 K1T  H5    C5   C4    109.41  3.000
 K1T  C7    C5   C4    111.19  3.000
 K1T  C20   C5   C4    111.17  3.000
 K1T  H7A   C7   H7    106.52  3.000
 K1T  H7A   C7   C8    109.42  3.000
 K1T  H7    C7   C8    109.19  3.000
 K1T  H7A   C7   C5    108.41  3.000
 K1T  H7    C7   C5    109.27  3.000
 K1T  C8    C7   C5    113.78  3.000
 K1T  C13   C8   C9    120.06  3.000
 K1T  C9    C8   C7    120.12  3.000
 K1T  C13   C8   C7    119.77  3.000
 K1T  C17   C9   C10   120.06  3.000
 K1T  C17   C9   C8    123.89  3.000
 K1T  C10   C9   C8    116.04  3.000
 K1T  O16   C10  C11   108.89  3.000
 K1T  O16   C10  C9    127.63  3.000
 K1T  C11   C10  C9    123.38  3.000
 K1T  O14   C11  C12   128.93  3.000
 K1T  C12   C11  C10   121.49  3.000
 K1T  O14   C11  C10   109.55  3.000
 K1T  H12   C12  C13   121.57  3.000
 K1T  H12   C12  C11   122.26  3.000
 K1T  C13   C12  C11   116.17  3.000
 K1T  H13   C13  C12   118.39  3.000
 K1T  H13   C13  C8    118.78  3.000
 K1T  C12   C13  C8    122.83  3.000
 K1T  C15   O14  C11   105.57  3.000
 K1T  H15A  C15  H15   110.38  3.000
 K1T  H15A  C15  O16   109.92  3.000
 K1T  H15   C15  O16   109.91  3.000
 K1T  H15A  C15  O14   109.77  3.000
 K1T  H15   C15  O14   109.82  3.000
 K1T  O16   C15  O14   106.98  3.000
 K1T  C15   O16  C10   105.87  3.000
 K1T  O19   C17  O18   127.95  3.000
 K1T  O18   C17  C9    115.92  3.000
 K1T  O19   C17  C9    116.11  3.000
 K1T  H20A  C20  H20   106.98  3.000
 K1T  H20A  C20  N21   108.30  3.000
 K1T  H20   C20  N21   108.49  3.000
 K1T  H20A  C20  C5    110.11  3.000
 K1T  H20   C20  C5    109.68  3.000
 K1T  N21   C20  C5    113.08  3.000
 K1T  HN21  N21  C22   117.95  3.000
 K1T  HN21  N21  C20   116.76  3.000
 K1T  C22   N21  C20   125.21  3.000
 K1T  C24   C22  O23   121.74  3.000
 K1T  C24   C22  N21   114.91  3.000
 K1T  O23   C22  N21   123.34  3.000
 K1T  H24A  C24  H24   106.01  3.000
 K1T  H24A  C24  C25   110.21  3.000
 K1T  H24   C24  C25   109.60  3.000
 K1T  H24A  C24  C22   110.83  3.000
 K1T  H24   C24  C22   106.91  3.000
 K1T  C25   C24  C22   112.98  3.000
 K1T  H25A  C25  H25   106.76  3.000
 K1T  H25A  C25  C26   109.40  3.000
 K1T  H25   C25  C26   109.10  3.000
 K1T  H25A  C25  C24   109.42  3.000
 K1T  H25   C25  C24   110.05  3.000
 K1T  C26   C25  C24   111.96  3.000
 K1T  H26A  C26  H26   106.09  3.000
 K1T  H26A  C26  N27   108.14  3.000
 K1T  H26   C26  N27   113.60  3.000
 K1T  H26A  C26  C25   109.31  3.000
 K1T  H26   C26  C25   108.80  3.000
 K1T  N27   C26  C25   110.74  3.000
 K1T  HN2A  N27  HN27  105.59  3.000
 K1T  HN2A  N27  C26   109.54  3.000
 K1T  HN27  N27  C26   109.24  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  O23   C22  N21  C20     0.00   0.0  0
 K1T  CONST_15  C24   C22  N21  C20   180.00   0.0  0
 K1T  CONST_16  HN21  N21  C22  O23   180.00   0.0  0
 K1T  Var_01    O14   C15  O16  C10   -17.38  30.0  1
 K1T  Var_02    O16   C15  O14  C11    17.14  30.0  1
 K1T  Var_03    C13   C8   C7   C5   -105.87  30.0  2
 K1T  Var_04    O19   C17  C9   C8     61.17  30.0  2
 K1T  Var_05    C5    C4   C2   C1     67.52  30.0  2
 K1T  Var_06    C22   N21  C20  C5   -112.28  30.0  3
 K1T  Var_07    C25   C24  C22  N21   143.14  30.0  3
 K1T  Var_08    C26   C25  C24  C22   176.12  30.0  3
 K1T  Var_09    N27   C26  C25  C24   179.56  30.0  3
 K1T  Var_10    H3    C3   C2   C1     62.55  30.0  3
 K1T  Var_11    H1    C1   C2   C3    173.98  30.0  3
 K1T  Var_12    HN27  N27  C26  C25    67.21  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

