# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:25:53 2020
#   Inital geometry file: a 129 line input string
#   Ligand name: 5-[(2S)-2-{[(1H-imidazol-4-ylacetyl)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)Cc1c[nH]cn1)Cc2ccc3OCOc3c2C(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
 Q31  Q31  '5-[(2S)-2-{[(1H-imidazol-4-ylacetyl)amino]methyl}-4-methylpentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  52  28  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q31
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
 Q31  C1    C  CR16   0  -0.342  -2.2967  -1.0751  -2.0383
 Q31  C2    C  CR16   0  -0.349  -2.8978  -2.3032  -1.7357
 Q31  C3    C  CR15   0  -0.132   6.3034  -0.8543   0.4634
 Q31  C4    C  CR15   0   0.082   5.7861  -2.9611   0.7360
 Q31  C5    C  CR6    0  -0.185  -3.0546  -0.0681   0.0388
 Q31  C6    C  CR6    0   0.093  -2.3652   0.0257  -1.1920
 Q31  C7    C  CR6    0   0.282  -3.5559  -2.3751  -0.5355
 Q31  C8    C  CR6    0   0.287  -3.6132  -1.2916   0.3257
 Q31  C9    C  CR5    0   0.176   4.9681  -0.9903   0.7173
 Q31  C10   C  C      0   0.365  -3.2031   1.0883   1.0205
 Q31  C11   C  C      0   0.556   2.9947   0.0664  -0.3969
 Q31  C12   C  CH2    0   0.068  -4.5599  -3.0333   1.3276
 Q31  C13   C  CH3    0  -0.648   1.4933   5.0032  -0.4471
 Q31  C14   C  CH3    0  -0.656   0.8469   3.5228   1.4619
 Q31  C15   C  CH2    0  -0.511  -1.6524   1.2994  -1.5612
 Q31  C16   C  CH2    0  -0.697   3.9338   0.0742   0.7993
 Q31  C17   C  CH2    0  -0.389   0.0086   3.0404  -0.8830
 Q31  C18   C  CH2    0  -0.232   0.7019   0.5905  -1.1283
 Q31  C19   C  CH1    0  -0.247   1.1630   3.5731  -0.0298
 Q31  C20   C  CH1    0  -0.292  -0.3943   1.5720  -0.7150
 Q31  N21   N  N      0  -0.455   4.6593  -2.3123   0.8861
 Q31  N22   N  NR15   0  -0.562   6.8071  -2.1226   0.4790
 Q31  N23   N  NH1    0  -0.641   1.7413   0.4586  -0.1284
 Q31  O24   O  O      0  -0.584  -3.7288   2.1252   0.5793
 Q31  O25   O  OC    -1  -0.592  -2.8013   0.8715   2.1768
 Q31  O26   O  O      0  -0.494   3.3765  -0.2339  -1.5188
 Q31  O27   O  O2     0  -0.491  -4.2482  -3.4168  -0.0043
 Q31  O28   O  O2     0  -0.484  -4.3557  -1.6335   1.4151
 Q31  H1    H  HCR6   0   0.245  -1.7519  -0.9846  -2.9708
 Q31  H2    H  HCR6   0   0.264  -2.8437  -3.1427  -2.4152
 Q31  H22   H  HNR5   0   0.419   7.7695  -2.3830   0.3351
 Q31  H151  H  HCH2   0   0.234  -1.3676   1.2655  -2.6175
 Q31  H152  H  HCH2   0   0.253  -2.3343   2.1412  -1.4450
 Q31  H161  H  HCH2   0   0.267   3.3681  -0.0097   1.7311
 Q31  H162  H  HCH2   0   0.289   4.4166   1.0557   0.8219
 Q31  H23   H  HNH1   0   0.394   1.4862   0.6214   0.8320
 Q31  H121  H  HCH2   0   0.240  -5.6009  -3.2707   1.5464
 Q31  H122  H  HCH2   0   0.225  -3.8957  -3.5528   2.0285
 Q31  H131  H  HCH3   0   0.224   2.3131   5.4094   0.1479
 Q31  H132  H  HCH3   0   0.223   1.7867   5.0541  -1.4971
 Q31  H133  H  HCH3   0   0.211   0.6297   5.6591  -0.3124
 Q31  H19   H  HCH1   0   0.221   2.0515   2.9621  -0.2136
 Q31  H141  H  HCH3   0   0.216   0.6190   2.5159   1.8154
 Q31  H142  H  HCH3   0   0.227   1.6880   3.8901   2.0528
 Q31  H143  H  HCH3   0   0.216  -0.0184   4.1479   1.6972
 Q31  H20   H  HCH1   0   0.238  -0.6543   1.3834   0.3333
 Q31  H171  H  HCH2   0   0.215  -0.8749   3.6554  -0.6741
 Q31  H172  H  HCH2   0   0.215   0.2468   3.2055  -1.9411
 Q31  H181  H  HCH2   0   0.244   0.2601  -0.3921  -1.3210
 Q31  H182  H  HCH2   0   0.235   1.1507   0.9223  -2.0675
 Q31  H3    H  HCR5   0   0.284   6.9163   0.0113   0.2771
 Q31  H4    H  HCR5   0   0.276   5.9188  -4.0297   0.8055

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
 Q31  C1   C2    aromatic  1.400  0.020  1.400
 Q31  C1   C6    aromatic  1.390  0.020  1.390
 Q31  C2   C7    aromatic  1.371  0.020  1.371
 Q31  C3   C9    aromatic  1.366  0.020  1.366
 Q31  C3   N22   aromatic  1.365  0.020  1.365
 Q31  C4   N21   aromatic  1.309  0.020  1.309
 Q31  C4   N22   aromatic  1.346  0.020  1.346
 Q31  C5   C6    aromatic  1.414  0.020  1.414
 Q31  C5   C8    aromatic  1.375  0.020  1.375
 Q31  C5   C10   single    1.524  0.020  1.524
 Q31  C6   C15   single    1.505  0.020  1.505
 Q31  C7   C8    aromatic  1.385  0.020  1.385
 Q31  C7   O27   single    1.359  0.020  1.359
 Q31  C8   O28   single    1.362  0.020  1.362
 Q31  C9   C16   single    1.486  0.020  1.486
 Q31  C9   N21   aromatic  1.368  0.020  1.368
 Q31  C10  O24   deloc     1.243  0.020  1.243
 Q31  C10  O25   deloc     1.243  0.020  1.243
 Q31  C11  C16   single    1.521  0.020  1.521
 Q31  C11  N23   single    1.341  0.020  1.341
 Q31  C11  O26   double    1.222  0.020  1.222
 Q31  C12  O27   single    1.421  0.020  1.421
 Q31  C12  O28   single    1.417  0.020  1.417
 Q31  C13  C19   single    1.526  0.020  1.526
 Q31  C14  C19   single    1.526  0.020  1.526
 Q31  C15  C20   single    1.541  0.020  1.541
 Q31  C17  C19   single    1.531  0.020  1.531
 Q31  C17  C20   single    1.532  0.020  1.532
 Q31  C18  C20   single    1.528  0.020  1.528
 Q31  C18  N23   single    1.448  0.020  1.448
 Q31  C1   H1    single    0.930  0.020  1.080
 Q31  C2   H2    single    0.930  0.020  1.080
 Q31  C3   H3    single    0.930  0.020  1.080
 Q31  N22  H22   single    0.860  0.020  1.020
 Q31  C4   H4    single    0.930  0.020  1.080
 Q31  C15  H151  single    0.970  0.020  1.090
 Q31  C15  H152  single    0.970  0.020  1.090
 Q31  C16  H161  single    0.970  0.020  1.090
 Q31  C16  H162  single    0.970  0.020  1.090
 Q31  N23  H23   single    0.860  0.020  1.020
 Q31  C12  H121  single    0.970  0.020  1.090
 Q31  C12  H122  single    0.970  0.020  1.090
 Q31  C13  H131  single    0.970  0.020  1.090
 Q31  C13  H132  single    0.970  0.020  1.090
 Q31  C13  H133  single    0.970  0.020  1.090
 Q31  C19  H19   single    0.970  0.020  1.090
 Q31  C14  H141  single    0.970  0.020  1.090
 Q31  C14  H142  single    0.970  0.020  1.090
 Q31  C14  H143  single    0.970  0.020  1.090
 Q31  C20  H20   single    0.970  0.020  1.090
 Q31  C17  H171  single    0.970  0.020  1.090
 Q31  C17  H172  single    0.970  0.020  1.090
 Q31  C18  H181  single    0.970  0.020  1.090
 Q31  C18  H182  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
 Q31  H1    C1   C6    118.84  3.000
 Q31  H1    C1   C2    118.36  3.000
 Q31  C6    C1   C2    122.80  3.000
 Q31  H2    C2   C7    122.24  3.000
 Q31  H2    C2   C1    121.57  3.000
 Q31  C7    C2   C1    116.19  3.000
 Q31  H3    C3   N22   122.61  3.000
 Q31  H3    C3   C9    131.95  3.000
 Q31  N22   C3   C9    105.44  3.000
 Q31  H4    C4   N22   122.41  3.000
 Q31  H4    C4   N21   126.11  3.000
 Q31  N22   C4   N21   111.48  3.000
 Q31  C10   C5   C8    120.07  3.000
 Q31  C10   C5   C6    123.91  3.000
 Q31  C8    C5   C6    116.02  3.000
 Q31  C15   C6   C5    120.03  3.000
 Q31  C15   C6   C1    119.82  3.000
 Q31  C5    C6   C1    120.10  3.000
 Q31  O27   C7   C8    109.61  3.000
 Q31  O27   C7   C2    128.84  3.000
 Q31  C8    C7   C2    121.54  3.000
 Q31  O28   C8   C7    108.87  3.000
 Q31  O28   C8   C5    127.71  3.000
 Q31  C7    C8   C5    123.33  3.000
 Q31  N21   C9   C16   121.88  3.000
 Q31  N21   C9   C3    109.86  3.000
 Q31  C16   C9   C3    128.26  3.000
 Q31  O25   C10  O24   127.74  3.000
 Q31  O25   C10  C5    115.80  3.000
 Q31  O24   C10  C5    116.44  3.000
 Q31  O26   C11  N23   123.21  3.000
 Q31  O26   C11  C16   122.02  3.000
 Q31  N23   C11  C16   114.73  3.000
 Q31  H122  C12  H121  110.31  3.000
 Q31  H122  C12  O28   109.95  3.000
 Q31  H121  C12  O28   109.90  3.000
 Q31  H122  C12  O27   109.79  3.000
 Q31  H121  C12  O27   109.81  3.000
 Q31  O28   C12  O27   107.03  3.000
 Q31  H133  C13  H132  107.64  3.000
 Q31  H133  C13  H131  107.65  3.000
 Q31  H132  C13  H131  107.77  3.000
 Q31  H133  C13  C19   110.97  3.000
 Q31  H132  C13  C19   111.41  3.000
 Q31  H131  C13  C19   111.24  3.000
 Q31  H143  C14  H142  107.53  3.000
 Q31  H143  C14  H141  107.01  3.000
 Q31  H142  C14  H141  107.22  3.000
 Q31  H143  C14  C19   110.83  3.000
 Q31  H142  C14  C19   111.00  3.000
 Q31  H141  C14  C19   112.98  3.000
 Q31  H152  C15  H151  106.84  3.000
 Q31  H152  C15  C20   108.41  3.000
 Q31  H151  C15  C20   108.84  3.000
 Q31  H152  C15  C6    109.35  3.000
 Q31  H151  C15  C6    109.49  3.000
 Q31  C20   C15  C6    113.68  3.000
 Q31  H162  C16  H161  106.23  3.000
 Q31  H162  C16  C11   107.05  3.000
 Q31  H161  C16  C11   110.51  3.000
 Q31  H162  C16  C9    109.67  3.000
 Q31  H161  C16  C9    110.62  3.000
 Q31  C11   C16  C9    112.50  3.000
 Q31  H172  C17  H171  105.92  3.000
 Q31  H172  C17  C20   107.88  3.000
 Q31  H171  C17  C20   107.75  3.000
 Q31  H172  C17  C19   108.74  3.000
 Q31  H171  C17  C19   107.83  3.000
 Q31  C20   C17  C19   118.08  3.000
 Q31  H182  C18  H181  106.69  3.000
 Q31  H182  C18  N23   109.05  3.000
 Q31  H181  C18  N23   109.24  3.000
 Q31  H182  C18  C20   109.39  3.000
 Q31  H181  C18  C20   109.55  3.000
 Q31  N23   C18  C20   112.74  3.000
 Q31  H19   C19  C17   108.93  3.000
 Q31  H19   C19  C14   108.31  3.000
 Q31  C17   C19  C14   112.15  3.000
 Q31  H19   C19  C13   107.57  3.000
 Q31  C17   C19  C13   109.68  3.000
 Q31  C14   C19  C13   110.07  3.000
 Q31  H20   C20  C18   108.55  3.000
 Q31  H20   C20  C17   109.39  3.000
 Q31  C18   C20  C17   113.41  3.000
 Q31  H20   C20  C15   107.52  3.000
 Q31  C18   C20  C15   108.88  3.000
 Q31  C17   C20  C15   108.92  3.000
 Q31  C9    N21  C4    105.69  3.000
 Q31  H22   N22  C4    126.23  3.000
 Q31  H22   N22  C3    126.25  3.000
 Q31  C4    N22  C3    107.52  3.000
 Q31  H23   N23  C18   117.52  3.000
 Q31  H23   N23  C11   118.37  3.000
 Q31  C18   N23  C11   124.01  3.000
 Q31  C12   O27  C7    105.74  3.000
 Q31  C12   O28  C8    106.08  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
 Q31  CONST_01  C8    C7   C2   C1      0.00   0.0  0
 Q31  CONST_02  C8    C5   C6   C1      0.00   0.0  0
 Q31  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 Q31  CONST_04  C5    C8   C7   C2      0.00   0.0  0
 Q31  CONST_05  C4    N21  C9   C3      0.00   0.0  0
 Q31  CONST_06  N21   C4   N22  C3      0.00   0.0  0
 Q31  CONST_07  C9    C3   N22  C4      0.00   0.0  0
 Q31  CONST_08  C7    C2   C1   C6      0.00   0.0  0
 Q31  CONST_09  C7    C8   C5   C6      0.00   0.0  0
 Q31  CONST_10  N22   C4   N21  C9      0.00   0.0  0
 Q31  CONST_11  N22   C3   C9   N21     0.00   0.0  0
 Q31  CONST_12  C10   C5   C6   C1    180.00   0.0  0
 Q31  CONST_13  C15   C6   C1   C2    180.00   0.0  0
 Q31  CONST_14  C16   C9   N21  C4    180.00   0.0  0
 Q31  CONST_15  C10   C5   C8   C7    180.00   0.0  0
 Q31  CONST_16  C15   C6   C5   C8    180.00   0.0  0
 Q31  CONST_17  O28   C8   C5   C10     0.00   0.0  0
 Q31  CONST_18  N22   C3   C9   C16   180.00   0.0  0
 Q31  CONST_19  H4    C4   N22  C3    180.00   0.0  0
 Q31  CONST_20  H3    C3   N22  C4    180.00   0.0  0
 Q31  CONST_21  H1    C1   C6   C5    180.00   0.0  0
 Q31  CONST_22  H2    C2   C1   C6    180.00   0.0  0
 Q31  CONST_23  H22   N22  C3   C9    180.00   0.0  0
 Q31  CONST_24  C18   N23  C11  C16   180.00   0.0  0
 Q31  CONST_25  O26   C11  N23  C18     0.00   0.0  0
 Q31  CONST_26  H23   N23  C11  C16     0.00   0.0  0
 Q31  Var_01    O28   C12  O27  C7     15.72  30.0  1
 Q31  Var_02    O27   C12  O28  C8    -16.05  30.0  1
 Q31  Var_03    C20   C15  C6   C1   -107.17  30.0  2
 Q31  Var_04    C11   C16  C9   C3    107.73  30.0  2
 Q31  Var_05    O24   C10  C5   C6     56.84  30.0  2
 Q31  Var_06    N23   C11  C16  C9    147.93  30.0  2
 Q31  Var_07    C20   C18  N23  C11  -155.65  30.0  1
 Q31  Var_08    C20   C17  C19  C13   174.36  30.0  3
 Q31  Var_09    H141  C14  C19  C13  -179.07  30.0  3
 Q31  Var_10    H131  C13  C19  C14    56.02  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
 Q31  chir_01  C20  C15  C17  C18  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
 Q31  plan-1  C3   0.020
 Q31  plan-1  C4   0.020
 Q31  plan-1  C9   0.020
 Q31  plan-1  C16  0.020
 Q31  plan-1  N21  0.020
 Q31  plan-1  N22  0.020
 Q31  plan-1  H22  0.020
 Q31  plan-1  H3   0.020
 Q31  plan-1  H4   0.020
 Q31  plan-2  C1   0.020
 Q31  plan-2  C2   0.020
 Q31  plan-2  C5   0.020
 Q31  plan-2  C6   0.020
 Q31  plan-2  C7   0.020
 Q31  plan-2  C8   0.020
 Q31  plan-2  C10  0.020
 Q31  plan-2  C15  0.020
 Q31  plan-2  O27  0.020
 Q31  plan-2  O28  0.020
 Q31  plan-2  H1   0.020
 Q31  plan-2  H2   0.020
 Q31  plan-3  C11  0.020
 Q31  plan-3  C16  0.020
 Q31  plan-3  C18  0.020
 Q31  plan-3  N23  0.020
 Q31  plan-3  O26  0.020
 Q31  plan-3  H23  0.020
 Q31  plan-4  C5   0.020
 Q31  plan-4  C10  0.020
 Q31  plan-4  O24  0.020
 Q31  plan-4  O25  0.020

