# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 02:02:11 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  53  28  .  2021-08-20  2021-08-20  
;
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  -0.344  -2.5524  -1.0079  -2.0361
 Q31  C2    C  CR16  0  -0.325  -3.2745  -2.1704  -1.7368
 Q31  C3    C  CR15  0  -0.131   6.2979  -0.2241   0.8193
 Q31  C4    C  CR15  0   0.082   6.4006  -2.3531   0.3323
 Q31  C5    C  CR6   0  -0.201  -3.1746   0.0328   0.0558
 Q31  C6    C  CR6   0   0.129  -2.4898   0.0853  -1.1866
 Q31  C7    C  CR56  0   0.298  -3.9212  -2.1988  -0.5326
 Q31  C8    C  CR56  0   0.338  -3.8629  -1.1287   0.3489
 Q31  C9    C  CR5   0   0.177   5.0465  -0.7711   0.7978
 Q31  C10   C  C     0   0.485  -3.2165   1.1838   0.9932
 Q31  C11   C  C     0   0.555   2.9274   0.0710  -0.2321
 Q31  C12   C  CH2   0   0.071  -5.0774  -2.7457   1.2875
 Q31  C13   C  CH3   0  -0.647   1.8609   4.6676  -0.6382
 Q31  C14   C  CH3   0  -0.654   1.1183   3.3072   1.3253
 Q31  C15   C  CH2   0  -0.521  -1.6388   1.2640  -1.5811
 Q31  C16   C  CH2   0  -0.696   3.7433  -0.0989   1.0403
 Q31  C17   C  CH2   0  -0.394   0.2176   2.8267  -0.9984
 Q31  C18   C  CH2   0  -0.259   0.6058   0.2914  -1.0662
 Q31  C19   C  CH1   0  -0.252   1.4205   3.2834  -0.1691
 Q31  C20   C  CH1   0  -0.263  -0.3613   1.4338  -0.7365
 Q31  N21   N  N     0  -0.455   5.1260  -2.1024   0.4929
 Q31  N22   N  NR15  0  -0.562   7.1475  -1.2492   0.5197
 Q31  N23   N  NH1   0  -0.634   1.5985   0.0535  -0.0428
 Q31  O24   O  O     0  -0.424  -3.2878   2.3398   0.6564
 Q31  O25   O  OH1   0  -0.583  -3.1766   0.7986   2.2609
 Q31  O26   O  O     0  -0.493   3.4581   0.2573  -1.3169
 Q31  O27   O  O     0  -0.483  -4.7026  -3.1736  -0.0127
 Q31  O28   O  O     0  -0.471  -4.6125  -1.4079   1.4335
 Q31  H1    H  HCR6  0   0.261  -2.0148  -0.9658  -2.9747
 Q31  H2    H  HCR6  0   0.281  -3.3144  -3.0002  -2.4289
 Q31  H22   H  HNR5  0   0.419   8.1511  -1.1928   0.4563
 Q31  H4    H  HCR5  0   0.276   6.8344  -3.3099   0.0862
 Q31  H151  H  HCH2  0   0.248  -1.3474   1.1420  -2.6286
 Q31  H152  H  HCH2  0   0.262  -2.2215   2.1831  -1.5359
 Q31  H161  H  HCH2  0   0.268   3.1667  -0.6373   1.7970
 Q31  H162  H  HCH2  0   0.287   3.9139   0.9047   1.4425
 Q31  H25   H  HOH1  0   0.487  -3.2591   1.5701   2.8424
 Q31  H23   H  HNH1  0   0.396   1.2569  -0.1713   0.8778
 Q31  H121  H  HCH2  0   0.247  -6.1632  -2.7695   1.3901
 Q31  H122  H  HCH2  0   0.241  -4.6070  -3.3820   2.0425
 Q31  H131  H  HCH3  0   0.224   2.7265   5.0186  -0.0739
 Q31  H132  H  HCH3  0   0.223   2.1323   4.6633  -1.6954
 Q31  H133  H  HCH3  0   0.211   1.0598   5.3987  -0.5041
 Q31  H19   H  HCH1  0   0.228   2.2568   2.6013  -0.3407
 Q31  H141  H  HCH3  0   0.220   0.8666   2.3215   1.7176
 Q31  H142  H  HCH3  0   0.225   1.9793   3.6687   1.8909
 Q31  H143  H  HCH3  0   0.212   0.2787   3.9729   1.5422
 Q31  H20   H  HCH1  0   0.228  -0.6328   1.3568   0.3222
 Q31  H171  H  HCH2  0   0.215  -0.5863   3.5569  -0.8436
 Q31  H172  H  HCH2  0   0.218   0.4775   2.8920  -2.0622
 Q31  H181  H  HCH2  0   0.249   0.0420  -0.6332  -1.2168
 Q31  H182  H  HCH2  0   0.247   1.1215   0.5032  -2.0029
 Q31  H3    H  HCR5  0   0.284   6.6425   0.7768   1.0172

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  1.401  0.020  1.401
 Q31  C1   C6    aromatic  1.386  0.020  1.386
 Q31  C2   C7    aromatic  1.367  0.020  1.367
 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  1.420  0.020  1.420
 Q31  C5   C8    aromatic  1.382  0.020  1.382
 Q31  C5   C10   single    1.485  0.020  1.485
 Q31  C6   C15   single    1.506  0.020  1.506
 Q31  C7   C8    aromatic  1.388  0.020  1.388
 Q31  C7   O27   single    1.353  0.020  1.353
 Q31  C8   O28   single    1.348  0.020  1.348
 Q31  C9   C16   single    1.486  0.020  1.486
 Q31  C9   N21   aromatic  1.368  0.020  1.368
 Q31  C10  O24   double    1.206  0.020  1.206
 Q31  C10  O25   single    1.326  0.020  1.326
 Q31  C11  C16   single    1.521  0.020  1.521
 Q31  C11  N23   single    1.342  0.020  1.342
 Q31  C11  O26   double    1.222  0.020  1.222
 Q31  C12  O27   single    1.419  0.020  1.419
 Q31  C12  O28   single    1.424  0.020  1.424
 Q31  C13  C19   single    1.526  0.020  1.526
 Q31  C14  C19   single    1.525  0.020  1.525
 Q31  C15  C20   single    1.541  0.020  1.541
 Q31  C17  C19   single    1.531  0.020  1.531
 Q31  C17  C20   single    1.531  0.020  1.531
 Q31  C18  C20   single    1.533  0.020  1.533
 Q31  C18  N23   single    1.445  0.020  1.445
 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  O25  H25   single    0.850  0.020  0.980
 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    118.58  3.000
 Q31  H1    C1   C2    118.26  3.000
 Q31  C6    C1   C2    123.15  3.000
 Q31  H2    C2   C7    122.03  3.000
 Q31  H2    C2   C1    121.27  3.000
 Q31  C7    C2   C1    116.70  3.000
 Q31  H3    C3   N22   122.64  3.000
 Q31  H3    C3   C9    131.93  3.000
 Q31  N22   C3   C9    105.43  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    120.24  3.000
 Q31  C10   C5   C6    122.51  3.000
 Q31  C8    C5   C6    117.20  3.000
 Q31  C15   C6   C5    122.05  3.000
 Q31  C15   C6   C1    118.83  3.000
 Q31  C5    C6   C1    119.05  3.000
 Q31  O27   C7   C8    109.61  3.000
 Q31  O27   C7   C2    128.79  3.000
 Q31  C8    C7   C2    121.58  3.000
 Q31  O28   C8   C7    109.16  3.000
 Q31  O28   C8   C5    128.47  3.000
 Q31  C7    C8   C5    122.30  3.000
 Q31  N21   C9   C16   121.84  3.000
 Q31  N21   C9   C3    109.87  3.000
 Q31  C16   C9   C3    128.29  3.000
 Q31  O25   C10  O24   123.18  3.000
 Q31  O25   C10  C5    112.19  3.000
 Q31  O24   C10  C5    124.63  3.000
 Q31  O26   C11  N23   123.85  3.000
 Q31  O26   C11  C16   121.79  3.000
 Q31  N23   C11  C16   114.30  3.000
 Q31  H122  C12  H121  110.52  3.000
 Q31  H122  C12  O28   109.60  3.000
 Q31  H121  C12  O28   109.62  3.000
 Q31  H122  C12  O27   110.09  3.000
 Q31  H121  C12  O27   110.03  3.000
 Q31  O28   C12  O27   106.92  3.000
 Q31  H133  C13  H132  107.68  3.000
 Q31  H133  C13  H131  107.63  3.000
 Q31  H132  C13  H131  107.75  3.000
 Q31  H133  C13  C19   110.94  3.000
 Q31  H132  C13  C19   111.46  3.000
 Q31  H131  C13  C19   111.20  3.000
 Q31  H143  C14  H142  107.53  3.000
 Q31  H143  C14  H141  107.57  3.000
 Q31  H142  C14  H141  107.16  3.000
 Q31  H143  C14  C19   110.86  3.000
 Q31  H142  C14  C19   110.89  3.000
 Q31  H141  C14  C19   112.60  3.000
 Q31  H152  C15  H151  106.04  3.000
 Q31  H152  C15  C20   109.14  3.000
 Q31  H151  C15  C20   108.44  3.000
 Q31  H152  C15  C6    110.31  3.000
 Q31  H151  C15  C6    108.30  3.000
 Q31  C20   C15  C6    114.27  3.000
 Q31  H162  C16  H161  106.22  3.000
 Q31  H162  C16  C11   106.77  3.000
 Q31  H161  C16  C11   110.56  3.000
 Q31  H162  C16  C9    109.75  3.000
 Q31  H161  C16  C9    110.65  3.000
 Q31  C11   C16  C9    112.60  3.000
 Q31  H172  C17  H171  105.72  3.000
 Q31  H172  C17  C20   108.04  3.000
 Q31  H171  C17  C20   107.72  3.000
 Q31  H172  C17  C19   108.75  3.000
 Q31  H171  C17  C19   107.51  3.000
 Q31  C20   C17  C19   118.42  3.000
 Q31  H182  C18  H181  106.85  3.000
 Q31  H182  C18  N23   108.39  3.000
 Q31  H181  C18  N23   108.21  3.000
 Q31  H182  C18  C20   109.79  3.000
 Q31  H181  C18  C20   109.55  3.000
 Q31  N23   C18  C20   113.81  3.000
 Q31  H19   C19  C17   109.28  3.000
 Q31  H19   C19  C14   108.38  3.000
 Q31  C17   C19  C14   112.33  3.000
 Q31  H19   C19  C13   107.27  3.000
 Q31  C17   C19  C13   109.32  3.000
 Q31  C14   C19  C13   110.14  3.000
 Q31  H20   C20  C18   108.17  3.000
 Q31  H20   C20  C17   108.84  3.000
 Q31  C18   C20  C17   113.75  3.000
 Q31  H20   C20  C15   108.45  3.000
 Q31  C18   C20  C15   108.85  3.000
 Q31  C17   C20  C15   108.66  3.000
 Q31  C9    N21  C4    105.69  3.000
 Q31  H22   N22  C4    126.16  3.000
 Q31  H22   N22  C3    126.31  3.000
 Q31  C4    N22  C3    107.53  3.000
 Q31  H23   N23  C18   116.80  3.000
 Q31  H23   N23  C11   117.87  3.000
 Q31  C18   N23  C11   125.30  3.000
 Q31  H25   O25  C10   109.87  3.000
 Q31  C12   O27  C7    106.70  3.000
 Q31  C12   O28  C8    107.08  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  H25   O25  C10  C5    180.00   0.0  0
 Q31  CONST_25  C18   N23  C11  C16   180.00   0.0  0
 Q31  CONST_26  O26   C11  N23  C18     0.00   0.0  0
 Q31  CONST_27  H23   N23  C11  C16     0.00   0.0  0
 Q31  Var_01    O28   C12  O27  C7      6.96  30.0  1
 Q31  Var_02    O27   C12  O28  C8     -7.23  30.0  1
 Q31  Var_03    C20   C15  C6   C1   -109.17  30.0  2
 Q31  Var_04    C11   C16  C9   C3    107.82  30.0  2
 Q31  Var_05    O24   C10  C5   C6     36.65  30.0  2
 Q31  Var_06    N23   C11  C16  C9    149.76  30.0  1
 Q31  Var_07    C20   C18  N23  C11  -123.48  30.0  1
 Q31  Var_08    C20   C17  C19  C13   177.63  30.0  3
 Q31  Var_09    H141  C14  C19  C13  -175.99  30.0  3
 Q31  Var_10    H131  C13  C19  C14    56.81  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  H4   0.020
 Q31  plan-1  H3   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
 Q31  plan-4  H25  0.020

