# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:09:48 2020
#   Inital geometry file: a 132 line input string
#   Ligand name: 5-[(2S)-4-methyl-2-{[(1H-pyrrol-3-ylacetyl)amino]methyl}pentyl]-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]cc1)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
 H39  H39  '5-[(2S)-4-methyl-2-{[(1H-pyrrol-3-ylacetyl)amino]methyl}pentyl]-1,3-benzodioxole-4-carboxylic acid'  ligand  54  28  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_H39
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
 H39  C1    C  CR16  0  -0.344  -2.9456   0.8299   2.0601
 H39  C2    C  CR16  0  -0.324  -3.9271   1.7782   1.7450
 H39  C3    C  CR15  0  -0.400   4.9330  -0.5870  -1.3485
 H39  C4    C  CR15  0  -0.051   6.2435  -0.9747  -1.2172
 H39  C5    C  CR15  0  -0.102   6.0676   1.0667  -0.3447
 H39  C6    C  CR6   0  -0.196  -3.2313  -0.3093  -0.0533
 H39  C7    C  CR6   0   0.126  -2.5906  -0.2048   1.2089
 H39  C8    C  CR5   0   0.055   4.8177   0.7169  -0.7939
 H39  C9    C  CR56  0   0.295  -4.5291   1.6568   0.5235
 H39  C10   C  CR56  0   0.337  -4.1812   0.6453  -0.3609
 H39  C11   C  C     0   0.482  -2.9565  -1.4182  -1.0019
 H39  C12   C  C     0   0.542   2.7244   1.0919   0.5067
 H39  C13   C  CH2   0   0.068  -5.9069   1.7576  -1.2095
 H39  C14   C  CH3   0  -0.647   2.6656  -3.6876   0.6315
 H39  C15   C  CH3   0  -0.667   1.5157  -2.5537  -1.2805
 H39  C16   C  CH2   0  -0.681   3.5704   1.5307  -0.6786
 H39  C17   C  CH2   0  -0.520  -1.4950  -1.1501   1.6272
 H39  C18   C  CH2   0  -0.393   0.7059  -2.2151   1.0944
 H39  C19   C  CH2   0  -0.252   0.4583   0.3406   1.1624
 H39  C20   C  CH1   0  -0.250   1.9190  -2.4334   0.1854
 H39  C21   C  CH1   0  -0.267  -0.1902  -1.0041   0.8211
 H39  N22   N  NR15  0  -0.574   6.9158   0.0367  -0.6082
 H39  N23   N  NH1   0  -0.629   1.4574   0.7629   0.2076
 H39  O24   O  OH1   0  -0.583  -2.9572  -1.0067  -2.2623
 H39  O25   O  O     0  -0.423  -2.7634  -2.5646  -0.6815
 H39  O26   O  O     0  -0.494   3.1872   1.0476   1.6373
 H39  O27   O  O     0  -0.483  -5.4900   2.4321  -0.0335
 H39  O28   O  O     0  -0.470  -4.9271   0.7608  -1.4786
 H39  H1    H  HCR6  0   0.262  -2.4441   0.9106   3.0157
 H39  H2    H  HCR6  0   0.280  -4.1885   2.5654   2.4388
 H39  H4    H  HCR5  0   0.267   6.7424  -1.8826  -1.5139
 H39  H5    H  HCR5  0   0.265   6.4099   1.9682   0.1373
 H39  H13   H  HCH2  0   0.238  -6.8801   1.2826  -1.0465
 H39  H13A  H  HCH2  0   0.251  -5.9553   2.4570  -2.0431
 H39  H14   H  HCH3  0   0.222   3.5535  -3.8572   0.0196
 H39  H14A  H  HCH3  0   0.222   2.9900  -3.6111   1.6711
 H39  H14B  H  HCH3  0   0.210   2.0311  -4.5740   0.5479
 H39  H15   H  HCH3  0   0.227   2.3736  -2.8195  -1.9015
 H39  H15A  H  HCH3  0   0.218   0.7586  -3.3313  -1.4143
 H39  H15B  H  HCH3  0   0.219   1.1055  -1.6254  -1.6789
 H39  H16   H  HCH2  0   0.276   3.8245   2.5818  -0.5184
 H39  H16A  H  HCH2  0   0.258   2.9963   1.4907  -1.6079
 H39  H17   H  HCH2  0   0.249  -1.2742  -0.9765   2.6845
 H39  H17A  H  HCH2  0   0.262  -1.8404  -2.1807   1.5586
 H39  H18   H  HCH2  0   0.215   0.0819  -3.1135   1.0159
 H39  H18A  H  HCH2  0   0.219   1.0415  -2.1734   2.1373
 H39  H19   H  HCH2  0   0.248  -0.3147   1.1131   1.2160
 H39  H19A  H  HCH2  0   0.245   0.9234   0.2904   2.1470
 H39  H20   H  HCH1  0   0.234   2.6085  -1.5923   0.2845
 H39  H21   H  HCH1  0   0.229  -0.4444  -0.9933  -0.2444
 H39  HN23  H  HNH1  0   0.394   1.1557   0.8591  -0.7483
 H39  HO24  H  HOH1  0   0.486  -2.8279  -1.7620  -2.8563
 H39  HN22  H  HNR5  0   0.408   7.8986   0.0300  -0.3945
 H39  H3    H  HCR5  0   0.241   4.1418  -1.1695  -1.7956

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
 H39  C7   C1    aromatic  1.386  0.020  1.386
 H39  C1   C2    aromatic  1.401  0.020  1.401
 H39  C1   H1    single    0.930  0.020  1.080
 H39  C9   C2    aromatic  1.367  0.020  1.367
 H39  C2   H2    single    0.930  0.020  1.080
 H39  C4   C3    aromatic  1.373  0.020  1.373
 H39  C3   C8    aromatic  1.422  0.020  1.422
 H39  C3   H3    single    0.930  0.020  1.080
 H39  C4   N22   aromatic  1.359  0.020  1.359
 H39  C4   H4    single    0.930  0.020  1.080
 H39  N22  C5    aromatic  1.360  0.020  1.360
 H39  C5   C8    aromatic  1.373  0.020  1.373
 H39  C5   H5    single    0.930  0.020  1.080
 H39  C11  C6    single    1.485  0.020  1.485
 H39  C6   C7    aromatic  1.419  0.020  1.419
 H39  C6   C10   aromatic  1.381  0.020  1.381
 H39  C17  C7    single    1.506  0.020  1.506
 H39  C8   C16   single    1.494  0.020  1.494
 H39  C10  C9    aromatic  1.388  0.020  1.388
 H39  C9   O27   single    1.355  0.020  1.355
 H39  O28  C10   single    1.349  0.020  1.349
 H39  O25  C11   double    1.206  0.020  1.206
 H39  O24  C11   single    1.326  0.020  1.326
 H39  C16  C12   single    1.521  0.020  1.521
 H39  C12  O26   double    1.222  0.020  1.222
 H39  C12  N23   single    1.343  0.020  1.343
 H39  O28  C13   single    1.423  0.020  1.423
 H39  C13  O27   single    1.418  0.020  1.418
 H39  C13  H13   single    0.970  0.020  1.090
 H39  C13  H13A  single    0.970  0.020  1.090
 H39  C20  C14   single    1.526  0.020  1.526
 H39  C14  H14   single    0.970  0.020  1.090
 H39  C14  H14A  single    0.970  0.020  1.090
 H39  C14  H14B  single    0.970  0.020  1.090
 H39  C15  C20   single    1.525  0.020  1.525
 H39  C15  H15   single    0.970  0.020  1.090
 H39  C15  H15A  single    0.970  0.020  1.090
 H39  C15  H15B  single    0.970  0.020  1.090
 H39  C16  H16   single    0.970  0.020  1.090
 H39  C16  H16A  single    0.970  0.020  1.090
 H39  C17  C21   single    1.541  0.020  1.541
 H39  C17  H17   single    0.970  0.020  1.090
 H39  C17  H17A  single    0.970  0.020  1.090
 H39  C20  C18   single    1.532  0.020  1.532
 H39  C18  C21   single    1.531  0.020  1.531
 H39  C18  H18   single    0.970  0.020  1.090
 H39  C18  H18A  single    0.970  0.020  1.090
 H39  N23  C19   single    1.445  0.020  1.445
 H39  C21  C19   single    1.531  0.020  1.531
 H39  C19  H19   single    0.970  0.020  1.090
 H39  C19  H19A  single    0.970  0.020  1.090
 H39  C20  H20   single    0.970  0.020  1.090
 H39  C21  H21   single    0.970  0.020  1.090
 H39  N23  HN23  single    0.860  0.020  1.020
 H39  O24  HO24  single    0.850  0.020  0.980
 H39  N22  HN22  single    0.860  0.020  1.020

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
 H39  H1    C1   C7    118.64  3.000
 H39  H1    C1   C2    118.22  3.000
 H39  C7    C1   C2    123.15  3.000
 H39  H2    C2   C9    122.10  3.000
 H39  H2    C2   C1    121.20  3.000
 H39  C9    C2   C1    116.70  3.000
 H39  H3    C3   C8    126.66  3.000
 H39  H3    C3   C4    125.93  3.000
 H39  C8    C3   C4    107.41  3.000
 H39  H4    C4   N22   121.43  3.000
 H39  H4    C4   C3    130.81  3.000
 H39  N22   C4   C3    107.76  3.000
 H39  H5    C5   N22   121.46  3.000
 H39  H5    C5   C8    130.41  3.000
 H39  N22   C5   C8    108.14  3.000
 H39  C11   C6   C10   120.07  3.000
 H39  C10   C6   C7    117.23  3.000
 H39  C11   C6   C7    122.65  3.000
 H39  C17   C7   C6    121.94  3.000
 H39  C17   C7   C1    118.96  3.000
 H39  C6    C7   C1    119.04  3.000
 H39  C16   C8   C5    126.58  3.000
 H39  C16   C8   C3    126.69  3.000
 H39  C5    C8   C3    106.70  3.000
 H39  O27   C9   C10   109.45  3.000
 H39  O27   C9   C2    128.97  3.000
 H39  C10   C9   C2    121.58  3.000
 H39  O28   C10  C9    109.09  3.000
 H39  O28   C10  C6    128.62  3.000
 H39  C9    C10  C6    122.28  3.000
 H39  O25   C11  O24   123.21  3.000
 H39  O24   C11  C6    112.05  3.000
 H39  O25   C11  C6    124.74  3.000
 H39  O26   C12  N23   123.66  3.000
 H39  N23   C12  C16   114.96  3.000
 H39  O26   C12  C16   121.38  3.000
 H39  H13A  C13  H13   110.67  3.000
 H39  H13A  C13  O28   109.61  3.000
 H39  H13   C13  O28   109.64  3.000
 H39  H13A  C13  O27   110.01  3.000
 H39  H13   C13  O27   110.13  3.000
 H39  O28   C13  O27   106.71  3.000
 H39  H14B  C14  H14A  107.58  3.000
 H39  H14B  C14  H14   107.65  3.000
 H39  H14A  C14  H14   107.64  3.000
 H39  H14B  C14  C20   111.10  3.000
 H39  H14A  C14  C20   111.48  3.000
 H39  H14   C14  C20   111.21  3.000
 H39  H15B  C15  H15A  107.47  3.000
 H39  H15B  C15  H15   107.16  3.000
 H39  H15A  C15  H15   107.54  3.000
 H39  H15B  C15  C20   112.55  3.000
 H39  H15A  C15  C20   110.90  3.000
 H39  H15   C15  C20   110.98  3.000
 H39  H16A  C16  H16   106.38  3.000
 H39  H16A  C16  C12   111.09  3.000
 H39  H16   C16  C12   107.01  3.000
 H39  H16A  C16  C8    110.67  3.000
 H39  H16   C16  C8    109.94  3.000
 H39  C12   C16  C8    111.56  3.000
 H39  H17A  C17  H17   105.97  3.000
 H39  H17A  C17  C21   108.99  3.000
 H39  H17   C17  C21   108.64  3.000
 H39  H17A  C17  C7    110.23  3.000
 H39  H17   C17  C7    108.40  3.000
 H39  C21   C17  C7    114.28  3.000
 H39  H18A  C18  H18   105.87  3.000
 H39  H18A  C18  C21   108.60  3.000
 H39  H18   C18  C21   107.59  3.000
 H39  H18A  C18  C20   109.11  3.000
 H39  H18   C18  C20   106.95  3.000
 H39  C21   C18  C20   118.06  3.000
 H39  H19A  C19  H19   106.84  3.000
 H39  H19A  C19  N23   108.38  3.000
 H39  H19   C19  N23   108.33  3.000
 H39  H19A  C19  C21   109.97  3.000
 H39  H19   C19  C21   109.37  3.000
 H39  N23   C19  C21   113.71  3.000
 H39  H20   C20  C18   109.66  3.000
 H39  H20   C20  C15   108.36  3.000
 H39  C18   C20  C15   111.85  3.000
 H39  H20   C20  C14   107.31  3.000
 H39  C18   C20  C14   109.34  3.000
 H39  C15   C20  C14   110.21  3.000
 H39  H21   C21  C19   107.85  3.000
 H39  H21   C21  C18   108.49  3.000
 H39  C19   C21  C18   114.01  3.000
 H39  H21   C21  C17   108.26  3.000
 H39  C19   C21  C17   108.98  3.000
 H39  C18   C21  C17   109.10  3.000
 H39  HN22  N22  C5    124.98  3.000
 H39  HN22  N22  C4    125.02  3.000
 H39  C5    N22  C4    110.00  3.000
 H39  HN23  N23  C19   116.62  3.000
 H39  HN23  N23  C12   118.08  3.000
 H39  C19   N23  C12   125.23  3.000
 H39  HO24  O24  C11   109.91  3.000
 H39  C13   O27  C9    106.10  3.000
 H39  C13   O28  C10   106.50  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
 H39  CONST_01  C10   C6   C7   C1      0.00   0.0  0
 H39  CONST_02  C10   C9   C2   C1      0.00   0.0  0
 H39  CONST_03  C6    C7   C1   C2      0.00   0.0  0
 H39  CONST_04  C6    C10  C9   C2      0.00   0.0  0
 H39  CONST_05  C5    N22  C4   C3      0.00   0.0  0
 H39  CONST_06  N22   C5   C8   C3      0.00   0.0  0
 H39  CONST_07  C5    C8   C3   C4      0.00   0.0  0
 H39  CONST_08  C8    C5   N22  C4      0.00   0.0  0
 H39  CONST_09  C9    C2   C1   C7      0.00   0.0  0
 H39  CONST_10  C9    C10  C6   C7      0.00   0.0  0
 H39  CONST_11  N22   C4   C3   C8      0.00   0.0  0
 H39  CONST_12  C11   C6   C7   C1    180.00   0.0  0
 H39  CONST_13  C17   C7   C1   C2    180.00   0.0  0
 H39  CONST_14  C16   C8   C3   C4    180.00   0.0  0
 H39  CONST_15  C11   C6   C10  C9    180.00   0.0  0
 H39  CONST_16  C17   C7   C6   C10   180.00   0.0  0
 H39  CONST_17  O28   C10  C6   C11     0.00   0.0  0
 H39  CONST_18  N22   C5   C8   C16   180.00   0.0  0
 H39  CONST_19  HN22  N22  C4   C3    180.00   0.0  0
 H39  CONST_20  H5    C5   C8   C3    180.00   0.0  0
 H39  CONST_21  H4    C4   N22  C5    180.00   0.0  0
 H39  CONST_22  H3    C3   C8   C5    180.00   0.0  0
 H39  CONST_23  H1    C1   C7   C6    180.00   0.0  0
 H39  CONST_24  H2    C2   C1   C7    180.00   0.0  0
 H39  CONST_25  HO24  O24  C11  C6    180.00   0.0  0
 H39  CONST_26  C19   N23  C12  C16   180.00   0.0  0
 H39  CONST_27  O26   C12  N23  C19     0.00   0.0  0
 H39  CONST_28  HN23  N23  C12  C16     0.00   0.0  0
 H39  Var_01    O28   C13  O27  C9    -14.45  30.0  1
 H39  Var_02    O27   C13  O28  C10    14.12  30.0  1
 H39  Var_03    C21   C17  C7   C1   -109.66  30.0  2
 H39  Var_04    C12   C16  C8   C3     79.57  30.0  2
 H39  Var_05    O25   C11  C6   C7     37.91  30.0  2
 H39  Var_06    O26   C12  C16  C8     54.97  30.0  3
 H39  Var_07    C21   C19  N23  C12  -125.32  30.0  3
 H39  Var_08    C21   C18  C20  C14  -179.95  30.0  3
 H39  Var_09    H15   C15  C20  C14   -51.80  30.0  3
 H39  Var_10    H14   C14  C20  C15    58.20  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
 H39  chir_01  C21  C17  C18  C19  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
 H39  plan-1  C3    0.020
 H39  plan-1  C4    0.020
 H39  plan-1  C5    0.020
 H39  plan-1  C8    0.020
 H39  plan-1  C16   0.020
 H39  plan-1  N22   0.020
 H39  plan-1  H4    0.020
 H39  plan-1  H5    0.020
 H39  plan-1  HN22  0.020
 H39  plan-1  H3    0.020
 H39  plan-2  C1    0.020
 H39  plan-2  C2    0.020
 H39  plan-2  C6    0.020
 H39  plan-2  C7    0.020
 H39  plan-2  C9    0.020
 H39  plan-2  C10   0.020
 H39  plan-2  C11   0.020
 H39  plan-2  C17   0.020
 H39  plan-2  O27   0.020
 H39  plan-2  O28   0.020
 H39  plan-2  H1    0.020
 H39  plan-2  H2    0.020
 H39  plan-3  C12   0.020
 H39  plan-3  C16   0.020
 H39  plan-3  C19   0.020
 H39  plan-3  N23   0.020
 H39  plan-3  O26   0.020
 H39  plan-3  HN23  0.020
 H39  plan-4  C6    0.020
 H39  plan-4  C11   0.020
 H39  plan-4  O24   0.020
 H39  plan-4  O25   0.020
 H39  plan-4  HO24  0.020

