# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 17:48:45 2020
#   Inital geometry file: a 64 line input string
#   Ligand name: 3-(1,3-benzodioxol-5-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCc1ccc2OCOc2c1
#
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
 I2E  I2E  '3-(1,3-benzodioxol-5-yl)propanoic acid'  ligand  23  14  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_I2E
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
 I2E  C4    C  CR56   0   0.276  -2.5086  -0.6362  -0.1421
 I2E  C5    C  CR16   0  -0.329  -1.7357  -1.7695  -0.1384
 I2E  C6    C  CR16   0  -0.329  -0.3843  -1.6123   0.1967
 I2E  C3    C  CR56   0   0.311  -1.9759   0.6031   0.1720
 I2E  C2    C  CR16   0  -0.395  -0.6535   0.7679   0.4995
 I2E  C1    C  CR6    0   0.116   0.1646  -0.3751   0.5122
 I2E  C7    C  CH2    0  -0.497   1.6330  -0.2378   0.8101
 I2E  C8    C  CH2    0  -0.575   2.4346   0.0869  -0.4474
 I2E  C9    C  C      0   0.413   3.9474   0.2861  -0.2402
 I2E  O1    O  OC    -1  -0.630   4.6117   0.5044  -1.2751
 I2E  C20   C  CH2    0   0.070  -4.1668   0.8393  -0.1056
 I2E  O2    O  O      0  -0.607   4.3905   0.2219   0.9229
 I2E  O4    O  O      0  -0.490  -3.8268  -0.4974  -0.4440
 I2E  O3    O  O      0  -0.490  -2.9481   1.5461   0.0793
 I2E  H5    H  HCR6   0   0.267  -2.1446  -2.7407  -0.3825
 I2E  H6    H  HCR6   0   0.246   0.2513  -2.4894   0.2133
 I2E  H2    H  HCR6   0   0.261  -0.2521   1.7439   0.7435
 I2E  H71C  H  HCH2   0   0.228   1.7878   0.5451   1.5552
 I2E  H72C  H  HCH2   0   0.228   2.0053  -1.1641   1.2530
 I2E  H81C  H  HCH2   0   0.227   2.2868  -0.7059  -1.1888
 I2E  H82C  H  HCH2   0   0.228   2.0311   0.9925  -0.9147
 I2E  H201  H  HCH2   0   0.243  -4.7370   1.2921  -0.9169
 I2E  H202  H  HCH2   0   0.229  -4.7484   0.8528   0.8231

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
 I2E  C4   C5    aromatic  1.372  0.020  1.372
 I2E  C4   C3    aromatic  1.385  0.020  1.385
 I2E  C4   O4    single    1.359  0.020  1.359
 I2E  C5   C6    aromatic  1.401  0.020  1.401
 I2E  C6   C1    aromatic  1.390  0.020  1.390
 I2E  C3   C2    aromatic  1.372  0.020  1.372
 I2E  C3   O3    single    1.358  0.020  1.358
 I2E  C2   C1    aromatic  1.406  0.020  1.406
 I2E  C1   C7    single    1.505  0.020  1.505
 I2E  C7   C8    single    1.526  0.020  1.526
 I2E  C8   C9    single    1.540  0.020  1.540
 I2E  C9   O1    deloc     1.249  0.020  1.249
 I2E  C9   O2    deloc     1.246  0.020  1.246
 I2E  C20  O4    single    1.420  0.020  1.420
 I2E  C20  O3    single    1.421  0.020  1.421
 I2E  C5   H5    single    0.930  0.020  1.080
 I2E  C6   H6    single    0.930  0.020  1.080
 I2E  C2   H2    single    0.930  0.020  1.080
 I2E  C7   H71C  single    0.970  0.020  1.090
 I2E  C7   H72C  single    0.970  0.020  1.090
 I2E  C8   H81C  single    0.970  0.020  1.090
 I2E  C8   H82C  single    0.970  0.020  1.090
 I2E  C20  H201  single    0.970  0.020  1.090
 I2E  C20  H202  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
 I2E  O4    C4   C3    109.39  3.000
 I2E  O4    C4   C5    129.15  3.000
 I2E  C3    C4   C5    121.46  3.000
 I2E  H5    C5   C6    121.29  3.000
 I2E  H5    C5   C4    121.88  3.000
 I2E  C6    C5   C4    116.83  3.000
 I2E  H6    C6   C1    119.05  3.000
 I2E  H6    C6   C5    118.60  3.000
 I2E  C1    C6   C5    122.35  3.000
 I2E  O3    C3   C2    128.53  3.000
 I2E  O3    C3   C4    109.31  3.000
 I2E  C2    C3   C4    122.16  3.000
 I2E  H2    C2   C1    121.00  3.000
 I2E  H2    C2   C3    121.27  3.000
 I2E  C1    C2   C3    117.73  3.000
 I2E  C7    C1   C2    119.70  3.000
 I2E  C7    C1   C6    120.77  3.000
 I2E  C2    C1   C6    119.47  3.000
 I2E  H72C  C7   H71C  106.44  3.000
 I2E  H72C  C7   C8    109.61  3.000
 I2E  H71C  C7   C8    109.59  3.000
 I2E  H72C  C7   C1    109.60  3.000
 I2E  H71C  C7   C1    109.81  3.000
 I2E  C8    C7   C1    111.64  3.000
 I2E  H82C  C8   H81C  105.06  3.000
 I2E  H82C  C8   C9    108.19  3.000
 I2E  H81C  C8   C9    108.49  3.000
 I2E  H82C  C8   C7    109.49  3.000
 I2E  H81C  C8   C7    109.44  3.000
 I2E  C9    C8   C7    115.63  3.000
 I2E  O2    C9   O1    126.38  3.000
 I2E  O2    C9   C8    117.92  3.000
 I2E  O1    C9   C8    115.70  3.000
 I2E  H202  C20  H201  110.36  3.000
 I2E  H202  C20  O3    109.80  3.000
 I2E  H201  C20  O3    109.81  3.000
 I2E  H202  C20  O4    109.91  3.000
 I2E  H201  C20  O4    109.81  3.000
 I2E  O3    C20  O4    107.09  3.000
 I2E  C20   O4   C4    105.98  3.000
 I2E  C20   O3   C3    106.11  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
 I2E  CONST_01  C1  C6   C5  C4    0.00   0.0  0
 I2E  CONST_02  C1  C2   C3  C4    0.00   0.0  0
 I2E  CONST_03  C2  C3   C4  C5    0.00   0.0  0
 I2E  CONST_04  C2  C1   C6  C5    0.00   0.0  0
 I2E  CONST_05  C3  C4   C5  C6    0.00   0.0  0
 I2E  CONST_06  C3  C2   C1  C6    0.00   0.0  0
 I2E  CONST_07  C7  C1   C6  C5  180.00   0.0  0
 I2E  CONST_08  C7  C1   C2  C3  180.00   0.0  0
 I2E  CONST_09  H6  C6   C5  C4  180.00   0.0  0
 I2E  CONST_10  H2  C2   C3  C4  180.00   0.0  0
 I2E  CONST_11  H5  C5   C4  C3  180.00   0.0  0
 I2E  Var_01    O3  C20  O4  C4   14.23  30.0  1
 I2E  Var_02    O4  C20  O3  C3  -14.12  30.0  1
 I2E  Var_03    C8  C7   C1  C6   91.51  30.0  2
 I2E  Var_04    C9  C8   C7  C1  178.38  30.0  3
 I2E  Var_05    O1  C9   C8  C7  177.54  30.0  3

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
 I2E  plan-1  C8  0.020
 I2E  plan-1  C9  0.020
 I2E  plan-1  O1  0.020
 I2E  plan-1  O2  0.020
 I2E  plan-2  C4  0.020
 I2E  plan-2  C5  0.020
 I2E  plan-2  C6  0.020
 I2E  plan-2  C3  0.020
 I2E  plan-2  C2  0.020
 I2E  plan-2  C1  0.020
 I2E  plan-2  C7  0.020
 I2E  plan-2  O4  0.020
 I2E  plan-2  O3  0.020
 I2E  plan-2  H5  0.020
 I2E  plan-2  H6  0.020
 I2E  plan-2  H2  0.020

