# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 05:54:29 2020
#   Inital geometry file: a 50 line input string
#   Ligand name: 1,3-benzodioxole-5-carbaldehyde
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=Cc1ccc2OCOc2c1
#
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
 5XC  5XC  1,3-benzodioxole-5-carbaldehyde  ligand  17  11  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5XC
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
 5XC  O01  O  O     0  -0.483   1.9772  -1.3142  -0.2750
 5XC  O02  O  O     0  -0.473   2.3829   0.9365  -0.2452
 5XC  O03  O  O     0  -0.392  -3.8754  -0.0240   0.1631
 5XC  C04  C  CR56  0   0.316   0.8076  -0.6433  -0.1675
 5XC  C05  C  CR56  0   0.322   1.0596   0.7224  -0.1532
 5XC  C06  C  CR16  0  -0.367  -0.4644  -1.1411  -0.0951
 5XC  C07  C  CH2   0   0.071   3.0129  -0.3426  -0.2265
 5XC  C08  C  CR16  0  -0.329   0.0490   1.6547  -0.0666
 5XC  C09  C  CR6   0  -0.032  -1.5113  -0.2052  -0.0049
 5XC  C10  C  CR16  0  -0.275  -1.2517   1.1635   0.0087
 5XC  C11  C  C1    0   0.115  -2.8837  -0.7129   0.0751
 5XC  H2   H  HCR6  0   0.285  -0.6622  -2.2058  -0.1081
 5XC  H3   H  HCH2  0   0.244   3.5886  -0.4540   0.6962
 5XC  H4   H  HCR6  0   0.284   0.2537   2.7163  -0.0592
 5XC  H5   H  HCR6  0   0.272  -2.0748   1.8619   0.0786
 5XC  H6   H  H     0   0.195  -2.9634  -1.8148   0.0493
 5XC  H1   H  HCH2  0   0.249   3.6606  -0.4448  -1.0978

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
 5XC  O03  C11  double    1.211  0.020  1.211
 5XC  O01  C04  single    1.353  0.020  1.353
 5XC  O01  C07  single    1.421  0.020  1.421
 5XC  C06  C04  aromatic  1.368  0.020  1.368
 5XC  C06  C09  aromatic  1.407  0.020  1.407
 5XC  C04  C05  aromatic  1.389  0.020  1.389
 5XC  C11  C09  single    1.465  0.020  1.465
 5XC  C07  O02  single    1.426  0.020  1.426
 5XC  C09  C10  aromatic  1.393  0.020  1.393
 5XC  C05  O02  single    1.344  0.020  1.344
 5XC  C05  C08  aromatic  1.378  0.020  1.378
 5XC  C10  C08  aromatic  1.392  0.020  1.392
 5XC  C06  H2   single    0.930  0.020  1.080
 5XC  C07  H3   single    0.970  0.020  1.090
 5XC  C08  H4   single    0.930  0.020  1.080
 5XC  C10  H5   single    0.930  0.020  1.080
 5XC  C11  H6   single    0.930  0.020  1.080
 5XC  C07  H1   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
 5XC  C07  O01  C04  106.76  3.000
 5XC  C07  O02  C05  106.94  3.000
 5XC  C06  C04  C05  121.74  3.000
 5XC  C05  C04  O01  109.37  3.000
 5XC  C06  C04  O01  128.89  3.000
 5XC  C08  C05  C04  122.21  3.000
 5XC  C08  C05  O02  128.24  3.000
 5XC  C04  C05  O02  109.55  3.000
 5XC  H2   C06  C09  121.25  3.000
 5XC  H2   C06  C04  121.80  3.000
 5XC  C09  C06  C04  116.95  3.000
 5XC  H1   C07  H3   110.61  3.000
 5XC  H1   C07  O02  109.63  3.000
 5XC  H3   C07  O02  109.58  3.000
 5XC  H1   C07  O01  109.97  3.000
 5XC  H3   C07  O01  110.06  3.000
 5XC  O02  C07  O01  106.91  3.000
 5XC  H4   C08  C10  121.53  3.000
 5XC  H4   C08  C05  121.73  3.000
 5XC  C10  C08  C05  116.74  3.000
 5XC  C11  C09  C10  120.95  3.000
 5XC  C10  C09  C06  121.03  3.000
 5XC  C11  C09  C06  118.02  3.000
 5XC  H5   C10  C09  119.55  3.000
 5XC  H5   C10  C08  119.11  3.000
 5XC  C09  C10  C08  121.34  3.000
 5XC  H6   C11  C09  114.32  3.000
 5XC  H6   C11  O03  120.67  3.000
 5XC  C09  C11  O03  125.02  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
 5XC  CONST_01  C10  C09  C06  C04    0.00   0.0  0
 5XC  CONST_02  C10  C08  C05  C04    0.00   0.0  0
 5XC  CONST_03  C09  C06  C04  C05    0.00   0.0  0
 5XC  CONST_04  C09  C10  C08  C05    0.00   0.0  0
 5XC  CONST_05  C08  C05  C04  C06    0.00   0.0  0
 5XC  CONST_06  C08  C10  C09  C06    0.00   0.0  0
 5XC  CONST_07  C11  C09  C06  C04  180.00   0.0  0
 5XC  CONST_08  C11  C09  C10  C08  180.00   0.0  0
 5XC  CONST_09  H2   C06  C04  O01    0.00   0.0  0
 5XC  CONST_10  H4   C08  C05  O02    0.00   0.0  0
 5XC  CONST_11  H5   C10  C08  C05  180.00   0.0  0
 5XC  Var_01    C08  C05  O02  C07  176.52  30.0  1
 5XC  Var_02    H3   C07  O01  C04  112.21  30.0  1
 5XC  Var_03    C06  C09  C11  O03  179.60  30.0  2

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
 5XC  plan-1  O03  0.020
 5XC  plan-1  C09  0.020
 5XC  plan-1  C11  0.020
 5XC  plan-1  H6   0.020
 5XC  plan-2  O01  0.020
 5XC  plan-2  O02  0.020
 5XC  plan-2  C04  0.020
 5XC  plan-2  C05  0.020
 5XC  plan-2  C06  0.020
 5XC  plan-2  C08  0.020
 5XC  plan-2  C09  0.020
 5XC  plan-2  C10  0.020
 5XC  plan-2  C11  0.020
 5XC  plan-2  H2   0.020
 5XC  plan-2  H4   0.020
 5XC  plan-2  H5   0.020

