# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 11:23:48 2020
#   Inital geometry file: a 57 line input string
#   Ligand name: 2,3-dihydro-1,4-benzodioxin-5-ylmethanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCc1cccc2OCCOc12
#
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
 DBJ  DBJ  2,3-dihydro-1,4-benzodioxin-5-ylmethanol  ligand  22  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DBJ
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
 DBJ  O1   O  OH1   0  -0.669  -3.4663  -0.9549   0.0560
 DBJ  C2   C  CH2   0  -0.168  -2.1139  -1.3325   0.0530
 DBJ  C3   C  CR6   0  -0.091  -1.2432  -0.1054   0.0217
 DBJ  C4   C  CR6   0   0.296   0.1424  -0.2735   0.0031
 DBJ  O5   O  O2    0  -0.478   0.6251  -1.5419   0.0052
 DBJ  C5   C  CH2   0  -0.223   1.9935  -1.6508  -0.3545
 DBJ  C7   C  CH2   0  -0.227   2.7996  -0.5915   0.3560
 DBJ  O8   O  O2    0  -0.482   2.3415   0.6988  -0.0156
 DBJ  C9   C  CR6   0   0.323   0.9925   0.8342  -0.0171
 DBJ  C10  C  CR16  0  -0.373   0.4555   2.1155  -0.0379
 DBJ  C11  C  CR16  0  -0.256  -0.9182   2.2852  -0.0304
 DBJ  C12  C  CR16  0  -0.321  -1.7636   1.1825   0.0097
 DBJ  H1   H  HOH1  0   0.462  -3.9972  -1.7558   0.0847
 DBJ  H2   H  HCH2  0   0.217  -1.8640  -1.9284   0.9415
 DBJ  H3   H  HCH2  0   0.216  -1.8765  -1.9648  -0.8133
 DBJ  H4   H  HCH2  0   0.260   2.3253  -2.6457  -0.0616
 DBJ  H5   H  HCH2  0   0.243   2.1068  -1.5527  -1.4395
 DBJ  H6   H  HCH2  0   0.242   2.7261  -0.7202   1.4414
 DBJ  H7   H  HCH2  0   0.261   3.8495  -0.6559   0.0734
 DBJ  H8   H  HCR6  0   0.263   1.1240   2.9671  -0.0576
 DBJ  H9   H  HCR6  0   0.252  -1.3337   3.2842  -0.0453
 DBJ  H10  H  HCR6  0   0.253  -2.8338   1.3301   0.0229

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
 DBJ  C7   C5   single    1.509  0.020  1.509
 DBJ  C7   O8   single    1.419  0.020  1.419
 DBJ  C5   O5   single    1.419  0.020  1.419
 DBJ  O8   C9   single    1.356  0.020  1.356
 DBJ  O5   C4   single    1.357  0.020  1.357
 DBJ  C9   C4   aromatic  1.396  0.020  1.396
 DBJ  C9   C10  aromatic  1.389  0.020  1.389
 DBJ  C4   C3   aromatic  1.396  0.020  1.396
 DBJ  C10  C11  aromatic  1.384  0.020  1.384
 DBJ  C3   C2   single    1.505  0.020  1.505
 DBJ  C3   C12  aromatic  1.389  0.020  1.389
 DBJ  C2   O1   single    1.404  0.020  1.404
 DBJ  C11  C12  aromatic  1.390  0.020  1.390
 DBJ  O1   H1   single    0.850  0.020  0.980
 DBJ  C2   H2   single    0.970  0.020  1.090
 DBJ  C2   H3   single    0.970  0.020  1.090
 DBJ  C5   H4   single    0.970  0.020  1.090
 DBJ  C5   H5   single    0.970  0.020  1.090
 DBJ  C7   H6   single    0.970  0.020  1.090
 DBJ  C7   H7   single    0.970  0.020  1.090
 DBJ  C10  H8   single    0.930  0.020  1.080
 DBJ  C11  H9   single    0.930  0.020  1.080
 DBJ  C12  H10  single    0.930  0.020  1.080

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
 DBJ  H1   O1   C2   107.93  3.000
 DBJ  H3   C2   H2   106.05  3.000
 DBJ  H3   C2   C3   109.14  3.000
 DBJ  H2   C2   C3   109.11  3.000
 DBJ  H3   C2   O1   111.38  3.000
 DBJ  H2   C2   O1   111.30  3.000
 DBJ  C3   C2   O1   109.75  3.000
 DBJ  C12  C3   C4   118.91  3.000
 DBJ  C12  C3   C2   122.64  3.000
 DBJ  C4   C3   C2   118.45  3.000
 DBJ  C9   C4   O5   121.66  3.000
 DBJ  C9   C4   C3   120.59  3.000
 DBJ  O5   C4   C3   117.75  3.000
 DBJ  C5   O5   C4   114.48  3.000
 DBJ  H5   C5   H4   108.47  3.000
 DBJ  H5   C5   C7   110.38  3.000
 DBJ  H4   C5   C7   110.60  3.000
 DBJ  H5   C5   O5   110.12  3.000
 DBJ  H4   C5   O5   107.21  3.000
 DBJ  C7   C5   O5   109.99  3.000
 DBJ  H7   C7   H6   108.36  3.000
 DBJ  H7   C7   O8   107.28  3.000
 DBJ  H6   C7   O8   110.17  3.000
 DBJ  H7   C7   C5   110.57  3.000
 DBJ  H6   C7   C5   110.38  3.000
 DBJ  O8   C7   C5   110.03  3.000
 DBJ  C9   O8   C7   114.36  3.000
 DBJ  C10  C9   O8   118.47  3.000
 DBJ  C10  C9   C4   119.76  3.000
 DBJ  O8   C9   C4   121.77  3.000
 DBJ  H8   C10  C11  121.09  3.000
 DBJ  H8   C10  C9   119.14  3.000
 DBJ  C11  C10  C9   119.77  3.000
 DBJ  H9   C11  C12  119.95  3.000
 DBJ  H9   C11  C10  119.61  3.000
 DBJ  C12  C11  C10  120.43  3.000
 DBJ  H10  C12  C11  119.64  3.000
 DBJ  H10  C12  C3   119.84  3.000
 DBJ  C11  C12  C3   120.52  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
 DBJ  CONST_01  C10  C9   C4   C3     0.00   0.0  0
 DBJ  CONST_02  C10  C11  C12  C3     0.00   0.0  0
 DBJ  CONST_03  C11  C10  C9   C4     0.00   0.0  0
 DBJ  CONST_04  C11  C12  C3   C4     0.00   0.0  0
 DBJ  CONST_05  C12  C3   C4   C9     0.00   0.0  0
 DBJ  CONST_06  C12  C11  C10  C9     0.00   0.0  0
 DBJ  CONST_07  O5   C4   C3   C2     0.00   0.0  0
 DBJ  CONST_08  C9   C4   C3   C2   180.00   0.0  0
 DBJ  CONST_09  C11  C12  C3   C2   180.00   0.0  0
 DBJ  CONST_10  H9   C11  C12  C3   180.00   0.0  0
 DBJ  CONST_11  H8   C10  C9   C4   180.00   0.0  0
 DBJ  CONST_12  H10  C12  C3   C4   180.00   0.0  0
 DBJ  Var_01    C7   C5   O5   C4    44.79  30.0  1
 DBJ  Var_02    O8   C7   C5   O5   -60.71  30.0  1
 DBJ  Var_03    C9   C4   O5   C5   -15.29  30.0  1
 DBJ  Var_04    C10  C9   O8   C7   164.26  30.0  1
 DBJ  Var_05    C4   C3   C2   O1  -179.47  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
 DBJ  plan-1  C2   0.020
 DBJ  plan-1  C3   0.020
 DBJ  plan-1  C4   0.020
 DBJ  plan-1  O5   0.020
 DBJ  plan-1  O8   0.020
 DBJ  plan-1  C9   0.020
 DBJ  plan-1  C10  0.020
 DBJ  plan-1  C11  0.020
 DBJ  plan-1  C12  0.020
 DBJ  plan-1  H8   0.020
 DBJ  plan-1  H9   0.020
 DBJ  plan-1  H10  0.020

