# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 10:38:13 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: 3-hydroxy-2H-chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC1=Cc2ccccc2OC1=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
 SE2  SE2  3-hydroxy-2H-chromen-2-one  ligand  18  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SE2
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
 SE2  O8   O  O     0  -0.433  -2.6499   1.5090   0.1639
 SE2  C8   C  CR6   0   0.482  -1.6795   0.7934   0.1006
 SE2  O1   O  O     0  -0.449  -0.4591   1.3417   0.0944
 SE2  C11  C  CR66  0   0.363   0.6903   0.6144   0.0273
 SE2  C10  C  CR16  0  -0.314   1.8904   1.3074   0.0290
 SE2  C1   C  CR16  0  -0.265   3.0717   0.5893  -0.0373
 SE2  C2   C  CR16  0  -0.248   3.0505  -0.8038  -0.1041
 SE2  C3   C  CR16  0  -0.326   1.8462  -1.4791  -0.1041
 SE2  C4   C  CR66  0   0.029   0.6379  -0.7765  -0.0387
 SE2  C5   C  CR16  0  -0.261  -0.6484  -1.4137  -0.0354
 SE2  C7   C  CR6   0   0.171  -1.7657  -0.6670   0.0293
 SE2  O11  O  OH1   0  -0.610  -2.9917  -1.1974   0.0348
 SE2  H10  H  HCR6  0   0.284   1.8957   2.3882   0.0815
 SE2  H1   H  HCR6  0   0.271   4.0154   1.1178  -0.0360
 SE2  H2   H  HCR6  0   0.266   3.9785  -1.3568  -0.1564
 SE2  H3   H  HCR6  0   0.269   1.8234  -2.5603  -0.1547
 SE2  H5   H  HCR6  0   0.294  -0.7082  -2.4940  -0.0862
 SE2  H11  H  HOH1  0   0.477  -3.6545  -0.4946   0.0855

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
 SE2  O8   C8   double    1.207  0.020  1.207
 SE2  C8   O1   single    1.338  0.020  1.338
 SE2  C8   C7   single    1.465  0.020  1.465
 SE2  O1   C11  single    1.362  0.020  1.362
 SE2  C11  C10  aromatic  1.386  0.020  1.386
 SE2  C11  C4   aromatic  1.393  0.020  1.393
 SE2  C10  C1   aromatic  1.384  0.020  1.384
 SE2  C1   C2   aromatic  1.395  0.020  1.395
 SE2  C2   C3   aromatic  1.381  0.020  1.381
 SE2  C3   C4   aromatic  1.399  0.020  1.399
 SE2  C4   C5   single    1.435  0.020  1.435
 SE2  C5   C7   double    1.345  0.020  1.345
 SE2  C7   O11  single    1.336  0.020  1.336
 SE2  C10  H10  single    0.930  0.020  1.080
 SE2  C1   H1   single    0.930  0.020  1.080
 SE2  C2   H2   single    0.930  0.020  1.080
 SE2  C3   H3   single    0.930  0.020  1.080
 SE2  C5   H5   single    0.930  0.020  1.080
 SE2  O11  H11  single    0.850  0.020  0.980

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
 SE2  C7   C8   O1   117.52  3.000
 SE2  C7   C8   O8   123.11  3.000
 SE2  O1   C8   O8   119.37  3.000
 SE2  C11  O1   C8   123.45  3.000
 SE2  C4   C11  C10  122.12  3.000
 SE2  C4   C11  O1   120.25  3.000
 SE2  C10  C11  O1   117.63  3.000
 SE2  H10  C10  C1   121.09  3.000
 SE2  H10  C10  C11  120.25  3.000
 SE2  C1   C10  C11  118.66  3.000
 SE2  H1   C1   C2   120.09  3.000
 SE2  H1   C1   C10  119.42  3.000
 SE2  C2   C1   C10  120.50  3.000
 SE2  H2   C2   C3   119.89  3.000
 SE2  H2   C2   C1   119.99  3.000
 SE2  C3   C2   C1   120.12  3.000
 SE2  H3   C3   C4   119.04  3.000
 SE2  H3   C3   C2   120.46  3.000
 SE2  C4   C3   C2   120.50  3.000
 SE2  C5   C4   C3   123.43  3.000
 SE2  C5   C4   C11  118.47  3.000
 SE2  C3   C4   C11  118.10  3.000
 SE2  H5   C5   C7   120.66  3.000
 SE2  H5   C5   C4   119.48  3.000
 SE2  C7   C5   C4   119.86  3.000
 SE2  O11  C7   C5   122.82  3.000
 SE2  O11  C7   C8   116.72  3.000
 SE2  C5   C7   C8   120.46  3.000
 SE2  H11  O11  C7   109.91  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
 SE2  CONST_01  C2   C1   C10  C11     0.00   0.0  0
 SE2  CONST_02  C2   C3   C4   C11     0.00   0.0  0
 SE2  CONST_03  C3   C4   C11  C10     0.00   0.0  0
 SE2  CONST_04  C3   C2   C1   C10     0.00   0.0  0
 SE2  CONST_05  C4   C11  C10  C1      0.00   0.0  0
 SE2  CONST_06  C4   C3   C2   C1      0.00   0.0  0
 SE2  CONST_07  H10  C10  C11  O1      0.00   0.0  0
 SE2  CONST_08  H1   C1   C10  C11   180.00   0.0  0
 SE2  CONST_09  H3   C3   C4   C11   180.00   0.0  0
 SE2  CONST_10  H2   C2   C1   C10   180.00   0.0  0
 SE2  Var_01    C10  C11  O1   C8   -179.99  30.0  1
 SE2  Var_02    C4   C5   C7   C8     -0.18  30.0  1
 SE2  Var_03    C5   C7   C8   O1      0.19  30.0  1
 SE2  Var_04    C7   C8   O1   C11    -0.07  30.0  1
 SE2  Var_05    C7   C5   C4   C11     0.06  30.0  1

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
 SE2  plan-1  O8   0.020
 SE2  plan-1  C8   0.020
 SE2  plan-1  O1   0.020
 SE2  plan-1  C7   0.020
 SE2  plan-2  O1   0.020
 SE2  plan-2  C11  0.020
 SE2  plan-2  C10  0.020
 SE2  plan-2  C1   0.020
 SE2  plan-2  C2   0.020
 SE2  plan-2  C3   0.020
 SE2  plan-2  C4   0.020
 SE2  plan-2  C5   0.020
 SE2  plan-2  H10  0.020
 SE2  plan-2  H1   0.020
 SE2  plan-2  H2   0.020
 SE2  plan-2  H3   0.020

