# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 21:53:49 2020
#   Inital geometry file: a 51 line input string
#   Ligand name: 1H-indene
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1C=Cc2ccccc12
#
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
 DEN  DEN  '1H-indene                '  ligand  17  9  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_DEN
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
 DEN  C1   C  CH2   0  -0.516   1.1585  -0.0045  -1.6461
 DEN  C2   C  CR15  0  -0.264  -0.1259  -0.0262  -2.4203
 DEN  C3   C  CR15  0  -0.255  -1.1827  -0.0340  -1.5956
 DEN  C4   C  CR16  0  -0.328  -1.4147  -0.0194   0.9892
 DEN  C5   C  CR16  0  -0.262  -0.6940  -0.0029   2.1785
 DEN  C6   C  CR16  0  -0.268   0.6979   0.0145   2.1667
 DEN  C7   C  CR16  0  -0.312   1.3978   0.0160   0.9617
 DEN  C8   C  CR56  0   0.054   0.6854  -0.0006  -0.2229
 DEN  C9   C  CR56  0   0.101  -0.7165  -0.0184  -0.2115
 DEN  H11  H  HCH2  0   0.272   1.7857  -0.8731  -1.8722
 DEN  H12  H  HCH2  0   0.273   1.7662   0.8738  -1.8865
 DEN  H2   H  HCR5  0   0.255  -0.1648  -0.0346  -3.5003
 DEN  H3   H  HCR5  0   0.251  -2.2233  -0.0491  -1.8900
 DEN  H4   H  HCR6  0   0.249  -2.4977  -0.0326   1.0047
 DEN  H5   H  HCR6  0   0.252  -1.2208  -0.0032   3.1244
 DEN  H6   H  HCR6  0   0.251   1.2419   0.0264   3.1025
 DEN  H7   H  HCR6  0   0.249   2.4811   0.0293   0.9605

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
 DEN  C1  C2   single    1.500  0.020  1.500
 DEN  C1  C8   single    1.500  0.020  1.500
 DEN  C1  H11  single    0.970  0.020  1.090
 DEN  C1  H12  single    0.970  0.020  1.090
 DEN  C2  C3   double    1.341  0.020  1.341
 DEN  C2  H2   single    0.930  0.020  1.080
 DEN  C3  C9   single    1.461  0.020  1.461
 DEN  C3  H3   single    0.930  0.020  1.080
 DEN  C4  C5   aromatic  1.391  0.020  1.391
 DEN  C4  C9   aromatic  1.389  0.020  1.389
 DEN  C4  H4   single    0.930  0.020  1.080
 DEN  C5  C6   aromatic  1.392  0.020  1.392
 DEN  C5  H5   single    0.930  0.020  1.080
 DEN  C6  C7   aromatic  1.394  0.020  1.394
 DEN  C6  H6   single    0.930  0.020  1.080
 DEN  C7  C8   aromatic  1.382  0.020  1.382
 DEN  C7  H7   single    0.930  0.020  1.080
 DEN  C8  C9   aromatic  1.402  0.020  1.402

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
 DEN  H12  C1  H11  105.84  3.000
 DEN  H12  C1  C8   112.42  3.000
 DEN  H11  C1  C8   112.25  3.000
 DEN  H12  C1  C2   111.94  3.000
 DEN  H11  C1  C2   111.87  3.000
 DEN  C8   C1  C2   102.70  3.000
 DEN  H2   C2  C3   125.90  3.000
 DEN  H2   C2  C1   123.15  3.000
 DEN  C3   C2  C1   110.95  3.000
 DEN  H3   C3  C9   124.42  3.000
 DEN  H3   C3  C2   126.23  3.000
 DEN  C9   C3  C2   109.35  3.000
 DEN  H4   C4  C9   121.00  3.000
 DEN  H4   C4  C5   120.40  3.000
 DEN  C9   C4  C5   118.60  3.000
 DEN  H5   C5  C6   119.60  3.000
 DEN  H5   C5  C4   119.66  3.000
 DEN  C6   C5  C4   120.74  3.000
 DEN  H6   C6  C7   119.67  3.000
 DEN  H6   C6  C5   119.69  3.000
 DEN  C7   C6  C5   120.63  3.000
 DEN  H7   C7  C8   120.97  3.000
 DEN  H7   C7  C6   120.21  3.000
 DEN  C8   C7  C6   118.82  3.000
 DEN  C9   C8  C7   120.57  3.000
 DEN  C9   C8  C1   108.85  3.000
 DEN  C7   C8  C1   130.59  3.000
 DEN  C8   C9  C4   120.64  3.000
 DEN  C8   C9  C3   108.16  3.000
 DEN  C4   C9  C3   131.20  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
 DEN  CONST_01  C7  C6  C5  C4    0.00  0.0  0
 DEN  CONST_02  C7  C8  C9  C4    0.00  0.0  0
 DEN  CONST_03  C8  C9  C4  C5    0.00  0.0  0
 DEN  CONST_04  C8  C7  C6  C5    0.00  0.0  0
 DEN  CONST_05  C9  C4  C5  C6    0.00  0.0  0
 DEN  CONST_06  C9  C8  C7  C6    0.00  0.0  0
 DEN  CONST_07  H7  C7  C8  C1    0.00  0.0  0
 DEN  CONST_08  H4  C4  C9  C3    0.00  0.0  0
 DEN  CONST_09  H6  C6  C5  C4  180.00  0.0  0
 DEN  CONST_10  H5  C5  C6  C7  180.00  0.0  0

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
 DEN  plan-1  C1   0.020
 DEN  plan-1  C2   0.020
 DEN  plan-1  C3   0.020
 DEN  plan-1  C4   0.020
 DEN  plan-1  C5   0.020
 DEN  plan-1  C6   0.020
 DEN  plan-1  C7   0.020
 DEN  plan-1  C8   0.020
 DEN  plan-1  C9   0.020
 DEN  plan-1  H11  0.020
 DEN  plan-1  H12  0.020
 DEN  plan-1  H2   0.020
 DEN  plan-1  H3   0.020
 DEN  plan-1  H4   0.020
 DEN  plan-1  H5   0.020
 DEN  plan-1  H6   0.020
 DEN  plan-1  H7   0.020

