# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 30 21:33:25 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: (1~{S})-2,3-dihydro-1~{H}-inden-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCc2ccccc12
#
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
 GQR  GQR  "(1~{S})-2,3-dihydro-1~{H}-inden-1-amine"
  ligand  21  10  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_GQR
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
 GQR  N1   N  NH2   0  -0.777  33.5583  14.8819  -61.9945
 GQR  C9   C  CR15  0  -0.180  34.0541  16.1360  -62.5561
 GQR  C5   C  CR56  0   0.106  34.5029  17.1414  -61.5166
 GQR  C6   C  CR16  0  -0.321  35.6634  17.1409  -60.7572
 GQR  C1   C  CR16  0  -0.260  35.8499  18.1394  -59.8065
 GQR  C8   C  CH2   0  -0.460  32.9389  16.9085  -63.2836
 GQR  C7   C  CH2   0  -0.499  32.3691  17.8977  -62.2536
 GQR  C4   C  CR56  0   0.087  33.5323  18.1214  -61.3270
 GQR  C3   C  CR16  0  -0.321  33.7131  19.1139  -60.3751
 GQR  C2   C  CR16  0  -0.257  34.8794  19.1185  -59.6163
 GQR  H1   H  HNH2  0   0.345  34.3039  14.4261  -61.4815
 GQR  H2   H  HNH2  0   0.339  32.8379  15.0768  -61.3074
 GQR  H4   H  HCR5  0   0.241  34.8650  15.8816  -63.2432
 GQR  H5   H  HCR6  0   0.245  36.4208  16.3795  -60.9052
 GQR  H6   H  HCR6  0   0.247  36.7553  18.1578  -59.2130
 GQR  H7   H  HCH2  0   0.243  33.3761  17.4689  -64.1120
 GQR  H8   H  HCH2  0   0.236  32.1875  16.2392  -63.7031
 GQR  H9   H  HCH2  0   0.249  32.0085  18.8191  -62.7132
 GQR  H10  H  HCH2  0   0.246  31.5234  17.4689  -61.7070
 GQR  H11  H  HCR6  0   0.243  32.9629  19.8815  -60.2250
 GQR  H12  H  HCR6  0   0.248  35.0365  19.8923  -58.8755

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
 GQR  C8  C9   single    1.539  0.020  1.539
 GQR  C8  C7   single    1.538  0.020  1.538
 GQR  C9  N1   single    1.461  0.020  1.461
 GQR  C9  C5   single    1.514  0.020  1.514
 GQR  C7  C4   single    1.504  0.020  1.504
 GQR  C5  C4   aromatic  1.392  0.020  1.392
 GQR  C5  C6   aromatic  1.387  0.020  1.387
 GQR  C4  C3   aromatic  1.387  0.020  1.387
 GQR  C6  C1   aromatic  1.391  0.020  1.391
 GQR  C3  C2   aromatic  1.391  0.020  1.391
 GQR  C1  C2   aromatic  1.392  0.020  1.392
 GQR  N1  H1   single    0.890  0.020  1.040
 GQR  N1  H2   single    0.890  0.020  1.040
 GQR  C9  H4   single    0.970  0.020  1.090
 GQR  C6  H5   single    0.930  0.020  1.080
 GQR  C1  H6   single    0.930  0.020  1.080
 GQR  C8  H7   single    0.970  0.020  1.090
 GQR  C8  H8   single    0.970  0.020  1.090
 GQR  C7  H9   single    0.970  0.020  1.090
 GQR  C7  H10  single    0.970  0.020  1.090
 GQR  C3  H11  single    0.930  0.020  1.080
 GQR  C2  H12  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
 GQR  H2   N1  H1  105.43  3.000
 GQR  H2   N1  C9  109.66  3.000
 GQR  H1   N1  C9  109.33  3.000
 GQR  H4   C9  C8  110.93  3.000
 GQR  H4   C9  C5  111.48  3.000
 GQR  C8   C9  C5  101.88  3.000
 GQR  H4   C9  N1  107.08  3.000
 GQR  C5   C9  N1  114.00  3.000
 GQR  C8   C9  N1  111.51  3.000
 GQR  C4   C5  C6  120.60  3.000
 GQR  C6   C5  C9  128.58  3.000
 GQR  C4   C5  C9  110.75  3.000
 GQR  H5   C6  C1  120.24  3.000
 GQR  H5   C6  C5  120.67  3.000
 GQR  C1   C6  C5  119.08  3.000
 GQR  H6   C1  C2  119.76  3.000
 GQR  H6   C1  C6  119.93  3.000
 GQR  C2   C1  C6  120.32  3.000
 GQR  H8   C8  H7  107.41  3.000
 GQR  H8   C8  C7  113.41  3.000
 GQR  H7   C8  C7  109.06  3.000
 GQR  H8   C8  C9  111.90  3.000
 GQR  H7   C8  C9  109.04  3.000
 GQR  C7   C8  C9  105.95  3.000
 GQR  H10  C7  H9  106.61  3.000
 GQR  H10  C7  C4  110.38  3.000
 GQR  H9   C7  C4  112.93  3.000
 GQR  H10  C7  C8  111.65  3.000
 GQR  H9   C7  C8  112.56  3.000
 GQR  C4   C7  C8  102.81  3.000
 GQR  C3   C4  C7  129.05  3.000
 GQR  C3   C4  C5  120.42  3.000
 GQR  C7   C4  C5  110.53  3.000
 GQR  H11  C3  C2  120.16  3.000
 GQR  H11  C3  C4  120.78  3.000
 GQR  C2   C3  C4  119.06  3.000
 GQR  H12  C2  C3  119.81  3.000
 GQR  H12  C2  C1  119.68  3.000
 GQR  C3   C2  C1  120.51  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
 GQR  CONST_01  C2   C3  C4  C5     0.00   0.0  0
 GQR  CONST_02  C2   C1  C6  C5     0.00   0.0  0
 GQR  CONST_03  C3   C4  C5  C6     0.00   0.0  0
 GQR  CONST_04  C3   C2  C1  C6     0.00   0.0  0
 GQR  CONST_05  C4   C5  C6  C1     0.00   0.0  0
 GQR  CONST_06  C4   C3  C2  C1     0.00   0.0  0
 GQR  CONST_07  H5   C6  C5  C9     0.00   0.0  0
 GQR  CONST_08  H11  C3  C4  C5   180.00   0.0  0
 GQR  CONST_09  H6   C1  C6  C5   180.00   0.0  0
 GQR  CONST_10  H12  C2  C1  C6   180.00   0.0  0
 GQR  CONST_11  H11  C3  C2  C1   180.00   0.0  0
 GQR  CONST_12  H11  C3  C4  C7     0.00   0.0  0
 GQR  CONST_13  H5   C6  C5  C4   180.00   0.0  0
 GQR  CONST_14  H12  C2  C3  C4   180.00   0.0  0
 GQR  CONST_15  H6   C1  C2  C3   180.00   0.0  0
 GQR  CONST_16  H5   C6  C1  C2   180.00   0.0  0
 GQR  Var_01    C4   C7  C8  C9    26.67  30.0  1
 GQR  Var_02    C8   C7  C4  C5   -15.45  30.0  1
 GQR  Var_03    C3   C4  C7  C8   165.19  30.0  1
 GQR  Var_04    H9   C7  C8  C9   148.48  30.0  1
 GQR  Var_05    H10  C7  C8  C9   -91.65  30.0  1
 GQR  Var_06    H9   C7  C4  C5  -137.01  30.0  1
 GQR  Var_07    H10  C7  C4  C5   103.76  30.0  1
 GQR  Var_08    H7   C8  C7  C4   -90.56  30.0  1
 GQR  Var_09    H8   C8  C7  C4   149.80  30.0  1
 GQR  Var_10    H9   C7  C4  C3    43.63  30.0  1
 GQR  Var_11    H10  C7  C4  C3   -75.59  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 GQR  chir_01  C9  C8  N1  C5  positiv

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
 GQR  plan-1  C9   0.020
 GQR  plan-1  C5   0.020
 GQR  plan-1  C6   0.020
 GQR  plan-1  C1   0.020
 GQR  plan-1  C7   0.020
 GQR  plan-1  C4   0.020
 GQR  plan-1  C3   0.020
 GQR  plan-1  C2   0.020
 GQR  plan-1  H5   0.020
 GQR  plan-1  H6   0.020
 GQR  plan-1  H11  0.020
 GQR  plan-1  H12  0.020

