# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 17:59:48 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: 1,3-dihydro-2H-isoindol-2-yl(2,4-dihydroxyphenyl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1ccc(c(O)c1)C(=O)N2Cc3ccccc3C2
#
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
 PFT  PFT  1,3-dihydro-2H-isoindol-2-yl(2,4-dihydroxyphenyl)methanone  ligand  32  19  .  2021-08-19  2021-08-19  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PFT
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
 PFT  N1    N  NR5   0  -0.488   0.8046   0.6912   0.4243
 PFT  C2    C  C     0   0.519  -0.3970   1.2285   0.6714
 PFT  C3    C  CH2   0  -0.278   2.0290   1.4495   0.6594
 PFT  C4    C  CH2   0  -0.264   1.0310  -0.6206  -0.1785
 PFT  C5    C  CR6   0  -0.200  -1.5770   0.3551   0.3822
 PFT  O6    O  O     0  -0.491  -0.5297   2.3605   1.1181
 PFT  C7    C  CR56  0   0.044   3.0877   0.5082   0.1775
 PFT  C8    C  CR56  0   0.049   2.5221  -0.6635  -0.2992
 PFT  C9    C  CR6   0   0.376  -2.3185   0.5510  -0.7844
 PFT  C10   C  CR16  0  -0.231  -1.9922  -0.6163   1.2810
 PFT  C11   C  CR16  0  -0.314   4.4617   0.6876   0.1650
 PFT  C12   C  CR16  0  -0.311   3.3160  -1.6835  -0.7987
 PFT  C13   C  CR16  0  -0.470  -3.4480  -0.2153  -1.0386
 PFT  O14   O  OH1   0  -0.622  -1.8771   1.4904  -1.6397
 PFT  C15   C  CR16  0  -0.408  -3.1211  -1.3856   1.0481
 PFT  C16   C  CR16  0  -0.255   5.2633  -0.3314  -0.3353
 PFT  C17   C  CR16  0  -0.256   4.6944  -1.5088  -0.8133
 PFT  C18   C  CR6   0   0.369  -3.8513  -1.1806  -0.1201
 PFT  O19   O  OH1   0  -0.627  -4.9560  -1.8878  -0.4163
 PFT  H3    H  HCH2  0   0.262   2.0247   2.3898   0.1006
 PFT  H2    H  HCH2  0   0.263   2.1441   1.7002   1.7176
 PFT  H4    H  HCH2  0   0.268   0.6510  -1.4287   0.4515
 PFT  H41   H  HCH2  0   0.265   0.5391  -0.7077  -1.1512
 PFT  H10   H  HCR6  0   0.269  -1.4251  -0.7791   2.1895
 PFT  H11   H  HCR6  0   0.255   4.9060   1.6016   0.5391
 PFT  H12   H  HCR6  0   0.255   2.8756  -2.5999  -1.1712
 PFT  H13   H  HCR6  0   0.280  -4.0198  -0.0699  -1.9485
 PFT  HO14  H  HOH1  0   0.480  -2.4454   1.5409  -2.4169
 PFT  H15   H  HCR6  0   0.272  -3.4284  -2.1317   1.7710
 PFT  H16   H  HCR6  0   0.258   6.3385  -0.2089  -0.3528
 PFT  H17   H  HCR6  0   0.258   5.3304  -2.2954  -1.1984
 PFT  HO19  H  HOH1  0   0.476  -5.1388  -2.5320   0.2767

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
 PFT  N1   C2    single    1.339  0.020  1.339
 PFT  N1   C3    single    1.459  0.020  1.459
 PFT  N1   C4    single    1.461  0.020  1.461
 PFT  C2   C5    single    1.496  0.020  1.496
 PFT  C2   O6    double    1.224  0.020  1.224
 PFT  C3   C7    single    1.496  0.020  1.496
 PFT  C4   C8    single    1.497  0.020  1.497
 PFT  C5   C9    aromatic  1.396  0.020  1.396
 PFT  C5   C10   aromatic  1.387  0.020  1.387
 PFT  C7   C8    aromatic  1.386  0.020  1.386
 PFT  C7   C11   aromatic  1.386  0.020  1.386
 PFT  C8   C12   aromatic  1.386  0.020  1.386
 PFT  C9   C13   aromatic  1.388  0.020  1.388
 PFT  C9   O14   single    1.345  0.020  1.345
 PFT  C10  C15   aromatic  1.386  0.020  1.386
 PFT  C11  C16   aromatic  1.390  0.020  1.390
 PFT  C12  C17   aromatic  1.390  0.020  1.390
 PFT  C13  C18   aromatic  1.392  0.020  1.392
 PFT  C15  C18   aromatic  1.393  0.020  1.393
 PFT  C16  C17   aromatic  1.392  0.020  1.392
 PFT  C18  O19   single    1.345  0.020  1.345
 PFT  C3   H3    single    0.970  0.020  1.090
 PFT  C3   H2    single    0.970  0.020  1.090
 PFT  C4   H4    single    0.970  0.020  1.090
 PFT  C4   H41   single    0.970  0.020  1.090
 PFT  C10  H10   single    0.930  0.020  1.080
 PFT  C11  H11   single    0.930  0.020  1.080
 PFT  C12  H12   single    0.930  0.020  1.080
 PFT  C13  H13   single    0.930  0.020  1.080
 PFT  O14  HO14  single    0.850  0.020  0.980
 PFT  C15  H15   single    0.930  0.020  1.080
 PFT  C16  H16   single    0.930  0.020  1.080
 PFT  C17  H17   single    0.930  0.020  1.080
 PFT  O19  HO19  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
 PFT  C4    N1   C3   113.77  3.000
 PFT  C4    N1   C2   125.12  3.000
 PFT  C3    N1   C2   120.97  3.000
 PFT  O6    C2   C5   121.65  3.000
 PFT  O6    C2   N1   122.39  3.000
 PFT  C5    C2   N1   115.96  3.000
 PFT  H2    C3   H3   107.32  3.000
 PFT  H2    C3   C7   112.42  3.000
 PFT  H3    C3   C7   112.27  3.000
 PFT  H2    C3   N1   111.31  3.000
 PFT  H3    C3   N1   111.17  3.000
 PFT  C7    C3   N1   102.40  3.000
 PFT  H41   C4   H4   107.30  3.000
 PFT  H41   C4   C8   111.97  3.000
 PFT  H4    C4   C8   111.82  3.000
 PFT  H41   C4   N1   111.64  3.000
 PFT  H4    C4   N1   111.85  3.000
 PFT  C8    C4   N1   102.32  3.000
 PFT  C10   C5   C9   118.74  3.000
 PFT  C10   C5   C2   121.31  3.000
 PFT  C9    C5   C2   119.89  3.000
 PFT  C11   C7   C8   120.74  3.000
 PFT  C11   C7   C3   128.53  3.000
 PFT  C8    C7   C3   110.73  3.000
 PFT  C12   C8   C7   120.83  3.000
 PFT  C12   C8   C4   128.39  3.000
 PFT  C7    C8   C4   110.77  3.000
 PFT  O14   C9   C13  122.42  3.000
 PFT  O14   C9   C5   117.07  3.000
 PFT  C13   C9   C5   120.50  3.000
 PFT  H10   C10  C15  118.94  3.000
 PFT  H10   C10  C5   119.47  3.000
 PFT  C15   C10  C5   121.59  3.000
 PFT  H11   C11  C16  120.44  3.000
 PFT  H11   C11  C7   120.86  3.000
 PFT  C16   C11  C7   118.70  3.000
 PFT  H12   C12  C17  120.41  3.000
 PFT  H12   C12  C8   120.93  3.000
 PFT  C17   C12  C8   118.66  3.000
 PFT  H13   C13  C18  119.59  3.000
 PFT  H13   C13  C9   120.57  3.000
 PFT  C18   C13  C9   119.84  3.000
 PFT  HO14  O14  C9   110.84  3.000
 PFT  H15   C15  C18  120.82  3.000
 PFT  H15   C15  C10  120.09  3.000
 PFT  C18   C15  C10  119.10  3.000
 PFT  H16   C16  C17  119.74  3.000
 PFT  H16   C16  C11  119.73  3.000
 PFT  C17   C16  C11  120.53  3.000
 PFT  H17   C17  C16  119.78  3.000
 PFT  H17   C17  C12  119.69  3.000
 PFT  C16   C17  C12  120.53  3.000
 PFT  O19   C18  C15  122.55  3.000
 PFT  O19   C18  C13  117.21  3.000
 PFT  C15   C18  C13  120.23  3.000
 PFT  HO19  O19  C18  110.42  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
 PFT  CONST_01  C18  C13  C9   C5      0.00   0.0  0
 PFT  CONST_02  C18  C15  C10  C5      0.00   0.0  0
 PFT  CONST_03  C17  C12  C8   C7      0.00   0.0  0
 PFT  CONST_04  C17  C16  C11  C7      0.00   0.0  0
 PFT  CONST_05  C16  C11  C7   C8      0.00   0.0  0
 PFT  CONST_06  C16  C17  C12  C8      0.00   0.0  0
 PFT  CONST_07  C15  C10  C5   C9      0.00   0.0  0
 PFT  CONST_08  C15  C18  C13  C9      0.00   0.0  0
 PFT  CONST_09  C13  C9   C5   C10     0.00   0.0  0
 PFT  CONST_10  C13  C18  C15  C10     0.00   0.0  0
 PFT  CONST_11  C12  C8   C7   C11     0.00   0.0  0
 PFT  CONST_12  C12  C17  C16  C11     0.00   0.0  0
 PFT  CONST_13  C13  C9   C5   C2    180.00   0.0  0
 PFT  CONST_14  C15  C10  C5   C2    180.00   0.0  0
 PFT  CONST_15  O19  C18  C13  C9    180.00   0.0  0
 PFT  CONST_16  O14  C9   C5   C10   180.00   0.0  0
 PFT  CONST_17  O19  C18  C15  C10   180.00   0.0  0
 PFT  CONST_18  C18  C13  C9   O14   180.00   0.0  0
 PFT  CONST_19  C5   C2   N1   C3    180.00   0.0  0
 PFT  CONST_20  C5   C2   N1   C4      0.00   0.0  0
 PFT  CONST_21  H11  C11  C7   C3      0.00   0.0  0
 PFT  CONST_22  H12  C12  C8   C4      0.00   0.0  0
 PFT  CONST_23  H13  C13  C9   C5    180.00   0.0  0
 PFT  CONST_24  H15  C15  C10  C5    180.00   0.0  0
 PFT  CONST_25  H16  C16  C11  C7    180.00   0.0  0
 PFT  CONST_26  H17  C17  C12  C8    180.00   0.0  0
 PFT  CONST_27  H10  C10  C5   C9    180.00   0.0  0
 PFT  CONST_28  O6   C2   N1   C3      0.00   0.0  0
 PFT  CONST_29  O6   C2   N1   C4    180.00   0.0  0
 PFT  Var_01    C8   C7   C3   N1      0.63  30.0  1
 PFT  Var_02    C7   C8   C4   N1     -0.38  30.0  1
 PFT  Var_03    C8   C4   N1   C3      0.83  30.0  1
 PFT  Var_04    C7   C3   N1   C4     -0.92  30.0  1
 PFT  Var_05    C9   C5   C2   N1   -101.88  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
 PFT  plan-1  C2   0.020
 PFT  plan-1  C5   0.020
 PFT  plan-1  C9   0.020
 PFT  plan-1  C10  0.020
 PFT  plan-1  C13  0.020
 PFT  plan-1  O14  0.020
 PFT  plan-1  C15  0.020
 PFT  plan-1  C18  0.020
 PFT  plan-1  O19  0.020
 PFT  plan-1  H10  0.020
 PFT  plan-1  H13  0.020
 PFT  plan-1  H15  0.020
 PFT  plan-2  C3   0.020
 PFT  plan-2  C4   0.020
 PFT  plan-2  C7   0.020
 PFT  plan-2  C8   0.020
 PFT  plan-2  C11  0.020
 PFT  plan-2  C12  0.020
 PFT  plan-2  C16  0.020
 PFT  plan-2  C17  0.020
 PFT  plan-2  H11  0.020
 PFT  plan-2  H12  0.020
 PFT  plan-2  H16  0.020
 PFT  plan-2  H17  0.020
 PFT  plan-3  N1   0.020
 PFT  plan-3  C2   0.020
 PFT  plan-3  C3   0.020
 PFT  plan-3  C4   0.020
 PFT  plan-3  C5   0.020
 PFT  plan-3  O6   0.020

