# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 20:23:55 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: (5-bromo-2,4-dihydroxyphenyl)(1,3-dihydro-2H-isoindol-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Oc1cc(O)c(cc1Br)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
 PV1  PV1  (5-bromo-2,4-dihydroxyphenyl)(1,3-dihydro-2H-isoindol-2-yl)methanone  ligand  32  20  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_PV1
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
 PV1  C6   C   CR16  0  -0.254   5.8848   1.0736   0.4262
 PV1  C5   C   CR16  0  -0.313   5.3344  -0.0730  -0.1338
 PV1  O1   O   O     0  -0.547   1.0405  -2.9620  -0.7214
 PV1  C4   C   CR56  0   0.048   3.9550  -0.1726  -0.2194
 PV1  C3   C   CR56  0   0.064   3.1417   0.8478   0.2408
 PV1  C2   C   CR16  0  -0.311   3.6825   1.9944   0.7994
 PV1  C1   C   CR16  0  -0.257   5.0651   2.0987   0.8908
 PV1  N1   N   NR5   0  -0.508   1.7623  -0.8617  -0.4809
 PV1  C7   C   CH2   0  -0.318   1.7019   0.5191   0.0031
 PV1  C8   C   CH2   0  -0.284   3.1338  -1.2976  -0.7614
 PV1  C9   C   C     0   0.606   0.7808  -1.7713  -0.4768
 PV1  C14  C   CR6   0  -0.265  -2.4952   0.1214  -0.0713
 PV1  C13  C   CR6   0   0.425  -3.2978  -0.8520   0.5401
 PV1  C12  C   CR16  0  -0.438  -2.7563  -2.1106   0.7629
 PV1  C11  C   CR6   0   0.376  -1.4488  -2.4108   0.4027
 PV1  C15  C   CR16  0  -0.225  -1.1849  -0.1601  -0.3984
 PV1  C10  C   CR6   0  -0.203  -0.6162  -1.4052  -0.1428
 PV1  H1   H   HCR6  0   0.259   6.9598   1.1698   0.5042
 PV1  H2   H   HCR6  0   0.256   5.9734  -0.8706  -0.4919
 PV1  H3   H   HOH1  0   0.477  -4.8764   0.2307   0.7195
 PV1  H4   H   HCR6  0   0.255   3.0469   2.7940   1.1592
 PV1  H5   H   HOH1  0   0.478  -0.1574  -3.7355   0.1352
 PV1  H6   H   HCR6  0   0.259   5.5082   2.9840   1.3271
 PV1  H7   H   HCH2  0   0.283   1.0896   0.5947   0.9039
 PV1  H8   H   HCH2  0   0.276   1.2843   1.1958  -0.7469
 PV1  H9   H   HCH2  0   0.269   3.2885  -1.4480  -1.8340
 PV1  H10  H   HCH2  0   0.271   3.3527  -2.2445  -0.2649
 PV1  H11  H   HCR6  0   0.286  -3.3760  -2.8815   1.2045
 PV1  H12  H   HCR6  0   0.291  -0.6084   0.6069  -0.8927
 PV1  O3   O   OH1   0  -0.602  -4.5638  -0.6627   0.9115
 PV1  O2   O   OH1   0  -0.628  -1.0245  -3.6557   0.6011
 PV1  BR1  BR  BR    0  -0.029  -3.2063   1.8278  -0.4565

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
 PV1  O2   C11  single    1.330  0.020  1.330
 PV1  C1   C2   aromatic  1.390  0.020  1.390
 PV1  C1   C6   aromatic  1.392  0.020  1.392
 PV1  C2   C3   aromatic  1.385  0.020  1.385
 PV1  C6   C5   aromatic  1.390  0.020  1.390
 PV1  C11  C12  aromatic  1.389  0.020  1.389
 PV1  C11  C10  aromatic  1.415  0.020  1.415
 PV1  C3   C7   single    1.496  0.020  1.496
 PV1  C3   C4   aromatic  1.384  0.020  1.384
 PV1  C12  C13  aromatic  1.388  0.020  1.388
 PV1  C7   N1   single    1.464  0.020  1.464
 PV1  O1   C9   double    1.243  0.020  1.243
 PV1  C5   C4   aromatic  1.386  0.020  1.386
 PV1  C4   C8   single    1.495  0.020  1.495
 PV1  C9   N1   single    1.338  0.020  1.338
 PV1  C9   C10  single    1.482  0.020  1.482
 PV1  N1   C8   single    1.466  0.020  1.466
 PV1  C10  C15  aromatic  1.392  0.020  1.392
 PV1  C13  O3   single    1.333  0.020  1.333
 PV1  C13  C14  aromatic  1.402  0.020  1.402
 PV1  C15  C14  aromatic  1.380  0.020  1.380
 PV1  C14  BR1  single    1.888  0.020  1.888
 PV1  C6   H1   single    0.930  0.020  1.080
 PV1  C5   H2   single    0.930  0.020  1.080
 PV1  O3   H3   single    0.850  0.020  0.980
 PV1  C2   H4   single    0.930  0.020  1.080
 PV1  O2   H5   single    0.850  0.020  0.980
 PV1  C1   H6   single    0.930  0.020  1.080
 PV1  C7   H7   single    0.970  0.020  1.090
 PV1  C7   H8   single    0.970  0.020  1.090
 PV1  C8   H9   single    0.970  0.020  1.090
 PV1  C8   H10  single    0.970  0.020  1.090
 PV1  C12  H11  single    0.930  0.020  1.080
 PV1  C15  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
 PV1  H1   C6   C1   119.69  3.000
 PV1  H1   C6   C5   119.72  3.000
 PV1  C1   C6   C5   120.58  3.000
 PV1  H2   C5   C4   120.93  3.000
 PV1  H2   C5   C6   120.48  3.000
 PV1  C4   C5   C6   118.59  3.000
 PV1  C8   C4   C3   110.66  3.000
 PV1  C8   C4   C5   128.57  3.000
 PV1  C3   C4   C5   120.77  3.000
 PV1  C7   C3   C2   128.44  3.000
 PV1  C7   C3   C4   110.54  3.000
 PV1  C2   C3   C4   121.00  3.000
 PV1  H4   C2   C1   120.45  3.000
 PV1  H4   C2   C3   121.07  3.000
 PV1  C1   C2   C3   118.49  3.000
 PV1  H6   C1   C2   119.70  3.000
 PV1  H6   C1   C6   119.73  3.000
 PV1  C2   C1   C6   120.57  3.000
 PV1  C9   N1   C8   118.98  3.000
 PV1  C8   N1   C7   112.47  3.000
 PV1  C9   N1   C7   127.56  3.000
 PV1  H8   C7   H7   108.00  3.000
 PV1  H8   C7   N1   111.88  3.000
 PV1  H7   C7   N1   111.17  3.000
 PV1  H8   C7   C3   109.92  3.000
 PV1  H7   C7   C3   113.17  3.000
 PV1  N1   C7   C3   102.71  3.000
 PV1  H10  C8   H9   107.36  3.000
 PV1  H10  C8   N1   111.01  3.000
 PV1  H9   C8   N1   111.14  3.000
 PV1  H10  C8   C4   112.21  3.000
 PV1  H9   C8   C4   112.42  3.000
 PV1  N1   C8   C4   102.75  3.000
 PV1  C10  C9   N1   121.60  3.000
 PV1  C10  C9   O1   118.55  3.000
 PV1  N1   C9   O1   119.82  3.000
 PV1  C15  C14  C13  120.36  3.000
 PV1  C15  C14  BR1  119.58  3.000
 PV1  C13  C14  BR1  120.05  3.000
 PV1  C12  C13  C14  118.44  3.000
 PV1  C14  C13  O3   124.52  3.000
 PV1  C12  C13  O3   117.03  3.000
 PV1  H11  C12  C11  119.36  3.000
 PV1  H11  C12  C13  119.19  3.000
 PV1  C11  C12  C13  121.43  3.000
 PV1  C10  C11  C12  120.02  3.000
 PV1  C10  C11  O2   122.35  3.000
 PV1  C12  C11  O2   117.64  3.000
 PV1  H12  C15  C10  120.09  3.000
 PV1  H12  C15  C14  118.09  3.000
 PV1  C10  C15  C14  121.79  3.000
 PV1  C15  C10  C11  117.77  3.000
 PV1  C15  C10  C9   124.36  3.000
 PV1  C11  C10  C9   117.76  3.000
 PV1  H3   O3   C13  112.54  3.000
 PV1  H5   O2   C11  106.57  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
 PV1  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 PV1  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 PV1  CONST_03  C2   C1   C6   C5      0.00   0.0  0
 PV1  CONST_04  C2   C3   C4   C5      0.00   0.0  0
 PV1  CONST_05  C1   C2   C3   C4      0.00   0.0  0
 PV1  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 PV1  CONST_07  C11  C12  C13  C14     0.00   0.0  0
 PV1  CONST_08  C11  C10  C15  C14     0.00   0.0  0
 PV1  CONST_09  C10  C11  C12  C13     0.00   0.0  0
 PV1  CONST_10  C10  C15  C14  C13     0.00   0.0  0
 PV1  CONST_11  C15  C10  C11  C12     0.00   0.0  0
 PV1  CONST_12  C15  C14  C13  C12     0.00   0.0  0
 PV1  CONST_13  C11  C12  C13  O3    180.00   0.0  0
 PV1  CONST_14  C15  C14  C13  O3    180.00   0.0  0
 PV1  CONST_15  C13  C12  C11  O2    180.00   0.0  0
 PV1  CONST_16  C15  C10  C11  O2    180.00   0.0  0
 PV1  CONST_17  C12  C11  C10  C9    180.00   0.0  0
 PV1  CONST_18  C14  C15  C10  C9    180.00   0.0  0
 PV1  CONST_19  C12  C13  C14  BR1   180.00   0.0  0
 PV1  CONST_20  C10  C15  C14  BR1   180.00   0.0  0
 PV1  CONST_21  C10  C9   N1   C7      0.00   0.0  0
 PV1  CONST_22  C10  C9   N1   C8    180.00   0.0  0
 PV1  CONST_23  H4   C2   C1   C6    180.00   0.0  0
 PV1  CONST_24  H6   C1   C6   C5    180.00   0.0  0
 PV1  CONST_25  H1   C6   C5   C4    180.00   0.0  0
 PV1  CONST_26  H2   C5   C4   C3    180.00   0.0  0
 PV1  CONST_27  H11  C12  C13  C14   180.00   0.0  0
 PV1  CONST_28  H12  C15  C14  C13   180.00   0.0  0
 PV1  CONST_29  C7   N1   C9   O1    180.00   0.0  0
 PV1  CONST_30  C8   N1   C9   O1      0.00   0.0  0
 PV1  Var_01    N1   C8   C4   C5    175.67  30.0  1
 PV1  Var_02    N1   C7   C3   C4      6.97  30.0  1
 PV1  Var_03    C7   N1   C8   C4      8.53  30.0  1
 PV1  Var_04    C8   N1   C7   C3     -9.64  30.0  1
 PV1  Var_05    C11  C10  C9   N1   -153.05  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
 PV1  plan-1  C9   0.020
 PV1  plan-1  C14  0.020
 PV1  plan-1  C13  0.020
 PV1  plan-1  C12  0.020
 PV1  plan-1  C11  0.020
 PV1  plan-1  C15  0.020
 PV1  plan-1  C10  0.020
 PV1  plan-1  H11  0.020
 PV1  plan-1  H12  0.020
 PV1  plan-1  O3   0.020
 PV1  plan-1  O2   0.020
 PV1  plan-1  BR1  0.020
 PV1  plan-2  C6   0.020
 PV1  plan-2  C5   0.020
 PV1  plan-2  C4   0.020
 PV1  plan-2  C3   0.020
 PV1  plan-2  C2   0.020
 PV1  plan-2  C1   0.020
 PV1  plan-2  C7   0.020
 PV1  plan-2  C8   0.020
 PV1  plan-2  H1   0.020
 PV1  plan-2  H2   0.020
 PV1  plan-2  H4   0.020
 PV1  plan-2  H6   0.020
 PV1  plan-3  O1   0.020
 PV1  plan-3  N1   0.020
 PV1  plan-3  C7   0.020
 PV1  plan-3  C8   0.020
 PV1  plan-3  C9   0.020
 PV1  plan-3  C10  0.020

