# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 07:43:15 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 4-{[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]oxy}-3,5-dimethylphenyl acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](COc1c(C)cc(OC(C)=O)cc1C)N2C(=O)c3ccccc3C2=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
 SS7  SS7  '4-{[(2S)-2-(1,3-dioxo-1,3-dihydro-2H-isoindol-2-yl)propyl]oxy}-3,5-dimethylphenyl acetate'  ligand  48  27  .  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_SS7
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
 SS7  O11  O  O     0  -0.402  -3.1050  -0.6628   2.3805
 SS7  C8   C  CR5   0   0.572  -3.1590  -0.3760   1.2107
 SS7  C5   C  CR56  0  -0.026  -3.8214   0.7892   0.5857
 SS7  C4   C  CR16  0  -0.297  -4.5393   1.8207   1.1532
 SS7  C3   C  CR16  0  -0.242  -5.0388   2.7945   0.2909
 SS7  C2   C  CR16  0  -0.240  -4.8194   2.7216  -1.0822
 SS7  C1   C  CR16  0  -0.298  -4.0927   1.6722  -1.6417
 SS7  C6   C  CR56  0  -0.018  -3.6039   0.7159  -0.7776
 SS7  C7   C  CR5   0   0.588  -2.8017  -0.5007  -1.0563
 SS7  O10  O  O     0  -0.397  -2.4290  -0.8905  -2.1321
 SS7  N9   N  NR5   0  -0.609  -2.5803  -1.1052   0.1770
 SS7  C12  C  CH1   0  -0.144  -1.7572  -2.2814   0.4501
 SS7  C14  C  CH3   0  -0.672  -1.9290  -3.4010  -0.5665
 SS7  C13  C  CH2   0  -0.160  -0.3100  -1.8723   0.6642
 SS7  O15  O  O2    0  -0.484   0.1973  -1.3235  -0.5390
 SS7  C16  C  CR6   0   0.290   1.4167  -0.7190  -0.4345
 SS7  C17  C  CR6   0   0.026   2.5730  -1.4733  -0.6391
 SS7  C22  C  CH3   0  -0.724   2.4935  -2.9391  -0.9500
 SS7  C18  C  CR16  0  -0.385   3.8042  -0.8298  -0.5625
 SS7  C21  C  CR6   0   0.037   1.4664   0.6507  -0.1689
 SS7  C23  C  CH3   0  -0.730   0.2082   1.4454   0.0233
 SS7  C20  C  CR16  0  -0.389   2.7113   1.2672  -0.1005
 SS7  C19  C  CR6   0   0.394   3.8610   0.5242  -0.2916
 SS7  O24  O  O2    0  -0.496   5.0900   1.1595  -0.2713
 SS7  C25  C  C     0   0.542   5.7308   1.2574   0.9106
 SS7  O27  O  O     0  -0.423   5.2797   0.8160   1.9310
 SS7  C26  C  CH3   0  -0.774   7.0360   1.9694   0.7517
 SS7  H1   H  HCR6  0   0.276  -4.7094   1.8779   2.2201
 SS7  H2   H  HCR6  0   0.279  -5.6053   3.6232   0.6936
 SS7  H3   H  HCR6  0   0.279  -5.2201   3.4950  -1.7235
 SS7  H4   H  HCR6  0   0.275  -3.9211   1.6172  -2.7085
 SS7  H5   H  HCH1  0   0.282  -2.1033  -2.6601   1.4140
 SS7  H6   H  HCH3  0   0.244  -1.4322  -4.2907  -0.1798
 SS7  H7   H  HCH3  0   0.245  -2.9822  -3.6441  -0.7019
 SS7  H8   H  HCH3  0   0.248  -1.4986  -3.1681  -1.5352
 SS7  H9   H  HCH2  0   0.238  -0.2466  -1.1413   1.4787
 SS7  H10  H  HCH2  0   0.240   0.2632  -2.7540   0.9721
 SS7  H11  H  HCH3  0   0.251   1.7832  -3.1421  -1.7513
 SS7  H12  H  HCH3  0   0.252   3.4653  -3.3252  -1.2524
 SS7  H13  H  HCH3  0   0.249   2.1689  -3.5171  -0.0824
 SS7  H14  H  HCR6  0   0.266   4.7177  -1.3892  -0.7247
 SS7  H15  H  HCH3  0   0.244  -0.3193   1.1494   0.9321
 SS7  H16  H  HCH3  0   0.258   0.4315   2.5071   0.1123
 SS7  H17  H  HCH3  0   0.248  -0.4823   1.3183  -0.8106
 SS7  H18  H  HCR6  0   0.267   2.7784   2.3312   0.0927
 SS7  H19  H  HCH3  0   0.277   6.8807   2.9580   0.3190
 SS7  H20  H  HCH3  0   0.266   7.5303   2.0733   1.7131
 SS7  H21  H  HCH3  0   0.279   7.6868   1.4169   0.0731

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
 SS7  C4   C3   aromatic  1.393  0.020  1.393
 SS7  C4   C5   aromatic  1.379  0.020  1.379
 SS7  C3   C2   aromatic  1.392  0.020  1.392
 SS7  O11  C8   double    1.206  0.020  1.206
 SS7  C5   C8   single    1.479  0.020  1.479
 SS7  C5   C6   aromatic  1.382  0.020  1.382
 SS7  C2   C1   aromatic  1.394  0.020  1.394
 SS7  C8   N9   single    1.391  0.020  1.391
 SS7  C6   C1   aromatic  1.379  0.020  1.379
 SS7  C6   C7   single    1.484  0.020  1.484
 SS7  C23  C21  single    1.501  0.020  1.501
 SS7  N9   C12  single    1.461  0.020  1.461
 SS7  N9   C7   single    1.391  0.020  1.391
 SS7  C12  C13  single    1.519  0.020  1.519
 SS7  C12  C14  single    1.522  0.020  1.522
 SS7  C7   O10  double    1.203  0.020  1.203
 SS7  O15  C13  single    1.416  0.020  1.416
 SS7  O15  C16  single    1.365  0.020  1.365
 SS7  C21  C16  aromatic  1.396  0.020  1.396
 SS7  C21  C20  aromatic  1.391  0.020  1.391
 SS7  C16  C17  aromatic  1.396  0.020  1.396
 SS7  C20  C19  aromatic  1.382  0.020  1.382
 SS7  C17  C22  single    1.501  0.020  1.501
 SS7  C17  C18  aromatic  1.391  0.020  1.391
 SS7  C26  C25  single    1.495  0.020  1.495
 SS7  C19  C18  aromatic  1.382  0.020  1.382
 SS7  C19  O24  single    1.384  0.020  1.384
 SS7  C25  O24  single    1.348  0.020  1.348
 SS7  C25  O27  double    1.200  0.020  1.200
 SS7  C4   H1   single    0.930  0.020  1.080
 SS7  C3   H2   single    0.930  0.020  1.080
 SS7  C2   H3   single    0.930  0.020  1.080
 SS7  C1   H4   single    0.930  0.020  1.080
 SS7  C12  H5   single    0.970  0.020  1.090
 SS7  C14  H6   single    0.970  0.020  1.090
 SS7  C14  H7   single    0.970  0.020  1.090
 SS7  C14  H8   single    0.970  0.020  1.090
 SS7  C13  H9   single    0.970  0.020  1.090
 SS7  C13  H10  single    0.970  0.020  1.090
 SS7  C22  H11  single    0.970  0.020  1.090
 SS7  C22  H12  single    0.970  0.020  1.090
 SS7  C22  H13  single    0.970  0.020  1.090
 SS7  C18  H14  single    0.930  0.020  1.080
 SS7  C23  H15  single    0.970  0.020  1.090
 SS7  C23  H16  single    0.970  0.020  1.090
 SS7  C23  H17  single    0.970  0.020  1.090
 SS7  C20  H18  single    0.930  0.020  1.080
 SS7  C26  H19  single    0.970  0.020  1.090
 SS7  C26  H20  single    0.970  0.020  1.090
 SS7  C26  H21  single    0.970  0.020  1.090

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
 SS7  N9   C8   C5   106.57  3.000
 SS7  N9   C8   O11  125.29  3.000
 SS7  C5   C8   O11  128.14  3.000
 SS7  C6   C5   C4   121.83  3.000
 SS7  C6   C5   C8   107.73  3.000
 SS7  C4   C5   C8   130.44  3.000
 SS7  H1   C4   C3   121.13  3.000
 SS7  H1   C4   C5   121.82  3.000
 SS7  C3   C4   C5   117.05  3.000
 SS7  H2   C3   C2   119.32  3.000
 SS7  H2   C3   C4   119.53  3.000
 SS7  C2   C3   C4   121.15  3.000
 SS7  H3   C2   C1   119.57  3.000
 SS7  H3   C2   C3   119.26  3.000
 SS7  C1   C2   C3   121.16  3.000
 SS7  H4   C1   C6   121.78  3.000
 SS7  H4   C1   C2   121.12  3.000
 SS7  C6   C1   C2   117.10  3.000
 SS7  C7   C6   C1   130.00  3.000
 SS7  C7   C6   C5   108.29  3.000
 SS7  C1   C6   C5   121.71  3.000
 SS7  N9   C7   O10  127.04  3.000
 SS7  O10  C7   C6   126.95  3.000
 SS7  N9   C7   C6   106.01  3.000
 SS7  C12  N9   C7   127.23  3.000
 SS7  C7   N9   C8   111.40  3.000
 SS7  C12  N9   C8   121.15  3.000
 SS7  H5   C12  C13  105.72  3.000
 SS7  H5   C12  C14  107.38  3.000
 SS7  C13  C12  C14  113.56  3.000
 SS7  H5   C12  N9   105.41  3.000
 SS7  C14  C12  N9   113.81  3.000
 SS7  C13  C12  N9   110.25  3.000
 SS7  H8   C14  H7   108.68  3.000
 SS7  H8   C14  H6   108.12  3.000
 SS7  H7   C14  H6   107.61  3.000
 SS7  H8   C14  C12  113.18  3.000
 SS7  H7   C14  C12  110.87  3.000
 SS7  H6   C14  C12  108.18  3.000
 SS7  H10  C13  H9   107.31  3.000
 SS7  H10  C13  O15  111.29  3.000
 SS7  H9   C13  O15  110.61  3.000
 SS7  H10  C13  C12  108.74  3.000
 SS7  H9   C13  C12  109.83  3.000
 SS7  O15  C13  C12  109.02  3.000
 SS7  C16  O15  C13  115.24  3.000
 SS7  C21  C16  C17  121.91  3.000
 SS7  C17  C16  O15  119.32  3.000
 SS7  C21  C16  O15  118.74  3.000
 SS7  C18  C17  C22  120.67  3.000
 SS7  C18  C17  C16  118.37  3.000
 SS7  C22  C17  C16  120.95  3.000
 SS7  H13  C22  H12  107.36  3.000
 SS7  H13  C22  H11  106.97  3.000
 SS7  H12  C22  H11  108.15  3.000
 SS7  H13  C22  C17  111.61  3.000
 SS7  H12  C22  C17  110.90  3.000
 SS7  H11  C22  C17  111.65  3.000
 SS7  H14  C18  C19  120.04  3.000
 SS7  H14  C18  C17  119.94  3.000
 SS7  C19  C18  C17  120.02  3.000
 SS7  C20  C21  C23  120.63  3.000
 SS7  C20  C21  C16  118.43  3.000
 SS7  C23  C21  C16  120.94  3.000
 SS7  H17  C23  H16  107.83  3.000
 SS7  H17  C23  H15  107.41  3.000
 SS7  H16  C23  H15  107.19  3.000
 SS7  H17  C23  C21  111.80  3.000
 SS7  H16  C23  C21  110.79  3.000
 SS7  H15  C23  C21  111.60  3.000
 SS7  H18  C20  C19  120.07  3.000
 SS7  H18  C20  C21  119.97  3.000
 SS7  C19  C20  C21  119.96  3.000
 SS7  O24  C19  C20  119.34  3.000
 SS7  O24  C19  C18  119.29  3.000
 SS7  C20  C19  C18  121.30  3.000
 SS7  C25  O24  C19  117.93  3.000
 SS7  C26  C25  O27  126.42  3.000
 SS7  O27  C25  O24  122.70  3.000
 SS7  C26  C25  O24  110.88  3.000
 SS7  H21  C26  H20  109.13  3.000
 SS7  H21  C26  H19  107.30  3.000
 SS7  H20  C26  H19  109.24  3.000
 SS7  H21  C26  C25  110.22  3.000
 SS7  H20  C26  C25  110.41  3.000
 SS7  H19  C26  C25  110.46  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
 SS7  CONST_01  C2   C3   C4   C5      0.00   0.0  0
 SS7  CONST_02  C2   C1   C6   C5      0.00   0.0  0
 SS7  CONST_03  C1   C2   C3   C4      0.00   0.0  0
 SS7  CONST_04  C1   C6   C5   C4      0.00   0.0  0
 SS7  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 SS7  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 SS7  CONST_07  C19  C20  C21  C16     0.00   0.0  0
 SS7  CONST_08  C19  C18  C17  C16     0.00   0.0  0
 SS7  CONST_09  C20  C21  C16  C17     0.00   0.0  0
 SS7  CONST_10  C20  C19  C18  C17     0.00   0.0  0
 SS7  CONST_11  C21  C16  C17  C18     0.00   0.0  0
 SS7  CONST_12  C21  C20  C19  C18     0.00   0.0  0
 SS7  CONST_13  C7   N9   C8   C5      0.00   0.0  0
 SS7  CONST_14  C20  C21  C16  O15   180.00   0.0  0
 SS7  CONST_15  C18  C17  C16  O15   180.00   0.0  0
 SS7  CONST_16  C23  C21  C16  C17   180.00   0.0  0
 SS7  CONST_17  O24  C19  C18  C17   180.00   0.0  0
 SS7  CONST_18  C21  C16  C17  C22   180.00   0.0  0
 SS7  CONST_19  C19  C18  C17  C22   180.00   0.0  0
 SS7  CONST_20  O24  C19  C20  C21   180.00   0.0  0
 SS7  CONST_21  C19  C20  C21  C23   180.00   0.0  0
 SS7  CONST_22  C7   N9   C8   O11   180.00   0.0  0
 SS7  CONST_23  C12  N9   C8   C5    180.00   0.0  0
 SS7  CONST_24  H1   C4   C5   C8      0.00   0.0  0
 SS7  CONST_25  H2   C3   C4   C5    180.00   0.0  0
 SS7  CONST_26  H4   C1   C6   C5    180.00   0.0  0
 SS7  CONST_27  H3   C2   C3   C4    180.00   0.0  0
 SS7  CONST_28  H18  C20  C21  C16   180.00   0.0  0
 SS7  CONST_29  H14  C18  C17  C16   180.00   0.0  0
 SS7  CONST_30  C12  N9   C8   O11     0.00   0.0  0
 SS7  Var_01    C21  C16  O15  C13   -91.90  30.0  2
 SS7  Var_02    H15  C23  C21  C16    66.80  30.0  2
 SS7  Var_03    H11  C22  C17  C16    49.16  30.0  2
 SS7  Var_04    C26  C25  O24  C19  -179.95  30.0  1
 SS7  Var_05    H9   C13  O15  C16    49.13  30.0  3
 SS7  Var_06    H19  C26  C25  O24    57.18  30.0  3

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
 SS7  chir_01  C12  N9  C13  C14  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
 SS7  plan-1  O15  0.020
 SS7  plan-1  C16  0.020
 SS7  plan-1  C17  0.020
 SS7  plan-1  C22  0.020
 SS7  plan-1  C18  0.020
 SS7  plan-1  C21  0.020
 SS7  plan-1  C23  0.020
 SS7  plan-1  C20  0.020
 SS7  plan-1  C19  0.020
 SS7  plan-1  O24  0.020
 SS7  plan-1  H14  0.020
 SS7  plan-1  H18  0.020
 SS7  plan-2  O11  0.020
 SS7  plan-2  C8   0.020
 SS7  plan-2  C5   0.020
 SS7  plan-2  C4   0.020
 SS7  plan-2  C3   0.020
 SS7  plan-2  C2   0.020
 SS7  plan-2  C1   0.020
 SS7  plan-2  C6   0.020
 SS7  plan-2  C7   0.020
 SS7  plan-2  O10  0.020
 SS7  plan-2  N9   0.020
 SS7  plan-2  C12  0.020
 SS7  plan-2  H1   0.020
 SS7  plan-2  H2   0.020
 SS7  plan-2  H3   0.020
 SS7  plan-2  H4   0.020
 SS7  plan-3  O24  0.020
 SS7  plan-3  C25  0.020
 SS7  plan-3  O27  0.020
 SS7  plan-3  C26  0.020

