# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 05:13:01 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 3-[(4-chlorophenyl)methoxy]-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)benzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc(OCc2ccc(Cl)cc2)c1N3Cc4ccccc4C3=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
 7HM  7HM  '3-[(4-chlorophenyl)methoxy]-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)benzoic acid'  ligand  44  28  .  2022-07-23  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_7HM
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
 7HM  C13  C   CH2   0  -0.272   1.5438   2.3881   0.0157
 7HM  C18  C   CR16  0  -0.196   4.5688   0.3669   1.0857
 7HM  C17  C   CR6   0  -0.049   4.8903  -0.2625  -0.1056
 7HM  C16  C   CR16  0  -0.197   4.1545  -0.0374  -1.2601
 7HM  C15  C   CR16  0  -0.288   3.0791   0.8347  -1.2108
 7HM  C19  C   CR16  0  -0.302   3.4857   1.2345   1.1161
 7HM  C20  C   CH2   0  -0.284  -1.0938  -0.8541  -1.2274
 7HM  C21  C   CR56  0   0.084  -1.0862  -2.2786  -0.7725
 7HM  C22  C   CR56  0  -0.064  -1.5958  -2.3536   0.5132
 7HM  C23  C   CR5   0   0.534  -1.9579  -0.9969   0.9620
 7HM  C27  C   CR16  0  -0.259  -1.3057  -4.7092   0.5258
 7HM  CL1  CL  CL    0  -0.126   6.2392  -1.3491  -0.1570
 7HM  C2   C   CR16  0  -0.304  -3.4456   3.0616  -0.0240
 7HM  C3   C   CR6   0  -0.057  -3.2061   1.6893  -0.0687
 7HM  C4   C   CR6   0   0.244  -1.8974   1.2098  -0.0556
 7HM  C5   C   CR6   0   0.390  -0.8242   2.1093   0.0104
 7HM  C6   C   CR16  0  -0.385  -1.0714   3.4787   0.0209
 7HM  C7   C   CR16  0  -0.228  -2.3786   3.9415   0.0046
 7HM  O9   O   OH1   0  -0.586  -5.4338   1.1907   0.4197
 7HM  O10  O   O     0  -0.425  -4.3119  -0.2974  -0.8042
 7HM  N11  N   NR5   0  -0.607  -1.6127  -0.1648  -0.0594
 7HM  O12  O   O2    0  -0.453   0.3933   1.5519   0.0657
 7HM  C14  C   CR6   0   0.108   2.7340   1.4795  -0.0263
 7HM  C25  C   CR16  0  -0.318  -0.6726  -3.4224  -1.4333
 7HM  C26  C   CR16  0  -0.240  -0.7890  -4.6376  -0.7686
 7HM  C28  C   CR16  0  -0.298  -1.7168  -3.5598   1.1846
 7HM  H34  H   HCH2  0   0.251   1.5130   3.0225  -0.8757
 7HM  H33  H   HCH2  0   0.252   1.5858   3.0387   0.8942
 7HM  H37  H   HCR6  0   0.282   5.1498   0.1856   1.9796
 7HM  H36  H   HCR6  0   0.283   4.4165  -0.5322  -2.1854
 7HM  H35  H   HCR6  0   0.265   2.5091   1.0169  -2.1138
 7HM  H38  H   HCR6  0   0.268   3.2315   1.7259   2.0472
 7HM  H39  H   HCH2  0   0.275  -0.0969  -0.4989  -1.4951
 7HM  H40  H   HCH2  0   0.277  -1.7511  -0.7056  -2.0880
 7HM  H43  H   HCR6  0   0.265  -1.3875  -5.6705   1.0154
 7HM  H29  H   HCR6  0   0.271  -4.4558   3.4450  -0.0362
 7HM  H30  H   HCR6  0   0.296  -0.2617   4.1940   0.0594
 7HM  H31  H   HCR6  0   0.273  -2.5602   5.0076   0.0193
 7HM  H32  H   HOH1  0   0.489  -6.1729   0.5811   0.2715
 7HM  H41  H   HCR6  0   0.262  -0.2710  -3.3793  -2.4378
 7HM  H42  H   HCR6  0   0.267  -0.4760  -5.5474  -1.2640
 7HM  H44  H   HCR6  0   0.261  -2.1209  -3.6041   2.1878
 7HM  C8   C   C     0   0.505  -4.3491   0.7421  -0.1949
 7HM  O24  O   O     0  -0.467  -2.4649  -0.6595   2.0157

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
 7HM  C26  C27  aromatic  1.396  0.020  1.396
 7HM  C26  C25  aromatic  1.390  0.020  1.390
 7HM  C27  C28  aromatic  1.387  0.020  1.387
 7HM  C25  C21  aromatic  1.384  0.020  1.384
 7HM  C28  C22  aromatic  1.386  0.020  1.386
 7HM  CL1  C17  single    1.733  0.020  1.733
 7HM  C21  C22  aromatic  1.385  0.020  1.385
 7HM  C21  C20  single    1.495  0.020  1.495
 7HM  C22  C23  single    1.474  0.020  1.474
 7HM  C20  N11  single    1.452  0.020  1.452
 7HM  C16  C17  aromatic  1.387  0.020  1.387
 7HM  C16  C15  aromatic  1.385  0.020  1.385
 7HM  C17  C18  aromatic  1.385  0.020  1.385
 7HM  O10  C8   double    1.205  0.020  1.205
 7HM  C23  N11  single    1.362  0.020  1.362
 7HM  C23  O24  double    1.217  0.020  1.217
 7HM  N11  C4   single    1.404  0.020  1.404
 7HM  C15  C14  aromatic  1.392  0.020  1.392
 7HM  C18  C19  aromatic  1.388  0.020  1.388
 7HM  C8   O9   single    1.325  0.020  1.325
 7HM  C8   C3   single    1.490  0.020  1.490
 7HM  C4   C3   aromatic  1.394  0.020  1.394
 7HM  C4   C5   aromatic  1.402  0.020  1.402
 7HM  C14  C19  aromatic  1.389  0.020  1.389
 7HM  C14  C13  single    1.498  0.020  1.498
 7HM  C3   C2   aromatic  1.394  0.020  1.394
 7HM  O12  C5   single    1.340  0.020  1.340
 7HM  O12  C13  single    1.423  0.020  1.423
 7HM  C5   C6   aromatic  1.392  0.020  1.392
 7HM  C2   C7   aromatic  1.383  0.020  1.383
 7HM  C6   C7   aromatic  1.387  0.020  1.387
 7HM  C13  H34  single    0.970  0.020  1.090
 7HM  C13  H33  single    0.970  0.020  1.090
 7HM  C18  H37  single    0.930  0.020  1.080
 7HM  C16  H36  single    0.930  0.020  1.080
 7HM  C15  H35  single    0.930  0.020  1.080
 7HM  C19  H38  single    0.930  0.020  1.080
 7HM  C20  H39  single    0.970  0.020  1.090
 7HM  C20  H40  single    0.970  0.020  1.090
 7HM  C27  H43  single    0.930  0.020  1.080
 7HM  C2   H29  single    0.930  0.020  1.080
 7HM  C6   H30  single    0.930  0.020  1.080
 7HM  C7   H31  single    0.930  0.020  1.080
 7HM  O9   H32  single    0.850  0.020  0.980
 7HM  C25  H41  single    0.930  0.020  1.080
 7HM  C26  H42  single    0.930  0.020  1.080
 7HM  C28  H44  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
 7HM  H33  C13  H34  108.08  3.000
 7HM  H33  C13  C14  110.65  3.000
 7HM  H34  C13  C14  110.55  3.000
 7HM  H33  C13  O12  110.62  3.000
 7HM  H34  C13  O12  110.27  3.000
 7HM  C14  C13  O12  106.67  3.000
 7HM  H37  C18  C19  120.39  3.000
 7HM  H37  C18  C17  120.66  3.000
 7HM  C19  C18  C17  118.94  3.000
 7HM  CL1  C17  C16  119.33  3.000
 7HM  C16  C17  C18  121.25  3.000
 7HM  CL1  C17  C18  119.41  3.000
 7HM  H36  C16  C15  120.43  3.000
 7HM  H36  C16  C17  120.61  3.000
 7HM  C15  C16  C17  118.96  3.000
 7HM  H35  C15  C14  120.06  3.000
 7HM  H35  C15  C16  118.99  3.000
 7HM  C14  C15  C16  120.95  3.000
 7HM  H38  C19  C14  119.99  3.000
 7HM  H38  C19  C18  119.05  3.000
 7HM  C14  C19  C18  120.96  3.000
 7HM  H40  C20  H39  108.17  3.000
 7HM  H40  C20  N11  110.72  3.000
 7HM  H39  C20  N11  111.66  3.000
 7HM  H40  C20  C21  111.84  3.000
 7HM  H39  C20  C21  112.33  3.000
 7HM  N11  C20  C21  102.08  3.000
 7HM  C25  C21  C22  120.55  3.000
 7HM  C22  C21  C20  109.40  3.000
 7HM  C25  C21  C20  130.05  3.000
 7HM  C28  C22  C23  129.21  3.000
 7HM  C23  C22  C21  108.85  3.000
 7HM  C28  C22  C21  121.94  3.000
 7HM  O24  C23  N11  125.84  3.000
 7HM  O24  C23  C22  128.39  3.000
 7HM  N11  C23  C22  105.76  3.000
 7HM  H43  C27  C28  119.94  3.000
 7HM  H43  C27  C26  119.55  3.000
 7HM  C28  C27  C26  120.51  3.000
 7HM  H29  C2   C7   119.71  3.000
 7HM  H29  C2   C3   120.64  3.000
 7HM  C7   C2   C3   119.64  3.000
 7HM  C8   C3   C4   120.16  3.000
 7HM  C4   C3   C2   119.98  3.000
 7HM  C8   C3   C2   119.80  3.000
 7HM  N11  C4   C5   118.24  3.000
 7HM  C5   C4   C3   119.90  3.000
 7HM  N11  C4   C3   121.82  3.000
 7HM  O12  C5   C6   124.77  3.000
 7HM  C6   C5   C4   119.72  3.000
 7HM  O12  C5   C4   115.51  3.000
 7HM  H30  C6   C7   119.05  3.000
 7HM  H30  C6   C5   121.22  3.000
 7HM  C7   C6   C5   119.72  3.000
 7HM  H31  C7   C6   119.15  3.000
 7HM  H31  C7   C2   119.85  3.000
 7HM  C6   C7   C2   121.00  3.000
 7HM  H32  O9   C8   109.90  3.000
 7HM  C4   N11  C23  123.01  3.000
 7HM  C4   N11  C20  122.65  3.000
 7HM  C23  N11  C20  113.81  3.000
 7HM  C5   O12  C13  119.25  3.000
 7HM  C19  C14  C15  118.94  3.000
 7HM  C19  C14  C13  120.92  3.000
 7HM  C15  C14  C13  120.12  3.000
 7HM  H41  C25  C26  120.63  3.000
 7HM  H41  C25  C21  121.39  3.000
 7HM  C26  C25  C21  117.97  3.000
 7HM  H42  C26  C25  119.46  3.000
 7HM  H42  C26  C27  119.25  3.000
 7HM  C25  C26  C27  121.29  3.000
 7HM  H44  C28  C27  121.12  3.000
 7HM  H44  C28  C22  121.15  3.000
 7HM  C27  C28  C22  117.73  3.000
 7HM  O10  C8   O9   123.48  3.000
 7HM  O9   C8   C3   111.93  3.000
 7HM  O10  C8   C3   124.57  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
 7HM  CONST_01  C15  C16  C17  C18     0.00   0.0  0
 7HM  CONST_02  C15  C14  C19  C18     0.00   0.0  0
 7HM  CONST_03  C14  C15  C16  C17     0.00   0.0  0
 7HM  CONST_04  C14  C19  C18  C17     0.00   0.0  0
 7HM  CONST_05  C19  C18  C17  C16     0.00   0.0  0
 7HM  CONST_06  C19  C14  C15  C16     0.00   0.0  0
 7HM  CONST_07  C27  C26  C25  C21     0.00   0.0  0
 7HM  CONST_08  C27  C28  C22  C21     0.00   0.0  0
 7HM  CONST_09  C26  C27  C28  C22     0.00   0.0  0
 7HM  CONST_10  C26  C25  C21  C22     0.00   0.0  0
 7HM  CONST_11  C5   C4   C3   C2      0.00   0.0  0
 7HM  CONST_12  C5   C6   C7   C2      0.00   0.0  0
 7HM  CONST_13  C6   C5   C4   C3      0.00   0.0  0
 7HM  CONST_14  C6   C7   C2   C3      0.00   0.0  0
 7HM  CONST_15  C7   C2   C3   C4      0.00   0.0  0
 7HM  CONST_16  C7   C6   C5   C4      0.00   0.0  0
 7HM  CONST_17  C28  C27  C26  C25     0.00   0.0  0
 7HM  CONST_18  C28  C22  C21  C25     0.00   0.0  0
 7HM  CONST_19  N11  C4   C3   C2    180.00   0.0  0
 7HM  CONST_20  N11  C4   C5   C6    180.00   0.0  0
 7HM  CONST_21  C22  C23  N11  C20     0.00   0.0  0
 7HM  CONST_22  C4   N11  C23  C22   180.00   0.0  0
 7HM  CONST_23  C16  C15  C14  C13   180.00   0.0  0
 7HM  CONST_24  C18  C19  C14  C13   180.00   0.0  0
 7HM  CONST_25  CL1  C17  C16  C15   180.00   0.0  0
 7HM  CONST_26  CL1  C17  C18  C19   180.00   0.0  0
 7HM  CONST_27  O12  C5   C4   C3    180.00   0.0  0
 7HM  CONST_28  C8   C3   C4   C5    180.00   0.0  0
 7HM  CONST_29  C8   C3   C2   C7    180.00   0.0  0
 7HM  CONST_30  O12  C5   C6   C7    180.00   0.0  0
 7HM  CONST_31  N11  C4   C3   C8      0.00   0.0  0
 7HM  CONST_32  O12  C5   C4   N11     0.00   0.0  0
 7HM  CONST_33  O24  C23  N11  C20   180.00   0.0  0
 7HM  CONST_34  O24  C23  N11  C4      0.00   0.0  0
 7HM  CONST_35  H36  C16  C17  C18   180.00   0.0  0
 7HM  CONST_36  H35  C15  C16  C17   180.00   0.0  0
 7HM  CONST_37  H38  C19  C18  C17   180.00   0.0  0
 7HM  CONST_38  H37  C18  C17  C16   180.00   0.0  0
 7HM  CONST_39  H41  C25  C21  C20     0.00   0.0  0
 7HM  CONST_40  H42  C26  C25  C21   180.00   0.0  0
 7HM  CONST_41  H44  C28  C22  C21   180.00   0.0  0
 7HM  CONST_42  H43  C27  C28  C22   180.00   0.0  0
 7HM  CONST_43  H30  C6   C7   C2    180.00   0.0  0
 7HM  CONST_44  H31  C7   C2   C3    180.00   0.0  0
 7HM  CONST_45  H29  C2   C3   C4    180.00   0.0  0
 7HM  CONST_46  H32  O9   C8   C3    180.00   0.0  0
 7HM  Var_01    C3   C4   N11  C20   106.80  30.0  2
 7HM  Var_02    H39  C20  C21  C22   121.43  30.0  1
 7HM  Var_03    C4   C5   O12  C13   174.50  30.0  2
 7HM  Var_04    O12  C13  C14  C15    77.05  30.0  2
 7HM  Var_05    O10  C8   C3   C2    145.45  30.0  3
 7HM  Var_06    C14  C13  O12  C5   -175.08  30.0  3

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
 7HM  plan-1  C13  0.020
 7HM  plan-1  C18  0.020
 7HM  plan-1  C17  0.020
 7HM  plan-1  C16  0.020
 7HM  plan-1  C15  0.020
 7HM  plan-1  C19  0.020
 7HM  plan-1  CL1  0.020
 7HM  plan-1  C14  0.020
 7HM  plan-1  H37  0.020
 7HM  plan-1  H36  0.020
 7HM  plan-1  H35  0.020
 7HM  plan-1  H38  0.020
 7HM  plan-2  C2   0.020
 7HM  plan-2  C3   0.020
 7HM  plan-2  C4   0.020
 7HM  plan-2  C5   0.020
 7HM  plan-2  C6   0.020
 7HM  plan-2  C7   0.020
 7HM  plan-2  N11  0.020
 7HM  plan-2  O12  0.020
 7HM  plan-2  H29  0.020
 7HM  plan-2  H30  0.020
 7HM  plan-2  H31  0.020
 7HM  plan-2  C8   0.020
 7HM  plan-3  C20  0.020
 7HM  plan-3  C21  0.020
 7HM  plan-3  C22  0.020
 7HM  plan-3  C23  0.020
 7HM  plan-3  C27  0.020
 7HM  plan-3  C4   0.020
 7HM  plan-3  N11  0.020
 7HM  plan-3  C25  0.020
 7HM  plan-3  C26  0.020
 7HM  plan-3  C28  0.020
 7HM  plan-3  H43  0.020
 7HM  plan-3  H41  0.020
 7HM  plan-3  H42  0.020
 7HM  plan-3  H44  0.020
 7HM  plan-3  O24  0.020
 7HM  plan-4  C3   0.020
 7HM  plan-4  O9   0.020
 7HM  plan-4  O10  0.020
 7HM  plan-4  H32  0.020
 7HM  plan-4  C8   0.020

