# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 15 02:18:34 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: N-[4-({[(3S)-oxolan-3-yl]methyl}carbamoyl)phenyl]-1,3-dihydro-2H-isoindole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1ccc(cc1)C(=O)NC[C@@H]2CCOC2)N3Cc4ccccc4C3
#
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
 7T7  7T7  N-[4-({[(3S)-oxolan-3-yl]methyl}carbamoyl)phenyl]-1,3-dihydro-2H-isoindole-2-carboxamide  ligand  50  27  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7T7
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
 7T7  N1   N  NH1   0  -0.650  -4.4341  -0.6247   0.7761
 7T7  C4   C  CR6   0  -0.050  -2.2369  -0.8605  -0.1716
 7T7  C5   C  CR16  0  -0.281  -1.6927   0.2557   0.4556
 7T7  C6   C  CR16  0  -0.309  -0.3274   0.4926   0.4775
 7T7  C7   C  C     0   0.531  -3.7014  -1.1328  -0.2301
 7T7  C8   C  CH2   0  -0.291  -5.8765  -0.7051   0.8542
 7T7  C10  C  CH2   0  -0.497  -8.0901   0.5063   0.4856
 7T7  C13  C  CH2   0  -0.321   4.6889  -0.5796  -0.4858
 7T7  C15  C  CR16  0  -0.311   7.2365  -0.9328  -0.8330
 7T7  C17  C  CR16  0  -0.255   8.6660   0.7830   0.0876
 7T7  C20  C  CH2   0  -0.268   4.9708   1.5212   0.7314
 7T7  C16  C  CR16  0  -0.257   8.5055  -0.4163  -0.6013
 7T7  C3   C  CR16  0  -0.258  -1.3628  -1.7412  -0.8068
 7T7  C18  C  CR16  0  -0.314   7.5606   1.4819   0.5571
 7T7  C2   C  CR16  0  -0.352  -0.0007  -1.5291  -0.7801
 7T7  C19  C  CR56  0   0.049   6.2972   0.9619   0.3253
 7T7  C14  C  CR56  0   0.052   6.1390  -0.2305  -0.3622
 7T7  C1   C  CR6   0   0.388   0.5450  -0.4105  -0.1358
 7T7  C    C  C     0   0.771   2.7123   0.6998   0.3754
 7T7  C11  C  CH2   0  -0.150  -8.5352   1.5622  -0.5186
 7T7  C12  C  CH2   0  -0.128  -6.4367   0.7858  -1.1581
 7T7  C9   C  CH1   0  -0.296  -6.5716   0.5456   0.3408
 7T7  N2   N  NR5   0  -0.552   4.0416   0.5311   0.2015
 7T7  N    N  NH1   0  -0.812   1.9280  -0.2930  -0.1644
 7T7  O1   O  O     0  -0.496  -4.1848  -1.7954  -1.1407
 7T7  O    O  O     0  -0.524   2.2579   1.6688   0.9688
 7T7  O2   O  O2    0  -0.506  -7.5216   1.6254  -1.5164
 7T7  H1   H  HNH1  0   0.406  -3.9648  -0.1597   1.5353
 7T7  H2   H  HCR6  0   0.256  -2.3311   0.9918   0.9287
 7T7  H3   H  HCR6  0   0.287   0.0431   1.3777   0.9651
 7T7  H4   H  HCH2  0   0.244  -6.2147  -1.5799   0.2969
 7T7  H5   H  HCH2  0   0.260  -6.1436  -0.8692   1.8990
 7T7  H6   H  HCH2  0   0.255  -8.4307   0.7236   1.4979
 7T7  H7   H  HCH2  0   0.235  -8.4710  -0.4816   0.2094
 7T7  H9   H  HCH2  0   0.271   4.4650  -1.5416  -0.0114
 7T7  H10  H  HCR6  0   0.254   7.1117  -1.8640  -1.3716
 7T7  H11  H  HCR6  0   0.258   9.6602   1.1741   0.2590
 7T7  H12  H  HCH2  0   0.259   4.8812   1.6164   1.8174
 7T7  H13  H  HCH2  0   0.259   4.7915   2.5117   0.3034
 7T7  H14  H  HCR6  0   0.259   9.3763  -0.9504  -0.9586
 7T7  H15  H  HCR6  0   0.260  -1.7495  -2.6129  -1.3179
 7T7  H16  H  HCR6  0   0.255   7.6887   2.4136   1.0942
 7T7  H17  H  HCR6  0   0.273   0.6556  -2.2404  -1.2684
 7T7  H18  H  HCH2  0   0.218  -9.4970   1.3210  -0.9792
 7T7  H19  H  HCH2  0   0.206  -8.6339   2.5413  -0.0377
 7T7  H20  H  HCH2  0   0.223  -5.5001   1.2770  -1.4328
 7T7  H21  H  HCH2  0   0.196  -6.4876  -0.1660  -1.7035
 7T7  H22  H  HCH1  0   0.245  -6.1820   1.4155   0.8820
 7T7  H23  H  HNH1  0   0.437   2.3926  -1.0535  -0.6345
 7T7  H8   H  HCH2  0   0.271   4.3805  -0.6472  -1.5351

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
 7T7  O2   C12  single    1.418  0.020  1.418
 7T7  O2   C11  single    1.424  0.020  1.424
 7T7  C12  C9   single    1.524  0.020  1.524
 7T7  C11  C10  single    1.524  0.020  1.524
 7T7  C9   C10  single    1.526  0.020  1.526
 7T7  C9   C8   single    1.520  0.020  1.520
 7T7  C8   N1   single    1.447  0.020  1.447
 7T7  O1   C7   double    1.226  0.020  1.226
 7T7  N1   C7   single    1.344  0.020  1.344
 7T7  C7   C4   single    1.491  0.020  1.491
 7T7  C4   C3   aromatic  1.394  0.020  1.394
 7T7  C4   C5   aromatic  1.391  0.020  1.391
 7T7  C3   C2   aromatic  1.379  0.020  1.379
 7T7  C5   C6   aromatic  1.386  0.020  1.386
 7T7  C2   C1   aromatic  1.401  0.020  1.401
 7T7  C6   C1   aromatic  1.397  0.020  1.397
 7T7  C1   N    single    1.388  0.020  1.388
 7T7  O    C    double    1.224  0.020  1.224
 7T7  N    C    single    1.376  0.020  1.376
 7T7  C    N2   single    1.351  0.020  1.351
 7T7  N2   C20  single    1.458  0.020  1.458
 7T7  N2   C13  single    1.458  0.020  1.458
 7T7  C20  C19  single    1.496  0.020  1.496
 7T7  C13  C14  single    1.497  0.020  1.497
 7T7  C19  C14  aromatic  1.385  0.020  1.385
 7T7  C19  C18  aromatic  1.386  0.020  1.386
 7T7  C14  C15  aromatic  1.385  0.020  1.385
 7T7  C18  C17  aromatic  1.390  0.020  1.390
 7T7  C15  C16  aromatic  1.390  0.020  1.390
 7T7  C17  C16  aromatic  1.392  0.020  1.392
 7T7  N1   H1   single    0.860  0.020  1.020
 7T7  C5   H2   single    0.930  0.020  1.080
 7T7  C6   H3   single    0.930  0.020  1.080
 7T7  C8   H4   single    0.970  0.020  1.090
 7T7  C8   H5   single    0.970  0.020  1.090
 7T7  C10  H6   single    0.970  0.020  1.090
 7T7  C10  H7   single    0.970  0.020  1.090
 7T7  C13  H8   single    0.970  0.020  1.090
 7T7  C13  H9   single    0.970  0.020  1.090
 7T7  C15  H10  single    0.930  0.020  1.080
 7T7  C17  H11  single    0.930  0.020  1.080
 7T7  C20  H12  single    0.970  0.020  1.090
 7T7  C20  H13  single    0.970  0.020  1.090
 7T7  C16  H14  single    0.930  0.020  1.080
 7T7  C3   H15  single    0.930  0.020  1.080
 7T7  C18  H16  single    0.930  0.020  1.080
 7T7  C2   H17  single    0.930  0.020  1.080
 7T7  C11  H18  single    0.970  0.020  1.090
 7T7  C11  H19  single    0.970  0.020  1.090
 7T7  C12  H20  single    0.970  0.020  1.090
 7T7  C12  H21  single    0.970  0.020  1.090
 7T7  C9   H22  single    0.970  0.020  1.090
 7T7  N    H23  single    0.860  0.020  1.020

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
 7T7  H1   N1   C8   116.73  3.000
 7T7  H1   N1   C7   119.02  3.000
 7T7  C8   N1   C7   124.24  3.000
 7T7  C3   C4   C7   118.86  3.000
 7T7  C3   C4   C5   117.85  3.000
 7T7  C7   C4   C5   123.27  3.000
 7T7  H2   C5   C6   117.23  3.000
 7T7  H2   C5   C4   120.77  3.000
 7T7  C6   C5   C4   121.98  3.000
 7T7  H3   C6   C1   121.02  3.000
 7T7  H3   C6   C5   119.13  3.000
 7T7  C1   C6   C5   119.84  3.000
 7T7  O1   C7   C4   121.03  3.000
 7T7  C4   C7   N1   115.91  3.000
 7T7  O1   C7   N1   123.06  3.000
 7T7  H5   C8   H4   107.02  3.000
 7T7  H5   C8   C9   109.59  3.000
 7T7  H4   C8   C9   110.21  3.000
 7T7  H5   C8   N1   107.71  3.000
 7T7  H4   C8   N1   109.03  3.000
 7T7  C9   C8   N1   113.07  3.000
 7T7  H7   C10  H6   107.80  3.000
 7T7  H7   C10  C9   110.22  3.000
 7T7  H6   C10  C9   113.21  3.000
 7T7  H7   C10  C11  110.95  3.000
 7T7  H6   C10  C11  112.50  3.000
 7T7  C9   C10  C11  102.14  3.000
 7T7  H9   C13  H8   107.63  3.000
 7T7  H9   C13  N2   111.97  3.000
 7T7  H8   C13  N2   111.94  3.000
 7T7  H9   C13  C14  111.53  3.000
 7T7  H8   C13  C14  111.48  3.000
 7T7  N2   C13  C14  102.33  3.000
 7T7  H10  C15  C14  120.91  3.000
 7T7  H10  C15  C16  120.52  3.000
 7T7  C14  C15  C16  118.58  3.000
 7T7  H11  C17  C18  119.71  3.000
 7T7  H11  C17  C16  119.71  3.000
 7T7  C18  C17  C16  120.58  3.000
 7T7  H13  C20  H12  107.23  3.000
 7T7  H13  C20  N2   111.62  3.000
 7T7  H12  C20  N2   111.58  3.000
 7T7  H13  C20  C19  112.19  3.000
 7T7  H12  C20  C19  112.01  3.000
 7T7  N2   C20  C19  102.27  3.000
 7T7  H14  C16  C17  119.72  3.000
 7T7  H14  C16  C15  119.76  3.000
 7T7  C17  C16  C15  120.53  3.000
 7T7  H15  C3   C2   119.09  3.000
 7T7  H15  C3   C4   120.02  3.000
 7T7  C2   C3   C4   120.89  3.000
 7T7  H16  C18  C19  120.91  3.000
 7T7  H16  C18  C17  120.41  3.000
 7T7  C19  C18  C17  118.68  3.000
 7T7  H17  C2   C1   119.67  3.000
 7T7  H17  C2   C3   119.24  3.000
 7T7  C1   C2   C3   121.08  3.000
 7T7  C14  C19  C18  120.67  3.000
 7T7  C18  C19  C20  128.52  3.000
 7T7  C14  C19  C20  110.81  3.000
 7T7  C19  C14  C15  120.96  3.000
 7T7  C15  C14  C13  128.40  3.000
 7T7  C19  C14  C13  110.63  3.000
 7T7  N    C1   C2   116.48  3.000
 7T7  N    C1   C6   125.19  3.000
 7T7  C2   C1   C6   118.33  3.000
 7T7  O    C    N    123.37  3.000
 7T7  N    C    N2   114.86  3.000
 7T7  O    C    N2   121.77  3.000
 7T7  H19  C11  H18  107.63  3.000
 7T7  H19  C11  O2   109.40  3.000
 7T7  H18  C11  O2   109.93  3.000
 7T7  H19  C11  C10  110.88  3.000
 7T7  H18  C11  C10  112.45  3.000
 7T7  O2   C11  C10  106.54  3.000
 7T7  H21  C12  H20  107.73  3.000
 7T7  H21  C12  O2   110.63  3.000
 7T7  H20  C12  O2   109.04  3.000
 7T7  H21  C12  C9   110.35  3.000
 7T7  H20  C12  C9   113.20  3.000
 7T7  O2   C12  C9   105.91  3.000
 7T7  H22  C9   C12  109.21  3.000
 7T7  H22  C9   C10  109.10  3.000
 7T7  C12  C9   C10  100.69  3.000
 7T7  H22  C9   C8   108.89  3.000
 7T7  C10  C9   C8   113.69  3.000
 7T7  C12  C9   C8   114.92  3.000
 7T7  C    N2   C20  119.70  3.000
 7T7  C20  N2   C13  113.95  3.000
 7T7  C    N2   C13  126.35  3.000
 7T7  H23  N    C    117.70  3.000
 7T7  H23  N    C1   113.90  3.000
 7T7  C    N    C1   128.39  3.000
 7T7  C12  O2   C11  109.96  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
 7T7  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 7T7  CONST_02  C1   C6   C5   C4      0.00   0.0  0
 7T7  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 7T7  CONST_04  C2   C1   C6   C5      0.00   0.0  0
 7T7  CONST_05  C3   C4   C5   C6      0.00   0.0  0
 7T7  CONST_06  C3   C2   C1   C6      0.00   0.0  0
 7T7  CONST_07  C18  C19  C14  C15     0.00   0.0  0
 7T7  CONST_08  C18  C17  C16  C15     0.00   0.0  0
 7T7  CONST_09  C14  C19  C18  C17     0.00   0.0  0
 7T7  CONST_10  C14  C15  C16  C17     0.00   0.0  0
 7T7  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 7T7  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 7T7  CONST_13  N    C1   C6   C5    180.00   0.0  0
 7T7  CONST_14  C7   C4   C5   C6    180.00   0.0  0
 7T7  CONST_15  C2   C3   C4   C7    180.00   0.0  0
 7T7  CONST_16  N    C1   C2   C3    180.00   0.0  0
 7T7  CONST_17  H17  C2   C3   C4    180.00   0.0  0
 7T7  CONST_18  H3   C6   C5   C4    180.00   0.0  0
 7T7  CONST_19  H15  C3   C4   C5    180.00   0.0  0
 7T7  CONST_20  H10  C15  C14  C13     0.00   0.0  0
 7T7  CONST_21  H11  C17  C16  C15   180.00   0.0  0
 7T7  CONST_22  H16  C18  C19  C20     0.00   0.0  0
 7T7  CONST_23  H2   C5   C4   C3    180.00   0.0  0
 7T7  CONST_24  H14  C16  C17  C18   180.00   0.0  0
 7T7  CONST_25  O    C    N2   C13   180.00   0.0  0
 7T7  CONST_26  O    C    N2   C20     0.00   0.0  0
 7T7  CONST_27  C    N    C1   C6      0.00   0.0  0
 7T7  CONST_28  C    N    C1   C2    180.00   0.0  0
 7T7  CONST_29  N2   C    N    C1    180.00   0.0  0
 7T7  CONST_30  N    C    N2   C13     0.00   0.0  0
 7T7  CONST_31  N    C    N2   C20   180.00   0.0  0
 7T7  CONST_32  H23  N    C1   C6    180.00   0.0  0
 7T7  CONST_33  C8   N1   C7   C4    180.00   0.0  0
 7T7  CONST_34  O    C    N    C1      0.00   0.0  0
 7T7  CONST_35  H1   N1   C7   C4      0.00   0.0  0
 7T7  CONST_36  O1   C7   N1   C8      0.00   0.0  0
 7T7  Var_01    C19  C20  N2   C13     0.17  30.0  1
 7T7  Var_02    N2   C13  C14  C15   179.89  30.0  1
 7T7  Var_03    C14  C13  N2   C20    -0.05  30.0  1
 7T7  Var_04    N2   C20  C19  C18   179.92  30.0  1
 7T7  Var_05    C9   C12  O2   C11   -19.35  30.0  1
 7T7  Var_06    O2   C11  C10  C9     26.86  30.0  1
 7T7  Var_07    H18  C11  O2   C12  -127.06  30.0  1
 7T7  Var_08    C3   C4   C7   N1    154.44  30.0  2
 7T7  Var_09    C9   C8   N1   C7    -96.56  30.0  2

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
 7T7  chir_01  C9  C12  C10  C8  negativ

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
 7T7  plan-1  C4   0.020
 7T7  plan-1  C5   0.020
 7T7  plan-1  C6   0.020
 7T7  plan-1  C7   0.020
 7T7  plan-1  C3   0.020
 7T7  plan-1  C2   0.020
 7T7  plan-1  C1   0.020
 7T7  plan-1  N    0.020
 7T7  plan-1  H2   0.020
 7T7  plan-1  H3   0.020
 7T7  plan-1  H15  0.020
 7T7  plan-1  H17  0.020
 7T7  plan-2  C13  0.020
 7T7  plan-2  C15  0.020
 7T7  plan-2  C17  0.020
 7T7  plan-2  C20  0.020
 7T7  plan-2  C16  0.020
 7T7  plan-2  C18  0.020
 7T7  plan-2  C19  0.020
 7T7  plan-2  C14  0.020
 7T7  plan-2  H10  0.020
 7T7  plan-2  H11  0.020
 7T7  plan-2  H14  0.020
 7T7  plan-2  H16  0.020
 7T7  plan-3  N1   0.020
 7T7  plan-3  C4   0.020
 7T7  plan-3  C7   0.020
 7T7  plan-3  C8   0.020
 7T7  plan-3  O1   0.020
 7T7  plan-3  H1   0.020
 7T7  plan-4  C13  0.020
 7T7  plan-4  C20  0.020
 7T7  plan-4  C1   0.020
 7T7  plan-4  C    0.020
 7T7  plan-4  N2   0.020
 7T7  plan-4  N    0.020
 7T7  plan-4  O    0.020
 7T7  plan-4  H23  0.020

