# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 02:05:46 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: (2R)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-2-phenyl-N-(1,3-thiazol-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(Nc1sccn1)[C@H](N2Cc3ccccc3C2=O)c4ccccc4
#
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
 57N  57N  (2R)-2-(1-oxo-1,3-dihydro-2H-isoindol-2-yl)-2-phenyl-N-(1,3-thiazol-2-yl)acetamide  ligand  40  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_57N
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
 57N  C14  C  CR5   0   0.299  -3.3810   0.8259   0.3190
 57N  C11  C  C     0   0.561  -1.0066   0.3716   0.2413
 57N  C10  C  CR6   0   0.102  -0.2110  -2.0140   0.0262
 57N  C01  C  CR16  0  -0.259   5.3520   2.0931   0.2043
 57N  C02  C  CR16  0  -0.298   4.2714   1.8760   1.0463
 57N  C03  C  CR56  0  -0.076   3.2495   1.0615   0.5851
 57N  C04  C  CR56  0   0.095   3.2851   0.4772  -0.6698
 57N  C05  C  CR16  0  -0.318   4.3617   0.6906  -1.5137
 57N  C06  C  CR16  0  -0.240   5.3930   1.5054  -1.0611
 57N  C07  C  CR5   0   0.567   1.9946   0.6696   1.2525
 57N  O08  O  O     0  -0.475   1.5866   1.0109   2.3489
 57N  C09  C  CH1   0  -0.294   0.0382  -0.6628   0.6611
 57N  N12  N  NH1   0  -0.682  -2.2775   0.0516   0.5926
 57N  O13  O  O     0  -0.429  -0.7336   1.4000  -0.3407
 57N  N15  N  N     0  -0.420  -4.5695   0.4589   0.6723
 57N  C16  C  CR15  0  -0.021  -5.4913   1.3930   0.2888
 57N  C17  C  CR15  0  -0.512  -4.9988   2.4748  -0.3585
 57N  S18  S  S2    0   0.229  -3.2872   2.3415  -0.5101
 57N  C19  C  CR16  0  -0.272  -0.6354  -2.1305  -1.2950
 57N  C20  C  CR16  0  -0.244  -0.8207  -3.3828  -1.8626
 57N  C21  C  CR16  0  -0.255  -0.5843  -4.5288  -1.1141
 57N  C22  C  CR16  0  -0.244  -0.1625  -4.4186   0.2040
 57N  C23  C  CR16  0  -0.290   0.0221  -3.1652   0.7712
 57N  C24  C  CH2   0  -0.278   2.0428  -0.3302  -0.8770
 57N  N25  N  NR5   0  -0.503   1.3600  -0.1727   0.3930
 57N  H2   H  HCR6  0   0.261   4.2277   2.3278   2.0292
 57N  H3   H  HCR6  0   0.262   4.4051   0.2414  -2.4976
 57N  H4   H  HCR6  0   0.267   6.2443   1.6897  -1.7038
 57N  H5   H  HCH1  0   0.321  -0.0519  -0.7784   1.7461
 57N  H6   H  HNH1  0   0.430  -2.4644  -0.8148   1.0810
 57N  H7   H  HCR5  0   0.274  -6.5354   1.2287   0.5136
 57N  H8   H  HCR5  0   0.304  -5.5324   3.3268  -0.7483
 57N  H9   H  HCR6  0   0.262  -0.8187  -1.2473  -1.8967
 57N  H10  H  HCR6  0   0.264  -1.1497  -3.4621  -2.8904
 57N  H11  H  HCR6  0   0.264  -0.7330  -5.5050  -1.5570
 57N  H12  H  HCR6  0   0.263   0.0190  -5.3077   0.7935
 57N  H13  H  HCR6  0   0.265   0.3462  -3.0815   1.8017
 57N  H14  H  HCH2  0   0.275   1.4485   0.0586  -1.7080
 57N  H15  H  HCH2  0   0.281   2.2630  -1.3794  -1.0872
 57N  H1   H  HCR6  0   0.265   6.1710   2.7225   0.5267

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
 57N  C17  S18  aromatic  1.724  0.020  1.724
 57N  C17  C16  aromatic  1.353  0.020  1.353
 57N  S18  C14  aromatic  1.730  0.020  1.730
 57N  C16  N15  aromatic  1.367  0.020  1.367
 57N  O13  C11  double    1.213  0.020  1.213
 57N  C20  C19  aromatic  1.387  0.020  1.387
 57N  C20  C21  aromatic  1.389  0.020  1.389
 57N  C14  N15  aromatic  1.293  0.020  1.293
 57N  C14  N12  single    1.376  0.020  1.376
 57N  C19  C10  aromatic  1.393  0.020  1.393
 57N  C05  C06  aromatic  1.390  0.020  1.390
 57N  C05  C04  aromatic  1.384  0.020  1.384
 57N  C21  C22  aromatic  1.388  0.020  1.388
 57N  C24  C04  single    1.496  0.020  1.496
 57N  C24  N25  single    1.450  0.020  1.450
 57N  C11  N12  single    1.357  0.020  1.357
 57N  C11  C09  single    1.529  0.020  1.529
 57N  C06  C01  aromatic  1.396  0.020  1.396
 57N  C04  C03  aromatic  1.385  0.020  1.385
 57N  C10  C09  single    1.514  0.020  1.514
 57N  C10  C23  aromatic  1.391  0.020  1.391
 57N  N25  C09  single    1.435  0.020  1.435
 57N  N25  C07  single    1.360  0.020  1.360
 57N  C22  C23  aromatic  1.388  0.020  1.388
 57N  C01  C02  aromatic  1.387  0.020  1.387
 57N  C03  C07  single    1.474  0.020  1.474
 57N  C03  C02  aromatic  1.386  0.020  1.386
 57N  C07  O08  double    1.219  0.020  1.219
 57N  C01  H1   single    0.930  0.020  1.080
 57N  C02  H2   single    0.930  0.020  1.080
 57N  C05  H3   single    0.930  0.020  1.080
 57N  C06  H4   single    0.930  0.020  1.080
 57N  C09  H5   single    0.970  0.020  1.090
 57N  N12  H6   single    0.860  0.020  1.020
 57N  C16  H7   single    0.930  0.020  1.080
 57N  C17  H8   single    0.930  0.020  1.080
 57N  C19  H9   single    0.930  0.020  1.080
 57N  C20  H10  single    0.930  0.020  1.080
 57N  C21  H11  single    0.930  0.020  1.080
 57N  C22  H12  single    0.930  0.020  1.080
 57N  C23  H13  single    0.930  0.020  1.080
 57N  C24  H14  single    0.970  0.020  1.090
 57N  C24  H15  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
 57N  S18  C14  N15  115.43  3.000
 57N  N15  C14  N12  121.55  3.000
 57N  S18  C14  N12  123.02  3.000
 57N  O13  C11  N12  122.35  3.000
 57N  N12  C11  C09  114.17  3.000
 57N  O13  C11  C09  123.48  3.000
 57N  C23  C10  C19  119.34  3.000
 57N  C23  C10  C09  119.12  3.000
 57N  C19  C10  C09  121.52  3.000
 57N  H1   C01  C06  119.52  3.000
 57N  H1   C01  C02  119.99  3.000
 57N  C06  C01  C02  120.48  3.000
 57N  H2   C02  C03  121.18  3.000
 57N  H2   C02  C01  121.14  3.000
 57N  C03  C02  C01  117.67  3.000
 57N  C07  C03  C04  108.66  3.000
 57N  C07  C03  C02  129.28  3.000
 57N  C04  C03  C02  122.06  3.000
 57N  C24  C04  C05  130.13  3.000
 57N  C24  C04  C03  109.39  3.000
 57N  C05  C04  C03  120.48  3.000
 57N  H3   C05  C06  120.62  3.000
 57N  H3   C05  C04  121.42  3.000
 57N  C06  C05  C04  117.96  3.000
 57N  H4   C06  C05  119.34  3.000
 57N  H4   C06  C01  119.32  3.000
 57N  C05  C06  C01  121.34  3.000
 57N  N25  C07  O08  125.85  3.000
 57N  O08  C07  C03  128.16  3.000
 57N  N25  C07  C03  106.00  3.000
 57N  H5   C09  N25  107.28  3.000
 57N  H5   C09  C10  107.93  3.000
 57N  N25  C09  C10  112.22  3.000
 57N  H5   C09  C11  106.70  3.000
 57N  N25  C09  C11  110.31  3.000
 57N  C10  C09  C11  112.11  3.000
 57N  H6   N12  C11  120.00  3.000
 57N  H6   N12  C14  115.44  3.000
 57N  C11  N12  C14  124.56  3.000
 57N  C16  N15  C14  110.43  3.000
 57N  H7   C16  C17  124.93  3.000
 57N  H7   C16  N15  119.29  3.000
 57N  C17  C16  N15  115.78  3.000
 57N  H8   C17  S18  121.38  3.000
 57N  H8   C17  C16  128.64  3.000
 57N  S18  C17  C16  109.98  3.000
 57N  C17  S18  C14   88.38  3.000
 57N  H9   C19  C20  119.05  3.000
 57N  H9   C19  C10  120.66  3.000
 57N  C20  C19  C10  120.29  3.000
 57N  H10  C20  C21  120.20  3.000
 57N  H10  C20  C19  119.69  3.000
 57N  C21  C20  C19  120.11  3.000
 57N  H11  C21  C22  120.13  3.000
 57N  H11  C21  C20  120.02  3.000
 57N  C22  C21  C20  119.85  3.000
 57N  H12  C22  C23  119.80  3.000
 57N  H12  C22  C21  120.20  3.000
 57N  C23  C22  C21  120.00  3.000
 57N  H13  C23  C22  119.88  3.000
 57N  H13  C23  C10  119.71  3.000
 57N  C22  C23  C10  120.41  3.000
 57N  H15  C24  H14  107.75  3.000
 57N  H15  C24  N25  111.57  3.000
 57N  H14  C24  N25  111.78  3.000
 57N  H15  C24  C04  112.18  3.000
 57N  H14  C24  C04  111.39  3.000
 57N  N25  C24  C04  102.18  3.000
 57N  C24  N25  C09  124.06  3.000
 57N  C09  N25  C07  121.53  3.000
 57N  C24  N25  C07  113.63  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
 57N  CONST_01  C16  C17  S18  C14    0.00   0.0  0
 57N  CONST_02  C17  C16  N15  C14    0.00   0.0  0
 57N  CONST_03  C21  C20  C19  C10    0.00   0.0  0
 57N  CONST_04  C21  C22  C23  C10    0.00   0.0  0
 57N  CONST_05  C04  C05  C06  C01    0.00   0.0  0
 57N  CONST_06  C04  C03  C02  C01    0.00   0.0  0
 57N  CONST_07  C05  C06  C01  C02    0.00   0.0  0
 57N  CONST_08  C05  C04  C03  C02    0.00   0.0  0
 57N  CONST_09  C06  C05  C04  C03    0.00   0.0  0
 57N  CONST_10  C06  C01  C02  C03    0.00   0.0  0
 57N  CONST_11  S18  C17  C16  N15    0.00   0.0  0
 57N  CONST_12  C17  S18  C14  N15    0.00   0.0  0
 57N  CONST_13  S18  C14  N15  C16    0.00   0.0  0
 57N  CONST_14  C22  C21  C20  C19    0.00   0.0  0
 57N  CONST_15  C22  C23  C10  C19    0.00   0.0  0
 57N  CONST_16  C23  C10  C19  C20    0.00   0.0  0
 57N  CONST_17  C23  C22  C21  C20    0.00   0.0  0
 57N  CONST_18  C24  N25  C07  C03    0.00   0.0  0
 57N  CONST_19  C20  C19  C10  C09  180.00   0.0  0
 57N  CONST_20  C22  C23  C10  C09  180.00   0.0  0
 57N  CONST_21  C17  S18  C14  N12  180.00   0.0  0
 57N  CONST_22  C16  N15  C14  N12  180.00   0.0  0
 57N  CONST_23  C09  N25  C07  C03  180.00   0.0  0
 57N  CONST_24  C24  N25  C07  O08  180.00   0.0  0
 57N  CONST_25  H8   C17  S18  C14  180.00   0.0  0
 57N  CONST_26  H7   C16  N15  C14  180.00   0.0  0
 57N  CONST_27  H10  C20  C19  C10  180.00   0.0  0
 57N  CONST_28  H12  C22  C23  C10  180.00   0.0  0
 57N  CONST_29  H3   C05  C06  C01  180.00   0.0  0
 57N  CONST_30  H4   C06  C01  C02  180.00   0.0  0
 57N  CONST_31  H1   C01  C02  C03  180.00   0.0  0
 57N  CONST_32  H2   C02  C03  C04  180.00   0.0  0
 57N  CONST_33  H11  C21  C20  C19  180.00   0.0  0
 57N  CONST_34  H13  C23  C10  C19  180.00   0.0  0
 57N  CONST_35  H9   C19  C20  C21  180.00   0.0  0
 57N  CONST_36  S18  C14  N12  C11    0.00   0.0  0
 57N  CONST_37  N15  C14  N12  C11  180.00   0.0  0
 57N  CONST_38  C09  N25  C07  O08    0.00   0.0  0
 57N  CONST_39  H6   N12  C14  N15    0.00   0.0  0
 57N  CONST_40  O13  C11  N12  C14    0.00   0.0  0
 57N  CONST_41  C09  C11  N12  C14  180.00   0.0  0
 57N  Var_01    H14  C24  C04  C03  117.37  30.0  1

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
 57N  chir_01  C09  C11  C10  N25  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
 57N  plan-1  C14  0.020
 57N  plan-1  N12  0.020
 57N  plan-1  N15  0.020
 57N  plan-1  C16  0.020
 57N  plan-1  C17  0.020
 57N  plan-1  S18  0.020
 57N  plan-1  H7   0.020
 57N  plan-1  H8   0.020
 57N  plan-2  C10  0.020
 57N  plan-2  C09  0.020
 57N  plan-2  C19  0.020
 57N  plan-2  C20  0.020
 57N  plan-2  C21  0.020
 57N  plan-2  C22  0.020
 57N  plan-2  C23  0.020
 57N  plan-2  H9   0.020
 57N  plan-2  H10  0.020
 57N  plan-2  H11  0.020
 57N  plan-2  H12  0.020
 57N  plan-2  H13  0.020
 57N  plan-3  C14  0.020
 57N  plan-3  C11  0.020
 57N  plan-3  C09  0.020
 57N  plan-3  N12  0.020
 57N  plan-3  O13  0.020
 57N  plan-3  H6   0.020
 57N  plan-4  C01  0.020
 57N  plan-4  C02  0.020
 57N  plan-4  C03  0.020
 57N  plan-4  C04  0.020
 57N  plan-4  C05  0.020
 57N  plan-4  C06  0.020
 57N  plan-4  C07  0.020
 57N  plan-4  O08  0.020
 57N  plan-4  C09  0.020
 57N  plan-4  C24  0.020
 57N  plan-4  N25  0.020
 57N  plan-4  H2   0.020
 57N  plan-4  H3   0.020
 57N  plan-4  H4   0.020
 57N  plan-4  H1   0.020

