# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 08:18:08 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: 5-amino-2-{4-[(4-aminophenyl)sulfanyl]phenyl}-1H-isoindole-1,3(2H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc(Sc2ccc(cc2)N3C(=O)c4ccc(N)cc4C3=O)cc1
#
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
 II2  II2  5-amino-2-{4-[(4-aminophenyl)sulfanyl]phenyl}-1H-isoindole-1,3(2H)-dione  ligand  41  26  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_II2
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
 II2  O1    O  O     0  -0.395   2.5725  -1.4672  -1.5003
 II2  C7    C  CR5   0   0.560   2.8792  -0.6696  -0.6518
 II2  C6    C  CR56  0  -0.009   4.1915  -0.0179  -0.4275
 II2  C5    C  CR16  0  -0.388   5.3555  -0.1618  -1.1342
 II2  C4    C  CR6   0   0.376   6.4750   0.5933  -0.7186
 II2  N1    N  NH2   0  -0.856   7.6360   0.5257  -1.4071
 II2  C3    C  CR16  0  -0.326   6.3496   1.4463   0.4001
 II2  C2    C  CR16  0  -0.288   5.1585   1.5702   1.0909
 II2  C1    C  CR56  0  -0.079   4.0677   0.8332   0.6614
 II2  N2    N  NR5   0  -0.726   2.0375  -0.1736   0.3364
 II2  C20   C  CR5   0   0.556   2.7010   0.7415   1.1725
 II2  O2    O  O     0  -0.403   2.1941   1.2893   2.1193
 II2  C8    C  CR6   0   0.328   0.6862  -0.5537   0.4933
 II2  C9    C  CR16  0  -0.263  -0.3181   0.4041   0.4372
 II2  C10   C  CR16  0  -0.237  -1.6460   0.0343   0.5773
 II2  C11   C  CR6   0  -0.116  -1.9850  -1.3035   0.7518
 II2  C18   C  CR16  0  -0.270  -0.9751  -2.2632   0.8014
 II2  C19   C  CR16  0  -0.265   0.3525  -1.8897   0.6843
 II2  S     S  S2    0   0.067  -3.6492  -1.8713   0.9416
 II2  C12   C  CR6   0  -0.214  -4.6151  -0.5289   0.3271
 II2  C13   C  CR16  0  -0.203  -4.7439  -0.3163  -1.0440
 II2  C14   C  CR16  0  -0.321  -5.5168   0.7211  -1.5273
 II2  C15   C  CR6   0   0.323  -6.2006   1.5765  -0.6480
 II2  N3    N  NH2   0  -0.856  -7.0166   2.5669  -1.1231
 II2  C16   C  CR16  0  -0.324  -6.0652   1.3555   0.7303
 II2  C17   C  CR16  0  -0.215  -5.2819   0.3202   1.2063
 II2  H5    H  HCR6  0   0.277   5.4281  -0.8307  -1.9823
 II2  H11N  H  HNH2  0   0.401   7.7837  -0.2297  -2.0550
 II2  H12N  H  HNH2  0   0.400   8.4708   0.9260  -1.0140
 II2  H3    H  HCR6  0   0.275   7.2131   2.0173   0.7182
 II2  H2    H  HCR6  0   0.271   5.0922   2.2355   1.9419
 II2  H9    H  HCR6  0   0.273  -0.0711   1.4440   0.2722
 II2  H19   H  HCR6  0   0.274   1.1258  -2.6434   0.7406
 II2  H10   H  HCR6  0   0.271  -2.4145   0.7937   0.5340
 II2  H18   H  HCR6  0   0.271  -1.2216  -3.3101   0.9289
 II2  H13   H  HCR6  0   0.268  -4.2290  -0.9644  -1.7422
 II2  H17   H  HCR6  0   0.267  -5.1853   0.1708   2.2744
 II2  H14   H  HCR6  0   0.263  -5.6031   0.8729  -2.5963
 II2  H31N  H  HNH2  0   0.386  -6.8582   2.8769  -2.0674
 II2  H32N  H  HNH2  0   0.386  -7.2344   3.3192  -0.4907
 II2  H16   H  HCR6  0   0.263  -6.5795   2.0036   1.4298

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
 II2  O1   C7    double    1.204  0.020  1.204
 II2  C7   C6    single    1.482  0.020  1.482
 II2  C7   N2    single    1.390  0.020  1.390
 II2  C6   C5    aromatic  1.369  0.020  1.369
 II2  C6   C1    aromatic  1.388  0.020  1.388
 II2  C5   C4    aromatic  1.413  0.020  1.413
 II2  C4   N1    single    1.351  0.020  1.351
 II2  C4   C3    aromatic  1.412  0.020  1.412
 II2  C3   C2    aromatic  1.383  0.020  1.383
 II2  C2   C1    aromatic  1.385  0.020  1.385
 II2  C1   C20   single    1.462  0.020  1.462
 II2  N2   C20   single    1.406  0.020  1.406
 II2  N2   C8    single    1.412  0.020  1.412
 II2  C20  O2    double    1.206  0.020  1.206
 II2  C8   C9    aromatic  1.389  0.020  1.389
 II2  C8   C19   aromatic  1.390  0.020  1.390
 II2  C9   C10   aromatic  1.385  0.020  1.385
 II2  C10  C11   aromatic  1.391  0.020  1.391
 II2  C11  C18   aromatic  1.394  0.020  1.394
 II2  C11  S     single    1.769  0.020  1.769
 II2  C18  C19   aromatic  1.384  0.020  1.384
 II2  S    C12   single    1.764  0.020  1.764
 II2  C12  C13   aromatic  1.393  0.020  1.393
 II2  C12  C17   aromatic  1.392  0.020  1.392
 II2  C13  C14   aromatic  1.381  0.020  1.381
 II2  C14  C15   aromatic  1.404  0.020  1.404
 II2  C15  N3    single    1.368  0.020  1.368
 II2  C15  C16   aromatic  1.402  0.020  1.402
 II2  C16  C17   aromatic  1.383  0.020  1.383
 II2  C5   H5    single    0.930  0.020  1.080
 II2  N1   H11N  single    0.890  0.020  1.040
 II2  N1   H12N  single    0.890  0.020  1.040
 II2  C3   H3    single    0.930  0.020  1.080
 II2  C2   H2    single    0.930  0.020  1.080
 II2  C9   H9    single    0.930  0.020  1.080
 II2  C19  H19   single    0.930  0.020  1.080
 II2  C10  H10   single    0.930  0.020  1.080
 II2  C18  H18   single    0.930  0.020  1.080
 II2  C13  H13   single    0.930  0.020  1.080
 II2  C17  H17   single    0.930  0.020  1.080
 II2  C14  H14   single    0.930  0.020  1.080
 II2  N3   H31N  single    0.890  0.020  1.040
 II2  N3   H32N  single    0.890  0.020  1.040
 II2  C16  H16   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
 II2  N2    C7   C6    105.76  3.000
 II2  N2    C7   O1    125.67  3.000
 II2  C6    C7   O1    128.56  3.000
 II2  C1    C6   C5    123.05  3.000
 II2  C1    C6   C7    108.03  3.000
 II2  C5    C6   C7    128.92  3.000
 II2  H5    C5   C4    120.50  3.000
 II2  H5    C5   C6    121.75  3.000
 II2  C4    C5   C6    117.75  3.000
 II2  C3    C4   N1    120.66  3.000
 II2  C3    C4   C5    119.04  3.000
 II2  N1    C4   C5    120.27  3.000
 II2  H12N  N1   H11N  115.38  3.000
 II2  H12N  N1   C4    119.60  3.000
 II2  H11N  N1   C4    119.46  3.000
 II2  H3    C3   C2    119.53  3.000
 II2  H3    C3   C4    118.70  3.000
 II2  C2    C3   C4    121.76  3.000
 II2  H2    C2   C1    121.52  3.000
 II2  H2    C2   C3    120.05  3.000
 II2  C1    C2   C3    118.42  3.000
 II2  C20   C1   C2    131.40  3.000
 II2  C20   C1   C6    108.62  3.000
 II2  C2    C1   C6    119.97  3.000
 II2  C8    N2   C20   124.09  3.000
 II2  C8    N2   C7    124.23  3.000
 II2  C20   N2   C7    111.67  3.000
 II2  O2    C20  N2    124.35  3.000
 II2  O2    C20  C1    129.73  3.000
 II2  N2    C20  C1    105.91  3.000
 II2  C19   C8   C9    119.65  3.000
 II2  C19   C8   N2    120.23  3.000
 II2  C9    C8   N2    120.11  3.000
 II2  H9    C9   C10   119.40  3.000
 II2  H9    C9   C8    120.27  3.000
 II2  C10   C9   C8    120.33  3.000
 II2  H10   C10  C11   120.48  3.000
 II2  H10   C10  C9    119.32  3.000
 II2  C11   C10  C9    120.19  3.000
 II2  S     C11  C18   117.18  3.000
 II2  S     C11  C10   123.47  3.000
 II2  C18   C11  C10   119.34  3.000
 II2  H18   C18  C19   119.29  3.000
 II2  H18   C18  C11   120.31  3.000
 II2  C19   C18  C11   120.40  3.000
 II2  H19   C19  C18   119.57  3.000
 II2  H19   C19  C8    120.35  3.000
 II2  C18   C19  C8    120.08  3.000
 II2  C12   S    C11   103.50  3.000
 II2  C17   C12  C13   118.95  3.000
 II2  C17   C12  S     120.42  3.000
 II2  C13   C12  S     120.63  3.000
 II2  H13   C13  C14   119.34  3.000
 II2  H13   C13  C12   119.94  3.000
 II2  C14   C13  C12   120.71  3.000
 II2  H14   C14  C15   119.59  3.000
 II2  H14   C14  C13   119.68  3.000
 II2  C15   C14  C13   120.73  3.000
 II2  C16   C15  N3    120.85  3.000
 II2  C16   C15  C14   118.19  3.000
 II2  N3    C15  C14   120.92  3.000
 II2  H32N  N3   H31N  113.16  3.000
 II2  H32N  N3   C15   116.86  3.000
 II2  H31N  N3   C15   117.05  3.000
 II2  H16   C16  C17   119.64  3.000
 II2  H16   C16  C15   119.63  3.000
 II2  C17   C16  C15   120.73  3.000
 II2  H17   C17  C16   119.56  3.000
 II2  H17   C17  C12   119.74  3.000
 II2  C16   C17  C12   120.70  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
 II2  CONST_01  C3    C4   C5   C6      0.00   0.0  0
 II2  CONST_02  C3    C2   C1   C6      0.00   0.0  0
 II2  CONST_03  C2    C1   C6   C5      0.00   0.0  0
 II2  CONST_04  C2    C3   C4   C5      0.00   0.0  0
 II2  CONST_05  C1    C6   C5   C4      0.00   0.0  0
 II2  CONST_06  C1    C2   C3   C4      0.00   0.0  0
 II2  CONST_07  C11   C10  C9   C8      0.00   0.0  0
 II2  CONST_08  C11   C18  C19  C8      0.00   0.0  0
 II2  CONST_09  C18   C19  C8   C9      0.00   0.0  0
 II2  CONST_10  C18   C11  C10  C9      0.00   0.0  0
 II2  CONST_11  C19   C8   C9   C10     0.00   0.0  0
 II2  CONST_12  C19   C18  C11  C10     0.00   0.0  0
 II2  CONST_13  C15   C14  C13  C12     0.00   0.0  0
 II2  CONST_14  C15   C16  C17  C12     0.00   0.0  0
 II2  CONST_15  C16   C17  C12  C13     0.00   0.0  0
 II2  CONST_16  C16   C15  C14  C13     0.00   0.0  0
 II2  CONST_17  C17   C12  C13  C14     0.00   0.0  0
 II2  CONST_18  C17   C16  C15  C14     0.00   0.0  0
 II2  CONST_19  C10   C9   C8   N2    180.00   0.0  0
 II2  CONST_20  C18   C19  C8   N2    180.00   0.0  0
 II2  CONST_21  C20   N2   C7   C6      0.00   0.0  0
 II2  CONST_22  C8    N2   C7   C6    180.00   0.0  0
 II2  CONST_23  N1    C4   C5   C6    180.00   0.0  0
 II2  CONST_24  C2    C3   C4   N1    180.00   0.0  0
 II2  CONST_25  S     C11  C10  C9    180.00   0.0  0
 II2  CONST_26  S     C11  C18  C19   180.00   0.0  0
 II2  CONST_27  C14   C13  C12  S     180.00   0.0  0
 II2  CONST_28  C16   C17  C12  S     180.00   0.0  0
 II2  CONST_29  N3    C15  C14  C13   180.00   0.0  0
 II2  CONST_30  C17   C16  C15  N3    180.00   0.0  0
 II2  CONST_31  C20   N2   C7   O1    180.00   0.0  0
 II2  CONST_32  C8    N2   C7   O1      0.00   0.0  0
 II2  CONST_33  H5    C5   C6   C7      0.00   0.0  0
 II2  CONST_34  H2    C2   C1   C6    180.00   0.0  0
 II2  CONST_35  H3    C3   C4   C5    180.00   0.0  0
 II2  CONST_36  H9    C9   C8   N2      0.00   0.0  0
 II2  CONST_37  H19   C19  C8   N2      0.00   0.0  0
 II2  CONST_38  H10   C10  C9   C8    180.00   0.0  0
 II2  CONST_39  H18   C18  C19  C8    180.00   0.0  0
 II2  CONST_40  H14   C14  C13  C12   180.00   0.0  0
 II2  CONST_41  H16   C16  C17  C12   180.00   0.0  0
 II2  CONST_42  H17   C17  C12  C13   180.00   0.0  0
 II2  CONST_43  H13   C13  C14  C15   180.00   0.0  0
 II2  CONST_45  H12N  N1   C4   C5    180.00   0.0  0
 II2  Var_01    C9    C8   N2   C7   -121.45  30.0  2
 II2  Var_02    C13   C12  S    C11    77.12  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
 II2  plan-1  N2    0.020
 II2  plan-1  C8    0.020
 II2  plan-1  C9    0.020
 II2  plan-1  C10   0.020
 II2  plan-1  C11   0.020
 II2  plan-1  C18   0.020
 II2  plan-1  C19   0.020
 II2  plan-1  S     0.020
 II2  plan-1  H9    0.020
 II2  plan-1  H19   0.020
 II2  plan-1  H10   0.020
 II2  plan-1  H18   0.020
 II2  plan-2  S     0.020
 II2  plan-2  C12   0.020
 II2  plan-2  C13   0.020
 II2  plan-2  C14   0.020
 II2  plan-2  C15   0.020
 II2  plan-2  N3    0.020
 II2  plan-2  C16   0.020
 II2  plan-2  C17   0.020
 II2  plan-2  H13   0.020
 II2  plan-2  H17   0.020
 II2  plan-2  H14   0.020
 II2  plan-2  H16   0.020
 II2  plan-3  O1    0.020
 II2  plan-3  C7    0.020
 II2  plan-3  C6    0.020
 II2  plan-3  C5    0.020
 II2  plan-3  C4    0.020
 II2  plan-3  N1    0.020
 II2  plan-3  C3    0.020
 II2  plan-3  C2    0.020
 II2  plan-3  C1    0.020
 II2  plan-3  N2    0.020
 II2  plan-3  C20   0.020
 II2  plan-3  O2    0.020
 II2  plan-3  C8    0.020
 II2  plan-3  H5    0.020
 II2  plan-3  H3    0.020
 II2  plan-3  H2    0.020
 II2  plan-4  C4    0.020
 II2  plan-4  N1    0.020
 II2  plan-4  H11N  0.020
 II2  plan-4  H12N  0.020
 II2  plan-5  C15   0.020
 II2  plan-5  N3    0.020
 II2  plan-5  H31N  0.020
 II2  plan-5  H32N  0.020

