# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 08:32:06 2020
#   Inital geometry file: a 97 line input string
#   Ligand name: 5-[2-(4-methylphenyl)sulfanylethanoyl]-1,3-dihydroindol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(SCC(=O)c2ccc3NC(=O)Cc3c2)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
 JQN  JQN  5-[2-(4-methylphenyl)sulfanylethanoyl]-1,3-dihydroindol-2-one  ligand  36  21  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JQN
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
 JQN  C1    C  CH3   0  -0.721   7.3374  -1.9166  -0.0238
 JQN  C2    C  CR6   0   0.084   6.0735  -1.1078  -0.0148
 JQN  C3    C  CR16  0  -0.284   6.1047   0.2827  -0.1174
 JQN  C4    C  CR16  0  -0.255   4.9436   1.0352  -0.0827
 JQN  C5    C  CR6   0  -0.118   3.7001   0.4159   0.0596
 JQN  C6    C  CR16  0  -0.245   3.6545  -0.9714   0.1606
 JQN  C7    C  CR16  0  -0.282   4.8292  -1.7129   0.1197
 JQN  S8    S  S2    0   0.073   2.3010   1.4896   0.1098
 JQN  C9    C  CH2   0  -0.745   0.9207   0.3284   0.0970
 JQN  C10   C  C     0   0.403  -0.3683   1.1197   0.0799
 JQN  O11   O  O     0  -0.394  -0.3385   2.3325   0.1120
 JQN  C12   C  CR6   0  -0.011  -1.6399   0.3724   0.0296
 JQN  C13   C  CR16  0  -0.297  -1.6788  -1.0226  -0.0206
 JQN  C14   C  CR16  0  -0.286  -2.8792  -1.7168  -0.0723
 JQN  C15   C  CR56  0   0.431  -4.0472  -0.9752  -0.0723
 JQN  C16   C  CR56  0   0.023  -4.0354   0.4231  -0.0191
 JQN  C17   C  CR16  0  -0.336  -2.8435   1.0977   0.0306
 JQN  C18   C  CH2   0  -0.622  -5.4517   0.9005  -0.0319
 JQN  C19   C  CR5   0   0.522  -6.2541  -0.3880  -0.1062
 JQN  O20   O  O     0  -0.443  -7.4574  -0.5093  -0.1436
 JQN  N21   N  NR15  0  -0.739  -5.3513  -1.4182  -0.1215
 JQN  H11C  H  HCH3  0   0.248   7.7381  -2.0298   0.9860
 JQN  H12C  H  HCH3  0   0.243   7.1693  -2.9184  -0.4186
 JQN  H13C  H  HCH3  0   0.243   8.1122  -1.4425  -0.6258
 JQN  H3    H  HCR6  0   0.252   7.0540   0.7923  -0.2348
 JQN  H7    H  HCR6  0   0.251   4.7631  -2.7920   0.1943
 JQN  H4    H  HCR6  0   0.262   5.0080   2.1133  -0.1715
 JQN  H6    H  HCR6  0   0.262   2.7176  -1.4997   0.2718
 JQN  H91C  H  HCH2  0   0.314   0.9744  -0.3204  -0.7803
 JQN  H92C  H  HCH2  0   0.315   0.9406  -0.3099   0.9838
 JQN  H13   H  HCR6  0   0.270  -0.7645  -1.6011  -0.0213
 JQN  H17   H  HCR6  0   0.265  -2.8267   2.1793   0.0698
 JQN  H14   H  HCR6  0   0.279  -2.8924  -2.7972  -0.1117
 JQN  H21   H  HNR5  0   0.419  -5.6227  -2.3896  -0.1661
 JQN  H181  H  HCH2  0   0.310  -5.7273   1.4568   0.8672
 JQN  H182  H  HCH2  0   0.310  -5.6863   1.5393  -0.8865

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
 JQN  C1   C2    single    1.501  0.020  1.501
 JQN  C2   C3    aromatic  1.395  0.020  1.395
 JQN  C2   C7    aromatic  1.390  0.020  1.390
 JQN  C3   C4    aromatic  1.384  0.020  1.384
 JQN  C4   C5    aromatic  1.396  0.020  1.396
 JQN  C5   C6    aromatic  1.392  0.020  1.392
 JQN  C5   S8    single    1.764  0.020  1.764
 JQN  C6   C7    aromatic  1.390  0.020  1.390
 JQN  S8   C9    single    1.804  0.020  1.804
 JQN  C9   C10   single    1.513  0.020  1.513
 JQN  C10  O11   double    1.214  0.020  1.214
 JQN  C10  C12   single    1.476  0.020  1.476
 JQN  C12  C13   aromatic  1.396  0.020  1.396
 JQN  C12  C17   aromatic  1.405  0.020  1.405
 JQN  C13  C14   aromatic  1.388  0.020  1.388
 JQN  C14  C15   aromatic  1.384  0.020  1.384
 JQN  C15  C16   aromatic  1.399  0.020  1.399
 JQN  C15  N21   single    1.378  0.020  1.378
 JQN  C16  C17   aromatic  1.370  0.020  1.370
 JQN  C16  C18   single    1.495  0.020  1.495
 JQN  C18  C19   single    1.520  0.020  1.520
 JQN  C19  O20   double    1.210  0.020  1.210
 JQN  C19  N21   single    1.370  0.020  1.370
 JQN  C1   H11C  single    0.970  0.020  1.090
 JQN  C1   H12C  single    0.970  0.020  1.090
 JQN  C1   H13C  single    0.970  0.020  1.090
 JQN  C3   H3    single    0.930  0.020  1.080
 JQN  C7   H7    single    0.930  0.020  1.080
 JQN  C4   H4    single    0.930  0.020  1.080
 JQN  C6   H6    single    0.930  0.020  1.080
 JQN  C9   H91C  single    0.970  0.020  1.090
 JQN  C9   H92C  single    0.970  0.020  1.090
 JQN  C13  H13   single    0.930  0.020  1.080
 JQN  C17  H17   single    0.930  0.020  1.080
 JQN  C14  H14   single    0.930  0.020  1.080
 JQN  N21  H21   single    0.860  0.020  1.020
 JQN  C18  H181  single    0.970  0.020  1.090
 JQN  C18  H182  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
 JQN  H13C  C1   H12C  108.03  3.000
 JQN  H13C  C1   H11C  107.16  3.000
 JQN  H12C  C1   H11C  107.23  3.000
 JQN  H13C  C1   C2    111.57  3.000
 JQN  H12C  C1   C2    111.57  3.000
 JQN  H11C  C1   C2    111.06  3.000
 JQN  C7    C2   C3    117.46  3.000
 JQN  C7    C2   C1    121.33  3.000
 JQN  C3    C2   C1    121.21  3.000
 JQN  H3    C3   C4    118.81  3.000
 JQN  H3    C3   C2    119.76  3.000
 JQN  C4    C3   C2    121.43  3.000
 JQN  H4    C4   C5    120.16  3.000
 JQN  H4    C4   C3    119.27  3.000
 JQN  C5    C4   C3    120.57  3.000
 JQN  S8    C5   C6    125.35  3.000
 JQN  S8    C5   C4    116.05  3.000
 JQN  C6    C5   C4    118.59  3.000
 JQN  H6    C6   C7    118.34  3.000
 JQN  H6    C6   C5    121.52  3.000
 JQN  C7    C6   C5    120.14  3.000
 JQN  H7    C7   C6    118.54  3.000
 JQN  H7    C7   C2    119.65  3.000
 JQN  C6    C7   C2    121.82  3.000
 JQN  C9    S8   C5    102.41  3.000
 JQN  H92C  C9   H91C  107.69  3.000
 JQN  H92C  C9   C10   109.28  3.000
 JQN  H91C  C9   C10   110.09  3.000
 JQN  H92C  C9   S8    110.87  3.000
 JQN  H91C  C9   S8    110.51  3.000
 JQN  C10   C9   S8    108.39  3.000
 JQN  C12   C10  O11   121.88  3.000
 JQN  C12   C10  C9    118.02  3.000
 JQN  O11   C10  C9    120.10  3.000
 JQN  C17   C12  C13   119.46  3.000
 JQN  C17   C12  C10   118.46  3.000
 JQN  C13   C12  C10   122.08  3.000
 JQN  H13   C13  C14   117.61  3.000
 JQN  H13   C13  C12   120.71  3.000
 JQN  C14   C13  C12   121.68  3.000
 JQN  H14   C14  C15   121.69  3.000
 JQN  H14   C14  C13   120.79  3.000
 JQN  C15   C14  C13   117.53  3.000
 JQN  N21   C15  C16   109.30  3.000
 JQN  N21   C15  C14   128.80  3.000
 JQN  C16   C15  C14   121.90  3.000
 JQN  C18   C16  C17   131.85  3.000
 JQN  C18   C16  C15   108.11  3.000
 JQN  C17   C16  C15   120.04  3.000
 JQN  H17   C17  C16   120.44  3.000
 JQN  H17   C17  C12   120.17  3.000
 JQN  C16   C17  C12   119.39  3.000
 JQN  H182  C18  H181  106.96  3.000
 JQN  H182  C18  C19   110.13  3.000
 JQN  H181  C18  C19   109.80  3.000
 JQN  H182  C18  C16   113.39  3.000
 JQN  H181  C18  C16   113.24  3.000
 JQN  C19   C18  C16   103.30  3.000
 JQN  N21   C19  O20   125.43  3.000
 JQN  N21   C19  C18   106.87  3.000
 JQN  O20   C19  C18   127.71  3.000
 JQN  H21   N21  C19   123.16  3.000
 JQN  H21   N21  C15   124.41  3.000
 JQN  C19   N21  C15   112.43  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
 JQN  CONST_01  C5    C4   C3   C2      0.00   0.0  0
 JQN  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 JQN  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 JQN  CONST_04  C6    C5   C4   C3      0.00   0.0  0
 JQN  CONST_05  C7    C2   C3   C4      0.00   0.0  0
 JQN  CONST_06  C7    C6   C5   C4      0.00   0.0  0
 JQN  CONST_07  C15   C14  C13  C12     0.00   0.0  0
 JQN  CONST_08  C15   C16  C17  C12     0.00   0.0  0
 JQN  CONST_09  C16   C17  C12  C13     0.00   0.0  0
 JQN  CONST_10  C16   C15  C14  C13     0.00   0.0  0
 JQN  CONST_11  C17   C12  C13  C14     0.00   0.0  0
 JQN  CONST_12  C17   C16  C15  C14     0.00   0.0  0
 JQN  CONST_13  C18   C19  N21  C15     0.00   0.0  0
 JQN  CONST_14  C4    C3   C2   C1    180.00   0.0  0
 JQN  CONST_15  C6    C7   C2   C1    180.00   0.0  0
 JQN  CONST_16  S8    C5   C4   C3    180.00   0.0  0
 JQN  CONST_17  S8    C5   C6   C7    180.00   0.0  0
 JQN  CONST_18  C14   C13  C12  C10   180.00   0.0  0
 JQN  CONST_19  C16   C17  C12  C10   180.00   0.0  0
 JQN  CONST_20  O20   C19  N21  C15   180.00   0.0  0
 JQN  CONST_21  H4    C4   C3   C2    180.00   0.0  0
 JQN  CONST_22  H6    C6   C7   C2    180.00   0.0  0
 JQN  CONST_23  H7    C7   C2   C3    180.00   0.0  0
 JQN  CONST_24  H3    C3   C4   C5    180.00   0.0  0
 JQN  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 JQN  CONST_26  H17   C17  C12  C13   180.00   0.0  0
 JQN  CONST_27  H13   C13  C14  C15   180.00   0.0  0
 JQN  CONST_28  H21   N21  C19  C18   180.00   0.0  0
 JQN  Var_01    H181  C18  C16  C15   118.39  30.0  1
 JQN  Var_02    C13   C12  C10  C9     -0.90  30.0  2
 JQN  Var_03    H11C  C1   C2   C3     88.34  30.0  2
 JQN  Var_04    C10   C9   S8   C5   -177.70  30.0  3
 JQN  Var_05    C12   C10  C9   S8    178.35  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
 JQN  plan-1  C1   0.020
 JQN  plan-1  C2   0.020
 JQN  plan-1  C3   0.020
 JQN  plan-1  C4   0.020
 JQN  plan-1  C5   0.020
 JQN  plan-1  C6   0.020
 JQN  plan-1  C7   0.020
 JQN  plan-1  S8   0.020
 JQN  plan-1  H3   0.020
 JQN  plan-1  H7   0.020
 JQN  plan-1  H4   0.020
 JQN  plan-1  H6   0.020
 JQN  plan-2  C9   0.020
 JQN  plan-2  C10  0.020
 JQN  plan-2  O11  0.020
 JQN  plan-2  C12  0.020
 JQN  plan-3  C10  0.020
 JQN  plan-3  C12  0.020
 JQN  plan-3  C13  0.020
 JQN  plan-3  C14  0.020
 JQN  plan-3  C15  0.020
 JQN  plan-3  C16  0.020
 JQN  plan-3  C17  0.020
 JQN  plan-3  C18  0.020
 JQN  plan-3  C19  0.020
 JQN  plan-3  O20  0.020
 JQN  plan-3  N21  0.020
 JQN  plan-3  H13  0.020
 JQN  plan-3  H17  0.020
 JQN  plan-3  H14  0.020
 JQN  plan-3  H21  0.020

