# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:32:27 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: 1,5-dimethyl-3~{H}-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)Cc2cc(C)ccc12
#
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
 IS7  IS7  1,5-dimethyl-3~{H}-indol-2-one  ligand  23  12  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_IS7
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
 IS7  C2   C  CH2   0  -0.609  -13.1389  -22.3230  -3.9995
 IS7  C1   C  CR5   0   0.512  -13.1949  -22.9926  -5.3616
 IS7  O    O  O     0  -0.460  -13.8820  -22.6747  -6.3105
 IS7  C3   C  CR56  0   0.012  -12.1283  -23.1370  -3.2592
 IS7  C9   C  CR56  0   0.418  -11.6697  -24.1392  -4.1144
 IS7  N    N  NR5   0  -0.582  -12.3224  -24.0423  -5.3433
 IS7  C    C  CH3   0  -0.534  -12.0906  -24.9023  -6.4769
 IS7  C8   C  CR16  0  -0.304  -10.7073  -25.0409  -3.7067
 IS7  C7   C  CR16  0  -0.308  -10.2172  -24.9238  -2.4057
 IS7  C5   C  CR6   0   0.086  -10.6608  -23.9385  -1.5304
 IS7  C6   C  CH3   0  -0.719  -10.1319  -23.8494  -0.1273
 IS7  C4   C  CR16  0  -0.362  -11.6298  -23.0322  -1.9803
 IS7  H1   H  HCH2  0   0.298  -12.8466  -21.2761  -4.1146
 IS7  H2   H  HCH2  0   0.299  -14.1290  -22.3261  -3.5373
 IS7  H3   H  HCH3  0   0.257  -11.7632  -25.8815  -6.1363
 IS7  H4   H  HCH3  0   0.261  -13.0139  -25.0291  -7.0368
 IS7  H5   H  HCH3  0   0.252  -11.3289  -24.4933  -7.1419
 IS7  H6   H  HCR6  0   0.264  -10.3268  -25.8136  -4.3618
 IS7  H7   H  HCR6  0   0.247   -9.4625  -25.6258  -2.0718
 IS7  H8   H  HCH3  0   0.240   -9.9222  -22.8174   0.1560
 IS7  H9   H  HCH3  0   0.243  -10.8542  -24.2373   0.5941
 IS7  H10  H  HCH3  0   0.242   -9.2132  -24.4229  -0.0092
 IS7  H11  H  HCR6  0   0.244  -11.9842  -22.2472  -1.3212

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
 IS7  C   N    single    1.442  0.020  1.442
 IS7  O   C1   double    1.214  0.020  1.214
 IS7  N   C1   single    1.365  0.020  1.365
 IS7  N   C9   single    1.395  0.020  1.395
 IS7  C1  C2   single    1.519  0.020  1.519
 IS7  C9  C8   aromatic  1.380  0.020  1.380
 IS7  C9  C3   aromatic  1.395  0.020  1.395
 IS7  C2  C3   single    1.494  0.020  1.494
 IS7  C8  C7   aromatic  1.395  0.020  1.395
 IS7  C3  C4   aromatic  1.377  0.020  1.377
 IS7  C7  C5   aromatic  1.391  0.020  1.391
 IS7  C4  C5   aromatic  1.401  0.020  1.401
 IS7  C5  C6   single    1.502  0.020  1.502
 IS7  C2  H1   single    0.970  0.020  1.090
 IS7  C2  H2   single    0.970  0.020  1.090
 IS7  C   H3   single    0.970  0.020  1.090
 IS7  C   H4   single    0.970  0.020  1.090
 IS7  C   H5   single    0.970  0.020  1.090
 IS7  C8  H6   single    0.930  0.020  1.080
 IS7  C7  H7   single    0.930  0.020  1.080
 IS7  C6  H8   single    0.970  0.020  1.090
 IS7  C6  H9   single    0.970  0.020  1.090
 IS7  C6  H10  single    0.970  0.020  1.090
 IS7  C4  H11  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
 IS7  H2   C2  H1  106.82  3.000
 IS7  H2   C2  C3  113.69  3.000
 IS7  H1   C2  C3  113.15  3.000
 IS7  H2   C2  C1  110.17  3.000
 IS7  H1   C2  C1  109.74  3.000
 IS7  C3   C2  C1  103.25  3.000
 IS7  N    C1  O   125.00  3.000
 IS7  N    C1  C2  107.66  3.000
 IS7  O    C1  C2  127.33  3.000
 IS7  C4   C3  C9  120.34  3.000
 IS7  C4   C3  C2  131.59  3.000
 IS7  C9   C3  C2  108.06  3.000
 IS7  C8   C9  N   129.19  3.000
 IS7  C8   C9  C3  121.16  3.000
 IS7  N    C9  C3  109.65  3.000
 IS7  C    N   C9  125.18  3.000
 IS7  C9   N   C1  111.36  3.000
 IS7  C    N   C1  123.43  3.000
 IS7  H5   C   H4  108.84  3.000
 IS7  H5   C   H3  108.56  3.000
 IS7  H4   C   H3  108.18  3.000
 IS7  H5   C   N   111.59  3.000
 IS7  H4   C   N   109.76  3.000
 IS7  H3   C   N   109.84  3.000
 IS7  H6   C8  C7  120.06  3.000
 IS7  H6   C8  C9  122.20  3.000
 IS7  C7   C8  C9  117.74  3.000
 IS7  H7   C7  C5  119.16  3.000
 IS7  H7   C7  C8  118.54  3.000
 IS7  C5   C7  C8  122.30  3.000
 IS7  C4   C5  C6  120.34  3.000
 IS7  C6   C5  C7  121.18  3.000
 IS7  C4   C5  C7  118.48  3.000
 IS7  H10  C6  H9  107.41  3.000
 IS7  H10  C6  H8  107.93  3.000
 IS7  H9   C6  H8  106.96  3.000
 IS7  H10  C6  C5  111.53  3.000
 IS7  H9   C6  C5  111.29  3.000
 IS7  H8   C6  C5  111.50  3.000
 IS7  H11  C4  C5  119.94  3.000
 IS7  H11  C4  C3  120.09  3.000
 IS7  C5   C4  C3  119.97  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
 IS7  CONST_01  C7   C8  C9  C3     0.00   0.0  0
 IS7  CONST_02  C7   C5  C4  C3     0.00   0.0  0
 IS7  CONST_03  C5   C7  C8  C9     0.00   0.0  0
 IS7  CONST_04  C5   C4  C3  C9     0.00   0.0  0
 IS7  CONST_05  C4   C3  C9  C8     0.00   0.0  0
 IS7  CONST_06  C4   C5  C7  C8     0.00   0.0  0
 IS7  CONST_07  C9   N   C1  C2     0.00   0.0  0
 IS7  CONST_08  C6   C5  C4  C3   180.00   0.0  0
 IS7  CONST_09  C6   C5  C7  C8   180.00   0.0  0
 IS7  CONST_10  C    N   C1  C2   180.00   0.0  0
 IS7  CONST_11  C9   N   C1  O    180.00   0.0  0
 IS7  CONST_12  H11  C4  C3  C2     0.00   0.0  0
 IS7  CONST_13  H6   C8  C9  C3   180.00   0.0  0
 IS7  CONST_14  H7   C7  C8  C9   180.00   0.0  0
 IS7  CONST_15  C    N   C1  O      0.00   0.0  0
 IS7  Var_01    H1   C2  C3  C9  -118.25  30.0  1
 IS7  Var_02    H3   C   N   C1  -153.46  30.0  3
 IS7  Var_03    H8   C6  C5  C7   137.08  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
 IS7  plan-1  C2   0.020
 IS7  plan-1  C1   0.020
 IS7  plan-1  O    0.020
 IS7  plan-1  C3   0.020
 IS7  plan-1  C9   0.020
 IS7  plan-1  N    0.020
 IS7  plan-1  C    0.020
 IS7  plan-1  C8   0.020
 IS7  plan-1  C7   0.020
 IS7  plan-1  C5   0.020
 IS7  plan-1  C6   0.020
 IS7  plan-1  C4   0.020
 IS7  plan-1  H6   0.020
 IS7  plan-1  H7   0.020
 IS7  plan-1  H11  0.020

