# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 03:40:24 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (3E)-3-[(2,4,6-trimethoxyphenyl)methylidene]-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cc(OC)c(/C=C2/C(=O)Nc3ccccc23)c(OC)c1
#
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
 IC1  IC1  (3E)-3-[(2,4,6-trimethoxyphenyl)methylidene]-1,3-dihydro-2H-indol-2-one  ligand  40  23  .  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_IC1
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
 IC1  N1    N  NR15  0  -0.772  -0.7080  -0.1171  -3.9250
 IC1  C2    C  CR5   0   0.514  -1.5171  -0.4819  -2.8889
 IC1  O2    O  O     0  -0.457  -2.6260  -0.9730  -2.9902
 IC1  C3    C  CR5   0  -0.012  -0.7555  -0.1696  -1.6413
 IC1  C4    C  CR16  0  -0.360   1.5781   0.9979  -1.4123
 IC1  C5    C  CR16  0  -0.266   2.6250   1.5366  -2.1552
 IC1  C6    C  CR16  0  -0.270   2.5969   1.5082  -3.5446
 IC1  C7    C  CR16  0  -0.306   1.5143   0.9623  -4.2297
 IC1  C8    C  CR56  0   0.373   0.4809   0.4391  -3.4778
 IC1  C9    C  CR56  0   0.053   0.5011   0.4268  -2.0738
 IC1  C10   C  C1    0  -0.281  -1.3109  -0.4081  -0.4403
 IC1  C1'   C  CR6   0  -0.179  -0.7152  -0.2739   0.8789
 IC1  C2'   C  CR6   0   0.402  -1.4619   0.3255   1.9132
 IC1  C3'   C  CR16  0  -0.518  -0.9560   0.4470   3.1961
 IC1  C4'   C  CR6   0   0.448   0.3154  -0.0580   3.4746
 IC1  C5'   C  CR16  0  -0.566   1.0668  -0.6937   2.4919
 IC1  C6'   C  CR6   0   0.415   0.5392  -0.8105   1.2063
 IC1  O2'   O  O2    0  -0.461  -2.6659   0.7863   1.5473
 IC1  O4'   O  O2    0  -0.467   0.7366   0.1103   4.7352
 IC1  O6'   O  O2    0  -0.455   1.1686  -1.4636   0.2241
 IC1  C11   C  CH3   0  -0.439  -3.5118   1.3568   2.5288
 IC1  C12   C  CH3   0  -0.442   2.0186  -0.3633   5.1054
 IC1  C13   C  CH3   0  -0.444   2.4728  -1.9663   0.4407
 IC1  HN1   H  HNR5  0   0.410  -0.9691  -0.2059  -4.8948
 IC1  H41   H  HCR6  0   0.247   1.6112   1.0523  -0.3335
 IC1  H51   H  HCR6  0   0.254   3.4687   1.9806  -1.6443
 IC1  H61   H  HCR6  0   0.259   3.4228   1.9251  -4.1060
 IC1  H71   H  HCR6  0   0.266   1.4825   0.9571  -5.3114
 IC1  H101  H  H     0   0.270  -2.3464  -0.7370  -0.4645
 IC1  H3'1  H  HCR6  0   0.285  -1.5072   0.9362   3.9873
 IC1  H5'1  H  HCR6  0   0.303   2.0357  -1.1091   2.7223
 IC1  H111  H  HCH3  0   0.265  -4.4362   1.6183   2.0206
 IC1  H112  H  HCH3  0   0.233  -3.7367   0.6505   3.3311
 IC1  H113  H  HCH3  0   0.233  -3.0776   2.2613   2.9607
 IC1  H121  H  HCH3  0   0.265   2.1500  -0.1041   6.1525
 IC1  H122  H  HCH3  0   0.233   2.0980  -1.4479   4.9999
 IC1  H123  H  HCH3  0   0.234   2.8113   0.1096   4.5212
 IC1  H131  H  HCH3  0   0.265   2.7806  -2.4237  -0.4958
 IC1  H132  H  HCH3  0   0.232   3.1796  -1.1716   0.6922
 IC1  H133  H  HCH3  0   0.236   2.4936  -2.7249   1.2267

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
 IC1  N1   C2    single    1.364  0.020  1.364
 IC1  N1   C8    single    1.387  0.020  1.387
 IC1  N1   HN1   single    0.860  0.020  1.020
 IC1  C2   O2    double    1.217  0.020  1.217
 IC1  C2   C3    single    1.495  0.020  1.495
 IC1  C3   C9    single    1.457  0.020  1.457
 IC1  C3   C10   double    1.345  0.020  1.345
 IC1  C4   C5    aromatic  1.392  0.020  1.392
 IC1  C4   C9    aromatic  1.387  0.020  1.387
 IC1  C4   H41   single    0.930  0.020  1.080
 IC1  C5   C6    aromatic  1.390  0.020  1.390
 IC1  C5   H51   single    0.930  0.020  1.080
 IC1  C6   C7    aromatic  1.393  0.020  1.393
 IC1  C6   H61   single    0.930  0.020  1.080
 IC1  C7   C8    aromatic  1.381  0.020  1.381
 IC1  C7   H71   single    0.930  0.020  1.080
 IC1  C8   C9    aromatic  1.404  0.020  1.404
 IC1  C10  C1'   single    1.454  0.020  1.454
 IC1  C10  H101  single    0.930  0.020  1.080
 IC1  C1'  C2'   aromatic  1.409  0.020  1.409
 IC1  C1'  C6'   aromatic  1.403  0.020  1.403
 IC1  C2'  C3'   aromatic  1.384  0.020  1.384
 IC1  C2'  O2'   single    1.340  0.020  1.340
 IC1  C3'  C4'   aromatic  1.396  0.020  1.396
 IC1  C3'  H3'1  single    0.930  0.020  1.080
 IC1  C4'  C5'   aromatic  1.391  0.020  1.391
 IC1  C4'  O4'   single    1.340  0.020  1.340
 IC1  C5'  C6'   aromatic  1.395  0.020  1.395
 IC1  C5'  H5'1  single    0.930  0.020  1.080
 IC1  C6'  O6'   single    1.337  0.020  1.337
 IC1  O2'  C11   single    1.416  0.020  1.416
 IC1  O4'  C12   single    1.416  0.020  1.416
 IC1  O6'  C13   single    1.414  0.020  1.414
 IC1  C11  H111  single    0.970  0.020  1.090
 IC1  C11  H112  single    0.970  0.020  1.090
 IC1  C11  H113  single    0.970  0.020  1.090
 IC1  C12  H121  single    0.970  0.020  1.090
 IC1  C12  H122  single    0.970  0.020  1.090
 IC1  C12  H123  single    0.970  0.020  1.090
 IC1  C13  H131  single    0.970  0.020  1.090
 IC1  C13  H132  single    0.970  0.020  1.090
 IC1  C13  H133  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
 IC1  HN1   N1   C8    124.59  3.000
 IC1  HN1   N1   C2    123.60  3.000
 IC1  C8    N1   C2    111.76  3.000
 IC1  C3    C2   O2    128.18  3.000
 IC1  C3    C2   N1    106.02  3.000
 IC1  O2    C2   N1    125.81  3.000
 IC1  C10   C3   C9    133.96  3.000
 IC1  C10   C3   C2    119.87  3.000
 IC1  C9    C3   C2    106.10  3.000
 IC1  H41   C4   C9    121.37  3.000
 IC1  H41   C4   C5    119.36  3.000
 IC1  C9    C4   C5    119.26  3.000
 IC1  H51   C5   C6    119.75  3.000
 IC1  H51   C5   C4    119.56  3.000
 IC1  C6    C5   C4    120.69  3.000
 IC1  H61   C6   C7    119.28  3.000
 IC1  H61   C6   C5    119.69  3.000
 IC1  C7    C6   C5    121.03  3.000
 IC1  H71   C7   C8    121.36  3.000
 IC1  H71   C7   C6    121.09  3.000
 IC1  C8    C7   C6    117.54  3.000
 IC1  C9    C8   C7    122.47  3.000
 IC1  C9    C8   N1    109.35  3.000
 IC1  C7    C8   N1    128.17  3.000
 IC1  C8    C9   C4    118.98  3.000
 IC1  C8    C9   C3    106.74  3.000
 IC1  C4    C9   C3    134.17  3.000
 IC1  H101  C10  C1'   116.02  3.000
 IC1  H101  C10  C3    115.30  3.000
 IC1  C1'   C10  C3    128.68  3.000
 IC1  C6'   C1'  C2'   117.71  3.000
 IC1  C6'   C1'  C10   122.87  3.000
 IC1  C2'   C1'  C10   119.22  3.000
 IC1  O2'   C2'  C3'   123.45  3.000
 IC1  O2'   C2'  C1'   114.95  3.000
 IC1  C3'   C2'  C1'   121.59  3.000
 IC1  H3'1  C3'  C4'   118.81  3.000
 IC1  H3'1  C3'  C2'   122.11  3.000
 IC1  C4'   C3'  C2'   119.07  3.000
 IC1  O4'   C4'  C5'   123.53  3.000
 IC1  O4'   C4'  C3'   115.37  3.000
 IC1  C5'   C4'  C3'   121.09  3.000
 IC1  H5'1  C5'  C6'   120.29  3.000
 IC1  H5'1  C5'  C4'   120.67  3.000
 IC1  C6'   C5'  C4'   119.03  3.000
 IC1  O6'   C6'  C5'   122.69  3.000
 IC1  O6'   C6'  C1'   115.87  3.000
 IC1  C5'   C6'  C1'   121.42  3.000
 IC1  C11   O2'  C2'   119.09  3.000
 IC1  C12   O4'  C4'   119.25  3.000
 IC1  C13   O6'  C6'   119.69  3.000
 IC1  H113  C11  H112  109.07  3.000
 IC1  H113  C11  H111  108.90  3.000
 IC1  H112  C11  H111  108.90  3.000
 IC1  H113  C11  O2'   111.73  3.000
 IC1  H112  C11  O2'   111.82  3.000
 IC1  H111  C11  O2'   106.32  3.000
 IC1  H123  C12  H122  108.99  3.000
 IC1  H123  C12  H121  108.92  3.000
 IC1  H122  C12  H121  108.73  3.000
 IC1  H123  C12  O4'   111.86  3.000
 IC1  H122  C12  O4'   111.88  3.000
 IC1  H121  C12  O4'   106.35  3.000
 IC1  H133  C13  H132  109.09  3.000
 IC1  H133  C13  H131  108.80  3.000
 IC1  H132  C13  H131  108.74  3.000
 IC1  H133  C13  O6'   111.99  3.000
 IC1  H132  C13  O6'   111.91  3.000
 IC1  H131  C13  O6'   106.19  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
 IC1  CONST_01  C7    C6   C5   C4      0.00   0.0  0
 IC1  CONST_02  C7    C8   C9   C4      0.00   0.0  0
 IC1  CONST_03  C8    C9   C4   C5      0.00   0.0  0
 IC1  CONST_04  C8    C7   C6   C5      0.00   0.0  0
 IC1  CONST_05  C9    C4   C5   C6      0.00   0.0  0
 IC1  CONST_06  C9    C8   C7   C6      0.00   0.0  0
 IC1  CONST_07  C4'   C3'  C2'  C1'     0.00   0.0  0
 IC1  CONST_08  C4'   C5'  C6'  C1'     0.00   0.0  0
 IC1  CONST_09  C5'   C6'  C1'  C2'     0.00   0.0  0
 IC1  CONST_10  C5'   C4'  C3'  C2'     0.00   0.0  0
 IC1  CONST_11  C6'   C1'  C2'  C3'     0.00   0.0  0
 IC1  CONST_12  C6'   C5'  C4'  C3'     0.00   0.0  0
 IC1  CONST_13  C8    N1   C2   C3      0.00   0.0  0
 IC1  CONST_14  C3'   C2'  C1'  C10   180.00   0.0  0
 IC1  CONST_15  C5'   C6'  C1'  C10   180.00   0.0  0
 IC1  CONST_16  O6'   C6'  C1'  C2'   180.00   0.0  0
 IC1  CONST_17  O4'   C4'  C3'  C2'   180.00   0.0  0
 IC1  CONST_18  O2'   C2'  C3'  C4'   180.00   0.0  0
 IC1  CONST_19  O6'   C6'  C5'  C4'   180.00   0.0  0
 IC1  CONST_20  O2'   C2'  C1'  C6'   180.00   0.0  0
 IC1  CONST_21  O4'   C4'  C5'  C6'   180.00   0.0  0
 IC1  CONST_22  C8    N1   C2   O2    180.00   0.0  0
 IC1  CONST_23  H71   C7   C8   N1      0.00   0.0  0
 IC1  CONST_24  H41   C4   C9   C3      0.00   0.0  0
 IC1  CONST_25  H61   C6   C5   C4    180.00   0.0  0
 IC1  CONST_26  H51   C5   C6   C7    180.00   0.0  0
 IC1  CONST_27  H3'1  C3'  C2'  C1'   180.00   0.0  0
 IC1  CONST_28  H5'1  C5'  C6'  C1'   180.00   0.0  0
 IC1  CONST_29  HN1   N1   C2   C3    180.00   0.0  0
 IC1  Var_01    C1'   C10  C3   C2    174.95  30.0  2
 IC1  Var_02    C2'   C1'  C10  C3    136.45  30.0  2
 IC1  Var_03    H111  C11  O2'  C2'  -177.68  30.0  3
 IC1  Var_04    H121  C12  O4'  C4'   178.99  30.0  3
 IC1  Var_05    H131  C13  O6'  C6'  -178.38  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
 IC1  plan-1  C10   0.020
 IC1  plan-1  C1'   0.020
 IC1  plan-1  C2'   0.020
 IC1  plan-1  C3'   0.020
 IC1  plan-1  C4'   0.020
 IC1  plan-1  C5'   0.020
 IC1  plan-1  C6'   0.020
 IC1  plan-1  O2'   0.020
 IC1  plan-1  O4'   0.020
 IC1  plan-1  O6'   0.020
 IC1  plan-1  H3'1  0.020
 IC1  plan-1  H5'1  0.020
 IC1  plan-2  N1    0.020
 IC1  plan-2  C2    0.020
 IC1  plan-2  O2    0.020
 IC1  plan-2  C3    0.020
 IC1  plan-2  C4    0.020
 IC1  plan-2  C5    0.020
 IC1  plan-2  C6    0.020
 IC1  plan-2  C7    0.020
 IC1  plan-2  C8    0.020
 IC1  plan-2  C9    0.020
 IC1  plan-2  C10   0.020
 IC1  plan-2  HN1   0.020
 IC1  plan-2  H41   0.020
 IC1  plan-2  H51   0.020
 IC1  plan-2  H61   0.020
 IC1  plan-2  H71   0.020

