# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 12:19:32 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (3Z)-3-(1H-imidazol-5-ylmethylidene)-5-methoxy-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2NC(=O)\C(=C/c3[nH]cnc3)c2c1
#
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
 SU9  SU9  (3Z)-3-(1H-imidazol-5-ylmethylidene)-5-methoxy-1,3-dihydro-2H-indol-2-one  ligand  29  18  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SU9
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
 SU9  N5'   N  NR15  0  -0.642  -0.1572  -0.1200  -3.6559
 SU9  C4'   C  CR15  0   0.103   0.3837  -0.1265  -4.8757
 SU9  N3'   N  N     0  -0.436   1.7025  -0.0570  -4.8347
 SU9  C2'   C  CR15  0  -0.187   2.0126  -0.0036  -3.5238
 SU9  C1'   C  CR5   0   0.304   0.8655  -0.0407  -2.7471
 SU9  C6'   C  C1    0  -0.370   0.7768  -0.0131  -1.3280
 SU9  C9    C  C     0  -0.060  -0.2876  -0.0537  -0.4927
 SU9  C8    C  C     0   0.540  -1.7309  -0.1369  -0.8399
 SU9  O10   O  O     0  -0.490  -2.2630  -0.1844  -1.9445
 SU9  N7    N  NH1   0  -0.761  -2.4040  -0.1517   0.3390
 SU9  C5    C  CR6   0   0.363  -1.5460  -0.0870   1.4323
 SU9  C6    C  CR16  0  -0.284  -1.8317  -0.0809   2.7777
 SU9  C1    C  CR16  0  -0.402  -0.7691  -0.0109   3.6806
 SU9  C2    C  CR6   0   0.399   0.5480   0.0509   3.2276
 SU9  O11   O  O2    0  -0.478   1.6264   0.1183   4.0390
 SU9  C12   C  CH3   0  -0.435   1.4215   0.1027   5.4358
 SU9  C3    C  CR16  0  -0.481   0.8223   0.0447   1.8561
 SU9  C4    C  CR6   0   0.108  -0.2289  -0.0242   0.9632
 SU9  H5'   H  HNR5  0   0.439  -1.1398  -0.1621  -3.3862
 SU9  H4'   H  HCR5  0   0.288  -0.2133  -0.1831  -5.7728
 SU9  H2'   H  HCR5  0   0.273   3.0322   0.0582  -3.1726
 SU9  H6'   H  H     0   0.274   1.7524   0.0506  -0.8560
 SU9  HN7   H  HNH1  0   0.414  -3.4093  -0.1997   0.4004
 SU9  H6    H  HCR6  0   0.272  -2.8498  -0.1292   3.1413
 SU9  H1    H  HCR6  0   0.281  -0.9954  -0.0065   4.7379
 SU9  H121  H  HCH3  0   0.258   2.4069   0.1449   5.8937
 SU9  H122  H  HCH3  0   0.226   0.8403   0.9647   5.7755
 SU9  H123  H  HCH3  0   0.226   0.9194  -0.8109   5.7661
 SU9  H3    H  HCR6  0   0.258   1.8513   0.0920   1.5188

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
 SU9  N5'  C4'   aromatic  1.334  0.020  1.334
 SU9  N5'  C1'   aromatic  1.370  0.020  1.370
 SU9  N5'  H5'   single    0.860  0.020  1.020
 SU9  C4'  N3'   aromatic  1.321  0.020  1.321
 SU9  C4'  H4'   single    0.930  0.020  1.080
 SU9  N3'  C2'   aromatic  1.348  0.020  1.348
 SU9  C2'  C1'   aromatic  1.386  0.020  1.386
 SU9  C2'  H2'   single    0.930  0.020  1.080
 SU9  C1'  C6'   single    1.422  0.020  1.422
 SU9  C6'  C9    double    1.354  0.020  1.354
 SU9  C6'  H6'   single    0.930  0.020  1.080
 SU9  C9   C8    single    1.487  0.020  1.487
 SU9  C9   C4    single    1.457  0.020  1.457
 SU9  C8   O10   double    1.227  0.020  1.227
 SU9  C8   N7    single    1.358  0.020  1.358
 SU9  N7   C5    single    1.391  0.020  1.391
 SU9  N7   HN7   single    0.860  0.020  1.020
 SU9  C5   C6    aromatic  1.375  0.020  1.375
 SU9  C5   C4    aromatic  1.400  0.020  1.400
 SU9  C6   C1    aromatic  1.396  0.020  1.396
 SU9  C6   H6    single    0.930  0.020  1.080
 SU9  C1   C2    aromatic  1.394  0.020  1.394
 SU9  C1   H1    single    0.930  0.020  1.080
 SU9  C2   O11   single    1.351  0.020  1.351
 SU9  C2   C3    aromatic  1.399  0.020  1.399
 SU9  O11  C12   single    1.412  0.020  1.412
 SU9  C12  H121  single    0.970  0.020  1.090
 SU9  C12  H122  single    0.970  0.020  1.090
 SU9  C12  H123  single    0.970  0.020  1.090
 SU9  C3   C4    aromatic  1.381  0.020  1.381
 SU9  C3   H3    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
 SU9  H5'   N5'  C1'   123.09  3.000
 SU9  H5'   N5'  C4'   129.21  3.000
 SU9  C1'   N5'  C4'   107.70  3.000
 SU9  H4'   C4'  N3'   125.50  3.000
 SU9  H4'   C4'  N5'   122.41  3.000
 SU9  N3'   C4'  N5'   112.08  3.000
 SU9  C2'   N3'  C4'   105.18  3.000
 SU9  H2'   C2'  C1'   126.92  3.000
 SU9  H2'   C2'  N3'   122.38  3.000
 SU9  C1'   C2'  N3'   110.70  3.000
 SU9  C6'   C1'  C2'   127.62  3.000
 SU9  C6'   C1'  N5'   128.05  3.000
 SU9  C2'   C1'  N5'   104.33  3.000
 SU9  H6'   C6'  C9    116.11  3.000
 SU9  H6'   C6'  C1'   112.27  3.000
 SU9  C9    C6'  C1'   131.63  3.000
 SU9  C4    C9   C8    105.87  3.000
 SU9  C4    C9   C6'   125.75  3.000
 SU9  C8    C9   C6'   128.38  3.000
 SU9  N7    C8   O10   124.50  3.000
 SU9  N7    C8   C9    106.21  3.000
 SU9  O10   C8   C9    129.29  3.000
 SU9  HN7   N7   C5    124.70  3.000
 SU9  HN7   N7   C8    123.21  3.000
 SU9  C5    N7   C8    112.10  3.000
 SU9  C4    C5   C6    121.54  3.000
 SU9  C4    C5   N7    108.61  3.000
 SU9  C6    C5   N7    129.85  3.000
 SU9  H6    C6   C1    120.07  3.000
 SU9  H6    C6   C5    121.59  3.000
 SU9  C1    C6   C5    118.34  3.000
 SU9  H1    C1   C2    121.02  3.000
 SU9  H1    C1   C6    118.25  3.000
 SU9  C2    C1   C6    120.74  3.000
 SU9  C3    C2   O11   115.63  3.000
 SU9  C3    C2   C1    120.25  3.000
 SU9  O11   C2   C1    124.13  3.000
 SU9  C12   O11  C2    118.53  3.000
 SU9  H123  C12  H122  108.71  3.000
 SU9  H123  C12  H121  108.74  3.000
 SU9  H122  C12  H121  108.67  3.000
 SU9  H123  C12  O11   112.00  3.000
 SU9  H122  C12  O11   112.07  3.000
 SU9  H121  C12  O11   106.54  3.000
 SU9  H3    C3   C4    121.58  3.000
 SU9  H3    C3   C2    119.42  3.000
 SU9  C4    C3   C2    119.01  3.000
 SU9  C3    C4   C5    120.13  3.000
 SU9  C3    C4   C9    132.65  3.000
 SU9  C5    C4   C9    107.22  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
 SU9  CONST_01  C2'   N3'  C4'  N5'     0.00   0.0  0
 SU9  CONST_02  N3'   C2'  C1'  N5'     0.00   0.0  0
 SU9  CONST_03  C2'   C1'  N5'  C4'     0.00   0.0  0
 SU9  CONST_04  C1'   C2'  N3'  C4'     0.00   0.0  0
 SU9  CONST_05  C1'   N5'  C4'  N3'     0.00   0.0  0
 SU9  CONST_06  C2    C1   C6   C5      0.00   0.0  0
 SU9  CONST_07  C2    C3   C4   C5      0.00   0.0  0
 SU9  CONST_08  C3    C4   C5   C6      0.00   0.0  0
 SU9  CONST_09  C3    C2   C1   C6      0.00   0.0  0
 SU9  CONST_10  C4    C5   C6   C1      0.00   0.0  0
 SU9  CONST_11  C4    C3   C2   C1      0.00   0.0  0
 SU9  CONST_12  C5    N7   C8   C9      0.00   0.0  0
 SU9  CONST_13  C6'   C1'  N5'  C4'   180.00   0.0  0
 SU9  CONST_14  C6'   C1'  C2'  N3'   180.00   0.0  0
 SU9  CONST_15  O11   C2   C1   C6    180.00   0.0  0
 SU9  CONST_16  C4    C3   C2   O11   180.00   0.0  0
 SU9  CONST_17  C8    C9   C6'  C1'     0.00   0.0  0
 SU9  CONST_18  C4    C9   C6'  C1'   180.00   0.0  0
 SU9  CONST_19  C5    N7   C8   O10   180.00   0.0  0
 SU9  CONST_20  H2'   C2'  C1'  N5'   180.00   0.0  0
 SU9  CONST_21  H5'   N5'  C4'  N3'   180.00   0.0  0
 SU9  CONST_22  H4'   C4'  N3'  C2'   180.00   0.0  0
 SU9  CONST_23  H3    C3   C4   C9      0.00   0.0  0
 SU9  CONST_24  H6    C6   C5   N7      0.00   0.0  0
 SU9  CONST_25  H1    C1   C6   C5    180.00   0.0  0
 SU9  CONST_26  HN7   N7   C8   C9    180.00   0.0  0
 SU9  CONST_27  H6'   C6'  C9   C8    180.00   0.0  0
 SU9  Var_01    C9    C6'  C1'  N5'    -0.05  30.0  2
 SU9  Var_02    C3    C2   O11  C12  -178.82  30.0  1
 SU9  Var_03    H121  C12  O11  C2    178.91  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
 SU9  plan-1  N5'  0.020
 SU9  plan-1  C4'  0.020
 SU9  plan-1  N3'  0.020
 SU9  plan-1  C2'  0.020
 SU9  plan-1  C1'  0.020
 SU9  plan-1  C6'  0.020
 SU9  plan-1  H5'  0.020
 SU9  plan-1  H4'  0.020
 SU9  plan-1  H2'  0.020
 SU9  plan-2  C1'  0.020
 SU9  plan-2  C6'  0.020
 SU9  plan-2  C9   0.020
 SU9  plan-2  C8   0.020
 SU9  plan-2  O10  0.020
 SU9  plan-2  N7   0.020
 SU9  plan-2  C5   0.020
 SU9  plan-2  C6   0.020
 SU9  plan-2  C1   0.020
 SU9  plan-2  C2   0.020
 SU9  plan-2  O11  0.020
 SU9  plan-2  C3   0.020
 SU9  plan-2  C4   0.020
 SU9  plan-2  H6'  0.020
 SU9  plan-2  HN7  0.020
 SU9  plan-2  H6   0.020
 SU9  plan-2  H1   0.020
 SU9  plan-2  H3   0.020

