# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 17:53:31 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (3Z)-3-[(3,5-dimethyl-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]c(\C=C2/C(=O)Nc3ccccc23)c(C)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
 X2M  X2M  (3Z)-3-[(3,5-dimethyl-1H-pyrrol-2-yl)methylidene]-1,3-dihydro-2H-indol-2-one  ligand  32  18  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_X2M
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
 X2M  C3    C  CR5   0   0.524  -0.7038   1.5820  -0.2230
 X2M  C5    C  CR5   0  -0.075  -0.6879   0.1173  -0.0690
 X2M  C6    C  CR56  0   0.375  -2.8648   0.8625  -0.1120
 X2M  C7    C  CR56  0   0.077  -2.0811  -0.2946  -0.0024
 X2M  C8    C  CR16  0  -0.381  -2.7021  -1.5263   0.1402
 X2M  C9    C  CR16  0  -0.261  -4.0923  -1.5822   0.1712
 X2M  C10   C  CR16  0  -0.279  -4.8520  -0.4212   0.0609
 X2M  C11   C  CR16  0  -0.301  -4.2455   0.8245  -0.0832
 X2M  C19   C  C1    0  -0.371   0.3866  -0.7221   0.0027
 X2M  C21   C  CR5   0   0.301   1.7756  -0.4970  -0.0370
 X2M  O4    O  O     0  -0.500   0.2309   2.3763  -0.3193
 X2M  N1    N  NR15  0  -0.761  -2.0183   1.9506  -0.2420
 X2M  C26   C  CR5   0   0.049   2.7864  -1.4687   0.0502
 X2M  C25   C  CR15  0  -0.426   4.0037  -0.7859  -0.0180
 X2M  C24   C  CR5   0   0.342   3.7300   0.5737  -0.1446
 X2M  N22   N  NR15  0  -0.708   2.3985   0.7241  -0.1553
 X2M  CAB   C  CH3   0  -0.756   2.5970  -2.9434   0.1724
 X2M  CAA   C  CH3   0  -0.742   4.6677   1.7211  -0.2442
 X2M  H1    H  HNR5  0   0.410  -2.3199   2.9081  -0.3375
 X2M  H19   H  H     0   0.260   0.1373  -1.7731   0.1177
 X2M  H11   H  HCR6  0   0.265  -4.8384   1.7257  -0.1699
 X2M  H8    H  HCR6  0   0.248  -2.1202  -2.4362   0.2288
 X2M  H9    H  HCR6  0   0.252  -4.5868  -2.5380   0.2844
 X2M  H10   H  HCR6  0   0.255  -5.9319  -0.4831   0.0870
 X2M  H22   H  HNR5  0   0.427   1.8686   1.5918  -0.2356
 X2M  H25   H  HCR5  0   0.252   4.9909  -1.2209   0.0236
 X2M  HAB1  H  HCH3  0   0.251   2.2819  -3.3885  -0.7736
 X2M  HAB2  H  HCH3  0   0.254   3.5274  -3.4275   0.4648
 X2M  HAB3  H  HCH3  0   0.245   1.8433  -3.2024   0.9167
 X2M  HAA1  H  HCH3  0   0.258   4.5164   2.2852  -1.1660
 X2M  HAA2  H  HCH3  0   0.258   4.5376   2.4156   0.5875
 X2M  HAA3  H  HCH3  0   0.258   5.6967   1.3692  -0.2306

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
 X2M  C3   C5    single    1.473  0.020  1.473
 X2M  C3   O4    double    1.230  0.020  1.230
 X2M  C3   N1    single    1.365  0.020  1.365
 X2M  C5   C7    single    1.454  0.020  1.454
 X2M  C5   C19   double    1.365  0.020  1.365
 X2M  C6   C7    aromatic  1.402  0.020  1.402
 X2M  C6   C11   aromatic  1.381  0.020  1.381
 X2M  C6   N1    single    1.385  0.020  1.385
 X2M  C7   C8    aromatic  1.387  0.020  1.387
 X2M  C8   C9    aromatic  1.392  0.020  1.392
 X2M  C9   C10   aromatic  1.392  0.020  1.392
 X2M  C10  C11   aromatic  1.393  0.020  1.393
 X2M  C19  C21   single    1.408  0.020  1.408
 X2M  C21  C26   aromatic  1.405  0.020  1.405
 X2M  C21  N22   aromatic  1.376  0.020  1.376
 X2M  C26  C25   aromatic  1.397  0.020  1.397
 X2M  C26  CAB   single    1.492  0.020  1.492
 X2M  C25  C24   aromatic  1.393  0.020  1.393
 X2M  C24  N22   aromatic  1.340  0.020  1.340
 X2M  C24  CAA   single    1.485  0.020  1.485
 X2M  N1   H1    single    0.860  0.020  1.020
 X2M  C19  H19   single    0.930  0.020  1.080
 X2M  C11  H11   single    0.930  0.020  1.080
 X2M  C8   H8    single    0.930  0.020  1.080
 X2M  C9   H9    single    0.930  0.020  1.080
 X2M  C10  H10   single    0.930  0.020  1.080
 X2M  N22  H22   single    0.860  0.020  1.020
 X2M  C25  H25   single    0.930  0.020  1.080
 X2M  CAB  HAB1  single    0.970  0.020  1.090
 X2M  CAB  HAB2  single    0.970  0.020  1.090
 X2M  CAB  HAB3  single    0.970  0.020  1.090
 X2M  CAA  HAA1  single    0.970  0.020  1.090
 X2M  CAA  HAA2  single    0.970  0.020  1.090
 X2M  CAA  HAA3  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
 X2M  N1    C3   O4    123.79  3.000
 X2M  N1    C3   C5    106.28  3.000
 X2M  O4    C3   C5    129.94  3.000
 X2M  C19   C5   C7    125.27  3.000
 X2M  C19   C5   C3    128.71  3.000
 X2M  C7    C5   C3    106.03  3.000
 X2M  N1    C6   C11   129.39  3.000
 X2M  N1    C6   C7    108.31  3.000
 X2M  C11   C6   C7    122.30  3.000
 X2M  C8    C7   C6    119.39  3.000
 X2M  C8    C7   C5    133.25  3.000
 X2M  C6    C7   C5    107.35  3.000
 X2M  H8    C8   C9    120.06  3.000
 X2M  H8    C8   C7    120.91  3.000
 X2M  C9    C8   C7    119.03  3.000
 X2M  H9    C9   C10   119.71  3.000
 X2M  H9    C9   C8    119.62  3.000
 X2M  C10   C9   C8    120.67  3.000
 X2M  H10   C10  C11   119.22  3.000
 X2M  H10   C10  C9    119.68  3.000
 X2M  C11   C10  C9    121.10  3.000
 X2M  H11   C11  C10   120.96  3.000
 X2M  H11   C11  C6    121.53  3.000
 X2M  C10   C11  C6    117.51  3.000
 X2M  H19   C19  C21   112.59  3.000
 X2M  H19   C19  C5    114.82  3.000
 X2M  C21   C19  C5    132.59  3.000
 X2M  N22   C21  C26   107.06  3.000
 X2M  N22   C21  C19   126.23  3.000
 X2M  C26   C21  C19   126.71  3.000
 X2M  H1    N1   C6    124.90  3.000
 X2M  H1    N1   C3    123.06  3.000
 X2M  C6    N1   C3    112.03  3.000
 X2M  CAB   C26  C25   126.70  3.000
 X2M  CAB   C26  C21   126.68  3.000
 X2M  C25   C26  C21   106.61  3.000
 X2M  H25   C25  C24   125.21  3.000
 X2M  H25   C25  C26   126.72  3.000
 X2M  C24   C25  C26   108.07  3.000
 X2M  CAA   C24  N22   122.69  3.000
 X2M  CAA   C24  C25   129.51  3.000
 X2M  N22   C24  C25   107.79  3.000
 X2M  H22   N22  C24   127.77  3.000
 X2M  H22   N22  C21   121.77  3.000
 X2M  C24   N22  C21   110.46  3.000
 X2M  HAB3  CAB  HAB2  107.55  3.000
 X2M  HAB3  CAB  HAB1  107.16  3.000
 X2M  HAB2  CAB  HAB1  107.34  3.000
 X2M  HAB3  CAB  C26   112.24  3.000
 X2M  HAB2  CAB  C26   110.67  3.000
 X2M  HAB1  CAB  C26   111.64  3.000
 X2M  HAA3  CAA  HAA2  108.01  3.000
 X2M  HAA3  CAA  HAA1  108.00  3.000
 X2M  HAA2  CAA  HAA1  107.36  3.000
 X2M  HAA3  CAA  C24   110.28  3.000
 X2M  HAA2  CAA  C24   111.42  3.000
 X2M  HAA1  CAA  C24   111.62  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
 X2M  CONST_01  C9    C8   C7   C6     0.00   0.0  0
 X2M  CONST_02  C9    C10  C11  C6     0.00   0.0  0
 X2M  CONST_03  C10   C11  C6   C7     0.00   0.0  0
 X2M  CONST_04  C10   C9   C8   C7     0.00   0.0  0
 X2M  CONST_05  C11   C6   C7   C8     0.00   0.0  0
 X2M  CONST_06  C11   C10  C9   C8     0.00   0.0  0
 X2M  CONST_07  C24   C25  C26  C21    0.00   0.0  0
 X2M  CONST_08  C25   C24  N22  C21    0.00   0.0  0
 X2M  CONST_09  C24   N22  C21  C26    0.00   0.0  0
 X2M  CONST_10  N22   C24  C25  C26    0.00   0.0  0
 X2M  CONST_11  N22   C21  C26  C25    0.00   0.0  0
 X2M  CONST_12  C6    N1   C3   C5     0.00   0.0  0
 X2M  CONST_13  C25   C26  C21  C19  180.00   0.0  0
 X2M  CONST_14  C24   N22  C21  C19  180.00   0.0  0
 X2M  CONST_15  CAA   C24  N22  C21  180.00   0.0  0
 X2M  CONST_16  CAA   C24  C25  C26  180.00   0.0  0
 X2M  CONST_17  CAB   C26  C25  C24  180.00   0.0  0
 X2M  CONST_18  CAB   C26  C21  N22  180.00   0.0  0
 X2M  CONST_19  O4    C3   N1   C6   180.00   0.0  0
 X2M  CONST_20  H8    C8   C7   C5     0.00   0.0  0
 X2M  CONST_21  H10   C10  C11  C6   180.00   0.0  0
 X2M  CONST_22  H11   C11  C6   C7   180.00   0.0  0
 X2M  CONST_23  H9    C9   C8   C7   180.00   0.0  0
 X2M  CONST_24  H25   C25  C26  C21  180.00   0.0  0
 X2M  CONST_25  H22   N22  C21  C26  180.00   0.0  0
 X2M  CONST_26  H1    N1   C3   C5   180.00   0.0  0
 X2M  Var_01    C21   C19  C5   C3     0.30  30.0  2
 X2M  Var_02    C26   C21  C19  C5   179.93  30.0  2
 X2M  Var_03    HAB1  CAB  C26  C21   74.45  30.0  2
 X2M  Var_04    HAA1  CAA  C24  C25  121.46  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
 X2M  plan-1  C19  0.020
 X2M  plan-1  C21  0.020
 X2M  plan-1  C26  0.020
 X2M  plan-1  C25  0.020
 X2M  plan-1  C24  0.020
 X2M  plan-1  N22  0.020
 X2M  plan-1  CAB  0.020
 X2M  plan-1  CAA  0.020
 X2M  plan-1  H22  0.020
 X2M  plan-1  H25  0.020
 X2M  plan-2  C3   0.020
 X2M  plan-2  C5   0.020
 X2M  plan-2  C6   0.020
 X2M  plan-2  C7   0.020
 X2M  plan-2  C8   0.020
 X2M  plan-2  C9   0.020
 X2M  plan-2  C10  0.020
 X2M  plan-2  C11  0.020
 X2M  plan-2  C19  0.020
 X2M  plan-2  O4   0.020
 X2M  plan-2  N1   0.020
 X2M  plan-2  H1   0.020
 X2M  plan-2  H11  0.020
 X2M  plan-2  H8   0.020
 X2M  plan-2  H9   0.020
 X2M  plan-2  H10  0.020

