# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 12 22:07:21 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN\1CCCC\1=C\2C=Nc3ccccc\23
#
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
 9UL  9UL  (3~{Z})-3-(1-methylpyrrolidin-2-ylidene)indole  ligand  29  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9UL
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
 9UL  C10  C  CR56  0   0.183   2.1113  -0.8318   0.1582
 9UL  C11  C  CR56  0   0.077   1.1549   0.2002   0.0033
 9UL  C12  C  CR16  0  -0.398   1.5954   1.5081  -0.2151
 9UL  C13  C  CR16  0  -0.265   2.9578   1.7641  -0.2535
 9UL  C14  C  CR16  0  -0.285   3.8944   0.7386  -0.0862
 9UL  C15  C  CR16  0  -0.326   3.4779  -0.5663   0.1166
 9UL  N02  N  NT    0  -0.458  -2.5638  -0.4651  -0.0232
 9UL  C03  C  CH2   0  -0.277  -3.6903   0.4634  -0.0861
 9UL  C04  C  CH2   0  -0.486  -3.0811   1.7829   0.3586
 9UL  C05  C  CH2   0  -0.564  -1.5980   1.6185   0.0313
 9UL  C06  C  C     0   0.386  -1.3850   0.1311   0.0412
 9UL  C07  C  CR5   0  -0.073  -0.1275  -0.4671   0.0879
 9UL  C08  C  CR15  0  -0.126   0.2235  -1.8445   0.2872
 9UL  N09  N  N     0  -0.475   1.5124  -2.0612   0.3393
 9UL  H1   H  HCR6  0   0.245   0.9050   2.3269  -0.3630
 9UL  H2   H  HCR6  0   0.243   3.3011   2.7772  -0.4215
 9UL  H3   H  HCR6  0   0.242   4.9519   0.9676  -0.1222
 9UL  H4   H  HCR6  0   0.240   4.1953  -1.3689   0.2375
 9UL  H5   H  HCH3  0   0.263  -2.6130  -2.4217   0.7446
 9UL  H6   H  HCH3  0   0.281  -3.8394  -2.0322  -0.4612
 9UL  H7   H  HCH3  0   0.259  -2.1695  -2.2925  -0.9694
 9UL  H8   H  HCH2  0   0.260  -4.0744   0.4992  -1.1096
 9UL  H9   H  HCH2  0   0.267  -3.5311   2.6370  -0.1419
 9UL  H10  H  HCH2  0   0.283  -1.3549   2.0026  -0.9641
 9UL  H11  H  HCR5  0   0.249  -0.4611  -2.6686   0.4291
 9UL  H13  H  HCH2  0   0.281  -0.9504   2.1274   0.7429
 9UL  H14  H  HCH2  0   0.261  -3.2134   1.9134   1.4326
 9UL  H15  H  HCH2  0   0.266  -4.4952   0.1191   0.5630
 9UL  C01  C  CH3   0  -0.554  -2.8006  -1.8789  -0.1822

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
 9UL  C04  C03  single    1.520  0.020  1.520
 9UL  C04  C05  single    1.528  0.020  1.528
 9UL  C03  N02  single    1.461  0.020  1.461
 9UL  C05  C06  single    1.503  0.020  1.503
 9UL  N02  C01  single    1.442  0.020  1.442
 9UL  N02  C06  single    1.323  0.020  1.323
 9UL  C06  C07  double    1.393  0.020  1.393
 9UL  C07  C11  single    1.448  0.020  1.448
 9UL  C07  C08  single    1.435  0.020  1.435
 9UL  C12  C11  aromatic  1.397  0.020  1.397
 9UL  C12  C13  aromatic  1.387  0.020  1.387
 9UL  C11  C10  aromatic  1.416  0.020  1.416
 9UL  C08  N09  double    1.308  0.020  1.308
 9UL  C13  C14  aromatic  1.399  0.020  1.399
 9UL  C10  N09  single    1.379  0.020  1.379
 9UL  C10  C15  aromatic  1.393  0.020  1.393
 9UL  C14  C15  aromatic  1.385  0.020  1.385
 9UL  C12  H1   single    0.930  0.020  1.080
 9UL  C13  H2   single    0.930  0.020  1.080
 9UL  C14  H3   single    0.930  0.020  1.080
 9UL  C15  H4   single    0.930  0.020  1.080
 9UL  C01  H5   single    0.970  0.020  1.090
 9UL  C01  H6   single    0.970  0.020  1.090
 9UL  C01  H7   single    0.970  0.020  1.090
 9UL  C03  H8   single    0.970  0.020  1.090
 9UL  C04  H9   single    0.970  0.020  1.090
 9UL  C05  H10  single    0.970  0.020  1.090
 9UL  C08  H11  single    0.930  0.020  1.080
 9UL  C05  H13  single    0.970  0.020  1.090
 9UL  C04  H14  single    0.970  0.020  1.090
 9UL  C03  H15  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
 9UL  N09  C10  C15  126.86  3.000
 9UL  C15  C10  C11  121.38  3.000
 9UL  N09  C10  C11  111.76  3.000
 9UL  C07  C11  C12  136.03  3.000
 9UL  C12  C11  C10  119.11  3.000
 9UL  C07  C11  C10  104.83  3.000
 9UL  H1   C12  C13  118.93  3.000
 9UL  H1   C12  C11  121.93  3.000
 9UL  C13  C12  C11  119.13  3.000
 9UL  H2   C13  C14  119.48  3.000
 9UL  H2   C13  C12  119.24  3.000
 9UL  C14  C13  C12  121.27  3.000
 9UL  H3   C14  C15  119.87  3.000
 9UL  H3   C14  C13  119.67  3.000
 9UL  C15  C14  C13  120.46  3.000
 9UL  H4   C15  C14  121.02  3.000
 9UL  H4   C15  C10  120.35  3.000
 9UL  C14  C15  C10  118.63  3.000
 9UL  C06  N02  C03  113.75  3.000
 9UL  C06  N02  C01  126.41  3.000
 9UL  C03  N02  C01  119.45  3.000
 9UL  H15  C03  H8   107.96  3.000
 9UL  H15  C03  C04  113.33  3.000
 9UL  H8   C03  C04  112.71  3.000
 9UL  H15  C03  N02  110.06  3.000
 9UL  H8   C03  N02  109.37  3.000
 9UL  C04  C03  N02  103.30  3.000
 9UL  H14  C04  H9   108.01  3.000
 9UL  H14  C04  C05  109.99  3.000
 9UL  H9   C04  C05  112.81  3.000
 9UL  H14  C04  C03  110.09  3.000
 9UL  H9   C04  C03  112.41  3.000
 9UL  C05  C04  C03  103.48  3.000
 9UL  H13  C05  H10  107.36  3.000
 9UL  H13  C05  C06  111.97  3.000
 9UL  H10  C05  C06  108.79  3.000
 9UL  H13  C05  C04  112.78  3.000
 9UL  H10  C05  C04  111.88  3.000
 9UL  C06  C05  C04  104.05  3.000
 9UL  C07  C06  C05  123.59  3.000
 9UL  C07  C06  N02  127.77  3.000
 9UL  C05  C06  N02  108.64  3.000
 9UL  C08  C07  C06  129.60  3.000
 9UL  C08  C07  C11  103.52  3.000
 9UL  C06  C07  C11  126.83  3.000
 9UL  H11  C08  N09  119.51  3.000
 9UL  H11  C08  C07  126.52  3.000
 9UL  N09  C08  C07  113.92  3.000
 9UL  C08  N09  C10  105.96  3.000
 9UL  H7   C01  H6   108.33  3.000
 9UL  H7   C01  H5   108.98  3.000
 9UL  H6   C01  H5   108.22  3.000
 9UL  H7   C01  N02  110.88  3.000
 9UL  H6   C01  N02  108.88  3.000
 9UL  H5   C01  N02  111.47  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
 9UL  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 9UL  CONST_02  C13  C14  C15  C10     0.00   0.0  0
 9UL  CONST_03  C14  C13  C12  C11     0.00   0.0  0
 9UL  CONST_04  C14  C15  C10  C11     0.00   0.0  0
 9UL  CONST_05  C15  C10  C11  C12     0.00   0.0  0
 9UL  CONST_06  C15  C14  C13  C12     0.00   0.0  0
 9UL  CONST_07  H1   C12  C11  C10   180.00   0.0  0
 9UL  CONST_08  H3   C14  C15  C10   180.00   0.0  0
 9UL  CONST_09  H2   C13  C12  C11   180.00   0.0  0
 9UL  CONST_10  H4   C15  C10  C11   180.00   0.0  0
 9UL  Var_01    C05  C06  C07  C11    -6.46  30.0  3
 9UL  Var_02    C05  C04  C03  N02    24.49  30.0  1
 9UL  Var_03    C04  C05  C06  N02    15.93  30.0  1
 9UL  Var_04    C06  C05  C04  C03   -24.68  30.0  1
 9UL  Var_05    C06  N02  C03  C04   -16.16  30.0  1
 9UL  Var_06    H5   C01  N02  C03  -112.16  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
 9UL  plan-1  C10  0.020
 9UL  plan-1  C11  0.020
 9UL  plan-1  C12  0.020
 9UL  plan-1  C13  0.020
 9UL  plan-1  C14  0.020
 9UL  plan-1  C15  0.020
 9UL  plan-1  C06  0.020
 9UL  plan-1  C07  0.020
 9UL  plan-1  C08  0.020
 9UL  plan-1  N09  0.020
 9UL  plan-1  H1   0.020
 9UL  plan-1  H2   0.020
 9UL  plan-1  H3   0.020
 9UL  plan-1  H4   0.020
 9UL  plan-1  H11  0.020
 9UL  plan-2  N02  0.020
 9UL  plan-2  C03  0.020
 9UL  plan-2  C06  0.020
 9UL  plan-2  C01  0.020

