# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 00:46:51 2020
#   Inital geometry file: a 49 line input string
#   Ligand name: 2,3-dihydro-1H-indole
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C1Cc2ccccc2N1
#
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
 IDM  IDM  '2,3-dihydro-1H-indole    '  ligand  18  9  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IDM
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
 IDM  N1   N  NR15  0  -0.711   1.1308   0.2939  -1.5097
 IDM  C2   C  CH2   0  -0.216   0.0552  -0.0568  -2.4393
 IDM  C3   C  CH2   0  -0.521  -1.2373   0.0813  -1.6038
 IDM  C4A  C  CR56  0  -0.022  -0.7261   0.0413  -0.1890
 IDM  C4   C  CR16  0  -0.328  -1.3986  -0.0552   1.0112
 IDM  C5   C  CR16  0  -0.290  -0.6734  -0.0721   2.2051
 IDM  C6   C  CR16  0  -0.214   0.7103   0.0041   2.1725
 IDM  C7   C  CR16  0  -0.363   1.4004   0.1113   0.9663
 IDM  C7A  C  CR56  0   0.425   0.6675   0.1410  -0.2129
 IDM  HN1  H  HNR5  0   0.377   2.0332  -0.1158  -1.7028
 IDM  H21  H  HCH2  0   0.175   0.1593  -1.0818  -2.8110
 IDM  H22  H  HCH2  0   0.234   0.0631   0.6070  -3.3031
 IDM  H31  H  HCH2  0   0.239  -1.7615   1.0155  -1.8223
 IDM  H32  H  HCH2  0   0.231  -1.9348  -0.7291  -1.8180
 IDM  H4   H  HCR6  0   0.247  -2.4799  -0.1299   1.0349
 IDM  H5   H  HCR6  0   0.250  -1.1921  -0.1552   3.1506
 IDM  H6   H  HCR6  0   0.260   1.2718  -0.0163   3.0960
 IDM  H7   H  HCR6  0   0.226   2.4818   0.1760   0.9541

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
 IDM  N1   C2   single    1.464  0.020  1.464
 IDM  N1   C7A  single    1.386  0.020  1.386
 IDM  N1   HN1  single    0.890  0.020  1.040
 IDM  C2   C3   single    1.545  0.020  1.545
 IDM  C2   H21  single    0.970  0.020  1.090
 IDM  C2   H22  single    0.970  0.020  1.090
 IDM  C3   C4A  single    1.505  0.020  1.505
 IDM  C3   H31  single    0.970  0.020  1.090
 IDM  C3   H32  single    0.970  0.020  1.090
 IDM  C4A  C4   aromatic  1.379  0.020  1.379
 IDM  C4A  C7A  aromatic  1.397  0.020  1.397
 IDM  C4   C5   aromatic  1.397  0.020  1.397
 IDM  C4   H4   single    0.930  0.020  1.080
 IDM  C5   C6   aromatic  1.386  0.020  1.386
 IDM  C5   H5   single    0.930  0.020  1.080
 IDM  C6   C7   aromatic  1.394  0.020  1.394
 IDM  C6   H6   single    0.930  0.020  1.080
 IDM  C7   C7A  aromatic  1.389  0.020  1.389
 IDM  C7   H7   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
 IDM  HN1  N1   C7A  115.66  3.000
 IDM  HN1  N1   C2   115.97  3.000
 IDM  C7A  N1   C2   108.79  3.000
 IDM  H22  C2   H21  107.49  3.000
 IDM  H22  C2   C3   112.35  3.000
 IDM  H21  C2   C3   110.28  3.000
 IDM  H22  C2   N1   110.62  3.000
 IDM  H21  C2   N1   111.71  3.000
 IDM  C3   C2   N1   104.47  3.000
 IDM  H32  C3   H31  106.81  3.000
 IDM  H32  C3   C4A  112.47  3.000
 IDM  H31  C3   C4A  111.93  3.000
 IDM  H32  C3   C2   111.25  3.000
 IDM  H31  C3   C2   111.68  3.000
 IDM  C4A  C3   C2   102.81  3.000
 IDM  C7A  C4A  C4   120.41  3.000
 IDM  C7A  C4A  C3   108.71  3.000
 IDM  C4   C4A  C3   130.87  3.000
 IDM  H4   C4   C5   119.88  3.000
 IDM  H4   C4   C4A  120.68  3.000
 IDM  C5   C4   C4A  119.43  3.000
 IDM  H5   C5   C6   120.23  3.000
 IDM  H5   C5   C4   119.94  3.000
 IDM  C6   C5   C4   119.83  3.000
 IDM  H6   C6   C7   118.92  3.000
 IDM  H6   C6   C5   119.82  3.000
 IDM  C7   C6   C5   121.26  3.000
 IDM  H7   C7   C7A  121.07  3.000
 IDM  H7   C7   C6   120.57  3.000
 IDM  C7A  C7   C6   118.37  3.000
 IDM  C7   C7A  C4A  120.68  3.000
 IDM  C7   C7A  N1   128.36  3.000
 IDM  C4A  C7A  N1   110.94  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
 IDM  CONST_01  C6   C5   C4   C4A     0.00   0.0  0
 IDM  CONST_02  C6   C7   C7A  C4A     0.00   0.0  0
 IDM  CONST_03  C7   C7A  C4A  C4      0.00   0.0  0
 IDM  CONST_04  C7   C6   C5   C4      0.00   0.0  0
 IDM  CONST_05  C7A  C4A  C4   C5      0.00   0.0  0
 IDM  CONST_06  C7A  C7   C6   C5      0.00   0.0  0
 IDM  CONST_07  H7   C7   C7A  N1      0.00   0.0  0
 IDM  CONST_08  H4   C4   C4A  C3      0.00   0.0  0
 IDM  CONST_09  H5   C5   C4   C4A   180.00   0.0  0
 IDM  CONST_10  H6   C6   C5   C4    180.00   0.0  0
 IDM  Var_01    C4A  C3   C2   N1    -18.50  30.0  1
 IDM  Var_02    C4A  C7A  N1   C2    -15.03  30.0  1
 IDM  Var_03    C4   C4A  C3   C2   -170.40  30.0  1
 IDM  Var_04    C7A  N1   C2   C3     20.91  30.0  1

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
 IDM  plan-1  N1   0.020
 IDM  plan-1  C3   0.020
 IDM  plan-1  C4A  0.020
 IDM  plan-1  C4   0.020
 IDM  plan-1  C5   0.020
 IDM  plan-1  C6   0.020
 IDM  plan-1  C7   0.020
 IDM  plan-1  C7A  0.020
 IDM  plan-1  H4   0.020
 IDM  plan-1  H5   0.020
 IDM  plan-1  H6   0.020
 IDM  plan-1  H7   0.020

