# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 09:05:50 2020
#   Inital geometry file: a 59 line input string
#   Ligand name: 1H-indol-3-ylacetonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N#CCc1c[nH]c2ccccc12
#
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
 3BO  3BO  1H-indol-3-ylacetonitrile  ligand  20  12  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_3BO
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
 3BO  C01  C  CR16  0  -0.267   1.9785   1.8098   0.0743
 3BO  C02  C  CR16  0  -0.281   2.9155   0.8392  -0.3187
 3BO  C03  C  CR16  0  -0.302   2.5649  -0.4915  -0.4408
 3BO  C04  C  CR56  0   0.357   1.2438  -0.8357  -0.1586
 3BO  C05  C  CR56  0   0.050   0.2879   0.1240   0.2392
 3BO  C06  C  CR16  0  -0.366   0.6706   1.4653   0.3531
 3BO  C07  C  CR5   0  -0.007  -0.9399  -0.5803   0.4463
 3BO  C08  C  CR15  0  -0.057  -0.6883  -1.8941   0.1715
 3BO  N09  N  NR15  0  -0.685   0.6168  -2.0480  -0.1893
 3BO  C10  C  CH2   0  -0.648  -2.2451   0.0045   0.8818
 3BO  C11  C  CSP   0   0.126  -2.8129   0.8824  -0.1367
 3BO  N12  N  NS    0  -0.277  -3.2472   1.5737  -0.9475
 3BO  H1   H  HCR6  0   0.249   2.2898   2.8431   0.1565
 3BO  H2   H  HCR6  0   0.252   3.9329   1.1401  -0.5322
 3BO  H3   H  HCR6  0   0.262   3.2892  -1.2373  -0.7433
 3BO  H4   H  HCR6  0   0.243  -0.0438   2.2228   0.6534
 3BO  H5   H  HCR5  0   0.292  -1.3550  -2.7410   0.2119
 3BO  H6   H  HNR5  0   0.413   1.0467  -2.9259  -0.4274
 3BO  H7   H  HCH2  0   0.327  -2.9738  -0.7811   1.0903
 3BO  H8   H  HCH2  0   0.320  -2.1414   0.5875   1.8010

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
 3BO  N12  C11  triple    1.151  0.020  1.151
 3BO  C11  C10  single    1.460  0.020  1.460
 3BO  C10  C07  single    1.495  0.020  1.495
 3BO  C07  C05  aromatic  1.431  0.020  1.431
 3BO  C07  C08  aromatic  1.366  0.020  1.366
 3BO  C06  C05  aromatic  1.399  0.020  1.399
 3BO  C06  C01  aromatic  1.381  0.020  1.381
 3BO  C05  C04  aromatic  1.412  0.020  1.412
 3BO  C08  N09  aromatic  1.363  0.020  1.363
 3BO  C01  C02  aromatic  1.405  0.020  1.405
 3BO  C04  N09  aromatic  1.365  0.020  1.365
 3BO  C04  C03  aromatic  1.394  0.020  1.394
 3BO  C02  C03  aromatic  1.381  0.020  1.381
 3BO  C01  H1   single    0.930  0.020  1.080
 3BO  C02  H2   single    0.930  0.020  1.080
 3BO  C03  H3   single    0.930  0.020  1.080
 3BO  C06  H4   single    0.930  0.020  1.080
 3BO  C08  H5   single    0.930  0.020  1.080
 3BO  N09  H6   single    0.860  0.020  1.020
 3BO  C10  H7   single    0.970  0.020  1.090
 3BO  C10  H8   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
 3BO  H1   C01  C06  119.68  3.000
 3BO  H1   C01  C02  119.27  3.000
 3BO  C06  C01  C02  121.05  3.000
 3BO  H2   C02  C03  119.27  3.000
 3BO  H2   C02  C01  119.34  3.000
 3BO  C03  C02  C01  121.39  3.000
 3BO  H3   C03  C04  121.36  3.000
 3BO  H3   C03  C02  121.23  3.000
 3BO  C04  C03  C02  117.42  3.000
 3BO  N09  C04  C05  107.40  3.000
 3BO  N09  C04  C03  130.54  3.000
 3BO  C05  C04  C03  122.06  3.000
 3BO  C07  C05  C06  134.01  3.000
 3BO  C06  C05  C04  119.30  3.000
 3BO  C07  C05  C04  106.69  3.000
 3BO  H4   C06  C05  120.82  3.000
 3BO  H4   C06  C01  120.39  3.000
 3BO  C05  C06  C01  118.79  3.000
 3BO  C10  C07  C08  126.56  3.000
 3BO  C08  C07  C05  106.64  3.000
 3BO  C10  C07  C05  126.79  3.000
 3BO  H5   C08  N09  120.88  3.000
 3BO  H5   C08  C07  129.35  3.000
 3BO  N09  C08  C07  109.77  3.000
 3BO  H6   N09  C08  124.78  3.000
 3BO  H6   N09  C04  125.73  3.000
 3BO  C08  N09  C04  109.49  3.000
 3BO  H8   C10  H7   106.64  3.000
 3BO  H8   C10  C11  107.62  3.000
 3BO  H7   C10  C11  107.84  3.000
 3BO  H8   C10  C07  111.76  3.000
 3BO  H7   C10  C07  110.92  3.000
 3BO  C11  C10  C07  111.82  3.000
 3BO  N12  C11  C10  180.00  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
 3BO  CONST_01  C07  C05  C06  C01  180.00   0.0  0
 3BO  CONST_02  C04  C05  C06  C01    0.00   0.0  0
 3BO  CONST_03  C04  C03  C02  C01    0.00   0.0  0
 3BO  CONST_04  C05  C06  C01  C02    0.00   0.0  0
 3BO  CONST_05  C05  C04  C03  C02    0.00   0.0  0
 3BO  CONST_06  N09  C04  C03  C02  180.00   0.0  0
 3BO  CONST_07  C07  C05  C04  C03  180.00   0.0  0
 3BO  CONST_08  C06  C05  C04  C03    0.00   0.0  0
 3BO  CONST_09  C08  N09  C04  C03  180.00   0.0  0
 3BO  CONST_10  C06  C01  C02  C03    0.00   0.0  0
 3BO  CONST_11  C08  C07  C05  C04    0.00   0.0  0
 3BO  CONST_12  C07  C08  N09  C04    0.00   0.0  0
 3BO  CONST_13  N09  C08  C07  C05    0.00   0.0  0
 3BO  CONST_14  C08  N09  C04  C05    0.00   0.0  0
 3BO  CONST_15  C08  C07  C05  C06  180.00   0.0  0
 3BO  CONST_16  N09  C04  C05  C06  180.00   0.0  0
 3BO  CONST_17  N09  C04  C05  C07    0.00   0.0  0
 3BO  CONST_18  C10  C07  C05  C04  180.00   0.0  0
 3BO  CONST_19  C10  C07  C05  C06    0.00   0.0  0
 3BO  CONST_20  C10  C07  C08  N09  180.00   0.0  0
 3BO  CONST_21  H3   C03  C02  C01  180.00   0.0  0
 3BO  CONST_22  H4   C06  C01  C02  180.00   0.0  0
 3BO  CONST_23  H6   N09  C04  C03    0.00   0.0  0
 3BO  CONST_24  H1   C01  C02  C03  180.00   0.0  0
 3BO  CONST_25  H5   C08  N09  C04  180.00   0.0  0
 3BO  CONST_26  H2   C02  C03  C04  180.00   0.0  0
 3BO  Var_01    C11  C10  C07  C05   67.39  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
 3BO  plan-1  C01  0.020
 3BO  plan-1  C02  0.020
 3BO  plan-1  C03  0.020
 3BO  plan-1  C04  0.020
 3BO  plan-1  C05  0.020
 3BO  plan-1  C06  0.020
 3BO  plan-1  C07  0.020
 3BO  plan-1  C08  0.020
 3BO  plan-1  N09  0.020
 3BO  plan-1  C10  0.020
 3BO  plan-1  H1   0.020
 3BO  plan-1  H2   0.020
 3BO  plan-1  H3   0.020
 3BO  plan-1  H4   0.020
 3BO  plan-1  H5   0.020
 3BO  plan-1  H6   0.020

