# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 10:42:35 2021
#   Inital geometry file: a 86 line input string
#   Ligand name: 4-({[(4-fluorophenyl)methyl]amino}methyl)benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(CNCc2ccc(cc2)C#N)cc1
#
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
 WHD  WHD  4-({[(4-fluorophenyl)methyl]amino}methyl)benzonitrile  ligand  31  18  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_WHD
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
 WHD  N1   N  NS    0  -0.255  27.9474  -0.3319  -26.4776
 WHD  C4   C  CH2   0  -0.317  23.2651   7.2733  -25.5671
 WHD  C5   C  CH2   0  -0.310  25.0929   5.9154  -26.3599
 WHD  C6   C  CR6   0   0.097  25.7138   4.5450  -26.3496
 WHD  C7   C  CR16  0  -0.298  27.0946   4.3999  -26.4578
 WHD  C8   C  CR16  0  -0.224  27.6796   3.1463  -26.4931
 WHD  C10  C  CSP   0   0.053  27.4662   0.7151  -26.4484
 WHD  C13  C  CR16  0  -0.269  21.1211   6.2938  -24.6831
 WHD  N    N  NH1   0  -0.588  23.9559   6.0019  -25.4698
 WHD  C    C  CR6   0   0.509  19.8580   7.3925  -22.9901
 WHD  C1   C  CR16  0  -0.397  20.7782   8.4178  -22.9254
 WHD  C11  C  CR16  0  -0.224  25.4885   2.1417  -26.2966
 WHD  C12  C  CR16  0  -0.282  24.9200   3.4017  -26.2642
 WHD  C14  C  CR16  0  -0.397  20.0085   6.3252  -23.8571
 WHD  C2   C  CR16  0  -0.298  21.8870   8.3654  -23.7622
 WHD  C3   C  CR6   0   0.076  22.0718   7.3138  -24.6520
 WHD  C9   C  CR6   0  -0.012  26.8732   2.0120  -26.4137
 WHD  H3   H  HCH2  0   0.243  22.9321   7.3928  -26.6035
 WHD  H2   H  HCH2  0   0.218  23.9158   8.1355  -25.3580
 WHD  H6   H  HCH2  0   0.254  24.7413   6.1251  -27.3763
 WHD  H5   H  HCH2  0   0.224  25.8697   6.6663  -26.1526
 WHD  H7   H  HCR6  0   0.267  27.7248   5.2787  -26.5114
 WHD  H8   H  HCR6  0   0.280  28.7535   3.0470  -26.5748
 WHD  H11  H  HCR6  0   0.260  21.2539   5.4614  -25.3624
 WHD  H4   H  HNH1  0   0.349  24.2661   5.8628  -24.5150
 WHD  H    H  HCR6  0   0.277  20.6405   9.2388  -22.2343
 WHD  H9   H  HCR6  0   0.278  24.8641   1.2609  -26.2322
 WHD  H10  H  HCR6  0   0.266  23.8476   3.5036  -26.1670
 WHD  H12  H  HCR6  0   0.277  19.2700   5.5346  -23.8868
 WHD  H1   H  HCR6  0   0.262  22.6181   9.1630  -23.7128
 WHD  F    F  F     0  -0.318  18.7819   7.4287  -22.1848

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
 WHD  F    C    single    1.344  0.020  1.344
 WHD  C    C1   aromatic  1.379  0.020  1.379
 WHD  C1   C2   aromatic  1.390  0.020  1.390
 WHD  C2   C3   aromatic  1.390  0.020  1.390
 WHD  C3   C4   single    1.504  0.020  1.504
 WHD  C4   N    single    1.450  0.020  1.450
 WHD  N    C5   single    1.447  0.020  1.447
 WHD  C5   C6   single    1.504  0.020  1.504
 WHD  C6   C7   aromatic  1.393  0.020  1.393
 WHD  C7   C8   aromatic  1.384  0.020  1.384
 WHD  C8   C9   aromatic  1.394  0.020  1.394
 WHD  C9   C10  single    1.426  0.020  1.426
 WHD  C10  N1   triple    1.153  0.020  1.153
 WHD  C11  C9   aromatic  1.396  0.020  1.396
 WHD  C12  C11  aromatic  1.383  0.020  1.383
 WHD  C6   C12  aromatic  1.394  0.020  1.394
 WHD  C13  C3   aromatic  1.395  0.020  1.395
 WHD  C14  C13  aromatic  1.386  0.020  1.386
 WHD  C    C14  aromatic  1.383  0.020  1.383
 WHD  C4   H3   single    0.970  0.020  1.090
 WHD  C4   H2   single    0.970  0.020  1.090
 WHD  C5   H6   single    0.970  0.020  1.090
 WHD  C5   H5   single    0.970  0.020  1.090
 WHD  C7   H7   single    0.930  0.020  1.080
 WHD  C8   H8   single    0.930  0.020  1.080
 WHD  C13  H11  single    0.930  0.020  1.080
 WHD  N    H4   single    0.890  0.020  1.040
 WHD  C1   H    single    0.930  0.020  1.080
 WHD  C11  H9   single    0.930  0.020  1.080
 WHD  C12  H10  single    0.930  0.020  1.080
 WHD  C14  H12  single    0.930  0.020  1.080
 WHD  C2   H1   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
 WHD  H2   C4   H3   105.91  3.000
 WHD  H2   C4   C3   109.42  3.000
 WHD  H3   C4   C3   109.36  3.000
 WHD  H2   C4   N    113.11  3.000
 WHD  H3   C4   N    107.70  3.000
 WHD  C3   C4   N    111.14  3.000
 WHD  H5   C5   H6   105.71  3.000
 WHD  H5   C5   N    113.47  3.000
 WHD  H6   C5   N    107.89  3.000
 WHD  H5   C5   C6   109.21  3.000
 WHD  H6   C5   C6   108.24  3.000
 WHD  N    C5   C6   112.00  3.000
 WHD  C12  C6   C7   118.93  3.000
 WHD  C12  C6   C5   120.82  3.000
 WHD  C7   C6   C5   120.24  3.000
 WHD  H7   C7   C8   119.21  3.000
 WHD  H7   C7   C6   119.76  3.000
 WHD  C8   C7   C6   121.03  3.000
 WHD  H8   C8   C9   120.26  3.000
 WHD  H8   C8   C7   120.32  3.000
 WHD  C9   C8   C7   119.42  3.000
 WHD  C9   C10  N1   180.00  3.000
 WHD  H11  C13  C3   119.52  3.000
 WHD  H11  C13  C14  119.33  3.000
 WHD  C3   C13  C14  121.15  3.000
 WHD  H4   N    C5   109.32  3.000
 WHD  H4   N    C4   109.23  3.000
 WHD  C5   N    C4   112.68  3.000
 WHD  F    C    C14  118.90  3.000
 WHD  C14  C    C1   122.03  3.000
 WHD  F    C    C1   119.07  3.000
 WHD  H    C1   C2   120.97  3.000
 WHD  H    C1   C    120.61  3.000
 WHD  C2   C1   C    118.42  3.000
 WHD  H9   C11  C9   120.13  3.000
 WHD  H9   C11  C12  120.23  3.000
 WHD  C9   C11  C12  119.64  3.000
 WHD  H10  C12  C11  119.71  3.000
 WHD  H10  C12  C6   119.52  3.000
 WHD  C11  C12  C6   120.78  3.000
 WHD  H12  C14  C    120.43  3.000
 WHD  H12  C14  C13  120.99  3.000
 WHD  C    C14  C13  118.58  3.000
 WHD  H1   C2   C3   119.78  3.000
 WHD  H1   C2   C1   118.89  3.000
 WHD  C3   C2   C1   121.33  3.000
 WHD  C2   C3   C13  118.49  3.000
 WHD  C13  C3   C4   120.49  3.000
 WHD  C2   C3   C4   121.01  3.000
 WHD  C11  C9   C10  119.94  3.000
 WHD  C11  C9   C8   120.20  3.000
 WHD  C10  C9   C8   119.86  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
 WHD  CONST_01  C9   C8   C7   C6      0.00   0.0  0
 WHD  CONST_02  C9   C11  C12  C6      0.00   0.0  0
 WHD  CONST_03  C11  C12  C6   C7      0.00   0.0  0
 WHD  CONST_04  C11  C9   C8   C7      0.00   0.0  0
 WHD  CONST_05  C12  C6   C7   C8      0.00   0.0  0
 WHD  CONST_06  C12  C11  C9   C8      0.00   0.0  0
 WHD  CONST_07  C1   C2   C3   C13     0.00   0.0  0
 WHD  CONST_08  C1   C    C14  C13     0.00   0.0  0
 WHD  CONST_09  C3   C2   C1   C       0.00   0.0  0
 WHD  CONST_10  C3   C13  C14  C       0.00   0.0  0
 WHD  CONST_11  C2   C3   C13  C14     0.00   0.0  0
 WHD  CONST_12  C2   C1   C    C14     0.00   0.0  0
 WHD  CONST_13  C1   C2   C3   C4    180.00   0.0  0
 WHD  CONST_14  C14  C13  C3   C4    180.00   0.0  0
 WHD  CONST_15  C8   C7   C6   C5    180.00   0.0  0
 WHD  CONST_16  C11  C12  C6   C5    180.00   0.0  0
 WHD  CONST_17  C10  C9   C8   C7    180.00   0.0  0
 WHD  CONST_18  C12  C11  C9   C10   180.00   0.0  0
 WHD  CONST_19  F    C    C14  C13   180.00   0.0  0
 WHD  CONST_20  F    C    C1   C2    180.00   0.0  0
 WHD  CONST_21  H8   C8   C7   C6    180.00   0.0  0
 WHD  CONST_22  H9   C11  C12  C6    180.00   0.0  0
 WHD  CONST_23  H10  C12  C6   C7    180.00   0.0  0
 WHD  CONST_24  H1   C2   C3   C13   180.00   0.0  0
 WHD  CONST_25  H11  C13  C14  C     180.00   0.0  0
 WHD  CONST_26  H12  C14  C    C1    180.00   0.0  0
 WHD  CONST_27  H7   C7   C6   C12   180.00   0.0  0
 WHD  CONST_28  H    C1   C    C14   180.00   0.0  0
 WHD  Var_01    N    C5   C6   C7   -143.59  30.0  3
 WHD  Var_02    N    C4   C3   C13   -51.72  30.0  2
 WHD  Var_03    C6   C5   N    C4   -174.21  30.0  3
 WHD  Var_04    C3   C4   N    C5    178.67  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
 WHD  plan-1  N1   0.020
 WHD  plan-1  C5   0.020
 WHD  plan-1  C6   0.020
 WHD  plan-1  C7   0.020
 WHD  plan-1  C8   0.020
 WHD  plan-1  C10  0.020
 WHD  plan-1  C11  0.020
 WHD  plan-1  C12  0.020
 WHD  plan-1  C9   0.020
 WHD  plan-1  H7   0.020
 WHD  plan-1  H8   0.020
 WHD  plan-1  H9   0.020
 WHD  plan-1  H10  0.020
 WHD  plan-2  C4   0.020
 WHD  plan-2  C13  0.020
 WHD  plan-2  C    0.020
 WHD  plan-2  C1   0.020
 WHD  plan-2  C14  0.020
 WHD  plan-2  C2   0.020
 WHD  plan-2  C3   0.020
 WHD  plan-2  H11  0.020
 WHD  plan-2  H    0.020
 WHD  plan-2  H12  0.020
 WHD  plan-2  H1   0.020
 WHD  plan-2  F    0.020

