# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 16:18:15 2022
#   Inital geometry file: a 51 line input string
#   Ligand name: benzenecarboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccccc1
#
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
 BEN  BEN  'benzenecarboximidamide   '  ligand  17  9  .  2022-03-07  2022-03-07
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BEN
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
 BEN  C1    C  CR6   0  -0.163  6.7130   9.9939  20.6158
 BEN  C2    C  CR16  0  -0.222  5.9846   9.1141  19.8170
 BEN  C3    C  CR16  0  -0.206  6.5558   8.5690  18.6755
 BEN  C4    C  CR16  0  -0.260  7.8521   8.9088  18.3135
 BEN  C5    C  CR16  0  -0.198  8.5804   9.7898  19.1024
 BEN  C6    C  CR16  0  -0.309  8.0164  10.3245  20.2510
 BEN  C     C  C     0   0.188  6.1313  10.5539  21.8683
 BEN  N1    N  N     0  -0.473  6.7685  10.6825  22.9680
 BEN  N2    N  NH2   0  -0.807  4.8172  10.8984  21.7852
 BEN  H2    H  HCR6  0   0.249  4.9744   8.8391  20.0929
 BEN  H3    H  HCR6  0   0.266  5.9860   7.8768  18.0694
 BEN  H4    H  HCR6  0   0.258  8.2954   8.4890  17.4199
 BEN  H5    H  HCR6  0   0.282  9.5889  10.0652  18.8227
 BEN  H6    H  HCR6  0   0.292  8.5870  11.0165  20.8582
 BEN  HN1   H  H     0   0.364  7.6974  10.2859  22.8978
 BEN  HN21  H  HNH2  0   0.367  4.4137  11.3724  22.5772
 BEN  HN22  H  HNH2  0   0.373  4.4240  11.1388  20.8916

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
 BEN  C1  C2    aromatic  1.394  0.020  1.394
 BEN  C1  C6    aromatic  1.393  0.020  1.393
 BEN  C1  C     single    1.490  0.020  1.490
 BEN  C2  C3    aromatic  1.388  0.020  1.388
 BEN  C2  H2    single    0.930  0.020  1.080
 BEN  C3  C4    aromatic  1.388  0.020  1.388
 BEN  C3  H3    single    0.930  0.020  1.080
 BEN  C4  C5    aromatic  1.389  0.020  1.389
 BEN  C4  H4    single    0.930  0.020  1.080
 BEN  C5  C6    aromatic  1.387  0.020  1.387
 BEN  C5  H5    single    0.930  0.020  1.080
 BEN  C6  H6    single    0.930  0.020  1.080
 BEN  C   N1    double    1.277  0.020  1.277
 BEN  C   N2    single    1.361  0.020  1.361
 BEN  N1  HN1   single    0.890  0.020  1.040
 BEN  N2  HN21  single    0.890  0.020  1.040
 BEN  N2  HN22  single    0.890  0.020  1.040

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
 BEN  C     C1  C6    119.74  3.000
 BEN  C     C1  C2    120.99  3.000
 BEN  C6    C1  C2    119.25  3.000
 BEN  H2    C2  C3    119.59  3.000
 BEN  H2    C2  C1    120.13  3.000
 BEN  C3    C2  C1    120.27  3.000
 BEN  H3    C3  C4    120.15  3.000
 BEN  H3    C3  C2    119.68  3.000
 BEN  C4    C3  C2    120.17  3.000
 BEN  H4    C4  C5    120.02  3.000
 BEN  H4    C4  C3    120.19  3.000
 BEN  C5    C4  C3    119.80  3.000
 BEN  H5    C5  C6    119.66  3.000
 BEN  H5    C5  C4    120.22  3.000
 BEN  C6    C5  C4    120.12  3.000
 BEN  H6    C6  C5    119.76  3.000
 BEN  H6    C6  C1    119.84  3.000
 BEN  C5    C6  C1    120.38  3.000
 BEN  N2    C   N1    120.58  3.000
 BEN  N2    C   C1    114.88  3.000
 BEN  N1    C   C1    124.52  3.000
 BEN  HN1   N1  C     111.02  3.000
 BEN  HN22  N2  HN21  115.44  3.000
 BEN  HN22  N2  C     119.49  3.000
 BEN  HN21  N2  C     117.25  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
 BEN  CONST_01  C4    C3  C2  C1    0.00   0.0  0
 BEN  CONST_02  C4    C5  C6  C1    0.00   0.0  0
 BEN  CONST_03  C5    C6  C1  C2    0.00   0.0  0
 BEN  CONST_04  C5    C4  C3  C2    0.00   0.0  0
 BEN  CONST_05  C6    C1  C2  C3    0.00   0.0  0
 BEN  CONST_06  C6    C5  C4  C3    0.00   0.0  0
 BEN  CONST_07  C     C1  C2  C3  180.00   0.0  0
 BEN  CONST_08  C     C1  C6  C5  180.00   0.0  0
 BEN  CONST_09  H3    C3  C2  C1  180.00   0.0  0
 BEN  CONST_10  H5    C5  C6  C1  180.00   0.0  0
 BEN  CONST_11  H6    C6  C1  C2  180.00   0.0  0
 BEN  CONST_12  H4    C4  C3  C2  180.00   0.0  0
 BEN  CONST_13  H2    C2  C3  C4  180.00   0.0  0
 BEN  CONST_14  HN1   N1  C   C1    0.00   0.0  0
 BEN  CONST_15  HN21  N2  C   C1  180.00   0.0  0
 BEN  Var_01    N1    C   C1  C2  138.11  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
 BEN  plan-1  C1    0.020
 BEN  plan-1  C2    0.020
 BEN  plan-1  C3    0.020
 BEN  plan-1  C4    0.020
 BEN  plan-1  C5    0.020
 BEN  plan-1  C6    0.020
 BEN  plan-1  C     0.020
 BEN  plan-1  H2    0.020
 BEN  plan-1  H3    0.020
 BEN  plan-1  H4    0.020
 BEN  plan-1  H5    0.020
 BEN  plan-1  H6    0.020
 BEN  plan-2  C1    0.020
 BEN  plan-2  C     0.020
 BEN  plan-2  N1    0.020
 BEN  plan-2  N2    0.020
 BEN  plan-2  HN1   0.020
 BEN  plan-2  HN21  0.020
 BEN  plan-2  HN22  0.020

