# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 04:43:16 2020
#   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
 BDN  BDN  'benzenecarboximidamide   '  ligand  17  9  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_BDN
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
 BDN  C1    C  CR6   0   0.007  -0.0288  -0.0561   0.2248
 BDN  C2    C  CR16  0  -0.290  -1.1826   0.2120  -0.5095
 BDN  C3    C  CR16  0  -0.244  -1.1403   0.2549  -1.8949
 BDN  C4    C  CR16  0  -0.255   0.0551   0.0214  -2.5630
 BDN  C5    C  CR16  0  -0.241   1.2082  -0.2488  -1.8384
 BDN  C6    C  CR16  0  -0.282   1.1691  -0.2813  -0.4515
 BDN  C     C  C     0   0.329  -0.0973  -0.1190   1.7124
 BDN  N1    N  N     0  -0.642  -1.0878  -0.5827   2.3740
 BDN  N2    N  NH2   0  -0.803   1.0191   0.3217   2.3569
 BDN  H2    H  HCR6  0   0.262  -2.1166   0.4092   0.0022
 BDN  H3    H  HCR6  0   0.262  -2.0406   0.4755  -2.4531
 BDN  H4    H  HCR6  0   0.262   0.0875   0.0504  -3.6442
 BDN  H5    H  HCR6  0   0.262   2.1407  -0.4393  -2.3533
 BDN  H6    H  HCR6  0   0.263   2.0729  -0.5039   0.1015
 BDN  HN1   H  H     0   0.332  -1.7876  -0.9679   1.7507
 BDN  HN21  H  HNH2  0   0.384   0.9544   0.4041   3.3592
 BDN  HN22  H  HNH2  0   0.393   1.5796   1.0321   1.9167

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
 BDN  C1  C2    aromatic  1.394  0.020  1.394
 BDN  C1  C6    aromatic  1.394  0.020  1.394
 BDN  C1  C     single    1.491  0.020  1.491
 BDN  C2  C3    aromatic  1.387  0.020  1.387
 BDN  C2  H2    single    0.930  0.020  1.080
 BDN  C3  C4    aromatic  1.389  0.020  1.389
 BDN  C3  H3    single    0.930  0.020  1.080
 BDN  C4  C5    aromatic  1.388  0.020  1.388
 BDN  C4  H4    single    0.930  0.020  1.080
 BDN  C5  C6    aromatic  1.388  0.020  1.388
 BDN  C5  H5    single    0.930  0.020  1.080
 BDN  C6  H6    single    0.930  0.020  1.080
 BDN  C   N1    double    1.278  0.020  1.278
 BDN  C   N2    single    1.362  0.020  1.362
 BDN  N1  HN1   single    0.890  0.020  1.040
 BDN  N2  HN21  single    0.890  0.020  1.040
 BDN  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
 BDN  C     C1  C6    121.12  3.000
 BDN  C     C1  C2    119.74  3.000
 BDN  C6    C1  C2    119.13  3.000
 BDN  H2    C2  C3    119.52  3.000
 BDN  H2    C2  C1    120.00  3.000
 BDN  C3    C2  C1    120.47  3.000
 BDN  H3    C3  C4    120.14  3.000
 BDN  H3    C3  C2    119.76  3.000
 BDN  C4    C3  C2    120.10  3.000
 BDN  H4    C4  C5    120.12  3.000
 BDN  H4    C4  C3    120.12  3.000
 BDN  C5    C4  C3    119.76  3.000
 BDN  H5    C5  C6    119.71  3.000
 BDN  H5    C5  C4    120.11  3.000
 BDN  C6    C5  C4    120.18  3.000
 BDN  H6    C6  C5    119.46  3.000
 BDN  H6    C6  C1    120.18  3.000
 BDN  C5    C6  C1    120.35  3.000
 BDN  N2    C   N1    120.50  3.000
 BDN  N2    C   C1    114.89  3.000
 BDN  N1    C   C1    124.57  3.000
 BDN  HN1   N1  C     110.78  3.000
 BDN  HN22  N2  HN21  114.40  3.000
 BDN  HN22  N2  C     118.55  3.000
 BDN  HN21  N2  C     116.38  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
 BDN  CONST_01  C4    C3  C2  C1    0.00   0.0  0
 BDN  CONST_02  C4    C5  C6  C1    0.00   0.0  0
 BDN  CONST_03  C5    C6  C1  C2    0.00   0.0  0
 BDN  CONST_04  C5    C4  C3  C2    0.00   0.0  0
 BDN  CONST_05  C6    C1  C2  C3    0.00   0.0  0
 BDN  CONST_06  C6    C5  C4  C3    0.00   0.0  0
 BDN  CONST_07  C     C1  C2  C3  180.00   0.0  0
 BDN  CONST_08  C     C1  C6  C5  180.00   0.0  0
 BDN  CONST_09  H3    C3  C2  C1  180.00   0.0  0
 BDN  CONST_10  H5    C5  C6  C1  180.00   0.0  0
 BDN  CONST_11  H6    C6  C1  C2  180.00   0.0  0
 BDN  CONST_12  H4    C4  C3  C2  180.00   0.0  0
 BDN  CONST_13  H2    C2  C3  C4  180.00   0.0  0
 BDN  CONST_14  HN1   N1  C   C1    0.00   0.0  0
 BDN  CONST_15  HN21  N2  C   C1  180.00   0.0  0
 BDN  Var_01    N1    C   C1  C2   35.72  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
 BDN  plan-1  C1    0.020
 BDN  plan-1  C2    0.020
 BDN  plan-1  C3    0.020
 BDN  plan-1  C4    0.020
 BDN  plan-1  C5    0.020
 BDN  plan-1  C6    0.020
 BDN  plan-1  C     0.020
 BDN  plan-1  H2    0.020
 BDN  plan-1  H3    0.020
 BDN  plan-1  H4    0.020
 BDN  plan-1  H5    0.020
 BDN  plan-1  H6    0.020
 BDN  plan-2  C1    0.020
 BDN  plan-2  C     0.020
 BDN  plan-2  N1    0.020
 BDN  plan-2  N2    0.020
 BDN  plan-2  HN1   0.020
 BDN  plan-2  HN21  0.020
 BDN  plan-2  HN22  0.020

