# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 17:53:09 2020
#   Inital geometry file: a 65 line input string
#   Ligand name: naphthalene-2-carboximidamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=N)c1ccc2ccccc2c1
#
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
 2UP  2UP  naphthalene-2-carboximidamide  ligand  23  13  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2UP
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
 2UP  CAI  C  CR16  0  -0.349  -0.4699  -0.8691   0.0284
 2UP  CAM  C  CR66  0   0.139   0.9014  -0.5353   0.0079
 2UP  CAG  C  CR16  0  -0.309   1.9086  -1.5259  -0.0901
 2UP  CAD  C  CR16  0  -0.258   3.2303  -1.1747  -0.1094
 2UP  CAC  C  CR16  0  -0.255   3.6089   0.1831  -0.0307
 2UP  CAF  C  CR16  0  -0.308   2.6581   1.1621   0.0655
 2UP  CAL  C  CR66  0   0.108   1.2833   0.8293   0.0861
 2UP  CAH  C  CR16  0  -0.299   0.2714   1.8114   0.1826
 2UP  CAE  C  CR16  0  -0.292  -1.0495   1.4599   0.1905
 2UP  CAK  C  CR6   0   0.046  -1.4378   0.1004   0.1083
 2UP  CAJ  C  C     0   0.335  -2.8742  -0.2943   0.1164
 2UP  NAB  N  N     0  -0.652  -3.1939  -1.4432   0.5745
 2UP  NAA  N  NH2   0  -0.822  -3.7389   0.6603  -0.3383
 2UP  H1   H  HCR6  0   0.253  -0.7613  -1.9105  -0.0320
 2UP  H2   H  HCR6  0   0.256   1.6180  -2.5678  -0.1506
 2UP  H3   H  HCR6  0   0.261   3.9934  -1.9380  -0.1842
 2UP  H4   H  HCR6  0   0.260   4.6587   0.4454  -0.0464
 2UP  H5   H  HCR6  0   0.257   2.9484   2.2042   0.1261
 2UP  H6   H  HCR6  0   0.258   0.5534   2.8547   0.2562
 2UP  H7   H  HCR6  0   0.260  -1.7996   2.2344   0.2825
 2UP  H8   H  H     0   0.323  -4.1941  -1.6057   0.4924
 2UP  H9   H  HNH2  0   0.395  -3.4030   1.3294  -1.0115
 2UP  H10  H  HNH2  0   0.392  -4.6948   0.3810  -0.4928

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
 2UP  CAH  CAE  aromatic  1.367  0.020  1.367
 2UP  CAH  CAL  aromatic  1.413  0.020  1.413
 2UP  CAE  CAK  aromatic  1.416  0.020  1.416
 2UP  CAF  CAL  aromatic  1.415  0.020  1.415
 2UP  CAF  CAC  aromatic  1.368  0.020  1.368
 2UP  CAL  CAM  aromatic  1.419  0.020  1.419
 2UP  CAC  CAD  aromatic  1.412  0.020  1.412
 2UP  CAK  CAJ  single    1.490  0.020  1.490
 2UP  CAK  CAI  aromatic  1.372  0.020  1.372
 2UP  CAJ  NAB  double    1.278  0.020  1.278
 2UP  CAJ  NAA  single    1.366  0.020  1.366
 2UP  CAM  CAI  aromatic  1.411  0.020  1.411
 2UP  CAM  CAG  aromatic  1.416  0.020  1.416
 2UP  CAD  CAG  aromatic  1.368  0.020  1.368
 2UP  CAI  H1   single    0.930  0.020  1.080
 2UP  CAG  H2   single    0.930  0.020  1.080
 2UP  CAD  H3   single    0.930  0.020  1.080
 2UP  CAC  H4   single    0.930  0.020  1.080
 2UP  CAF  H5   single    0.930  0.020  1.080
 2UP  CAH  H6   single    0.930  0.020  1.080
 2UP  CAE  H7   single    0.930  0.020  1.080
 2UP  NAB  H8   single    0.890  0.020  1.040
 2UP  NAA  H9   single    0.890  0.020  1.040
 2UP  NAA  H10  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
 2UP  H1   CAI  CAK  119.52  3.000
 2UP  H1   CAI  CAM  119.21  3.000
 2UP  CAK  CAI  CAM  121.26  3.000
 2UP  CAL  CAM  CAG  119.02  3.000
 2UP  CAG  CAM  CAI  121.77  3.000
 2UP  CAL  CAM  CAI  119.21  3.000
 2UP  H2   CAG  CAD  120.35  3.000
 2UP  H2   CAG  CAM  119.07  3.000
 2UP  CAD  CAG  CAM  120.58  3.000
 2UP  H3   CAD  CAC  119.55  3.000
 2UP  H3   CAD  CAG  120.10  3.000
 2UP  CAC  CAD  CAG  120.35  3.000
 2UP  H4   CAC  CAF  120.12  3.000
 2UP  H4   CAC  CAD  119.50  3.000
 2UP  CAF  CAC  CAD  120.38  3.000
 2UP  H5   CAF  CAL  119.07  3.000
 2UP  H5   CAF  CAC  120.40  3.000
 2UP  CAL  CAF  CAC  120.53  3.000
 2UP  CAH  CAL  CAF  122.22  3.000
 2UP  CAF  CAL  CAM  119.14  3.000
 2UP  CAH  CAL  CAM  118.64  3.000
 2UP  H6   CAH  CAE  119.92  3.000
 2UP  H6   CAH  CAL  119.18  3.000
 2UP  CAE  CAH  CAL  120.90  3.000
 2UP  H7   CAE  CAK  120.13  3.000
 2UP  H7   CAE  CAH  119.10  3.000
 2UP  CAK  CAE  CAH  120.76  3.000
 2UP  CAJ  CAK  CAE  121.22  3.000
 2UP  CAJ  CAK  CAI  119.55  3.000
 2UP  CAE  CAK  CAI  119.22  3.000
 2UP  NAA  CAJ  NAB  126.12  3.000
 2UP  NAA  CAJ  CAK  115.06  3.000
 2UP  NAB  CAJ  CAK  118.78  3.000
 2UP  H8   NAB  CAJ  111.16  3.000
 2UP  H10  NAA  H9   113.46  3.000
 2UP  H10  NAA  CAJ  117.25  3.000
 2UP  H9   NAA  CAJ  118.41  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
 2UP  CONST_01  CAH  CAE  CAK  CAI    0.00   0.0  0
 2UP  CONST_02  CAH  CAL  CAM  CAI    0.00   0.0  0
 2UP  CONST_03  CAF  CAL  CAM  CAI  180.00   0.0  0
 2UP  CONST_04  CAD  CAG  CAM  CAI  180.00   0.0  0
 2UP  CONST_05  CAE  CAH  CAL  CAM    0.00   0.0  0
 2UP  CONST_06  CAC  CAF  CAL  CAM    0.00   0.0  0
 2UP  CONST_07  CAE  CAK  CAI  CAM    0.00   0.0  0
 2UP  CONST_08  CAC  CAD  CAG  CAM    0.00   0.0  0
 2UP  CONST_09  CAH  CAL  CAM  CAG  180.00   0.0  0
 2UP  CONST_10  CAF  CAL  CAM  CAG    0.00   0.0  0
 2UP  CONST_11  CAK  CAI  CAM  CAG  180.00   0.0  0
 2UP  CONST_12  CAF  CAC  CAD  CAG    0.00   0.0  0
 2UP  CONST_13  CAL  CAF  CAC  CAD    0.00   0.0  0
 2UP  CONST_14  CAL  CAM  CAG  CAD    0.00   0.0  0
 2UP  CONST_15  CAH  CAL  CAF  CAC  180.00   0.0  0
 2UP  CONST_16  CAE  CAH  CAL  CAF  180.00   0.0  0
 2UP  CONST_17  CAK  CAE  CAH  CAL    0.00   0.0  0
 2UP  CONST_18  CAK  CAI  CAM  CAL    0.00   0.0  0
 2UP  CONST_19  CAJ  CAK  CAI  CAM  180.00   0.0  0
 2UP  CONST_20  CAJ  CAK  CAE  CAH  180.00   0.0  0
 2UP  CONST_21  H7   CAE  CAK  CAI  180.00   0.0  0
 2UP  CONST_22  H2   CAG  CAM  CAI    0.00   0.0  0
 2UP  CONST_23  H6   CAH  CAL  CAM  180.00   0.0  0
 2UP  CONST_24  H5   CAF  CAL  CAM  180.00   0.0  0
 2UP  CONST_25  H3   CAD  CAG  CAM  180.00   0.0  0
 2UP  CONST_26  H1   CAI  CAM  CAG    0.00   0.0  0
 2UP  CONST_27  H4   CAC  CAD  CAG  180.00   0.0  0
 2UP  CONST_28  H8   NAB  CAJ  CAK  180.00   0.0  0
 2UP  CONST_30  H10  NAA  CAJ  CAK  180.00   0.0  0
 2UP  Var_01    NAB  CAJ  CAK  CAI   27.63  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
 2UP  plan-1  CAI  0.020
 2UP  plan-1  CAM  0.020
 2UP  plan-1  CAG  0.020
 2UP  plan-1  CAD  0.020
 2UP  plan-1  CAC  0.020
 2UP  plan-1  CAF  0.020
 2UP  plan-1  CAL  0.020
 2UP  plan-1  CAH  0.020
 2UP  plan-1  CAE  0.020
 2UP  plan-1  CAK  0.020
 2UP  plan-1  CAJ  0.020
 2UP  plan-1  H1   0.020
 2UP  plan-1  H2   0.020
 2UP  plan-1  H3   0.020
 2UP  plan-1  H4   0.020
 2UP  plan-1  H5   0.020
 2UP  plan-1  H6   0.020
 2UP  plan-1  H7   0.020
 2UP  plan-2  CAK  0.020
 2UP  plan-2  CAJ  0.020
 2UP  plan-2  NAB  0.020
 2UP  plan-2  NAA  0.020
 2UP  plan-2  H8   0.020
 2UP  plan-2  H9   0.020
 2UP  plan-2  H10  0.020

