# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 21:31:27 2022
#   Inital geometry file: a 55 line input string
#   Ligand name: 1-(quinoxalin-6-yl)methanamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCc1ccc2nccnc2c1
#
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
 KX3  KX3  "1-(quinoxalin-6-yl)methanamine"
  ligand  21  12  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_KX3
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
 KX3  N1   N  N     0  -0.378  -12.2092   -9.4340   0.3413
 KX3  C5   C  CR16  0  -0.289  -15.6569  -10.5091   1.0573
 KX3  C6   C  CR16  0  -0.281  -15.5108  -11.8598   0.9038
 KX3  C7   C  CR6   0   0.123  -14.2650  -12.4354   0.5535
 KX3  C8   C  CR16  0  -0.356  -13.1815  -11.6171   0.3637
 KX3  C10  C  CR66  0   0.214  -14.5485   -9.6574   0.8693
 KX3  C11  C  CH2   0  -0.368  -14.1688  -13.9237   0.3525
 KX3  C9   C  CR66  0   0.246  -13.2968  -10.2207   0.5222
 KX3  C3   C  CR16  0  -0.119  -13.6278   -7.5894   0.8464
 KX3  C2   C  CR16  0  -0.117  -12.3750   -8.1520   0.5008
 KX3  N12  N  NH2   0  -0.789  -14.5214  -14.2699  -1.0203
 KX3  N4   N  N     0  -0.375  -14.6906   -8.3207   1.0277
 KX3  H1   H  HCR6  0   0.266  -16.6105  -10.0736   1.3274
 KX3  H2   H  HCR6  0   0.262  -16.3632  -12.5111   1.0580
 KX3  H3   H  HCR6  0   0.260  -12.2144  -12.0264   0.0959
 KX3  H4   H  HCH2  0   0.216  -14.7897  -14.4238   1.1073
 KX3  H5   H  HCH2  0   0.241  -13.1409  -14.2455   0.5290
 KX3  H6   H  HCR6  0   0.275  -13.7216   -6.5162   0.9689
 KX3  H7   H  HCR6  0   0.275  -11.5152   -7.5064   0.3604
 KX3  H8   H  HNH2  0   0.352  -14.4121  -15.2692  -1.1437
 KX3  H9   H  HNH2  0   0.344  -15.5053  -14.0832  -1.1729

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
 KX3  N12  C11  single    1.459  0.020  1.459
 KX3  N1   C2   aromatic  1.303  0.020  1.303
 KX3  N1   C9   aromatic  1.354  0.020  1.354
 KX3  C11  C7   single    1.505  0.020  1.505
 KX3  C8   C9   aromatic  1.410  0.020  1.410
 KX3  C8   C7   aromatic  1.371  0.020  1.371
 KX3  C2   C3   aromatic  1.416  0.020  1.416
 KX3  C9   C10  aromatic  1.416  0.020  1.416
 KX3  C7   C6   aromatic  1.416  0.020  1.416
 KX3  C3   N4   aromatic  1.303  0.020  1.303
 KX3  C10  N4   aromatic  1.354  0.020  1.354
 KX3  C10  C5   aromatic  1.410  0.020  1.410
 KX3  C6   C5   aromatic  1.367  0.020  1.367
 KX3  C5   H1   single    0.930  0.020  1.080
 KX3  C6   H2   single    0.930  0.020  1.080
 KX3  C8   H3   single    0.930  0.020  1.080
 KX3  C11  H4   single    0.970  0.020  1.090
 KX3  C11  H5   single    0.970  0.020  1.090
 KX3  C3   H6   single    0.930  0.020  1.080
 KX3  C2   H7   single    0.930  0.020  1.080
 KX3  N12  H8   single    0.890  0.020  1.040
 KX3  N12  H9   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
 KX3  C2   N1   C9   116.95  3.000
 KX3  H1   C5   C10  118.85  3.000
 KX3  H1   C5   C6   121.31  3.000
 KX3  C10  C5   C6   119.84  3.000
 KX3  H2   C6   C7   118.87  3.000
 KX3  H2   C6   C5   119.58  3.000
 KX3  C7   C6   C5   121.55  3.000
 KX3  C11  C7   C8   121.42  3.000
 KX3  C8   C7   C6   119.13  3.000
 KX3  C11  C7   C6   119.42  3.000
 KX3  H3   C8   C9   118.34  3.000
 KX3  H3   C8   C7   120.93  3.000
 KX3  C9   C8   C7   120.72  3.000
 KX3  N4   C10  C9   120.96  3.000
 KX3  N4   C10  C5   119.89  3.000
 KX3  C9   C10  C5   119.16  3.000
 KX3  H5   C11  H4   106.69  3.000
 KX3  H5   C11  N12  108.05  3.000
 KX3  H4   C11  N12  113.72  3.000
 KX3  H5   C11  C7   109.28  3.000
 KX3  H4   C11  C7   108.81  3.000
 KX3  N12  C11  C7   110.17  3.000
 KX3  C10  C9   C8   119.59  3.000
 KX3  C10  C9   N1   120.77  3.000
 KX3  C8   C9   N1   119.64  3.000
 KX3  H6   C3   N4   117.99  3.000
 KX3  H6   C3   C2   119.82  3.000
 KX3  N4   C3   C2   122.19  3.000
 KX3  H7   C2   C3   119.77  3.000
 KX3  H7   C2   N1   117.99  3.000
 KX3  C3   C2   N1   122.24  3.000
 KX3  H9   N12  H8   105.55  3.000
 KX3  H9   N12  C11  109.44  3.000
 KX3  H8   N12  C11  108.82  3.000
 KX3  C3   N4   C10  116.90  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
 KX3  CONST_01  N4   C3   C2   N1      0.00   0.0  0
 KX3  CONST_02  C7   C8   C9   N1    180.00   0.0  0
 KX3  CONST_03  N4   C10  C9   N1      0.00   0.0  0
 KX3  CONST_04  C5   C10  C9   N1    180.00   0.0  0
 KX3  CONST_05  C8   C9   C10  C5      0.00   0.0  0
 KX3  CONST_06  C3   N4   C10  C5    180.00   0.0  0
 KX3  CONST_07  C8   C7   C6   C5      0.00   0.0  0
 KX3  CONST_08  C9   C8   C7   C6      0.00   0.0  0
 KX3  CONST_09  C9   C10  C5   C6      0.00   0.0  0
 KX3  CONST_10  N4   C10  C5   C6    180.00   0.0  0
 KX3  CONST_11  C10  C9   C8   C7      0.00   0.0  0
 KX3  CONST_12  C10  C5   C6   C7      0.00   0.0  0
 KX3  CONST_13  C2   N1   C9   C8    180.00   0.0  0
 KX3  CONST_14  N4   C10  C9   C8    180.00   0.0  0
 KX3  CONST_15  C2   N1   C9   C10     0.00   0.0  0
 KX3  CONST_16  C2   C3   N4   C10     0.00   0.0  0
 KX3  CONST_17  C3   C2   N1   C9      0.00   0.0  0
 KX3  CONST_18  C3   N4   C10  C9      0.00   0.0  0
 KX3  CONST_19  C11  C7   C6   C5    180.00   0.0  0
 KX3  CONST_20  C9   C8   C7   C11   180.00   0.0  0
 KX3  CONST_21  H6   C3   C2   N1    180.00   0.0  0
 KX3  CONST_22  H3   C8   C9   N1      0.00   0.0  0
 KX3  CONST_23  H3   C8   C7   C6    180.00   0.0  0
 KX3  CONST_24  H1   C5   C6   C7    180.00   0.0  0
 KX3  CONST_25  H2   C6   C7   C8    180.00   0.0  0
 KX3  CONST_26  H3   C8   C9   C10   180.00   0.0  0
 KX3  CONST_27  H6   C3   N4   C10   180.00   0.0  0
 KX3  CONST_28  H2   C6   C5   C10   180.00   0.0  0
 KX3  CONST_29  H7   C2   N1   C9    180.00   0.0  0
 KX3  CONST_30  H1   C5   C10  C9    180.00   0.0  0
 KX3  CONST_31  H7   C2   C3   N4    180.00   0.0  0
 KX3  CONST_32  H1   C5   C10  N4      0.00   0.0  0
 KX3  Var_01    N12  C11  C7   C6     86.30  30.0  2
 KX3  Var_02    N12  C11  C7   C8    -91.62  30.0  2
 KX3  Var_03    H4   C11  C7   C6    -39.00  30.0  2
 KX3  Var_04    H5   C11  C7   C6   -155.13  30.0  2
 KX3  Var_05    H4   C11  C7   C8    143.09  30.0  2
 KX3  Var_06    H5   C11  C7   C8     26.96  30.0  2
 KX3  Var_07    H8   N12  C11  C7    177.63  30.0  3
 KX3  Var_08    H9   N12  C11  C7    -67.49  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
 KX3  plan-1  N1   0.020
 KX3  plan-1  C5   0.020
 KX3  plan-1  C6   0.020
 KX3  plan-1  C7   0.020
 KX3  plan-1  C8   0.020
 KX3  plan-1  C10  0.020
 KX3  plan-1  C11  0.020
 KX3  plan-1  C9   0.020
 KX3  plan-1  C3   0.020
 KX3  plan-1  C2   0.020
 KX3  plan-1  N4   0.020
 KX3  plan-1  H1   0.020
 KX3  plan-1  H2   0.020
 KX3  plan-1  H3   0.020
 KX3  plan-1  H6   0.020
 KX3  plan-1  H7   0.020

