# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 17 13:30:09 2020
#   Inital geometry file: a 54 line input string
#   Ligand name: (4S,5Z)-4-amino-5-iminopentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCC(N)=O)C=N
#
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
 0JU  0JU  (4S,5Z)-4-amino-5-iminopentanamide  ligand  20  9  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_0JU
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
 0JU  C    C  C1    0  -0.039  -2.5620   0.6286   0.5116
 0JU  NF   N  N     0  -0.546  -3.6086   0.5749  -0.1927
 0JU  CA   C  CH1   0  -0.149  -1.4562  -0.3888   0.3903
 0JU  N    N  NH2   0  -0.779  -1.6982  -1.4486  -0.5642
 0JU  CB   C  CH2   0  -0.431  -0.1456   0.3408   0.0816
 0JU  CG   C  CH2   0  -0.568   1.0597  -0.5847   0.1353
 0JU  CD   C  C     0   0.525   2.3583   0.1136  -0.2053
 0JU  OE   O  O     0  -0.499   2.4085   1.0671  -0.9707
 0JU  NE   N  NH2   0  -0.805   3.4519  -0.4081   0.3720
 0JU  H1   H  H     0   0.216  -2.3830   1.4066   1.2608
 0JU  H2   H  H     0   0.344  -4.2326   1.3427   0.0384
 0JU  H3   H  HCH1  0   0.247  -1.3545  -0.8443   1.3847
 0JU  H4   H  HNH2  0   0.347  -2.5603  -1.9224  -0.3236
 0JU  H5   H  HNH2  0   0.336  -1.8707  -1.0386  -1.4753
 0JU  H7   H  HCH2  0   0.236  -0.2193   0.8050  -0.9056
 0JU  H8   H  HCH2  0   0.239  -0.0179   1.1554   0.7995
 0JU  H9   H  HCH2  0   0.249   1.1278  -1.0556   1.1195
 0JU  H10  H  HCH2  0   0.277   0.9269  -1.4010  -0.5803
 0JU  H11  H  HNH2  0   0.404   3.4002  -1.1967   0.9920
 0JU  H12  H  HNH2  0   0.396   4.3658  -0.0436   0.1586

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
 0JU  OE  CD   double  1.224  0.020  1.224
 0JU  NE  CD   single  1.342  0.020  1.342
 0JU  CD  CG   single  1.513  0.020  1.513
 0JU  CG  CB   single  1.521  0.020  1.521
 0JU  CB  CA   single  1.531  0.020  1.531
 0JU  CA  N    single  1.447  0.020  1.447
 0JU  CA  C    single  1.508  0.020  1.508
 0JU  C   NF   double  1.263  0.020  1.263
 0JU  C   H1   single  0.930  0.020  1.080
 0JU  NF  H2   single  0.890  0.020  1.040
 0JU  CA  H3   single  0.970  0.020  1.090
 0JU  N   H4   single  0.890  0.020  1.040
 0JU  N   H5   single  0.890  0.020  1.040
 0JU  CB  H7   single  0.970  0.020  1.090
 0JU  CB  H8   single  0.970  0.020  1.090
 0JU  CG  H9   single  0.970  0.020  1.090
 0JU  CG  H10  single  0.970  0.020  1.090
 0JU  NE  H11  single  0.860  0.020  1.020
 0JU  NE  H12  single  0.860  0.020  1.020

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
 0JU  H1   C   CA   114.50  3.000
 0JU  H1   C   NF   123.20  3.000
 0JU  CA   C   NF   122.30  3.000
 0JU  H2   NF  C    110.49  3.000
 0JU  H3   CA  CB   107.51  3.000
 0JU  H3   CA  N    108.00  3.000
 0JU  CB   CA  N    111.05  3.000
 0JU  H3   CA  C    105.95  3.000
 0JU  N    CA  C    115.14  3.000
 0JU  CB   CA  C    108.81  3.000
 0JU  H5   N   H4   104.95  3.000
 0JU  H5   N   CA   108.97  3.000
 0JU  H4   N   CA   109.17  3.000
 0JU  H8   CB  H7   106.52  3.000
 0JU  H8   CB  CG   109.74  3.000
 0JU  H7   CB  CG   110.11  3.000
 0JU  H8   CB  CA   108.82  3.000
 0JU  H7   CB  CA   109.06  3.000
 0JU  CG   CB  CA   112.41  3.000
 0JU  H10  CG  H9   105.97  3.000
 0JU  H10  CG  CD   107.54  3.000
 0JU  H9   CG  CD   110.36  3.000
 0JU  H10  CG  CB   109.57  3.000
 0JU  H9   CG  CB   110.09  3.000
 0JU  CD   CG  CB   113.04  3.000
 0JU  NE   CD  OE   122.58  3.000
 0JU  NE   CD  CG   115.03  3.000
 0JU  OE   CD  CG   122.38  3.000
 0JU  H12  NE  H11  117.50  3.000
 0JU  H12  NE  CD   120.52  3.000
 0JU  H11  NE  CD   121.92  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
 0JU  CONST_01  H11  NE  CD  CG    0.00   0.0  0
 0JU  CONST_02  H12  NE  CD  CG  180.00   0.0  0
 0JU  Var_01    CD   CG  CB  CA  178.41  30.0  1
 0JU  Var_02    OE   CD  CG  CB  -29.94  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 0JU  chir_01  CA  CB  N  C  positiv

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
 0JU  plan-1  CG   0.020
 0JU  plan-1  CD   0.020
 0JU  plan-1  OE   0.020
 0JU  plan-1  NE   0.020
 0JU  plan-1  H11  0.020
 0JU  plan-1  H12  0.020
 0JU  plan-2  C    0.020
 0JU  plan-2  NF   0.020
 0JU  plan-2  CA   0.020
 0JU  plan-2  H1   0.020
 0JU  plan-2  H2   0.020

