# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:22:56 2022
#   Inital geometry file: a 86 line input string
#   Ligand name: N-(4-cyanobenzyl)-L-asparagine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CC(=O)NCc1ccc(cc1)C#N)C(O)=O
#
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
 AS7  AS7  N-(4-cyanobenzyl)-L-asparagine  L-peptide  30  18  .  2016-04-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_AS7
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
 AS7  C     C  C      0   0.415  16.6791  -13.6325  22.5375
 AS7  N     N  NH2    0  -0.797  17.4581  -15.7658  23.5667
 AS7  O     O  O      0  -0.602  16.3407  -13.3293  23.6979
 AS7  C1    C  CH2    0  -0.334  14.4985  -18.5916  21.7515
 AS7  C2    C  C      0   0.088  14.3008  -18.9284  23.2114
 AS7  C3    C  C1     0  -0.274  13.3111  -19.8515  23.5507
 AS7  C4    C  C1     0  -0.230  13.0738  -20.1895  24.8683
 AS7  C5    C  C      0  -0.007  13.8384  -19.5981  25.8757
 AS7  C6    C  C1     0  -0.232  14.8315  -18.6771  25.5485
 AS7  C7    C  C1     0  -0.311  15.0588  -18.3458  24.2222
 AS7  C8    C  CSP    0   0.050  13.6003  -19.9397  27.2400
 AS7  N9    N  NS     0  -0.253  13.4029  -20.2169  28.3412
 AS7  CA    C  CH1    0  -0.210  17.4722  -14.9538  22.3597
 AS7  CB    C  CH2    0  -0.558  16.9784  -15.7907  21.1774
 AS7  CG    C  C      0   0.555  15.6508  -16.4439  21.4824
 AS7  OD1   O  O      0  -0.488  14.6371  -15.8033  21.7204
 AS7  ND2   N  NH1    0  -0.636  15.6555  -17.7942  21.4601
 AS7  OXT   O  OC    -1  -0.608  16.5072  -12.9572  21.5050
 AS7  H     H  HNH2   0   0.335  18.2990  -16.3248  23.6271
 AS7  H2    H  HNH2   0   0.339  17.4428  -15.1499  24.3685
 AS7  H1    H  HCH2   0   0.275  14.5676  -19.5199  21.1817
 AS7  H1A   H  HCH2   0   0.270  13.6080  -18.0763  21.3864
 AS7  H3    H  H      0   0.263  12.7175  -20.3141  22.7710
 AS7  H4    H  H      0   0.277  12.3039  -20.9074  25.1182
 AS7  H6    H  H      0   0.274  15.4242  -18.2193  26.3297
 AS7  H7    H  H      0   0.293  15.8347  -17.6248  23.9855
 AS7  HA    H  HCH1   0   0.218  18.4928  -14.6314  22.0968
 AS7  HB    H  HCH2   0   0.252  16.8637  -15.1494  20.3026
 AS7  HBA   H  HCH2   0   0.238  17.7275  -16.5447  20.9239
 AS7  HND2  H  HNH1   0   0.400  16.5275  -18.2744  21.3128

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
 AS7  C    O     deloc     1.231  0.020  1.231
 AS7  C    CA    single    1.525  0.021  1.525
 AS7  C    OXT   deloc     1.246  0.020  1.246
 AS7  N    CA    single    1.458  0.019  1.458
 AS7  C1   C2    single    1.511  0.020  1.511
 AS7  C1   ND2   single    1.435  0.020  1.435
 AS7  C2   C3    aromatic  1.395  0.020  1.395
 AS7  C2   C7    aromatic  1.391  0.020  1.391
 AS7  C3   C4    aromatic  1.381  0.020  1.381
 AS7  C4   C5    aromatic  1.396  0.020  1.396
 AS7  C5   C6    aromatic  1.393  0.020  1.393
 AS7  C5   C8    single    1.426  0.020  1.426
 AS7  C6   C7    aromatic  1.386  0.020  1.386
 AS7  C8   N9    triple    1.153  0.020  1.153
 AS7  CA   CB    single    1.530  0.020  1.530
 AS7  CB   CG    single    1.511  0.020  1.511
 AS7  CG   OD1   double    1.223  0.020  1.223
 AS7  CG   ND2   single    1.350  0.020  1.350
 AS7  N    H     single    0.860  0.020  0.860
 AS7  N    H2    single    0.890  0.020  1.040
 AS7  C1   H1    single    0.970  0.020  1.090
 AS7  C1   H1A   single    0.970  0.020  1.090
 AS7  C3   H3    single    0.930  0.020  1.080
 AS7  C4   H4    single    0.930  0.020  1.080
 AS7  C6   H6    single    0.930  0.020  1.080
 AS7  C7   H7    single    0.930  0.020  1.080
 AS7  CA   HA    single    0.970  0.020  0.970
 AS7  CB   HB    single    0.970  0.020  1.090
 AS7  CB   HBA   single    0.970  0.020  1.090
 AS7  ND2  HND2  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
 AS7  OXT   C    CA   115.93  3.000
 AS7  OXT   C    O    127.05  3.000
 AS7  CA    C    O    120.80  1.700
 AS7  H2    N    H    107.57  3.000
 AS7  H2    N    CA   108.54  3.000
 AS7  H     N    CA   114.00  3.000
 AS7  H1A   C1   H1   106.17  3.000
 AS7  H1A   C1   ND2  109.11  3.000
 AS7  H1    C1   ND2  108.40  3.000
 AS7  H1A   C1   C2   108.75  3.000
 AS7  H1    C1   C2   108.85  3.000
 AS7  ND2   C1   C2   115.18  3.000
 AS7  C7    C2   C3   119.13  3.000
 AS7  C7    C2   C1   122.50  3.000
 AS7  C3    C2   C1   118.37  3.000
 AS7  H3    C3   C4   119.20  3.000
 AS7  H3    C3   C2   119.74  3.000
 AS7  C4    C3   C2   121.06  3.000
 AS7  H4    C4   C5   120.27  3.000
 AS7  H4    C4   C3   120.34  3.000
 AS7  C5    C4   C3   119.39  3.000
 AS7  C8    C5   C6   120.13  3.000
 AS7  C8    C5   C4   119.82  3.000
 AS7  C6    C5   C4   120.06  3.000
 AS7  H6    C6   C7   120.00  3.000
 AS7  H6    C6   C5   120.02  3.000
 AS7  C7    C6   C5   119.98  3.000
 AS7  H7    C7   C6   119.00  3.000
 AS7  H7    C7   C2   120.61  3.000
 AS7  C6    C7   C2   120.39  3.000
 AS7  N9    C8   C5   180.00  3.000
 AS7  HA    CA   CB   109.00  3.000
 AS7  HA    CA   N    110.00  3.000
 AS7  CB    CA   N    110.50  1.700
 AS7  HA    CA   C    109.00  3.000
 AS7  CB    CA   C    110.10  1.900
 AS7  N     CA   C    111.00  2.800
 AS7  HBA   CB   HB   106.96  3.000
 AS7  HBA   CB   CG   110.55  3.000
 AS7  HB    CB   CG   108.89  3.000
 AS7  HBA   CB   CA   109.60  3.000
 AS7  HB    CB   CA   109.39  3.000
 AS7  CG    CB   CA   111.35  3.000
 AS7  ND2   CG   OD1  122.01  3.000
 AS7  ND2   CG   CB   115.21  3.000
 AS7  OD1   CG   CB   122.78  3.000
 AS7  HND2  ND2  CG   118.85  3.000
 AS7  HND2  ND2  C1   117.59  3.000
 AS7  CG    ND2  C1   123.33  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
 AS7  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 AS7  CONST_02  C5    C6   C7   C2     0.00   0.0  0
 AS7  CONST_03  C6    C7   C2   C3     0.00   0.0  0
 AS7  CONST_04  C6    C5   C4   C3     0.00   0.0  0
 AS7  CONST_05  C7    C2   C3   C4     0.00   0.0  0
 AS7  CONST_06  C7    C6   C5   C4     0.00   0.0  0
 AS7  CONST_07  C4    C3   C2   C1   180.00   0.0  0
 AS7  CONST_08  C6    C7   C2   C1   180.00   0.0  0
 AS7  CONST_09  C8    C5   C4   C3   180.00   0.0  0
 AS7  CONST_10  C8    C5   C6   C7   180.00   0.0  0
 AS7  CONST_11  H4    C4   C3   C2   180.00   0.0  0
 AS7  CONST_12  H6    C6   C7   C2   180.00   0.0  0
 AS7  CONST_13  H7    C7   C2   C3   180.00   0.0  0
 AS7  CONST_14  H3    C3   C4   C5   180.00   0.0  0
 AS7  CONST_15  CB    CG   ND2  C1   180.00   0.0  0
 AS7  CONST_16  OD1   CG   ND2  C1     0.00   0.0  0
 AS7  CONST_17  HND2  ND2  CG   CB     0.00   0.0  0
 AS7  Var_01    ND2   C1   C2   C3  -171.11  30.0  2
 AS7  Var_02    CG    ND2  C1   C2   -87.92  30.0  3
 AS7  Var_03    OD1   CG   CB   CA    62.09  30.0  3

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
 AS7  chir_01  CA  C  N  CB  negativ

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
 AS7  plan-1  C1    0.020
 AS7  plan-1  C2    0.020
 AS7  plan-1  C3    0.020
 AS7  plan-1  C4    0.020
 AS7  plan-1  C5    0.020
 AS7  plan-1  C6    0.020
 AS7  plan-1  C7    0.020
 AS7  plan-1  C8    0.020
 AS7  plan-1  N9    0.020
 AS7  plan-1  H3    0.020
 AS7  plan-1  H4    0.020
 AS7  plan-1  H6    0.020
 AS7  plan-1  H7    0.020
 AS7  plan-2  C1    0.020
 AS7  plan-2  CB    0.020
 AS7  plan-2  CG    0.020
 AS7  plan-2  OD1   0.020
 AS7  plan-2  ND2   0.020
 AS7  plan-2  HND2  0.020
 AS7  plan-3  C     0.020
 AS7  plan-3  O     0.020
 AS7  plan-3  CA    0.020
 AS7  plan-3  OXT   0.020

