# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:57:22 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-[(benzyloxy)carbonyl]-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@H](NC(=O)OCc1ccccc1)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
 NX6  NX6  'N-[(benzyloxy)carbonyl]-L-aspartic acid'  ligand  30  19  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NX6
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
 NX6  C    C  C      0   0.410   2.8624   1.7706  -0.1253
 NX6  N    N  NH1    0  -0.648   1.1692  -0.0599  -0.0087
 NX6  O    O  O      0  -0.602   1.9760   2.4450  -0.6786
 NX6  C1   C  C      0   0.755   0.2282   0.4740   0.7821
 NX6  O1   O  O      0  -0.535   0.4323   1.0460   1.8356
 NX6  C2   C  CH2    0  -0.235  -2.1043   0.7189   1.0727
 NX6  O2   O  O2     0  -0.488  -1.0027   0.2575   0.2873
 NX6  C3   C  C      0   0.077  -3.3540   0.2501   0.3907
 NX6  C4   C  C1     0  -0.289  -3.8303  -1.0406   0.6060
 NX6  C5   C  C1     0  -0.243  -4.9720  -1.4888  -0.0428
 NX6  C6   C  C1     0  -0.262  -5.6506  -0.6482  -0.9168
 NX6  C7   C  C1     0  -0.242  -5.1821   0.6400  -1.1380
 NX6  C8   C  C1     0  -0.295  -4.0382   1.0843  -0.4876
 NX6  CA   C  CH1    0  -0.184   2.5646   0.2796   0.1678
 NX6  CB   C  CH2    0  -0.597   3.4046  -0.6253  -0.7248
 NX6  CG   C  C      0   0.408   3.2860  -2.1225  -0.3842
 NX6  OD1  O  OC    -1  -0.620   3.1929  -2.9156  -1.3434
 NX6  OD2  O  O      0  -0.613   3.3266  -2.4261   0.8248
 NX6  OXT  O  OC    -1  -0.622   4.0003   2.1562   0.2135
 NX6  HN   H  HNH1   0   0.382   0.8798  -0.3811  -0.9196
 NX6  H2   H  HCH2   0   0.242  -2.0437   0.3165   2.0861
 NX6  H2A  H  HCH2   0   0.242  -2.0886   1.8090   1.1422
 NX6  H4   H  H      0   0.254  -3.3091  -1.6985   1.2917
 NX6  H5   H  H      0   0.258  -5.3337  -2.4933   0.1350
 NX6  H6   H  H      0   0.258  -6.5437  -0.9952  -1.4200
 NX6  H7   H  H      0   0.258  -5.7063   1.2994  -1.8174
 NX6  H8   H  H      0   0.255  -3.6780   2.0917  -0.6615
 NX6  HA   H  HCH1   0   0.228   2.8413   0.0700   1.2031
 NX6  HB   H  HCH2   0   0.208   3.1553  -0.4508  -1.7768
 NX6  HBA  H  HCH2   0   0.241   4.4510  -0.3304  -0.6048

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
 NX6  O    C    deloc     1.244  0.020  1.244
 NX6  C    CA   single    1.548  0.020  1.548
 NX6  C    OXT  deloc     1.248  0.020  1.248
 NX6  CA   N    single    1.447  0.020  1.447
 NX6  N    C1   single    1.340  0.020  1.340
 NX6  N    HN   single    0.890  0.020  1.040
 NX6  O1   C1   double    1.216  0.020  1.216
 NX6  C1   O2   single    1.344  0.020  1.344
 NX6  O2   C2   single    1.429  0.020  1.429
 NX6  C2   C3   single    1.499  0.020  1.499
 NX6  C2   H2   single    0.970  0.020  1.090
 NX6  C2   H2A  single    0.970  0.020  1.090
 NX6  C8   C3   aromatic  1.391  0.020  1.391
 NX6  C3   C4   aromatic  1.393  0.020  1.393
 NX6  C4   C5   aromatic  1.388  0.020  1.388
 NX6  C4   H4   single    0.930  0.020  1.080
 NX6  C6   C5   aromatic  1.390  0.020  1.390
 NX6  C5   H5   single    0.930  0.020  1.080
 NX6  C7   C6   aromatic  1.388  0.020  1.388
 NX6  C6   H6   single    0.930  0.020  1.080
 NX6  C8   C7   aromatic  1.389  0.020  1.389
 NX6  C7   H7   single    0.930  0.020  1.080
 NX6  C8   H8   single    0.930  0.020  1.080
 NX6  CB   CA   single    1.524  0.020  1.524
 NX6  CA   HA   single    0.970  0.020  1.090
 NX6  CG   CB   single    1.540  0.020  1.540
 NX6  CB   HB   single    0.970  0.020  1.090
 NX6  CB   HBA  single    0.970  0.020  1.090
 NX6  OD2  CG   deloc     1.247  0.020  1.247
 NX6  CG   OD1  deloc     1.248  0.020  1.248

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
 NX6  OXT  C   CA   114.92  3.000
 NX6  OXT  C   O    127.08  3.000
 NX6  CA   C   O    117.99  3.000
 NX6  HN   N   CA   117.50  3.000
 NX6  HN   N   C1   117.29  3.000
 NX6  CA   N   C1   120.78  3.000
 NX6  O2   C1  O1   123.25  3.000
 NX6  O2   C1  N    111.20  3.000
 NX6  O1   C1  N    125.50  3.000
 NX6  H2A  C2  H2   107.93  3.000
 NX6  H2A  C2  C3   110.67  3.000
 NX6  H2   C2  C3   110.69  3.000
 NX6  H2A  C2  O2   110.24  3.000
 NX6  H2   C2  O2   110.38  3.000
 NX6  C3   C2  O2   106.95  3.000
 NX6  C2   O2  C1   116.84  3.000
 NX6  C8   C3  C4   119.02  3.000
 NX6  C4   C3  C2   120.31  3.000
 NX6  C8   C3  C2   120.65  3.000
 NX6  H4   C4  C5   119.70  3.000
 NX6  H4   C4  C3   119.73  3.000
 NX6  C5   C4  C3   120.57  3.000
 NX6  H5   C5  C6   120.10  3.000
 NX6  H5   C5  C4   119.86  3.000
 NX6  C6   C5  C4   120.03  3.000
 NX6  H6   C6  C7   120.12  3.000
 NX6  H6   C6  C5   120.10  3.000
 NX6  C7   C6  C5   119.78  3.000
 NX6  H7   C7  C8   119.87  3.000
 NX6  H7   C7  C6   120.13  3.000
 NX6  C8   C7  C6   120.00  3.000
 NX6  H8   C8  C7   119.73  3.000
 NX6  H8   C8  C3   119.68  3.000
 NX6  C7   C8  C3   120.59  3.000
 NX6  HA   CA  CB   107.56  3.000
 NX6  HA   CA  N    108.35  3.000
 NX6  CB   CA  N    108.72  3.000
 NX6  HA   CA  C    108.40  3.000
 NX6  CB   CA  C    110.79  3.000
 NX6  N    CA  C    112.85  3.000
 NX6  HBA  CB  HB   106.27  3.000
 NX6  HBA  CB  CG   108.15  3.000
 NX6  HB   CB  CG   110.48  3.000
 NX6  HBA  CB  CA   107.64  3.000
 NX6  HB   CB  CA   110.03  3.000
 NX6  CG   CB  CA   113.92  3.000
 NX6  OD2  CG  OD1  126.36  3.000
 NX6  OD1  CG  CB   116.97  3.000
 NX6  OD2  CG  CB   116.65  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
 NX6  CONST_01  C6   C7  C8  C3     0.00   0.0  0
 NX6  CONST_02  C6   C5  C4  C3     0.00   0.0  0
 NX6  CONST_03  C7   C8  C3  C4     0.00   0.0  0
 NX6  CONST_04  C7   C6  C5  C4     0.00   0.0  0
 NX6  CONST_05  C8   C3  C4  C5     0.00   0.0  0
 NX6  CONST_06  C8   C7  C6  C5     0.00   0.0  0
 NX6  CONST_07  C7   C8  C3  C2   180.00   0.0  0
 NX6  CONST_08  C5   C4  C3  C2   180.00   0.0  0
 NX6  CONST_09  H7   C7  C8  C3   180.00   0.0  0
 NX6  CONST_10  H5   C5  C4  C3   180.00   0.0  0
 NX6  CONST_11  H8   C8  C3  C4   180.00   0.0  0
 NX6  CONST_12  H6   C6  C5  C4   180.00   0.0  0
 NX6  CONST_13  H4   C4  C5  C6   180.00   0.0  0
 NX6  Var_01    C8   C3  C2  O2   -95.38  30.0  2
 NX6  Var_02    C3   C2  O2  C1  -174.60  30.0  3
 NX6  Var_03    CA   N   C1  O1   -15.15  30.0  2
 NX6  Var_04    OD2  CG  CB  CA   -44.05  30.0  2

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
 NX6  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
 NX6  plan-1  C2   0.020
 NX6  plan-1  C3   0.020
 NX6  plan-1  C4   0.020
 NX6  plan-1  C5   0.020
 NX6  plan-1  C6   0.020
 NX6  plan-1  C7   0.020
 NX6  plan-1  C8   0.020
 NX6  plan-1  H4   0.020
 NX6  plan-1  H5   0.020
 NX6  plan-1  H6   0.020
 NX6  plan-1  H7   0.020
 NX6  plan-1  H8   0.020
 NX6  plan-2  C    0.020
 NX6  plan-2  O    0.020
 NX6  plan-2  CA   0.020
 NX6  plan-2  OXT  0.020
 NX6  plan-3  CB   0.020
 NX6  plan-3  CG   0.020
 NX6  plan-3  OD1  0.020
 NX6  plan-3  OD2  0.020
 NX6  plan-4  N    0.020
 NX6  plan-4  C1   0.020
 NX6  plan-4  O1   0.020
 NX6  plan-4  O2   0.020

