# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 00:49:54 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  32  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   0.555   2.8613   1.7189  -0.3154
 NX6  N     N  NH1   0  -0.657   1.1535  -0.0101  -0.1151
 NX6  O     O  O     0  -0.425   2.0894   2.4579  -0.8651
 NX6  C1    C  C     0   0.770   0.2282   0.5143   0.7161
 NX6  O1    O  O     0  -0.515   0.4860   1.1306   1.7288
 NX6  C2    C  CH2   0  -0.243  -2.0907   0.7375   1.0898
 NX6  O2    O  O2    0  -0.477  -1.0060   0.2444   0.2909
 NX6  C3    C  CR6   0   0.075  -3.3564   0.2431   0.4595
 NX6  C4    C  CR16  0  -0.287  -3.8280  -1.0369   0.7379
 NX6  C5    C  CR16  0  -0.242  -4.9865  -1.5071   0.1360
 NX6  C6    C  CR16  0  -0.261  -5.6860  -0.6994  -0.7522
 NX6  C7    C  CR16  0  -0.242  -5.2225   0.5786  -1.0349
 NX6  C8    C  CR16  0  -0.293  -4.0617   1.0451  -0.4322
 NX6  CA    C  CH1   0  -0.196   2.5451   0.2778   0.0727
 NX6  CB    C  CH2   0  -0.616   3.3900  -0.6923  -0.7460
 NX6  CG    C  C     0   0.567   3.2749  -2.1093  -0.2435
 NX6  OD1   O  OH1   0  -0.589   3.6474  -2.9827  -1.1681
 NX6  OD2   O  O     0  -0.433   2.9273  -2.4183   0.8671
 NX6  OXT   O  OH1   0  -0.589   4.0956   2.0491   0.0309
 NX6  HN    H  HNH1  0   0.406   0.8523  -0.3642  -1.0106
 NX6  H2    H  HCH2  0   0.251  -1.9968   0.3730   2.1144
 NX6  H2A   H  HCH2  0   0.251  -2.0692   1.8288   1.1134
 NX6  H4    H  HCR6  0   0.256  -3.2907  -1.6693   1.4348
 NX6  H5    H  HCR6  0   0.259  -5.3443  -2.5032   0.3620
 NX6  H6    H  HCR6  0   0.259  -6.5918  -1.0638  -1.2191
 NX6  H7    H  HCR6  0   0.259  -5.7638   1.2130  -1.7245
 NX6  H8    H  HCR6  0   0.256  -3.7052   2.0442  -0.6536
 NX6  HA    H  HCH1  0   0.306   2.8003   0.1573   1.1287
 NX6  HB    H  HCH2  0   0.298   3.1276  -0.6419  -1.8054
 NX6  HBA   H  HCH2  0   0.325   4.4465  -0.4183  -0.6836
 NX6  HOD1  H  HOH1  0   0.484   3.6161  -3.8823  -0.8085
 NX6  HOXT  H  HOH1  0   0.488   4.2911   2.9599  -0.2369

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     double    1.202  0.020  1.202
 NX6  C    CA    single    1.526  0.020  1.526
 NX6  C    OXT   single    1.324  0.020  1.324
 NX6  CA   N     single    1.433  0.020  1.433
 NX6  N    C1    single    1.350  0.020  1.350
 NX6  N    HN    single    0.860  0.020  1.020
 NX6  O1   C1    double    1.213  0.020  1.213
 NX6  C1   O2    single    1.333  0.020  1.333
 NX6  O2   C2    single    1.435  0.020  1.435
 NX6  C2   C3    single    1.498  0.020  1.498
 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  1.392  0.020  1.392
 NX6  C4   C5    aromatic  1.388  0.020  1.388
 NX6  C4   H4    single    0.930  0.020  1.080
 NX6  C6   C5    aromatic  1.389  0.020  1.389
 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    1.525  0.020  1.525
 NX6  CA   HA    single    0.970  0.020  1.090
 NX6  CG   CB    single    1.508  0.020  1.508
 NX6  CB   HB    single    0.970  0.020  1.090
 NX6  CB   HBA   single    0.970  0.020  1.090
 NX6  OD2  CG    double    1.204  0.020  1.204
 NX6  CG   OD1   single    1.325  0.020  1.325
 NX6  OD1  HOD1  single    0.850  0.020  0.980
 NX6  OXT  HOXT  single    0.850  0.020  0.980

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   111.24  3.000
 NX6  OXT   C    O    124.41  3.000
 NX6  CA    C    O    124.35  3.000
 NX6  HN    N    CA   118.46  3.000
 NX6  HN    N    C1   118.57  3.000
 NX6  CA    N    C1   120.45  3.000
 NX6  O2    C1   O1   124.47  3.000
 NX6  O2    C1   N    111.07  3.000
 NX6  O1    C1   N    124.45  3.000
 NX6  H2A   C2   H2   108.16  3.000
 NX6  H2A   C2   C3   110.84  3.000
 NX6  H2    C2   C3   110.95  3.000
 NX6  H2A   C2   O2   109.92  3.000
 NX6  H2    C2   O2   110.05  3.000
 NX6  C3    C2   O2   106.93  3.000
 NX6  C2    O2   C1   116.93  3.000
 NX6  C8    C3   C4   119.10  3.000
 NX6  C4    C3   C2   120.37  3.000
 NX6  C8    C3   C2   120.52  3.000
 NX6  H4    C4   C5   119.68  3.000
 NX6  H4    C4   C3   119.81  3.000
 NX6  C5    C4   C3   120.51  3.000
 NX6  H5    C5   C6   120.14  3.000
 NX6  H5    C5   C4   119.83  3.000
 NX6  C6    C5   C4   120.04  3.000
 NX6  H6    C6   C7   120.09  3.000
 NX6  H6    C6   C5   120.09  3.000
 NX6  C7    C6   C5   119.81  3.000
 NX6  H7    C7   C8   119.85  3.000
 NX6  H7    C7   C6   120.16  3.000
 NX6  C8    C7   C6   119.99  3.000
 NX6  H8    C8   C7   119.74  3.000
 NX6  H8    C8   C3   119.71  3.000
 NX6  C7    C8   C3   120.55  3.000
 NX6  HA    CA   CB   108.61  3.000
 NX6  HA    CA   N    109.34  3.000
 NX6  CB    CA   N    109.86  3.000
 NX6  HA    CA   C    107.55  3.000
 NX6  CB    CA   C    110.46  3.000
 NX6  N     CA   C    110.95  3.000
 NX6  HBA   CB   HB   106.01  3.000
 NX6  HBA   CB   CG   106.88  3.000
 NX6  HB    CB   CG   110.38  3.000
 NX6  HBA   CB   CA   110.20  3.000
 NX6  HB    CB   CA   110.99  3.000
 NX6  CG    CB   CA   112.12  3.000
 NX6  OD2   CG   OD1  123.75  3.000
 NX6  OD1   CG   CB   111.42  3.000
 NX6  OD2   CG   CB   124.79  3.000
 NX6  HOD1  OD1  CG   110.10  3.000
 NX6  HOXT  OXT  C    110.49  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  CONST_14  HOXT  OXT  C   O      0.00   0.0  0
 NX6  CONST_15  HOD1  OD1  CG  CB   180.00   0.0  0
 NX6  Var_01    C8    C3   C2  O2   -95.34  30.0  2
 NX6  Var_02    C3    C2   O2  C1  -176.72  30.0  3
 NX6  Var_03    CA    N    C1  O1    -7.75  30.0  1
 NX6  Var_04    OD2   CG   CB  CA   -21.70  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
 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-2  HOXT  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-3  HOD1  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

