# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 20:46:03 2020
#   Inital geometry file: a 84 line input string
#   Ligand name: 4-{[(R)-carboxy(phenyl)methyl]amino}-4-oxobutanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCC(=O)N[C@@H](C(O)=O)c1ccccc1
#
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
 NPG  NPG  '4-{[(R)-carboxy(phenyl)methyl]amino}-4-oxobutanoic acid'  ligand  29  18  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_NPG
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
 NPG  O61  O  O      0  -0.611   1.8425   0.5413   4.6429
 NPG  O62  O  OC    -1  -0.627   0.3980  -0.5157   5.9666
 NPG  C6   C  C      0   0.412   0.8131  -0.1307   4.8540
 NPG  C5   C  CH2    0  -0.573  -0.0221  -0.5659   3.6357
 NPG  C4   C  CH2    0  -0.575   0.2235   0.2569   2.3810
 NPG  O31  O  O      0  -0.519  -1.7701  -0.5557   1.3031
 NPG  C3   C  C      0   0.572  -0.6055  -0.1880   1.1968
 NPG  N1   N  NH1    0  -0.646   0.0233  -0.1480   0.0124
 NPG  C2   C  C      0   0.412  -1.8371   0.6195  -1.4828
 NPG  C1   C  CH1    0  -0.206  -0.6740  -0.3872  -1.2287
 NPG  CG   C  CR6    0   0.087   0.2813  -0.2737  -2.3878
 NPG  CD1  C  CR16   0  -0.294   1.0518   0.8764  -2.5628
 NPG  CD2  C  CR16   0  -0.326   0.3796  -1.2927  -3.3296
 NPG  CE1  C  CR16   0  -0.241   1.9102   0.9943  -3.6465
 NPG  CE2  C  CR16   0  -0.241   1.2320  -1.1733  -4.4201
 NPG  CZ   C  CR16   0  -0.271   2.0028  -0.0302  -4.5808
 NPG  H51  H  HCH2   0   0.232   0.2124  -1.6181   3.4340
 NPG  H52  H  HCH2   0   0.221  -1.0811  -0.5483   3.9001
 NPG  H41  H  HCH2   0   0.254  -0.0330   1.3049   2.5708
 NPG  H42  H  HCH2   0   0.238   1.2850   0.2521   2.1311
 NPG  HN1  H  HNH1   0   0.392   0.9774   0.1719  -0.0156
 NPG  H1   H  HCH1   0   0.243  -1.0930  -1.3973  -1.2196
 NPG  HD1  H  HCR6   0   0.252   0.9711   1.6930  -1.8556
 NPG  HD2  H  HCR6   0   0.248  -0.2126  -2.1918  -3.2081
 NPG  HE1  H  HCR6   0   0.253   2.5028   1.8925  -3.7662
 NPG  HE2  H  HCR6   0   0.254   1.2966  -1.9774  -5.1419
 NPG  HZ   H  HCR6   0   0.253   2.6702   0.0631  -5.4277
 NPG  O11  O  O      0  -0.604  -2.7307   0.1985  -2.2395
 NPG  O12  O  OC    -1  -0.592  -1.7357   1.7429  -0.9670

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
 NPG  O61  C6   deloc     1.247  0.020  1.247
 NPG  O62  C6   deloc     1.248  0.020  1.248
 NPG  C6   C5   single    1.540  0.020  1.540
 NPG  C5   C4   single    1.520  0.020  1.520
 NPG  C5   H51  single    0.970  0.020  1.090
 NPG  C5   H52  single    0.970  0.020  1.090
 NPG  C4   C3   single    1.512  0.020  1.512
 NPG  C4   H41  single    0.970  0.020  1.090
 NPG  C4   H42  single    0.970  0.020  1.090
 NPG  O31  C3   double    1.226  0.020  1.226
 NPG  C3   N1   single    1.342  0.020  1.342
 NPG  N1   C1   single    1.443  0.020  1.443
 NPG  N1   HN1  single    0.860  0.020  1.020
 NPG  O11  C2   deloc     1.244  0.020  1.244
 NPG  O12  C2   deloc     1.240  0.020  1.240
 NPG  C2   C1   single    1.559  0.020  1.559
 NPG  C1   CG   single    1.506  0.020  1.506
 NPG  C1   H1   single    0.970  0.020  1.090
 NPG  CG   CD1  aromatic  1.395  0.020  1.395
 NPG  CG   CD2  aromatic  1.391  0.020  1.391
 NPG  CD1  CE1  aromatic  1.388  0.020  1.388
 NPG  CD1  HD1  single    0.930  0.020  1.080
 NPG  CD2  CE2  aromatic  1.389  0.020  1.389
 NPG  CD2  HD2  single    0.930  0.020  1.080
 NPG  CE1  CZ   aromatic  1.390  0.020  1.390
 NPG  CE1  HE1  single    0.930  0.020  1.080
 NPG  CE2  CZ   aromatic  1.388  0.020  1.388
 NPG  CE2  HE2  single    0.930  0.020  1.080
 NPG  CZ   HZ   single    0.930  0.020  1.080

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
 NPG  C5   C6   O62  115.95  3.000
 NPG  C5   C6   O61  117.78  3.000
 NPG  O62  C6   O61  126.26  3.000
 NPG  H52  C5   H51  105.51  3.000
 NPG  H52  C5   C4   110.35  3.000
 NPG  H51  C5   C4   109.44  3.000
 NPG  H52  C5   C6   109.27  3.000
 NPG  H51  C5   C6   107.50  3.000
 NPG  C4   C5   C6   114.35  3.000
 NPG  H42  C4   H41  105.77  3.000
 NPG  H42  C4   C3   110.66  3.000
 NPG  H41  C4   C3   106.79  3.000
 NPG  H42  C4   C5   110.11  3.000
 NPG  H41  C4   C5   109.69  3.000
 NPG  C3   C4   C5   113.48  3.000
 NPG  N1   C3   O31  122.06  3.000
 NPG  N1   C3   C4   115.19  3.000
 NPG  O31  C3   C4   122.75  3.000
 NPG  HN1  N1   C1   119.11  3.000
 NPG  HN1  N1   C3   118.57  3.000
 NPG  C1   N1   C3   121.85  3.000
 NPG  C1   C2   O12  117.13  3.000
 NPG  C1   C2   O11  114.60  3.000
 NPG  O12  C2   O11  128.18  3.000
 NPG  H1   C1   CG   108.60  3.000
 NPG  H1   C1   C2   108.17  3.000
 NPG  CG   C1   C2   107.40  3.000
 NPG  H1   C1   N1   109.33  3.000
 NPG  CG   C1   N1   110.05  3.000
 NPG  C2   C1   N1   113.17  3.000
 NPG  CD2  CG   CD1  118.68  3.000
 NPG  CD2  CG   C1   120.71  3.000
 NPG  CD1  CG   C1   120.58  3.000
 NPG  HD1  CD1  CE1  119.46  3.000
 NPG  HD1  CD1  CG   119.89  3.000
 NPG  CE1  CD1  CG   120.64  3.000
 NPG  HD2  CD2  CE2  119.65  3.000
 NPG  HD2  CD2  CG   119.56  3.000
 NPG  CE2  CD2  CG   120.79  3.000
 NPG  HE1  CE1  CZ   120.05  3.000
 NPG  HE1  CE1  CD1  119.71  3.000
 NPG  CZ   CE1  CD1  120.24  3.000
 NPG  HE2  CE2  CZ   120.09  3.000
 NPG  HE2  CE2  CD2  119.75  3.000
 NPG  CZ   CE2  CD2  120.16  3.000
 NPG  HZ   CZ   CE2  120.27  3.000
 NPG  HZ   CZ   CE1  120.24  3.000
 NPG  CE2  CZ   CE1  119.50  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
 NPG  CONST_01  CZ   CE1  CD1  CG     0.00   0.0  0
 NPG  CONST_02  CZ   CE2  CD2  CG     0.00   0.0  0
 NPG  CONST_03  CE2  CD2  CG   CD1    0.00   0.0  0
 NPG  CONST_04  CE2  CZ   CE1  CD1    0.00   0.0  0
 NPG  CONST_05  CE1  CD1  CG   CD2    0.00   0.0  0
 NPG  CONST_06  CE1  CZ   CE2  CD2    0.00   0.0  0
 NPG  CONST_07  CE1  CD1  CG   C1   180.00   0.0  0
 NPG  CONST_08  CE2  CD2  CG   C1   180.00   0.0  0
 NPG  CONST_09  HE1  CE1  CD1  CG   180.00   0.0  0
 NPG  CONST_10  HE2  CE2  CD2  CG   180.00   0.0  0
 NPG  CONST_11  HD2  CD2  CG   CD1  180.00   0.0  0
 NPG  CONST_12  HZ   CZ   CE1  CD1  180.00   0.0  0
 NPG  CONST_13  HD1  CD1  CG   CD2  180.00   0.0  0
 NPG  CONST_14  C1   N1   C3   C4   180.00   0.0  0
 NPG  CONST_15  C1   N1   C3   O31    0.00   0.0  0
 NPG  CONST_16  HN1  N1   C3   C4     0.00   0.0  0
 NPG  Var_01    C4   C5   C6   O61  -20.16  30.0  3
 NPG  Var_02    C3   C4   C5   C6   179.94  30.0  3
 NPG  Var_03    O31  C3   C4   C5    38.60  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
 NPG  chir_01  C1  N1  C2  CG  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
 NPG  plan-1  C1   0.020
 NPG  plan-1  CG   0.020
 NPG  plan-1  CD1  0.020
 NPG  plan-1  CD2  0.020
 NPG  plan-1  CE1  0.020
 NPG  plan-1  CE2  0.020
 NPG  plan-1  CZ   0.020
 NPG  plan-1  HD1  0.020
 NPG  plan-1  HD2  0.020
 NPG  plan-1  HE1  0.020
 NPG  plan-1  HE2  0.020
 NPG  plan-1  HZ   0.020
 NPG  plan-2  C4   0.020
 NPG  plan-2  O31  0.020
 NPG  plan-2  C3   0.020
 NPG  plan-2  N1   0.020
 NPG  plan-2  C1   0.020
 NPG  plan-2  HN1  0.020
 NPG  plan-3  O61  0.020
 NPG  plan-3  O62  0.020
 NPG  plan-3  C6   0.020
 NPG  plan-3  C5   0.020
 NPG  plan-4  C2   0.020
 NPG  plan-4  C1   0.020
 NPG  plan-4  O11  0.020
 NPG  plan-4  O12  0.020

