# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 11:29:34 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  31  18  .  2021-08-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

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  -0.444   1.8274   0.2834   4.8416
 NPG  O62  O  OH1   0  -0.596  -0.0037  -0.1667   6.0309
 NPG  C6   C  C     0   0.556   0.6576  -0.0055   4.8895
 NPG  C5   C  CH2   0  -0.577  -0.2338  -0.2278   3.6999
 NPG  C4   C  CH2   0  -0.587   0.5018  -0.0757   2.3831
 NPG  O31  O  O     0  -0.491  -1.5812  -0.6089   1.2868
 NPG  C3   C  C     0   0.595  -0.3968  -0.3246   1.1936
 NPG  N1   N  NH1   0  -0.660   0.1997  -0.2043  -0.0080
 NPG  O12  O  OH1   0  -0.580  -1.6796   1.5431  -0.9036
 NPG  C2   C  C     0   0.546  -1.7973   0.3105  -1.3643
 NPG  C1   C  CH1   0  -0.196  -0.5199  -0.5080  -1.2166
 NPG  CG   C  CR6   0   0.059   0.3366  -0.2527  -2.4375
 NPG  CD1  C  CR16  0  -0.284   1.0250   0.9484  -2.5968
 NPG  CD2  C  CR16  0  -0.302   0.4161  -1.2205  -3.4325
 NPG  CE1  C  CR16  0  -0.237   1.7897   1.1688  -3.7333
 NPG  CE2  C  CR16  0  -0.239   1.1769  -0.9964  -4.5722
 NPG  CZ   C  CR16  0  -0.260   1.8662   0.1984  -4.7244
 NPG  H62  H  HOH1  0   0.480   0.5909  -0.0181   6.7813
 NPG  H51  H  HCH2  0   0.288  -0.6795  -1.2218   3.7874
 NPG  H52  H  HCH2  0   0.289  -1.0678   0.4758   3.7648
 NPG  H41  H  HCH2  0   0.285   0.9297   0.9260   2.2921
 NPG  H42  H  HCH2  0   0.283   1.3455  -0.7690   2.3309
 NPG  HN1  H  HNH1  0   0.412   1.1943  -0.0508  -0.0638
 NPG  H12  H  HOH1  0   0.485  -2.4949   2.0387  -1.0728
 NPG  H1   H  HCH1  0   0.302  -0.8337  -1.5560  -1.2252
 NPG  HD1  H  HCR6  0   0.264   0.9713   1.7176  -1.8367
 NPG  HD2  H  HCR6  0   0.260  -0.1130  -2.1584  -3.3152
 NPG  HE1  H  HCR6  0   0.262   2.3241   2.1031  -3.8458
 NPG  HE2  H  HCR6  0   0.262   1.2344  -1.7591  -5.3375
 NPG  HZ   H  HCR6  0   0.261   2.4629   0.3731  -5.6102
 NPG  O11  O  O     0  -0.436  -2.7777  -0.1166  -1.9180

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   double    1.206  0.020  1.206
 NPG  O62  C6   single    1.329  0.020  1.329
 NPG  O62  H62  single    0.850  0.020  0.980
 NPG  C6   C5   single    1.503  0.020  1.503
 NPG  C5   C4   single    1.516  0.020  1.516
 NPG  C5   H51  single    0.970  0.020  1.090
 NPG  C5   H52  single    0.970  0.020  1.090
 NPG  C4   C3   single    1.511  0.020  1.511
 NPG  C4   H41  single    0.970  0.020  1.090
 NPG  C4   H42  single    0.970  0.020  1.090
 NPG  O31  C3   double    1.222  0.020  1.222
 NPG  C3   N1   single    1.347  0.020  1.347
 NPG  N1   C1   single    1.439  0.020  1.439
 NPG  N1   HN1  single    0.860  0.020  1.020
 NPG  O11  C2   double    1.204  0.020  1.204
 NPG  O12  C2   single    1.321  0.020  1.321
 NPG  O12  H12  single    0.850  0.020  0.980
 NPG  C2   C1   single    1.524  0.020  1.524
 NPG  C1   CG   single    1.513  0.020  1.513
 NPG  C1   H1   single    0.970  0.020  1.090
 NPG  CG   CD1  aromatic  1.393  0.020  1.393
 NPG  CG   CD2  aromatic  1.390  0.020  1.390
 NPG  CD1  CE1  aromatic  1.387  0.020  1.387
 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  1.389  0.020  1.389
 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  H62  O62  C6   109.95  3.000
 NPG  C5   C6   O62  111.52  3.000
 NPG  C5   C6   O61  125.41  3.000
 NPG  O62  C6   O61  123.08  3.000
 NPG  H52  C5   H51  105.64  3.000
 NPG  H52  C5   C4   110.93  3.000
 NPG  H51  C5   C4   111.02  3.000
 NPG  H52  C5   C6   108.07  3.000
 NPG  H51  C5   C6   108.24  3.000
 NPG  C4   C5   C6   112.63  3.000
 NPG  H42  C4   H41  105.96  3.000
 NPG  H42  C4   C3   108.47  3.000
 NPG  H41  C4   C3   108.55  3.000
 NPG  H42  C4   C5   110.63  3.000
 NPG  H41  C4   C5   110.75  3.000
 NPG  C3   C4   C5   112.25  3.000
 NPG  N1   C3   O31  121.21  3.000
 NPG  N1   C3   C4   115.10  3.000
 NPG  O31  C3   C4   123.69  3.000
 NPG  HN1  N1   C1   118.63  3.000
 NPG  HN1  N1   C3   120.00  3.000
 NPG  C1   N1   C3   120.60  3.000
 NPG  H12  O12  C2   109.96  3.000
 NPG  C1   C2   O12  113.11  3.000
 NPG  C1   C2   O11  122.44  3.000
 NPG  O12  C2   O11  124.32  3.000
 NPG  H1   C1   CG   108.53  3.000
 NPG  H1   C1   C2   105.86  3.000
 NPG  CG   C1   C2   107.79  3.000
 NPG  H1   C1   N1   110.62  3.000
 NPG  CG   C1   N1   111.04  3.000
 NPG  C2   C1   N1   112.77  3.000
 NPG  CD2  CG   CD1  119.34  3.000
 NPG  CD2  CG   C1   119.49  3.000
 NPG  CD1  CG   C1   121.15  3.000
 NPG  HD1  CD1  CE1  119.31  3.000
 NPG  HD1  CD1  CG   120.50  3.000
 NPG  CE1  CD1  CG   120.19  3.000
 NPG  HD2  CD2  CE2  119.75  3.000
 NPG  HD2  CD2  CG   119.82  3.000
 NPG  CE2  CD2  CG   120.42  3.000
 NPG  HE1  CE1  CZ   120.11  3.000
 NPG  HE1  CE1  CD1  119.64  3.000
 NPG  CZ   CE1  CD1  120.25  3.000
 NPG  HE2  CE2  CZ   120.19  3.000
 NPG  HE2  CE2  CD2  119.73  3.000
 NPG  CZ   CE2  CD2  120.07  3.000
 NPG  HZ   CZ   CE2  120.18  3.000
 NPG  HZ   CZ   CE1  120.10  3.000
 NPG  CE2  CZ   CE1  119.72  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  CONST_17  H62  O62  C6   O61    0.00   0.0  0
 NPG  CONST_18  H12  O12  C2   O11    0.00   0.0  0
 NPG  Var_01    C4   C5   C6   O61    1.08  30.0  3
 NPG  Var_02    C3   C4   C5   C6   179.01  30.0  3
 NPG  Var_03    O31  C3   C4   C5     0.34  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-3  H62  0.020
 NPG  plan-4  O12  0.020
 NPG  plan-4  C2   0.020
 NPG  plan-4  C1   0.020
 NPG  plan-4  H12  0.020
 NPG  plan-4  O11  0.020

