# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 02:32:59 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (2R)-2-benzyl-3-nitropropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=O)[C@H](Cc1ccccc1)C[N+]([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
 ZNP  ZNP  (2R)-2-benzyl-3-nitropropanamide  ligand  27  15  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_ZNP
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
 ZNP  CAF   C  CR16   0  -0.287  -2.3697   0.1419   1.2769
 ZNP  CAG   C  CR16   0  -0.215  -3.6140  -0.4492   1.0922
 ZNP  CAH   C  CR16   0  -0.244  -4.1520  -0.5539  -0.1826
 ZNP  CAI   C  CR16   0  -0.212  -3.4407  -0.0598  -1.2700
 ZNP  CAJ   C  CR16   0  -0.264  -2.1999   0.5309  -1.0811
 ZNP  CAE   C  CR6    0   0.135  -1.6480   0.6372   0.1949
 ZNP  CAD   C  CH2    0  -0.492  -0.2910   1.2580   0.3883
 ZNP  CAB   C  CH1    0  -0.442   0.8482   0.3963  -0.1963
 ZNP  CAA   C  CH2    0  -0.283   0.8669  -0.9428   0.5049
 ZNP  NAK   N  N      1   0.449   1.9709  -1.8346   0.0509
 ZNP  OAN   O  O     -1  -0.356   2.2020  -2.8060   0.7279
 ZNP  OAM   O  O      0  -0.402   2.5530  -1.5640  -0.9710
 ZNP  CAC   C  C      0   0.566   2.1692   1.1268   0.0068
 ZNP  OAO   O  O      0  -0.479   2.8544   0.9361   1.0014
 ZNP  NAL   N  NH2    0  -0.795   2.4772   2.0067  -0.9505
 ZNP  HAF   H  HCR6   0   0.228  -1.9580   0.2228   2.2763
 ZNP  HAG   H  HCR6   0   0.242  -4.1613  -0.8268   1.9465
 ZNP  HAH   H  HCR6   0   0.241  -5.1193  -1.0163  -0.3308
 ZNP  HAI   H  HCR6   0   0.238  -3.8547  -0.1341  -2.2674
 ZNP  HAJ   H  HCR6   0   0.209  -1.6571   0.9177  -1.9363
 ZNP  HAD   H  HCH2   0   0.260  -0.2608   2.2370  -0.0944
 ZNP  HADA  H  HCH2   0   0.257  -0.1063   1.4253   1.4520
 ZNP  HAB   H  HCH1   0   0.271   0.6610   0.2562  -1.2643
 ZNP  HAA   H  HCH2   0   0.285   0.9810  -0.8434   1.5829
 ZNP  HAAA  H  HCH2   0   0.327  -0.0478  -1.5055   0.3121
 ZNP  HNAL  H  HNH2   0   0.383   1.9054   2.1243  -1.7694
 ZNP  HNAA  H  HNH2   0   0.381   3.3104   2.5688  -0.8831

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
 ZNP  CAF  CAG   aromatic  1.390  0.020  1.390
 ZNP  CAF  CAE   aromatic  1.392  0.020  1.392
 ZNP  CAG  CAH   aromatic  1.388  0.020  1.388
 ZNP  CAH  CAI   aromatic  1.390  0.020  1.390
 ZNP  CAI  CAJ   aromatic  1.387  0.020  1.387
 ZNP  CAJ  CAE   aromatic  1.394  0.020  1.394
 ZNP  CAE  CAD   single    1.505  0.020  1.505
 ZNP  CAD  CAB   single    1.543  0.020  1.543
 ZNP  CAB  CAA   single    1.512  0.020  1.512
 ZNP  CAB  CAC   single    1.523  0.020  1.523
 ZNP  CAA  NAK   single    1.490  0.020  1.490
 ZNP  NAK  OAN   single    1.206  0.020  1.206
 ZNP  NAK  OAM   double    1.207  0.020  1.207
 ZNP  CAC  OAO   double    1.223  0.020  1.223
 ZNP  CAC  NAL   single    1.336  0.020  1.336
 ZNP  CAF  HAF   single    0.930  0.020  1.080
 ZNP  CAG  HAG   single    0.930  0.020  1.080
 ZNP  CAH  HAH   single    0.930  0.020  1.080
 ZNP  CAI  HAI   single    0.930  0.020  1.080
 ZNP  CAJ  HAJ   single    0.930  0.020  1.080
 ZNP  CAD  HAD   single    0.970  0.020  1.090
 ZNP  CAD  HADA  single    0.970  0.020  1.090
 ZNP  CAB  HAB   single    0.970  0.020  1.090
 ZNP  CAA  HAA   single    0.970  0.020  1.090
 ZNP  CAA  HAAA  single    0.970  0.020  1.090
 ZNP  NAL  HNAL  single    0.860  0.020  1.020
 ZNP  NAL  HNAA  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
 ZNP  HAF   CAF  CAE   119.56  3.000
 ZNP  HAF   CAF  CAG   119.63  3.000
 ZNP  CAE   CAF  CAG   120.81  3.000
 ZNP  HAG   CAG  CAH   120.18  3.000
 ZNP  HAG   CAG  CAF   119.73  3.000
 ZNP  CAH   CAG  CAF   120.09  3.000
 ZNP  HAH   CAH  CAI   120.13  3.000
 ZNP  HAH   CAH  CAG   120.30  3.000
 ZNP  CAI   CAH  CAG   119.57  3.000
 ZNP  HAI   CAI  CAJ   119.79  3.000
 ZNP  HAI   CAI  CAH   120.04  3.000
 ZNP  CAJ   CAI  CAH   120.17  3.000
 ZNP  HAJ   CAJ  CAE   119.77  3.000
 ZNP  HAJ   CAJ  CAI   119.49  3.000
 ZNP  CAE   CAJ  CAI   120.74  3.000
 ZNP  CAD   CAE  CAJ   120.40  3.000
 ZNP  CAD   CAE  CAF   120.96  3.000
 ZNP  CAJ   CAE  CAF   118.63  3.000
 ZNP  HADA  CAD  HAD   106.76  3.000
 ZNP  HADA  CAD  CAB   109.24  3.000
 ZNP  HAD   CAD  CAB   108.22  3.000
 ZNP  HADA  CAD  CAE   109.92  3.000
 ZNP  HAD   CAD  CAE   109.75  3.000
 ZNP  CAB   CAD  CAE   112.75  3.000
 ZNP  HAB   CAB  CAC   109.89  3.000
 ZNP  HAB   CAB  CAA   109.99  3.000
 ZNP  CAC   CAB  CAA   110.63  3.000
 ZNP  HAB   CAB  CAD   108.37  3.000
 ZNP  CAC   CAB  CAD   108.78  3.000
 ZNP  CAA   CAB  CAD   109.15  3.000
 ZNP  HAAA  CAA  HAA   108.06  3.000
 ZNP  HAAA  CAA  NAK   104.99  3.000
 ZNP  HAA   CAA  NAK   106.18  3.000
 ZNP  HAAA  CAA  CAB   111.38  3.000
 ZNP  HAA   CAA  CAB   112.32  3.000
 ZNP  NAK   CAA  CAB   113.45  3.000
 ZNP  OAM   NAK  OAN   124.29  3.000
 ZNP  OAM   NAK  CAA   118.77  3.000
 ZNP  OAN   NAK  CAA   116.93  3.000
 ZNP  NAL   CAC  OAO   123.80  3.000
 ZNP  NAL   CAC  CAB   114.85  3.000
 ZNP  OAO   CAC  CAB   121.31  3.000
 ZNP  HNAA  NAL  HNAL  117.36  3.000
 ZNP  HNAA  NAL  CAC   120.68  3.000
 ZNP  HNAL  NAL  CAC   121.95  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
 ZNP  CONST_01  CAI   CAH  CAG  CAF    0.00   0.0  0
 ZNP  CONST_02  CAI   CAJ  CAE  CAF    0.00   0.0  0
 ZNP  CONST_03  CAJ   CAE  CAF  CAG    0.00   0.0  0
 ZNP  CONST_04  CAJ   CAI  CAH  CAG    0.00   0.0  0
 ZNP  CONST_05  CAE   CAF  CAG  CAH    0.00   0.0  0
 ZNP  CONST_06  CAE   CAJ  CAI  CAH    0.00   0.0  0
 ZNP  CONST_07  CAD   CAE  CAF  CAG  180.00   0.0  0
 ZNP  CONST_08  CAD   CAE  CAJ  CAI  180.00   0.0  0
 ZNP  CONST_09  HAH   CAH  CAG  CAF  180.00   0.0  0
 ZNP  CONST_10  HAJ   CAJ  CAE  CAF  180.00   0.0  0
 ZNP  CONST_11  HAI   CAI  CAH  CAG  180.00   0.0  0
 ZNP  CONST_12  HAF   CAF  CAG  CAH  180.00   0.0  0
 ZNP  CONST_13  HAG   CAG  CAH  CAI  180.00   0.0  0
 ZNP  CONST_14  HNAL  NAL  CAC  CAB    0.00   0.0  0
 ZNP  CONST_15  HNAA  NAL  CAC  CAB  180.00   0.0  0
 ZNP  Var_01    CAB   CAD  CAE  CAF  110.70  30.0  2
 ZNP  Var_02    OAN   NAK  CAA  CAB  166.62  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
 ZNP  chir_01  CAB  CAD  CAA  CAC  positiv

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
 ZNP  plan-1  CAF   0.020
 ZNP  plan-1  CAG   0.020
 ZNP  plan-1  CAH   0.020
 ZNP  plan-1  CAI   0.020
 ZNP  plan-1  CAJ   0.020
 ZNP  plan-1  CAE   0.020
 ZNP  plan-1  CAD   0.020
 ZNP  plan-1  HAF   0.020
 ZNP  plan-1  HAG   0.020
 ZNP  plan-1  HAH   0.020
 ZNP  plan-1  HAI   0.020
 ZNP  plan-1  HAJ   0.020
 ZNP  plan-2  CAB   0.020
 ZNP  plan-2  CAC   0.020
 ZNP  plan-2  OAO   0.020
 ZNP  plan-2  NAL   0.020
 ZNP  plan-2  HNAL  0.020
 ZNP  plan-2  HNAA  0.020
 ZNP  plan-3  CAA   0.020
 ZNP  plan-3  NAK   0.020
 ZNP  plan-3  OAN   0.020
 ZNP  plan-3  OAM   0.020

