# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 13:04:52 2020
#   Inital geometry file: a 71 line input string
#   Ligand name: (2R)-2-benzyl-3-nitropropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=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
 23N  23N  '(2R)-2-benzyl-3-nitropropanoic acid'  ligand  26  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_23N
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
 23N  CAH   C  CR16   0  -0.301  -1.6873   1.4306   0.5760
 23N  CAF   C  CR16   0  -0.239  -3.0240   1.5017   0.9398
 23N  CAE   C  CR16   0  -0.269  -3.9644   0.7018   0.3014
 23N  CAG   C  CR16   0  -0.240  -3.5578  -0.1644  -0.7035
 23N  CAI   C  CR16   0  -0.301  -2.2179  -0.2327  -1.0644
 23N  CAM   C  CR6    0   0.114  -1.2680   0.5616  -0.4294
 23N  CAJ   C  CH2    0  -0.504   0.1872   0.4600  -0.7945
 23N  CAN   C  CH1    0  -0.410   0.9988  -0.3380   0.2441
 23N  CAL   C  C      0   0.570   0.3755  -1.7105   0.3960
 23N  OAD   O  O      0  -0.435   0.4425  -2.5673  -0.4500
 23N  OAA   O  OH1    0  -0.574  -0.2672  -1.8534   1.5412
 23N  CAK   C  CH2    0  -0.327   2.4436  -0.5384  -0.1921
 23N  NAO   N  N      1   0.443   3.2228   0.7335  -0.2410
 23N  OAC   O  O     -1  -0.381   2.9349   1.6163   0.5297
 23N  OAB   O  O      0  -0.376   4.1334   0.7870  -1.0292
 23N  HAH   H  HCR6   0   0.250  -0.9634   2.0630   1.0775
 23N  HAF   H  HCR6   0   0.255  -3.3333   2.1835   1.7218
 23N  HAE   H  HCR6   0   0.255  -5.0077   0.7570   0.5841
 23N  HAG   H  HCR6   0   0.256  -4.2821  -0.7895  -1.2098
 23N  HAI   H  HCR6   0   0.251  -1.9101  -0.9076  -1.8545
 23N  HAJ1  H  HCH2   0   0.265   0.2956  -0.0125  -1.7731
 23N  HAJ2  H  HCH2   0   0.274   0.6136   1.4612  -0.8789
 23N  HAN   H  HCH1   0   0.302   0.9718   0.1730   1.2070
 23N  HOAA  H  HOH1   0   0.484  -0.6901  -2.7256   1.5801
 23N  HAK1  H  HCH2   0   0.336   2.9921  -1.1673   0.5130
 23N  HAK2  H  HCH2   0   0.302   2.5174  -0.9858  -1.1804

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
 23N  CAF  CAH   aromatic  1.387  0.020  1.387
 23N  CAF  CAE   aromatic  1.390  0.020  1.390
 23N  CAH  CAM   aromatic  1.393  0.020  1.393
 23N  OAB  NAO   double    1.206  0.020  1.206
 23N  CAE  CAG   aromatic  1.388  0.020  1.388
 23N  CAK  NAO   single    1.492  0.020  1.492
 23N  CAK  CAN   single    1.522  0.020  1.522
 23N  CAM  CAJ   single    1.504  0.020  1.504
 23N  CAM  CAI   aromatic  1.392  0.020  1.392
 23N  NAO  OAC   single    1.207  0.020  1.207
 23N  CAJ  CAN   single    1.541  0.020  1.541
 23N  CAG  CAI   aromatic  1.389  0.020  1.389
 23N  CAN  CAL   single    1.515  0.020  1.515
 23N  CAL  OAD   double    1.206  0.020  1.206
 23N  CAL  OAA   single    1.321  0.020  1.321
 23N  CAH  HAH   single    0.930  0.020  1.080
 23N  CAF  HAF   single    0.930  0.020  1.080
 23N  CAE  HAE   single    0.930  0.020  1.080
 23N  CAG  HAG   single    0.930  0.020  1.080
 23N  CAI  HAI   single    0.930  0.020  1.080
 23N  CAJ  HAJ1  single    0.970  0.020  1.090
 23N  CAJ  HAJ2  single    0.970  0.020  1.090
 23N  CAN  HAN   single    0.970  0.020  1.090
 23N  OAA  HOAA  single    0.850  0.020  0.980
 23N  CAK  HAK1  single    0.970  0.020  1.090
 23N  CAK  HAK2  single    0.970  0.020  1.090

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
 23N  HAH   CAH  CAM   119.77  3.000
 23N  HAH   CAH  CAF   119.49  3.000
 23N  CAM   CAH  CAF   120.74  3.000
 23N  HAF   CAF  CAE   120.07  3.000
 23N  HAF   CAF  CAH   119.80  3.000
 23N  CAE   CAF  CAH   120.13  3.000
 23N  HAE   CAE  CAG   120.23  3.000
 23N  HAE   CAE  CAF   120.19  3.000
 23N  CAG   CAE  CAF   119.58  3.000
 23N  HAG   CAG  CAI   119.70  3.000
 23N  HAG   CAG  CAE   120.21  3.000
 23N  CAI   CAG  CAE   120.09  3.000
 23N  HAI   CAI  CAM   119.62  3.000
 23N  HAI   CAI  CAG   119.60  3.000
 23N  CAM   CAI  CAG   120.78  3.000
 23N  CAJ   CAM  CAI   120.74  3.000
 23N  CAI   CAM  CAH   118.67  3.000
 23N  CAJ   CAM  CAH   120.57  3.000
 23N  HAJ2  CAJ  HAJ1  106.79  3.000
 23N  HAJ2  CAJ  CAN   108.75  3.000
 23N  HAJ1  CAJ  CAN   109.13  3.000
 23N  HAJ2  CAJ  CAM   109.56  3.000
 23N  HAJ1  CAJ  CAM   110.05  3.000
 23N  CAN   CAJ  CAM   112.40  3.000
 23N  HAN   CAN  CAK   109.77  3.000
 23N  HAN   CAN  CAL   109.01  3.000
 23N  CAK   CAN  CAL   107.46  3.000
 23N  HAN   CAN  CAJ   109.84  3.000
 23N  CAL   CAN  CAJ   108.66  3.000
 23N  CAK   CAN  CAJ   112.02  3.000
 23N  OAA   CAL  OAD   123.94  3.000
 23N  OAA   CAL  CAN   112.65  3.000
 23N  OAD   CAL  CAN   123.40  3.000
 23N  HOAA  OAA  CAL   110.13  3.000
 23N  HAK2  CAK  HAK1  108.40  3.000
 23N  HAK2  CAK  NAO   106.59  3.000
 23N  HAK1  CAK  NAO   104.46  3.000
 23N  HAK2  CAK  CAN   112.27  3.000
 23N  HAK1  CAK  CAN   111.55  3.000
 23N  NAO   CAK  CAN   113.12  3.000
 23N  OAB   NAO  OAC   124.43  3.000
 23N  OAC   NAO  CAK   118.55  3.000
 23N  OAB   NAO  CAK   116.98  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
 23N  CONST_01  CAG   CAE  CAF  CAH     0.00   0.0  0
 23N  CONST_02  CAG   CAI  CAM  CAH     0.00   0.0  0
 23N  CONST_03  CAI   CAM  CAH  CAF     0.00   0.0  0
 23N  CONST_04  CAI   CAG  CAE  CAF     0.00   0.0  0
 23N  CONST_05  CAM   CAH  CAF  CAE     0.00   0.0  0
 23N  CONST_06  CAM   CAI  CAG  CAE     0.00   0.0  0
 23N  CONST_07  CAJ   CAM  CAH  CAF   180.00   0.0  0
 23N  CONST_08  CAJ   CAM  CAI  CAG   180.00   0.0  0
 23N  CONST_09  HAE   CAE  CAF  CAH   180.00   0.0  0
 23N  CONST_10  HAI   CAI  CAM  CAH   180.00   0.0  0
 23N  CONST_11  HAG   CAG  CAE  CAF   180.00   0.0  0
 23N  CONST_12  HAH   CAH  CAF  CAE   180.00   0.0  0
 23N  CONST_13  HAF   CAF  CAE  CAG   180.00   0.0  0
 23N  CONST_14  HOAA  OAA  CAL  CAN   180.00   0.0  0
 23N  Var_01    CAN   CAJ  CAM  CAH    75.55  30.0  2
 23N  Var_02    OAB   NAO  CAK  CAN  -151.48  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
 23N  chir_01  CAN  CAK  CAJ  CAL  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
 23N  plan-1  CAH   0.020
 23N  plan-1  CAF   0.020
 23N  plan-1  CAE   0.020
 23N  plan-1  CAG   0.020
 23N  plan-1  CAI   0.020
 23N  plan-1  CAM   0.020
 23N  plan-1  CAJ   0.020
 23N  plan-1  HAH   0.020
 23N  plan-1  HAF   0.020
 23N  plan-1  HAE   0.020
 23N  plan-1  HAG   0.020
 23N  plan-1  HAI   0.020
 23N  plan-2  CAN   0.020
 23N  plan-2  CAL   0.020
 23N  plan-2  OAD   0.020
 23N  plan-2  OAA   0.020
 23N  plan-2  HOAA  0.020
 23N  plan-3  CAK   0.020
 23N  plan-3  NAO   0.020
 23N  plan-3  OAC   0.020
 23N  plan-3  OAB   0.020

