# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 11:33:02 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: (2R)-2-benzyl-4,4-dihydroxy-5-nitropentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@H](Cc1ccccc1)CC(O)(O)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
 BPX  BPX  '(2R)-2-benzyl-4,4-dihydroxy-5-nitropentanoic acid'  ligand  34  19  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BPX
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
 BPX  CAJ   C  CR16   0  -0.304  -2.6281  -1.6419  -0.5523
 BPX  CAI   C  CR16   0  -0.240  -3.9355  -1.9782  -0.8722
 BPX  CAE   C  CR16   0  -0.271  -4.9930  -1.4105  -0.1713
 BPX  CAD   C  CR16   0  -0.240  -4.7305  -0.5073   0.8490
 BPX  CAL   C  CR16   0  -0.302  -3.4193  -0.1719   1.1639
 BPX  CAK   C  CR6    0   0.114  -2.3519  -0.7338   0.4688
 BPX  CAF   C  CH2    0  -0.506  -0.9305  -0.3548   0.7843
 BPX  CAB   C  CH1    0  -0.345  -0.3430   0.6179  -0.2547
 BPX  CAC   C  C      0   0.558  -1.2595   1.8188  -0.3583
 BPX  OAO   O  O      0  -0.444  -1.4463   2.5969   0.5451
 BPX  OAN   O  OH1    0  -0.579  -1.8392   1.9284  -1.5443
 BPX  CAA   C  CH2    0  -0.528   1.0593   1.1334   0.0920
 BPX  CAG   C  CT     0   0.471   2.1780   0.0818   0.0563
 BPX  OAP   O  OH1    0  -0.642   2.1142  -0.8352   1.0991
 BPX  OAQ   O  OH1    0  -0.640   2.1227  -0.7277  -1.0698
 BPX  CAH   C  CH2    0  -0.379   3.5195   0.8640   0.1145
 BPX  NAM   N  N      1   0.444   4.6505  -0.0865   0.1587
 BPX  OAS   O  O      0  -0.387   5.0770  -0.5002  -0.8928
 BPX  OAR   O  O     -1  -0.387   5.0616  -0.4261   1.2421
 BPX  HAJ   H  HCR6   0   0.247  -1.8106  -2.0959  -1.1012
 BPX  HAI   H  HCR6   0   0.254  -4.1286  -2.6870  -1.6673
 BPX  HAE   H  HCR6   0   0.254  -6.0136  -1.6734  -0.4174
 BPX  HAD   H  HCR6   0   0.254  -5.5463  -0.0638   1.4055
 BPX  HAL   H  HCR6   0   0.248  -3.2255   0.5324   1.9643
 BPX  HAF   H  HCH2   0   0.249  -0.8741   0.0969   1.7775
 BPX  HAFA  H  HCH2   0   0.275  -0.3106  -1.2498   0.8082
 BPX  HAB   H  HCH1   0   0.274  -0.3137   0.1192  -1.2253
 BPX  HOAN  H  HOH1   0   0.479  -2.4188   2.7058  -1.5591
 BPX  HAA   H  HCH2   0   0.273   1.3217   1.9235  -0.6188
 BPX  HAAA  H  HCH2   0   0.267   1.0478   1.6098   1.0764
 BPX  HOAP  H  HOH1   0   0.464   2.0128  -0.3719   1.9377
 BPX  HOAQ  H  HOH1   0   0.464   2.1700  -0.1880  -1.8667
 BPX  HAH   H  HCH2   0   0.305   3.6455   1.4918  -0.7657
 BPX  HAHA  H  HCH2   0   0.305   3.5662   1.4834   1.0083

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
 BPX  CAJ  CAI   aromatic  1.387  0.020  1.387
 BPX  CAJ  CAK   aromatic  1.394  0.020  1.394
 BPX  CAI  CAE   aromatic  1.390  0.020  1.390
 BPX  CAE  CAD   aromatic  1.388  0.020  1.388
 BPX  CAD  CAL   aromatic  1.390  0.020  1.390
 BPX  CAL  CAK   aromatic  1.392  0.020  1.392
 BPX  CAK  CAF   single    1.505  0.020  1.505
 BPX  CAF  CAB   single    1.540  0.020  1.540
 BPX  CAB  CAC   single    1.514  0.020  1.514
 BPX  CAB  CAA   single    1.534  0.020  1.534
 BPX  CAC  OAO   double    1.207  0.020  1.207
 BPX  CAC  OAN   single    1.325  0.020  1.325
 BPX  CAA  CAG   single    1.536  0.020  1.536
 BPX  CAG  OAP   single    1.390  0.020  1.390
 BPX  CAG  OAQ   single    1.388  0.020  1.388
 BPX  CAG  CAH   single    1.554  0.020  1.554
 BPX  CAH  NAM   single    1.478  0.020  1.478
 BPX  NAM  OAS   double    1.208  0.020  1.208
 BPX  NAM  OAR   single    1.208  0.020  1.208
 BPX  CAJ  HAJ   single    0.930  0.020  1.080
 BPX  CAI  HAI   single    0.930  0.020  1.080
 BPX  CAE  HAE   single    0.930  0.020  1.080
 BPX  CAD  HAD   single    0.930  0.020  1.080
 BPX  CAL  HAL   single    0.930  0.020  1.080
 BPX  CAF  HAF   single    0.970  0.020  1.090
 BPX  CAF  HAFA  single    0.970  0.020  1.090
 BPX  CAB  HAB   single    0.970  0.020  1.090
 BPX  OAN  HOAN  single    0.850  0.020  0.980
 BPX  CAA  HAA   single    0.970  0.020  1.090
 BPX  CAA  HAAA  single    0.970  0.020  1.090
 BPX  OAP  HOAP  single    0.850  0.020  0.980
 BPX  OAQ  HOAQ  single    0.850  0.020  0.980
 BPX  CAH  HAH   single    0.970  0.020  1.090
 BPX  CAH  HAHA  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
 BPX  HAJ   CAJ  CAK  119.61  3.000
 BPX  HAJ   CAJ  CAI  119.49  3.000
 BPX  CAK   CAJ  CAI  120.89  3.000
 BPX  HAI   CAI  CAE  120.14  3.000
 BPX  HAI   CAI  CAJ  119.75  3.000
 BPX  CAE   CAI  CAJ  120.12  3.000
 BPX  HAE   CAE  CAD  120.24  3.000
 BPX  HAE   CAE  CAI  120.24  3.000
 BPX  CAD   CAE  CAI  119.52  3.000
 BPX  HAD   CAD  CAL  119.72  3.000
 BPX  HAD   CAD  CAE  120.13  3.000
 BPX  CAL   CAD  CAE  120.15  3.000
 BPX  HAL   CAL  CAK  119.61  3.000
 BPX  HAL   CAL  CAD  119.54  3.000
 BPX  CAK   CAL  CAD  120.86  3.000
 BPX  CAF   CAK  CAL  121.20  3.000
 BPX  CAF   CAK  CAJ  120.32  3.000
 BPX  CAL   CAK  CAJ  118.47  3.000
 BPX  HAFA  CAF  HAF  106.89  3.000
 BPX  HAFA  CAF  CAB  108.47  3.000
 BPX  HAF   CAF  CAB  109.42  3.000
 BPX  HAFA  CAF  CAK  109.60  3.000
 BPX  HAF   CAF  CAK  110.09  3.000
 BPX  CAB   CAF  CAK  112.22  3.000
 BPX  HAB   CAB  CAA  109.27  3.000
 BPX  HAB   CAB  CAC  108.53  3.000
 BPX  CAA   CAB  CAC  107.60  3.000
 BPX  HAB   CAB  CAF  108.76  3.000
 BPX  CAA   CAB  CAF  114.12  3.000
 BPX  CAC   CAB  CAF  108.43  3.000
 BPX  OAN   CAC  OAO  123.31  3.000
 BPX  OAN   CAC  CAB  113.06  3.000
 BPX  OAO   CAC  CAB  123.63  3.000
 BPX  HOAN  OAN  CAC  109.97  3.000
 BPX  HAAA  CAA  HAA  105.82  3.000
 BPX  HAAA  CAA  CAG  109.08  3.000
 BPX  HAA   CAA  CAG  107.73  3.000
 BPX  HAAA  CAA  CAB  109.89  3.000
 BPX  HAA   CAA  CAB  108.36  3.000
 BPX  CAG   CAA  CAB  115.51  3.000
 BPX  CAH   CAG  OAQ  111.00  3.000
 BPX  CAH   CAG  OAP  110.10  3.000
 BPX  OAQ   CAG  OAP  102.83  3.000
 BPX  CAH   CAG  CAA  106.46  3.000
 BPX  OAQ   CAG  CAA  112.90  3.000
 BPX  OAP   CAG  CAA  113.63  3.000
 BPX  HOAP  OAP  CAG  109.91  3.000
 BPX  HOAQ  OAQ  CAG  110.02  3.000
 BPX  HAHA  CAH  HAH  109.32  3.000
 BPX  HAHA  CAH  NAM  107.98  3.000
 BPX  HAH   CAH  NAM  107.85  3.000
 BPX  HAHA  CAH  CAG  110.75  3.000
 BPX  HAH   CAH  CAG  111.10  3.000
 BPX  NAM   CAH  CAG  109.75  3.000
 BPX  OAR   NAM  OAS  124.38  3.000
 BPX  OAR   NAM  CAH  117.91  3.000
 BPX  OAS   NAM  CAH  117.67  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
 BPX  CONST_01  CAD   CAE  CAI  CAJ    0.00   0.0  0
 BPX  CONST_02  CAD   CAL  CAK  CAJ    0.00   0.0  0
 BPX  CONST_03  CAL   CAK  CAJ  CAI    0.00   0.0  0
 BPX  CONST_04  CAL   CAD  CAE  CAI    0.00   0.0  0
 BPX  CONST_05  CAK   CAJ  CAI  CAE    0.00   0.0  0
 BPX  CONST_06  CAK   CAL  CAD  CAE    0.00   0.0  0
 BPX  CONST_07  CAF   CAK  CAJ  CAI  180.00   0.0  0
 BPX  CONST_08  CAF   CAK  CAL  CAD  180.00   0.0  0
 BPX  CONST_09  HAE   CAE  CAI  CAJ  180.00   0.0  0
 BPX  CONST_10  HAL   CAL  CAK  CAJ  180.00   0.0  0
 BPX  CONST_11  HAD   CAD  CAE  CAI  180.00   0.0  0
 BPX  CONST_12  HAJ   CAJ  CAI  CAE  180.00   0.0  0
 BPX  CONST_13  HAI   CAI  CAE  CAD  180.00   0.0  0
 BPX  CONST_14  HOAN  OAN  CAC  CAB  180.00   0.0  0
 BPX  Var_01    CAB   CAF  CAK  CAJ   75.65  30.0  2
 BPX  Var_02    OAP   CAG  CAA  CAB  -71.18  30.0  3
 BPX  Var_03    NAM   CAH  CAG  CAA  176.93  30.0  3
 BPX  Var_04    OAS   NAM  CAH  CAG   86.07  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
 BPX  chir_01  CAB  CAF  CAC  CAA  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
 BPX  plan-1  CAJ   0.020
 BPX  plan-1  CAI   0.020
 BPX  plan-1  CAE   0.020
 BPX  plan-1  CAD   0.020
 BPX  plan-1  CAL   0.020
 BPX  plan-1  CAK   0.020
 BPX  plan-1  CAF   0.020
 BPX  plan-1  HAJ   0.020
 BPX  plan-1  HAI   0.020
 BPX  plan-1  HAE   0.020
 BPX  plan-1  HAD   0.020
 BPX  plan-1  HAL   0.020
 BPX  plan-2  CAB   0.020
 BPX  plan-2  CAC   0.020
 BPX  plan-2  OAO   0.020
 BPX  plan-2  OAN   0.020
 BPX  plan-2  HOAN  0.020
 BPX  plan-3  CAH   0.020
 BPX  plan-3  NAM   0.020
 BPX  plan-3  OAS   0.020
 BPX  plan-3  OAR   0.020

