# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 06:09:32 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  33  19  .  2021-08-06  2021-08-06  
;
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  -0.315  -2.5710  -1.7339  -0.5003
 BPX  CAI   C  CR16   0  -0.242  -3.8596  -2.1266  -0.8354
 BPX  CAE   C  CR16   0  -0.277  -4.9526  -1.5215  -0.2272
 BPX  CAD   C  CR16   0  -0.244  -4.7418  -0.5239   0.7152
 BPX  CAL   C  CR16   0  -0.300  -3.4497  -0.1324   1.0429
 BPX  CAK   C  CR6    0   0.135  -2.3450  -0.7314   0.4421
 BPX  CAF   C  CH2    0  -0.496  -0.9418  -0.3047   0.7731
 BPX  CAB   C  CH1    0  -0.321  -0.3621   0.6464  -0.2825
 BPX  CAC   C  C      0   0.425  -1.2570   1.8972  -0.4380
 BPX  OAO   O  O      0  -0.613  -1.4659   2.5556   0.6017
 BPX  OAN   O  OC    -1  -0.609  -1.6715   2.1672  -1.5819
 BPX  CAA   C  CH2    0  -0.533   1.0526   1.1334   0.0505
 BPX  CAG   C  CT     0   0.474   2.1744   0.0857   0.0236
 BPX  OAP   O  OH1    0  -0.647   2.1265  -0.8181   1.0808
 BPX  OAQ   O  OH1    0  -0.645   2.1275  -0.7399  -1.0929
 BPX  CAH   C  CH2    0  -0.371   3.5185   0.8714   0.0613
 BPX  NAM   N  N      1   0.442   4.6534  -0.0726   0.0957
 BPX  OAS   O  O      0  -0.391   5.0858  -0.4721  -0.9593
 BPX  OAR   O  O     -1  -0.392   5.0637  -0.4259   1.1758
 BPX  HAJ   H  HCR6   0   0.240  -1.7248  -2.2180  -0.9752
 BPX  HAI   H  HCR6   0   0.248  -4.0093  -2.9098  -1.5681
 BPX  HAE   H  HCR6   0   0.249  -5.9590  -1.8284  -0.4818
 BPX  HAD   H  HCR6   0   0.248  -5.5859  -0.0485   1.1991
 BPX  HAL   H  HCR6   0   0.238  -3.2965   0.6512   1.7742
 BPX  HAF   H  HCH2   0   0.225  -0.9240   0.1876   1.7483
 BPX  HAFA  H  HCH2   0   0.243  -0.3129  -1.1916   0.8531
 BPX  HAB   H  HCH1   0   0.210  -0.3383   0.1228  -1.2422
 BPX  HAA   H  HCH2   0   0.251   1.3200   1.9162  -0.6684
 BPX  HAAA  H  HCH2   0   0.247   1.0511   1.6231   1.0294
 BPX  HOAP  H  HOH1   0   0.462   1.9857  -0.3418   1.9059
 BPX  HOAQ  H  HOH1   0   0.462   2.0533  -0.2031  -1.8895
 BPX  HAH   H  HCH2   0   0.300   3.6291   1.4933  -0.8247
 BPX  HAHA  H  HCH2   0   0.298   3.5746   1.4956   0.9514

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  1.388  0.020  1.388
 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  1.389  0.020  1.389
 BPX  CAL  CAK   aromatic  1.393  0.020  1.393
 BPX  CAK  CAF   single    1.504  0.020  1.504
 BPX  CAF  CAB   single    1.535  0.020  1.535
 BPX  CAB  CAC   single    1.546  0.020  1.546
 BPX  CAB  CAA   single    1.533  0.020  1.533
 BPX  CAC  OAO   deloc     1.248  0.020  1.248
 BPX  CAC  OAN   deloc     1.246  0.020  1.246
 BPX  CAA  CAG   single    1.535  0.020  1.535
 BPX  CAG  OAP   single    1.392  0.020  1.392
 BPX  CAG  OAQ   single    1.389  0.020  1.389
 BPX  CAG  CAH   single    1.557  0.020  1.557
 BPX  CAH  NAM   single    1.477  0.020  1.477
 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  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  119.37  3.000
 BPX  HAJ   CAJ  CAI  119.49  3.000
 BPX  CAK   CAJ  CAI  121.14  3.000
 BPX  HAI   CAI  CAE  120.15  3.000
 BPX  HAI   CAI  CAJ  119.76  3.000
 BPX  CAE   CAI  CAJ  120.08  3.000
 BPX  HAE   CAE  CAD  120.30  3.000
 BPX  HAE   CAE  CAI  120.32  3.000
 BPX  CAD   CAE  CAI  119.38  3.000
 BPX  HAD   CAD  CAL  119.73  3.000
 BPX  HAD   CAD  CAE  120.03  3.000
 BPX  CAL   CAD  CAE  120.25  3.000
 BPX  HAL   CAL  CAK  119.37  3.000
 BPX  HAL   CAL  CAD  119.65  3.000
 BPX  CAK   CAL  CAD  120.98  3.000
 BPX  CAF   CAK  CAL  121.55  3.000
 BPX  CAF   CAK  CAJ  120.27  3.000
 BPX  CAL   CAK  CAJ  118.17  3.000
 BPX  HAFA  CAF  HAF  106.96  3.000
 BPX  HAFA  CAF  CAB  109.68  3.000
 BPX  HAF   CAF  CAB  109.18  3.000
 BPX  HAFA  CAF  CAK  108.88  3.000
 BPX  HAF   CAF  CAK  109.85  3.000
 BPX  CAB   CAF  CAK  112.15  3.000
 BPX  HAB   CAB  CAA  108.82  3.000
 BPX  HAB   CAB  CAC  108.16  3.000
 BPX  CAA   CAB  CAC  107.40  3.000
 BPX  HAB   CAB  CAF  108.38  3.000
 BPX  CAA   CAB  CAF  113.34  3.000
 BPX  CAC   CAB  CAF  110.61  3.000
 BPX  OAN   CAC  OAO  126.48  3.000
 BPX  OAN   CAC  CAB  117.40  3.000
 BPX  OAO   CAC  CAB  116.10  3.000
 BPX  HAAA  CAA  HAA  105.51  3.000
 BPX  HAAA  CAA  CAG  108.78  3.000
 BPX  HAA   CAA  CAG  107.32  3.000
 BPX  HAAA  CAA  CAB  109.58  3.000
 BPX  HAA   CAA  CAB  108.04  3.000
 BPX  CAG   CAA  CAB  116.99  3.000
 BPX  CAH   CAG  OAQ  110.39  3.000
 BPX  CAH   CAG  OAP  109.81  3.000
 BPX  OAQ   CAG  OAP  102.91  3.000
 BPX  CAH   CAG  CAA  106.61  3.000
 BPX  OAQ   CAG  CAA  113.26  3.000
 BPX  OAP   CAG  CAA  113.88  3.000
 BPX  HOAP  OAP  CAG  109.55  3.000
 BPX  HOAQ  OAQ  CAG  109.63  3.000
 BPX  HAHA  CAH  HAH  109.44  3.000
 BPX  HAHA  CAH  NAM  107.93  3.000
 BPX  HAH   CAH  NAM  107.83  3.000
 BPX  HAHA  CAH  CAG  110.71  3.000
 BPX  HAH   CAH  CAG  110.88  3.000
 BPX  NAM   CAH  CAG  109.96  3.000
 BPX  OAR   NAM  OAS  124.22  3.000
 BPX  OAR   NAM  CAH  117.95  3.000
 BPX  OAS   NAM  CAH  117.79  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  Var_01    CAB  CAF  CAK  CAJ   79.33  30.0  2
 BPX  Var_02    OAP  CAG  CAA  CAB  -71.63  30.0  3
 BPX  Var_03    NAM  CAH  CAG  CAA  177.62  30.0  3
 BPX  Var_04    OAS  NAM  CAH  CAG   87.37  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-3  CAH  0.020
 BPX  plan-3  NAM  0.020
 BPX  plan-3  OAS  0.020
 BPX  plan-3  OAR  0.020

