# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 01:15:57 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: [(2~{R})-2-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-ethyl]azanium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [NH3+]C[C@H](O)c1ccc(O)c(O)c1
#
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
 E5E  E5E  '[(2~{R})-2-[3,4-bis(oxidanyl)phenyl]-2-oxidanyl-ethyl]azanium'  ligand  24  12  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_E5E
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
 E5E  OAC   O  OH1   0  -0.630  -2.6857  -1.7202  -0.8815
 E5E  CAJ   C  CR6   0   0.200  -1.8198  -0.7840  -0.4380
 E5E  CAG   C  CR16  0  -0.331  -0.4589  -0.9803  -0.6136
 E5E  CAI   C  CR6   0   0.306  -2.2722   0.4016   0.1556
 E5E  OAB   O  OH1   0  -0.654  -3.6115   0.5294   0.3095
 E5E  CAE   C  CR16  0  -0.336  -1.3569   1.3641   0.5490
 E5E  CAF   C  CR16  0  -0.254   0.0042   1.1615   0.3616
 E5E  CAK   C  CR6   0   0.064   0.4629  -0.0131  -0.2238
 E5E  CAL   C  CH1   0  -0.083   1.9371  -0.2568  -0.4289
 E5E  OAD   O  OH1   0  -0.702   2.5461   0.6485  -1.3227
 E5E  CAH   C  CH2   0  -0.340   2.6566  -0.2340   0.9171
 E5E  NAA   N  NT3   1  -0.753   4.1062  -0.4977   0.7207
 E5E  HOAC  H  HOH1  0   0.477  -3.5148  -1.6642  -0.3912
 E5E  HAG   H  HCR6  0   0.276  -0.1196  -1.9063  -1.0638
 E5E  HOAB  H  HOH1  0   0.477  -3.8080   1.1789   0.9947
 E5E  HAE   H  HCR6  0   0.265  -1.7076   2.2846   0.9992
 E5E  HAF   H  HCR6  0   0.253   0.6874   1.9377   0.6830
 E5E  HAL   H  HCH1  0   0.269   2.0675  -1.2499  -0.8680
 E5E  HOAD  H  HOH1  0   0.461   2.2119   1.5371  -1.1583
 E5E  HAH   H  HCH2  0   0.305   2.5808   0.7424   1.3912
 E5E  HAHA  H  HCH2  0   0.302   2.2724  -1.0038   1.5815
 E5E  HNAA  H  HNT3  0   0.472   4.2819  -1.4372   0.3660
 E5E  HNAB  H  HNT3  0   0.471   4.5124   0.1609   0.0551
 E5E  HNAC  H  HNT3  0   0.484   4.6232  -0.4121   1.5950

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
 E5E  OAD  CAL   single    1.410  0.020  1.410
 E5E  CAL  CAK   single    1.508  0.020  1.508
 E5E  CAL  CAH   single    1.526  0.020  1.526
 E5E  CAK  CAF   aromatic  1.390  0.020  1.390
 E5E  CAK  CAG   aromatic  1.392  0.020  1.392
 E5E  CAF  CAE   aromatic  1.389  0.020  1.389
 E5E  CAG  CAJ   aromatic  1.386  0.020  1.386
 E5E  CAE  CAI   aromatic  1.385  0.020  1.385
 E5E  CAJ  CAI   aromatic  1.401  0.020  1.401
 E5E  CAJ  OAC   single    1.350  0.020  1.350
 E5E  CAI  OAB   single    1.354  0.020  1.354
 E5E  CAH  NAA   single    1.486  0.020  1.486
 E5E  OAC  HOAC  single    0.850  0.020  0.980
 E5E  CAG  HAG   single    0.930  0.020  1.080
 E5E  OAB  HOAB  single    0.850  0.020  0.980
 E5E  CAE  HAE   single    0.930  0.020  1.080
 E5E  CAF  HAF   single    0.930  0.020  1.080
 E5E  CAL  HAL   single    0.970  0.020  1.090
 E5E  OAD  HOAD  single    0.850  0.020  0.980
 E5E  CAH  HAH   single    0.970  0.020  1.090
 E5E  CAH  HAHA  single    0.970  0.020  1.090
 E5E  NAA  HNAA  single    0.890  0.020  1.040
 E5E  NAA  HNAB  single    0.890  0.020  1.040
 E5E  NAA  HNAC  single    0.890  0.020  1.040

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
 E5E  HOAC  OAC  CAJ   110.12  3.000
 E5E  CAI   CAJ  CAG   119.38  3.000
 E5E  CAI   CAJ  OAC   121.26  3.000
 E5E  CAG   CAJ  OAC   119.33  3.000
 E5E  HAG   CAG  CAK   120.17  3.000
 E5E  HAG   CAG  CAJ   118.74  3.000
 E5E  CAK   CAG  CAJ   121.08  3.000
 E5E  CAE   CAI  OAB   123.76  3.000
 E5E  OAB   CAI  CAJ   116.58  3.000
 E5E  CAE   CAI  CAJ   119.66  3.000
 E5E  HOAB  OAB  CAI   110.23  3.000
 E5E  HAE   CAE  CAF   119.83  3.000
 E5E  HAE   CAE  CAI   119.64  3.000
 E5E  CAF   CAE  CAI   120.53  3.000
 E5E  HAF   CAF  CAK   121.50  3.000
 E5E  HAF   CAF  CAE   118.28  3.000
 E5E  CAK   CAF  CAE   120.23  3.000
 E5E  CAL   CAK  CAF   121.08  3.000
 E5E  CAF   CAK  CAG   119.11  3.000
 E5E  CAL   CAK  CAG   119.80  3.000
 E5E  HAL   CAL  CAH   108.14  3.000
 E5E  HAL   CAL  OAD   106.07  3.000
 E5E  CAH   CAL  OAD   110.22  3.000
 E5E  HAL   CAL  CAK   108.54  3.000
 E5E  CAH   CAL  CAK   109.78  3.000
 E5E  OAD   CAL  CAK   113.86  3.000
 E5E  HOAD  OAD  CAL   109.52  3.000
 E5E  HAHA  CAH  HAH   110.15  3.000
 E5E  HAHA  CAH  NAA   107.45  3.000
 E5E  HAH   CAH  NAA   106.54  3.000
 E5E  HAHA  CAH  CAL   111.21  3.000
 E5E  HAH   CAH  CAL   111.40  3.000
 E5E  NAA   CAH  CAL   109.91  3.000
 E5E  HNAC  NAA  HNAB  107.65  3.000
 E5E  HNAC  NAA  HNAA  106.76  3.000
 E5E  HNAB  NAA  HNAA  107.41  3.000
 E5E  HNAC  NAA  CAH   111.50  3.000
 E5E  HNAB  NAA  CAH   111.09  3.000
 E5E  HNAA  NAA  CAH   112.18  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
 E5E  CONST_01  CAF   CAK  CAG  CAJ    0.00   0.0  0
 E5E  CONST_02  CAF   CAE  CAI  CAJ    0.00   0.0  0
 E5E  CONST_03  CAE   CAF  CAK  CAG    0.00   0.0  0
 E5E  CONST_04  CAE   CAI  CAJ  CAG    0.00   0.0  0
 E5E  CONST_05  CAK   CAF  CAE  CAI    0.00   0.0  0
 E5E  CONST_06  CAK   CAG  CAJ  CAI    0.00   0.0  0
 E5E  CONST_07  CAK   CAG  CAJ  OAC  180.00   0.0  0
 E5E  CONST_08  CAE   CAI  CAJ  OAC  180.00   0.0  0
 E5E  CONST_09  CAL   CAK  CAG  CAJ  180.00   0.0  0
 E5E  CONST_10  OAB   CAI  CAJ  CAG  180.00   0.0  0
 E5E  CONST_11  CAF   CAE  CAI  OAB  180.00   0.0  0
 E5E  CONST_12  CAL   CAK  CAF  CAE  180.00   0.0  0
 E5E  CONST_13  HAE   CAE  CAI  CAJ  180.00   0.0  0
 E5E  CONST_14  HAF   CAF  CAK  CAG  180.00   0.0  0
 E5E  CONST_15  HAG   CAG  CAJ  CAI  180.00   0.0  0
 E5E  Var_01    HNAA  NAA  CAH  CAL  -65.01  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
 E5E  chir_01  CAL  OAD  CAK  CAH  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
 E5E  plan-1  OAC  0.020
 E5E  plan-1  CAJ  0.020
 E5E  plan-1  CAG  0.020
 E5E  plan-1  CAI  0.020
 E5E  plan-1  OAB  0.020
 E5E  plan-1  CAE  0.020
 E5E  plan-1  CAF  0.020
 E5E  plan-1  CAK  0.020
 E5E  plan-1  CAL  0.020
 E5E  plan-1  HAG  0.020
 E5E  plan-1  HAE  0.020
 E5E  plan-1  HAF  0.020

