# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 20:27:41 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@@H](CC=O)N[C@@](O)(CC(O)=O)C(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
 5XR  5XR  '2-hydroxy-N-[(1S)-1-hydroxy-3-oxopropyl]-L-aspartic acid'  ligand  26  15  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5XR
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
 5XR  OAI  O  O     0  -0.431   3.4569   0.5483   0.3726
 5XR  CAH  C  C     0   0.566   3.1972  -0.4177  -0.2997
 5XR  OAJ  O  OH1   0  -0.590   4.1117  -1.2636  -0.7511
 5XR  CAD  C  CH2   0  -0.633   1.8169  -0.7890  -0.7616
 5XR  CAB  C  CT    0   0.302   0.7099  -0.2505   0.1526
 5XR  CAA  C  C     0   0.549   0.8047   1.2787   0.3138
 5XR  OAG  O  O     0  -0.432   0.7747   1.8654   1.3595
 5XR  OAF  O  OH1   0  -0.601   0.8819   1.8658  -0.8731
 5XR  OAC  O  OH1   0  -0.644   0.8240  -0.7630   1.4399
 5XR  NAE  N  NH1   0  -0.647  -0.5457  -0.6623  -0.4407
 5XR  CAK  C  CH1   0   0.156  -1.7730  -0.2188   0.1500
 5XR  OAO  O  OH1   0  -0.650  -2.0178   1.1719   0.0714
 5XR  CAL  C  CH2   0  -0.603  -2.9300  -0.9960  -0.4719
 5XR  CAM  C  C1    0   0.194  -4.2359  -0.5595   0.1198
 5XR  OAN  O  O     0  -0.376  -5.2250  -0.2929  -0.5150
 5XR  H1   H  HOH1  0   0.483   4.9963  -0.9754  -0.4784
 5XR  H2   H  HCH2  0   0.308   1.7011  -0.4204  -1.7852
 5XR  H3   H  HCH2  0   0.302   1.7181  -1.8753  -0.8235
 5XR  H4   H  HOH1  0   0.484   0.9009   2.8284  -0.7671
 5XR  H5   H  HOH1  0   0.455   0.6746  -1.7148   1.3893
 5XR  H6   H  HNH1  0   0.369  -0.5477  -0.5888  -1.4504
 5XR  H8   H  HCH1  0   0.253  -1.7294  -0.4298   1.2202
 5XR  H9   H  HOH1  0   0.444  -2.1204   1.4227  -0.8542
 5XR  H10  H  HCH2  0   0.263  -2.9509  -0.8803  -1.5595
 5XR  H11  H  HCH2  0   0.290  -2.8056  -2.0611  -0.2516
 5XR  H13  H  H     0   0.189  -4.2476  -0.5201   1.2243

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
 5XR  OAG  CAA  double  1.199  0.020  1.199
 5XR  OAI  CAH  double  1.205  0.020  1.205
 5XR  OAC  CAB  single  1.390  0.020  1.390
 5XR  OAN  CAM  double  1.205  0.020  1.205
 5XR  CAD  CAH  single  1.502  0.020  1.502
 5XR  CAD  CAB  single  1.533  0.020  1.533
 5XR  CAA  CAB  single  1.541  0.020  1.541
 5XR  CAA  OAF  single  1.326  0.020  1.326
 5XR  CAH  OAJ  single  1.325  0.020  1.325
 5XR  CAB  NAE  single  1.448  0.020  1.448
 5XR  CAM  CAL  single  1.499  0.020  1.499
 5XR  NAE  CAK  single  1.433  0.020  1.433
 5XR  CAL  CAK  single  1.526  0.020  1.526
 5XR  CAK  OAO  single  1.414  0.020  1.414
 5XR  OAJ  H1   single  0.850  0.020  0.980
 5XR  CAD  H2   single  0.970  0.020  1.090
 5XR  CAD  H3   single  0.970  0.020  1.090
 5XR  OAF  H4   single  0.850  0.020  0.980
 5XR  OAC  H5   single  0.850  0.020  0.980
 5XR  NAE  H6   single  0.890  0.020  1.040
 5XR  CAK  H8   single  0.970  0.020  1.090
 5XR  OAO  H9   single  0.850  0.020  0.980
 5XR  CAL  H10  single  0.970  0.020  1.090
 5XR  CAL  H11  single  0.970  0.020  1.090
 5XR  CAM  H13  single  0.930  0.020  1.080

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
 5XR  CAD  CAH  OAJ  111.82  3.000
 5XR  OAJ  CAH  OAI  123.57  3.000
 5XR  CAD  CAH  OAI  124.58  3.000
 5XR  H1   OAJ  CAH  110.13  3.000
 5XR  H3   CAD  H2   105.81  3.000
 5XR  H3   CAD  CAB  108.52  3.000
 5XR  H2   CAD  CAB  111.28  3.000
 5XR  H3   CAD  CAH  110.26  3.000
 5XR  H2   CAD  CAH  107.56  3.000
 5XR  CAB  CAD  CAH  113.16  3.000
 5XR  NAE  CAB  OAC  110.22  3.000
 5XR  NAE  CAB  CAA  112.24  3.000
 5XR  OAC  CAB  CAA  105.30  3.000
 5XR  NAE  CAB  CAD  106.36  3.000
 5XR  CAA  CAB  CAD  111.51  3.000
 5XR  OAC  CAB  CAD  111.30  3.000
 5XR  OAF  CAA  OAG  124.41  3.000
 5XR  OAF  CAA  CAB  110.44  3.000
 5XR  OAG  CAA  CAB  125.12  3.000
 5XR  H4   OAF  CAA  110.06  3.000
 5XR  H5   OAC  CAB  107.60  3.000
 5XR  H6   NAE  CAK  112.77  3.000
 5XR  H6   NAE  CAB  112.93  3.000
 5XR  CAK  NAE  CAB  119.06  3.000
 5XR  H8   CAK  CAL  109.35  3.000
 5XR  H8   CAK  OAO  104.57  3.000
 5XR  CAL  CAK  OAO  110.30  3.000
 5XR  H8   CAK  NAE  108.07  3.000
 5XR  OAO  CAK  NAE  115.46  3.000
 5XR  CAL  CAK  NAE  108.89  3.000
 5XR  H9   OAO  CAK  109.11  3.000
 5XR  H11  CAL  H10  107.77  3.000
 5XR  H11  CAL  CAM  107.64  3.000
 5XR  H10  CAL  CAM  110.19  3.000
 5XR  H11  CAL  CAK  109.10  3.000
 5XR  H10  CAL  CAK  111.45  3.000
 5XR  CAM  CAL  CAK  110.57  3.000
 5XR  H13  CAM  OAN  120.65  3.000
 5XR  H13  CAM  CAL  114.47  3.000
 5XR  OAN  CAM  CAL  124.86  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
 5XR  CONST_01  H1   OAJ  CAH  OAI    0.00   0.0  0
 5XR  CONST_02  H4   OAF  CAA  CAB  180.00   0.0  0
 5XR  Var_01    CAB  CAD  CAH  OAI  -25.76  30.0  1
 5XR  Var_02    OAN  CAM  CAL  CAK  132.94  30.0  2

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
 5XR  chir_01  CAB  CAD  CAA  NAE  negativ
 5XR  chir_02  CAK  OAO  NAE  CAL  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
 5XR  plan-1  OAI  0.020
 5XR  plan-1  CAH  0.020
 5XR  plan-1  OAJ  0.020
 5XR  plan-1  CAD  0.020
 5XR  plan-1  H1   0.020
 5XR  plan-2  CAB  0.020
 5XR  plan-2  CAA  0.020
 5XR  plan-2  OAG  0.020
 5XR  plan-2  OAF  0.020
 5XR  plan-2  H4   0.020
 5XR  plan-3  CAL  0.020
 5XR  plan-3  CAM  0.020
 5XR  plan-3  OAN  0.020
 5XR  plan-3  H13  0.020

