# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 07:34:15 2022
#   Inital geometry file: a 56 line input string
#   Ligand name: (2~{S},4~{R})-2-azanyl-4-methyl-5-oxidanyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](CO)C[C@H](N)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
 HL5  HL5  '(2~{S},4~{R})-2-azanyl-4-methyl-5-oxidanyl-pentanoic acid'  L-peptide  22  10  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_HL5
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
 HL5  N     N  NH2    0  -0.814  132.4509  -33.4259  82.7503
 HL5  CA    C  CH1    0  -0.232  131.3258  -32.6240  83.2115
 HL5  C     C  C      0   0.416  129.9825  -33.1935  82.6821
 HL5  OXT   O  OC     0  -0.607  128.9769  -32.4736  82.8392
 HL5  CB    C  CH2    0  -0.386  131.5165  -31.1609  82.8034
 HL5  CG    C  CH1    0  -0.274  132.8293  -30.5127  83.2534
 HL5  CD1   C  CH2    0  -0.130  132.9177  -30.4648  84.7715
 HL5  CD2   C  CH3    0  -0.648  132.9595  -29.1193  82.6429
 HL5  O     O  O     -1  -0.601  130.0066  -34.3375  82.1845
 HL5  H2    H  HNH2   0   0.329  133.1989  -33.4029  83.4310
 HL5  H1    H  HNH2   0   0.332  132.1412  -34.3868  82.6849
 HL5  HA    H  HCH1   0   0.194  131.2267  -32.6587  84.3102
 HL5  HB2   H  HCH2   0   0.205  131.4678  -31.0985  81.7106
 HL5  HB3   H  HCH2   0   0.201  130.6802  -30.5692  83.1853
 HL5  HG1   H  HCH1   0   0.211  133.6602  -31.1244  82.8823
 HL5  HD1   H  HOH1   0   0.447  134.1831  -29.8925  86.1244
 HL5  HD12  H  HCH2   0   0.177  132.0781  -29.8642  85.1531
 HL5  HD13  H  HCH2   0   0.199  132.7916  -31.4756  85.1805
 HL5  HD23  H  HCH3   0   0.226  133.9087  -28.6474  82.8946
 HL5  HD22  H  HCH3   0   0.220  132.8951  -29.1668  81.5545
 HL5  HD21  H  HCH3   0   0.207  132.1574  -28.4639  82.9920
 HL5  OD    O  OH1    0  -0.672  134.1610  -29.9221  85.1641

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
 HL5  O    C     deloc   1.231  0.020  1.231
 HL5  CD2  CG    single  1.527  0.020  1.527
 HL5  C    OXT   deloc   1.247  0.020  1.247
 HL5  C    CA    single  1.525  0.021  1.525
 HL5  N    CA    single  1.458  0.019  1.458
 HL5  CB   CA    single  1.530  0.020  1.530
 HL5  CB   CG    single  1.532  0.020  1.532
 HL5  CG   CD1   single  1.521  0.020  1.521
 HL5  CD1  OD    single  1.412  0.020  1.412
 HL5  N    H2    single  0.890  0.020  1.040
 HL5  N    H1    single  0.890  0.020  1.040
 HL5  CA   HA    single  0.970  0.020  0.970
 HL5  CB   HB2   single  0.970  0.020  1.090
 HL5  CB   HB3   single  0.970  0.020  1.090
 HL5  CG   HG1   single  0.970  0.020  1.090
 HL5  OD   HD1   single  0.850  0.020  0.980
 HL5  CD1  HD12  single  0.970  0.020  1.090
 HL5  CD1  HD13  single  0.970  0.020  1.090
 HL5  CD2  HD23  single  0.970  0.020  1.090
 HL5  CD2  HD22  single  0.970  0.020  1.090
 HL5  CD2  HD21  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
 HL5  H1    N    H2    106.95  3.000
 HL5  H1    N    CA    107.87  3.000
 HL5  H2    N    CA    110.22  3.000
 HL5  HA    CA   CB    109.00  3.000
 HL5  HA    CA   C     109.00  3.000
 HL5  CB    CA   C     110.10  1.900
 HL5  HA    CA   N     110.00  3.000
 HL5  CB    CA   N     110.50  1.700
 HL5  C     CA   N     111.00  2.800
 HL5  O     C    OXT   126.53  3.000
 HL5  OXT   C    CA    116.31  3.000
 HL5  O     C    CA    120.80  1.700
 HL5  HB3   CB   HB2   106.47  3.000
 HL5  HB3   CB   CG    108.90  3.000
 HL5  HB2   CB   CG    107.88  3.000
 HL5  HB3   CB   CA    109.20  3.000
 HL5  HB2   CB   CA    108.35  3.000
 HL5  CG    CB   CA    115.65  3.000
 HL5  HG1   CG   CD2   108.01  3.000
 HL5  HG1   CG   CD1   108.14  3.000
 HL5  CD2   CG   CD1   111.43  3.000
 HL5  HG1   CG   CB    108.30  3.000
 HL5  CD1   CG   CB    110.87  3.000
 HL5  CD2   CG   CB    109.98  3.000
 HL5  HD13  CD1  HD12  106.61  3.000
 HL5  HD13  CD1  OD    110.57  3.000
 HL5  HD12  CD1  OD    111.43  3.000
 HL5  HD13  CD1  CG    109.64  3.000
 HL5  HD12  CD1  CG    108.59  3.000
 HL5  OD    CD1  CG    109.92  3.000
 HL5  HD21  CD2  HD22  107.54  3.000
 HL5  HD21  CD2  HD23  107.80  3.000
 HL5  HD22  CD2  HD23  107.49  3.000
 HL5  HD21  CD2  CG    110.91  3.000
 HL5  HD22  CD2  CG    110.74  3.000
 HL5  HD23  CD2  CG    112.16  3.000
 HL5  HD1   OD   CD1   108.05  3.000

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
 HL5  chir_01  CA  C    N   CB   negativ
 HL5  chir_02  CG  CD1  CB  CD2  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
 HL5  plan-1  CA   0.020
 HL5  plan-1  C    0.020
 HL5  plan-1  OXT  0.020
 HL5  plan-1  O    0.020

