# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 19:04:04 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: (2S,4S,5R)-2-[(2-hydroxyethoxy)methyl]-5-methyl-1,3-oxazolidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H]1O[C@@H](COCCO)N[C@@H]1C(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
 SL5  SL5  '(2S,4S,5R)-2-[(2-hydroxyethoxy)methyl]-5-methyl-1,3-oxazolidine-4-carboxylic acid'  ligand  28  14  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SL5
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
 SL5  C     C  C      0   0.396  -2.4403   1.0777  -0.6245
 SL5  N     N  NH1    0  -0.621  -0.8062   0.7626   1.2353
 SL5  O     O  O      0  -0.601  -3.1838   1.5990   0.2304
 SL5  C5    C  CH1    0   0.118  -0.1996  -0.4013   1.8245
 SL5  C6    C  CH2    0  -0.131   1.3172  -0.3766   1.7674
 SL5  O7    O  O2     0  -0.469   1.7453  -0.2745   0.4396
 SL5  C8    C  CH2    0  -0.154   3.1363  -0.1662   0.2971
 SL5  C9    C  CH2    0  -0.180   3.4842  -0.0566  -1.1657
 SL5  CA    C  CH1    0  -0.248  -1.1598   0.3902  -0.1222
 SL5  CB    C  CH1    0   0.060  -1.3590  -1.1426  -0.0539
 SL5  O10   O  OH1    0  -0.669   2.9654   1.1452  -1.6860
 SL5  OG1   O  O2     0  -0.521  -0.6958  -1.5445   1.1373
 SL5  CG2   C  CH3    0  -0.688  -0.8201  -1.8799  -1.2601
 SL5  OXT   O  OC    -1  -0.606  -2.6415   1.0079  -1.8517
 SL5  HN    H  HNH1   0   0.343  -1.6731   0.9867   1.7129
 SL5  H5    H  HCH1   0   0.232  -0.4762  -0.4675   2.8835
 SL5  H6    H  HCH2   0   0.192   1.6682   0.4752   2.3681
 SL5  H6A   H  HCH2   0   0.194   1.7139  -1.2856   2.2454
 SL5  H8    H  HCH2   0   0.199   3.5216   0.7070   0.8443
 SL5  H8A   H  HCH2   0   0.199   3.6502  -1.0484   0.7056
 SL5  H9A   H  HCH2   0   0.198   4.5779  -0.1008  -1.2493
 SL5  H9B   H  HCH2   0   0.199   3.0891  -0.9338  -1.6946
 SL5  HA    H  HCH1   0   0.232  -0.3366   0.6143  -0.8069
 SL5  HB    H  HCH1   0   0.197  -2.4274  -1.3753   0.0625
 SL5  HO10  H  HOH1   0   0.454   3.1718   1.1770  -2.6240
 SL5  HG2   H  HCH3   0   0.228   0.2475  -1.6911  -1.3783
 SL5  HG2A  H  HCH3   0   0.224  -0.9787  -2.9567  -1.1846
 SL5  HG2B  H  HCH3   0   0.223  -1.3323  -1.5275  -2.1560

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
 SL5  C    O     deloc   1.247  0.020  1.247
 SL5  C    CA    single  1.538  0.020  1.538
 SL5  C    OXT   deloc   1.245  0.020  1.245
 SL5  N    C5    single  1.439  0.020  1.439
 SL5  N    CA    single  1.451  0.020  1.451
 SL5  C5   C6    single  1.518  0.020  1.518
 SL5  C5   OG1   single  1.423  0.020  1.423
 SL5  C6   O7    single  1.399  0.020  1.399
 SL5  O7   C8    single  1.402  0.020  1.402
 SL5  C8   C9    single  1.508  0.020  1.508
 SL5  CA   CB    single  1.547  0.020  1.547
 SL5  CB   OG1   single  1.421  0.020  1.421
 SL5  CB   CG2   single  1.513  0.020  1.513
 SL5  N    HN    single  0.890  0.020  1.040
 SL5  C5   H5    single  0.970  0.020  1.090
 SL5  C6   H6    single  0.970  0.020  1.090
 SL5  C6   H6A   single  0.970  0.020  1.090
 SL5  C8   H8    single  0.970  0.020  1.090
 SL5  C8   H8A   single  0.970  0.020  1.090
 SL5  C9   H9A   single  0.970  0.020  1.090
 SL5  C9   H9B   single  0.970  0.020  1.090
 SL5  CA   HA    single  0.970  0.020  1.090
 SL5  CB   HB    single  0.970  0.020  1.090
 SL5  C9   O10   single  1.409  0.020  1.409
 SL5  O10  HO10  single  0.850  0.020  0.980
 SL5  CG2  HG2   single  0.970  0.020  1.090
 SL5  CG2  HG2A  single  0.970  0.020  1.090
 SL5  CG2  HG2B  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
 SL5  OXT   C    CA    115.55  3.000
 SL5  OXT   C    O     127.05  3.000
 SL5  CA    C    O     117.35  3.000
 SL5  HN    N    CA    106.78  3.000
 SL5  HN    N    C5    110.25  3.000
 SL5  CA    N    C5    106.16  3.000
 SL5  H5    C5   OG1   109.26  3.000
 SL5  H5    C5   C6    106.82  3.000
 SL5  OG1   C5   C6    110.07  3.000
 SL5  H5    C5   N     109.76  3.000
 SL5  OG1   C5   N     107.77  3.000
 SL5  C6    C5   N     113.13  3.000
 SL5  H6A   C6   H6    106.70  3.000
 SL5  H6A   C6   O7    111.23  3.000
 SL5  H6    C6   O7    111.36  3.000
 SL5  H6A   C6   C5    109.28  3.000
 SL5  H6    C6   C5    108.11  3.000
 SL5  O7    C6   C5    110.04  3.000
 SL5  C8    O7   C6    113.93  3.000
 SL5  H8A   C8   H8    106.75  3.000
 SL5  H8A   C8   C9    108.11  3.000
 SL5  H8    C8   C9    110.12  3.000
 SL5  H8A   C8   O7    111.34  3.000
 SL5  H8    C8   O7    110.99  3.000
 SL5  C9    C8   O7    109.46  3.000
 SL5  H9B   C9   H9A   106.84  3.000
 SL5  H9B   C9   O10   111.79  3.000
 SL5  H9A   C9   O10   111.92  3.000
 SL5  O10   C9   C8    109.59  3.000
 SL5  H9B   C9   C8    109.04  3.000
 SL5  H9A   C9   C8    107.51  3.000
 SL5  HA    CA   CB    109.11  3.000
 SL5  HA    CA   N     110.45  3.000
 SL5  CB    CA   N     104.13  3.000
 SL5  HA    CA   C     109.31  3.000
 SL5  CB    CA   C     110.50  3.000
 SL5  N     CA   C     113.19  3.000
 SL5  HB    CB   CG2   109.11  3.000
 SL5  HB    CB   OG1   107.75  3.000
 SL5  CG2   CB   OG1   111.36  3.000
 SL5  HB    CB   CA    109.84  3.000
 SL5  CG2   CB   CA    113.69  3.000
 SL5  OG1   CB   CA    104.90  3.000
 SL5  HO10  O10  C9    108.03  3.000
 SL5  CB    OG1  C5    109.89  3.000
 SL5  HG2B  CG2  HG2A  107.91  3.000
 SL5  HG2B  CG2  HG2   108.35  3.000
 SL5  HG2A  CG2  HG2   108.71  3.000
 SL5  HG2B  CG2  CB    109.28  3.000
 SL5  HG2A  CG2  CB    111.96  3.000
 SL5  HG2   CG2  CB    110.53  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
 SL5  Var_01  C9   C8  O7  C6  -179.76  30.0  3
 SL5  Var_02  O10  C9  C8  O7    65.13  30.0  3
 SL5  Var_03  H6   C6  O7  C8    56.60  30.0  1

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
 SL5  chir_01  C5  N    C6  OG1  positiv
 SL5  chir_02  CA  N    CB  C    negativ
 SL5  chir_03  CB  OG1  CA  CG2  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
 SL5  plan-1  C    0.020
 SL5  plan-1  O    0.020
 SL5  plan-1  CA   0.020
 SL5  plan-1  OXT  0.020

