# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 07:42:29 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  29  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 PERFECT
;

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   0.528  -2.3976   1.1090  -0.4249
 SL5  N     N  NH1   0  -0.611  -0.7869   0.7280   1.3733
 SL5  O     O  O     0  -0.435  -3.1378   1.7155   0.3081
 SL5  C5    C  CH1   0   0.107  -0.1804  -0.4596   1.9237
 SL5  C6    C  CH2   0  -0.127   1.3309  -0.4556   1.7985
 SL5  O7    O  O2    0  -0.473   1.6884  -0.3203   0.4536
 SL5  C8    C  CH2   0  -0.156   3.0622  -0.1290   0.2379
 SL5  C9    C  CH2   0  -0.181   3.3179   0.0215  -1.2400
 SL5  CA    C  CH1   0  -0.242  -1.1574   0.3781   0.0187
 SL5  CB    C  CH1   0   0.057  -1.3936  -1.1610   0.0582
 SL5  O10   O  OH1   0  -0.668   2.6810   1.1865  -1.7106
 SL5  OG1   O  O2    0  -0.507  -0.7377  -1.5767   1.2420
 SL5  CG2   C  CH3   0  -0.687  -0.8627  -1.8919  -1.1559
 SL5  OXT   O  OH1   0  -0.585  -2.5943   0.9755  -1.7271
 SL5  HN    H  HNH1  0   0.363  -1.6229   0.9556   1.8997
 SL5  H5    H  HCH1  0   0.252  -0.4206  -0.5327   2.9891
 SL5  H6    H  HCH2  0   0.199   1.7181   0.3766   2.4031
 SL5  H6A   H  HCH2  0   0.203   1.7373  -1.3814   2.2320
 SL5  H8    H  HCH2  0   0.203   3.4222   0.7585   0.7783
 SL5  H8A   H  HCH2  0   0.203   3.6469  -0.9843   0.6046
 SL5  H9A   H  HCH2  0   0.201   4.4055   0.0621  -1.3831
 SL5  H9B   H  HCH2  0   0.201   2.9610  -0.8767  -1.7602
 SL5  HA    H  HCH1  0   0.291  -0.3440   0.6046  -0.6767
 SL5  HB    H  HCH1  0   0.222  -2.4655  -1.3743   0.1689
 SL5  HO10  H  HOH1  0   0.454   2.8061   1.2306  -2.6624
 SL5  HG2   H  HCH3  0   0.237   0.2025  -1.7028  -1.2864
 SL5  HG2A  H  HCH3  0   0.238  -1.0179  -2.9674  -1.0656
 SL5  HG2B  H  HCH3  0   0.228  -1.3847  -1.5603  -2.0538
 SL5  HXT   H  HOH1  0   0.487  -3.4216   1.4071  -1.9902

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     double  1.205  0.020  1.205
 SL5  C    CA    single  1.506  0.020  1.506
 SL5  C    OXT   single  1.324  0.020  1.324
 SL5  N    C5    single  1.443  0.020  1.443
 SL5  N    CA    single  1.447  0.020  1.447
 SL5  C5   C6    single  1.516  0.020  1.516
 SL5  C5   OG1   single  1.422  0.020  1.422
 SL5  C6   O7    single  1.398  0.020  1.398
 SL5  O7   C8    single  1.404  0.020  1.404
 SL5  C8   C9    single  1.507  0.020  1.507
 SL5  CA   CB    single  1.558  0.020  1.558
 SL5  CB   OG1   single  1.416  0.020  1.416
 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
 SL5  OXT  HXT   single  0.850  0.020  0.980

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    111.29  3.000
 SL5  OXT   C    O     123.90  3.000
 SL5  CA    C    O     124.79  3.000
 SL5  HN    N    CA    109.22  3.000
 SL5  HN    N    C5    109.47  3.000
 SL5  CA    N    C5    105.40  3.000
 SL5  H5    C5   OG1   109.16  3.000
 SL5  H5    C5   C6    107.41  3.000
 SL5  OG1   C5   C6    110.67  3.000
 SL5  H5    C5   N     109.51  3.000
 SL5  OG1   C5   N     107.40  3.000
 SL5  C6    C5   N     112.66  3.000
 SL5  H6A   C6   H6    106.87  3.000
 SL5  H6A   C6   O7    111.47  3.000
 SL5  H6    C6   O7    111.45  3.000
 SL5  H6A   C6   C5    109.48  3.000
 SL5  H6    C6   C5    107.92  3.000
 SL5  O7    C6   C5    109.54  3.000
 SL5  C8    O7   C6    114.29  3.000
 SL5  H8A   C8   H8    106.85  3.000
 SL5  H8A   C8   C9    108.34  3.000
 SL5  H8    C8   C9    110.23  3.000
 SL5  H8A   C8   O7    111.30  3.000
 SL5  H8    C8   O7    110.78  3.000
 SL5  C9    C8   O7    109.29  3.000
 SL5  H9B   C9   H9A   106.89  3.000
 SL5  H9B   C9   O10   111.80  3.000
 SL5  H9A   C9   O10   111.96  3.000
 SL5  O10   C9   C8    109.48  3.000
 SL5  H9B   C9   C8    109.13  3.000
 SL5  H9A   C9   C8    107.44  3.000
 SL5  HA    CA   CB    109.48  3.000
 SL5  HA    CA   N     110.77  3.000
 SL5  CB    CA   N     104.72  3.000
 SL5  HA    CA   C     108.94  3.000
 SL5  CB    CA   C     111.22  3.000
 SL5  N     CA   C     111.66  3.000
 SL5  HB    CB   CG2   109.23  3.000
 SL5  HB    CB   OG1   108.11  3.000
 SL5  CG2   CB   OG1   111.50  3.000
 SL5  HB    CB   CA    110.03  3.000
 SL5  CG2   CB   CA    113.81  3.000
 SL5  OG1   CB   CA    103.95  3.000
 SL5  HO10  O10  C9    108.06  3.000
 SL5  CB    OG1  C5    110.59  3.000
 SL5  HG2B  CG2  HG2A  107.46  3.000
 SL5  HG2B  CG2  HG2   108.46  3.000
 SL5  HG2A  CG2  HG2   108.68  3.000
 SL5  HG2B  CG2  CB    110.23  3.000
 SL5  HG2A  CG2  CB    111.10  3.000
 SL5  HG2   CG2  CB    110.81  3.000
 SL5  HXT   OXT  C     110.42  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  CONST_01  HXT  OXT  C   CA   180.00   0.0  0
 SL5  Var_01    C9   C8   O7  C6  -179.22  30.0  3
 SL5  Var_02    O10  C9   C8  O7    64.11  30.0  3
 SL5  Var_03    H6   C6   O7  C8    52.72  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
 SL5  plan-1  HXT  0.020

