# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 29 21:14:08 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (3R)-3-amino-5-(methylsulfanyl)pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](N)CC(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
 B3M  B3M  '(3R)-3-amino-5-(methylsulfanyl)pentanoic acid'  L-peptide  23  10  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_B3M
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
 B3M  N    N  NH2   0  -0.788  -0.7330   1.3415   0.8547
 B3M  CA   C  CH2   0  -0.582  -1.8620  -0.7562   0.0660
 B3M  C    C  C     0   0.548  -3.2103  -0.1480  -0.2045
 B3M  O    O  O     0  -0.447  -3.4014   0.8805  -0.8071
 B3M  CB   C  CH1   0  -0.091  -0.6947   0.2247  -0.0744
 B3M  CG   C  CH2   0  -0.413   0.6180  -0.5414   0.0898
 B3M  CD   C  CH2   0  -0.537   1.8392   0.3258  -0.1690
 B3M  SE   S  S2    0  -0.052   3.3448  -0.6764  -0.0075
 B3M  CF   C  CH3   0  -0.763   4.5938   0.5769  -0.3682
 B3M  HN   H  HNH2  0   0.349  -1.5500   1.9134   0.6866
 B3M  HA   H  HCH2  0   0.268  -1.8599  -1.2108   1.0612
 B3M  HAA  H  HCH2  0   0.285  -1.7470  -1.5859  -0.6414
 B3M  HB   H  HCH1  0   0.234  -0.7157   0.6430  -1.0853
 B3M  HG   H  HCH2  0   0.229   0.6679  -0.9624   1.1002
 B3M  HGA  H  HCH2  0   0.237   0.6205  -1.3904  -0.5996
 B3M  HD   H  HCH2  0   0.252   1.8005   0.7467  -1.1769
 B3M  HDA  H  HCH2  0   0.261   1.8788   1.1536   0.5388
 B3M  HF   H  HCH3  0   0.259   4.4586   0.9916  -1.3662
 B3M  HFA  H  HCH3  0   0.259   4.5677   1.3833   0.3635
 B3M  HFB  H  HCH3  0   0.271   5.5694   0.0962  -0.3214
 B3M  HNA  H  HNH2  0   0.337  -0.8132   0.9973   1.8049
 B3M  OXT  O  OH1   0  -0.594  -4.1982  -0.8978   0.2727
 B3M  HXT  H  HOH1  0   0.479  -5.0535  -0.5013   0.0487

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
 B3M  N    HN   single  0.890  0.020  1.040
 B3M  N    HNA  single  0.890  0.020  1.040
 B3M  CA   HA   single  0.970  0.020  0.970
 B3M  CA   C    single  1.525  0.021  1.525
 B3M  C    OXT  single  1.329  0.020  1.329
 B3M  O    C    double  1.231  0.020  1.231
 B3M  CB   N    single  1.453  0.020  1.453
 B3M  CB   CA   single  1.521  0.033  1.521
 B3M  CG   CB   single  1.529  0.020  1.529
 B3M  CG   HGA  single  0.970  0.020  1.090
 B3M  CD   CG   single  1.520  0.020  1.520
 B3M  CD   HDA  single  0.970  0.020  1.090
 B3M  SE   CD   single  1.816  0.020  1.816
 B3M  SE   CF   single  1.806  0.020  1.806
 B3M  CF   HF   single  0.970  0.020  1.090
 B3M  CF   HFA  single  0.970  0.020  1.090
 B3M  HAA  CA   single  0.970  0.020  1.090
 B3M  HB   CB   single  0.970  0.020  1.090
 B3M  HG   CG   single  0.970  0.020  1.090
 B3M  HD   CD   single  0.970  0.020  1.090
 B3M  HFB  CF   single  0.970  0.020  1.090
 B3M  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
 B3M  HNA  N    HN   106.49  3.000
 B3M  HNA  N    CB   109.90  3.000
 B3M  HN   N    CB   110.46  3.000
 B3M  HAA  CA   HA   105.80  3.000
 B3M  HAA  CA   CB   110.22  3.000
 B3M  HA   CA   CB   109.00  3.000
 B3M  HAA  CA   C    106.51  3.000
 B3M  CB   CA   C    110.50  1.500
 B3M  HA   CA   C    110.00  3.000
 B3M  OXT  C    O    122.84  3.000
 B3M  O    C    CA   120.80  1.700
 B3M  OXT  C    CA   120.80  1.700
 B3M  HB   CB   CG   107.89  3.000
 B3M  HB   CB   CA   108.36  3.000
 B3M  CG   CB   CA   108.89  3.000
 B3M  HB   CB   N    107.24  3.000
 B3M  CG   CB   N    109.82  3.000
 B3M  CA   CB   N    110.40  1.500
 B3M  HGA  CG   HG   106.44  3.000
 B3M  HG   CG   CD   109.86  3.000
 B3M  HGA  CG   CD   109.50  3.000
 B3M  HG   CG   CB   109.31  3.000
 B3M  CD   CG   CB   112.68  3.000
 B3M  HGA  CG   CB   108.86  3.000
 B3M  HDA  CD   HD   107.92  3.000
 B3M  HD   CD   SE   108.90  3.000
 B3M  HDA  CD   SE   109.34  3.000
 B3M  HD   CD   CG   110.39  3.000
 B3M  SE   CD   CG   109.64  3.000
 B3M  HDA  CD   CG   110.61  3.000
 B3M  CF   SE   CD    99.94  3.000
 B3M  HFB  CF   HFA  108.64  3.000
 B3M  HFB  CF   HF   108.59  3.000
 B3M  HFA  CF   HF   109.31  3.000
 B3M  HFB  CF   SE   107.75  3.000
 B3M  HFA  CF   SE   111.29  3.000
 B3M  HF   CF   SE   111.18  3.000
 B3M  HXT  OXT  C    110.02  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
 B3M  CONST_01  HXT  OXT  C   CA   180.00   0.0  0
 B3M  Var_01    CB   CA   C   O     18.88  30.0  2
 B3M  Var_02    SE   CD   CG  CB  -178.09  30.0  1
 B3M  Var_03    HF   CF   SE  CD   -60.16  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
 B3M  chir_01  CB  N  CA  CG  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
 B3M  plan-1  CA   0.020
 B3M  plan-1  C    0.020
 B3M  plan-1  O    0.020
 B3M  plan-1  OXT  0.020
 B3M  plan-1  HXT  0.020

