# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 16 17:41:18 2020
#   Inital geometry file: a 55 line input string
#   Ligand name: (2S)-2-amino-4-(methylseleninyl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[Se](=O)CC[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
 MSO  MSO  '(2S)-2-amino-4-(methylseleninyl)butanoic acid'  L-peptide  21  10  .  2022-09-22  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_MSO
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
 MSO  N    N   NH2   0  -0.782   1.9284  -0.1402  -2.2494
 MSO  CA   C   CH1   0  -0.210   0.5278  -0.4855  -2.1784
 MSO  CB   C   CH2   0  -0.451  -0.2036  -0.0428  -0.8908
 MSO  C    C   C     0   0.548  -0.1953   0.1077  -3.3724
 MSO  CG   C   CH2   0  -0.655   0.4140  -0.6855   0.3392
 MSO  SE   SE  SE    0   0.880  -0.4945  -0.0754   1.9640
 MSO  OE   O   O     0  -0.819  -0.1439   1.5303   2.0438
 MSO  CE   C   CH3   0  -0.860   0.7721  -0.9192   3.1779
 MSO  O    O   O     0  -0.435   0.2272   1.0055  -4.0543
 MSO  OXT  O   OH1   0  -0.594  -1.3793  -0.4625  -3.5625
 MSO  H    H   HNH2  0   0.348   2.0662   0.8382  -2.0260
 MSO  H2   H   HNH2  0   0.361   2.4484  -0.6692  -1.5628
 MSO  HCA  H   HCH1  0   0.278   0.4454  -1.5744  -2.2528
 MSO  HB2  H   HCH2  0   0.258  -1.2602  -0.3114  -0.9580
 MSO  HB3  H   HCH2  0   0.250  -0.1506   1.0471  -0.8089
 MSO  HG2  H   HCH2  0   0.277   1.4701  -0.4271   0.4500
 MSO  HG3  H   HCH2  0   0.281   0.3236  -1.7751   0.3082
 MSO  HE1  H   HCH3  0   0.286   0.5164  -0.6340   4.1975
 MSO  HE2  H   HCH3  0   0.276   0.7064  -2.0028   3.0792
 MSO  HE3  H   HCH3  0   0.280   1.7815  -0.5829   2.9411
 MSO  HXT  H   HOH1  0   0.482  -1.8434  -0.0312  -4.2956

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
 MSO  N    CA   single  1.458  0.019  1.458
 MSO  N    H    single  0.860  0.020  0.860
 MSO  N    H2   single  0.890  0.020  1.040
 MSO  CA   CB   single  1.530  0.020  1.530
 MSO  CA   C    single  1.525  0.021  1.525
 MSO  CA   HCA  single  0.970  0.020  1.090
 MSO  CB   CG   single  1.519  0.020  1.519
 MSO  CB   HB2  single  0.970  0.020  1.090
 MSO  CB   HB3  single  0.970  0.020  1.090
 MSO  C    O    double  1.231  0.020  1.231
 MSO  C    OXT  single  1.328  0.020  1.328
 MSO  CG   SE   single  1.959  0.020  1.959
 MSO  CG   HG2  single  0.970  0.020  1.090
 MSO  CG   HG3  single  0.970  0.020  1.090
 MSO  SE   OE   double  1.646  0.020  1.646
 MSO  SE   CE   single  1.947  0.020  1.947
 MSO  CE   HE1  single  0.970  0.020  1.090
 MSO  CE   HE2  single  0.970  0.020  1.090
 MSO  CE   HE3  single  0.970  0.020  1.090
 MSO  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
 MSO  H2   N    H    106.60  3.000
 MSO  H2   N    CA   109.90  3.000
 MSO  H    N    CA   114.00  3.000
 MSO  HCA  CA   C    107.43  3.000
 MSO  HCA  CA   CB   107.81  3.000
 MSO  C    CA   CB   110.10  1.900
 MSO  HCA  CA   N    107.91  3.000
 MSO  C    CA   N    111.00  2.800
 MSO  CB   CA   N    110.50  1.700
 MSO  HB3  CB   HB2  107.24  3.000
 MSO  HB3  CB   CG   109.94  3.000
 MSO  HB2  CB   CG   109.82  3.000
 MSO  HB3  CB   CA   108.95  3.000
 MSO  HB2  CB   CA   109.64  3.000
 MSO  CG   CB   CA   111.16  3.000
 MSO  OXT  C    O    123.50  3.000
 MSO  OXT  C    CA   111.71  3.000
 MSO  O    C    CA   120.80  1.700
 MSO  HG3  CG   HG2  108.56  3.000
 MSO  HG3  CG   SE   107.18  3.000
 MSO  HG2  CG   SE   106.88  3.000
 MSO  HG3  CG   CB   111.40  3.000
 MSO  HG2  CG   CB   112.03  3.000
 MSO  SE   CG   CB   110.57  3.000
 MSO  CE   SE   OE   104.72  3.000
 MSO  CE   SE   CG    94.62  3.000
 MSO  OE   SE   CG   104.20  3.000
 MSO  HE3  CE   HE2  110.05  3.000
 MSO  HE3  CE   HE1  109.88  3.000
 MSO  HE2  CE   HE1  109.32  3.000
 MSO  HE3  CE   SE   109.47  3.000
 MSO  HE2  CE   SE   109.59  3.000
 MSO  HE1  CE   SE   108.51  3.000
 MSO  HXT  OXT  C    110.13  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
 MSO  CONST_01  HXT  OXT  C   CA  180.00   0.0  0
 MSO  Var_01    SE   CG   CB  CA  178.47  30.0  3
 MSO  Var_02    OE   SE   CG  CB  -65.73  30.0  3
 MSO  Var_03    HE1  CE   SE  CG  174.81  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
 MSO  chir_01  CA  N  CB  C  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
 MSO  plan-1  CA   0.020
 MSO  plan-1  C    0.020
 MSO  plan-1  O    0.020
 MSO  plan-1  OXT  0.020
 MSO  plan-1  HXT  0.020
 MSO  plan-2  CG   0.020
 MSO  plan-2  SE   0.020
 MSO  plan-2  OE   0.020
 MSO  plan-2  CE   0.020

