# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 01:26:31 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  20  10  .  2022-09-22  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_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  -0.741   1.9200  -0.2049  -2.3033
 MSO  CA   C   CH1    0  -0.211   0.5027  -0.5244  -2.1887
 MSO  CB   C   CH2    0  -0.414  -0.1814  -0.0470  -0.8877
 MSO  C    C   C      0   0.435  -0.2980   0.0791  -3.3676
 MSO  CG   C   CH2    0  -0.633   0.3856  -0.7101   0.3571
 MSO  SE   SE  SE     0   0.861  -0.4881  -0.0146   1.9692
 MSO  OE   O   O      0  -0.825  -0.0260   1.5642   2.0191
 MSO  CE   C   CH3    0  -0.808   0.7170  -0.9123   3.2131
 MSO  O    O   O      0  -0.573   0.1553   1.1157  -3.8977
 MSO  OXT  O   OC    -1  -0.756  -1.3418  -0.5029  -3.6501
 MSO  H    H   HNH2   0   0.344   2.0247   0.7959  -2.4030
 MSO  H2   H   HNH2   0   0.258   2.4300  -0.4754  -1.4659
 MSO  HCA  H   HCH1   0   0.237   0.3959  -1.6126  -2.2369
 MSO  HB2  H   HCH2   0   0.236  -1.2506  -0.2636  -0.9564
 MSO  HB3  H   HCH2   0   0.273  -0.0758   1.0398  -0.8142
 MSO  HG2  H   HCH2   0   0.281   1.4542  -0.5166   0.4806
 MSO  HG3  H   HCH2   0   0.223   0.2335  -1.7903   0.3361
 MSO  HE1  H   HCH3   0   0.244   0.4602  -0.6016   4.2251
 MSO  HE2  H   HCH3   0   0.277   0.5980  -1.9923   3.1286
 MSO  HE3  H   HCH3   0   0.291   1.7464  -0.6312   2.9915

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  1.520  0.020  1.520
 MSO  CB  HB2  single  0.970  0.020  1.090
 MSO  CB  HB3  single  0.970  0.020  1.090
 MSO  C   O    deloc   1.231  0.020  1.231
 MSO  C   OXT  deloc   1.228  0.020  1.228
 MSO  CG  SE   single  1.961  0.020  1.961
 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  1.951  0.020  1.951
 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

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    107.00  3.000
 MSO  H2   N   CA   111.38  3.000
 MSO  H    N   CA   114.00  3.000
 MSO  HCA  CA  C    107.68  3.000
 MSO  HCA  CA  CB   107.52  3.000
 MSO  C    CA  CB   110.10  1.900
 MSO  HCA  CA  N    108.02  3.000
 MSO  C    CA  N    111.00  2.800
 MSO  CB   CA  N    110.50  1.700
 MSO  HB3  CB  HB2  107.18  3.000
 MSO  HB3  CB  CG   110.01  3.000
 MSO  HB2  CB  CG   109.26  3.000
 MSO  HB3  CB  CA   108.70  3.000
 MSO  HB2  CB  CA   108.60  3.000
 MSO  CG   CB  CA   112.93  3.000
 MSO  OXT  C   O    127.15  3.000
 MSO  OXT  C   CA   115.48  3.000
 MSO  O    C   CA   120.80  1.700
 MSO  HG3  CG  HG2  108.29  3.000
 MSO  HG3  CG  SE   107.74  3.000
 MSO  HG2  CG  SE   106.25  3.000
 MSO  HG3  CG  CB   111.35  3.000
 MSO  HG2  CG  CB   112.33  3.000
 MSO  SE   CG  CB   110.63  3.000
 MSO  CE   SE  OE   104.40  3.000
 MSO  CE   SE  CG    94.92  3.000
 MSO  OE   SE  CG   103.88  3.000
 MSO  HE3  CE  HE2  110.06  3.000
 MSO  HE3  CE  HE1  109.75  3.000
 MSO  HE2  CE  HE1  109.20  3.000
 MSO  HE3  CE  SE   109.59  3.000
 MSO  HE2  CE  SE   109.83  3.000
 MSO  HE1  CE  SE   108.39  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  Var_01  SE   CG  CB  CA  178.17  30.0  3
 MSO  Var_02  OE   SE  CG  CB  -65.73  30.0  3
 MSO  Var_03  HE1  CE  SE  CG  175.73  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-2  CG   0.020
 MSO  plan-2  SE   0.020
 MSO  plan-2  OE   0.020
 MSO  plan-2  CE   0.020

