# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:16:41 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: [(3S)-3-amino-3-carboxypropyl](ethyl)methylsulfonium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[S@@+](C)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
 MT2  MT2  '[(3S)-3-amino-3-carboxypropyl](ethyl)methylsulfonium'  L-peptide  26  11  .  2019-03-22  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_MT2
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
 MT2  O     O  O      0  -0.598  23.3912  8.1593  17.9883
 MT2  C     C  C      0   0.413  22.3472  7.9807  17.3326
 MT2  OXT   O  OC    -1  -0.592  21.9878  8.5930  16.3087
 MT2  CA    C  CH1    0  -0.234  21.3660  6.9109  17.8870
 MT2  N     N  NH2    0  -0.807  20.4179  6.4803  16.8732
 MT2  CB    C  CH2    0  -0.409  22.0919  5.6938  18.4652
 MT2  CG    C  CH2    0  -0.587  22.9275  5.0163  17.3904
 MT2  SD    S  S3     1   0.379  23.4129  3.3420  17.8931
 MT2  CE    C  CH3    0  -0.757  24.8334  3.0045  16.8477
 MT2  C15   C  CH2   -1  -0.550  22.1526  2.2845  17.1190
 MT2  HA    H  HCH1   0   0.230  20.8588  7.3962  18.7361
 MT2  HN2   H  HNH2   0   0.338  19.5182  6.2847  17.2901
 MT2  H     H  HNH2   0   0.340  20.2921  7.2420  16.2189
 MT2  HB1   H  HCH2   0   0.249  22.7331  5.9885  19.2949
 MT2  HB2   H  HCH2   0   0.245  21.3421  5.0097  18.8692
 MT2  HG1   H  HCH2   0   0.315  22.3962  4.9363  16.4407
 MT2  HG2   H  HCH2   0   0.322  23.8617  5.5556  17.2292
 MT2  HE1   H  HCH3   0   0.311  24.5918  3.2158  15.8086
 MT2  HE2   H  HCH3   0   0.323  25.6508  3.6339  17.1911
 MT2  HE3   H  HCH3   0   0.320  25.0969  1.9573  16.9777
 MT2  H14   H  HCH3   0   0.256  20.7174  2.4285  18.7460
 MT2  H14A  H  HCH3   0   0.254  20.4046  3.5406  17.3993
 MT2  H14B  H  HCH3   0   0.279  20.0857  1.8229  17.2172
 MT2  H15   H  HCH2   0   0.315  22.2072  2.4592  16.0440
 MT2  H15A  H  HCH2   0   0.323  22.4859  1.2676  17.3295
 MT2  C14   C  CH3    0  -0.678  20.7646  2.5478  17.6646

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
 MT2  O    C     deloc   1.231  0.020  1.231
 MT2  C    OXT   deloc   1.246  0.020  1.246
 MT2  C    CA    single  1.525  0.021  1.525
 MT2  CA   N     single  1.458  0.019  1.458
 MT2  CA   CB    single  1.530  0.020  1.530
 MT2  CA   HA    single  0.970  0.020  0.970
 MT2  N    HN2   single  0.890  0.020  1.040
 MT2  N    H     single  0.860  0.020  0.860
 MT2  CB   CG    single  1.521  0.020  1.521
 MT2  CB   HB1   single  0.970  0.020  1.090
 MT2  CB   HB2   single  0.970  0.020  1.090
 MT2  CG   SD    single  1.814  0.020  1.814
 MT2  CG   HG1   single  0.970  0.020  1.090
 MT2  CG   HG2   single  0.970  0.020  1.090
 MT2  SD   CE    single  1.796  0.020  1.796
 MT2  SD   C15   single  1.818  0.020  1.818
 MT2  CE   HE1   single  0.970  0.020  1.090
 MT2  CE   HE2   single  0.970  0.020  1.090
 MT2  CE   HE3   single  0.970  0.020  1.090
 MT2  C14  C15   single  1.514  0.020  1.514
 MT2  C14  H14   single  0.970  0.020  1.090
 MT2  C14  H14A  single  0.970  0.020  1.090
 MT2  C14  H14B  single  0.970  0.020  1.090
 MT2  C15  H15   single  0.970  0.020  1.090
 MT2  C15  H15A  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
 MT2  CA    C    OXT   116.70  3.000
 MT2  CA    C    O     120.80  1.700
 MT2  OXT   C    O     127.15  3.000
 MT2  HA    CA   CB    109.00  3.000
 MT2  HA    CA   N     110.00  3.000
 MT2  CB    CA   N     110.50  1.700
 MT2  HA    CA   C     110.00  3.000
 MT2  CB    CA   C     110.10  1.900
 MT2  N     CA   C     111.00  2.800
 MT2  H     N    HN2   107.56  3.000
 MT2  H     N    CA    114.00  3.000
 MT2  HN2   N    CA    110.51  3.000
 MT2  HB2   CB   HB1   106.96  3.000
 MT2  HB2   CB   CG    111.07  3.000
 MT2  HB1   CB   CG    109.60  3.000
 MT2  HB2   CB   CA    108.19  3.000
 MT2  HB1   CB   CA    110.59  3.000
 MT2  CG    CB   CA    110.36  3.000
 MT2  HG2   CG   HG1   108.95  3.000
 MT2  HG2   CG   SD    105.55  3.000
 MT2  HG1   CG   SD    107.68  3.000
 MT2  HG2   CG   CB    110.79  3.000
 MT2  HG1   CG   CB    112.35  3.000
 MT2  SD    CG   CB    111.24  3.000
 MT2  C15   SD   CE    101.02  3.000
 MT2  C15   SD   CG    103.49  3.000
 MT2  CE    SD   CG    102.93  3.000
 MT2  HE3   CE   HE2   109.72  3.000
 MT2  HE3   CE   HE1   110.80  3.000
 MT2  HE2   CE   HE1   110.88  3.000
 MT2  HE3   CE   SD    107.64  3.000
 MT2  HE2   CE   SD    107.58  3.000
 MT2  HE1   CE   SD    110.12  3.000
 MT2  H15A  C15  H15   108.92  3.000
 MT2  H15A  C15  C14   111.88  3.000
 MT2  H15   C15  C14   111.91  3.000
 MT2  H15A  C15  SD    104.37  3.000
 MT2  H15   C15  SD    106.97  3.000
 MT2  C14   C15  SD    112.38  3.000
 MT2  H14B  C14  H14A  107.50  3.000
 MT2  H14B  C14  H14   107.94  3.000
 MT2  H14A  C14  H14   109.12  3.000
 MT2  H14B  C14  C15   107.91  3.000
 MT2  H14A  C14  C15   111.94  3.000
 MT2  H14   C14  C15   112.23  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
 MT2  Var_01  SD   CG   CB   CA  -163.85  30.0  3
 MT2  Var_02  H14  C14  C15  SD   -56.44  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
 MT2  chir_01  CA  C    N   CB  negativ
 MT2  chir_02  SD  C15  CE  CG  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
 MT2  plan-1  O    0.020
 MT2  plan-1  C    0.020
 MT2  plan-1  OXT  0.020
 MT2  plan-1  CA   0.020

