# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:34:39 2022
#   Inital geometry file: a 67 line input string
#   Ligand name: 3-{[(R)-methylsulfinyl]methyl}-L-valine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S@@](=O)CC(C)(C)[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
 M2S  M2S  3-{[(R)-methylsulfinyl]methyl}-L-valine  L-peptide  26  12  .  2012-08-28  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_M2S
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
 M2S  N     N  NH2    0  -0.801  -13.6308  -0.0874  4.0010
 M2S  CA    C  CH1    0  -0.162  -14.4468   1.0233  4.4864
 M2S  CB    C  CT     0  -0.093  -14.3889   1.1022  6.0420
 M2S  CG1   C  CH3    0  -0.640  -15.2169   2.2866  6.5464
 M2S  CG2   C  CH3    0  -0.638  -14.9906  -0.1869  6.6079
 M2S  CG    C  CH2    0  -0.593  -12.9222   1.2158  6.4724
 M2S  SD    S  S3     0   0.711  -12.6921   1.3743  8.2701
 M2S  OE    O  O      0  -0.786  -12.7695   2.8469  8.6149
 M2S  CE    C  CH3    0  -0.799  -10.9374   0.9449  8.2931
 M2S  C     C  C      0   0.399  -14.0939   2.3708  3.8034
 M2S  O     O  O      0  -0.602  -12.8804   2.5808  3.5818
 M2S  OXT   O  OC    -1  -0.603  -15.0409   3.1315  3.5238
 M2S  H     H  HNH2   0   0.339  -13.9992  -0.3943  3.1094
 M2S  H2    H  HNH2   0   0.330  -12.7100   0.2816  3.7900
 M2S  HA    H  HCH1   0   0.208  -15.4907   0.7940  4.2499
 M2S  HG11  H  HCH3   0   0.218  -15.3392   2.2482  7.6299
 M2S  HG12  H  HCH3   0   0.226  -14.7672   3.2480  6.3008
 M2S  HG13  H  HCH3   0   0.221  -16.2155   2.2611  6.1093
 M2S  HG21  H  HCH3   0   0.228  -14.4511  -1.0636  6.2511
 M2S  HG22  H  HCH3   0   0.220  -14.9728  -0.1957  7.6994
 M2S  HG23  H  HCH3   0   0.222  -16.0337  -0.2860  6.2995
 M2S  HG2   H  HCH2   0   0.273  -12.3833   0.3158  6.1675
 M2S  HG3   H  HCH2   0   0.290  -12.4251   2.0828  6.0318
 M2S  HE1   H  HCH3   0   0.271  -10.8126  -0.1018  8.0219
 M2S  HE2   H  HCH3   0   0.276  -10.3913   1.5833  7.5990
 M2S  HE3   H  HCH3   0   0.285  -10.5732   1.1012  9.3069

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
 M2S  N    CA    single  1.458  0.019  1.458
 M2S  CA   CB    single  1.530  0.020  1.530
 M2S  CA   C     single  1.525  0.021  1.525
 M2S  CB   CG1   single  1.531  0.020  1.531
 M2S  CB   CG2   single  1.531  0.020  1.531
 M2S  CB   CG    single  1.533  0.020  1.533
 M2S  CG   SD    single  1.819  0.020  1.819
 M2S  SD   OE    double  1.514  0.020  1.514
 M2S  SD   CE    single  1.807  0.020  1.807
 M2S  C    O     deloc   1.231  0.020  1.231
 M2S  C    OXT   deloc   1.246  0.020  1.246
 M2S  N    H     single  0.860  0.020  0.860
 M2S  N    H2    single  0.890  0.020  1.040
 M2S  CA   HA    single  0.970  0.020  0.970
 M2S  CG1  HG11  single  0.970  0.020  1.090
 M2S  CG1  HG12  single  0.970  0.020  1.090
 M2S  CG1  HG13  single  0.970  0.020  1.090
 M2S  CG2  HG21  single  0.970  0.020  1.090
 M2S  CG2  HG22  single  0.970  0.020  1.090
 M2S  CG2  HG23  single  0.970  0.020  1.090
 M2S  CG   HG2   single  0.970  0.020  1.090
 M2S  CG   HG3   single  0.970  0.020  1.090
 M2S  CE   HE1   single  0.970  0.020  1.090
 M2S  CE   HE2   single  0.970  0.020  1.090
 M2S  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
 M2S  H2    N    H     104.93  3.000
 M2S  H2    N    CA    107.44  3.000
 M2S  H     N    CA    114.00  3.000
 M2S  HA    CA   C     110.00  3.000
 M2S  HA    CA   CB    109.00  3.000
 M2S  C     CA   CB    110.10  1.900
 M2S  HA    CA   N     110.00  3.000
 M2S  C     CA   N     111.00  2.800
 M2S  CB    CA   N     110.50  1.700
 M2S  CG    CB   CG2   109.55  3.000
 M2S  CG    CB   CG1   111.58  3.000
 M2S  CG2   CB   CG1   108.49  3.000
 M2S  CG    CB   CA    108.64  3.000
 M2S  CG2   CB   CA    108.16  3.000
 M2S  CG1   CB   CA    110.37  3.000
 M2S  HG13  CG1  HG12  107.95  3.000
 M2S  HG13  CG1  HG11  107.14  3.000
 M2S  HG12  CG1  HG11  107.53  3.000
 M2S  HG13  CG1  CB    110.20  3.000
 M2S  HG12  CG1  CB    112.66  3.000
 M2S  HG11  CG1  CB    111.14  3.000
 M2S  HG23  CG2  HG22  107.29  3.000
 M2S  HG23  CG2  HG21  107.90  3.000
 M2S  HG22  CG2  HG21  108.23  3.000
 M2S  HG23  CG2  CB    110.33  3.000
 M2S  HG22  CG2  CB    111.71  3.000
 M2S  HG21  CG2  CB    111.22  3.000
 M2S  HG3   CG   HG2   108.47  3.000
 M2S  HG3   CG   SD    105.78  3.000
 M2S  HG2   CG   SD    106.57  3.000
 M2S  HG3   CG   CB    112.40  3.000
 M2S  HG2   CG   CB    109.43  3.000
 M2S  SD    CG   CB    113.89  3.000
 M2S  CE    SD   OE    106.13  3.000
 M2S  CE    SD   CG     96.59  3.000
 M2S  OE    SD   CG    107.65  3.000
 M2S  HE3   CE   HE2   109.97  3.000
 M2S  HE3   CE   HE1   109.37  3.000
 M2S  HE2   CE   HE1   110.32  3.000
 M2S  HE3   CE   SD    107.62  3.000
 M2S  HE2   CE   SD    109.84  3.000
 M2S  HE1   CE   SD    109.68  3.000
 M2S  OXT   C    O     126.49  3.000
 M2S  OXT   C    CA    117.13  3.000
 M2S  O     C    CA    120.80  1.700

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
 M2S  Var_01  SD    CG   CB  CA  178.05  30.0  3
 M2S  Var_02  OE    SD   CG  CB  -87.65  30.0  3
 M2S  Var_03  HG11  CG1  CB  CA  169.46  30.0  3
 M2S  Var_04  HG21  CG2  CB  CA   58.56  30.0  3
 M2S  Var_05  HE1   CE   SD  CG  -67.76  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
 M2S  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
 M2S  plan-1  CA   0.020
 M2S  plan-1  C    0.020
 M2S  plan-1  O    0.020
 M2S  plan-1  OXT  0.020
 M2S  plan-2  CG   0.020
 M2S  plan-2  SD   0.020
 M2S  plan-2  OE   0.020
 M2S  plan-2  CE   0.020

