# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:41:58 2020
#   Inital geometry file: a 76 line input string
#   Ligand name: (2S)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl]butanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H](CC[S@@](C)=O)NC(C)=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
 RSM  RSM  (2S)-2-(acetylamino)-N-methyl-4-[(R)-methylsulfinyl]butanamide  ligand  30  14  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RSM
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
 RSM  C2   C  CH3   0  -0.773   0.9564   3.4781   0.1435
 RSM  C    C  C     0   0.534   1.0740   1.9866  -0.0317
 RSM  O    O  O     0  -0.500   1.3477   1.4754  -1.1090
 RSM  N    N  NH1   0  -0.626   0.8555   1.2498   1.0710
 RSM  CA   C  CH1   0  -0.188   0.9333  -0.1898   1.0630
 RSM  CB   C  CH2   0  -0.477  -0.2474  -0.8479   0.3394
 RSM  CG   C  CH2   0  -0.602  -1.5774  -0.3233   0.8541
 RSM  SD   S  S3    0   0.727  -2.9389  -1.2063   0.0390
 RSM  OD1  O  O     0  -0.790  -2.8374  -0.8847  -1.4354
 RSM  CE   C  CH3   0  -0.804  -4.2803  -0.2011   0.7008
 RSM  C3   C  C     0   0.568   2.3298  -0.6209   0.5876
 RSM  O3   O  O     0  -0.501   3.3176   0.0110   0.9291
 RSM  N2   N  NH1   0  -0.640   2.4089  -1.7408  -0.1376
 RSM  C1   C  CH3   0  -0.512   3.6740  -2.2718  -0.5895
 RSM  H2   H  HCH3  0   0.267   0.2075   3.8637  -0.5476
 RSM  H2A  H  HCH3  0   0.250   0.6806   3.7776   1.1524
 RSM  H2B  H  HCH3  0   0.268   1.9060   3.9489  -0.1111
 RSM  HN   H  HNH1  0   0.407   0.6543   1.7109   1.9418
 RSM  HA   H  HCH1  0   0.304   0.8859  -0.4960   2.1127
 RSM  HB   H  HCH2  0   0.265  -0.1792  -0.6827  -0.7362
 RSM  HBA  H  HCH2  0   0.258  -0.2066  -1.9262   0.5163
 RSM  HG   H  HCH2  0   0.283  -1.6895  -0.4930   1.9275
 RSM  HGA  H  HCH2  0   0.288  -1.7034   0.7415   0.6494
 RSM  HE   H  HCH3  0   0.282  -4.1214   0.8434   0.4357
 RSM  HEA  H  HCH3  0   0.293  -5.2104  -0.5598   0.2644
 RSM  HEB  H  HCH3  0   0.278  -4.3218  -0.3163   1.7825
 RSM  HN2  H  HNH1  0   0.414   1.5742  -2.2195  -0.4260
 RSM  H1   H  HCH3  0   0.239   4.3289  -2.5136   0.2478
 RSM  H1A  H  HCH3  0   0.250   3.4824  -3.1830  -1.1485
 RSM  H1B  H  HCH3  0   0.238   4.1959  -1.5704  -1.2414

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
 RSM  C2  C    single  1.506  0.020  1.506
 RSM  C   O    double  1.223  0.020  1.223
 RSM  C   N    single  1.344  0.020  1.344
 RSM  N   CA   single  1.442  0.020  1.442
 RSM  CA  CB   single  1.533  0.020  1.533
 RSM  CA  C3   single  1.537  0.020  1.537
 RSM  CB  CG   single  1.520  0.020  1.520
 RSM  CG  SD   single  1.816  0.020  1.816
 RSM  SD  OD1  double  1.512  0.020  1.512
 RSM  SD  CE   single  1.802  0.020  1.802
 RSM  C3  O3   double  1.221  0.020  1.221
 RSM  C3  N2   single  1.337  0.020  1.337
 RSM  N2  C1   single  1.445  0.020  1.445
 RSM  C2  H2   single  0.970  0.020  1.090
 RSM  C2  H2A  single  0.970  0.020  1.090
 RSM  C2  H2B  single  0.970  0.020  1.090
 RSM  N   HN   single  0.860  0.020  1.020
 RSM  CA  HA   single  0.970  0.020  1.090
 RSM  CB  HB   single  0.970  0.020  1.090
 RSM  CB  HBA  single  0.970  0.020  1.090
 RSM  CG  HG   single  0.970  0.020  1.090
 RSM  CG  HGA  single  0.970  0.020  1.090
 RSM  CE  HE   single  0.970  0.020  1.090
 RSM  CE  HEA  single  0.970  0.020  1.090
 RSM  CE  HEB  single  0.970  0.020  1.090
 RSM  N2  HN2  single  0.860  0.020  1.020
 RSM  C1  H1   single  0.970  0.020  1.090
 RSM  C1  H1A  single  0.970  0.020  1.090
 RSM  C1  H1B  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
 RSM  H2B  C2  H2A  108.57  3.000
 RSM  H2B  C2  H2   107.32  3.000
 RSM  H2A  C2  H2   108.46  3.000
 RSM  H2B  C2  C    109.42  3.000
 RSM  H2A  C2  C    113.59  3.000
 RSM  H2   C2  C    109.28  3.000
 RSM  N    C   O    121.99  3.000
 RSM  N    C   C2   115.76  3.000
 RSM  O    C   C2   122.24  3.000
 RSM  HN   N   CA   118.25  3.000
 RSM  HN   N   C    119.45  3.000
 RSM  CA   N   C    122.28  3.000
 RSM  HA   CA  C3   104.92  3.000
 RSM  HA   CA  CB   107.41  3.000
 RSM  C3   CA  CB   115.68  3.000
 RSM  HA   CA  N    105.77  3.000
 RSM  C3   CA  N    109.32  3.000
 RSM  CB   CA  N    112.94  3.000
 RSM  HBA  CB  HB   107.86  3.000
 RSM  HBA  CB  CG   108.56  3.000
 RSM  HB   CB  CG   109.67  3.000
 RSM  HBA  CB  CA   108.56  3.000
 RSM  HB   CB  CA   110.63  3.000
 RSM  CG   CB  CA   111.47  3.000
 RSM  HGA  CG  HG   108.90  3.000
 RSM  HGA  CG  SD   107.67  3.000
 RSM  HG   CG  SD   106.77  3.000
 RSM  HGA  CG  CB   111.98  3.000
 RSM  HG   CG  CB   111.65  3.000
 RSM  SD   CG  CB   109.65  3.000
 RSM  CE   SD  OD1  106.82  3.000
 RSM  CE   SD  CG    97.01  3.000
 RSM  OD1  SD  CG   106.49  3.000
 RSM  HEB  CE  HEA  109.33  3.000
 RSM  HEB  CE  HE   110.42  3.000
 RSM  HEA  CE  HE   110.08  3.000
 RSM  HEB  CE  SD   109.52  3.000
 RSM  HEA  CE  SD   107.76  3.000
 RSM  HE   CE  SD   109.69  3.000
 RSM  N2   C3  O3   122.51  3.000
 RSM  N2   C3  CA   117.17  3.000
 RSM  O3   C3  CA   120.22  3.000
 RSM  HN2  N2  C1   117.57  3.000
 RSM  HN2  N2  C3   120.39  3.000
 RSM  C1   N2  C3   121.97  3.000
 RSM  H1B  C1  H1A  108.44  3.000
 RSM  H1B  C1  H1   108.32  3.000
 RSM  H1A  C1  H1   108.37  3.000
 RSM  H1B  C1  N2   111.70  3.000
 RSM  H1A  C1  N2   108.35  3.000
 RSM  H1   C1  N2   111.56  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
 RSM  CONST_01  CA   N   C   C2   180.00   0.0  0
 RSM  CONST_02  CA   N   C   O      0.00   0.0  0
 RSM  CONST_03  C1   N2  C3  CA   180.00   0.0  0
 RSM  CONST_04  C1   N2  C3  O3     0.00   0.0  0
 RSM  CONST_05  HN   N   C   C2     0.00   0.0  0
 RSM  CONST_06  HN2  N2  C3  CA     0.00   0.0  0
 RSM  Var_01    SD   CG  CB  CA  -176.54  30.0  3
 RSM  Var_02    OD1  SD  CG  CB   -62.93  30.0  3
 RSM  Var_03    H2   C2  C   O     57.14  30.0  3
 RSM  Var_04    HE   CE  SD  CG    57.10  30.0  3
 RSM  Var_05    H1   C1  N2  C3    60.39  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
 RSM  chir_01  CA  N  CB  C3  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
 RSM  plan-1  C2   0.020
 RSM  plan-1  C    0.020
 RSM  plan-1  O    0.020
 RSM  plan-1  N    0.020
 RSM  plan-1  CA   0.020
 RSM  plan-1  HN   0.020
 RSM  plan-2  CA   0.020
 RSM  plan-2  C3   0.020
 RSM  plan-2  O3   0.020
 RSM  plan-2  N2   0.020
 RSM  plan-2  C1   0.020
 RSM  plan-2  HN2  0.020
 RSM  plan-3  CG   0.020
 RSM  plan-3  SD   0.020
 RSM  plan-3  OD1  0.020
 RSM  plan-3  CE   0.020

