# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 21:07:05 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: N-(3-carboxypropanoyl)-D-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@@H](NC(=O)CCC(O)=O)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
 SMG  SMG  N-(3-carboxypropanoyl)-D-methionine  ligand  29  16  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_SMG
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
 SMG  O61  O  OC    -1  -0.631   1.4564   0.5896  -5.5422
 SMG  O62  O  O      0  -0.609   1.0998  -1.4096  -4.6288
 SMG  C6   C  C      0   0.415   1.0349  -0.1645  -4.6403
 SMG  C5   C  CH2    0  -0.579   0.3559   0.5339  -3.4493
 SMG  C4   C  CH2    0  -0.581   0.0485  -0.3651  -2.2651
 SMG  O31  O  O      0  -0.516  -1.3531   1.3394  -1.3038
 SMG  C3   C  C      0   0.570  -0.6381   0.3603  -1.1270
 SMG  N1   N  NH1    0  -0.633  -0.3915  -0.1394   0.0967
 SMG  C2   C  C      0   0.412  -2.6000  -0.2146   1.2691
 SMG  C1   C  CH1    0  -0.182  -1.1296   0.2836   1.2618
 SMG  CB   C  CH2    0  -0.461  -0.4135  -0.1759   2.5321
 SMG  CG   C  CH2    0  -0.537   1.0180   0.3332   2.6206
 SMG  SD   S  S2     0  -0.049   1.7299  -0.1249   4.2270
 SMG  CE   C  CH3    0  -0.763   3.4282   0.4390   3.9849
 SMG  H51  H  HCH2   0   0.231  -0.5684   0.9933  -3.8123
 SMG  H52  H  HCH2   0   0.223   0.9842   1.3716  -3.1319
 SMG  H41  H  HCH2   0   0.238   0.9605  -0.8440  -1.9009
 SMG  H42  H  HCH2   0   0.256  -0.6071  -1.1838  -2.5780
 SMG  HN1  H  HNH1   0   0.385   0.0883  -1.0248   0.1443
 SMG  H1   H  HCH1   0   0.235  -1.1485   1.3773   1.2683
 SMG  HB1  H  HCH2   0   0.235  -0.4199  -1.2696   2.5911
 SMG  HB2  H  HCH2   0   0.249  -0.9878   0.1882   3.3853
 SMG  HG1  H  HCH2   0   0.256   1.0455   1.4201   2.5101
 SMG  HG2  H  HCH2   0   0.257   1.6382  -0.0968   1.8319
 SMG  HE1  H  HCH3   0   0.272   3.9909   0.1976   4.8849
 SMG  HE2  H  HCH3   0   0.260   3.8905  -0.0678   3.1387
 SMG  HE3  H  HCH3   0   0.260   3.4695   1.5158   3.8261
 SMG  O11  O  O      0  -0.618  -3.3160   0.2848   2.1603
 SMG  O12  O  OC    -1  -0.594  -2.9287  -1.0615   0.4229

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
 SMG  O61  C6   deloc   1.249  0.020  1.249
 SMG  O62  C6   deloc   1.247  0.020  1.247
 SMG  C6   C5   single  1.539  0.020  1.539
 SMG  C5   C4   single  1.518  0.020  1.518
 SMG  C5   H51  single  0.970  0.020  1.090
 SMG  C5   H52  single  0.970  0.020  1.090
 SMG  C4   C3   single  1.514  0.020  1.514
 SMG  C4   H41  single  0.970  0.020  1.090
 SMG  C4   H42  single  0.970  0.020  1.090
 SMG  O31  C3   double  1.225  0.020  1.225
 SMG  C3   N1   single  1.345  0.020  1.345
 SMG  N1   C1   single  1.443  0.020  1.443
 SMG  N1   HN1  single  0.890  0.020  1.040
 SMG  O11  C2   deloc   1.247  0.020  1.247
 SMG  O12  C2   deloc   1.242  0.020  1.242
 SMG  C2   C1   single  1.552  0.020  1.552
 SMG  C1   CB   single  1.529  0.020  1.529
 SMG  C1   H1   single  0.970  0.020  1.090
 SMG  CB   CG   single  1.522  0.020  1.522
 SMG  CB   HB1  single  0.970  0.020  1.090
 SMG  CB   HB2  single  0.970  0.020  1.090
 SMG  CG   SD   single  1.816  0.020  1.816
 SMG  CG   HG1  single  0.970  0.020  1.090
 SMG  CG   HG2  single  0.970  0.020  1.090
 SMG  SD   CE   single  1.806  0.020  1.806
 SMG  CE   HE1  single  0.970  0.020  1.090
 SMG  CE   HE2  single  0.970  0.020  1.090
 SMG  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
 SMG  C5   C6  O62  117.98  3.000
 SMG  C5   C6  O61  115.71  3.000
 SMG  O62  C6  O61  126.30  3.000
 SMG  H52  C5  H51  105.07  3.000
 SMG  H52  C5  C4   110.08  3.000
 SMG  H51  C5  C4   109.66  3.000
 SMG  H52  C5  C6   108.58  3.000
 SMG  H51  C5  C6   107.85  3.000
 SMG  C4   C5  C6   115.11  3.000
 SMG  H42  C4  H41  105.51  3.000
 SMG  H42  C4  C3   107.55  3.000
 SMG  H41  C4  C3   109.75  3.000
 SMG  H42  C4  C5   109.95  3.000
 SMG  H41  C4  C5   110.52  3.000
 SMG  C3   C4  C5   113.23  3.000
 SMG  N1   C3  O31  122.37  3.000
 SMG  N1   C3  C4   115.01  3.000
 SMG  O31  C3  C4   122.61  3.000
 SMG  HN1  N1  C1   117.58  3.000
 SMG  HN1  N1  C3   117.17  3.000
 SMG  C1   N1  C3   122.15  3.000
 SMG  C1   C2  O12  117.81  3.000
 SMG  C1   C2  O11  114.74  3.000
 SMG  O12  C2  O11  127.44  3.000
 SMG  H1   C1  CB   107.68  3.000
 SMG  H1   C1  C2   107.73  3.000
 SMG  CB   C1  C2   110.07  3.000
 SMG  H1   C1  N1   107.86  3.000
 SMG  CB   C1  N1   110.08  3.000
 SMG  C2   C1  N1   113.22  3.000
 SMG  HB2  CB  HB1  106.74  3.000
 SMG  HB2  CB  CG   109.76  3.000
 SMG  HB1  CB  CG   109.65  3.000
 SMG  HB2  CB  C1   107.63  3.000
 SMG  HB1  CB  C1   110.00  3.000
 SMG  CG   CB  C1   112.85  3.000
 SMG  HG2  CG  HG1  107.72  3.000
 SMG  HG2  CG  SD   108.49  3.000
 SMG  HG1  CG  SD   109.30  3.000
 SMG  HG2  CG  CB   111.15  3.000
 SMG  HG1  CG  CB   110.52  3.000
 SMG  SD   CG  CB   109.62  3.000
 SMG  CE   SD  CG    99.86  3.000
 SMG  HE3  CE  HE2  109.30  3.000
 SMG  HE3  CE  HE1  108.68  3.000
 SMG  HE2  CE  HE1  108.64  3.000
 SMG  HE3  CE  SD   111.34  3.000
 SMG  HE2  CE  SD   110.98  3.000
 SMG  HE1  CE  SD   107.82  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
 SMG  CONST_01  C1   N1  C3  C4    180.00   0.0  0
 SMG  CONST_02  C1   N1  C3  O31     0.00   0.0  0
 SMG  CONST_03  HN1  N1  C3  C4      0.00   0.0  0
 SMG  Var_01    C4   C5  C6  O61  -170.67  30.0  3
 SMG  Var_02    C3   C4  C5  C6   -179.10  30.0  3
 SMG  Var_03    O31  C3  C4  C5     28.51  30.0  3
 SMG  Var_04    SD   CG  CB  C1    174.54  30.0  3
 SMG  Var_05    HE1  CE  SD  CG   -178.52  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
 SMG  chir_01  C1  N1  C2  CB  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
 SMG  plan-1  C4   0.020
 SMG  plan-1  O31  0.020
 SMG  plan-1  C3   0.020
 SMG  plan-1  N1   0.020
 SMG  plan-1  C1   0.020
 SMG  plan-1  HN1  0.020
 SMG  plan-2  O61  0.020
 SMG  plan-2  O62  0.020
 SMG  plan-2  C6   0.020
 SMG  plan-2  C5   0.020
 SMG  plan-3  C2   0.020
 SMG  plan-3  C1   0.020
 SMG  plan-3  O11  0.020
 SMG  plan-3  O12  0.020

