# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 27 08:01:20 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  31  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  OH1   0  -0.596   1.0874   0.6043  -5.6592
 SMG  O62  O  O     0  -0.444   1.3182  -1.3635  -4.6364
 SMG  C6   C  C     0   0.556   0.9311  -0.2215  -4.6298
 SMG  C5   C  CH2   0  -0.579   0.2206   0.4488  -3.4876
 SMG  C4   C  CH2   0  -0.589   0.0700  -0.4556  -2.2782
 SMG  O31  O  O     0  -0.492  -1.5347   1.0794  -1.3477
 SMG  C3   C  C     0   0.591  -0.6808   0.2266  -1.1580
 SMG  N1   N  NH1   0  -0.655  -0.3556  -0.1824   0.0830
 SMG  O12  O  OH1   0  -0.581  -2.7783  -1.1858   0.6265
 SMG  C2   C  C     0   0.538  -2.5250  -0.0504   1.2539
 SMG  C1   C  CH1   0  -0.159  -1.0498   0.3224   1.2367
 SMG  CB   C  CH2   0  -0.477  -0.3952  -0.1804   2.5271
 SMG  CG   C  CH2   0  -0.547   1.0525   0.2759   2.6482
 SMG  SD   S  S2    0  -0.035   1.7009  -0.2213   4.2679
 SMG  CE   C  CH3   0  -0.764   3.4193   0.2988   4.0764
 SMG  H61  H  HOH1  0   0.480   1.5513   0.1519  -6.3794
 SMG  H51  H  HCH2  0   0.290  -0.7551   0.7869  -3.8445
 SMG  H52  H  HCH2  0   0.290   0.7711   1.3567  -3.2266
 SMG  H41  H  HCH2  0   0.270   1.0450  -0.7943  -1.9240
 SMG  H42  H  HCH2  0   0.288  -0.4896  -1.3567  -2.5458
 SMG  HN1  H  HNH1  0   0.408   0.2821  -0.9547   0.1941
 SMG  H12  H  HOH1  0   0.486  -3.7223  -1.3966   0.6887
 SMG  H1   H  HCH1  0   0.292  -1.0099   1.4149   1.2376
 SMG  HB1  H  HCH2  0   0.264  -0.4519  -1.2714   2.5763
 SMG  HB2  H  HCH2  0   0.274  -0.9707   0.2091   3.3691
 SMG  HG1  H  HCH2  0   0.269   1.1204   1.3614   2.5465
 SMG  HG2  H  HCH2  0   0.265   1.6774  -0.1719   1.8731
 SMG  HE1  H  HCH3  0   0.275   3.9486   0.0313   4.9892
 SMG  HE2  H  HCH3  0   0.262   3.8902  -0.2118   3.2375
 SMG  HE3  H  HCH3  0   0.263   3.4932   1.3757   3.9326
 SMG  O11  O  O     0  -0.441  -3.3563   0.6046   1.8298

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   single  1.329  0.020  1.329
 SMG  O61  H61  single  0.850  0.020  0.980
 SMG  O62  C6   double  1.206  0.020  1.206
 SMG  C6   C5   single  1.503  0.020  1.503
 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  1.511  0.020  1.511
 SMG  C4   H41  single  0.970  0.020  1.090
 SMG  C4   H42  single  0.970  0.020  1.090
 SMG  O31  C3   double  1.222  0.020  1.222
 SMG  C3   N1   single  1.347  0.020  1.347
 SMG  N1   C1   single  1.438  0.020  1.438
 SMG  N1   HN1  single  0.860  0.020  1.020
 SMG  O11  C2   double  1.205  0.020  1.205
 SMG  O12  C2   single  1.322  0.020  1.322
 SMG  O12  H12  single  0.850  0.020  0.980
 SMG  C2   C1   single  1.522  0.020  1.522
 SMG  C1   CB   single  1.532  0.020  1.532
 SMG  C1   H1   single  0.970  0.020  1.090
 SMG  CB   CG   single  1.523  0.020  1.523
 SMG  CB   HB1  single  0.970  0.020  1.090
 SMG  CB   HB2  single  0.970  0.020  1.090
 SMG  CG   SD   single  1.814  0.020  1.814
 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  H61  O61  C6   110.00  3.000
 SMG  C5   C6   O62  125.33  3.000
 SMG  C5   C6   O61  111.54  3.000
 SMG  O62  C6   O61  123.13  3.000
 SMG  H52  C5   H51  105.70  3.000
 SMG  H52  C5   C4   110.76  3.000
 SMG  H51  C5   C4   110.86  3.000
 SMG  H52  C5   C6   108.29  3.000
 SMG  H51  C5   C6   108.18  3.000
 SMG  C4   C5   C6   112.76  3.000
 SMG  H42  C4   H41  106.31  3.000
 SMG  H42  C4   C3   107.40  3.000
 SMG  H41  C4   C3   110.09  3.000
 SMG  H42  C4   C5   110.28  3.000
 SMG  H41  C4   C5   110.79  3.000
 SMG  C3   C4   C5   111.78  3.000
 SMG  N1   C3   O31  121.60  3.000
 SMG  N1   C3   C4   115.22  3.000
 SMG  O31  C3   C4   123.18  3.000
 SMG  HN1  N1   C1   119.08  3.000
 SMG  HN1  N1   C3   119.16  3.000
 SMG  C1   N1   C3   121.08  3.000
 SMG  H12  O12  C2   110.06  3.000
 SMG  C1   C2   O12  113.01  3.000
 SMG  C1   C2   O11  122.76  3.000
 SMG  O12  C2   O11  124.17  3.000
 SMG  H1   C1   CB   108.17  3.000
 SMG  H1   C1   C2   106.27  3.000
 SMG  CB   C1   C2   108.93  3.000
 SMG  H1   C1   N1   109.50  3.000
 SMG  CB   C1   N1   110.76  3.000
 SMG  C2   C1   N1   113.02  3.000
 SMG  HB2  CB   HB1  107.09  3.000
 SMG  HB2  CB   CG   109.45  3.000
 SMG  HB1  CB   CG   110.16  3.000
 SMG  HB2  CB   C1   107.90  3.000
 SMG  HB1  CB   C1   110.07  3.000
 SMG  CG   CB   C1   112.01  3.000
 SMG  HG2  CG   HG1  107.81  3.000
 SMG  HG2  CG   SD   108.48  3.000
 SMG  HG1  CG   SD   109.47  3.000
 SMG  HG2  CG   CB   111.40  3.000
 SMG  HG1  CG   CB   110.46  3.000
 SMG  SD   CG   CB   109.19  3.000
 SMG  CE   SD   CG    99.59  3.000
 SMG  HE3  CE   HE2  109.42  3.000
 SMG  HE3  CE   HE1  108.71  3.000
 SMG  HE2  CE   HE1  108.69  3.000
 SMG  HE3  CE   SD   111.32  3.000
 SMG  HE2  CE   SD   110.98  3.000
 SMG  HE1  CE   SD   107.64  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  CONST_04  H61  O61  C6  O62     0.00   0.0  0
 SMG  CONST_05  H12  O12  C2  O11     0.00   0.0  0
 SMG  Var_01    C4   C5   C6  O61  -178.01  30.0  3
 SMG  Var_02    C3   C4   C5  C6   -178.40  30.0  3
 SMG  Var_03    O31  C3   C4  C5     29.95  30.0  3
 SMG  Var_04    SD   CG   CB  C1    174.55  30.0  3
 SMG  Var_05    HE1  CE   SD  CG   -178.53  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-2  H61  0.020
 SMG  plan-3  O12  0.020
 SMG  plan-3  C2   0.020
 SMG  plan-3  C1   0.020
 SMG  plan-3  H12  0.020
 SMG  plan-3  O11  0.020

