# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:31:39 2022
#   Inital geometry file: a 74 line input string
#   Ligand name: 2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCSC[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
 ML3  ML3  2-{[(2R)-2-amino-2-carboxyethyl]sulfanyl}-N,N,N-trimethylethanaminium  L-peptide  31  13  .  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_ML3
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
 ML3  N     N  NH2    0  -0.791  63.0052  47.6690  45.2421
 ML3  CA    C  CH1    0  -0.178  63.0458  46.5180  44.3463
 ML3  CB    C  CH2    0  -0.588  62.7332  45.2175  45.0891
 ML3  SG    S  S2     0  -0.018  62.8007  43.7171  44.0669
 ML3  CD    C  CH2    0  -0.628  64.5931  43.4972  43.8828
 ML3  CE    C  CH2    0  -0.292  65.3231  42.9916  45.1170
 ML3  NZ    N  NT     1  -0.380  65.4060  41.4950  45.2822
 ML3  CM1   C  CH3    0  -0.546  66.0072  41.2295  46.6220
 ML3  CM2   C  CH3    0  -0.540  64.0680  40.8427  45.2181
 ML3  CM3   C  CH3    0  -0.549  66.2926  40.9036  44.2405
 ML3  C     C  C      0   0.410  62.0321  46.7457  43.1999
 ML3  O     O  O      0  -0.599  62.4712  46.7654  42.0361
 ML3  OXT   O  OC    -1  -0.609  60.8463  46.8960  43.5625
 ML3  HN    H  HNH2   0   0.330  62.0579  47.7729  45.5867
 ML3  HNA   H  HNH2   0   0.336  63.5869  47.4977  46.0541
 ML3  HA    H  HCH1   0   0.209  64.0540  46.4572  43.9272
 ML3  HB    H  HCH2   0   0.265  63.3935  45.0955  45.9523
 ML3  HD    H  HCH2   0   0.308  64.7415  42.8527  43.0153
 ML3  HE    H  HCH2   0   0.307  66.3568  43.3366  45.0992
 ML3  HEA   H  HCH2   0   0.309  64.8625  43.3790  46.0254
 ML3  HM1   H  HCH3   0   0.295  66.9741  41.7226  46.6826
 ML3  HM1A  H  HCH3   0   0.296  65.3440  41.6172  47.3910
 ML3  HM1B  H  HCH3   0   0.296  66.1316  40.1574  46.7489
 ML3  HM2   H  HCH3   0   0.292  63.6591  40.9395  44.2174
 ML3  HM2A  H  HCH3   0   0.296  64.1913  39.7890  45.4560
 ML3  HM2B  H  HCH3   0   0.294  63.4033  41.3119  45.9375
 ML3  HM3   H  HCH3   0   0.295  65.8736  41.0748  43.2535
 ML3  HM3A  H  HCH3   0   0.295  67.2763  41.3602  44.3101
 ML3  HM3B  H  HCH3   0   0.298  66.3699  39.8335  44.4138
 ML3  H17   H  HCH2   0   0.269  61.7116  45.2547  45.4728
 ML3  H18   H  HCH2   0   0.316  65.0397  44.4541  43.6132

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
 ML3  N    CA    single  1.458  0.019  1.458
 ML3  N    HN    single  0.890  0.020  1.040
 ML3  N    HNA   single  0.890  0.020  1.040
 ML3  CA   CB    single  1.530  0.020  1.530
 ML3  CA   C     single  1.525  0.021  1.525
 ML3  CA   HA    single  0.970  0.020  0.970
 ML3  CB   SG    single  1.817  0.020  1.817
 ML3  CB   HB    single  0.970  0.020  1.090
 ML3  SG   CD    single  1.815  0.020  1.815
 ML3  CD   CE    single  1.520  0.020  1.520
 ML3  CD   HD    single  0.970  0.020  1.090
 ML3  CE   NZ    single  1.508  0.020  1.508
 ML3  CE   HE    single  0.970  0.020  1.090
 ML3  CE   HEA   single  0.970  0.020  1.090
 ML3  NZ   CM1   single  1.492  0.020  1.492
 ML3  NZ   CM2   single  1.490  0.020  1.490
 ML3  NZ   CM3   single  1.490  0.020  1.490
 ML3  CM1  HM1   single  0.970  0.020  1.090
 ML3  CM1  HM1A  single  0.970  0.020  1.090
 ML3  CM1  HM1B  single  0.970  0.020  1.090
 ML3  CM2  HM2   single  0.970  0.020  1.090
 ML3  CM2  HM2A  single  0.970  0.020  1.090
 ML3  CM2  HM2B  single  0.970  0.020  1.090
 ML3  CM3  HM3   single  0.970  0.020  1.090
 ML3  CM3  HM3A  single  0.970  0.020  1.090
 ML3  CM3  HM3B  single  0.970  0.020  1.090
 ML3  C    O     deloc   1.231  0.020  1.231
 ML3  C    OXT   deloc   1.249  0.020  1.249
 ML3  CB   H17   single  0.970  0.020  1.090
 ML3  CD   H18   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
 ML3  HNA   N    HN    106.35  3.000
 ML3  HNA   N    CA    110.04  3.000
 ML3  HN    N    CA    108.40  3.000
 ML3  HA    CA   C     109.00  3.000
 ML3  HA    CA   CB    109.00  3.000
 ML3  C     CA   CB    110.10  1.900
 ML3  HA    CA   N     110.00  3.000
 ML3  C     CA   N     111.00  2.800
 ML3  CB    CA   N     110.50  1.700
 ML3  H17   CB   HB    106.94  3.000
 ML3  H17   CB   SG    105.11  3.000
 ML3  HB    CB   SG    109.24  3.000
 ML3  H17   CB   CA    109.44  3.000
 ML3  HB    CB   CA    110.77  3.000
 ML3  SG    CB   CA    114.92  3.000
 ML3  CD    SG   CB    101.17  3.000
 ML3  H18   CD   HD    105.44  3.000
 ML3  H18   CD   CE    107.22  3.000
 ML3  HD    CD   CE    112.57  3.000
 ML3  H18   CD   SG    108.86  3.000
 ML3  HD    CD   SG    106.65  3.000
 ML3  CE    CD   SG    115.60  3.000
 ML3  HEA   CE   HE    107.57  3.000
 ML3  HEA   CE   NZ    106.55  3.000
 ML3  HE    CE   NZ    105.29  3.000
 ML3  HEA   CE   CD    110.83  3.000
 ML3  HE    CE   CD    109.69  3.000
 ML3  NZ    CE   CD    116.45  3.000
 ML3  CM3   NZ   CM2   109.30  3.000
 ML3  CM3   NZ   CM1   108.50  3.000
 ML3  CM2   NZ   CM1   108.81  3.000
 ML3  CM3   NZ   CE    110.49  3.000
 ML3  CM2   NZ   CE    112.36  3.000
 ML3  CM1   NZ   CE    107.28  3.000
 ML3  HM1B  CM1  HM1A  109.83  3.000
 ML3  HM1B  CM1  HM1   109.83  3.000
 ML3  HM1A  CM1  HM1   109.97  3.000
 ML3  HM1B  CM1  NZ    109.05  3.000
 ML3  HM1A  CM1  NZ    109.02  3.000
 ML3  HM1   CM1  NZ    109.12  3.000
 ML3  HM2B  CM2  HM2A  110.07  3.000
 ML3  HM2B  CM2  HM2   109.97  3.000
 ML3  HM2A  CM2  HM2   109.32  3.000
 ML3  HM2B  CM2  NZ    109.40  3.000
 ML3  HM2A  CM2  NZ    108.24  3.000
 ML3  HM2   CM2  NZ    109.81  3.000
 ML3  HM3B  CM3  HM3A  109.82  3.000
 ML3  HM3B  CM3  HM3   109.12  3.000
 ML3  HM3A  CM3  HM3   109.95  3.000
 ML3  HM3B  CM3  NZ    108.76  3.000
 ML3  HM3A  CM3  NZ    109.09  3.000
 ML3  HM3   CM3  NZ    110.08  3.000
 ML3  OXT   C    O     127.22  3.000
 ML3  OXT   C    CA    115.13  3.000
 ML3  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
 ML3  Var_01  CE   CD   SG  CB    73.72  30.0  3
 ML3  Var_02  NZ   CE   CD  SG    87.94  30.0  3
 ML3  Var_03  CM1  NZ   CE  CD  -173.28  30.0  3
 ML3  Var_04  HB   CB   SG  CD   -50.15  30.0  1
 ML3  Var_05  HM1  CM1  NZ  CE   -56.92  30.0  3
 ML3  Var_06  HM2  CM2  NZ  CE    67.06  30.0  3
 ML3  Var_07  HM3  CM3  NZ  CE   -63.15  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
 ML3  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
 ML3  plan-1  CA   0.020
 ML3  plan-1  C    0.020
 ML3  plan-1  O    0.020
 ML3  plan-1  OXT  0.020

