# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:32:31 2022
#   Inital geometry file: a 66 line input string
#   Ligand name: S-[2-(dimethylamino)ethyl]-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(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
 M2L  M2L  S-[2-(dimethylamino)ethyl]-L-cysteine  L-peptide  27  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_M2L
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
 M2L  N     N  NH2    0  -0.793  18.4409  -1.8064  50.8629
 M2L  CA    C  CH1    0  -0.192  17.2693  -1.7380  51.7130
 M2L  CB    C  CH2    0  -0.578  17.3906  -0.7371  52.8728
 M2L  SG    S  S2     0  -0.048  18.8182  -1.0135  53.9592
 M2L  CD    C  CH2    0  -0.564  18.3104  -2.5588  54.7797
 M2L  CE    C  CH2    0  -0.263  19.0692  -2.8230  56.0781
 M2L  NZ    N  NT     0  -0.399  20.2952  -3.5812  55.9201
 M2L  CM1   C  CH3    0  -0.524  21.3167  -2.8739  55.1774
 M2L  CM2   C  CH3    0  -0.518  20.7986  -3.9942  57.2126
 M2L  C     C  C      0   0.406  16.0050  -1.3430  50.9039
 M2L  O     O  O      0  -0.596  16.1877  -0.6700  49.8711
 M2L  OXT   O  OC    -1  -0.607  14.9143  -1.6966  51.3917
 M2L  HN    H  HNH2   0   0.324  18.4576  -0.9749  50.2850
 M2L  HNA   H  HNH2   0   0.326  19.2765  -1.7829  51.4375
 M2L  HA    H  HCH1   0   0.214  17.0901  -2.7280  52.1462
 M2L  HB    H  HCH2   0   0.266  17.5218   0.2744  52.4783
 M2L  HBA   H  HCH2   0   0.258  16.4850  -0.7389  53.4831
 M2L  HD    H  HCH2   0   0.273  17.2478  -2.4583  55.0079
 M2L  HDA   H  HCH2   0   0.264  18.4246  -3.4091  54.1058
 M2L  HE    H  HCH2   0   0.198  19.2355  -1.8692  56.6086
 M2L  HEA   H  HCH2   0   0.244  18.4083  -3.4132  56.7176
 M2L  HM1   H  HCH3   0   0.235  20.9905  -2.6730  54.1574
 M2L  HM1A  H  HCH3   0   0.189  21.5990  -1.9129  55.6371
 M2L  HM1B  H  HCH3   0   0.234  22.2150  -3.4893  55.1170
 M2L  HM2   H  HCH3   0   0.231  21.6863  -4.6155  57.0860
 M2L  HM2A  H  HCH3   0   0.190  21.0730  -3.1497  57.8647
 M2L  HM2B  H  HCH3   0   0.231  20.0494  -4.5887  57.7379

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
 M2L  N    CA    single  1.458  0.019  1.458
 M2L  N    HN    single  0.890  0.020  1.040
 M2L  N    HNA   single  0.890  0.020  1.040
 M2L  C    CA    single  1.525  0.021  1.525
 M2L  CA   CB    single  1.530  0.020  1.530
 M2L  CA   HA    single  0.970  0.020  0.970
 M2L  CB   SG    single  1.815  0.020  1.815
 M2L  CB   HB    single  0.970  0.020  1.090
 M2L  CB   HBA   single  0.970  0.020  1.090
 M2L  SG   CD    single  1.822  0.020  1.822
 M2L  CD   CE    single  1.527  0.020  1.527
 M2L  CD   HD    single  0.970  0.020  1.090
 M2L  CD   HDA   single  0.970  0.020  1.090
 M2L  NZ   CE    single  1.450  0.020  1.450
 M2L  CE   HE    single  0.970  0.020  1.090
 M2L  CE   HEA   single  0.970  0.020  1.090
 M2L  CM1  NZ    single  1.448  0.020  1.448
 M2L  NZ   CM2   single  1.447  0.020  1.447
 M2L  CM1  HM1   single  0.970  0.020  1.090
 M2L  CM1  HM1A  single  0.970  0.020  1.090
 M2L  CM1  HM1B  single  0.970  0.020  1.090
 M2L  CM2  HM2   single  0.970  0.020  1.090
 M2L  CM2  HM2A  single  0.970  0.020  1.090
 M2L  CM2  HM2B  single  0.970  0.020  1.090
 M2L  O    C     deloc   1.231  0.020  1.231
 M2L  C    OXT   deloc   1.246  0.020  1.246

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
 M2L  HNA   N    HN    106.90  3.000
 M2L  HNA   N    CA    109.43  3.000
 M2L  HN    N    CA    108.02  3.000
 M2L  HA    CA   C     109.00  3.000
 M2L  HA    CA   CB    109.00  3.000
 M2L  C     CA   CB    110.10  1.900
 M2L  HA    CA   N     110.00  3.000
 M2L  CB    CA   N     110.50  1.700
 M2L  C     CA   N     111.00  2.800
 M2L  HBA   CB   HB    107.62  3.000
 M2L  HBA   CB   SG    108.51  3.000
 M2L  HB    CB   SG    105.21  3.000
 M2L  HBA   CB   CA    110.81  3.000
 M2L  HB    CB   CA    109.85  3.000
 M2L  SG    CB   CA    114.50  3.000
 M2L  CD    SG   CB    100.34  3.000
 M2L  HDA   CD   HD    107.63  3.000
 M2L  HDA   CD   CE    109.78  3.000
 M2L  HD    CD   CE    108.78  3.000
 M2L  HDA   CD   SG    110.72  3.000
 M2L  HD    CD   SG    106.71  3.000
 M2L  CE    CD   SG    113.03  3.000
 M2L  HEA   CE   HE    106.06  3.000
 M2L  HEA   CE   NZ    107.02  3.000
 M2L  HE    CE   NZ    112.13  3.000
 M2L  HEA   CE   CD    106.89  3.000
 M2L  HE    CE   CD    109.51  3.000
 M2L  NZ    CE   CD    114.70  3.000
 M2L  CM2   NZ   CM1   110.62  3.000
 M2L  CM2   NZ   CE    110.24  3.000
 M2L  CM1   NZ   CE    113.39  3.000
 M2L  HM1B  CM1  HM1A  107.70  3.000
 M2L  HM1B  CM1  HM1   107.38  3.000
 M2L  HM1A  CM1  HM1   107.84  3.000
 M2L  HM1B  CM1  NZ    109.51  3.000
 M2L  HM1A  CM1  NZ    113.13  3.000
 M2L  HM1   CM1  NZ    111.05  3.000
 M2L  HM2B  CM2  HM2A  107.68  3.000
 M2L  HM2B  CM2  HM2   107.72  3.000
 M2L  HM2A  CM2  HM2   107.61  3.000
 M2L  HM2B  CM2  NZ    110.27  3.000
 M2L  HM2A  CM2  NZ    113.36  3.000
 M2L  HM2   CM2  NZ    109.99  3.000
 M2L  OXT   C    O     127.30  3.000
 M2L  OXT   C    CA    115.90  3.000
 M2L  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
 M2L  Var_01  CE   CD   SG  CB  -160.98  30.0  3
 M2L  Var_02  NZ   CE   CD  SG   -89.67  30.0  3
 M2L  Var_03  CM1  NZ   CE  CD    66.23  30.0  1
 M2L  Var_04  HB   CB   SG  CD   169.48  30.0  1
 M2L  Var_05  HM1  CM1  NZ  CE   -62.91  30.0  3
 M2L  Var_06  HM2  CM2  NZ  CE   176.54  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
 M2L  chir_01  CA  N  C  CB  positiv

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
 M2L  plan-1  CA   0.020
 M2L  plan-1  C    0.020
 M2L  plan-1  O    0.020
 M2L  plan-1  OXT  0.020

