# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 19:26:42 2022
#   Inital geometry file: a 53 line input string
#   Ligand name: (3R)-3-(methylsulfanyl)-L-aspartic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H]([C@H](N)C(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
 D2T  D2T  '(3R)-3-(methylsulfanyl)-L-aspartic acid'  L-peptide  18  11  .  2019-03-22  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D2T
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
 D2T  N    N  NH2    0  -0.793   -97.7239  16.9666  -38.8680
 D2T  CA   C  CH1    0  -0.210   -98.4938  16.4322  -37.7579
 D2T  C    C  C      0   0.409   -98.2539  14.9319  -37.4186
 D2T  O    O  O      0  -0.620   -98.9942  14.4422  -36.5388
 D2T  CB   C  CH1    0  -0.487   -99.9795  16.7450  -37.9021
 D2T  SB   S  S2     0  -0.051  -100.3779  18.5320  -37.9158
 D2T  CG   C  C      0   0.442  -100.6528  16.1552  -39.1680
 D2T  OD1  O  O      0  -0.584  -100.1042  15.1674  -39.6907
 D2T  OD2  O  OC    -1  -0.596  -101.7030  16.7125  -39.5402
 D2T  O1   O  OC    -1  -0.611   -97.2954  14.3656  -37.9796
 D2T  H1   H  HNH2   0   0.324   -96.7654  16.6626  -38.7488
 D2T  H2   H  HNH2   0   0.321   -98.0321  16.4950  -39.7106
 D2T  H4   H  HCH1   0   0.221   -98.1477  16.9541  -36.8549
 D2T  H5   H  HCH1   0   0.260  -100.4816  16.3130  -37.0317
 D2T  H6   H  HCH3   0   0.262   -99.7699  20.1653  -36.3117
 D2T  H7   H  HCH3   0   0.247   -99.6984  18.5592  -35.5832
 D2T  H8   H  HCH3   0   0.245   -98.3844  19.1219  -36.6356
 D2T  CB1  C  CH3    0  -0.780   -99.4626  19.1334  -36.4795

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
 D2T  OD1  CG   deloc   1.245  0.020  1.245
 D2T  OD2  CG   deloc   1.246  0.020  1.246
 D2T  CG   CB   single  1.550  0.020  1.550
 D2T  N    CA   single  1.458  0.019  1.458
 D2T  SB   CB   single  1.831  0.020  1.831
 D2T  SB   CB1  single  1.806  0.020  1.806
 D2T  CB   CA   single  1.530  0.020  1.530
 D2T  CA   C    single  1.525  0.021  1.525
 D2T  C    O    deloc   1.231  0.020  1.231
 D2T  C    O1   deloc   1.247  0.020  1.247
 D2T  N    H1   single  0.890  0.020  1.040
 D2T  N    H2   single  0.890  0.020  1.040
 D2T  CA   H4   single  0.970  0.020  1.090
 D2T  CB   H5   single  0.970  0.020  1.090
 D2T  CB1  H6   single  0.970  0.020  1.090
 D2T  CB1  H7   single  0.970  0.020  1.090
 D2T  CB1  H8   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
 D2T  H2   N    H1   104.24  3.000
 D2T  H2   N    CA   107.63  3.000
 D2T  H1   N    CA   107.53  3.000
 D2T  H4   CA   CB   106.68  3.000
 D2T  H4   CA   C    103.30  3.000
 D2T  CB   CA   C    110.10  1.900
 D2T  H4   CA   N    106.64  3.000
 D2T  C    CA   N    111.00  2.800
 D2T  CB   CA   N    110.50  1.700
 D2T  O1   C    O    126.46  3.000
 D2T  O1   C    CA   117.27  3.000
 D2T  O    C    CA   120.80  1.700
 D2T  H5   CB   CG   107.47  3.000
 D2T  H5   CB   SB   106.95  3.000
 D2T  CG   CB   SB   105.70  3.000
 D2T  H5   CB   CA   106.92  3.000
 D2T  SB   CB   CA   114.38  3.000
 D2T  CG   CB   CA   114.98  3.000
 D2T  CB1  SB   CB   102.05  3.000
 D2T  OD2  CG   OD1  126.93  3.000
 D2T  OD2  CG   CB   116.10  3.000
 D2T  OD1  CG   CB   116.95  3.000
 D2T  H8   CB1  H7   109.04  3.000
 D2T  H8   CB1  H6   108.13  3.000
 D2T  H7   CB1  H6   108.13  3.000
 D2T  H8   CB1  SB   112.59  3.000
 D2T  H7   CB1  SB   111.64  3.000
 D2T  H6   CB1  SB   107.14  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
 D2T  Var_01  H6  CB1  SB  CB  -170.97  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
 D2T  chir_01  CA  N   CB  C   negativ
 D2T  chir_02  CB  SB  CA  CG  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
 D2T  plan-1  CA   0.020
 D2T  plan-1  C    0.020
 D2T  plan-1  O    0.020
 D2T  plan-1  O1   0.020
 D2T  plan-2  CB   0.020
 D2T  plan-2  CG   0.020
 D2T  plan-2  OD1  0.020
 D2T  plan-2  OD2  0.020

