# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 04:52:18 2022
#   Inital geometry file: a 50 line input string
#   Ligand name: (2~{S})-2-azanyl-5-sulfanyl-pentanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCS)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
 QMB  QMB  "5-Mercapto-norvaline"  L-peptide  19  9  .  2022-09-22  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_QMB
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
 QMB  N    N  NH2    0  -0.814  -29.6377  -36.9047   8.7896
 QMB  CA   C  CH1    0  -0.227  -30.8564  -37.7008   8.8257
 QMB  CB   C  CH2    0  -0.399  -30.8860  -38.5714  10.0830
 QMB  CG   C  CH2    0  -0.434  -29.6904  -39.4995  10.2814
 QMB  CD   C  CH2    0  -0.544  -29.5917  -40.6801   9.3231
 QMB  SE   S  S2     0  -0.274  -29.0463  -40.2034   7.6372
 QMB  C    C  C      0   0.418  -32.1186  -36.8012   8.7366
 QMB  O    O  O      0  -0.606  -33.2071  -37.3589   8.9779
 QMB  OXT  O  OC    -1  -0.601  -31.9500  -35.6133   8.3944
 QMB  H    H  HNH2   0   0.326  -28.8877  -37.4357   8.3661
 QMB  H2   H  HNH2   0   0.331  -29.8071  -36.1045   8.1947
 QMB  HA   H  HCH1   0   0.193  -30.9361  -38.3688   7.9508
 QMB  HB1  H  HCH2   0   0.207  -30.9443  -37.9114  10.9548
 QMB  HB2  H  HCH2   0   0.207  -31.8000  -39.1683  10.0835
 QMB  H7   H  HCH2   0   0.239  -29.7672  -39.9294  11.2847
 QMB  H8   H  HCH2   0   0.224  -28.7542  -38.9352  10.2709
 QMB  H9   H  HCH2   0   0.257  -30.5507  -41.1956   9.2553
 QMB  H10  H  HCH2   0   0.276  -28.8592  -41.3924   9.6993
 QMB  H11  H  HSH1   0   0.220  -28.3588  -41.3153   7.3549

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
 QMB  SE  CD   single  1.835  0.020  1.835
 QMB  CA  N    single  1.458  0.019  1.458
 QMB  CA  C    single  1.525  0.021  1.525
 QMB  CA  CB   single  1.521  0.033  1.521
 QMB  O   C    deloc   1.231  0.020  1.231
 QMB  C   OXT  deloc   1.248  0.020  1.248
 QMB  CD  CG   single  1.524  0.020  1.524
 QMB  CB  CG   single  1.526  0.020  1.526
 QMB  N   H    single  0.860  0.020  0.860
 QMB  N   H2   single  0.890  0.020  1.040
 QMB  CA  HA   single  0.970  0.020  0.970
 QMB  CB  HB1  single  0.970  0.020  1.090
 QMB  CB  HB2  single  0.970  0.020  1.090
 QMB  CG  H7   single  0.970  0.020  1.090
 QMB  CG  H8   single  0.970  0.020  1.090
 QMB  CD  H9   single  0.970  0.020  1.090
 QMB  CD  H10  single  0.970  0.020  1.090
 QMB  SE  H11  single  1.200  0.020  1.300

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
 QMB  H2   N   H    107.05  3.000
 QMB  H2   N   CA   107.88  3.000
 QMB  H    N   CA   114.00  3.000
 QMB  HA   CA  C    109.00  3.000
 QMB  HA   CA  CB   109.00  3.000
 QMB  C    CA  CB   110.50  1.500
 QMB  HA   CA  N    110.00  3.000
 QMB  CB   CA  N    110.40  1.500
 QMB  C    CA  N    111.00  2.800
 QMB  HB2  CB  HB1  106.54  3.000
 QMB  HB2  CB  CG   108.86  3.000
 QMB  HB1  CB  CG   107.74  3.000
 QMB  HB2  CB  CA   109.13  3.000
 QMB  HB1  CB  CA   108.20  3.000
 QMB  CG   CB  CA   115.96  3.000
 QMB  H8   CG  H7   105.76  3.000
 QMB  H8   CG  CD   109.78  3.000
 QMB  H7   CG  CD   106.07  3.000
 QMB  H8   CG  CB   110.84  3.000
 QMB  H7   CG  CB   107.64  3.000
 QMB  CD   CG  CB   116.11  3.000
 QMB  H10  CD  H9   107.68  3.000
 QMB  H10  CD  SE   106.71  3.000
 QMB  H9   CD  SE   109.09  3.000
 QMB  H10  CD  CG   109.46  3.000
 QMB  H9   CD  CG   110.38  3.000
 QMB  SE   CD  CG   113.31  3.000
 QMB  H11  SE  CD    97.51  3.000
 QMB  OXT  C   O    126.65  3.000
 QMB  OXT  C   CA   117.23  3.000
 QMB  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
 QMB  Var_01  CD   CG  CB  CA   -70.48  30.0  3
 QMB  Var_02  SE   CD  CG  CB    74.62  30.0  1
 QMB  Var_03  H7   CG  CB  CA   170.88  30.0  3
 QMB  Var_04  H8   CG  CB  CA    55.66  30.0  3
 QMB  Var_05  H9   CD  CG  CB   -48.06  30.0  1
 QMB  Var_06  H10  CD  CG  CB  -166.42  30.0  1
 QMB  Var_07  HB1  CB  CG  CD   168.16  30.0  1
 QMB  Var_08  HB2  CB  CG  CD    53.00  30.0  1
 QMB  Var_09  H7   CG  CD  SE  -165.89  30.0  3
 QMB  Var_10  H8   CG  CD  SE   -52.05  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
 QMB  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
 QMB  plan-1  CA   0.020
 QMB  plan-1  C    0.020
 QMB  plan-1  O    0.020
 QMB  plan-1  OXT  0.020

