# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 16:43:32 2022
#   Inital geometry file: a 54 line input string
#   Ligand name: (2~{S})-2-azanyl-3-thiophen-3-yl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](Cc1cscc1)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
 Q78  Q78  '(2~{S})-2-azanyl-3-thiophen-3-yl-propanoic acid'  L-peptide  19  11  .  2022-08-10  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_Q78
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
 Q78  N    N  NH2    0  -0.826  -12.6321  5.8414  -6.8647
 Q78  CA   C  CH1    0  -0.112  -12.3581  4.8399  -7.8919
 Q78  C    C  C      0   0.387  -13.6560  4.2754  -8.5496
 Q78  CB   C  CH2    0  -0.473  -11.5696  3.6551  -7.3235
 Q78  CG   C  CR5    0   0.086  -10.2126  3.9827  -6.7715
 Q78  CD1  C  CR15   0  -0.493   -9.6162  3.2450  -5.7906
 Q78  CD2  C  CR15   0  -0.304   -9.3606  5.0365  -7.2183
 Q78  O1   O  O     -1  -0.662  -13.4813  3.4020  -9.4238
 Q78  CE   C  CR15   0  -0.420   -8.1546  5.0546  -6.5839
 Q78  SE   S  S2     0   0.266   -8.0367  3.8035  -5.4195
 Q78  OXT  O  OC     0  -0.687  -14.7425  4.7381  -8.1488
 Q78  H1   H  HNH2   0   0.358  -12.2553  6.7374  -7.1425
 Q78  H2   H  HNH2   0   0.352  -13.6419  5.9592  -6.8518
 Q78  H4   H  HCH1   0   0.228  -11.7697  5.2791  -8.7064
 Q78  H5   H  HCH2   0   0.192  -12.1719  3.1842  -6.5385
 Q78  H6   H  HCH2   0   0.280  -11.4528  2.9050  -8.0996
 Q78  H7   H  HCR5   0   0.296  -10.0111  2.3743  -5.2877
 Q78  H8   H  HCR5   0   0.245   -9.6184  5.7379  -7.9963
 Q78  H9   H  HCR5   0   0.287   -7.3418  5.7479  -6.7291

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
 Q78  O1   C    deloc     1.248  0.020  1.248
 Q78  C    CA   single    1.525  0.021  1.525
 Q78  CA   N    single    1.458  0.019  1.458
 Q78  CA   CB   single    1.530  0.020  1.530
 Q78  CB   CG   single    1.501  0.020  1.501
 Q78  CD2  CG   aromatic  1.427  0.020  1.427
 Q78  CD2  CE   aromatic  1.363  0.020  1.363
 Q78  CG   CD1  aromatic  1.365  0.020  1.365
 Q78  CE   SE   aromatic  1.713  0.020  1.713
 Q78  CD1  SE   aromatic  1.716  0.020  1.716
 Q78  C    OXT  deloc     1.247  0.020  1.247
 Q78  N    H1   single    0.890  0.020  1.040
 Q78  N    H2   single    0.890  0.020  1.040
 Q78  CA   H4   single    0.970  0.020  1.090
 Q78  CB   H5   single    0.970  0.020  1.090
 Q78  CB   H6   single    0.970  0.020  1.090
 Q78  CD1  H7   single    0.930  0.020  1.080
 Q78  CD2  H8   single    0.930  0.020  1.080
 Q78  CE   H9   single    0.930  0.020  1.080

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
 Q78  H2   N    H1   105.72  3.000
 Q78  H2   N    CA   105.95  3.000
 Q78  H1   N    CA   110.16  3.000
 Q78  H4   CA   CB   108.00  3.000
 Q78  H4   CA   C    106.14  3.000
 Q78  CB   CA   C    110.10  1.900
 Q78  H4   CA   N    110.39  3.000
 Q78  CB   CA   N    110.50  1.700
 Q78  C    CA   N    111.00  2.800
 Q78  OXT  C    O1   127.35  3.000
 Q78  OXT  C    CA   117.06  3.000
 Q78  O1   C    CA   115.59  3.000
 Q78  H6   CB   H5   105.93  3.000
 Q78  H6   CB   CG   108.44  3.000
 Q78  H5   CB   CG   109.10  3.000
 Q78  H6   CB   CA   108.93  3.000
 Q78  H5   CB   CA   108.37  3.000
 Q78  CG   CB   CA   115.64  3.000
 Q78  CD2  CG   CD1  111.31  3.000
 Q78  CD1  CG   CB   122.78  3.000
 Q78  CD2  CG   CB   125.86  3.000
 Q78  H7   CD1  SE   119.88  3.000
 Q78  H7   CD1  CG   127.63  3.000
 Q78  SE   CD1  CG   112.45  3.000
 Q78  H8   CD2  CE   122.58  3.000
 Q78  H8   CD2  CG   124.29  3.000
 Q78  CE   CD2  CG   113.11  3.000
 Q78  H9   CE   SE   120.62  3.000
 Q78  H9   CE   CD2  127.81  3.000
 Q78  SE   CE   CD2  111.56  3.000
 Q78  CE   SE   CD1   91.57  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
 Q78  CONST_01  SE   CE   CD2  CG     0.00   0.0  0
 Q78  CONST_02  CE   SE   CD1  CG     0.00   0.0  0
 Q78  CONST_03  CE   CD2  CG   CD1    0.00   0.0  0
 Q78  CONST_04  CD2  CE   SE   CD1    0.00   0.0  0
 Q78  CONST_05  SE   CD1  CG   CD2    0.00   0.0  0
 Q78  CONST_06  CE   CD2  CG   CB   180.00   0.0  0
 Q78  CONST_07  SE   CD1  CG   CB   180.00   0.0  0
 Q78  CONST_08  H9   CE   CD2  CG   180.00   0.0  0
 Q78  CONST_09  H8   CD2  CG   CD1  180.00   0.0  0
 Q78  CONST_10  H7   CD1  CG   CD2  180.00   0.0  0
 Q78  Var_01    CD2  CG   CB   CA   -29.90  30.0  2

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
 Q78  chir_01  CA  C  N  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
 Q78  plan-1  CB   0.020
 Q78  plan-1  CG   0.020
 Q78  plan-1  CD1  0.020
 Q78  plan-1  CD2  0.020
 Q78  plan-1  CE   0.020
 Q78  plan-1  SE   0.020
 Q78  plan-1  H7   0.020
 Q78  plan-1  H8   0.020
 Q78  plan-1  H9   0.020
 Q78  plan-2  CA   0.020
 Q78  plan-2  C    0.020
 Q78  plan-2  O1   0.020
 Q78  plan-2  OXT  0.020

