# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 12:57:43 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: N~6~-(5-carboxythiophen-3-yl)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNc1csc(c1)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
 KST  KST  N~6~-(5-carboxythiophen-3-yl)-L-lysine  L-peptide  32  18  .  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_KST
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
 KST  O2    O  O      0  -0.595  24.2116  12.4927  -10.5877
 KST  C9    C  C      0   0.390  23.7985  11.3241  -10.4551
 KST  O1    O  OC    -1  -0.580  24.1855  10.4552   -9.6544
 KST  C8    C  CR5    0  -0.303  22.6862  10.9303  -11.3931
 KST  S     S  S2     0   0.171  22.1032  12.0918  -12.5169
 KST  C6    C  CR15   0  -0.576  20.9528  10.9837  -13.1601
 KST  C7    C  CR15   0  -0.283  22.0126   9.7527  -11.5058
 KST  C5    C  CR5    0   0.389  21.0041   9.7696  -12.5216
 KST  N1    N  NH1    0  -0.680  20.1745   8.6889  -12.7649
 KST  C4    C  CH2    0  -0.254  19.3473   8.7225  -13.9498
 KST  C3    C  CH2    0  -0.469  18.4902   7.4740  -14.0808
 KST  C2    C  CH2    0  -0.422  17.5854   7.5625  -15.3050
 KST  C1    C  CH2    0  -0.440  16.7649   6.3183  -15.6360
 KST  CA    C  CH1    0  -0.197  15.7709   5.8713  -14.5419
 KST  N     N  NH2    0  -0.808  16.3330   4.9921  -13.5243
 KST  C     C  C      0   0.397  14.5655   5.1873  -15.2300
 KST  OXT   O  OC    -1  -0.613  13.6850   5.9469  -15.6814
 KST  O     O  O      0  -0.605  14.5998   3.9430  -15.3209
 KST  H6    H  HCR5   0   0.281  20.3010  11.2823  -13.9666
 KST  H7    H  HCR5   0   0.250  22.2186   8.8908  -10.8845
 KST  HN1   H  HNH1   0   0.367  20.6300   7.7992  -12.6197
 KST  H41   H  HCH2   0   0.220  18.6911   9.5960  -13.8857
 KST  H42   H  HCH2   0   0.203  19.9459   8.8555  -14.8642
 KST  H31   H  HCH2   0   0.219  19.1332   6.5899  -14.1545
 KST  H32   H  HCH2   0   0.225  17.8962   7.3631  -13.1692
 KST  H21   H  HCH2   0   0.213  16.9013   8.4076  -15.1728
 KST  H22   H  HCH2   0   0.218  18.2013   7.8100  -16.1759
 KST  H11   H  HCH2   0   0.220  16.2182   6.5412  -16.5568
 KST  H12   H  HCH2   0   0.208  17.4306   5.4807  -15.8715
 KST  HA    H  HCH1   0   0.194  15.3984   6.7751  -14.0447
 KST  HN1A  H  HNH2   0   0.323  16.4681   4.0823  -13.9484
 KST  HN2   H  HNH2   0   0.338  17.2492   5.3148  -13.2426

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
 KST  O2  C9    deloc     1.247  0.020  1.247
 KST  C9  C8    single    1.507  0.020  1.507
 KST  C9  O1    deloc     1.243  0.020  1.243
 KST  C8  S     aromatic  1.718  0.020  1.718
 KST  C8  C7    aromatic  1.361  0.020  1.361
 KST  S   C6    aromatic  1.722  0.020  1.722
 KST  C6  C5    aromatic  1.373  0.020  1.373
 KST  C6  H6    single    0.930  0.020  1.080
 KST  C7  C5    aromatic  1.432  0.020  1.432
 KST  C7  H7    single    0.930  0.020  1.080
 KST  C5  N1    single    1.384  0.020  1.384
 KST  N1  C4    single    1.445  0.020  1.445
 KST  N1  HN1   single    0.890  0.020  1.040
 KST  C4  C3    single    1.520  0.020  1.520
 KST  C4  H41   single    0.970  0.020  1.090
 KST  C4  H42   single    0.970  0.020  1.090
 KST  C3  C2    single    1.525  0.020  1.525
 KST  C3  H31   single    0.970  0.020  1.090
 KST  C3  H32   single    0.970  0.020  1.090
 KST  C2  C1    single    1.527  0.020  1.527
 KST  C2  H21   single    0.970  0.020  1.090
 KST  C2  H22   single    0.970  0.020  1.090
 KST  C1  CA    single    1.544  0.020  1.544
 KST  C1  H11   single    0.970  0.020  1.090
 KST  C1  H12   single    0.970  0.020  1.090
 KST  CA  C     single    1.525  0.021  1.525
 KST  CA  N     single    1.458  0.019  1.458
 KST  CA  HA    single    0.970  0.020  0.970
 KST  N   HN1A  single    0.890  0.020  1.040
 KST  N   HN2   single    0.890  0.020  1.040
 KST  C   O     deloc     1.231  0.020  1.231
 KST  C   OXT   deloc     1.247  0.020  1.247

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
 KST  C8    C9  O1    116.60  3.000
 KST  O1    C9  O2    128.36  3.000
 KST  C8    C9  O2    115.04  3.000
 KST  C7    C8  S     111.27  3.000
 KST  C7    C8  C9    129.99  3.000
 KST  S     C8  C9    118.74  3.000
 KST  C6    S   C8     92.06  3.000
 KST  H6    C6  C5    127.95  3.000
 KST  H6    C6  S     120.31  3.000
 KST  C5    C6  S     111.74  3.000
 KST  H7    C7  C5    123.43  3.000
 KST  H7    C7  C8    123.18  3.000
 KST  C5    C7  C8    113.40  3.000
 KST  N1    C5  C7    122.54  3.000
 KST  N1    C5  C6    125.90  3.000
 KST  C7    C5  C6    111.52  3.000
 KST  HN1   N1  C4    113.35  3.000
 KST  HN1   N1  C5    113.09  3.000
 KST  C4    N1  C5    117.97  3.000
 KST  H42   C4  H41   106.16  3.000
 KST  H42   C4  C3    109.53  3.000
 KST  H41   C4  C3    108.81  3.000
 KST  H42   C4  N1    111.87  3.000
 KST  H41   C4  N1    108.27  3.000
 KST  C3    C4  N1    111.98  3.000
 KST  H32   C3  H31   107.04  3.000
 KST  H32   C3  C2    110.66  3.000
 KST  H31   C3  C2    109.94  3.000
 KST  H32   C3  C4    108.52  3.000
 KST  H31   C3  C4    109.73  3.000
 KST  C2    C3  C4    110.86  3.000
 KST  H22   C2  H21   105.83  3.000
 KST  H22   C2  C1    108.30  3.000
 KST  H21   C2  C1    108.62  3.000
 KST  H22   C2  C3    108.53  3.000
 KST  H21   C2  C3    108.57  3.000
 KST  C1    C2  C3    116.47  3.000
 KST  H12   C1  H11   106.18  3.000
 KST  H12   C1  CA    108.79  3.000
 KST  H11   C1  CA    109.49  3.000
 KST  H12   C1  C2    110.07  3.000
 KST  H11   C1  C2    106.57  3.000
 KST  CA    C1  C2    115.35  3.000
 KST  HA    CA  C     109.00  3.000
 KST  HA    CA  N     110.00  3.000
 KST  C     CA  N     111.00  2.800
 KST  HA    CA  C1    107.54  3.000
 KST  N     CA  C1    114.90  3.000
 KST  C     CA  C1    108.32  3.000
 KST  HN2   N   HN1A  106.40  3.000
 KST  HN2   N   CA    110.57  3.000
 KST  HN1A  N   CA    107.51  3.000
 KST  O     C   OXT   126.88  3.000
 KST  OXT   C   CA    116.21  3.000
 KST  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
 KST  CONST_01  C5  C6  S   C8     0.00   0.0  0
 KST  CONST_02  C6  C5  C7  C8     0.00   0.0  0
 KST  CONST_03  C5  C7  C8  S      0.00   0.0  0
 KST  CONST_04  C7  C5  C6  S      0.00   0.0  0
 KST  CONST_05  C7  C8  S   C6     0.00   0.0  0
 KST  CONST_06  C6  S   C8  C9   180.00   0.0  0
 KST  CONST_07  C5  C7  C8  C9   180.00   0.0  0
 KST  CONST_08  N1  C5  C7  C8   180.00   0.0  0
 KST  CONST_09  N1  C5  C6  S    180.00   0.0  0
 KST  CONST_10  H6  C6  S   C8   180.00   0.0  0
 KST  CONST_11  H7  C7  C8  S    180.00   0.0  0
 KST  CONST_12  C4  N1  C5  C6     0.00   0.0  0
 KST  CONST_13  C4  N1  C5  C7   180.00   0.0  0
 KST  Var_01    S   C8  C9  O2    -0.29  30.0  2
 KST  Var_02    C3  C4  N1  C5  -179.82  30.0  3
 KST  Var_03    C2  C3  C4  N1   177.56  30.0  3
 KST  Var_04    C1  C2  C3  C4   174.31  30.0  3
 KST  Var_05    CA  C1  C2  C3    60.81  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
 KST  chir_01  CA  C1  C  N  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
 KST  plan-1  C9   0.020
 KST  plan-1  C8   0.020
 KST  plan-1  S    0.020
 KST  plan-1  C6   0.020
 KST  plan-1  C7   0.020
 KST  plan-1  C5   0.020
 KST  plan-1  N1   0.020
 KST  plan-1  H6   0.020
 KST  plan-1  H7   0.020
 KST  plan-2  C5   0.020
 KST  plan-2  N1   0.020
 KST  plan-2  C4   0.020
 KST  plan-2  HN1  0.020
 KST  plan-3  O2   0.020
 KST  plan-3  C9   0.020
 KST  plan-3  O1   0.020
 KST  plan-3  C8   0.020
 KST  plan-4  CA   0.020
 KST  plan-4  C    0.020
 KST  plan-4  OXT  0.020
 KST  plan-4  O    0.020

