# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:25:01 2022
#   Inital geometry file: a 82 line input string
#   Ligand name: (2R)-2-azanyl-3-[(1S,6R)-3,6-dihydroxy-4-methyl-2,5-dioxo-cyclohex-3-en-1-yl]sulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(O)C(=O)[C@@H](SC[C@H](N)C(O)=O)[C@H](O)C1=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
 C1T  C1T  '(2R)-2-azanyl-3-[(1S,6R)-3,6-dihydroxy-4-methyl-2,5-dioxo-cyclohex-3-en-1-yl]sulfanyl-propanoic acid'  L-peptide  30  18  .  2012-08-28  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C1T
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
 C1T  C    C  C      0   0.427  15.0853  49.3106  -129.4911
 C1T  N    N  NH2    0  -0.808  12.9667  48.0990  -129.8448
 C1T  O    O  O      0  -0.587  15.6810  50.3671  -129.7832
 C1T  C1   C  CH1    0  -0.624  13.7563  50.9941  -133.9063
 C1T  C2   C  CH1    0   0.004  13.4115  49.6903  -134.6308
 C1T  C3   C  C      0   0.313  12.6959  49.9907  -135.9379
 C1T  C4   C  C      0  -0.125  11.6390  50.9986  -135.9391
 C1T  C5   C  C      0   0.298  11.5586  51.8599  -134.9011
 C1T  C6   C  C      0   0.401  12.5351  51.8625  -133.7717
 C1T  C7   C  CH3    0  -0.702  10.7234  51.0450  -137.1189
 C1T  O8   O  OH1    0  -0.586  10.6106  52.7813  -134.8291
 C1T  O9   O  OH1    0  -0.651  14.5570  48.9347  -134.8420
 C1T  CA   C  CH1    0  -0.198  14.0400  48.8140  -130.5166
 C1T  CB   C  CH2    0  -0.545  13.4356  49.9685  -131.3072
 C1T  SG   S  S2     0   0.051  14.6722  50.7959  -132.3572
 C1T  O10  O  O      0  -0.399  12.9761  49.3494  -136.9324
 C1T  O11  O  O      0  -0.370  12.3188  52.5981  -132.8375
 C1T  OXT  O  OC    -1  -0.596  15.2686  48.6023  -128.4836
 C1T  H    H  HNH2   0   0.335  12.5184  47.4606  -130.4890
 C1T  H2   H  HNH2   0   0.337  13.3780  47.5371  -129.1105
 C1T  H1   H  HCH1   0   0.342  14.4430  51.5544  -134.5567
 C1T  H20  H  HCH1   0   0.258  12.6795  49.1365  -134.0194
 C1T  H7   H  HCH3   0   0.257   9.8999  51.7383  -136.9716
 C1T  H7A  H  HCH3   0   0.258  11.2657  51.3565  -138.0135
 C1T  HO8  H  HOH1   0   0.479  10.7229  53.2921  -134.0106
 C1T  HO9  H  HOH1   0   0.450  14.4838  48.5382  -135.7215
 C1T  HA   H  HCH1   0   0.209  14.5864  48.1757  -131.2327
 C1T  HB2  H  HCH2   0   0.256  12.6384  49.5846  -131.9474
 C1T  HB3  H  HCH2   0   0.259  12.9855  50.6969  -130.6318
 C1T  H13  H  HCH3   0   0.255  10.3043  50.0604  -137.3274

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
 C1T  C   O    deloc   1.231  0.020  1.231
 C1T  C   CA   single  1.525  0.021  1.525
 C1T  C   OXT  deloc   1.245  0.020  1.245
 C1T  N   CA   single  1.458  0.019  1.458
 C1T  N   H    single  0.860  0.020  0.860
 C1T  N   H2   single  0.890  0.020  1.040
 C1T  C1  C2   single  1.531  0.020  1.531
 C1T  C1  C6   single  1.505  0.020  1.505
 C1T  C1  SG   single  1.810  0.020  1.810
 C1T  C1  H1   single  0.970  0.020  1.090
 C1T  C2  C3   single  1.520  0.020  1.520
 C1T  C2  O9   single  1.388  0.020  1.388
 C1T  C2  H20  single  0.970  0.020  1.090
 C1T  C3  C4   single  1.460  0.020  1.460
 C1T  C3  O10  double  1.216  0.020  1.216
 C1T  C4  C5   double  1.351  0.020  1.351
 C1T  C4  C7   single  1.494  0.020  1.494
 C1T  C5  C6   single  1.493  0.020  1.493
 C1T  C5  O8   single  1.324  0.020  1.324
 C1T  C6  O11  double  1.209  0.020  1.209
 C1T  C7  H7   single  0.970  0.020  1.090
 C1T  C7  H7A  single  0.970  0.020  1.090
 C1T  C7  H13  single  0.970  0.020  1.090
 C1T  O8  HO8  single  0.850  0.020  0.980
 C1T  O9  HO9  single  0.850  0.020  0.980
 C1T  CA  CB   single  1.530  0.020  1.530
 C1T  CA  HA   single  0.970  0.020  0.970
 C1T  CB  SG   single  1.821  0.020  1.821
 C1T  CB  HB2  single  0.970  0.020  1.090
 C1T  CB  HB3  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
 C1T  OXT  C   CA   116.96  3.000
 C1T  OXT  C   O    126.94  3.000
 C1T  CA   C   O    120.80  1.700
 C1T  H2   N   H    106.96  3.000
 C1T  H2   N   CA   107.96  3.000
 C1T  H    N   CA   114.00  3.000
 C1T  H1   C1  SG   104.24  3.000
 C1T  H1   C1  C6   105.41  3.000
 C1T  SG   C1  C6   113.41  3.000
 C1T  H1   C1  C2   107.14  3.000
 C1T  SG   C1  C2   115.19  3.000
 C1T  C6   C1  C2   110.55  3.000
 C1T  H20  C2  O9   111.02  3.000
 C1T  H20  C2  C3   105.28  3.000
 C1T  O9   C2  C3   111.42  3.000
 C1T  H20  C2  C1   108.35  3.000
 C1T  O9   C2  C1   110.46  3.000
 C1T  C3   C2  C1   110.16  3.000
 C1T  O10  C3  C4   122.01  3.000
 C1T  O10  C3  C2   119.37  3.000
 C1T  C4   C3  C2   118.54  3.000
 C1T  C7   C4  C5   123.39  3.000
 C1T  C7   C4  C3   117.75  3.000
 C1T  C5   C4  C3   118.84  3.000
 C1T  O8   C5  C6   115.21  3.000
 C1T  O8   C5  C4   121.87  3.000
 C1T  C6   C5  C4   122.91  3.000
 C1T  O11  C6  C5   117.95  3.000
 C1T  O11  C6  C1   124.45  3.000
 C1T  C5   C6  C1   117.53  3.000
 C1T  H13  C7  H7A  106.98  3.000
 C1T  H13  C7  H7   108.12  3.000
 C1T  H7A  C7  H7   107.79  3.000
 C1T  H13  C7  C4   111.01  3.000
 C1T  H7A  C7  C4   110.58  3.000
 C1T  H7   C7  C4   112.17  3.000
 C1T  HO8  O8  C5   109.21  3.000
 C1T  HO9  O9  C2   107.38  3.000
 C1T  HA   CA  CB   109.00  3.000
 C1T  HA   CA  N    110.00  3.000
 C1T  CB   CA  N    110.50  1.700
 C1T  HA   CA  C    109.00  3.000
 C1T  CB   CA  C    110.10  1.900
 C1T  N    CA  C    111.00  2.800
 C1T  HB3  CB  HB2  107.25  3.000
 C1T  HB3  CB  SG   109.51  3.000
 C1T  HB2  CB  SG   108.50  3.000
 C1T  HB3  CB  CA   110.38  3.000
 C1T  HB2  CB  CA   109.10  3.000
 C1T  SG   CB  CA   111.96  3.000
 C1T  CB   SG  C1   101.51  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
 C1T  Var_01  C4  C5  C6  C1    8.62  30.0  1
 C1T  Var_02  C6  C5  C4  C3    2.35  30.0  1
 C1T  Var_03  H7  C7  C4  C3  172.79  30.0  3
 C1T  Var_04  CA  CB  SG  C1  135.91  30.0  1

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
 C1T  chir_01  C1  C2  C6  SG  negativ
 C1T  chir_02  C2  O9  C1  C3  negativ
 C1T  chir_03  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
 C1T  plan-1  C2   0.020
 C1T  plan-1  C3   0.020
 C1T  plan-1  C4   0.020
 C1T  plan-1  O10  0.020
 C1T  plan-2  C1   0.020
 C1T  plan-2  C5   0.020
 C1T  plan-2  C6   0.020
 C1T  plan-2  O11  0.020
 C1T  plan-3  C    0.020
 C1T  plan-3  O    0.020
 C1T  plan-3  CA   0.020
 C1T  plan-3  OXT  0.020

