# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Mar 20 12:38:13 2022
#   Inital geometry file: a 77 line input string
#   Ligand name: (2~{S})-2-azanyl-3-(2-methylsulfanyl-1~{H}-indol-3-yl)propanal
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSc1[nH]c2ccccc2c1C[C@H](N)C=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
 Q2E  Q2E  (2~{S})-2-azanyl-3-(2-methylsulfanyl-1~{H}-indol-3-yl)propanal  L-peptide  30  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_Q2E
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
 Q2E  C1   C  CR5   0   0.072  -3.7966  -35.8869  -3.0080
 Q2E  C2   C  CR56  0   0.350  -3.7700  -35.6464  -5.2263
 Q2E  C3   C  CR16  0  -0.307  -3.4250  -35.4266  -6.5596
 Q2E  C4   C  CR16  0  -0.280  -4.4144  -35.5939  -7.5089
 Q2E  C5   C  CR16  0  -0.265  -5.7182  -35.9749  -7.1478
 Q2E  C6   C  CR16  0  -0.372  -6.0546  -36.1947  -5.8269
 Q2E  C7   C  CR56  0   0.049  -5.0728  -36.0323  -4.8421
 Q2E  C8   C  CR5   0   0.069  -5.0672  -36.1903  -3.4202
 Q2E  C9   C  C1    0   0.161  -8.3913  -35.8886  -1.5871
 Q2E  N1   N  NH2   0  -0.773  -6.3844  -34.4175  -1.3844
 Q2E  CA   C  CH1   0  -0.195  -7.1091  -35.3647  -2.1915
 Q2E  O    O  O     0  -0.365  -8.7982  -35.6074  -0.4887
 Q2E  CB   C  CH2   0  -0.565  -6.2247  -36.5694  -2.5676
 Q2E  S    S  S2    0   0.014  -3.1897  -35.8194  -1.3758
 Q2E  C    C  CH3   0  -0.767  -1.9174  -37.1160  -1.4117
 Q2E  N    N  NR15  0  -0.709  -3.0199  -35.5572  -4.0930
 Q2E  H1   H  HCR6  0   0.258  -2.4208  -35.1347  -6.8402
 Q2E  H2   H  HCR6  0   0.248  -4.1805  -35.4287  -8.5527
 Q2E  H3   H  HCR6  0   0.245  -6.4662  -36.0960  -7.9205
 Q2E  H4   H  HCR6  0   0.241  -7.0623  -36.4878  -5.5577
 Q2E  H6   H  HNH2  0   0.352  -6.9617  -33.6094  -1.1882
 Q2E  H7   H  HNH2  0   0.342  -6.1569  -34.8289  -0.4873
 Q2E  H9   H  HCH1  0   0.270  -7.4105  -34.8758  -3.1283
 Q2E  H10  H  HCH2  0   0.258  -6.8365  -37.3123  -3.0875
 Q2E  H11  H  HCH2  0   0.257  -5.8742  -37.0448  -1.6470
 Q2E  H12  H  HCH3  0   0.278  -1.4940  -37.1649  -0.4099
 Q2E  H13  H  HCH3  0   0.271  -2.3568  -38.0795  -1.6594
 Q2E  H14  H  HCH3  0   0.270  -1.1232  -36.8760  -2.1147
 Q2E  H15  H  HNR5  0   0.409  -2.0521  -35.2822  -4.0489
 Q2E  H5   H  H     0   0.182  -8.9583  -36.5733  -2.2466

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
 Q2E  C4  C5   aromatic  1.405  0.020  1.405
 Q2E  C4  C3   aromatic  1.381  0.020  1.381
 Q2E  C5  C6   aromatic  1.381  0.020  1.381
 Q2E  C3  C2   aromatic  1.395  0.020  1.395
 Q2E  C6  C7   aromatic  1.400  0.020  1.400
 Q2E  C2  C7   aromatic  1.412  0.020  1.412
 Q2E  C2  N    aromatic  1.362  0.020  1.362
 Q2E  C7  C8   aromatic  1.431  0.020  1.431
 Q2E  N   C1   aromatic  1.374  0.020  1.374
 Q2E  C8  C1   aromatic  1.370  0.020  1.370
 Q2E  C8  CB   single    1.487  0.020  1.487
 Q2E  C1  S    single    1.743  0.020  1.743
 Q2E  CB  CA   single    1.530  0.020  1.530
 Q2E  CA  C9   single    1.511  0.020  1.511
 Q2E  CA  N1   single    1.440  0.020  1.440
 Q2E  C9  O    double    1.205  0.020  1.205
 Q2E  S   C    single    1.817  0.020  1.817
 Q2E  C3  H1   single    0.930  0.020  1.080
 Q2E  C4  H2   single    0.930  0.020  1.080
 Q2E  C5  H3   single    0.930  0.020  1.080
 Q2E  C6  H4   single    0.930  0.020  1.080
 Q2E  C9  H5   single    0.930  0.020  1.080
 Q2E  N1  H6   single    0.890  0.020  1.040
 Q2E  N1  H7   single    0.890  0.020  1.040
 Q2E  CA  H9   single    0.970  0.020  1.090
 Q2E  CB  H10  single    0.970  0.020  1.090
 Q2E  CB  H11  single    0.970  0.020  1.090
 Q2E  C   H12  single    0.970  0.020  1.090
 Q2E  C   H13  single    0.970  0.020  1.090
 Q2E  C   H14  single    0.970  0.020  1.090
 Q2E  N   H15  single    0.860  0.020  1.020

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
 Q2E  N    C1  S    122.23  3.000
 Q2E  S    C1  C8   127.83  3.000
 Q2E  N    C1  C8   109.86  3.000
 Q2E  N    C2  C7   107.43  3.000
 Q2E  N    C2  C3   130.46  3.000
 Q2E  C7   C2  C3   122.11  3.000
 Q2E  H1   C3  C4   121.26  3.000
 Q2E  H1   C3  C2   121.31  3.000
 Q2E  C4   C3  C2   117.43  3.000
 Q2E  H2   C4  C5   119.31  3.000
 Q2E  H2   C4  C3   119.31  3.000
 Q2E  C5   C4  C3   121.38  3.000
 Q2E  H3   C5  C6   119.79  3.000
 Q2E  H3   C5  C4   119.21  3.000
 Q2E  C6   C5  C4   121.00  3.000
 Q2E  H4   C6  C7   120.59  3.000
 Q2E  H4   C6  C5   120.50  3.000
 Q2E  C7   C6  C5   118.92  3.000
 Q2E  C8   C7  C6   133.55  3.000
 Q2E  C8   C7  C2   107.28  3.000
 Q2E  C6   C7  C2   119.16  3.000
 Q2E  CB   C8  C7   126.51  3.000
 Q2E  CB   C8  C1   127.31  3.000
 Q2E  C7   C8  C1   106.15  3.000
 Q2E  H5   C9  O    120.98  3.000
 Q2E  H5   C9  CA   114.25  3.000
 Q2E  O    C9  CA   124.77  3.000
 Q2E  H7   N1  H6   106.30  3.000
 Q2E  H7   N1  CA   110.01  3.000
 Q2E  H6   N1  CA   110.28  3.000
 Q2E  H9   CA  CB   107.29  3.000
 Q2E  H9   CA  N1   108.86  3.000
 Q2E  CB   CA  N1   111.24  3.000
 Q2E  H9   CA  C9   105.22  3.000
 Q2E  N1   CA  C9   115.52  3.000
 Q2E  CB   CA  C9   108.27  3.000
 Q2E  H11  CB  H10  106.50  3.000
 Q2E  H11  CB  CA   108.56  3.000
 Q2E  H10  CB  CA   109.03  3.000
 Q2E  H11  CB  C8   110.12  3.000
 Q2E  H10  CB  C8   109.64  3.000
 Q2E  CA   CB  C8   112.79  3.000
 Q2E  C    S   C1   101.40  3.000
 Q2E  H14  C   H13  110.08  3.000
 Q2E  H14  C   H12  108.71  3.000
 Q2E  H13  C   H12  109.08  3.000
 Q2E  H14  C   S    111.52  3.000
 Q2E  H13  C   S    110.72  3.000
 Q2E  H12  C   S    106.63  3.000
 Q2E  H15  N   C2   125.70  3.000
 Q2E  H15  N   C1   125.03  3.000
 Q2E  C2   N   C1   109.27  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
 Q2E  CONST_01  C3   C2  N   C1   180.00   0.0  0
 Q2E  CONST_02  C7   C2  N   C1     0.00   0.0  0
 Q2E  CONST_03  C6   C7  C8  C1   180.00   0.0  0
 Q2E  CONST_04  C2   C7  C8  C1     0.00   0.0  0
 Q2E  CONST_05  C5   C4  C3  C2     0.00   0.0  0
 Q2E  CONST_06  C5   C6  C7  C2     0.00   0.0  0
 Q2E  CONST_07  C8   C1  N   C2     0.00   0.0  0
 Q2E  CONST_08  C6   C5  C4  C3     0.00   0.0  0
 Q2E  CONST_09  C6   C7  C2  C3     0.00   0.0  0
 Q2E  CONST_10  C8   C7  C2  C3   180.00   0.0  0
 Q2E  CONST_11  C7   C6  C5  C4     0.00   0.0  0
 Q2E  CONST_12  C7   C2  C3  C4     0.00   0.0  0
 Q2E  CONST_13  N    C2  C3  C4   180.00   0.0  0
 Q2E  CONST_14  C8   C7  C6  C5   180.00   0.0  0
 Q2E  CONST_15  N    C2  C7  C6   180.00   0.0  0
 Q2E  CONST_16  N    C1  C8  C7     0.00   0.0  0
 Q2E  CONST_17  N    C2  C7  C8     0.00   0.0  0
 Q2E  CONST_18  CB   C8  C7  C2   180.00   0.0  0
 Q2E  CONST_19  S    C1  N   C2   180.00   0.0  0
 Q2E  CONST_20  CB   C8  C7  C6     0.00   0.0  0
 Q2E  CONST_21  S    C1  C8  C7   180.00   0.0  0
 Q2E  CONST_22  N    C1  C8  CB   180.00   0.0  0
 Q2E  CONST_23  H2   C4  C3  C2   180.00   0.0  0
 Q2E  CONST_24  H4   C6  C7  C2   180.00   0.0  0
 Q2E  CONST_25  H3   C5  C4  C3   180.00   0.0  0
 Q2E  CONST_26  H15  N   C2  C3     0.00   0.0  0
 Q2E  CONST_27  H1   C3  C4  C5   180.00   0.0  0
 Q2E  Var_01    CA   CB  C8  C1    93.98  30.0  2
 Q2E  Var_02    N    C1  S   C    -65.37  30.0  2
 Q2E  Var_03    H12  C   S   C1  -178.55  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
 Q2E  chir_01  CA  CB  C9  N1  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
 Q2E  plan-1  C1   0.020
 Q2E  plan-1  C2   0.020
 Q2E  plan-1  C3   0.020
 Q2E  plan-1  C4   0.020
 Q2E  plan-1  C5   0.020
 Q2E  plan-1  C6   0.020
 Q2E  plan-1  C7   0.020
 Q2E  plan-1  C8   0.020
 Q2E  plan-1  CB   0.020
 Q2E  plan-1  S    0.020
 Q2E  plan-1  N    0.020
 Q2E  plan-1  H1   0.020
 Q2E  plan-1  H2   0.020
 Q2E  plan-1  H3   0.020
 Q2E  plan-1  H4   0.020
 Q2E  plan-1  H15  0.020
 Q2E  plan-2  C9   0.020
 Q2E  plan-2  CA   0.020
 Q2E  plan-2  O    0.020
 Q2E  plan-2  H5   0.020

