# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 23:15:50 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: (2~{R})-3-(1~{H}-indol-3-yl)-2-methylsulfanyl-propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CS[C@H](Cc1c[nH]c2ccccc12)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
 D8L  D8L  '(2~{R})-3-(1~{H}-indol-3-yl)-2-methylsulfanyl-propanoic acid'  ligand  28  16  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8L
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
 D8L  C4   C  CR56   0   0.352  55.8260  25.0831  49.4451
 D8L  C5   C  CR56   0   0.022  55.0733  26.2772  49.3732
 D8L  C6   C  CR16   0  -0.372  53.7325  26.2599  49.7748
 D8L  C11  C  CH3    0  -0.770  57.9936  30.8764  49.5052
 D8L  C7   C  CR15   0  -0.085  57.1416  26.6913  48.6400
 D8L  C8   C  CR5    0   0.041  55.9366  27.2968  48.8523
 D8L  C9   C  CH2    0  -0.526  55.5707  28.7248  48.6323
 D8L  C10  C  CH1    0  -0.515  55.5449  29.5651  49.9155
 D8L  C12  C  C      0   0.445  54.7880  30.9252  49.7734
 D8L  N1   N  NR15   0  -0.689  57.0797  25.3691  48.9922
 D8L  C3   C  CR16   0  -0.306  55.2764  23.8869  49.9047
 D8L  C1   C  CR16   0  -0.268  53.1835  25.0766  50.2299
 D8L  C2   C  CR16   0  -0.284  53.9505  23.9012  50.2950
 D8L  O1   O  O      0  -0.588  55.0565  31.8152  50.5969
 D8L  O2   O  OC    -1  -0.590  53.9380  30.9742  48.8647
 D8L  S1   S  S2     0  -0.034  57.1996  29.7268  50.6484
 D8L  H4   H  HCR6   0   0.238  53.1311  27.1606  49.7277
 D8L  H10  H  HCH3   0   0.263  59.0301  30.9853  49.8214
 D8L  H11  H  HCH3   0   0.251  57.9913  30.5007  48.4825
 D8L  H12  H  HCH3   0   0.254  57.5130  31.8518  49.5350
 D8L  H6   H  HCR5   0   0.272  58.0581  27.1122  48.2564
 D8L  H7   H  HCH2   0   0.236  56.2510  29.1802  47.9077
 D8L  H8   H  HCH2   0   0.240  54.5778  28.7767  48.1824
 D8L  H9   H  HCH1   0   0.275  54.9983  28.9968  50.6795
 D8L  H5   H  HNR5   0   0.403  57.8393  24.7138  48.9163
 D8L  H3   H  HCR6   0   0.253  55.8646  22.9789  49.9529
 D8L  H1   H  HCR6   0   0.240  52.1471  25.0499  50.5414
 D8L  H2   H  HCR6   0   0.244  53.4936  22.9887  50.6562

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
 D8L  C9   C8   single    1.490  0.020  1.490
 D8L  C9   C10  single    1.534  0.020  1.534
 D8L  C11  S1   single    1.805  0.020  1.805
 D8L  C8   C7   aromatic  1.365  0.020  1.365
 D8L  C8   C5   aromatic  1.434  0.020  1.434
 D8L  C7   N1   aromatic  1.370  0.020  1.370
 D8L  N1   C4   aromatic  1.363  0.020  1.363
 D8L  C5   C6   aromatic  1.400  0.020  1.400
 D8L  C5   C4   aromatic  1.413  0.020  1.413
 D8L  C6   C1   aromatic  1.382  0.020  1.382
 D8L  C4   C3   aromatic  1.394  0.020  1.394
 D8L  C3   C2   aromatic  1.382  0.020  1.382
 D8L  C1   C2   aromatic  1.405  0.020  1.405
 D8L  O1   C12  deloc     1.242  0.020  1.242
 D8L  C12  C10  single    1.563  0.020  1.563
 D8L  C12  O2   deloc     1.245  0.020  1.245
 D8L  C10  S1   single    1.817  0.020  1.817
 D8L  C6   H4   single    0.930  0.020  1.080
 D8L  C11  H10  single    0.970  0.020  1.090
 D8L  C11  H11  single    0.970  0.020  1.090
 D8L  C11  H12  single    0.970  0.020  1.090
 D8L  C7   H6   single    0.930  0.020  1.080
 D8L  C9   H7   single    0.970  0.020  1.090
 D8L  C9   H8   single    0.970  0.020  1.090
 D8L  C10  H9   single    0.970  0.020  1.090
 D8L  N1   H5   single    0.860  0.020  1.020
 D8L  C3   H3   single    0.930  0.020  1.080
 D8L  C1   H1   single    0.930  0.020  1.080
 D8L  C2   H2   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
 D8L  C3   C4   N1   130.69  3.000
 D8L  C3   C4   C5   122.12  3.000
 D8L  N1   C4   C5   107.19  3.000
 D8L  C8   C5   C6   133.61  3.000
 D8L  C6   C5   C4   119.02  3.000
 D8L  C8   C5   C4   107.37  3.000
 D8L  H4   C6   C1   120.37  3.000
 D8L  H4   C6   C5   120.57  3.000
 D8L  C1   C6   C5   119.06  3.000
 D8L  H12  C11  H11  109.51  3.000
 D8L  H12  C11  H10  108.84  3.000
 D8L  H11  C11  H10  108.00  3.000
 D8L  H12  C11  S1   111.06  3.000
 D8L  H11  C11  S1   111.95  3.000
 D8L  H10  C11  S1   107.36  3.000
 D8L  H6   C7   N1   120.42  3.000
 D8L  H6   C7   C8   129.20  3.000
 D8L  N1   C7   C8   110.38  3.000
 D8L  C9   C8   C7   128.22  3.000
 D8L  C7   C8   C5   105.81  3.000
 D8L  C9   C8   C5   125.95  3.000
 D8L  H8   C9   H7   105.85  3.000
 D8L  H8   C9   C10  107.67  3.000
 D8L  H7   C9   C10  109.68  3.000
 D8L  H8   C9   C8   109.26  3.000
 D8L  H7   C9   C8   110.13  3.000
 D8L  C10  C9   C8   113.92  3.000
 D8L  H9   C10  S1   102.64  3.000
 D8L  H9   C10  C12  105.82  3.000
 D8L  S1   C10  C12  113.59  3.000
 D8L  H9   C10  C9   107.87  3.000
 D8L  S1   C10  C9   111.77  3.000
 D8L  C12  C10  C9   114.12  3.000
 D8L  O2   C12  O1   127.11  3.000
 D8L  O2   C12  C10  115.54  3.000
 D8L  O1   C12  C10  117.29  3.000
 D8L  H5   N1   C7   125.12  3.000
 D8L  H5   N1   C4   125.64  3.000
 D8L  C7   N1   C4   109.24  3.000
 D8L  H3   C3   C2   121.14  3.000
 D8L  H3   C3   C4   121.32  3.000
 D8L  C2   C3   C4   117.53  3.000
 D8L  H1   C1   C2   119.25  3.000
 D8L  H1   C1   C6   119.76  3.000
 D8L  C2   C1   C6   120.99  3.000
 D8L  H2   C2   C1   119.36  3.000
 D8L  H2   C2   C3   119.37  3.000
 D8L  C1   C2   C3   121.28  3.000
 D8L  C10  S1   C11  101.64  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
 D8L  CONST_01  C8   C7   N1  C4      0.00   0.0  0
 D8L  CONST_02  C7   C8   C5  C4      0.00   0.0  0
 D8L  CONST_03  C1   C6   C5  C4      0.00   0.0  0
 D8L  CONST_04  C1   C2   C3  C4      0.00   0.0  0
 D8L  CONST_05  N1   C7   C8  C5      0.00   0.0  0
 D8L  CONST_06  C2   C1   C6  C5      0.00   0.0  0
 D8L  CONST_07  C7   N1   C4  C5      0.00   0.0  0
 D8L  CONST_08  C2   C3   C4  C5      0.00   0.0  0
 D8L  CONST_09  C7   C8   C5  C6    180.00   0.0  0
 D8L  CONST_10  N1   C4   C5  C6    180.00   0.0  0
 D8L  CONST_11  C3   C4   C5  C6      0.00   0.0  0
 D8L  CONST_12  C3   C2   C1  C6      0.00   0.0  0
 D8L  CONST_13  C3   C4   N1  C7    180.00   0.0  0
 D8L  CONST_14  C1   C6   C5  C8    180.00   0.0  0
 D8L  CONST_15  N1   C4   C5  C8      0.00   0.0  0
 D8L  CONST_16  C3   C4   C5  C8    180.00   0.0  0
 D8L  CONST_17  C2   C3   C4  N1    180.00   0.0  0
 D8L  CONST_18  C9   C8   C5  C4    180.00   0.0  0
 D8L  CONST_19  C9   C8   C5  C6      0.00   0.0  0
 D8L  CONST_20  N1   C7   C8  C9    180.00   0.0  0
 D8L  CONST_21  H6   C7   N1  C4    180.00   0.0  0
 D8L  CONST_22  H4   C6   C5  C4    180.00   0.0  0
 D8L  CONST_23  H2   C2   C3  C4    180.00   0.0  0
 D8L  CONST_24  H1   C1   C6  C5    180.00   0.0  0
 D8L  CONST_25  H5   N1   C4  C5    180.00   0.0  0
 D8L  CONST_26  H3   C3   C4  C5    180.00   0.0  0
 D8L  Var_01    C10  C9   C8  C5     77.31  30.0  2
 D8L  Var_02    H10  C11  S1  C10  -175.97  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
 D8L  chir_01  C10  C9  C12  S1  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
 D8L  plan-1  C4   0.020
 D8L  plan-1  C5   0.020
 D8L  plan-1  C6   0.020
 D8L  plan-1  C7   0.020
 D8L  plan-1  C8   0.020
 D8L  plan-1  C9   0.020
 D8L  plan-1  N1   0.020
 D8L  plan-1  C3   0.020
 D8L  plan-1  C1   0.020
 D8L  plan-1  C2   0.020
 D8L  plan-1  H4   0.020
 D8L  plan-1  H6   0.020
 D8L  plan-1  H5   0.020
 D8L  plan-1  H3   0.020
 D8L  plan-1  H1   0.020
 D8L  plan-1  H2   0.020
 D8L  plan-2  C10  0.020
 D8L  plan-2  C12  0.020
 D8L  plan-2  O1   0.020
 D8L  plan-2  O2   0.020

