# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:36:35 2022
#   Inital geometry file: a 121 line input string
#   Ligand name: 5-[2-({(2S)-2-amino-3-[4-(trifluoromethyl)phenyl]propyl}amino)-1,3-thiazol-5-yl]-1,3-dihydro-2H-indol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](CNc1sc(cn1)c2ccc3NC(=O)Cc3c2)Cc4ccc(cc4)C(F)(F)F
#
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
 L9L  L9L  5-[2-({(2S)-2-amino-3-[4-(trifluoromethyl)phenyl]propyl}amino)-1,3-thiazol-5-yl]-1,3-dihydro-2H-indol-2-one  ligand  49  30  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L9L
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
 L9L  C1    C  CR16  0  -0.341   -6.0238  -1.6626   0.3892
 L9L  F1    F  F     0  -0.310    8.9849   1.7515   1.0516
 L9L  N1    N  NH1   0  -0.667   -0.0192  -0.2327  -0.1615
 L9L  O1    O  O     0  -0.457  -10.4369   2.0733  -0.2069
 L9L  S1    S  S2    0   0.158   -2.6038   0.5038   0.0354
 L9L  C2    C  CR16  0  -0.282   -7.4026  -1.5120   0.4649
 L9L  F2    F  F     0  -0.308    8.9840   1.7251  -1.1007
 L9L  N2    N  N     0  -0.451   -1.6778  -1.8785  -0.2660
 L9L  C3    C  CR56  0   0.399   -7.9326  -0.2678   0.1798
 L9L  F3    F  F     0  -0.317    9.7355   0.0366  -0.0030
 L9L  N3    N  NH2   0  -0.774    2.5022   0.3031   1.2971
 L9L  C4    C  CR56  0   0.025   -7.1176   0.8048  -0.1771
 L9L  N4    N  NR15  0  -0.739   -9.2569   0.1478   0.1941
 L9L  C5    C  CR16  0  -0.397   -5.7539   0.6418  -0.2641
 L9L  C6    C  CR6   0   0.144   -5.1823  -0.6086   0.0188
 L9L  C7    C  CH1   0  -0.148    2.4132  -0.4635   0.0703
 L9L  C8    C  CR5   0   0.515   -9.3909   1.4630  -0.1393
 L9L  C9    C  CR5   0  -0.280   -3.7426  -0.8187  -0.0702
 L9L  C10   C  CR15  0  -0.033   -3.0389  -1.9704  -0.2276
 L9L  C11   C  CR5   0   0.328   -1.2969  -0.6406  -0.1437
 L9L  C12   C  CH2   0  -0.238    1.0759  -1.1784  -0.1457
 L9L  C13   C  CR16  0  -0.287    5.5787  -0.6167   1.2132
 L9L  C14   C  CR16  0  -0.264    6.8224  -0.0077   1.2031
 L9L  C15   C  CR6   0  -0.216    7.4068   0.3596  -0.0047
 L9L  C16   C  CR16  0  -0.262    6.7418   0.0994  -1.1967
 L9L  C17   C  CR16  0  -0.299    5.4988  -0.5140  -1.1727
 L9L  C18   C  CR6   0   0.167    4.8974  -0.8809   0.0280
 L9L  C20   C  CH2   0  -0.516    3.5361  -1.5088   0.0344
 L9L  C21   C  CH2   0  -0.623   -7.9911   1.9967  -0.4057
 L9L  H1    H  HCR6  0   0.256   -5.5973  -2.6248   0.6416
 L9L  HN1   H  HNH1  0   0.396    0.1755   0.7302   0.0556
 L9L  H2    H  HCR6  0   0.271   -8.0302  -2.3447   0.7539
 L9L  HN3   H  HNH2  0   0.351    1.9333   1.1386   1.2669
 L9L  HN3A  H  HNH2  0   0.343    2.1787  -0.2447   2.0856
 L9L  HN4   H  HNR5  0   0.413  -10.0401  -0.4479   0.4174
 L9L  H5    H  HCR6  0   0.252   -5.1335   1.4805  -0.5597
 L9L  H7    H  HCH1  0   0.254    2.5671   0.2313  -0.7626
 L9L  H10   H  HCR5  0   0.264   -3.4972  -2.9447  -0.3359
 L9L  H12   H  HCH2  0   0.229    0.9259  -1.9164   0.6512
 L9L  H12A  H  HCH2  0   0.237    1.0989  -1.7302  -1.0897
 L9L  H13   H  HCR6  0   0.252    5.1347  -0.8933   2.1600
 L9L  H14   H  HCR6  0   0.268    7.3234   0.1798   2.1438
 L9L  H16   H  HCR6  0   0.268    7.1778   0.3661  -2.1501
 L9L  H17   H  HCR6  0   0.256    4.9919  -0.7116  -2.1095
 L9L  H20   H  HCH2  0   0.251    3.4297  -2.1696   0.8997
 L9L  H20A  H  HCH2  0   0.255    3.4155  -2.1338  -0.8538
 L9L  H21   H  HCH2  0   0.305   -7.7736   2.8254   0.2727
 L9L  H21A  H  HCH2  0   0.305   -7.9298   2.3933  -1.4219
 L9L  C19   C  CT    0   1.047    8.7698   0.9713  -0.0157

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
 L9L  C1   C2    aromatic  1.389  0.020  1.389
 L9L  C1   C6    aromatic  1.399  0.020  1.399
 L9L  C1   H1    single    0.930  0.020  1.080
 L9L  C19  F1    single    1.339  0.020  1.339
 L9L  N1   C11   single    1.341  0.020  1.341
 L9L  N1   C12   single    1.447  0.020  1.447
 L9L  N1   HN1   single    0.860  0.020  1.020
 L9L  C8   O1    double    1.213  0.020  1.213
 L9L  C11  S1    aromatic  1.746  0.020  1.746
 L9L  C9   S1    aromatic  1.748  0.020  1.748
 L9L  C2   C3    aromatic  1.382  0.020  1.382
 L9L  C2   H2    single    0.930  0.020  1.080
 L9L  C19  F2    single    1.338  0.020  1.338
 L9L  N2   C10   aromatic  1.365  0.020  1.365
 L9L  N2   C11   aromatic  1.301  0.020  1.301
 L9L  C3   C4    aromatic  1.394  0.020  1.394
 L9L  C3   N4    single    1.388  0.020  1.388
 L9L  F3   C19   single    1.344  0.020  1.344
 L9L  N3   C7    single    1.449  0.020  1.449
 L9L  N3   HN3   single    0.890  0.020  1.040
 L9L  N3   HN3A  single    0.890  0.020  1.040
 L9L  C4   C5    aromatic  1.376  0.020  1.376
 L9L  C4   C21   single    1.495  0.020  1.495
 L9L  N4   C8    single    1.363  0.020  1.363
 L9L  N4   HN4   single    0.860  0.020  1.020
 L9L  C5   C6    aromatic  1.404  0.020  1.404
 L9L  C5   H5    single    0.930  0.020  1.080
 L9L  C9   C6    single    1.458  0.020  1.458
 L9L  C7   C12   single    1.532  0.020  1.532
 L9L  C7   C20   single    1.535  0.020  1.535
 L9L  C7   H7    single    0.970  0.020  1.090
 L9L  C8   C21   single    1.522  0.020  1.522
 L9L  C10  C9    aromatic  1.359  0.020  1.359
 L9L  C10  H10   single    0.930  0.020  1.080
 L9L  C12  H12   single    0.970  0.020  1.090
 L9L  C12  H12A  single    0.970  0.020  1.090
 L9L  C13  C18   aromatic  1.392  0.020  1.392
 L9L  C13  C14   aromatic  1.385  0.020  1.385
 L9L  C13  H13   single    0.930  0.020  1.080
 L9L  C14  C15   aromatic  1.391  0.020  1.391
 L9L  C14  H14   single    0.930  0.020  1.080
 L9L  C15  C16   aromatic  1.390  0.020  1.390
 L9L  C15  C19   single    1.494  0.020  1.494
 L9L  C17  C16   aromatic  1.386  0.020  1.386
 L9L  C16  H16   single    0.930  0.020  1.080
 L9L  C18  C17   aromatic  1.392  0.020  1.392
 L9L  C17  H17   single    0.930  0.020  1.080
 L9L  C20  C18   single    1.499  0.020  1.499
 L9L  C20  H20   single    0.970  0.020  1.090
 L9L  C20  H20A  single    0.970  0.020  1.090
 L9L  C21  H21   single    0.970  0.020  1.090
 L9L  C21  H21A  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
 L9L  H1    C1   C6   119.64  3.000
 L9L  H1    C1   C2   118.35  3.000
 L9L  C6    C1   C2   122.00  3.000
 L9L  HN1   N1   C12  118.47  3.000
 L9L  HN1   N1   C11  118.20  3.000
 L9L  C12   N1   C11  121.47  3.000
 L9L  C11   S1   C9    89.17  3.000
 L9L  H2    C2   C3   121.70  3.000
 L9L  H2    C2   C1   120.46  3.000
 L9L  C3    C2   C1   117.84  3.000
 L9L  C11   N2   C10  110.69  3.000
 L9L  N4    C3   C4   109.28  3.000
 L9L  N4    C3   C2   129.29  3.000
 L9L  C4    C3   C2   121.43  3.000
 L9L  HN3A  N3   HN3  106.88  3.000
 L9L  HN3A  N3   C7   110.68  3.000
 L9L  HN3   N3   C7   112.16  3.000
 L9L  C21   C4   C5   131.58  3.000
 L9L  C21   C4   C3   108.12  3.000
 L9L  C5    C4   C3   120.30  3.000
 L9L  HN4   N4   C8   123.19  3.000
 L9L  HN4   N4   C3   124.47  3.000
 L9L  C8    N4   C3   112.34  3.000
 L9L  H5    C5   C6   120.73  3.000
 L9L  H5    C5   C4   119.51  3.000
 L9L  C6    C5   C4   119.76  3.000
 L9L  C9    C6   C5   121.22  3.000
 L9L  C9    C6   C1   120.12  3.000
 L9L  C5    C6   C1   118.66  3.000
 L9L  H7    C7   C20  108.15  3.000
 L9L  H7    C7   C12  108.15  3.000
 L9L  C20   C7   C12  108.52  3.000
 L9L  H7    C7   N3   107.42  3.000
 L9L  C20   C7   N3   109.59  3.000
 L9L  C12   C7   N3   114.82  3.000
 L9L  C21   C8   N4   106.90  3.000
 L9L  C21   C8   O1   127.38  3.000
 L9L  N4    C8   O1   125.72  3.000
 L9L  C10   C9   C6   129.84  3.000
 L9L  C10   C9   S1   108.11  3.000
 L9L  C6    C9   S1   122.05  3.000
 L9L  H10   C10  C9   123.74  3.000
 L9L  H10   C10  N2   118.69  3.000
 L9L  C9    C10  N2   117.56  3.000
 L9L  N2    C11  S1   114.46  3.000
 L9L  N2    C11  N1   124.54  3.000
 L9L  S1    C11  N1   120.99  3.000
 L9L  H12A  C12  H12  106.90  3.000
 L9L  H12A  C12  C7   109.80  3.000
 L9L  H12   C12  C7   109.33  3.000
 L9L  H12A  C12  N1   109.65  3.000
 L9L  H12   C12  N1   110.15  3.000
 L9L  C7    C12  N1   110.93  3.000
 L9L  H13   C13  C18  119.71  3.000
 L9L  H13   C13  C14  119.18  3.000
 L9L  C18   C13  C14  121.11  3.000
 L9L  H14   C14  C15  120.97  3.000
 L9L  H14   C14  C13  119.05  3.000
 L9L  C15   C14  C13  119.98  3.000
 L9L  C19   C15  C16  120.46  3.000
 L9L  C19   C15  C14  119.85  3.000
 L9L  C16   C15  C14  119.63  3.000
 L9L  H16   C16  C17  119.06  3.000
 L9L  H16   C16  C15  121.13  3.000
 L9L  C17   C16  C15  119.81  3.000
 L9L  H17   C17  C18  119.71  3.000
 L9L  H17   C17  C16  119.03  3.000
 L9L  C18   C17  C16  121.26  3.000
 L9L  C20   C18  C17  120.43  3.000
 L9L  C20   C18  C13  121.34  3.000
 L9L  C17   C18  C13  118.21  3.000
 L9L  H20A  C20  H20  106.66  3.000
 L9L  H20A  C20  C18  109.65  3.000
 L9L  H20   C20  C18  110.16  3.000
 L9L  H20A  C20  C7   109.14  3.000
 L9L  H20   C20  C7   108.77  3.000
 L9L  C18   C20  C7   112.29  3.000
 L9L  H21A  C21  H21  106.91  3.000
 L9L  H21A  C21  C8   109.99  3.000
 L9L  H21   C21  C8   109.90  3.000
 L9L  H21A  C21  C4   113.50  3.000
 L9L  H21   C21  C4   113.16  3.000
 L9L  C8    C21  C4   103.36  3.000
 L9L  C15   C19  F3   111.76  3.000
 L9L  C15   C19  F2   112.49  3.000
 L9L  F3    C19  F2   106.52  3.000
 L9L  C15   C19  F1   112.28  3.000
 L9L  F3    C19  F1   106.39  3.000
 L9L  F2    C19  F1   106.99  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
 L9L  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 L9L  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 L9L  CONST_05  C10  N2   C11  S1      0.00   0.0  0
 L9L  CONST_07  N2   C10  C9   S1      0.00   0.0  0
 L9L  CONST_08  C5   C6   C1   C2      0.00   0.0  0
 L9L  CONST_09  C9   C6   C1   C2    180.00   0.0  0
 L9L  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 L9L  CONST_11  C6   C9   C10  N2    180.00   0.0  0
 L9L  CONST_12  C9   S1   C11  N2      0.00   0.0  0
 L9L  CONST_13  C6   C1   C2   C3      0.00   0.0  0
 L9L  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 L9L  CONST_15  C9   C6   C5   C4    180.00   0.0  0
 L9L  CONST_17  C11  S1   C9   C6    180.00   0.0  0
 L9L  CONST_18  C11  N2   C10  C9      0.00   0.0  0
 L9L  CONST_19  C11  S1   C9   C10     0.00   0.0  0
 L9L  CONST_20  C16  C17  C18  C13     0.00   0.0  0
 L9L  CONST_21  C16  C15  C14  C13     0.00   0.0  0
 L9L  CONST_22  C17  C18  C13  C14     0.00   0.0  0
 L9L  CONST_23  C17  C16  C15  C14     0.00   0.0  0
 L9L  CONST_24  C18  C13  C14  C15     0.00   0.0  0
 L9L  CONST_25  C18  C17  C16  C15     0.00   0.0  0
 L9L  CONST_26  C21  C8   N4   C3      0.00   0.0  0
 L9L  CONST_27  C9   S1   C11  N1    180.00   0.0  0
 L9L  CONST_28  C10  N2   C11  N1    180.00   0.0  0
 L9L  CONST_29  C19  C15  C14  C13   180.00   0.0  0
 L9L  CONST_30  C20  C18  C13  C14   180.00   0.0  0
 L9L  CONST_31  C20  C18  C17  C16   180.00   0.0  0
 L9L  CONST_32  C19  C15  C16  C17   180.00   0.0  0
 L9L  CONST_33  C3   N4   C8   O1    180.00   0.0  0
 L9L  CONST_34  H5   C5   C6   C1    180.00   0.0  0
 L9L  CONST_35  H10  C10  C9   S1    180.00   0.0  0
 L9L  CONST_36  H1   C1   C2   C3    180.00   0.0  0
 L9L  CONST_37  H2   C2   C3   C4    180.00   0.0  0
 L9L  CONST_38  H17  C17  C18  C13   180.00   0.0  0
 L9L  CONST_39  H16  C16  C15  C14   180.00   0.0  0
 L9L  CONST_40  H13  C13  C14  C15   180.00   0.0  0
 L9L  CONST_41  H14  C14  C15  C16   180.00   0.0  0
 L9L  CONST_42  HN4  N4   C8   C21   180.00   0.0  0
 L9L  CONST_43  C12  N1   C11  S1    180.00   0.0  0
 L9L  CONST_44  C12  N1   C11  N2      0.00   0.0  0
 L9L  CONST_45  HN1  N1   C11  S1      0.00   0.0  0
 L9L  Var_01    H21  C21  C4   C3    118.64  30.0  1
 L9L  Var_02    C14  C15  C19  F1    -34.77  30.0  3
 L9L  Var_03    C13  C18  C20  C7     90.84  30.0  2
 L9L  Var_04    C11  N1   C12  C7   -170.28  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
 L9L  chir_01  C7  N3  C12  C20  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
 L9L  plan-1  N1   0.020
 L9L  plan-1  S1   0.020
 L9L  plan-1  N2   0.020
 L9L  plan-1  C6   0.020
 L9L  plan-1  C9   0.020
 L9L  plan-1  C10  0.020
 L9L  plan-1  C11  0.020
 L9L  plan-1  H10  0.020
 L9L  plan-2  C13  0.020
 L9L  plan-2  C14  0.020
 L9L  plan-2  C15  0.020
 L9L  plan-2  C16  0.020
 L9L  plan-2  C17  0.020
 L9L  plan-2  C18  0.020
 L9L  plan-2  C20  0.020
 L9L  plan-2  H13  0.020
 L9L  plan-2  H14  0.020
 L9L  plan-2  H16  0.020
 L9L  plan-2  H17  0.020
 L9L  plan-2  C19  0.020
 L9L  plan-3  N1   0.020
 L9L  plan-3  C11  0.020
 L9L  plan-3  C12  0.020
 L9L  plan-3  HN1  0.020
 L9L  plan-4  C1   0.020
 L9L  plan-4  O1   0.020
 L9L  plan-4  C2   0.020
 L9L  plan-4  C3   0.020
 L9L  plan-4  C4   0.020
 L9L  plan-4  N4   0.020
 L9L  plan-4  C5   0.020
 L9L  plan-4  C6   0.020
 L9L  plan-4  C8   0.020
 L9L  plan-4  C9   0.020
 L9L  plan-4  C21  0.020
 L9L  plan-4  H1   0.020
 L9L  plan-4  H2   0.020
 L9L  plan-4  HN4  0.020
 L9L  plan-4  H5   0.020

