# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 21:58:13 2022
#   Inital geometry file: a 89 line input string
#   Ligand name: (5~{S})-5-[(1~{R})-1-(4-chloranyl-1~{H}-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC1=NC(=O)[C@@H](O1)[C@H](C)c2c[nH]c3cccc(Cl)c23
#
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
 JE0  JE0  "(5S)-5-[(1R)-1-(4-chloranyl-1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4-one"
  ligand  34  20  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JE0
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
 JE0  C10  C   CR16  0  -0.298  19.4429  51.0853  13.9576
 JE0  C11  C   CR16  0  -0.231  18.0909  50.9840  13.6010
 JE0  C12  C   CR6   0  -0.241  17.1837  50.4096  14.4653
 JE0  C13  C   CR56  0   0.173  17.5870  49.9179  15.7137
 JE0  N    N   NH1   0  -0.637  14.1109  51.2378  20.6286
 JE0  C    C   CH3   0  -0.687  15.2938  47.8327  18.0608
 JE0  O    O   O     0  -0.455  15.1098  50.7277  18.6686
 JE0  C1   C   CH1   0  -0.371  15.5041  48.9469  17.0378
 JE0  C2   C   CR15  0  -0.115  14.7202  50.2120  17.3928
 JE0  C3   C   CR5   0   0.756  14.0003  50.7800  19.4014
 JE0  C4   C   CH3   0  -0.516  12.9765  51.3511  21.5206
 JE0  C5   C   CR5   0   0.411  13.2214  49.9956  17.5799
 JE0  C6   C   CR5   0   0.056  16.9552  49.2736  16.8337
 JE0  C7   C   CR15  0  -0.071  17.9524  49.0486  17.7421
 JE0  C8   C   CR56  0   0.351  18.9636  50.0406  16.0293
 JE0  C9   C   CR16  0  -0.289  19.8980  50.6166  15.1710
 JE0  N1   N   N     0  -0.534  12.8843  50.3771  18.8430
 JE0  N2   N   NR15  0  -0.688  19.1439  49.5037  17.2657
 JE0  O1   O   O     0  -0.448  12.4802  49.5525  16.7286
 JE0  CL   CL  CL    0  -0.145  15.5225  50.3062  13.9636
 JE0  H1   H   HCR6  0   0.259  20.1351  51.5394  13.2614
 JE0  H2   H   HCR6  0   0.270  17.7597  51.3576  12.6415
 JE0  H3   H   HNH1  0   0.422  15.0219  51.5176  20.9577
 JE0  H4   H   HCH3  0   0.248  14.2423  47.5538  18.1313
 JE0  H5   H   HCH3  0   0.251  15.8454  46.9420  17.7621
 JE0  H6   H   HCH3  0   0.234  15.6325  48.1116  19.0590
 JE0  H7   H   HCH1  0   0.264  15.0799  48.6080  16.0895
 JE0  H8   H   HCR5  0   0.297  14.8974  50.9897  16.6451
 JE0  H9   H   HCH3  0   0.264  13.3261  51.7700  22.4588
 JE0  H10  H   HCH3  0   0.252  12.2141  52.0099  21.1078
 JE0  H11  H   HCH3  0   0.251  12.5293  50.3781  21.7185
 JE0  H12  H   HCR5  0   0.287  17.8996  48.5862  18.7149
 JE0  H13  H   HCR6  0   0.265  20.9411  50.6919  15.4494
 JE0  H14  H   HNR5  0   0.413  20.0248  49.4324  17.7482

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
 JE0  C11  C10  aromatic  1.402  0.020  1.402
 JE0  C11  C12  aromatic  1.378  0.020  1.378
 JE0  CL   C12  single    1.738  0.020  1.738
 JE0  C10  C9   aromatic  1.378  0.020  1.378
 JE0  C12  C13  aromatic  1.401  0.020  1.401
 JE0  C9   C8   aromatic  1.393  0.020  1.393
 JE0  C13  C8   aromatic  1.418  0.020  1.418
 JE0  C13  C6   aromatic  1.438  0.020  1.438
 JE0  C8   N2   aromatic  1.360  0.020  1.360
 JE0  C6   C1   single    1.501  0.020  1.501
 JE0  C6   C7   aromatic  1.368  0.020  1.368
 JE0  O1   C5   double    1.213  0.020  1.213
 JE0  C1   C    single    1.527  0.020  1.527
 JE0  C1   C2   single    1.530  0.020  1.530
 JE0  N2   C7   aromatic  1.362  0.020  1.362
 JE0  C2   C5   single    1.526  0.020  1.526
 JE0  C2   O    single    1.430  0.020  1.430
 JE0  C5   N1   single    1.362  0.020  1.362
 JE0  O    C3   single    1.331  0.020  1.331
 JE0  N1   C3   double    1.311  0.020  1.311
 JE0  C3   N    single    1.314  0.020  1.314
 JE0  N    C4   single    1.448  0.020  1.448
 JE0  C10  H1   single    0.930  0.020  1.080
 JE0  C11  H2   single    0.930  0.020  1.080
 JE0  N    H3   single    0.860  0.020  1.020
 JE0  C    H4   single    0.970  0.020  1.090
 JE0  C    H5   single    0.970  0.020  1.090
 JE0  C    H6   single    0.970  0.020  1.090
 JE0  C1   H7   single    0.970  0.020  1.090
 JE0  C2   H8   single    0.970  0.020  1.090
 JE0  C4   H9   single    0.970  0.020  1.090
 JE0  C4   H10  single    0.970  0.020  1.090
 JE0  C4   H11  single    0.970  0.020  1.090
 JE0  C7   H12  single    0.930  0.020  1.080
 JE0  C9   H13  single    0.930  0.020  1.080
 JE0  N2   H14  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
 JE0  H1   C10  C9   119.88  3.000
 JE0  H1   C10  C11  118.93  3.000
 JE0  C9   C10  C11  121.19  3.000
 JE0  H2   C11  C12  119.92  3.000
 JE0  H2   C11  C10  119.73  3.000
 JE0  C12  C11  C10  120.35  3.000
 JE0  CL   C12  C13  120.75  3.000
 JE0  C13  C12  C11  121.04  3.000
 JE0  CL   C12  C11  118.21  3.000
 JE0  C8   C13  C6   106.97  3.000
 JE0  C6   C13  C12  136.44  3.000
 JE0  C8   C13  C12  116.58  3.000
 JE0  H3   N    C4   119.03  3.000
 JE0  H3   N    C3   118.52  3.000
 JE0  C4   N    C3   122.45  3.000
 JE0  H6   C    H5   107.63  3.000
 JE0  H6   C    H4   107.81  3.000
 JE0  H5   C    H4   107.27  3.000
 JE0  H6   C    C1   112.57  3.000
 JE0  H5   C    C1   110.06  3.000
 JE0  H4   C    C1   111.27  3.000
 JE0  C3   O    C2   106.15  3.000
 JE0  H7   C1   C6   108.95  3.000
 JE0  H7   C1   C2   105.01  3.000
 JE0  C6   C1   C2   110.30  3.000
 JE0  H7   C1   C    107.55  3.000
 JE0  C2   C1   C    112.16  3.000
 JE0  C6   C1   C    112.51  3.000
 JE0  H8   C2   C5   110.12  3.000
 JE0  H8   C2   C1   110.27  3.000
 JE0  C5   C2   C1   114.49  3.000
 JE0  H8   C2   O    108.02  3.000
 JE0  C5   C2   O    102.08  3.000
 JE0  C1   C2   O    111.44  3.000
 JE0  N1   C3   O    117.59  3.000
 JE0  N1   C3   N    125.18  3.000
 JE0  O    C3   N    117.23  3.000
 JE0  H11  C4   H10  108.78  3.000
 JE0  H11  C4   H9   108.67  3.000
 JE0  H10  C4   H9   108.64  3.000
 JE0  H11  C4   N    111.34  3.000
 JE0  H10  C4   N    111.25  3.000
 JE0  H9   C4   N    108.09  3.000
 JE0  O1   C5   N1   127.03  3.000
 JE0  N1   C5   C2   108.49  3.000
 JE0  O1   C5   C2   124.48  3.000
 JE0  C7   C6   C1   125.36  3.000
 JE0  C7   C6   C13  105.71  3.000
 JE0  C1   C6   C13  128.89  3.000
 JE0  H12  C7   N2   120.12  3.000
 JE0  H12  C7   C6   129.35  3.000
 JE0  N2   C7   C6   110.53  3.000
 JE0  N2   C8   C9   129.37  3.000
 JE0  N2   C8   C13  107.28  3.000
 JE0  C9   C8   C13  123.36  3.000
 JE0  H13  C9   C8   121.11  3.000
 JE0  H13  C9   C10  121.40  3.000
 JE0  C8   C9   C10  117.48  3.000
 JE0  C5   N1   C3   105.69  3.000
 JE0  H14  N2   C8   125.42  3.000
 JE0  H14  N2   C7   125.05  3.000
 JE0  C8   N2   C7   109.52  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
 JE0  CONST_01  C13  C12  C11  C10     0.00   0.0  0
 JE0  CONST_02  C13  C8   C9   C10     0.00   0.0  0
 JE0  CONST_03  N2   C8   C9   C10   180.00   0.0  0
 JE0  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 JE0  CONST_05  C8   C13  C12  C11     0.00   0.0  0
 JE0  CONST_06  C6   C13  C12  C11   180.00   0.0  0
 JE0  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 JE0  CONST_08  C9   C8   C13  C12     0.00   0.0  0
 JE0  CONST_09  N2   C8   C13  C12   180.00   0.0  0
 JE0  CONST_10  C7   C6   C13  C12   180.00   0.0  0
 JE0  CONST_11  C7   N2   C8   C13     0.00   0.0  0
 JE0  CONST_12  N2   C7   C6   C13     0.00   0.0  0
 JE0  CONST_13  C9   C8   C13  C6    180.00   0.0  0
 JE0  CONST_14  N2   C8   C13  C6      0.00   0.0  0
 JE0  CONST_15  C8   N2   C7   C6      0.00   0.0  0
 JE0  CONST_16  C8   C13  C6   C7      0.00   0.0  0
 JE0  CONST_17  C9   C8   N2   C7    180.00   0.0  0
 JE0  CONST_18  C5   N1   C3   O       0.00   0.0  0
 JE0  CONST_19  CL   C12  C11  C10   180.00   0.0  0
 JE0  CONST_20  C1   C6   C13  C12     0.00   0.0  0
 JE0  CONST_21  C8   C13  C6   C1    180.00   0.0  0
 JE0  CONST_22  N2   C7   C6   C1    180.00   0.0  0
 JE0  CONST_23  CL   C12  C13  C6      0.00   0.0  0
 JE0  CONST_24  CL   C12  C13  C8    180.00   0.0  0
 JE0  CONST_25  C5   N1   C3   N     180.00   0.0  0
 JE0  CONST_26  H13  C9   C10  C11   180.00   0.0  0
 JE0  CONST_27  H1   C10  C11  C12   180.00   0.0  0
 JE0  CONST_28  H2   C11  C12  C13   180.00   0.0  0
 JE0  CONST_29  H13  C9   C8   C13   180.00   0.0  0
 JE0  CONST_30  H14  N2   C8   C13   180.00   0.0  0
 JE0  CONST_31  H12  C7   C6   C13   180.00   0.0  0
 JE0  CONST_32  H14  N2   C7   C6    180.00   0.0  0
 JE0  CONST_33  H1   C10  C9   C8    180.00   0.0  0
 JE0  CONST_34  H12  C7   N2   C8    180.00   0.0  0
 JE0  CONST_35  H2   C11  C10  C9    180.00   0.0  0
 JE0  CONST_36  H14  N2   C8   C9      0.00   0.0  0
 JE0  CONST_37  H13  C9   C8   N2      0.00   0.0  0
 JE0  CONST_38  C4   N    C3   O     180.00   0.0  0
 JE0  CONST_39  N1   C3   N    C4      0.00   0.0  0
 JE0  CONST_40  H3   N    C3   O       0.00   0.0  0
 JE0  CONST_41  H3   N    C3   N1    180.00   0.0  0
 JE0  Var_01    C3   N1   C5   C2     -0.17  30.0  1
 JE0  Var_02    N1   C3   O    C2      0.19  30.0  1
 JE0  Var_03    C2   O    C3   N    -179.54  30.0  1
 JE0  Var_04    O1   C5   N1   C3    179.63  30.0  1
 JE0  Var_05    H9   C4   N    C3   -178.92  30.0  3
 JE0  Var_06    H10  C4   N    C3    -59.71  30.0  3
 JE0  Var_07    H11  C4   N    C3     61.80  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
 JE0  chir_01  C1  C6  C   C2  negativ
 JE0  chir_02  C2  O   C1  C5  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
 JE0  plan-1  C10  0.020
 JE0  plan-1  C11  0.020
 JE0  plan-1  C12  0.020
 JE0  plan-1  C13  0.020
 JE0  plan-1  C1   0.020
 JE0  plan-1  C6   0.020
 JE0  plan-1  C7   0.020
 JE0  plan-1  C8   0.020
 JE0  plan-1  C9   0.020
 JE0  plan-1  N2   0.020
 JE0  plan-1  CL   0.020
 JE0  plan-1  H1   0.020
 JE0  plan-1  H2   0.020
 JE0  plan-1  H12  0.020
 JE0  plan-1  H13  0.020
 JE0  plan-1  H14  0.020
 JE0  plan-2  N    0.020
 JE0  plan-2  O    0.020
 JE0  plan-2  C3   0.020
 JE0  plan-2  C4   0.020
 JE0  plan-2  C5   0.020
 JE0  plan-2  N1   0.020
 JE0  plan-2  H3   0.020
 JE0  plan-3  C2   0.020
 JE0  plan-3  C5   0.020
 JE0  plan-3  N1   0.020
 JE0  plan-3  O1   0.020

