# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 23:28:29 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: (5~{S})-2-(methylamino)-5-[(1~{R})-1-(4-methyl-1~{H}-indol-3-yl)ethyl]-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(C)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
 J9L  J9L  "(5S)-2-(methylamino)-5-[(1R)-1-(4-methyl-1H-indol-3-yl)ethyl]-1,3-oxazol-4-one"
  ligand  37  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
;

data_comp_J9L
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
 J9L  C4   C  CH3   0  -0.516  12.8311  51.1813  21.3691
 J9L  C5   C  CR5   0   0.411  13.2387  49.8673  17.4267
 J9L  C3   C  CR5   0   0.757  13.9394  50.6367  19.2852
 J9L  N    N  NH1   0  -0.638  13.9998  51.0807  20.5206
 J9L  C2   C  CR15  0  -0.117  14.7432  50.0871  17.3041
 J9L  C1   C  CH1   0  -0.385  15.5416  48.8243  16.9741
 J9L  C    C  CH3   0  -0.679  15.3156  47.7154  18.0005
 J9L  O    O  O     0  -0.455  15.0779  50.5974  18.5971
 J9L  C10  C  CR16  0  -0.270  19.5333  50.7078  13.8255
 J9L  C11  C  CR16  0  -0.331  18.1996  50.5003  13.4396
 J9L  C12  C  CR6   0   0.002  17.2445  49.9927  14.3042
 J9L  C13  C  CH3   0  -0.768  15.8437  49.7655  13.8151
 J9L  C14  C  CR56  0   0.016  17.6513  49.6880  15.6213
 J9L  C6   C  CR5   0   0.029  16.9933  49.1585  16.7890
 J9L  C7   C  CR15  0  -0.078  17.9510  49.0771  17.7616
 J9L  C8   C  CR56  0   0.361  19.0031  49.8980  15.9823
 J9L  C9   C  CR16  0  -0.322  19.9573  50.4055  15.1008
 J9L  N1   N  N     0  -0.535  12.8482  50.2358  18.6783
 J9L  N2   N  NR15  0  -0.689  19.1482  49.5179  17.2822
 J9L  H1   H  HCH3  0   0.264  13.1455  51.5767  22.3295
 J9L  H2   H  HCH3  0   0.252  12.0892  51.8539  20.9412
 J9L  H3   H  HCH3  0   0.252  12.3715  50.2068  21.5268
 J9L  H4   H  HNH1  0   0.422  14.8960  51.3605  20.8881
 J9L  H5   H  HCR5  0   0.303  14.9513  50.8708  16.5695
 J9L  H6   H  HCH1  0   0.272  15.1332  48.4750  16.0231
 J9L  H7   H  HCH3  0   0.244  14.2642  47.4316  18.0562
 J9L  H8   H  HCH3  0   0.250  15.8767  46.8265  17.7151
 J9L  H9   H  HCH3  0   0.234  15.6379  48.0011  19.0018
 J9L  H11  H  HCR6  0   0.236  17.9074  50.7430  12.4246
 J9L  H12  H  HCH3  0   0.245  15.5670  48.7107  13.8601
 J9L  H13  H  HCH3  0   0.242  15.1039  50.3148  14.3988
 J9L  H14  H  HCH3  0   0.256  15.7403  50.0851  12.7787
 J9L  H15  H  HCR5  0   0.280  17.8685  48.7314  18.7799
 J9L  H16  H  HCR6  0   0.254  20.9845  50.5548  15.4086
 J9L  H17  H  HNR5  0   0.406  20.0078  49.5388  17.8051
 J9L  O1   O  O     0  -0.447  12.5362  49.4300  16.5400
 J9L  H10  H  HCR6  0   0.244  20.2367  51.1072  13.1063

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
 J9L  C11  C10  aromatic  1.404  0.020  1.404
 J9L  C11  C12  aromatic  1.385  0.020  1.385
 J9L  C13  C12  single    1.501  0.020  1.501
 J9L  C10  C9   aromatic  1.378  0.020  1.378
 J9L  C12  C14  aromatic  1.412  0.020  1.412
 J9L  C9   C8   aromatic  1.395  0.020  1.395
 J9L  C14  C8   aromatic  1.415  0.020  1.415
 J9L  C14  C6   aromatic  1.441  0.020  1.441
 J9L  C8   N2   aromatic  1.362  0.020  1.362
 J9L  C6   C1   single    1.501  0.020  1.501
 J9L  C6   C7   aromatic  1.367  0.020  1.367
 J9L  C1   C    single    1.528  0.020  1.528
 J9L  C1   C2   single    1.530  0.020  1.530
 J9L  O1   C5   double    1.213  0.020  1.213
 J9L  N2   C7   aromatic  1.363  0.020  1.363
 J9L  C2   C5   single    1.525  0.020  1.525
 J9L  C2   O    single    1.430  0.020  1.430
 J9L  C5   N1   single    1.362  0.020  1.362
 J9L  O    C3   single    1.331  0.020  1.331
 J9L  N1   C3   double    1.311  0.020  1.311
 J9L  C3   N    single    1.314  0.020  1.314
 J9L  N    C4   single    1.448  0.020  1.448
 J9L  C4   H1   single    0.970  0.020  1.090
 J9L  C4   H2   single    0.970  0.020  1.090
 J9L  C4   H3   single    0.970  0.020  1.090
 J9L  N    H4   single    0.860  0.020  1.020
 J9L  C2   H5   single    0.970  0.020  1.090
 J9L  C1   H6   single    0.970  0.020  1.090
 J9L  C    H7   single    0.970  0.020  1.090
 J9L  C    H8   single    0.970  0.020  1.090
 J9L  C    H9   single    0.970  0.020  1.090
 J9L  C10  H10  single    0.930  0.020  1.080
 J9L  C11  H11  single    0.930  0.020  1.080
 J9L  C13  H12  single    0.970  0.020  1.090
 J9L  C13  H13  single    0.970  0.020  1.090
 J9L  C13  H14  single    0.970  0.020  1.090
 J9L  C7   H15  single    0.930  0.020  1.080
 J9L  C9   H16  single    0.930  0.020  1.080
 J9L  N2   H17  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
 J9L  H3   C4   H2   108.79  3.000
 J9L  H3   C4   H1   108.67  3.000
 J9L  H2   C4   H1   108.67  3.000
 J9L  H3   C4   N    111.31  3.000
 J9L  H2   C4   N    111.26  3.000
 J9L  H1   C4   N    108.07  3.000
 J9L  N1   C5   O1   127.11  3.000
 J9L  N1   C5   C2   108.52  3.000
 J9L  O1   C5   C2   124.37  3.000
 J9L  N1   C3   O    117.61  3.000
 J9L  N1   C3   N    125.21  3.000
 J9L  O    C3   N    117.17  3.000
 J9L  H4   N    C3   118.51  3.000
 J9L  H4   N    C4   118.99  3.000
 J9L  C3   N    C4   122.50  3.000
 J9L  H5   C2   O    107.88  3.000
 J9L  H5   C2   C1   110.31  3.000
 J9L  O    C2   C1   111.56  3.000
 J9L  H5   C2   C5   110.17  3.000
 J9L  O    C2   C5   102.10  3.000
 J9L  C1   C2   C5   114.40  3.000
 J9L  H6   C1   C6   108.99  3.000
 J9L  H6   C1   C    107.30  3.000
 J9L  C6   C1   C    112.80  3.000
 J9L  H6   C1   C2   104.87  3.000
 J9L  C    C1   C2   112.15  3.000
 J9L  C6   C1   C2   110.33  3.000
 J9L  H9   C    H8   107.59  3.000
 J9L  H9   C    H7   107.84  3.000
 J9L  H8   C    H7   107.32  3.000
 J9L  H9   C    C1   112.53  3.000
 J9L  H8   C    C1   109.89  3.000
 J9L  H7   C    C1   111.46  3.000
 J9L  C2   O    C3   106.13  3.000
 J9L  H10  C10  C9   119.74  3.000
 J9L  H10  C10  C11  119.30  3.000
 J9L  C9   C10  C11  120.96  3.000
 J9L  H11  C11  C12  118.74  3.000
 J9L  H11  C11  C10  118.72  3.000
 J9L  C12  C11  C10  122.54  3.000
 J9L  C14  C12  C13  122.70  3.000
 J9L  C14  C12  C11  117.57  3.000
 J9L  C13  C12  C11  119.72  3.000
 J9L  H14  C13  H13  107.28  3.000
 J9L  H14  C13  H12  107.38  3.000
 J9L  H13  C13  H12  107.02  3.000
 J9L  H14  C13  C12  110.74  3.000
 J9L  H13  C13  C12  112.48  3.000
 J9L  H12  C13  C12  111.68  3.000
 J9L  C8   C14  C6   106.50  3.000
 J9L  C6   C14  C12  134.72  3.000
 J9L  C8   C14  C12  118.77  3.000
 J9L  C7   C6   C14  106.16  3.000
 J9L  C7   C6   C1   125.20  3.000
 J9L  C14  C6   C1   128.56  3.000
 J9L  H15  C7   N2   120.20  3.000
 J9L  H15  C7   C6   129.57  3.000
 J9L  N2   C7   C6   110.23  3.000
 J9L  N2   C8   C9   129.19  3.000
 J9L  N2   C8   C14  107.69  3.000
 J9L  C9   C8   C14  123.12  3.000
 J9L  H16  C9   C8   121.31  3.000
 J9L  H16  C9   C10  121.67  3.000
 J9L  C8   C9   C10  117.03  3.000
 J9L  C3   N1   C5   105.63  3.000
 J9L  H17  N2   C8   125.52  3.000
 J9L  H17  N2   C7   125.05  3.000
 J9L  C8   N2   C7   109.41  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
 J9L  CONST_01  C14  C12  C11  C10     0.00   0.0  0
 J9L  CONST_02  C14  C8   C9   C10     0.00   0.0  0
 J9L  CONST_03  N2   C8   C9   C10   180.00   0.0  0
 J9L  CONST_04  C8   C9   C10  C11     0.00   0.0  0
 J9L  CONST_05  C8   C14  C12  C11     0.00   0.0  0
 J9L  CONST_06  C6   C14  C12  C11   180.00   0.0  0
 J9L  CONST_07  C9   C10  C11  C12     0.00   0.0  0
 J9L  CONST_08  C9   C8   C14  C12     0.00   0.0  0
 J9L  CONST_09  N2   C8   C14  C12   180.00   0.0  0
 J9L  CONST_10  C7   C6   C14  C12   180.00   0.0  0
 J9L  CONST_11  C7   N2   C8   C14     0.00   0.0  0
 J9L  CONST_12  N2   C7   C6   C14     0.00   0.0  0
 J9L  CONST_13  C9   C8   C14  C6    180.00   0.0  0
 J9L  CONST_14  N2   C8   C14  C6      0.00   0.0  0
 J9L  CONST_15  C8   N2   C7   C6      0.00   0.0  0
 J9L  CONST_16  C8   C14  C6   C7      0.00   0.0  0
 J9L  CONST_17  C9   C8   N2   C7    180.00   0.0  0
 J9L  CONST_18  O    C3   N1   C5      0.00   0.0  0
 J9L  CONST_19  C12  C14  C6   C1      0.00   0.0  0
 J9L  CONST_20  C8   C14  C6   C1    180.00   0.0  0
 J9L  CONST_21  N2   C7   C6   C1    180.00   0.0  0
 J9L  CONST_22  C13  C12  C11  C10   180.00   0.0  0
 J9L  CONST_23  C8   C14  C12  C13   180.00   0.0  0
 J9L  CONST_24  C6   C14  C12  C13     0.00   0.0  0
 J9L  CONST_25  N    C3   N1   C5    180.00   0.0  0
 J9L  CONST_26  H16  C9   C10  C11   180.00   0.0  0
 J9L  CONST_27  H10  C10  C11  C12   180.00   0.0  0
 J9L  CONST_28  H11  C11  C12  C14   180.00   0.0  0
 J9L  CONST_29  H16  C9   C8   C14   180.00   0.0  0
 J9L  CONST_30  H17  N2   C8   C14   180.00   0.0  0
 J9L  CONST_31  H15  C7   C6   C14   180.00   0.0  0
 J9L  CONST_32  H17  N2   C7   C6    180.00   0.0  0
 J9L  CONST_33  H10  C10  C9   C8    180.00   0.0  0
 J9L  CONST_34  H15  C7   N2   C8    180.00   0.0  0
 J9L  CONST_35  H11  C11  C10  C9    180.00   0.0  0
 J9L  CONST_36  H17  N2   C8   C9      0.00   0.0  0
 J9L  CONST_37  H16  C9   C8   N2      0.00   0.0  0
 J9L  CONST_38  O    C3   N    C4    180.00   0.0  0
 J9L  CONST_39  N1   C3   N    C4      0.00   0.0  0
 J9L  CONST_40  H4   N    C3   O       0.00   0.0  0
 J9L  CONST_41  H4   N    C3   N1    180.00   0.0  0
 J9L  Var_01    C2   C5   N1   C3     -0.05  30.0  1
 J9L  Var_02    N1   C3   O    C2     -0.16  30.0  1
 J9L  Var_03    O1   C5   N1   C3    179.65  30.0  1
 J9L  Var_04    C2   O    C3   N    -179.90  30.0  1
 J9L  Var_05    H12  C13  C12  C11   117.43  30.0  2
 J9L  Var_06    H13  C13  C12  C11  -122.22  30.0  2
 J9L  Var_07    H14  C13  C12  C11    -2.20  30.0  2
 J9L  Var_08    H12  C13  C12  C14   -61.46  30.0  2
 J9L  Var_09    H13  C13  C12  C14    58.90  30.0  2
 J9L  Var_10    H14  C13  C12  C14   178.92  30.0  2
 J9L  Var_11    H1   C4   N    C3   -179.74  30.0  3
 J9L  Var_12    H2   C4   N    C3    -60.51  30.0  3
 J9L  Var_13    H3   C4   N    C3     61.01  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
 J9L  chir_01  C2  C1  C5  O   negativ
 J9L  chir_02  C1  C2  C   C6  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
 J9L  plan-1  C1   0.020
 J9L  plan-1  C10  0.020
 J9L  plan-1  C11  0.020
 J9L  plan-1  C12  0.020
 J9L  plan-1  C13  0.020
 J9L  plan-1  C14  0.020
 J9L  plan-1  C6   0.020
 J9L  plan-1  C7   0.020
 J9L  plan-1  C8   0.020
 J9L  plan-1  C9   0.020
 J9L  plan-1  N2   0.020
 J9L  plan-1  H11  0.020
 J9L  plan-1  H15  0.020
 J9L  plan-1  H16  0.020
 J9L  plan-1  H17  0.020
 J9L  plan-1  H10  0.020
 J9L  plan-2  C4   0.020
 J9L  plan-2  C5   0.020
 J9L  plan-2  C3   0.020
 J9L  plan-2  N    0.020
 J9L  plan-2  O    0.020
 J9L  plan-2  N1   0.020
 J9L  plan-2  H4   0.020
 J9L  plan-3  C5   0.020
 J9L  plan-3  C2   0.020
 J9L  plan-3  N1   0.020
 J9L  plan-3  O1   0.020

