# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 11:07:49 2022
#   Inital geometry file: a 85 line input string
#   Ligand name: (5S)-5-[(1H-indol-3-yl)methyl]-4-methoxy-1,5-dihydro-2H-pyrrol-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC1=CC(=O)N[C@H]1Cc2c[nH]c3ccccc23
#
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
 84N  84N  "(5S)-5-[(1H-indol-3-yl)methyl]-4-methoxy-1,5-dihydro-2H-pyrrol-2-one"
  ligand  32  18  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_84N
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
 84N  N1   N  NR15  0  -0.686  49.6993  13.6102  47.5577
 84N  C2   C  CR15  0  -0.508  49.8855  17.3177  44.8051
 84N  C4   C  CR15  0  -0.107  48.7354  15.6065  43.6788
 84N  C5   C  CH2   0  -0.553  47.9959  14.4637  44.4015
 84N  C6   C  CR5   0   0.009  48.4575  14.2458  45.8027
 84N  C8   C  CR56  0   0.349  48.6795  14.3495  48.0801
 84N  N    N  NR15  0  -0.661  50.1569  15.4063  43.6119
 84N  C3   C  CR5   0   0.518  50.8616  16.3350  44.3134
 84N  O1   O  O     0  -0.494  52.0726  16.3389  44.4737
 84N  C1   C  CR5   0   0.380  48.6658  16.9094  44.4222
 84N  O    O  O2    0  -0.435  47.4710  17.4374  44.6009
 84N  C    C  CH3   0  -0.435  47.4117  18.6281  45.3742
 84N  C9   C  CR56  0   0.030  47.8697  14.7707  47.0010
 84N  C10  C  CR16  0  -0.362  46.7320  15.5415  47.2709
 84N  C11  C  CR16  0  -0.267  46.4437  15.8776  48.5792
 84N  C12  C  CR16  0  -0.284  47.2696  15.4565  49.6350
 84N  C13  C  CR16  0  -0.303  48.3929  14.6869  49.4023
 84N  C7   C  CR15  0  -0.070  49.5645  13.5485  46.2002
 84N  H1   H  HNR5  0   0.406  50.4301  13.1640  48.0866
 84N  H4   H  HCR5  0   0.282  48.3039  15.7202  42.6776
 84N  H5   H  HCH2  0   0.257  46.9260  14.6824  44.3793
 84N  H6   H  HCH2  0   0.267  48.1285  13.5594  43.8027
 84N  H58  H  HCH3  0   0.262  46.3652  18.9139  45.4313
 84N  H59  H  HCH3  0   0.237  47.7958  18.4590  46.3823
 84N  H60  H  HCH3  0   0.241  47.9819  19.4311  44.9023
 84N  H61  H  HCR6  0   0.237  46.0839  15.8700  46.4679
 84N  H62  H  HCR6  0   0.242  45.5681  16.4753  48.7984
 84N  H63  H  HCR6  0   0.245  47.0191  15.7372  50.6500
 84N  H64  H  HCR6  0   0.255  49.0262  14.3575  50.2166
 84N  H65  H  HCR5  0   0.278  50.2791  13.0030  45.6039
 84N  H3   H  HNR5  0   0.394  50.5703  14.5570  43.2621
 84N  H2   H  HCR5  0   0.278  50.1582  18.1978  45.3667

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
 84N  N    C4   single    1.437  0.020  1.437
 84N  N    C3   single    1.361  0.020  1.361
 84N  C4   C1   single    1.502  0.020  1.502
 84N  C4   C5   single    1.541  0.020  1.541
 84N  C3   O1   double    1.222  0.020  1.222
 84N  C3   C2   single    1.470  0.020  1.470
 84N  C1   C2   double    1.342  0.020  1.342
 84N  C1   O    single    1.318  0.020  1.318
 84N  C5   C6   single    1.491  0.020  1.491
 84N  O    C    single    1.421  0.020  1.421
 84N  C6   C7   aromatic  1.367  0.020  1.367
 84N  C6   C9   aromatic  1.434  0.020  1.434
 84N  C7   N1   aromatic  1.366  0.020  1.366
 84N  C9   C10  aromatic  1.400  0.020  1.400
 84N  C9   C8   aromatic  1.413  0.020  1.413
 84N  C10  C11  aromatic  1.381  0.020  1.381
 84N  N1   C8   aromatic  1.364  0.020  1.364
 84N  C8   C13  aromatic  1.394  0.020  1.394
 84N  C11  C12  aromatic  1.405  0.020  1.405
 84N  C13  C12  aromatic  1.381  0.020  1.381
 84N  N1   H1   single    0.860  0.020  1.020
 84N  C2   H2   single    0.930  0.020  1.080
 84N  C4   H4   single    0.970  0.020  1.090
 84N  C5   H5   single    0.970  0.020  1.090
 84N  C5   H6   single    0.970  0.020  1.090
 84N  C    H58  single    0.970  0.020  1.090
 84N  C    H59  single    0.970  0.020  1.090
 84N  C    H60  single    0.970  0.020  1.090
 84N  C10  H61  single    0.930  0.020  1.080
 84N  C11  H62  single    0.930  0.020  1.080
 84N  C12  H63  single    0.930  0.020  1.080
 84N  C13  H64  single    0.930  0.020  1.080
 84N  C7   H65  single    0.930  0.020  1.080
 84N  N    H3   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
 84N  H1   N1   C7   125.04  3.000
 84N  H1   N1   C8   125.60  3.000
 84N  C7   N1   C8   109.36  3.000
 84N  H2   C2   C1   128.78  3.000
 84N  H2   C2   C3   123.48  3.000
 84N  C1   C2   C3   107.74  3.000
 84N  H4   C4   C1   110.12  3.000
 84N  H4   C4   N    111.18  3.000
 84N  C1   C4   N    100.93  3.000
 84N  H4   C4   C5   108.45  3.000
 84N  C1   C4   C5   112.89  3.000
 84N  N    C4   C5   113.15  3.000
 84N  H6   C5   H5   105.87  3.000
 84N  H6   C5   C6   110.88  3.000
 84N  H5   C5   C6   110.58  3.000
 84N  H6   C5   C4   107.37  3.000
 84N  H5   C5   C4   108.18  3.000
 84N  C6   C5   C4   113.60  3.000
 84N  C7   C6   C9   106.00  3.000
 84N  C9   C6   C5   127.20  3.000
 84N  C7   C6   C5   126.75  3.000
 84N  C13  C8   C9   122.28  3.000
 84N  C13  C8   N1   130.40  3.000
 84N  C9   C8   N1   107.31  3.000
 84N  H3   N    C3   122.82  3.000
 84N  H3   N    C4   122.66  3.000
 84N  C3   N    C4   113.16  3.000
 84N  O1   C3   N    125.69  3.000
 84N  O1   C3   C2   127.76  3.000
 84N  N    C3   C2   106.55  3.000
 84N  O    C1   C4   117.16  3.000
 84N  O    C1   C2   131.54  3.000
 84N  C4   C1   C2   111.30  3.000
 84N  C    O    C1   116.56  3.000
 84N  H60  C    H59  109.21  3.000
 84N  H60  C    H58  109.40  3.000
 84N  H59  C    H58  109.34  3.000
 84N  H60  C    O    111.05  3.000
 84N  H59  C    O    110.98  3.000
 84N  H58  C    O    106.81  3.000
 84N  C10  C9   C8   118.84  3.000
 84N  C8   C9   C6   107.10  3.000
 84N  C10  C9   C6   134.06  3.000
 84N  H61  C10  C11  120.25  3.000
 84N  H61  C10  C9   120.68  3.000
 84N  C11  C10  C9   119.08  3.000
 84N  H62  C11  C12  119.26  3.000
 84N  H62  C11  C10  119.67  3.000
 84N  C12  C11  C10  121.08  3.000
 84N  H63  C12  C13  119.38  3.000
 84N  H63  C12  C11  119.39  3.000
 84N  C13  C12  C11  121.22  3.000
 84N  H64  C13  C12  121.22  3.000
 84N  H64  C13  C8   121.28  3.000
 84N  C12  C13  C8   117.49  3.000
 84N  H65  C7   C6   129.30  3.000
 84N  H65  C7   N1   120.46  3.000
 84N  C6   C7   N1   110.24  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
 84N  CONST_01  C9   C6   C7   N1      0.00   0.0  0
 84N  CONST_02  C6   C9   C8   N1      0.00   0.0  0
 84N  CONST_03  C10  C9   C8   N1    180.00   0.0  0
 84N  CONST_04  C12  C13  C8   N1    180.00   0.0  0
 84N  CONST_05  C8   N1   C7   C6      0.00   0.0  0
 84N  CONST_06  C11  C10  C9   C6    180.00   0.0  0
 84N  CONST_07  C13  C8   C9   C6    180.00   0.0  0
 84N  CONST_08  C7   C6   C9   C8      0.00   0.0  0
 84N  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 84N  CONST_10  C11  C12  C13  C8      0.00   0.0  0
 84N  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 84N  CONST_12  C7   N1   C8   C9      0.00   0.0  0
 84N  CONST_13  C12  C13  C8   C9      0.00   0.0  0
 84N  CONST_14  C7   C6   C9   C10   180.00   0.0  0
 84N  CONST_15  C13  C8   C9   C10     0.00   0.0  0
 84N  CONST_16  C13  C12  C11  C10     0.00   0.0  0
 84N  CONST_17  C7   N1   C8   C13   180.00   0.0  0
 84N  CONST_18  C4   N    C3   C2      0.00   0.0  0
 84N  CONST_19  C5   C6   C7   N1    180.00   0.0  0
 84N  CONST_20  C10  C9   C6   C5      0.00   0.0  0
 84N  CONST_21  C8   C9   C6   C5    180.00   0.0  0
 84N  CONST_22  O1   C3   N    C4    180.00   0.0  0
 84N  CONST_23  H64  C13  C8   N1      0.00   0.0  0
 84N  CONST_24  H1   N1   C7   C6    180.00   0.0  0
 84N  CONST_25  H61  C10  C9   C6      0.00   0.0  0
 84N  CONST_26  H61  C10  C9   C8    180.00   0.0  0
 84N  CONST_27  H65  C7   N1   C8    180.00   0.0  0
 84N  CONST_28  H63  C12  C13  C8    180.00   0.0  0
 84N  CONST_29  H65  C7   C6   C9    180.00   0.0  0
 84N  CONST_30  H62  C11  C10  C9    180.00   0.0  0
 84N  CONST_31  H1   N1   C8   C9    180.00   0.0  0
 84N  CONST_32  H64  C13  C8   C9    180.00   0.0  0
 84N  CONST_33  H63  C12  C11  C10   180.00   0.0  0
 84N  CONST_34  H64  C13  C12  C11   180.00   0.0  0
 84N  CONST_35  H61  C10  C11  C12   180.00   0.0  0
 84N  CONST_36  H1   N1   C8   C13     0.00   0.0  0
 84N  CONST_37  H62  C11  C12  C13   180.00   0.0  0
 84N  CONST_38  H3   N    C3   C2    180.00   0.0  0
 84N  CONST_39  H3   N    C3   O1      0.00   0.0  0
 84N  Var_01    C3   C2   C1   C4      1.50  30.0  1
 84N  Var_02    C1   C2   C3   N       2.17  30.0  1
 84N  Var_03    C7   C6   C5   C4    -81.11  30.0  2
 84N  Var_04    C9   C6   C5   C4     95.89  30.0  2
 84N  Var_05    O    C1   C2   C3   -179.41  30.0  1
 84N  Var_06    C1   C2   C3   O1   -178.75  30.0  1
 84N  Var_07    H2   C2   C1   C4   -178.77  30.0  1
 84N  Var_08    H2   C2   C3   N    -177.58  30.0  1
 84N  Var_09    C    O    C1   C2     -2.69  30.0  3
 84N  Var_10    C    O    C1   C4    176.36  30.0  3
 84N  Var_11    H2   C2   C3   O1      1.50  30.0  1
 84N  Var_12    H2   C2   C1   O       0.32  30.0  1
 84N  Var_13    H5   C5   C6   C9    -25.96  30.0  2
 84N  Var_14    H6   C5   C6   C9   -143.09  30.0  2
 84N  Var_15    H5   C5   C6   C7    157.04  30.0  2
 84N  Var_16    H6   C5   C6   C7     39.91  30.0  2
 84N  Var_17    H58  C    O    C1   -179.24  30.0  3
 84N  Var_18    H59  C    O    C1    -60.14  30.0  3
 84N  Var_19    H60  C    O    C1     61.54  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
 84N  chir_01  C4  N  C1  C5  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
 84N  plan-1  N1   0.020
 84N  plan-1  C5   0.020
 84N  plan-1  C6   0.020
 84N  plan-1  C8   0.020
 84N  plan-1  C9   0.020
 84N  plan-1  C10  0.020
 84N  plan-1  C11  0.020
 84N  plan-1  C12  0.020
 84N  plan-1  C13  0.020
 84N  plan-1  C7   0.020
 84N  plan-1  H1   0.020
 84N  plan-1  H61  0.020
 84N  plan-1  H62  0.020
 84N  plan-1  H63  0.020
 84N  plan-1  H64  0.020
 84N  plan-1  H65  0.020
 84N  plan-2  C2   0.020
 84N  plan-2  C4   0.020
 84N  plan-2  N    0.020
 84N  plan-2  C3   0.020
 84N  plan-2  O1   0.020
 84N  plan-2  H3   0.020

