# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 17:39:36 2020
#   Inital geometry file: a 96 line input string
#   Ligand name: N-{(3R)-3-[2-(acetylamino)ethyl]-2-oxo-2,3-dihydro-1H-indol-5-yl}acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCC[C@H]1C(=O)Nc2ccc(NC(C)=O)cc12
#
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
 M49  M49  N-{(3R)-3-[2-(acetylamino)ethyl]-2-oxo-2,3-dihydro-1H-indol-5-yl}acetamide  ligand  37  20  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M49
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
 M49  O12  O  O     0  -0.481   3.0719   2.6204   0.9105
 M49  C11  C  C     0   0.511   3.9975   2.1640   0.2594
 M49  C20  C  CH3   0  -0.781   5.2647   2.9480   0.0282
 M49  N10  N  NH1   0  -0.736   3.9827   0.9369  -0.3164
 M49  C6   C  CR6   0   0.368   2.9901  -0.0522  -0.2647
 M49  C1   C  CR16  0  -0.396   1.6726   0.1850   0.1477
 M49  C2   C  CR56  0   0.086   0.7820  -0.8673   0.1421
 M49  C5   C  CR16  0  -0.354   3.3606  -1.3341  -0.6762
 M49  C4   C  CR16  0  -0.293   2.4597  -2.3913  -0.6856
 M49  C3   C  CR56  0   0.372   1.1690  -2.1379  -0.2662
 M49  N9   N  NR15  0  -0.741   0.0854  -3.0029  -0.1651
 M49  C8   C  CR5   0   0.551  -1.0321  -2.3765   0.2914
 M49  O13  O  O     0  -0.453  -2.1153  -2.8994   0.4568
 M49  C7   C  CR15  0  -0.465  -0.6654  -0.9114   0.5375
 M49  C14  C  CH2   0  -0.478  -1.5536   0.0652  -0.2406
 M49  C15  C  CH2   0  -0.237  -2.9311   0.2386   0.3798
 M49  N16  N  NH1   0  -0.636  -3.6899   1.2168  -0.3702
 M49  C17  C  C     0   0.520  -4.9807   1.4795  -0.1171
 M49  O18  O  O     0  -0.512  -5.6009   0.9087   0.7723
 M49  C19  C  CH3   0  -0.777  -5.6272   2.5080  -1.0129
 M49  H1   H  HCH3  0   0.271   5.6861   3.2412   0.9894
 M49  H2   H  HCH3  0   0.253   6.0245   2.4081  -0.5333
 M49  H3   H  HCH3  0   0.272   5.0235   3.8632  -0.5130
 M49  H4   H  HNH1  0   0.413   4.8246   0.6623  -0.7983
 M49  H5   H  HCR6  0   0.276   1.3528   1.1652   0.4642
 M49  H6   H  HCR6  0   0.273   4.3802  -1.5151  -0.9951
 M49  H7   H  HCR6  0   0.272   2.7746  -3.3747  -1.0076
 M49  H8   H  HNR5  0   0.411   0.1080  -3.9799  -0.4155
 M49  H9   H  HCR5  0   0.312  -0.7717  -0.7126   1.6113
 M49  H10  H  HCH2  0   0.262  -1.0504   1.0357  -0.2570
 M49  H11  H  HCH2  0   0.257  -1.6409  -0.2586  -1.2813
 M49  H12  H  HCH2  0   0.247  -3.4703  -0.7090   0.3947
 M49  H13  H  HCH2  0   0.233  -2.8207   0.5594   1.4206
 M49  H14  H  HNH1  0   0.401  -3.2187   1.7360  -1.0927
 M49  H15  H  HCH3  0   0.267  -6.3517   2.0141  -1.6620
 M49  H16  H  HCH3  0   0.262  -6.1729   3.2294  -0.4064
 M49  H17  H  HCH3  0   0.248  -4.9194   3.0457  -1.6411

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
 M49  C4   C5   aromatic  1.389  0.020  1.389
 M49  C4   C3   aromatic  1.381  0.020  1.381
 M49  C5   C6   aromatic  1.396  0.020  1.396
 M49  C3   N9   single    1.390  0.020  1.390
 M49  C3   C2   aromatic  1.390  0.020  1.390
 M49  C6   N10  single    1.402  0.020  1.402
 M49  C6   C1   aromatic  1.401  0.020  1.401
 M49  N9   C8   single    1.360  0.020  1.360
 M49  N10  C11  single    1.356  0.020  1.356
 M49  O12  C11  double    1.220  0.020  1.220
 M49  C2   C1   aromatic  1.379  0.020  1.379
 M49  C2   C7   single    1.501  0.020  1.501
 M49  C11  C20  single    1.508  0.020  1.508
 M49  C8   O13  double    1.214  0.020  1.214
 M49  C8   C7   single    1.530  0.020  1.530
 M49  C14  C7   single    1.532  0.020  1.532
 M49  C14  C15  single    1.521  0.020  1.521
 M49  C15  N16  single    1.447  0.020  1.447
 M49  N16  C17  single    1.341  0.020  1.341
 M49  C19  C17  single    1.509  0.020  1.509
 M49  C17  O18  double    1.225  0.020  1.225
 M49  C20  H1   single    0.970  0.020  1.090
 M49  C20  H2   single    0.970  0.020  1.090
 M49  C20  H3   single    0.970  0.020  1.090
 M49  N10  H4   single    0.860  0.020  1.020
 M49  C1   H5   single    0.930  0.020  1.080
 M49  C5   H6   single    0.930  0.020  1.080
 M49  C4   H7   single    0.930  0.020  1.080
 M49  N9   H8   single    0.860  0.020  1.020
 M49  C7   H9   single    0.970  0.020  1.090
 M49  C14  H10  single    0.970  0.020  1.090
 M49  C14  H11  single    0.970  0.020  1.090
 M49  C15  H12  single    0.970  0.020  1.090
 M49  C15  H13  single    0.970  0.020  1.090
 M49  N16  H14  single    0.860  0.020  1.020
 M49  C19  H15  single    0.970  0.020  1.090
 M49  C19  H16  single    0.970  0.020  1.090
 M49  C19  H17  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
 M49  N10  C11  C20  114.50  3.000
 M49  C20  C11  O12  121.65  3.000
 M49  N10  C11  O12  123.85  3.000
 M49  H3   C20  H2   108.35  3.000
 M49  H3   C20  H1   107.31  3.000
 M49  H2   C20  H1   108.58  3.000
 M49  H3   C20  C11  109.06  3.000
 M49  H2   C20  C11  114.07  3.000
 M49  H1   C20  C11  109.25  3.000
 M49  H4   N10  C6   114.62  3.000
 M49  H4   N10  C11  116.14  3.000
 M49  C6   N10  C11  129.09  3.000
 M49  C5   C6   C1   119.45  3.000
 M49  C1   C6   N10  123.86  3.000
 M49  C5   C6   N10  116.67  3.000
 M49  H5   C1   C2   120.22  3.000
 M49  H5   C1   C6   121.28  3.000
 M49  C2   C1   C6   118.50  3.000
 M49  C7   C2   C3   108.61  3.000
 M49  C7   C2   C1   130.11  3.000
 M49  C3   C2   C1   121.28  3.000
 M49  H6   C5   C4   118.76  3.000
 M49  H6   C5   C6   119.32  3.000
 M49  C4   C5   C6   121.92  3.000
 M49  H7   C4   C3   121.97  3.000
 M49  H7   C4   C5   120.35  3.000
 M49  C3   C4   C5   117.69  3.000
 M49  N9   C3   C4   129.54  3.000
 M49  N9   C3   C2   109.30  3.000
 M49  C4   C3   C2   121.16  3.000
 M49  H8   N9   C8   123.22  3.000
 M49  H8   N9   C3   124.54  3.000
 M49  C8   N9   C3   112.23  3.000
 M49  C7   C8   O13  127.18  3.000
 M49  C7   C8   N9   107.34  3.000
 M49  O13  C8   N9   125.48  3.000
 M49  H9   C7   C14  108.99  3.000
 M49  H9   C7   C8   107.92  3.000
 M49  C14  C7   C8   112.93  3.000
 M49  H9   C7   C2   110.23  3.000
 M49  C14  C7   C2   113.98  3.000
 M49  C8   C7   C2   102.52  3.000
 M49  H11  C14  H10  106.58  3.000
 M49  H11  C14  C15  110.47  3.000
 M49  H10  C14  C15  108.77  3.000
 M49  H11  C14  C7   109.93  3.000
 M49  H10  C14  C7   107.85  3.000
 M49  C15  C14  C7   112.99  3.000
 M49  H13  C15  H12  106.95  3.000
 M49  H13  C15  N16  110.33  3.000
 M49  H12  C15  N16  109.59  3.000
 M49  H13  C15  C14  109.26  3.000
 M49  H12  C15  C14  110.76  3.000
 M49  N16  C15  C14  109.91  3.000
 M49  H14  N16  C17  119.00  3.000
 M49  H14  N16  C15  118.36  3.000
 M49  C17  N16  C15  122.62  3.000
 M49  C19  C17  O18  122.10  3.000
 M49  O18  C17  N16  122.20  3.000
 M49  C19  C17  N16  115.70  3.000
 M49  H17  C19  H16  108.67  3.000
 M49  H17  C19  H15  108.18  3.000
 M49  H16  C19  H15  107.37  3.000
 M49  H17  C19  C17  113.62  3.000
 M49  H16  C19  C17  109.60  3.000
 M49  H15  C19  C17  109.21  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
 M49  CONST_01  C3   C4   C5   C6     0.00   0.0  0
 M49  CONST_02  C3   C2   C1   C6     0.00   0.0  0
 M49  CONST_03  C4   C5   C6   C1     0.00   0.0  0
 M49  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 M49  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 M49  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 M49  CONST_07  C7   C8   N9   C3     0.00   0.0  0
 M49  CONST_08  C4   C5   C6   N10  180.00   0.0  0
 M49  CONST_09  C2   C1   C6   N10  180.00   0.0  0
 M49  CONST_10  O13  C8   N9   C3   180.00   0.0  0
 M49  CONST_11  H7   C4   C5   C6   180.00   0.0  0
 M49  CONST_12  H6   C5   C6   C1   180.00   0.0  0
 M49  CONST_13  H5   C1   C6   C5   180.00   0.0  0
 M49  CONST_14  H8   N9   C8   C7   180.00   0.0  0
 M49  CONST_15  C5   C6   N10  C11  180.00   0.0  0
 M49  CONST_17  H4   N10  C6   C1   180.00   0.0  0
 M49  CONST_18  C6   N10  C11  O12    0.00   0.0  0
 M49  CONST_19  C6   N10  C11  C20  180.00   0.0  0
 M49  CONST_20  C19  C17  N16  C15  180.00   0.0  0
 M49  CONST_21  O18  C17  N16  C15    0.00   0.0  0
 M49  CONST_22  H14  N16  C17  O18  180.00   0.0  0
 M49  Var_01    N16  C15  C14  C7   177.41  30.0  3
 M49  Var_02    C17  N16  C15  C14  173.90  30.0  3
 M49  Var_03    H1   C20  C11  O12   55.87  30.0  3
 M49  Var_04    H15  C19  C17  N16  110.32  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
 M49  chir_01  C7  C2  C8  C14  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
 M49  plan-1  O12  0.020
 M49  plan-1  C11  0.020
 M49  plan-1  C20  0.020
 M49  plan-1  N10  0.020
 M49  plan-1  C6   0.020
 M49  plan-1  H4   0.020
 M49  plan-2  C15  0.020
 M49  plan-2  N16  0.020
 M49  plan-2  C17  0.020
 M49  plan-2  O18  0.020
 M49  plan-2  C19  0.020
 M49  plan-2  H14  0.020
 M49  plan-3  N10  0.020
 M49  plan-3  C6   0.020
 M49  plan-3  C1   0.020
 M49  plan-3  C2   0.020
 M49  plan-3  C5   0.020
 M49  plan-3  C4   0.020
 M49  plan-3  C3   0.020
 M49  plan-3  N9   0.020
 M49  plan-3  C8   0.020
 M49  plan-3  O13  0.020
 M49  plan-3  C7   0.020
 M49  plan-3  H5   0.020
 M49  plan-3  H6   0.020
 M49  plan-3  H7   0.020
 M49  plan-3  H8   0.020

