# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 01:14:48 2020
#   Inital geometry file: a 86 line input string
#   Ligand name: N-[(3R)-3-(cyanomethyl)-1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)[C@H](CC#N)c2cc(NC(C)=O)ccc12
#
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
 372  372  N-[(3R)-3-(cyanomethyl)-1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl]acetamide  ligand  31  18  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_372
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
 372  N14  N  NS    0  -0.269  -4.0069  -3.1158   0.1396
 372  C13  C  CSP   0   0.131  -3.0480  -2.5092   0.3270
 372  C12  C  CH2   0  -0.538  -1.8197  -1.7754   0.5940
 372  C7   C  CR15  0  -0.458  -1.5618  -0.6487  -0.4123
 372  C8   C  CR5   0   0.557  -2.6069   0.4598  -0.3031
 372  O11  O  O     0  -0.449  -3.8083   0.3176  -0.3904
 372  N9   N  NR5   0  -0.579  -1.9504   1.6291  -0.0740
 372  C10  C  CH3   0  -0.542  -2.5782   2.9158   0.0871
 372  C2   C  CR56  0   0.078  -0.2771   0.0807  -0.1681
 372  C1   C  CR16  0  -0.396   1.0181  -0.3862  -0.1256
 372  C3   C  CR56  0   0.400  -0.5743   1.4251   0.0132
 372  C4   C  CR16  0  -0.302   0.4264   2.3483   0.2416
 372  C5   C  CR16  0  -0.353   1.7349   1.8833   0.2870
 372  C6   C  CR6   0   0.371   2.0493   0.5340   0.1099
 372  N15  N  NH1   0  -0.738   3.4054   0.1922   0.1792
 372  C16  C  C     0   0.515   3.9995  -1.0175   0.0301
 372  O17  O  O     0  -0.479   3.3913  -2.0517  -0.1918
 372  C18  C  CH3   0  -0.782   5.5016  -0.9935   0.1556
 372  H1   H  HCH2  0   0.326  -1.8621  -1.3849   1.6126
 372  H2   H  HCH2  0   0.332  -0.9975  -2.4923   0.5591
 372  H3   H  HCR5  0   0.337  -1.5938  -1.0576  -1.4275
 372  H4   H  HCH3  0   0.257  -2.2515   3.6046  -0.6923
 372  H5   H  HCH3  0   0.270  -3.6556   2.7985   0.0217
 372  H6   H  HCH3  0   0.257  -2.3294   3.3433   1.0585
 372  H7   H  HCR6  0   0.283   1.2237  -1.4341  -0.2743
 372  H8   H  HCR6  0   0.279   0.2203   3.4008   0.3831
 372  H9   H  HCR6  0   0.276   2.5320   2.5955   0.4652
 372  H10  H  HNH1  0   0.415   4.0235   0.9684   0.3572
 372  H11  H  HCH3  0   0.254   5.9108  -0.0151   0.3984
 372  H12  H  HCH3  0   0.271   5.8088  -1.6978   0.9283
 372  H13  H  HCH3  0   0.273   5.9448  -1.3275  -0.7827

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
 372  C10  N9   single    1.441  0.020  1.441
 372  C4   C5   aromatic  1.389  0.020  1.389
 372  C4   C3   aromatic  1.381  0.020  1.381
 372  C5   C6   aromatic  1.397  0.020  1.397
 372  N9   C3   single    1.394  0.020  1.394
 372  N9   C8   single    1.360  0.020  1.360
 372  C3   C2   aromatic  1.389  0.020  1.389
 372  C6   N15  single    1.400  0.020  1.400
 372  C6   C1   aromatic  1.402  0.020  1.402
 372  C8   O11  double    1.213  0.020  1.213
 372  C8   C7   single    1.527  0.020  1.527
 372  N15  C16  single    1.356  0.020  1.356
 372  C2   C1   aromatic  1.377  0.020  1.377
 372  C2   C7   single    1.497  0.020  1.497
 372  C7   C12  single    1.532  0.020  1.532
 372  C12  C13  single    1.455  0.020  1.455
 372  C16  C18  single    1.508  0.020  1.508
 372  C16  O17  double    1.220  0.020  1.220
 372  C13  N14  triple    1.150  0.020  1.150
 372  C12  H1   single    0.970  0.020  1.090
 372  C12  H2   single    0.970  0.020  1.090
 372  C7   H3   single    0.970  0.020  1.090
 372  C10  H4   single    0.970  0.020  1.090
 372  C10  H5   single    0.970  0.020  1.090
 372  C10  H6   single    0.970  0.020  1.090
 372  C1   H7   single    0.930  0.020  1.080
 372  C4   H8   single    0.930  0.020  1.080
 372  C5   H9   single    0.930  0.020  1.080
 372  N15  H10  single    0.860  0.020  1.020
 372  C18  H11  single    0.970  0.020  1.090
 372  C18  H12  single    0.970  0.020  1.090
 372  C18  H13  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
 372  C12  C13  N14  180.00  3.000
 372  H2   C12  H1   107.10  3.000
 372  H2   C12  C7   109.58  3.000
 372  H1   C12  C7   110.87  3.000
 372  H2   C12  C13  107.38  3.000
 372  H1   C12  C13  108.58  3.000
 372  C7   C12  C13  113.10  3.000
 372  H3   C7   C2   110.99  3.000
 372  H3   C7   C8   108.50  3.000
 372  C2   C7   C8   102.82  3.000
 372  H3   C7   C12  109.23  3.000
 372  C2   C7   C12  113.29  3.000
 372  C8   C7   C12  111.81  3.000
 372  N9   C8   O11  126.22  3.000
 372  O11  C8   C7   125.98  3.000
 372  N9   C8   C7   107.80  3.000
 372  C3   N9   C10  123.64  3.000
 372  C3   N9   C8   111.17  3.000
 372  C10  N9   C8   125.18  3.000
 372  H6   C10  H5   108.81  3.000
 372  H6   C10  H4   108.73  3.000
 372  H5   C10  H4   108.82  3.000
 372  H6   C10  N9   110.51  3.000
 372  H5   C10  N9   109.22  3.000
 372  H4   C10  N9   110.72  3.000
 372  C3   C2   C1   121.69  3.000
 372  C1   C2   C7   130.29  3.000
 372  C3   C2   C7   108.01  3.000
 372  H7   C1   C6   121.39  3.000
 372  H7   C1   C2   120.30  3.000
 372  C6   C1   C2   118.31  3.000
 372  C4   C3   C2   120.92  3.000
 372  C2   C3   N9   110.17  3.000
 372  C4   C3   N9   128.91  3.000
 372  H8   C4   C5   120.05  3.000
 372  H8   C4   C3   122.29  3.000
 372  C5   C4   C3   117.66  3.000
 372  H9   C5   C6   119.35  3.000
 372  H9   C5   C4   118.57  3.000
 372  C6   C5   C4   122.08  3.000
 372  N15  C6   C5   116.59  3.000
 372  N15  C6   C1   124.08  3.000
 372  C5   C6   C1   119.33  3.000
 372  H10  N15  C16  115.96  3.000
 372  H10  N15  C6   114.49  3.000
 372  C16  N15  C6   129.55  3.000
 372  C18  C16  O17  121.69  3.000
 372  O17  C16  N15  123.90  3.000
 372  C18  C16  N15  114.41  3.000
 372  H13  C18  H12  107.32  3.000
 372  H13  C18  H11  108.35  3.000
 372  H12  C18  H11  108.48  3.000
 372  H13  C18  C16  109.18  3.000
 372  H12  C18  C16  109.24  3.000
 372  H11  C18  C16  114.06  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
 372  CONST_01  C5   C4   C3   C2      0.00   0.0  0
 372  CONST_02  C5   C6   C1   C2      0.00   0.0  0
 372  CONST_03  C4   C5   C6   C1      0.00   0.0  0
 372  CONST_04  C4   C3   C2   C1      0.00   0.0  0
 372  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 372  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 372  CONST_07  C3   N9   C8   C7      0.00   0.0  0
 372  CONST_08  N15  C6   C1   C2    180.00   0.0  0
 372  CONST_09  N15  C6   C5   C4    180.00   0.0  0
 372  CONST_10  C10  N9   C8   C7    180.00   0.0  0
 372  CONST_11  C3   N9   C8   O11   180.00   0.0  0
 372  CONST_12  H7   C1   C2   C7      0.00   0.0  0
 372  CONST_13  H8   C4   C3   N9      0.00   0.0  0
 372  CONST_14  H9   C5   C6   C1    180.00   0.0  0
 372  CONST_15  C16  N15  C6   C1      0.00   0.0  0
 372  CONST_16  C16  N15  C6   C5    180.00   0.0  0
 372  CONST_17  C10  N9   C8   O11     0.00   0.0  0
 372  CONST_18  H10  N15  C6   C1    180.00   0.0  0
 372  CONST_19  C18  C16  N15  C6    180.00   0.0  0
 372  CONST_20  O17  C16  N15  C6      0.00   0.0  0
 372  Var_01    H4   C10  N9   C8   -118.38  30.0  3
 372  Var_02    C7   C12  C13  N14   165.81  30.0  1
 372  Var_03    H11  C18  C16  N15     2.85  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
 372  chir_01  C7  C8  C2  C12  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
 372  plan-1  C6   0.020
 372  plan-1  N15  0.020
 372  plan-1  C16  0.020
 372  plan-1  O17  0.020
 372  plan-1  C18  0.020
 372  plan-1  H10  0.020
 372  plan-2  C7   0.020
 372  plan-2  C8   0.020
 372  plan-2  O11  0.020
 372  plan-2  N9   0.020
 372  plan-2  C10  0.020
 372  plan-2  C2   0.020
 372  plan-2  C1   0.020
 372  plan-2  C3   0.020
 372  plan-2  C4   0.020
 372  plan-2  C5   0.020
 372  plan-2  C6   0.020
 372  plan-2  N15  0.020
 372  plan-2  H7   0.020
 372  plan-2  H8   0.020
 372  plan-2  H9   0.020

