# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:29:10 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: (5R)-5-[(5-methoxy-3-oxo-1H-indazol-2-yl)methyl]-5-methyl-imidazolidine-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2NN(C[C@@]3(C)NC(=O)NC3=O)C(=O)c2c1
#
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
 724  724  (5R)-5-[(5-methoxy-3-oxo-1H-indazol-2-yl)methyl]-5-methyl-imidazolidine-2,4-dione  ligand  35  21  .  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_724
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
 724  N1    N  NR5   0  -0.381  -0.2102   0.4613   0.4452
 724  N2    N  NR15  0  -0.534   0.3160  -0.7654   0.8543
 724  C3    C  CR5   0   0.596   0.7609   1.3526   0.0828
 724  N4    N  NR15  0  -0.695  -4.5641  -0.6232   0.2845
 724  C5    C  CR5   0   0.588  -3.9739   0.5995   0.3366
 724  C6    C  CR5   0  -0.061  -2.5795   0.4297  -0.2582
 724  N7    N  NR15  0  -0.668  -2.5560  -0.9928  -0.5378
 724  C8    C  CR5   0   0.672  -3.7513  -1.5908  -0.2968
 724  O9    O  O     0  -0.464  -4.0742  -2.7325  -0.5241
 724  C11   C  CH3   0  -0.639  -2.4169   1.2646  -1.5219
 724  C12   C  CH2   0  -0.269  -1.5525   0.8055   0.8236
 724  C13   C  CR56  0  -0.168   1.9991   0.5796   0.1245
 724  C14   C  CR56  0   0.367   1.6689  -0.6988   0.5499
 724  C15   C  CR16  0  -0.277   2.6415  -1.6830   0.6449
 724  C16   C  CR16  0  -0.377   3.9442  -1.3384   0.3225
 724  C17   C  CR6   0   0.389   4.2862  -0.0357  -0.0824
 724  C18   C  CR16  0  -0.411   3.3015   0.9382  -0.1849
 724  O19   O  O     0  -0.488   0.5744   2.5303  -0.1838
 724  O20   O  O2    0  -0.476   5.5428   0.3452  -0.3936
 724  C21   C  CH3   0  -0.439   6.5788  -0.6140  -0.3381
 724  HN2   H  HNR5  0   0.402  -0.1889  -1.5499   0.4568
 724  HN4   H  HNR5  0   0.432  -5.4996  -0.8213   0.6118
 724  HN7   H  HNR5  0   0.418  -1.9498  -1.3827  -1.2443
 724  H11   H  HCH3  0   0.253  -2.4963   2.3265  -1.2955
 724  H11A  H  HCH3  0   0.258  -1.4392   1.0843  -1.9681
 724  H11B  H  HCH3  0   0.259  -3.1780   1.0078  -2.2585
 724  H12   H  HCH2  0   0.294  -1.7865   0.2957   1.7600
 724  H12A  H  HCH2  0   0.283  -1.5984   1.8791   1.0062
 724  H15   H  HCR6  0   0.281   2.4045  -2.6911   0.9576
 724  H16   H  HCR6  0   0.290   4.7014  -2.1068   0.3941
 724  H18   H  HCR6  0   0.269   3.5474   1.9434  -0.5044
 724  H21   H  HCH3  0   0.261   7.4907  -0.0995  -0.6313
 724  H21A  H  HCH3  0   0.228   6.7135  -1.0164   0.6696
 724  H21B  H  HCH3  0   0.228   6.4068  -1.4437  -1.0290
 724  O10   O  O     0  -0.421  -4.4404   1.6203   0.7791

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
 724  N1   N2    single    1.396  0.020  1.396
 724  N1   C3    single    1.367  0.020  1.367
 724  N1   C12   single    1.436  0.020  1.436
 724  N2   C14   single    1.388  0.020  1.388
 724  C3   C13   single    1.460  0.020  1.460
 724  C3   O19   double    1.222  0.020  1.222
 724  N4   C5    single    1.359  0.020  1.359
 724  N4   C8    single    1.391  0.020  1.391
 724  C5   C6    single    1.525  0.020  1.525
 724  C5   O10   double    1.206  0.020  1.206
 724  C6   N7    single    1.450  0.020  1.450
 724  C6   C11   single    1.523  0.020  1.523
 724  C6   C12   single    1.538  0.020  1.538
 724  N7   C8    single    1.358  0.020  1.358
 724  C8   O9    double    1.208  0.020  1.208
 724  C13  C14   aromatic  1.387  0.020  1.387
 724  C13  C18   aromatic  1.386  0.020  1.386
 724  C14  C15   aromatic  1.387  0.020  1.387
 724  C15  C16   aromatic  1.385  0.020  1.385
 724  C16  C17   aromatic  1.406  0.020  1.406
 724  C17  C18   aromatic  1.389  0.020  1.389
 724  C17  O20   single    1.350  0.020  1.350
 724  O20  C21   single    1.413  0.020  1.413
 724  N2   HN2   single    0.890  0.020  1.040
 724  N4   HN4   single    0.860  0.020  1.020
 724  N7   HN7   single    0.890  0.020  1.040
 724  C11  H11   single    0.970  0.020  1.090
 724  C11  H11A  single    0.970  0.020  1.090
 724  C11  H11B  single    0.970  0.020  1.090
 724  C12  H12   single    0.970  0.020  1.090
 724  C12  H12A  single    0.970  0.020  1.090
 724  C15  H15   single    0.930  0.020  1.080
 724  C16  H16   single    0.930  0.020  1.080
 724  C18  H18   single    0.930  0.020  1.080
 724  C21  H21   single    0.970  0.020  1.090
 724  C21  H21A  single    0.970  0.020  1.090
 724  C21  H21B  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
 724  C12   N1   C3    125.27  3.000
 724  C12   N1   N2    119.05  3.000
 724  C3    N1   N2    112.51  3.000
 724  HN2   N2   C14   115.87  3.000
 724  HN2   N2   N1    112.17  3.000
 724  C14   N2   N1    105.13  3.000
 724  O19   C3   C13   130.23  3.000
 724  O19   C3   N1    125.30  3.000
 724  C13   C3   N1    104.45  3.000
 724  HN4   N4   C8    122.68  3.000
 724  HN4   N4   C5    124.47  3.000
 724  C8    N4   C5    112.84  3.000
 724  O10   C5   C6    126.21  3.000
 724  O10   C5   N4    127.41  3.000
 724  C6    C5   N4    106.38  3.000
 724  C12   C6   C11   112.23  3.000
 724  C12   C6   N7    111.38  3.000
 724  C11   C6   N7    112.09  3.000
 724  C12   C6   C5    107.99  3.000
 724  C11   C6   C5    111.10  3.000
 724  N7    C6   C5    101.49  3.000
 724  HN7   N7   C8    118.87  3.000
 724  HN7   N7   C6    121.58  3.000
 724  C8    N7   C6    112.55  3.000
 724  O9    C8   N7    128.17  3.000
 724  O9    C8   N4    125.44  3.000
 724  N7    C8   N4    106.39  3.000
 724  H11B  C11  H11A  108.11  3.000
 724  H11B  C11  H11   108.63  3.000
 724  H11A  C11  H11   108.17  3.000
 724  H11B  C11  C6    110.92  3.000
 724  H11A  C11  C6    110.17  3.000
 724  H11   C11  C6    110.75  3.000
 724  H12A  C12  H12   107.89  3.000
 724  H12A  C12  C6    109.29  3.000
 724  H12   C12  C6    110.25  3.000
 724  H12A  C12  N1    108.63  3.000
 724  H12   C12  N1    108.32  3.000
 724  C6    C12  N1    112.34  3.000
 724  C18   C13  C14   122.05  3.000
 724  C18   C13  C3    130.81  3.000
 724  C14   C13  C3    107.14  3.000
 724  C15   C14  C13   120.53  3.000
 724  C15   C14  N2    129.37  3.000
 724  C13   C14  N2    110.08  3.000
 724  H15   C15  C16   120.33  3.000
 724  H15   C15  C14   121.83  3.000
 724  C16   C15  C14   117.83  3.000
 724  H16   C16  C17   120.47  3.000
 724  H16   C16  C15   117.80  3.000
 724  C17   C16  C15   121.74  3.000
 724  O20   C17  C18   116.44  3.000
 724  O20   C17  C16   123.66  3.000
 724  C18   C17  C16   119.90  3.000
 724  H18   C18  C17   120.78  3.000
 724  H18   C18  C13   121.29  3.000
 724  C17   C18  C13   117.93  3.000
 724  C21   O20  C17   118.82  3.000
 724  H21B  C21  H21A  108.81  3.000
 724  H21B  C21  H21   108.70  3.000
 724  H21A  C21  H21   108.63  3.000
 724  H21B  C21  O20   112.03  3.000
 724  H21A  C21  O20   112.11  3.000
 724  H21   C21  O20   106.45  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
 724  CONST_01  C16  C15  C14  C13    0.00   0.0  0
 724  CONST_02  C16  C17  C18  C13    0.00   0.0  0
 724  CONST_03  C17  C18  C13  C14    0.00   0.0  0
 724  CONST_04  C17  C16  C15  C14    0.00   0.0  0
 724  CONST_05  C18  C13  C14  C15    0.00   0.0  0
 724  CONST_06  C18  C17  C16  C15    0.00   0.0  0
 724  CONST_07  C13  C3   N1   N2     0.00   0.0  0
 724  CONST_08  C6   N7   C8   N4     0.00   0.0  0
 724  CONST_09  N7   C8   N4   C5     0.00   0.0  0
 724  CONST_10  C8   N4   C5   C6     0.00   0.0  0
 724  CONST_11  O20  C17  C18  C13  180.00   0.0  0
 724  CONST_12  O20  C17  C16  C15  180.00   0.0  0
 724  CONST_13  O19  C3   N1   N2   180.00   0.0  0
 724  CONST_14  O9   C8   N4   C5   180.00   0.0  0
 724  CONST_15  O9   C8   N7   C6   180.00   0.0  0
 724  CONST_16  O10  C5   N4   C8   180.00   0.0  0
 724  CONST_17  C13  C3   N1   C12  180.00   0.0  0
 724  CONST_18  H15  C15  C14  N2     0.00   0.0  0
 724  CONST_19  H18  C18  C13  C3     0.00   0.0  0
 724  CONST_20  H16  C16  C15  C14  180.00   0.0  0
 724  CONST_22  HN4  N4   C5   C6   180.00   0.0  0
 724  CONST_23  O19  C3   N1   C12    0.00   0.0  0
 724  Var_01    C6   C12  N1   N2   -94.15  30.0  3
 724  Var_02    H21  C21  O20  C17  179.52  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
 724  chir_01  C6  N7  C5  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
 724  plan-1  N1   0.020
 724  plan-1  N2   0.020
 724  plan-1  C3   0.020
 724  plan-1  C12  0.020
 724  plan-1  C13  0.020
 724  plan-1  C14  0.020
 724  plan-1  C15  0.020
 724  plan-1  C16  0.020
 724  plan-1  C17  0.020
 724  plan-1  C18  0.020
 724  plan-1  O19  0.020
 724  plan-1  O20  0.020
 724  plan-1  HN2  0.020
 724  plan-1  H15  0.020
 724  plan-1  H16  0.020
 724  plan-1  H18  0.020
 724  plan-2  N4   0.020
 724  plan-2  C5   0.020
 724  plan-2  C6   0.020
 724  plan-2  N7   0.020
 724  plan-2  C8   0.020
 724  plan-2  O9   0.020
 724  plan-2  HN4  0.020
 724  plan-2  HN7  0.020
 724  plan-2  O10  0.020

