# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Aug  1 13:10:27 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: (3~{S})-6-chloranyl-3'-(1,2-oxazol-3-ylmethyl)spiro[1,2-dihydroindene-3,5'-imidazolidine]-2',4'-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Clc1ccc2c(CC[C@]23NC(=O)N(Cc4ccon4)C3=O)c1
#
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
 RY5  RY5  "(3~{S})-6-chloranyl-3'-(1,2-oxazol-3-ylmethyl)spiro[1,2-dihydroindene-3,5'-imidazolidine]-2',4'-dione"
  ligand  34  22  .  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_RY5
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
 RY5  C1   C   CR6   0  -0.035  12.4631  -0.5451  23.3102
 RY5  C10  C   CH2   0  -0.398   6.8784  -0.8197  18.9120
 RY5  C11  C   CR5   0   0.276   6.0020   0.3507  18.6063
 RY5  C12  C   CR15  0  -0.478   4.8959   0.8337  19.3523
 RY5  C13  C   CR15  0   0.103   4.4600   1.8736  18.6096
 RY5  C14  C   CR5   0   0.589   8.1985   0.0899  20.7993
 RY5  C15  C   CR16  0  -0.281  11.7183   0.5941  23.5837
 RY5  C2   C   CR16  0  -0.217  11.9099  -1.6578  22.6882
 RY5  C3   C   CR16  0  -0.316  10.5708  -1.6361  22.3225
 RY5  C4   C   CR56  0   0.174   9.8227  -0.5051  22.5946
 RY5  C5   C   CR56  0   0.092  10.3825   0.6010  23.2163
 RY5  C6   C   CH2   0  -0.496   9.3636   1.6906  23.3941
 RY5  C7   C   CH2   0  -0.451   8.0326   0.9580  23.1797
 RY5  C8   C   C     0  -0.059   8.3703  -0.2492  22.2767
 RY5  C9   C   CR5   0   0.714   6.8723  -1.7193  21.2600
 RY5  N1   N   NR15  0  -0.692   7.4967  -1.3814  22.4036
 RY5  N2   N   NR5   0  -0.557   7.3166  -0.8118  20.2858
 RY5  N3   N   N     0  -0.170   6.1890   1.0549  17.5294
 RY5  O1   O   O     0  -0.461   6.0830  -2.6122  21.0614
 RY5  O2   O   O     0  -0.313   5.2207   2.0082  17.5240
 RY5  O3   O   O     0  -0.408   8.7353   0.9859  20.1971
 RY5  CL1  CL  CL    0  -0.125  14.1346  -0.5856  23.7706
 RY5  H1   H   HCH2  0   0.305   6.3291  -1.7466  18.7465
 RY5  H2   H   HCH2  0   0.301   7.7416  -0.8266  18.2464
 RY5  H3   H   HCR5  0   0.287   4.4984   0.4620  20.2814
 RY5  H4   H   HCR5  0   0.309   3.6509   2.5775  18.7292
 RY5  H5   H   HCR6  0   0.275  12.1693   1.4457  24.0767
 RY5  H6   H   HCR6  0   0.280  12.5154  -2.5328  22.4946
 RY5  H7   H   HCR6  0   0.266  10.1287  -2.5004  21.8423
 RY5  H8   H   HCH2  0   0.265   9.4208   2.1670  24.3730
 RY5  H9   H   HCH2  0   0.266   9.5115   2.4732  22.6470
 RY5  H10  H   HCH2  0   0.267   7.2480   1.5882  22.7621
 RY5  H11  H   HCH2  0   0.274   7.6694   0.5645  24.1312
 RY5  H12  H   HNR5  0   0.414   7.3465  -1.8762  23.2690

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
 RY5  O2   N3   aromatic  1.359  0.020  1.359
 RY5  O2   C13  aromatic  1.332  0.020  1.332
 RY5  N3   C11  aromatic  1.300  0.020  1.300
 RY5  C13  C12  aromatic  1.350  0.020  1.350
 RY5  C11  C10  single    1.494  0.020  1.494
 RY5  C11  C12  aromatic  1.419  0.020  1.419
 RY5  C10  N2   single    1.442  0.020  1.442
 RY5  O3   C14  double    1.206  0.020  1.206
 RY5  N2   C14  single    1.362  0.020  1.362
 RY5  N2   C9   single    1.404  0.020  1.404
 RY5  C14  C8   single    1.526  0.020  1.526
 RY5  O1   C9   double    1.208  0.020  1.208
 RY5  C9   N1   single    1.346  0.020  1.346
 RY5  C3   C2   aromatic  1.388  0.020  1.388
 RY5  C3   C4   aromatic  1.383  0.020  1.383
 RY5  C2   C1   aromatic  1.390  0.020  1.390
 RY5  C8   N1   single    1.436  0.020  1.436
 RY5  C8   C4   single    1.509  0.020  1.509
 RY5  C8   C7   single    1.545  0.020  1.545
 RY5  C4   C5   aromatic  1.387  0.020  1.387
 RY5  C1   CL1  single    1.734  0.020  1.734
 RY5  C1   C15  aromatic  1.388  0.020  1.388
 RY5  C5   C15  aromatic  1.385  0.020  1.385
 RY5  C5   C6   single    1.502  0.020  1.502
 RY5  C7   C6   single    1.534  0.020  1.534
 RY5  C10  H1   single    0.970  0.020  1.090
 RY5  C10  H2   single    0.970  0.020  1.090
 RY5  C12  H3   single    0.930  0.020  1.080
 RY5  C13  H4   single    0.930  0.020  1.080
 RY5  C15  H5   single    0.930  0.020  1.080
 RY5  C2   H6   single    0.930  0.020  1.080
 RY5  C3   H7   single    0.930  0.020  1.080
 RY5  C6   H8   single    0.970  0.020  1.090
 RY5  C6   H9   single    0.970  0.020  1.090
 RY5  C7   H10  single    0.970  0.020  1.090
 RY5  C7   H11  single    0.970  0.020  1.090
 RY5  N1   H12  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
 RY5  CL1  C1   C2   118.93  3.000
 RY5  CL1  C1   C15  118.94  3.000
 RY5  C2   C1   C15  122.12  3.000
 RY5  H2   C10  H1   107.52  3.000
 RY5  H2   C10  N2   109.95  3.000
 RY5  H1   C10  N2   107.60  3.000
 RY5  H2   C10  C11  110.16  3.000
 RY5  H1   C10  C11  109.84  3.000
 RY5  N2   C10  C11  111.65  3.000
 RY5  N3   C11  C12  111.30  3.000
 RY5  C12  C11  C10  128.06  3.000
 RY5  N3   C11  C10  120.62  3.000
 RY5  H3   C12  C13  128.41  3.000
 RY5  H3   C12  C11  128.60  3.000
 RY5  C13  C12  C11  102.98  3.000
 RY5  H4   C13  O2   116.90  3.000
 RY5  H4   C13  C12  133.12  3.000
 RY5  O2   C13  C12  109.98  3.000
 RY5  O3   C14  N2   126.31  3.000
 RY5  N2   C14  C8   106.91  3.000
 RY5  O3   C14  C8   126.78  3.000
 RY5  H5   C15  C5   121.24  3.000
 RY5  H5   C15  C1   120.78  3.000
 RY5  C5   C15  C1   117.97  3.000
 RY5  H6   C2   C3   120.37  3.000
 RY5  H6   C2   C1   120.34  3.000
 RY5  C3   C2   C1   119.30  3.000
 RY5  H7   C3   C4   121.27  3.000
 RY5  H7   C3   C2   119.87  3.000
 RY5  C4   C3   C2   118.86  3.000
 RY5  C8   C4   C5   110.35  3.000
 RY5  C5   C4   C3   121.47  3.000
 RY5  C8   C4   C3   128.17  3.000
 RY5  C6   C5   C4   110.96  3.000
 RY5  C6   C5   C15  128.77  3.000
 RY5  C4   C5   C15  120.27  3.000
 RY5  H9   C6   H8   107.10  3.000
 RY5  H9   C6   C7   111.35  3.000
 RY5  H8   C6   C7   112.31  3.000
 RY5  H9   C6   C5   110.30  3.000
 RY5  H8   C6   C5   112.81  3.000
 RY5  C7   C6   C5   103.03  3.000
 RY5  H11  C7   H10  107.63  3.000
 RY5  H11  C7   C8   107.48  3.000
 RY5  H10  C7   C8   112.67  3.000
 RY5  H11  C7   C6   109.81  3.000
 RY5  H10  C7   C6   113.71  3.000
 RY5  C8   C7   C6   105.38  3.000
 RY5  N1   C8   C7   115.57  3.000
 RY5  C7   C8   C4   102.69  3.000
 RY5  N1   C8   C4   115.69  3.000
 RY5  C7   C8   C14  111.57  3.000
 RY5  C4   C8   C14  110.50  3.000
 RY5  N1   C8   C14  101.09  3.000
 RY5  O1   C9   N2   124.79  3.000
 RY5  O1   C9   N1   128.92  3.000
 RY5  N2   C9   N1   106.30  3.000
 RY5  H12  N1   C9   122.48  3.000
 RY5  H12  N1   C8   123.62  3.000
 RY5  C9   N1   C8   113.90  3.000
 RY5  C9   N2   C14  111.80  3.000
 RY5  C9   N2   C10  124.16  3.000
 RY5  C14  N2   C10  124.03  3.000
 RY5  O2   N3   C11  106.31  3.000
 RY5  N3   O2   C13  109.43  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
 RY5  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 RY5  CONST_02  C4   C5   C15  C1      0.00   0.0  0
 RY5  CONST_03  C13  O2   N3   C11     0.00   0.0  0
 RY5  CONST_04  O2   C13  C12  C11     0.00   0.0  0
 RY5  CONST_05  N3   O2   C13  C12     0.00   0.0  0
 RY5  CONST_06  O2   N3   C11  C12     0.00   0.0  0
 RY5  CONST_07  N3   C11  C12  C13     0.00   0.0  0
 RY5  CONST_08  C3   C2   C1   C15     0.00   0.0  0
 RY5  CONST_09  C3   C4   C5   C15     0.00   0.0  0
 RY5  CONST_10  C5   C4   C3   C2      0.00   0.0  0
 RY5  CONST_11  C5   C15  C1   C2      0.00   0.0  0
 RY5  CONST_12  N1   C9   N2   C14     0.00   0.0  0
 RY5  CONST_13  C9   N2   C14  C8      0.00   0.0  0
 RY5  CONST_14  N2   C9   N1   C8      0.00   0.0  0
 RY5  CONST_15  O2   N3   C11  C10   180.00   0.0  0
 RY5  CONST_16  C13  C12  C11  C10   180.00   0.0  0
 RY5  CONST_17  CL1  C1   C2   C3    180.00   0.0  0
 RY5  CONST_18  CL1  C1   C15  C5    180.00   0.0  0
 RY5  CONST_19  C8   C14  N2   C10   180.00   0.0  0
 RY5  CONST_20  N1   C9   N2   C10   180.00   0.0  0
 RY5  CONST_21  O1   C9   N2   C14   180.00   0.0  0
 RY5  CONST_22  O1   C9   N1   C8    180.00   0.0  0
 RY5  CONST_23  O3   C14  N2   C9    180.00   0.0  0
 RY5  CONST_24  H7   C3   C2   C1    180.00   0.0  0
 RY5  CONST_25  H4   C13  C12  C11   180.00   0.0  0
 RY5  CONST_26  H6   C2   C1   C15   180.00   0.0  0
 RY5  CONST_27  H5   C15  C1   C2    180.00   0.0  0
 RY5  CONST_28  H6   C2   C3   C4    180.00   0.0  0
 RY5  CONST_29  H5   C15  C5   C4    180.00   0.0  0
 RY5  CONST_30  H7   C3   C4   C5    180.00   0.0  0
 RY5  CONST_31  H5   C15  C5   C6      0.00   0.0  0
 RY5  CONST_32  H7   C3   C4   C8      0.00   0.0  0
 RY5  CONST_33  H4   C13  O2   N3    180.00   0.0  0
 RY5  CONST_34  H3   C12  C11  N3    180.00   0.0  0
 RY5  CONST_35  H3   C12  C13  O2    180.00   0.0  0
 RY5  CONST_36  H12  N1   C9   N2    180.00   0.0  0
 RY5  CONST_37  O3   C14  N2   C10     0.00   0.0  0
 RY5  CONST_38  O1   C9   N2   C10     0.00   0.0  0
 RY5  CONST_39  H12  N1   C9   O1      0.00   0.0  0
 RY5  Var_01    C7   C6   C5   C15  -163.91  30.0  1
 RY5  Var_02    C7   C6   C5   C4     16.05  30.0  1
 RY5  Var_03    C8   C7   C6   C5    -26.05  30.0  1
 RY5  Var_04    C14  N2   C10  C11   -69.63  30.0  3
 RY5  Var_05    C9   N2   C10  C11   109.42  30.0  3
 RY5  Var_06    N2   C10  C11  C12   -47.61  30.0  2
 RY5  Var_07    N3   C11  C10  N2    133.89  30.0  2
 RY5  Var_08    H8   C6   C5   C15   -42.57  30.0  1
 RY5  Var_09    H9   C6   C5   C15    77.14  30.0  1
 RY5  Var_10    H8   C6   C5   C4    137.39  30.0  1
 RY5  Var_11    H9   C6   C5   C4   -102.90  30.0  1
 RY5  Var_12    H10  C7   C6   C5   -149.91  30.0  1
 RY5  Var_13    H11  C7   C6   C5     89.43  30.0  1
 RY5  Var_14    H8   C6   C7   C8   -147.72  30.0  1
 RY5  Var_15    H9   C6   C7   C8     92.17  30.0  1
 RY5  Var_16    H1   C10  C11  C12    71.67  30.0  2
 RY5  Var_17    H2   C10  C11  C12  -170.08  30.0  2
 RY5  Var_18    H1   C10  N2   C14   169.77  30.0  2
 RY5  Var_19    H2   C10  N2   C14    52.95  30.0  2
 RY5  Var_20    H1   C10  N2   C9    -11.18  30.0  2
 RY5  Var_21    H2   C10  N2   C9   -128.00  30.0  2
 RY5  Var_22    H1   C10  C11  N3   -106.83  30.0  2
 RY5  Var_23    H2   C10  C11  N3     11.42  30.0  2

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
 RY5  chir_01  C8  N1  C4  C7  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
 RY5  plan-1  C10  0.020
 RY5  plan-1  C11  0.020
 RY5  plan-1  C12  0.020
 RY5  plan-1  C13  0.020
 RY5  plan-1  N3   0.020
 RY5  plan-1  O2   0.020
 RY5  plan-1  H3   0.020
 RY5  plan-1  H4   0.020
 RY5  plan-2  C1   0.020
 RY5  plan-2  C15  0.020
 RY5  plan-2  C2   0.020
 RY5  plan-2  C3   0.020
 RY5  plan-2  C4   0.020
 RY5  plan-2  C5   0.020
 RY5  plan-2  C6   0.020
 RY5  plan-2  C8   0.020
 RY5  plan-2  CL1  0.020
 RY5  plan-2  H5   0.020
 RY5  plan-2  H6   0.020
 RY5  plan-2  H7   0.020
 RY5  plan-3  C10  0.020
 RY5  plan-3  C14  0.020
 RY5  plan-3  C8   0.020
 RY5  plan-3  C9   0.020
 RY5  plan-3  N1   0.020
 RY5  plan-3  N2   0.020
 RY5  plan-3  O1   0.020
 RY5  plan-3  O3   0.020
 RY5  plan-3  H12  0.020

