# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:25:32 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]cyclopropa[a]azulene-4,8(3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=C)[C@@H]1[C@H]2OC(=O)[C@@H]1[C@]3(O)C[C@H]4O[C@]45C(=O)O[C@H]2[C@]35C
#
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
 RI5  RI5  (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]cyclopropa[a]azulene-4,8(3H)-dione  ligand  37  21  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RI5
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
 RI5  C01   C  CH3   0  -0.718   4.1118  -0.0689   0.1971
 RI5  C02   C  C     0   0.188   2.9694  -0.0012  -0.7741
 RI5  C03   C  C2    0  -0.606   3.0576   0.7236  -1.8868
 RI5  C04   C  CR15  0  -0.339   1.8439  -0.9530  -0.4810
 RI5  C05   C  CR15  0  -0.012   0.6129  -0.9930  -1.3806
 RI5  C06   C  CR15  0   0.035  -0.1162   0.3407  -1.4420
 RI5  C07   C  C     0  -0.182  -0.3064   1.0611  -0.0818
 RI5  C08   C  CR5   0   0.310   0.5071   0.5224   1.1490
 RI5  C09   C  CR15  0  -0.473   1.1123  -0.8777   0.8676
 RI5  C10   C  CR5   0   0.584   0.0232  -1.8974   0.6154
 RI5  O11   O  O     0  -0.403  -0.5594  -2.6009   1.3898
 RI5  O12   O  O     0  -0.436  -0.2437  -1.9272  -0.6978
 RI5  C13   C  CH2   0  -0.508  -0.5350   0.4208   2.2979
 RI5  C14   C  CR15  0  -0.058  -1.8722   0.2198   1.6223
 RI5  C15   C  C     0   0.118  -1.7250   0.6584   0.2339
 RI5  O16   O  O2    0  -0.456  -2.4537   1.4238   1.1463
 RI5  C17   C  CR5   0   0.575  -2.3723   0.1522  -1.0042
 RI5  O18   O  O     0  -0.405  -3.5221  -0.1204  -1.1922
 RI5  O19   O  O     0  -0.437  -1.4403   0.0884  -1.9533
 RI5  O20   O  OH1   0  -0.648   1.5419   1.4121   1.4371
 RI5  C21   C  CH3   0  -0.640  -0.1700   2.5680  -0.2739
 RI5  H01   H  HCH3  0   0.247   4.9417   0.5576  -0.1269
 RI5  H01A  H  HCH3  0   0.239   3.8237   0.2493   1.1975
 RI5  H01B  H  HCH3  0   0.241   4.4797  -1.0945   0.2825
 RI5  H03   H  H     0   0.238   2.3026   0.7419  -2.6601
 RI5  H03A  H  H     0   0.245   3.9362   1.3252  -2.0830
 RI5  H04   H  HCR5  0   0.313   2.2977  -1.9525  -0.5306
 RI5  H05   H  HCR5  0   0.312   0.8012  -1.3841  -2.3802
 RI5  H06   H  HCR5  0   0.293   0.3702   0.9930  -2.1633
 RI5  H09   H  HCR5  0   0.320   1.7085  -1.1894   1.7268
 RI5  H13   H  HCH2  0   0.275  -0.3046  -0.3905   2.9893
 RI5  H13A  H  HCH2  0   0.291  -0.5461   1.3450   2.8800
 RI5  H14   H  HCR5  0   0.292  -2.5682  -0.5514   1.9351
 RI5  HO20  H  HOH1  0   0.461   1.9226   1.1862   2.2927
 RI5  H21   H  HCH3  0   0.242  -0.8542   2.9111  -1.0522
 RI5  H21A  H  HCH3  0   0.250  -0.4000   3.1168   0.6371
 RI5  H21B  H  HCH3  0   0.253   0.8402   2.8280  -0.5850

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
 RI5  C01  C02   single  1.501  0.020  1.501
 RI5  C01  H01   single  0.970  0.020  1.090
 RI5  C01  H01A  single  0.970  0.020  1.090
 RI5  C01  H01B  single  0.970  0.020  1.090
 RI5  C02  C03   double  1.331  0.020  1.331
 RI5  C02  C04   single  1.503  0.020  1.503
 RI5  C03  H03   single  0.930  0.020  1.080
 RI5  C03  H03A  single  0.930  0.020  1.080
 RI5  C05  C04   single  1.525  0.020  1.525
 RI5  C04  C09   single  1.536  0.020  1.536
 RI5  C04  H04   single  0.970  0.020  1.090
 RI5  C06  C05   single  1.521  0.020  1.521
 RI5  C05  O12   single  1.440  0.020  1.440
 RI5  C05  H05   single  0.970  0.020  1.090
 RI5  C06  O19   single  1.442  0.020  1.442
 RI5  C06  C07   single  1.551  0.020  1.551
 RI5  C06  H06   single  0.970  0.020  1.090
 RI5  C21  C07   single  1.525  0.020  1.525
 RI5  C07  C15   single  1.508  0.020  1.508
 RI5  C07  C08   single  1.571  0.020  1.571
 RI5  O20  C08   single  1.395  0.020  1.395
 RI5  C08  C09   single  1.551  0.020  1.551
 RI5  C08  C13   single  1.554  0.020  1.554
 RI5  C09  C10   single  1.513  0.020  1.513
 RI5  C09  H09   single  0.970  0.020  1.090
 RI5  O12  C10   single  1.340  0.020  1.340
 RI5  C10  O11   double  1.197  0.020  1.197
 RI5  C14  C13   single  1.512  0.020  1.512
 RI5  C13  H13   single  0.970  0.020  1.090
 RI5  C13  H13A  single  0.970  0.020  1.090
 RI5  C15  C14   single  1.463  0.020  1.463
 RI5  O16  C14   single  1.419  0.020  1.419
 RI5  C14  H14   single  0.970  0.020  1.090
 RI5  C17  C15   single  1.486  0.020  1.486
 RI5  C15  O16   single  1.396  0.020  1.396
 RI5  O19  C17   single  1.332  0.020  1.332
 RI5  C17  O18   double  1.196  0.020  1.196
 RI5  O20  HO20  single  0.850  0.020  0.980
 RI5  C21  H21   single  0.970  0.020  1.090
 RI5  C21  H21A  single  0.970  0.020  1.090
 RI5  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
 RI5  H01B  C01  H01A  106.95  3.000
 RI5  H01B  C01  H01   107.85  3.000
 RI5  H01A  C01  H01   107.88  3.000
 RI5  H01B  C01  C02   110.43  3.000
 RI5  H01A  C01  C02   112.33  3.000
 RI5  H01   C01  C02   111.20  3.000
 RI5  C04   C02  C03   123.89  3.000
 RI5  C04   C02  C01   114.54  3.000
 RI5  C03   C02  C01   121.00  3.000
 RI5  H03A  C03  H03   115.33  3.000
 RI5  H03A  C03  C02   120.52  3.000
 RI5  H03   C03  C02   124.13  3.000
 RI5  H04   C04  C09   106.31  3.000
 RI5  H04   C04  C05   106.43  3.000
 RI5  C09   C04  C05    97.74  3.000
 RI5  H04   C04  C02   104.95  3.000
 RI5  C09   C04  C02   119.80  3.000
 RI5  C05   C04  C02   120.40  3.000
 RI5  H05   C05  O12   107.76  3.000
 RI5  H05   C05  C06   111.13  3.000
 RI5  O12   C05  C06   107.63  3.000
 RI5  H05   C05  C04   114.26  3.000
 RI5  O12   C05  C04   102.57  3.000
 RI5  C06   C05  C04   112.81  3.000
 RI5  H06   C06  O19   106.29  3.000
 RI5  H06   C06  C07   110.98  3.000
 RI5  O19   C06  C07   106.24  3.000
 RI5  H06   C06  C05   109.78  3.000
 RI5  C07   C06  C05   115.51  3.000
 RI5  O19   C06  C05   107.52  3.000
 RI5  C21   C07  C15   111.98  3.000
 RI5  C15   C07  C08   103.39  3.000
 RI5  C21   C07  C08   113.03  3.000
 RI5  C08   C07  C06   117.67  3.000
 RI5  C15   C07  C06   100.08  3.000
 RI5  C21   C07  C06   109.72  3.000
 RI5  O20   C08  C13   112.73  3.000
 RI5  C13   C08  C09   109.67  3.000
 RI5  O20   C08  C09   108.89  3.000
 RI5  C13   C08  C07   104.74  3.000
 RI5  C09   C08  C07   111.69  3.000
 RI5  O20   C08  C07   109.11  3.000
 RI5  H09   C09  C10   109.39  3.000
 RI5  H09   C09  C08   109.16  3.000
 RI5  C10   C09  C08   110.96  3.000
 RI5  H09   C09  C04   114.64  3.000
 RI5  C10   C09  C04    99.41  3.000
 RI5  C08   C09  C04   112.91  3.000
 RI5  O12   C10  O11   121.58  3.000
 RI5  O11   C10  C09   129.66  3.000
 RI5  O12   C10  C09   108.76  3.000
 RI5  C10   O12  C05   109.38  3.000
 RI5  H13A  C13  H13   107.08  3.000
 RI5  H13A  C13  C14   109.98  3.000
 RI5  H13   C13  C14   111.79  3.000
 RI5  H13A  C13  C08   110.20  3.000
 RI5  H13   C13  C08   112.07  3.000
 RI5  C14   C13  C08   105.75  3.000
 RI5  H14   C14  O16   115.90  3.000
 RI5  H14   C14  C15   123.44  3.000
 RI5  O16   C14  C15    57.91  3.000
 RI5  H14   C14  C13   122.22  3.000
 RI5  O16   C14  C13   113.55  3.000
 RI5  C15   C14  C13   107.17  3.000
 RI5  C17   C15  O16   120.26  3.000
 RI5  O16   C15  C14    59.46  3.000
 RI5  C17   C15  C14   130.13  3.000
 RI5  O16   C15  C07   118.77  3.000
 RI5  C17   C15  C07   109.04  3.000
 RI5  C14   C15  C07   111.91  3.000
 RI5  C15   O16  C14    62.63  3.000
 RI5  O19   C17  O18   123.34  3.000
 RI5  O18   C17  C15   128.84  3.000
 RI5  O19   C17  C15   107.77  3.000
 RI5  C17   O19  C06   112.43  3.000
 RI5  HO20  O20  C08   109.09  3.000
 RI5  H21B  C21  H21A  108.36  3.000
 RI5  H21B  C21  H21   107.63  3.000
 RI5  H21A  C21  H21   107.81  3.000
 RI5  H21B  C21  C07   110.79  3.000
 RI5  H21A  C21  C07   111.96  3.000
 RI5  H21   C21  C07   110.14  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
 RI5  Var_01  C09  C10  O12  C05    0.68  30.0  3
 RI5  Var_02  C15  C17  O19  C06    7.97  30.0  1
 RI5  Var_03  C13  C14  C15  C07    3.96  30.0  1
 RI5  Var_04  O19  C17  C15  C07    6.50  30.0  1
 RI5  Var_05  C15  C14  C13  C08  -19.21  30.0  1
 RI5  Var_06  H03  C03  C02  C04    3.70   0.0  2
 RI5  Var_07  H01  C01  C02  C04  173.58  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
 RI5  chir_01  C04  C02  C05  C09  positiv
 RI5  chir_02  C05  O12  C04  C06  positiv
 RI5  chir_03  C06  O19  C05  C07  positiv
 RI5  chir_04  C07  C15  C08  C06  negativ
 RI5  chir_05  C08  C07  C09  C13  positiv
 RI5  chir_06  C09  C04  C08  C10  negativ
 RI5  chir_07  C14  C13  C15  O16  both

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
 RI5  plan-1  C09   0.020
 RI5  plan-1  C10   0.020
 RI5  plan-1  O11   0.020
 RI5  plan-1  O12   0.020
 RI5  plan-2  C15   0.020
 RI5  plan-2  C17   0.020
 RI5  plan-2  O18   0.020
 RI5  plan-2  O19   0.020
 RI5  plan-3  C01   0.020
 RI5  plan-3  C02   0.020
 RI5  plan-3  C03   0.020
 RI5  plan-3  C04   0.020
 RI5  plan-3  H03   0.020
 RI5  plan-3  H03A  0.020

