# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 05:32:33 2020
#   Inital geometry file: a 78 line input string
#   Ligand name: 1-[(4aS,7aS,9S)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazol-6(5H)-yl]ethan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N1C[C@@H]2C[C@@H]3O[C@@]2(C1)Cc4[nH]cnc34
#
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
 RHY  RHY  1-[(4aS,7aS,9S)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazol-6(5H)-yl]ethan-1-one  ligand  32  17  .  2022-07-22  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_RHY
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
 RHY  C10  C  CT    0   0.205   0.0708  -0.5863   0.0010
 RHY  C17  C  CH2   0  -0.293   1.4416  -1.2336   0.0564
 RHY  C01  C  CH3   0  -0.797   4.4585   1.0593  -0.2219
 RHY  C02  C  C     0   0.510   3.6236  -0.1222   0.2076
 RHY  C05  C  CH2   0  -0.262   1.7394   0.7874  -1.1615
 RHY  C06  C  CH1   0  -0.321   0.2347   0.6786  -0.8916
 RHY  C07  C  CH2   0  -0.419  -0.3620   1.8069  -0.0329
 RHY  C08  C  CH1   0  -0.110  -1.1371   1.0162   1.0217
 RHY  C11  C  CH2   0  -0.505  -1.0550  -1.5162  -0.4683
 RHY  C12  C  CR5   0   0.309  -2.3155  -0.7655  -0.2216
 RHY  C14  C  CR15  0   0.059  -4.3683  -0.0135  -0.1565
 RHY  C16  C  CR5   0   0.103  -2.3862   0.4147   0.4580
 RHY  N04  N  NT    0  -0.455   2.3470  -0.1373  -0.2179
 RHY  N13  N  NR15  0  -0.629  -3.5964  -1.0282  -0.6065
 RHY  N15  N  N     0  -0.457  -3.6656   0.8837   0.4927
 RHY  O03  O  O     0  -0.511   4.0809  -1.0167   0.9100
 RHY  O09  O  O2    0  -0.490  -0.2525  -0.0666   1.2852
 RHY  H1   H  HCH2  0   0.270   1.6448  -1.6911   1.0231
 RHY  H2   H  HCH2  0   0.248   1.5271  -2.0131  -0.7100
 RHY  H3   H  HCH3  0   0.265   4.5417   1.1123  -1.3086
 RHY  H4   H  HCH3  0   0.264   4.0235   2.0009   0.1151
 RHY  H5   H  HCH3  0   0.266   5.4580   0.9700   0.1956
 RHY  H6   H  HCH2  0   0.250   1.9724   0.4927  -2.1893
 RHY  H7   H  HCH2  0   0.261   2.1074   1.8020  -1.0168
 RHY  H8   H  HCH1  0   0.275  -0.3064   0.5787  -1.8325
 RHY  H9   H  HCH2  0   0.245   0.4225   2.3979   0.4475
 RHY  H10  H  HCH2  0   0.251  -0.9906   2.4890  -0.6045
 RHY  H11  H  HCH1  0   0.255  -1.3129   1.5702   1.9459
 RHY  H12  H  HCH2  0   0.260  -0.9190  -1.7531  -1.5269
 RHY  H13  H  HCH2  0   0.265  -1.0312  -2.4648   0.0785
 RHY  H14  H  HCR5  0   0.273  -5.4333   0.0166  -0.3266
 RHY  H15  H  HNR5  0   0.416  -3.9200  -1.8280  -1.1273

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
 RHY  C07  C06  single    1.538  0.020  1.538
 RHY  C07  C08  single    1.529  0.020  1.529
 RHY  C05  C06  single    1.533  0.020  1.533
 RHY  C05  N04  single    1.454  0.020  1.454
 RHY  C06  C10  single    1.557  0.020  1.557
 RHY  N15  C14  aromatic  1.312  0.020  1.312
 RHY  N15  C16  aromatic  1.363  0.020  1.363
 RHY  C08  C16  single    1.497  0.020  1.497
 RHY  C08  O09  single    1.423  0.020  1.423
 RHY  C14  N13  aromatic  1.352  0.020  1.352
 RHY  C16  C12  aromatic  1.364  0.020  1.364
 RHY  O03  C02  double    1.226  0.020  1.226
 RHY  N13  C12  aromatic  1.363  0.020  1.363
 RHY  N04  C02  single    1.346  0.020  1.346
 RHY  N04  C17  single    1.448  0.020  1.448
 RHY  C12  C11  single    1.488  0.020  1.488
 RHY  C02  C01  single    1.509  0.020  1.509
 RHY  C10  C11  single    1.534  0.020  1.534
 RHY  C10  O09  single    1.423  0.020  1.423
 RHY  C10  C17  single    1.517  0.020  1.517
 RHY  C17  H1   single    0.970  0.020  1.090
 RHY  C17  H2   single    0.970  0.020  1.090
 RHY  C01  H3   single    0.970  0.020  1.090
 RHY  C01  H4   single    0.970  0.020  1.090
 RHY  C01  H5   single    0.970  0.020  1.090
 RHY  C05  H6   single    0.970  0.020  1.090
 RHY  C05  H7   single    0.970  0.020  1.090
 RHY  C06  H8   single    0.970  0.020  1.090
 RHY  C07  H9   single    0.970  0.020  1.090
 RHY  C07  H10  single    0.970  0.020  1.090
 RHY  C08  H11  single    0.970  0.020  1.090
 RHY  C11  H12  single    0.970  0.020  1.090
 RHY  C11  H13  single    0.970  0.020  1.090
 RHY  C14  H14  single    0.930  0.020  1.080
 RHY  N13  H15  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
 RHY  O09  C10  C11  109.32  3.000
 RHY  O09  C10  C06  104.16  3.000
 RHY  C11  C10  C06  113.24  3.000
 RHY  O09  C10  C17  109.17  3.000
 RHY  C11  C10  C17  114.57  3.000
 RHY  C06  C10  C17  105.81  3.000
 RHY  H2   C17  H1   107.90  3.000
 RHY  H2   C17  N04  110.92  3.000
 RHY  H1   C17  N04  111.70  3.000
 RHY  H2   C17  C10  110.38  3.000
 RHY  H1   C17  C10  112.36  3.000
 RHY  N04  C17  C10  103.59  3.000
 RHY  H5   C01  H4   108.60  3.000
 RHY  H5   C01  H3   108.44  3.000
 RHY  H4   C01  H3   107.23  3.000
 RHY  H5   C01  C02  109.58  3.000
 RHY  H4   C01  C02  111.55  3.000
 RHY  H3   C01  C02  111.33  3.000
 RHY  O03  C02  N04  121.79  3.000
 RHY  N04  C02  C01  116.33  3.000
 RHY  O03  C02  C01  121.87  3.000
 RHY  H7   C05  H6   107.68  3.000
 RHY  H7   C05  N04  111.41  3.000
 RHY  H6   C05  N04  110.45  3.000
 RHY  H7   C05  C06  111.99  3.000
 RHY  H6   C05  C06  110.81  3.000
 RHY  N04  C05  C06  104.53  3.000
 RHY  H8   C06  C07  110.89  3.000
 RHY  H8   C06  C05  109.99  3.000
 RHY  C07  C06  C05  115.28  3.000
 RHY  H8   C06  C10  111.60  3.000
 RHY  C05  C06  C10  105.18  3.000
 RHY  C07  C06  C10  103.60  3.000
 RHY  H10  C07  H9   107.82  3.000
 RHY  H10  C07  C08  113.14  3.000
 RHY  H9   C07  C08  109.88  3.000
 RHY  H10  C07  C06  112.96  3.000
 RHY  H9   C07  C06  111.31  3.000
 RHY  C08  C07  C06  101.67  3.000
 RHY  H11  C08  O09  109.24  3.000
 RHY  H11  C08  C16  112.85  3.000
 RHY  O09  C08  C16  106.43  3.000
 RHY  H11  C08  C07  113.77  3.000
 RHY  O09  C08  C07  101.89  3.000
 RHY  C16  C08  C07  111.79  3.000
 RHY  H13  C11  H12  107.05  3.000
 RHY  H13  C11  C12  111.88  3.000
 RHY  H12  C11  C12  112.04  3.000
 RHY  H13  C11  C10  110.88  3.000
 RHY  H12  C11  C10  109.65  3.000
 RHY  C12  C11  C10  105.38  3.000
 RHY  N13  C12  C16  105.00  3.000
 RHY  N13  C12  C11  130.70  3.000
 RHY  C16  C12  C11  124.29  3.000
 RHY  H14  C14  N15  126.01  3.000
 RHY  H14  C14  N13  122.14  3.000
 RHY  N15  C14  N13  111.86  3.000
 RHY  N15  C16  C12  111.05  3.000
 RHY  C12  C16  C08  119.49  3.000
 RHY  N15  C16  C08  129.45  3.000
 RHY  C05  N04  C02  126.47  3.000
 RHY  C02  N04  C17  122.80  3.000
 RHY  C05  N04  C17  110.07  3.000
 RHY  H15  N13  C14  125.75  3.000
 RHY  H15  N13  C12  126.92  3.000
 RHY  C14  N13  C12  107.33  3.000
 RHY  C16  N15  C14  104.76  3.000
 RHY  C08  O09  C10  104.60  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
 RHY  CONST_01  N15  C14  N13  C12    0.00   0.0  0
 RHY  CONST_02  N13  C14  N15  C16    0.00   0.0  0
 RHY  CONST_03  H14  C14  N13  C12  180.00   0.0  0
 RHY  CONST_04  H15  N13  C14  N15  180.00   0.0  0
 RHY  CONST_05  O03  C02  N04  C17    0.00   0.0  0
 RHY  CONST_06  C01  C02  N04  C17  180.00   0.0  0
 RHY  CONST_07  C05  N04  C02  C01    0.00   0.0  0
 RHY  CONST_08  O03  C02  N04  C05  180.00   0.0  0
 RHY  Var_01    C05  N04  C17  C10  -34.41  30.0  1
 RHY  Var_02    C06  C05  N04  C17   30.06  30.0  1
 RHY  Var_03    H3   C01  C02  N04  -61.11  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
 RHY  chir_01  C10  C11  C06  C17  positiv
 RHY  chir_02  C06  C10  C05  C07  positiv
 RHY  chir_03  C08  O09  C07  C16  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
 RHY  plan-1  C17  0.020
 RHY  plan-1  C01  0.020
 RHY  plan-1  C02  0.020
 RHY  plan-1  C05  0.020
 RHY  plan-1  N04  0.020
 RHY  plan-1  O03  0.020
 RHY  plan-2  C08  0.020
 RHY  plan-2  C11  0.020
 RHY  plan-2  C12  0.020
 RHY  plan-2  C14  0.020
 RHY  plan-2  C16  0.020
 RHY  plan-2  N13  0.020
 RHY  plan-2  N15  0.020
 RHY  plan-2  H14  0.020
 RHY  plan-2  H15  0.020

