# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 03:43:17 2020
#   Inital geometry file: a 82 line input string
#   Ligand name: methyl (5aS,8aS,10S)-8,8a,9,10-tetrahydro-5H-5a,10-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-b]pyrazine-7(6H)-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)N1C[C@@H]2C[C@@H]3O[C@@]2(C1)Cc4nccnc34
#
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
 RH7  RH7  'methyl (5aS,8aS,10S)-8,8a,9,10-tetrahydro-5H-5a,10-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-b]pyrazine-7(6H)-carboxylate'  ligand  34  19  .  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_RH7
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
 RH7  C13  C  CR6   0   0.221  -2.4975   0.7605   0.1594
 RH7  C15  C  CR16  0  -0.119  -4.7493   0.8524   0.3705
 RH7  C01  C  CH3   0  -0.413   5.7852  -0.3863   0.1108
 RH7  C03  C  C     0   0.765   3.6032   0.4504  -0.1464
 RH7  C06  C  CH2   0  -0.233   1.7601  -0.9971   0.6927
 RH7  C07  C  CR15  0  -0.300   0.2916  -0.6526   0.9618
 RH7  C08  C  CH2   0  -0.474  -0.6783  -1.7925   0.6192
 RH7  C09  C  CR15  0  -0.094  -1.3433  -1.2746  -0.6732
 RH7  C11  C  CR5   0   0.168  -0.0230   0.4331  -0.0826
 RH7  C12  C  CH2   0  -0.521  -1.1463   1.4012   0.2824
 RH7  C16  C  CR16  0  -0.122  -4.8555  -0.4437  -0.1079
 RH7  C18  C  CR6   0   0.222  -2.6110  -0.5437  -0.3296
 RH7  C19  C  CH2   0  -0.258   1.2892   1.1424  -0.3561
 RH7  N05  N  NT    0  -0.515   2.3041   0.2041   0.0801
 RH7  N14  N  N     0  -0.377  -3.5728   1.4528   0.5025
 RH7  N17  N  N     0  -0.370  -3.7818  -1.1424  -0.4583
 RH7  O02  O  O2    0  -0.479   4.3810  -0.5491   0.2776
 RH7  O04  O  O     0  -0.532   4.0271   1.4626  -0.6731
 RH7  O10  O  O     0  -0.487  -0.4248  -0.3388  -1.2092
 RH7  H1   H  HCR6  0   0.274  -5.6326   1.4139   0.6501
 RH7  H2   H  HCH3  0   0.234   6.1599   0.4794   0.6570
 RH7  H3   H  HCH3  0   0.247   6.2390  -1.2861   0.5166
 RH7  H4   H  HCH3  0   0.234   6.0589  -0.2924  -0.9402
 RH7  H5   H  HCH2  0   0.257   2.2854  -1.2527   1.6121
 RH7  H6   H  HCH2  0   0.241   1.8432  -1.8512   0.0144
 RH7  H7   H  HCR5  0   0.279   0.1664  -0.2847   1.9810
 RH7  H8   H  HCH2  0   0.265  -0.1541  -2.7323   0.4429
 RH7  H9   H  HCH2  0   0.269  -1.4103  -1.9727   1.4058
 RH7  H10  H  HCR5  0   0.272  -1.5337  -2.0547  -1.4111
 RH7  H11  H  HCH2  0   0.282  -1.1146   2.2688  -0.3854
 RH7  H12  H  HCH2  0   0.275  -1.0029   1.7855   1.2951
 RH7  H13  H  HCR6  0   0.274  -5.8221  -0.9209  -0.2128
 RH7  H14  H  HCH2  0   0.262   1.3885   1.4028  -1.4121
 RH7  H15  H  HCH2  0   0.254   1.3401   2.0712   0.2189

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
 RH7  C08  C07  single    1.535  0.020  1.535
 RH7  C08  C09  single    1.543  0.020  1.543
 RH7  N17  C16  aromatic  1.328  0.020  1.328
 RH7  N17  C18  aromatic  1.321  0.020  1.321
 RH7  C16  C15  aromatic  1.386  0.020  1.386
 RH7  C07  C06  single    1.532  0.020  1.532
 RH7  C07  C11  single    1.539  0.020  1.539
 RH7  C06  N05  single    1.454  0.020  1.454
 RH7  C09  C18  single    1.503  0.020  1.503
 RH7  C09  O10  single    1.416  0.020  1.416
 RH7  C18  C13  aromatic  1.397  0.020  1.397
 RH7  C15  N14  aromatic  1.327  0.020  1.327
 RH7  C13  N14  aromatic  1.324  0.020  1.324
 RH7  C13  C12  single    1.501  0.020  1.501
 RH7  O04  C03  double    1.217  0.020  1.217
 RH7  N05  C03  single    1.341  0.020  1.341
 RH7  N05  C19  single    1.449  0.020  1.449
 RH7  C11  O10  single    1.423  0.020  1.423
 RH7  C11  C12  single    1.527  0.020  1.527
 RH7  C11  C19  single    1.517  0.020  1.517
 RH7  C03  O02  single    1.336  0.020  1.336
 RH7  O02  C01  single    1.423  0.020  1.423
 RH7  C15  H1   single    0.930  0.020  1.080
 RH7  C01  H2   single    0.970  0.020  1.090
 RH7  C01  H3   single    0.970  0.020  1.090
 RH7  C01  H4   single    0.970  0.020  1.090
 RH7  C06  H5   single    0.970  0.020  1.090
 RH7  C06  H6   single    0.970  0.020  1.090
 RH7  C07  H7   single    0.970  0.020  1.090
 RH7  C08  H8   single    0.970  0.020  1.090
 RH7  C08  H9   single    0.970  0.020  1.090
 RH7  C09  H10  single    0.970  0.020  1.090
 RH7  C12  H11  single    0.970  0.020  1.090
 RH7  C12  H12  single    0.970  0.020  1.090
 RH7  C16  H13  single    0.930  0.020  1.080
 RH7  C19  H14  single    0.970  0.020  1.090
 RH7  C19  H15  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
 RH7  N14  C13  C18  120.85  3.000
 RH7  N14  C13  C12  119.13  3.000
 RH7  C18  C13  C12  120.02  3.000
 RH7  H1   C15  N14  117.55  3.000
 RH7  H1   C15  C16  120.76  3.000
 RH7  N14  C15  C16  121.69  3.000
 RH7  H4   C01  H3   109.06  3.000
 RH7  H4   C01  H2   109.17  3.000
 RH7  H3   C01  H2   109.08  3.000
 RH7  H4   C01  O02  111.75  3.000
 RH7  H3   C01  O02  105.88  3.000
 RH7  H2   C01  O02  111.79  3.000
 RH7  O04  C03  O02  123.84  3.000
 RH7  O02  C03  N05  111.89  3.000
 RH7  O04  C03  N05  124.27  3.000
 RH7  H6   C06  H5   107.67  3.000
 RH7  H6   C06  N05  110.82  3.000
 RH7  H5   C06  N05  111.65  3.000
 RH7  H6   C06  C07  110.93  3.000
 RH7  H5   C06  C07  111.51  3.000
 RH7  N05  C06  C07  104.29  3.000
 RH7  H7   C07  C11  111.88  3.000
 RH7  H7   C07  C08  112.73  3.000
 RH7  C11  C07  C08  104.07  3.000
 RH7  H7   C07  C06  110.49  3.000
 RH7  C11  C07  C06  103.61  3.000
 RH7  C08  C07  C06  113.54  3.000
 RH7  H9   C08  H8   107.29  3.000
 RH7  H9   C08  C09  111.76  3.000
 RH7  H8   C08  C09  111.16  3.000
 RH7  H9   C08  C07  112.71  3.000
 RH7  H8   C08  C07  111.85  3.000
 RH7  C09  C08  C07  102.12  3.000
 RH7  H10  C09  O10  109.25  3.000
 RH7  H10  C09  C18  110.81  3.000
 RH7  O10  C09  C18  108.19  3.000
 RH7  H10  C09  C08  113.69  3.000
 RH7  O10  C09  C08  105.02  3.000
 RH7  C18  C09  C08  109.58  3.000
 RH7  O10  C11  C19  110.80  3.000
 RH7  C19  C11  C12  112.52  3.000
 RH7  O10  C11  C12  108.99  3.000
 RH7  C19  C11  C07  105.99  3.000
 RH7  C12  C11  C07  115.81  3.000
 RH7  O10  C11  C07  102.26  3.000
 RH7  H12  C12  H11  106.42  3.000
 RH7  H12  C12  C11  110.37  3.000
 RH7  H11  C12  C11  109.58  3.000
 RH7  H12  C12  C13  110.14  3.000
 RH7  H11  C12  C13  108.32  3.000
 RH7  C11  C12  C13  111.84  3.000
 RH7  H13  C16  N17  117.65  3.000
 RH7  H13  C16  C15  120.93  3.000
 RH7  N17  C16  C15  121.42  3.000
 RH7  N17  C18  C09  120.32  3.000
 RH7  C09  C18  C13  117.73  3.000
 RH7  N17  C18  C13  121.93  3.000
 RH7  H15  C19  H14  107.56  3.000
 RH7  H15  C19  N05  111.04  3.000
 RH7  H14  C19  N05  112.44  3.000
 RH7  H15  C19  C11  110.04  3.000
 RH7  H14  C19  C11  111.38  3.000
 RH7  N05  C19  C11  104.41  3.000
 RH7  C19  N05  C06  113.56  3.000
 RH7  C19  N05  C03  120.55  3.000
 RH7  C06  N05  C03  125.82  3.000
 RH7  C15  N14  C13  117.22  3.000
 RH7  C18  N17  C16  116.89  3.000
 RH7  C03  O02  C01  116.85  3.000
 RH7  C11  O10  C09  103.99  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
 RH7  CONST_01  C16  C15  N14  C13     0.00   0.0  0
 RH7  CONST_02  C18  N17  C16  C15     0.00   0.0  0
 RH7  CONST_03  N17  C16  C15  N14     0.00   0.0  0
 RH7  CONST_04  H1   C15  N14  C13   180.00   0.0  0
 RH7  CONST_05  H13  C16  N17  C18   180.00   0.0  0
 RH7  Var_01    C11  C19  N05  C06    -4.10  30.0  1
 RH7  Var_02    C19  N05  C06  C07   -13.85  30.0  1
 RH7  Var_03    O04  C03  N05  C06   179.31  30.0  2
 RH7  Var_04    N05  C03  O02  C01  -178.89  30.0  1
 RH7  Var_05    H2   C01  O02  C03    60.91  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
 RH7  chir_01  C07  C08  C06  C11  negativ
 RH7  chir_02  C09  O10  C08  C18  negativ
 RH7  chir_03  C11  C07  C12  C19  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
 RH7  plan-1  C03  0.020
 RH7  plan-1  N05  0.020
 RH7  plan-1  O02  0.020
 RH7  plan-1  O04  0.020
 RH7  plan-2  C13  0.020
 RH7  plan-2  C15  0.020
 RH7  plan-2  C09  0.020
 RH7  plan-2  C12  0.020
 RH7  plan-2  C16  0.020
 RH7  plan-2  C18  0.020
 RH7  plan-2  N14  0.020
 RH7  plan-2  N17  0.020
 RH7  plan-2  H1   0.020
 RH7  plan-2  H13  0.020

