# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 07:12:55 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: methyl (4aS,7aS,9S)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazole-6(5H)-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=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
 RKG  RKG  'methyl (4aS,7aS,9S)-3,4,7,7a,8,9-hexahydro-4a,9-epoxypyrrolo[3',4':4,5]cyclohepta[1,2-d]imidazole-6(5H)-carboxylate'  ligand  33  18  .  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_RKG
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
 RKG  C13  C  CH2   0  -0.506   1.4339   1.5185  -0.4233
 RKG  C01  C  CH3   0  -0.413  -5.3777  -0.7637   0.1036
 RKG  C03  C  C     0   0.758  -3.2873   0.3052   0.2170
 RKG  C06  C  CH2   0  -0.254  -1.4501  -0.6765  -1.1593
 RKG  C07  C  C     0  -0.327   0.0644  -0.6146  -0.9227
 RKG  C08  C  CH2   0  -0.420   0.6523  -1.7958  -0.1310
 RKG  C09  C  CR15  0  -0.109   1.4556  -1.0768   0.9537
 RKG  C11  C  C     0   0.206   0.2851   0.6041   0.0207
 RKG  C12  C  CH2   0  -0.292  -1.0605   1.2953   0.1238
 RKG  C14  C  CR5   0   0.309   2.6755   0.7267  -0.2132
 RKG  C16  C  CR15  0   0.059   4.7085  -0.0792  -0.1906
 RKG  C18  C  CR5   0   0.103   2.7180  -0.4849   0.4108
 RKG  N05  N  NR5   0  -0.506  -2.0019   0.2368  -0.1703
 RKG  N15  N  NR15  0  -0.629   3.9615   0.9747  -0.5904
 RKG  N17  N  N     0  -0.457   3.9850  -0.9868   0.4199
 RKG  O02  O  O2    0  -0.478  -4.0113  -0.6971  -0.2881
 RKG  O04  O  O     0  -0.530  -3.7437   1.1641   0.9475
 RKG  O10  O  O     0  -0.491   0.6048   0.0170   1.2760
 RKG  H1   H  HCH2  0   0.261   1.2986   1.7989  -1.4711
 RKG  H2   H  HCH2  0   0.265   1.4393   2.4459   0.1595
 RKG  H3   H  HCH3  0   0.233  -5.9305   0.1248  -0.2020
 RKG  H4   H  HCH3  0   0.247  -5.7897  -1.6303  -0.4058
 RKG  H5   H  HCH3  0   0.234  -5.4843  -0.8981   1.1800
 RKG  H6   H  HCH2  0   0.246  -1.6990  -0.3446  -2.1717
 RKG  H7   H  HCH2  0   0.259  -1.8420  -1.6837  -1.0305
 RKG  H8   H  H     0   0.275   0.5825  -0.4841  -1.8728
 RKG  H9   H  HCH2  0   0.246  -0.1369  -2.3980   0.3268
 RKG  H10  H  HCH2  0   0.251   1.2631  -2.4569  -0.7452
 RKG  H11  H  HCR5  0   0.255   1.6201  -1.6797   1.8489
 RKG  H12  H  HCH2  0   0.271  -1.2271   1.7270   1.1096
 RKG  H13  H  HCH2  0   0.247  -1.1305   2.1028  -0.6150
 RKG  H14  H  HCR5  0   0.273   5.7718  -0.1288  -0.3668
 RKG  H15  H  HNR5  0   0.416   4.3011   1.7868  -1.0812

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
 RKG  C08  C07  single    1.539  0.020  1.539
 RKG  C08  C09  single    1.529  0.020  1.529
 RKG  C06  C07  single    1.534  0.020  1.534
 RKG  C06  N05  single    1.455  0.020  1.455
 RKG  N17  C16  aromatic  1.311  0.020  1.311
 RKG  N17  C18  aromatic  1.363  0.020  1.363
 RKG  C07  C11  single    1.557  0.020  1.557
 RKG  C16  N15  aromatic  1.352  0.020  1.352
 RKG  C18  C09  single    1.496  0.020  1.496
 RKG  C18  C14  aromatic  1.364  0.020  1.364
 RKG  C09  O10  single    1.423  0.020  1.423
 RKG  N15  C14  aromatic  1.363  0.020  1.363
 RKG  O04  C03  double    1.216  0.020  1.216
 RKG  C14  C13  single    1.487  0.020  1.487
 RKG  N05  C03  single    1.344  0.020  1.344
 RKG  N05  C12  single    1.447  0.020  1.447
 RKG  C11  C13  single    1.534  0.020  1.534
 RKG  C11  O10  single    1.422  0.020  1.422
 RKG  C11  C12  single    1.516  0.020  1.516
 RKG  C03  O02  single    1.336  0.020  1.336
 RKG  O02  C01  single    1.423  0.020  1.423
 RKG  C13  H1   single    0.970  0.020  1.090
 RKG  C13  H2   single    0.970  0.020  1.090
 RKG  C01  H3   single    0.970  0.020  1.090
 RKG  C01  H4   single    0.970  0.020  1.090
 RKG  C01  H5   single    0.970  0.020  1.090
 RKG  C06  H6   single    0.970  0.020  1.090
 RKG  C06  H7   single    0.970  0.020  1.090
 RKG  C07  H8   single    0.970  0.020  1.090
 RKG  C08  H9   single    0.970  0.020  1.090
 RKG  C08  H10  single    0.970  0.020  1.090
 RKG  C09  H11  single    0.970  0.020  1.090
 RKG  C12  H12  single    0.970  0.020  1.090
 RKG  C12  H13  single    0.970  0.020  1.090
 RKG  C16  H14  single    0.930  0.020  1.080
 RKG  N15  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
 RKG  H2   C13  H1   107.06  3.000
 RKG  H2   C13  C14  111.81  3.000
 RKG  H1   C13  C14  112.04  3.000
 RKG  H2   C13  C11  110.76  3.000
 RKG  H1   C13  C11  109.74  3.000
 RKG  C14  C13  C11  105.48  3.000
 RKG  H5   C01  H4   109.12  3.000
 RKG  H5   C01  H3   109.13  3.000
 RKG  H4   C01  H3   109.05  3.000
 RKG  H5   C01  O02  111.81  3.000
 RKG  H4   C01  O02  105.81  3.000
 RKG  H3   C01  O02  111.82  3.000
 RKG  O04  C03  O02  123.62  3.000
 RKG  O02  C03  N05  111.79  3.000
 RKG  O04  C03  N05  124.59  3.000
 RKG  H7   C06  H6   107.96  3.000
 RKG  H7   C06  N05  111.34  3.000
 RKG  H6   C06  N05  110.63  3.000
 RKG  H7   C06  C07  112.00  3.000
 RKG  H6   C06  C07  110.79  3.000
 RKG  N05  C06  C07  104.14  3.000
 RKG  H8   C07  C11  111.53  3.000
 RKG  H8   C07  C08  111.03  3.000
 RKG  C11  C07  C08  103.59  3.000
 RKG  H8   C07  C06  109.85  3.000
 RKG  C11  C07  C06  105.37  3.000
 RKG  C08  C07  C06  115.19  3.000
 RKG  H10  C08  H9   107.85  3.000
 RKG  H10  C08  C09  112.99  3.000
 RKG  H9   C08  C09  109.95  3.000
 RKG  H10  C08  C07  112.94  3.000
 RKG  H9   C08  C07  111.26  3.000
 RKG  C09  C08  C07  101.81  3.000
 RKG  H11  C09  O10  109.20  3.000
 RKG  H11  C09  C18  112.88  3.000
 RKG  O10  C09  C18  106.41  3.000
 RKG  H11  C09  C08  113.65  3.000
 RKG  O10  C09  C08  102.01  3.000
 RKG  C18  C09  C08  111.83  3.000
 RKG  O10  C11  C12  109.13  3.000
 RKG  C12  C11  C07  105.80  3.000
 RKG  O10  C11  C07  104.10  3.000
 RKG  C12  C11  C13  114.37  3.000
 RKG  O10  C11  C13  109.46  3.000
 RKG  C07  C11  C13  113.42  3.000
 RKG  H13  C12  H12  107.95  3.000
 RKG  H13  C12  N05  111.12  3.000
 RKG  H12  C12  N05  111.99  3.000
 RKG  H13  C12  C11  110.27  3.000
 RKG  H12  C12  C11  112.21  3.000
 RKG  N05  C12  C11  103.31  3.000
 RKG  N15  C14  C18  105.01  3.000
 RKG  N15  C14  C13  130.67  3.000
 RKG  C18  C14  C13  124.31  3.000
 RKG  H14  C16  N17  126.01  3.000
 RKG  H14  C16  N15  122.14  3.000
 RKG  N17  C16  N15  111.86  3.000
 RKG  N17  C18  C14  111.06  3.000
 RKG  C14  C18  C09  119.43  3.000
 RKG  N17  C18  C09  129.51  3.000
 RKG  C12  N05  C06  110.53  3.000
 RKG  C12  N05  C03  121.76  3.000
 RKG  C06  N05  C03  126.19  3.000
 RKG  H15  N15  C16  125.86  3.000
 RKG  H15  N15  C14  126.82  3.000
 RKG  C16  N15  C14  107.31  3.000
 RKG  C18  N17  C16  104.77  3.000
 RKG  C03  O02  C01  116.84  3.000
 RKG  C11  O10  C09  104.59  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
 RKG  CONST_01  C16  N17  C18  C14     0.00   0.0  0
 RKG  CONST_02  N17  C16  N15  C14     0.00   0.0  0
 RKG  CONST_03  C18  C14  N15  C16     0.00   0.0  0
 RKG  CONST_04  N15  C16  N17  C18     0.00   0.0  0
 RKG  CONST_05  N17  C18  C14  N15     0.00   0.0  0
 RKG  CONST_06  H15  N15  C14  C13     0.00   0.0  0
 RKG  CONST_07  H14  C16  N15  C14   180.00   0.0  0
 RKG  Var_01    C11  C12  N05  C06   -34.66  30.0  1
 RKG  Var_02    C12  N05  C06  C07    29.69  30.0  1
 RKG  Var_03    C18  C14  C13  C11    -7.48  30.0  1
 RKG  Var_04    O04  C03  N05  C06  -172.41  30.0  2
 RKG  Var_05    N05  C03  O02  C01   177.22  30.0  1
 RKG  Var_06    H3   C01  O02  C03    61.24  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
 RKG  chir_01  C07  C08  C06  C11  negativ
 RKG  chir_02  C09  O10  C08  C18  negativ
 RKG  chir_03  C11  C07  C13  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
 RKG  plan-1  C03  0.020
 RKG  plan-1  N05  0.020
 RKG  plan-1  O02  0.020
 RKG  plan-1  O04  0.020
 RKG  plan-2  C13  0.020
 RKG  plan-2  C09  0.020
 RKG  plan-2  C14  0.020
 RKG  plan-2  C16  0.020
 RKG  plan-2  C18  0.020
 RKG  plan-2  N15  0.020
 RKG  plan-2  N17  0.020
 RKG  plan-2  H14  0.020
 RKG  plan-2  H15  0.020

