# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:33:05 2022
#   Inital geometry file: a 88 line input string
#   Ligand name: (4aS,5aR,6R,8aS,8bS)-5a-(carboxymethyl)-8-oxo-2,4a,5a,6,7,8,8a,8b-octahydro-1H-pyrrolo[3',4':4,5]furo[3,2-b]pyridine-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)C[C@@]12O[C@H]3C=CCN[C@H]3[C@@H]1C(=O)N[C@H]2C(O)=O
#
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
 IKM  IKM  '(4aS,5aR,6R,8aS,8bS)-5a-(carboxymethyl)-8-oxo-2,4a,5a,6,7,8,8a,8b-octahydro-1H-pyrrolo[3',4':4,5]furo[3,2-b]pyridine-6-carboxylic acid'  ligand  32  20  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_IKM
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
 IKM  C1   C  CH2    0  -0.325   3.7662  -0.9465  -1.1137
 IKM  C2   C  C1     0  -0.249   2.9928  -1.0147   1.2337
 IKM  C3   C  C1     0  -0.237   3.8567  -1.4094   0.3051
 IKM  C4   C  CH1    0  -0.109   2.0391   0.5915  -0.4581
 IKM  C5   C  CH1    0   0.042   1.9444   0.0135   0.9490
 IKM  O1   O  O2     0  -0.512   0.6409  -0.5324   1.0776
 IKM  N2   N  NR15   0  -0.600  -0.6315   2.0978   0.9362
 IKM  C6   C  CR15   0  -0.231  -1.3330   0.8451   0.7516
 IKM  C7   C  CR5    0   0.324  -0.2455  -0.0263   0.0809
 IKM  C8   C  CR15   0  -0.476   0.5957   1.0055  -0.6924
 IKM  C9   C  CR5    0   0.545   0.2912   2.3285  -0.0101
 IKM  O2   O  O      0  -0.501   0.8389   3.3951  -0.2461
 IKM  C10  C  CH2    0  -0.623  -0.7820  -1.1675  -0.7638
 IKM  C11  C  C      0   0.421  -2.5532   1.0426  -0.1818
 IKM  O3   O  OC    -1  -0.595  -3.5877   0.4116   0.0945
 IKM  C12  C  C      0   0.428  -1.6861  -2.1952  -0.0608
 IKM  O4   O  OC    -1  -0.640  -2.3253  -2.9505  -0.8257
 IKM  O5   O  O      0  -0.602  -1.6932  -2.2351   1.1831
 IKM  O6   O  O      0  -0.599  -2.3741   1.8123  -1.1475
 IKM  N1   N  NH1    0  -0.596   2.4388  -0.4396  -1.3935
 IKM  H1   H  HCH2   0   0.212   4.5646  -0.2070  -1.2978
 IKM  H2   H  HCH2   0   0.246   3.9739  -1.7855  -1.7824
 IKM  H3   H  H      0   0.247   3.0704  -1.3866   2.2496
 IKM  H4   H  H      0   0.250   4.6620  -2.0910   0.5551
 IKM  H5   H  HCH1   0   0.233   2.7198   1.4573  -0.4693
 IKM  H6   H  HCH1   0   0.211   2.0713   0.8324   1.6735
 IKM  H7   H  HNR5   0   0.383  -1.0699   2.8714   1.4140
 IKM  H8   H  HCR5   0   0.242  -1.6336   0.4141   1.7049
 IKM  H9   H  HCR5   0   0.288   0.3441   1.0753  -1.7525
 IKM  H10  H  HCH2   0   0.220  -1.3153  -0.7600  -1.6265
 IKM  H11  H  HCH2   0   0.246   0.0825  -1.6920  -1.1841
 IKM  H14  H  HNH1   0   0.356   2.4055  -0.0715  -2.3356

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
 IKM  C1   N1   single  1.448  0.020  1.448
 IKM  C1   C3   single  1.495  0.020  1.495
 IKM  N1   C4   single  1.448  0.020  1.448
 IKM  C3   C2   double  1.328  0.020  1.328
 IKM  C4   C8   single  1.520  0.020  1.520
 IKM  C4   C5   single  1.524  0.020  1.524
 IKM  C2   C5   single  1.496  0.020  1.496
 IKM  O5   C12  deloc   1.245  0.020  1.245
 IKM  O2   C9   double  1.222  0.020  1.222
 IKM  C8   C9   single  1.519  0.020  1.519
 IKM  C8   C7   single  1.540  0.020  1.540
 IKM  C5   O1   single  1.419  0.020  1.419
 IKM  C9   N2   single  1.342  0.020  1.342
 IKM  C12  O4   deloc   1.251  0.020  1.251
 IKM  C12  C10  single  1.539  0.020  1.539
 IKM  O1   C7   single  1.427  0.020  1.427
 IKM  C7   C10  single  1.518  0.020  1.518
 IKM  C7   C6   single  1.547  0.020  1.547
 IKM  N2   C6   single  1.448  0.020  1.448
 IKM  C6   C11  single  1.549  0.020  1.549
 IKM  C11  O6   deloc   1.248  0.020  1.248
 IKM  C11  O3   deloc   1.243  0.020  1.243
 IKM  C1   H1   single  0.970  0.020  1.090
 IKM  C1   H2   single  0.970  0.020  1.090
 IKM  C2   H3   single  0.930  0.020  1.080
 IKM  C3   H4   single  0.930  0.020  1.080
 IKM  C4   H5   single  0.970  0.020  1.090
 IKM  C5   H6   single  0.970  0.020  1.090
 IKM  N2   H7   single  0.890  0.020  1.040
 IKM  C6   H8   single  0.970  0.020  1.090
 IKM  C8   H9   single  0.970  0.020  1.090
 IKM  C10  H10  single  0.970  0.020  1.090
 IKM  C10  H11  single  0.970  0.020  1.090
 IKM  N1   H14  single  0.890  0.020  1.040

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
 IKM  H2   C1   H1   105.95  3.000
 IKM  H2   C1   N1   108.95  3.000
 IKM  H1   C1   N1   113.35  3.000
 IKM  H2   C1   C3   109.35  3.000
 IKM  H1   C1   C3   108.77  3.000
 IKM  N1   C1   C3   110.31  3.000
 IKM  H3   C2   C5   117.65  3.000
 IKM  H3   C2   C3   120.42  3.000
 IKM  C5   C2   C3   121.80  3.000
 IKM  H4   C3   C2   120.58  3.000
 IKM  H4   C3   C1   117.28  3.000
 IKM  C2   C3   C1   122.14  3.000
 IKM  H5   C4   N1   112.49  3.000
 IKM  H5   C4   C8   111.80  3.000
 IKM  N1   C4   C8   110.88  3.000
 IKM  H5   C4   C5   110.24  3.000
 IKM  C8   C4   C5   100.76  3.000
 IKM  N1   C4   C5   110.08  3.000
 IKM  H6   C5   O1   109.42  3.000
 IKM  H6   C5   C4   108.56  3.000
 IKM  O1   C5   C4   106.65  3.000
 IKM  H6   C5   C2   107.78  3.000
 IKM  O1   C5   C2   111.23  3.000
 IKM  C4   C5   C2   113.13  3.000
 IKM  C7   O1   C5   111.77  3.000
 IKM  H7   N2   C9   120.05  3.000
 IKM  H7   N2   C6   120.87  3.000
 IKM  C9   N2   C6   113.09  3.000
 IKM  H8   C6   C11  111.15  3.000
 IKM  H8   C6   C7   110.54  3.000
 IKM  C11  C6   C7   111.37  3.000
 IKM  H8   C6   N2   111.39  3.000
 IKM  C11  C6   N2   110.38  3.000
 IKM  C7   C6   N2   101.66  3.000
 IKM  C10  C7   C8   114.68  3.000
 IKM  C10  C7   C6   114.61  3.000
 IKM  C8   C7   C6   102.97  3.000
 IKM  C6   C7   O1   109.50  3.000
 IKM  C10  C7   O1   109.98  3.000
 IKM  C8   C7   O1   104.43  3.000
 IKM  H9   C8   C9   109.52  3.000
 IKM  H9   C8   C7   113.87  3.000
 IKM  C9   C8   C7   104.39  3.000
 IKM  H9   C8   C4   112.70  3.000
 IKM  C7   C8   C4   105.00  3.000
 IKM  C9   C8   C4   111.00  3.000
 IKM  O2   C9   C8   125.70  3.000
 IKM  C8   C9   N2   107.75  3.000
 IKM  O2   C9   N2   126.48  3.000
 IKM  H11  C10  H10  105.12  3.000
 IKM  H11  C10  C12  108.62  3.000
 IKM  H10  C10  C12  108.84  3.000
 IKM  H11  C10  C7   107.14  3.000
 IKM  H10  C10  C7   109.36  3.000
 IKM  C12  C10  C7   117.10  3.000
 IKM  O6   C11  O3   127.21  3.000
 IKM  O3   C11  C6   117.20  3.000
 IKM  O6   C11  C6   115.59  3.000
 IKM  O5   C12  O4   126.09  3.000
 IKM  O4   C12  C10  115.10  3.000
 IKM  O5   C12  C10  118.78  3.000
 IKM  H14  N1   C4   109.46  3.000
 IKM  H14  N1   C1   109.72  3.000
 IKM  C4   N1   C1   112.17  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
 IKM  CONST_02  O2  C9   N2   C6  180.00   0.0  0
 IKM  CONST_03  H7  N2   C9   C8  180.00   0.0  0
 IKM  Var_01    C5  C2   C3   C1   -5.51  30.0  1
 IKM  Var_02    N1  C1   C3   C2  -19.22  30.0  1
 IKM  Var_03    C4  N1   C1   C3   54.30  30.0  1
 IKM  Var_04    O5  C12  C10  C7  -16.16  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
 IKM  chir_01  C4  N1  C8   C5  negativ
 IKM  chir_02  C5  O1  C2   C4  negativ
 IKM  chir_03  C6  N2  C11  C7  negativ
 IKM  chir_04  C7  C8  O1   C6  negativ
 IKM  chir_05  C8  C7  C9   C4  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
 IKM  plan-1  N2   0.020
 IKM  plan-1  C6   0.020
 IKM  plan-1  C8   0.020
 IKM  plan-1  C9   0.020
 IKM  plan-1  O2   0.020
 IKM  plan-1  H7   0.020
 IKM  plan-2  C6   0.020
 IKM  plan-2  C11  0.020
 IKM  plan-2  O3   0.020
 IKM  plan-2  O6   0.020
 IKM  plan-3  C10  0.020
 IKM  plan-3  C12  0.020
 IKM  plan-3  O4   0.020
 IKM  plan-3  O5   0.020

