# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 17:22:33 2020
#   Inital geometry file: a 83 line input string
#   Ligand name: methyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H]1C[C@]2(CN1)C(=O)Nc3ccccc23
#
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
 092  092  'methyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  32  18  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_092
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
 092  C5   C  CR16  0  -0.261  -3.6042   2.1150   0.3793
 092  C8   C  CR16  0  -0.268  -4.3886   1.2473  -0.3697
 092  C3   C  CR16  0  -0.352  -2.2748   1.7983   0.6607
 092  C6   C  CR16  0  -0.306  -3.8753   0.0463  -0.8565
 092  C1   C  CR56  0   0.140  -1.7546   0.6138   0.1819
 092  C17  C  CR56  0   0.365  -2.5566  -0.2466  -0.5659
 092  C14  C  CR5   0   0.578  -0.5326  -1.2918  -0.4729
 092  C9   C  C     0   0.579   3.1388  -0.2032   0.0836
 092  C4   C  CH2   0  -0.462   0.8030   0.8274  -0.1176
 092  C13  C  CH2   0  -0.288  -0.0094  -0.3393   1.8015
 092  C7   C  CR15  0  -0.179   1.9634   0.3844   0.8277
 092  C2   C  C     0  -0.342  -0.4024  -0.0049   0.3392
 092  C18  C  CH3   0  -0.423   4.7961   0.2882  -1.5168
 092  N16  N  NR15  0  -0.744  -1.8120  -1.3628  -0.9280
 092  N10  N  NR15  0  -0.585   1.4194  -0.5530   1.7946
 092  O15  O  O     0  -0.449   0.3426  -2.1091  -0.6756
 092  O11  O  O2    0  -0.450   3.6721   0.6909  -0.7324
 092  H1   H  HCR6  0   0.255  -4.0256   3.0410   0.7469
 092  H2   H  HCR6  0   0.259  -5.4183   1.5033  -0.5821
 092  H3   H  HCR6  0   0.254  -1.6639   2.4754   1.2460
 092  H4   H  HCR6  0   0.268  -4.4889  -0.6261  -1.4414
 092  H5   H  HCH2  0   0.275   0.5944   1.8871   0.0270
 092  H6   H  HCH2  0   0.273   1.0245   0.6886  -1.1757
 092  H7   H  HCH2  0   0.250  -0.2639   0.5242   2.4241
 092  H8   H  HCH2  0   0.267  -0.5374  -1.2028   2.2062
 092  H9   H  HCR5  0   0.285   2.3315   1.2779   1.3429
 092  H10  H  HCH3  0   0.241   4.5388  -0.5291  -2.1900
 092  H11  H  HCH3  0   0.253   5.0789   1.1593  -2.1000
 092  H12  H  HCH3  0   0.241   5.6327  -0.0123  -0.8866
 092  H13  H  HNR5  0   0.411  -2.1592  -2.1232  -1.4931
 092  H14  H  HNR5  0   0.359   1.6157  -1.4984   1.4891
 092  O12  O  O     0  -0.445   3.5500  -1.3281   0.2128

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
 092  N10  C7   single    1.452  0.020  1.452
 092  N10  C13  single    1.445  0.020  1.445
 092  C3   C5   aromatic  1.395  0.020  1.395
 092  C3   C1   aromatic  1.379  0.020  1.379
 092  C5   C8   aromatic  1.389  0.020  1.389
 092  C7   C4   single    1.561  0.020  1.561
 092  C7   C9   single    1.510  0.020  1.510
 092  C13  C2   single    1.551  0.020  1.551
 092  C4   C2   single    1.534  0.020  1.534
 092  C1   C2   single    1.495  0.020  1.495
 092  C1   C17  aromatic  1.394  0.020  1.394
 092  C9   O12  double    1.205  0.020  1.205
 092  C9   O11  single    1.323  0.020  1.323
 092  C8   C6   aromatic  1.394  0.020  1.394
 092  C2   C14  single    1.527  0.020  1.527
 092  O11  C18  single    1.429  0.020  1.429
 092  C17  C6   aromatic  1.382  0.020  1.382
 092  C17  N16  single    1.390  0.020  1.390
 092  C14  N16  single    1.360  0.020  1.360
 092  C14  O15  double    1.215  0.020  1.215
 092  C5   H1   single    0.930  0.020  1.080
 092  C8   H2   single    0.930  0.020  1.080
 092  C3   H3   single    0.930  0.020  1.080
 092  C6   H4   single    0.930  0.020  1.080
 092  C4   H5   single    0.970  0.020  1.090
 092  C4   H6   single    0.970  0.020  1.090
 092  C13  H7   single    0.970  0.020  1.090
 092  C13  H8   single    0.970  0.020  1.090
 092  C7   H9   single    0.970  0.020  1.090
 092  C18  H10  single    0.970  0.020  1.090
 092  C18  H11  single    0.970  0.020  1.090
 092  C18  H12  single    0.970  0.020  1.090
 092  N16  H13  single    0.860  0.020  1.020
 092  N10  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
 092  H1   C5   C3   119.80  3.000
 092  H1   C5   C8   119.87  3.000
 092  C3   C5   C8   120.33  3.000
 092  H2   C8   C6   119.06  3.000
 092  H2   C8   C5   119.70  3.000
 092  C6   C8   C5   121.25  3.000
 092  H3   C3   C1   120.76  3.000
 092  H3   C3   C5   120.28  3.000
 092  C1   C3   C5   118.96  3.000
 092  H4   C6   C17  121.54  3.000
 092  H4   C6   C8   121.03  3.000
 092  C17  C6   C8   117.43  3.000
 092  C2   C1   C17  108.74  3.000
 092  C17  C1   C3   119.95  3.000
 092  C2   C1   C3   131.28  3.000
 092  N16  C17  C1   109.10  3.000
 092  N16  C17  C6   128.81  3.000
 092  C1   C17  C6   122.08  3.000
 092  O15  C14  N16  125.94  3.000
 092  O15  C14  C2   126.47  3.000
 092  N16  C14  C2   107.59  3.000
 092  O11  C9   O12  124.04  3.000
 092  O11  C9   C7   110.78  3.000
 092  O12  C9   C7   125.18  3.000
 092  H6   C4   H5   106.95  3.000
 092  H6   C4   C2   112.31  3.000
 092  H5   C4   C2   109.73  3.000
 092  H6   C4   C7   113.62  3.000
 092  H5   C4   C7   109.75  3.000
 092  C2   C4   C7   104.47  3.000
 092  H8   C13  H7   107.53  3.000
 092  H8   C13  N10  111.33  3.000
 092  H7   C13  N10  110.45  3.000
 092  H8   C13  C2   113.46  3.000
 092  H7   C13  C2   107.90  3.000
 092  N10  C13  C2   106.14  3.000
 092  H9   C7   N10  109.83  3.000
 092  H9   C7   C4   107.65  3.000
 092  N10  C7   C4   107.93  3.000
 092  H9   C7   C9   106.72  3.000
 092  C4   C7   C9   113.00  3.000
 092  N10  C7   C9   111.61  3.000
 092  C13  C2   C4   101.45  3.000
 092  C4   C2   C14  111.46  3.000
 092  C13  C2   C14  109.95  3.000
 092  C14  C2   C1   102.45  3.000
 092  C4   C2   C1   117.05  3.000
 092  C13  C2   C1   114.68  3.000
 092  H12  C18  H11  109.38  3.000
 092  H12  C18  H10  109.38  3.000
 092  H11  C18  H10  109.36  3.000
 092  H12  C18  O11  111.36  3.000
 092  H11  C18  O11  105.88  3.000
 092  H10  C18  O11  111.40  3.000
 092  H13  N16  C14  123.40  3.000
 092  H13  N16  C17  124.53  3.000
 092  C14  N16  C17  112.02  3.000
 092  H14  N10  C7   109.21  3.000
 092  H14  N10  C13  109.34  3.000
 092  C7   N10  C13  106.15  3.000
 092  C18  O11  C9   117.74  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
 092  CONST_01  C17  C1   C3   C5     0.00   0.0  0
 092  CONST_02  C17  C6   C8   C5     0.00   0.0  0
 092  CONST_03  C1   C3   C5   C8     0.00   0.0  0
 092  CONST_04  C1   C17  C6   C8     0.00   0.0  0
 092  CONST_05  C6   C8   C5   C3     0.00   0.0  0
 092  CONST_06  C6   C17  C1   C3     0.00   0.0  0
 092  CONST_07  C2   C14  N16  C17    0.00   0.0  0
 092  CONST_08  O15  C14  N16  C17  180.00   0.0  0
 092  CONST_09  H4   C6   C8   C5   180.00   0.0  0
 092  CONST_10  H3   C3   C5   C8   180.00   0.0  0
 092  CONST_11  H2   C8   C5   C3   180.00   0.0  0
 092  CONST_12  H1   C5   C8   C6   180.00   0.0  0
 092  CONST_13  H13  N16  C14  C2   180.00   0.0  0
 092  Var_01    C2   C13  N10  C7    35.69  30.0  1
 092  Var_02    O12  C9   O11  C18    0.69  30.0  1
 092  Var_03    H10  C18  O11  C9    61.68  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
 092  chir_01  C7  N10  C4  C9   positiv
 092  chir_02  C2  C4   C1  C14  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
 092  plan-1  C5   0.020
 092  plan-1  C8   0.020
 092  plan-1  C3   0.020
 092  plan-1  C6   0.020
 092  plan-1  C1   0.020
 092  plan-1  C17  0.020
 092  plan-1  C14  0.020
 092  plan-1  C2   0.020
 092  plan-1  N16  0.020
 092  plan-1  O15  0.020
 092  plan-1  H1   0.020
 092  plan-1  H2   0.020
 092  plan-1  H3   0.020
 092  plan-1  H4   0.020
 092  plan-1  H13  0.020
 092  plan-2  C9   0.020
 092  plan-2  C7   0.020
 092  plan-2  O11  0.020
 092  plan-2  O12  0.020

