# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 12 19:45:20 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: tetrahydro-2H-pyran-4-yl (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: O=C(OC1CCOCC1)[C@H]2C[C@]3(CN2)C(=O)Nc4ccccc34
#
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
 095  095  'tetrahydro-2H-pyran-4-yl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  43  23  .  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_095
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
 095  C5   C  CR16  0  -0.262  -4.6250   2.5546   0.4021
 095  C8   C  CR16  0  -0.268  -5.4938   2.0049  -0.5318
 095  C3   C  CR16  0  -0.348  -3.4411   1.8958   0.7368
 095  C6   C  CR16  0  -0.306  -5.2094   0.7922  -1.1573
 095  C1   C  CR56  0   0.139  -3.1489   0.6951   0.1249
 095  C17  C  CR56  0   0.367  -4.0314   0.1588  -0.8112
 095  C14  C  CR5   0   0.575  -2.3191  -1.3434  -0.7164
 095  C9   C  C     0   0.577   1.5933  -0.8084   0.7460
 095  C19  C  CH2   0  -0.486   4.7038  -0.2734   0.8609
 095  C23  C  CH2   0  -0.477   4.0251   1.0789  -1.1138
 095  C4   C  CH2   0  -0.463  -0.5852   0.3325   0.0821
 095  C13  C  CH2   0  -0.303  -1.8927  -0.8766   1.7134
 095  C20  C  CH2   0  -0.190   6.0754  -0.3980   0.2081
 095  C22  C  CH2   0  -0.193   5.4365   0.8688  -1.6483
 095  C7   C  CR15  0  -0.196   0.2642  -0.2915   1.2342
 095  C18  C  CH1   0   0.032   3.6523  -0.0912  -0.2217
 095  C2   C  C     0  -0.329  -1.9973  -0.2446   0.2938
 095  N16  N  NR15  0  -0.743  -3.5170  -1.0424  -1.2844
 095  N10  N  NR15  0  -0.574  -0.5300  -1.3302   1.8563
 095  O15  O  O     0  -0.451  -1.6398  -2.3210  -0.9582
 095  O21  O  O2    0  -0.481   6.3745   0.7131  -0.6065
 095  O11  O  O2    0  -0.465   2.3614   0.1923   0.3452
 095  H1   H  HCR6  0   0.255  -4.8664   3.4989   0.8713
 095  H2   H  HCR6  0   0.259  -6.4092   2.5247  -0.7834
 095  H3   H  HCR6  0   0.252  -2.7646   2.3293   1.4640
 095  H4   H  HCR6  0   0.268  -5.8870   0.3669  -1.8859
 095  H5   H  HCH2  0   0.253   4.5118  -1.1678   1.4565
 095  H6   H  HCH2  0   0.239   4.6900   0.5875   1.5351
 095  H7   H  HCH2  0   0.239   3.9813   2.0134  -0.5470
 095  H8   H  HCH2  0   0.252   3.3300   1.1630  -1.9520
 095  H9   H  HCH2  0   0.274  -0.5919   1.4192   0.1547
 095  H10  H  HCH2  0   0.273  -0.1980   0.0819  -0.9063
 095  H11  H  HCH2  0   0.252  -2.1020  -0.0944   2.4491
 095  H12  H  HCH2  0   0.271  -2.6060  -1.6830   1.8830
 095  H13  H  HCH2  0   0.245   6.8530  -0.4585   0.9701
 095  H14  H  HCH2  0   0.205   6.1182  -1.3269  -0.3798
 095  H15  H  HCH2  0   0.205   5.4515  -0.0098  -2.3092
 095  H16  H  HCH2  0   0.245   5.7499   1.7298  -2.2396
 095  H17  H  HCR5  0   0.287   0.4583   0.4947   1.9707
 095  H18  H  HCH1  0   0.243   3.5877  -0.9999  -0.8287
 095  H19  H  HNR5  0   0.411  -3.9662  -1.6239  -1.9758
 095  H20  H  HNR5  0   0.355  -0.4075  -2.1997   1.3498
 095  O12  O  O     0  -0.441   1.9023  -1.9719   0.7036

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
 095  N10  C7   single    1.448  0.020  1.448
 095  N10  C13  single    1.443  0.020  1.443
 095  C3   C5   aromatic  1.396  0.020  1.396
 095  C3   C1   aromatic  1.379  0.020  1.379
 095  C5   C8   aromatic  1.389  0.020  1.389
 095  C7   C4   single    1.561  0.020  1.561
 095  C7   C9   single    1.507  0.020  1.507
 095  C13  C2   single    1.557  0.020  1.557
 095  C4   C2   single    1.540  0.020  1.540
 095  C1   C2   single    1.496  0.020  1.496
 095  C1   C17  aromatic  1.394  0.020  1.394
 095  C2   C14  single    1.527  0.020  1.527
 095  C8   C6   aromatic  1.394  0.020  1.394
 095  C9   O11  single    1.324  0.020  1.324
 095  C9   O12  double    1.205  0.020  1.205
 095  O11  C18  single    1.438  0.020  1.438
 095  C17  C6   aromatic  1.382  0.020  1.382
 095  C17  N16  single    1.390  0.020  1.390
 095  C23  C18  single    1.518  0.020  1.518
 095  C23  C22  single    1.524  0.020  1.524
 095  C14  N16  single    1.359  0.020  1.359
 095  C14  O15  double    1.215  0.020  1.215
 095  C18  C19  single    1.520  0.020  1.520
 095  O21  C22  single    1.410  0.020  1.410
 095  O21  C20  single    1.410  0.020  1.410
 095  C19  C20  single    1.524  0.020  1.524
 095  C5   H1   single    0.930  0.020  1.080
 095  C8   H2   single    0.930  0.020  1.080
 095  C3   H3   single    0.930  0.020  1.080
 095  C6   H4   single    0.930  0.020  1.080
 095  C19  H5   single    0.970  0.020  1.090
 095  C19  H6   single    0.970  0.020  1.090
 095  C23  H7   single    0.970  0.020  1.090
 095  C23  H8   single    0.970  0.020  1.090
 095  C4   H9   single    0.970  0.020  1.090
 095  C4   H10  single    0.970  0.020  1.090
 095  C13  H11  single    0.970  0.020  1.090
 095  C13  H12  single    0.970  0.020  1.090
 095  C20  H13  single    0.970  0.020  1.090
 095  C20  H14  single    0.970  0.020  1.090
 095  C22  H15  single    0.970  0.020  1.090
 095  C22  H16  single    0.970  0.020  1.090
 095  C7   H17  single    0.970  0.020  1.090
 095  C18  H18  single    0.970  0.020  1.090
 095  N16  H19  single    0.860  0.020  1.020
 095  N10  H20  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
 095  H1   C5   C3   119.83  3.000
 095  H1   C5   C8   119.84  3.000
 095  C3   C5   C8   120.34  3.000
 095  H2   C8   C6   119.09  3.000
 095  H2   C8   C5   119.68  3.000
 095  C6   C8   C5   121.23  3.000
 095  H3   C3   C1   120.91  3.000
 095  H3   C3   C5   120.11  3.000
 095  C1   C3   C5   118.97  3.000
 095  H4   C6   C17  121.50  3.000
 095  H4   C6   C8   121.08  3.000
 095  C17  C6   C8   117.42  3.000
 095  C2   C1   C17  108.76  3.000
 095  C17  C1   C3   119.93  3.000
 095  C2   C1   C3   131.30  3.000
 095  N16  C17  C1   109.08  3.000
 095  N16  C17  C6   128.80  3.000
 095  C1   C17  C6   122.12  3.000
 095  O15  C14  N16  126.00  3.000
 095  O15  C14  C2   126.37  3.000
 095  N16  C14  C2   107.62  3.000
 095  O11  C9   O12  124.80  3.000
 095  O12  C9   C7   124.67  3.000
 095  O11  C9   C7   110.52  3.000
 095  H6   C19  H5   107.84  3.000
 095  H6   C19  C18  109.63  3.000
 095  H5   C19  C18  111.42  3.000
 095  H6   C19  C20  109.86  3.000
 095  H5   C19  C20  108.97  3.000
 095  C18  C19  C20  109.10  3.000
 095  H8   C23  H7   107.84  3.000
 095  H8   C23  C18  110.74  3.000
 095  H7   C23  C18  110.13  3.000
 095  H8   C23  C22  109.33  3.000
 095  H7   C23  C22  109.67  3.000
 095  C18  C23  C22  109.11  3.000
 095  H10  C4   H9   106.97  3.000
 095  H10  C4   C2   111.34  3.000
 095  H9   C4   C2   111.04  3.000
 095  H10  C4   C7   112.56  3.000
 095  H9   C4   C7   110.67  3.000
 095  C2   C4   C7   104.33  3.000
 095  H12  C13  H11  107.40  3.000
 095  H12  C13  N10  111.71  3.000
 095  H11  C13  N10  109.80  3.000
 095  H12  C13  C2   113.46  3.000
 095  H11  C13  C2   108.06  3.000
 095  N10  C13  C2   106.34  3.000
 095  H14  C20  H13  107.39  3.000
 095  H14  C20  O21  110.39  3.000
 095  H13  C20  O21  107.23  3.000
 095  H14  C20  C19  109.44  3.000
 095  H13  C20  C19  110.30  3.000
 095  O21  C20  C19  111.96  3.000
 095  H16  C22  H15  107.52  3.000
 095  H16  C22  O21  107.25  3.000
 095  H15  C22  O21  110.29  3.000
 095  H16  C22  C23  110.33  3.000
 095  H15  C22  C23  109.49  3.000
 095  O21  C22  C23  111.85  3.000
 095  H17  C7   N10  108.87  3.000
 095  H17  C7   C4   107.81  3.000
 095  N10  C7   C4   107.77  3.000
 095  H17  C7   C9   107.93  3.000
 095  C4   C7   C9   112.19  3.000
 095  N10  C7   C9   112.14  3.000
 095  H18  C18  O11  109.22  3.000
 095  H18  C18  C23  109.18  3.000
 095  O11  C18  C23  107.47  3.000
 095  H18  C18  C19  109.65  3.000
 095  C23  C18  C19  109.94  3.000
 095  O11  C18  C19  111.33  3.000
 095  C13  C2   C4   102.46  3.000
 095  C4   C2   C14  111.83  3.000
 095  C13  C2   C14  108.98  3.000
 095  C14  C2   C1   102.42  3.000
 095  C4   C2   C1   117.06  3.000
 095  C13  C2   C1   114.18  3.000
 095  H19  N16  C14  123.44  3.000
 095  H19  N16  C17  124.52  3.000
 095  C14  N16  C17  112.04  3.000
 095  H20  N10  C7   109.53  3.000
 095  H20  N10  C13  109.53  3.000
 095  C7   N10  C13  104.47  3.000
 095  C22  O21  C20  111.88  3.000
 095  C18  O11  C9   119.42  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
 095  CONST_01  C17  C1   C3   C5     0.00   0.0  0
 095  CONST_02  C17  C6   C8   C5     0.00   0.0  0
 095  CONST_03  C1   C3   C5   C8     0.00   0.0  0
 095  CONST_04  C1   C17  C6   C8     0.00   0.0  0
 095  CONST_05  C6   C8   C5   C3     0.00   0.0  0
 095  CONST_06  C6   C17  C1   C3     0.00   0.0  0
 095  CONST_07  C2   C14  N16  C17    0.00   0.0  0
 095  CONST_08  O15  C14  N16  C17  180.00   0.0  0
 095  CONST_09  H4   C6   C8   C5   180.00   0.0  0
 095  CONST_10  H3   C3   C5   C8   180.00   0.0  0
 095  CONST_11  H2   C8   C5   C3   180.00   0.0  0
 095  CONST_12  H1   C5   C8   C6   180.00   0.0  0
 095  CONST_13  H19  N16  C14  C2   180.00   0.0  0
 095  Var_01    C2   C13  N10  C7    39.59  30.0  1
 095  Var_02    O21  C22  C23  C18  -57.00  30.0  1
 095  Var_03    O21  C20  C19  C18   56.66  30.0  1
 095  Var_04    H15  C22  O21  C20  -61.98  30.0  1
 095  Var_05    H13  C20  O21  C22  178.90  30.0  1
 095  Var_06    O12  C9   O11  C18    1.78  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
 095  chir_01  C7   N10  C4   C9   positiv
 095  chir_02  C18  O11  C19  C23  positiv
 095  chir_03  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
 095  plan-1  C5   0.020
 095  plan-1  C8   0.020
 095  plan-1  C3   0.020
 095  plan-1  C6   0.020
 095  plan-1  C1   0.020
 095  plan-1  C17  0.020
 095  plan-1  C14  0.020
 095  plan-1  C2   0.020
 095  plan-1  N16  0.020
 095  plan-1  O15  0.020
 095  plan-1  H1   0.020
 095  plan-1  H2   0.020
 095  plan-1  H3   0.020
 095  plan-1  H4   0.020
 095  plan-1  H19  0.020
 095  plan-2  C9   0.020
 095  plan-2  C7   0.020
 095  plan-2  O11  0.020
 095  plan-2  O12  0.020

