# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 13 03:17:55 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 1-cyanocyclohexyl (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=C1Nc2ccccc2[C@@]13CN[C@H](C3)C(=O)OC4(CCCCC4)C#N
#
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
 09F  09F  '1-cyanocyclohexyl (3S,5'R)-2-oxo-1,2-dihydrospiro[indole-3,3'-pyrrolidine]-5'-carboxylate'  ligand  46  25  .  2022-03-08  2022-03-08
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_09F
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
 09F  C24  C  CSP   0   0.115   3.2560  -0.9240  -1.1349
 09F  C5   C  CR16  0  -0.261  -5.0847   2.5076   0.1221
 09F  C8   C  CR16  0  -0.267  -5.8484   1.7979  -0.7957
 09F  C3   C  CR16  0  -0.350  -3.8780   1.9852   0.5878
 09F  C6   C  CR16  0  -0.306  -5.4352   0.5552  -1.2730
 09F  C1   C  CR56  0   0.140  -3.4575   0.7569   0.1214
 09F  C17  C  CR56  0   0.367  -4.2371   0.0573  -0.7980
 09F  C14  C  CR5   0   0.578  -2.4275  -1.2853  -0.4505
 09F  C9   C  C     0   0.581   1.2923  -0.5349   0.9108
 09F  C21  C  CH2   0  -0.431   6.2535   0.8377  -0.1907
 09F  C20  C  CH2   0  -0.459   5.7809  -0.4600   0.4519
 09F  C22  C  CH2   0  -0.462   5.2908   1.2866  -1.2829
 09F  C19  C  CH2   0  -0.456   4.3595  -0.3370   0.9950
 09F  C23  C  CH2   0  -0.457   3.8670   1.4101  -0.7538
 09F  C4   C  CH2   0  -0.464  -0.8801   0.6036   0.2345
 09F  C13  C  CH2   0  -0.298  -2.1607  -0.5194   1.9292
 09F  C7   C  CR15  0  -0.179   0.0010   0.0603   1.4065
 09F  C18  C  CT    0   0.167   3.3798   0.1136  -0.0940
 09F  C2   C  C     0  -0.335  -2.2496  -0.0627   0.4483
 09F  N25  N  NS    0  -0.245   3.2167  -1.6836  -1.9969
 09F  N16  N  NR15  0  -0.744  -3.6074  -1.1419  -1.1100
 09F  N10  N  NR15  0  -0.580  -0.7860  -0.9035   2.1491
 09F  O12  O  O     0  -0.420   1.5719  -1.7026   0.9111
 09F  O11  O  O2    0  -0.472   2.0869   0.4238   0.4328
 09F  H1   H  HCR6  0   0.255  -5.4252   3.4711   0.4766
 09F  H2   H  HCR6  0   0.260  -6.7825   2.2135  -1.1505
 09F  H3   H  HCR6  0   0.253  -3.2828   2.5402   1.3034
 09F  H4   H  HCR6  0   0.268  -6.0329   0.0054  -1.9882
 09F  H5   H  HCH2  0   0.222   6.3261   1.6173   0.5750
 09F  H6   H  HCH2  0   0.242   7.2559   0.7099  -0.6037
 09F  H7   H  HCH2  0   0.233   5.8346  -1.2758  -0.2766
 09F  H8   H  HCH2  0   0.254   6.4391  -0.7448   1.2744
 09F  H9   H  HCH2  0   0.255   5.5943   2.2531  -1.6882
 09F  H10  H  HCH2  0   0.234   5.3227   0.5804  -2.1186
 09F  H11  H  HCH2  0   0.272   4.0412  -1.2808   1.4362
 09F  H12  H  HCH2  0   0.263   4.3299   0.4217   1.7827
 09F  H13  H  HCH2  0   0.265   3.8251   2.1892   0.0128
 09F  H14  H  HCH2  0   0.270   3.1789   1.6996  -1.5505
 09F  H15  H  HCH2  0   0.278  -0.9693   1.6866   0.3036
 09F  H16  H  HCH2  0   0.275  -0.4724   0.3800  -0.7517
 09F  H17  H  HCH2  0   0.253  -2.4214   0.3320   2.5654
 09F  H18  H  HCH2  0   0.271  -2.8444  -1.3317   2.1760
 09F  H19  H  HCR5  0   0.291   0.2546   0.9033   2.0563
 09F  H20  H  HNR5  0   0.412  -3.9675  -1.8240  -1.7605
 09F  H21  H  HNR5  0   0.360  -0.6319  -1.8308   1.7702
 09F  O15  O  O     0  -0.448  -1.6624  -2.2230  -0.5508

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
 09F  N10  C7   single    1.449  0.020  1.449
 09F  N10  C13  single    1.444  0.020  1.444
 09F  C3   C5   aromatic  1.395  0.020  1.395
 09F  C3   C1   aromatic  1.379  0.020  1.379
 09F  C5   C8   aromatic  1.389  0.020  1.389
 09F  C7   C4   single    1.564  0.020  1.564
 09F  C7   C9   single    1.506  0.020  1.506
 09F  C13  C2   single    1.552  0.020  1.552
 09F  C4   C2   single    1.538  0.020  1.538
 09F  C1   C2   single    1.496  0.020  1.496
 09F  C1   C17  aromatic  1.394  0.020  1.394
 09F  C2   C14  single    1.528  0.020  1.528
 09F  C8   C6   aromatic  1.394  0.020  1.394
 09F  C9   O11  single    1.334  0.020  1.334
 09F  C9   O12  double    1.201  0.020  1.201
 09F  O11  C18  single    1.430  0.020  1.430
 09F  C23  C18  single    1.534  0.020  1.534
 09F  C23  C22  single    1.524  0.020  1.524
 09F  C17  C6   aromatic  1.382  0.020  1.382
 09F  C17  N16  single    1.390  0.020  1.390
 09F  C18  C19  single    1.533  0.020  1.533
 09F  C18  C24  single    1.475  0.020  1.475
 09F  C14  N16  single    1.359  0.020  1.359
 09F  C14  O15  double    1.214  0.020  1.214
 09F  C19  C20  single    1.527  0.020  1.527
 09F  C22  C21  single    1.524  0.020  1.524
 09F  C21  C20  single    1.523  0.020  1.523
 09F  C24  N25  triple    1.150  0.020  1.150
 09F  C5   H1   single    0.930  0.020  1.080
 09F  C8   H2   single    0.930  0.020  1.080
 09F  C3   H3   single    0.930  0.020  1.080
 09F  C6   H4   single    0.930  0.020  1.080
 09F  C21  H5   single    0.970  0.020  1.090
 09F  C21  H6   single    0.970  0.020  1.090
 09F  C20  H7   single    0.970  0.020  1.090
 09F  C20  H8   single    0.970  0.020  1.090
 09F  C22  H9   single    0.970  0.020  1.090
 09F  C22  H10  single    0.970  0.020  1.090
 09F  C19  H11  single    0.970  0.020  1.090
 09F  C19  H12  single    0.970  0.020  1.090
 09F  C23  H13  single    0.970  0.020  1.090
 09F  C23  H14  single    0.970  0.020  1.090
 09F  C4   H15  single    0.970  0.020  1.090
 09F  C4   H16  single    0.970  0.020  1.090
 09F  C13  H17  single    0.970  0.020  1.090
 09F  C13  H18  single    0.970  0.020  1.090
 09F  C7   H19  single    0.970  0.020  1.090
 09F  N16  H20  single    0.860  0.020  1.020
 09F  N10  H21  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
 09F  N25  C24  C18  180.00  3.000
 09F  H1   C5   C3   119.77  3.000
 09F  H1   C5   C8   119.91  3.000
 09F  C3   C5   C8   120.32  3.000
 09F  H2   C8   C6   119.08  3.000
 09F  H2   C8   C5   119.66  3.000
 09F  C6   C8   C5   121.25  3.000
 09F  H3   C3   C1   120.79  3.000
 09F  H3   C3   C5   120.25  3.000
 09F  C1   C3   C5   118.96  3.000
 09F  H4   C6   C17  121.54  3.000
 09F  H4   C6   C8   121.03  3.000
 09F  C17  C6   C8   117.43  3.000
 09F  C2   C1   C17  108.71  3.000
 09F  C17  C1   C3   119.97  3.000
 09F  C2   C1   C3   131.31  3.000
 09F  N16  C17  C1   109.13  3.000
 09F  N16  C17  C6   128.80  3.000
 09F  C1   C17  C6   122.07  3.000
 09F  O15  C14  N16  126.04  3.000
 09F  O15  C14  C2   126.38  3.000
 09F  N16  C14  C2   107.58  3.000
 09F  O11  C9   O12  124.08  3.000
 09F  O12  C9   C7   125.73  3.000
 09F  O11  C9   C7   110.17  3.000
 09F  H6   C21  H5   106.68  3.000
 09F  H6   C21  C22  110.09  3.000
 09F  H5   C21  C22  109.47  3.000
 09F  H6   C21  C20  110.17  3.000
 09F  H5   C21  C20  109.39  3.000
 09F  C22  C21  C20  110.94  3.000
 09F  H8   C20  H7   106.10  3.000
 09F  H8   C20  C19  108.33  3.000
 09F  H7   C20  C19  110.02  3.000
 09F  H8   C20  C21  110.68  3.000
 09F  H7   C20  C21  109.81  3.000
 09F  C19  C20  C21  111.74  3.000
 09F  H10  C22  H9   106.25  3.000
 09F  H10  C22  C23  110.15  3.000
 09F  H9   C22  C23  108.48  3.000
 09F  H10  C22  C21  109.81  3.000
 09F  H9   C22  C21  110.58  3.000
 09F  C23  C22  C21  111.43  3.000
 09F  H12  C19  H11  107.53  3.000
 09F  H12  C19  C18  106.89  3.000
 09F  H11  C19  C18  110.84  3.000
 09F  H12  C19  C20  109.70  3.000
 09F  H11  C19  C20  110.26  3.000
 09F  C18  C19  C20  111.48  3.000
 09F  H14  C23  H13  107.36  3.000
 09F  H14  C23  C18  109.74  3.000
 09F  H13  C23  C18  106.76  3.000
 09F  H14  C23  C22  110.92  3.000
 09F  H13  C23  C22  109.68  3.000
 09F  C18  C23  C22  112.18  3.000
 09F  H16  C4   H15  106.97  3.000
 09F  H16  C4   C2   111.71  3.000
 09F  H15  C4   C2   110.43  3.000
 09F  H16  C4   C7   113.33  3.000
 09F  H15  C4   C7   110.13  3.000
 09F  C2   C4   C7   104.31  3.000
 09F  H18  C13  H17  107.39  3.000
 09F  H18  C13  N10  111.37  3.000
 09F  H17  C13  N10  110.19  3.000
 09F  H18  C13  C2   113.54  3.000
 09F  H17  C13  C2   108.18  3.000
 09F  N10  C13  C2   106.14  3.000
 09F  H19  C7   N10  109.51  3.000
 09F  H19  C7   C4   107.94  3.000
 09F  N10  C7   C4   108.01  3.000
 09F  H19  C7   C9   107.53  3.000
 09F  C4   C7   C9   111.95  3.000
 09F  N10  C7   C9   111.81  3.000
 09F  O11  C18  C23  105.20  3.000
 09F  C23  C18  C19  110.55  3.000
 09F  O11  C18  C19  112.33  3.000
 09F  C19  C18  C24  110.38  3.000
 09F  C23  C18  C24  108.52  3.000
 09F  O11  C18  C24  109.67  3.000
 09F  C13  C2   C4   102.07  3.000
 09F  C4   C2   C14  111.63  3.000
 09F  C13  C2   C14  109.41  3.000
 09F  C14  C2   C1   102.47  3.000
 09F  C4   C2   C1   116.83  3.000
 09F  C13  C2   C1   114.58  3.000
 09F  H20  N16  C14  123.45  3.000
 09F  H20  N16  C17  124.49  3.000
 09F  C14  N16  C17  112.05  3.000
 09F  H21  N10  C7   109.54  3.000
 09F  H21  N10  C13  109.34  3.000
 09F  C7   N10  C13  105.20  3.000
 09F  C18  O11  C9   120.98  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
 09F  CONST_01  C17  C1   C3   C5     0.00   0.0  0
 09F  CONST_02  C17  C6   C8   C5     0.00   0.0  0
 09F  CONST_03  C1   C3   C5   C8     0.00   0.0  0
 09F  CONST_04  C1   C17  C6   C8     0.00   0.0  0
 09F  CONST_05  C6   C8   C5   C3     0.00   0.0  0
 09F  CONST_06  C6   C17  C1   C3     0.00   0.0  0
 09F  CONST_07  C2   C14  N16  C17    0.00   0.0  0
 09F  CONST_08  O15  C14  N16  C17  180.00   0.0  0
 09F  CONST_09  H4   C6   C8   C5   180.00   0.0  0
 09F  CONST_10  H3   C3   C5   C8   180.00   0.0  0
 09F  CONST_11  H2   C8   C5   C3   180.00   0.0  0
 09F  CONST_12  H1   C5   C8   C6   180.00   0.0  0
 09F  CONST_13  H20  N16  C14  C2   180.00   0.0  0
 09F  Var_01    C18  C23  C22  C21  -54.99  30.0  1
 09F  Var_02    C18  C19  C20  C21   55.67  30.0  1
 09F  Var_03    C23  C22  C21  C20   55.06  30.0  1
 09F  Var_04    C19  C20  C21  C22  -55.66  30.0  1
 09F  Var_05    C2   C13  N10  C7    38.41  30.0  1
 09F  Var_06    O12  C9   O11  C18   -1.75  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
 09F  chir_01  C7   N10  C4   C9   positiv
 09F  chir_02  C18  C24  C19  C23  negativ
 09F  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
 09F  plan-1  C5   0.020
 09F  plan-1  C8   0.020
 09F  plan-1  C3   0.020
 09F  plan-1  C6   0.020
 09F  plan-1  C1   0.020
 09F  plan-1  C17  0.020
 09F  plan-1  C14  0.020
 09F  plan-1  C2   0.020
 09F  plan-1  N16  0.020
 09F  plan-1  H1   0.020
 09F  plan-1  H2   0.020
 09F  plan-1  H3   0.020
 09F  plan-1  H4   0.020
 09F  plan-1  H20  0.020
 09F  plan-1  O15  0.020
 09F  plan-2  C9   0.020
 09F  plan-2  C7   0.020
 09F  plan-2  O12  0.020
 09F  plan-2  O11  0.020

