# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 00:49:03 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 2-[1-[(3~{S})-6'-azanyl-5'-cyano-7-fluoranyl-2,2,3'-trimethyl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5-yl]piperidin-4-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1[nH]nc2OC(=C(C#N)[C@]3(c4cc(cc(F)c4CC3(C)C)N5CCC(CC5)CC(O)=O)c12)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
 8UF  8UF  '2-[1-[(3~{S})-6'-azanyl-5'-cyano-7-fluoranyl-2,2,3'-trimethyl-spiro[1~{H}-indene-3,4'-2~{H}-pyrano[2,3-c]pyrazole]-5-yl]piperidin-4-yl]ethanoic acid'  ligand  62  34  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_8UF
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
 8UF  C2   C  CR6   0   0.593   3.4111   2.4737  -0.3719
 8UF  C3   C  CR6   0  -0.194   2.6270   1.4741  -0.8901
 8UF  C4   C  C     0  -0.166   2.6121   0.0532  -0.3496
 8UF  C5   C  CR56  0  -0.135   2.9830   0.1835   1.0998
 8UF  C6   C  CR56  0   0.460   3.7018   1.2866   1.5574
 8UF  N7   N  NH2   0  -0.831   3.6495   3.6641  -0.9362
 8UF  C8   C  CSP   0   0.018   1.8417   1.8062  -2.0085
 8UF  C10  C  CR5   0   0.356   2.8117  -0.5736   2.2482
 8UF  C13  C  CH3   0  -0.756   2.1294  -1.8652   2.5249
 8UF  C16  C  CR56  0   0.191   1.2732  -0.6392  -0.4847
 8UF  C17  C  CR56  0  -0.158   1.4703  -1.9858  -0.7687
 8UF  C18  C  CR6   0   0.541   0.3518  -2.7778  -0.8521
 8UF  C20  C  CR16  0  -0.426   0.0235  -0.1018  -0.2757
 8UF  O54  O  OH1   0  -0.596  -8.3450   1.1767   1.6118
 8UF  C52  C  C     0   0.550  -7.5300   0.7057   0.6721
 8UF  O53  O  O     0  -0.443  -7.8570  -0.1603  -0.1016
 8UF  C51  C  CH2   0  -0.577  -6.2018   1.4110   0.6780
 8UF  C38  C  CH1   0  -0.245  -5.0923   0.6798  -0.0636
 8UF  C37  C  CH2   0  -0.421  -3.8637   1.5751  -0.1885
 8UF  C36  C  CH2   0  -0.303  -2.7159   0.8499  -0.8682
 8UF  C39  C  CH2   0  -0.419  -4.6846  -0.6157   0.6310
 8UF  C40  C  CH2   0  -0.307  -3.5040  -1.2880  -0.0539
 8UF  N35  N  NT    0  -0.517  -2.3779  -0.3812  -0.1613
 8UF  C19  C  CR6   0   0.395  -1.1149  -0.9206  -0.3836
 8UF  C41  C  CR16  0  -0.560  -0.9284  -2.2775  -0.6831
 8UF  F29  F  F     0  -0.315   0.4934  -4.0895  -1.1193
 8UF  C44  C  CH2   0  -0.475   2.9261  -2.3154  -0.8742
 8UF  C14  C  CR5   0  -0.045   3.5702  -0.9374  -1.1326
 8UF  C30  C  CH3   0  -0.656   3.5220  -0.6600  -2.6366
 8UF  N9   N  NS    0  -0.287   1.1849   2.1077  -2.9137
 8UF  N11  N  NR15  0  -0.489   3.4321   0.1122   3.2277
 8UF  N12  N  N     0  -0.289   3.9818   1.2630   2.8320
 8UF  O1   O  O     0  -0.455   4.0724   2.3406   0.7900
 8UF  H1   H  HNH2  0   0.418   3.1974   3.9024  -1.8029
 8UF  H2   H  HNH2  0   0.415   3.9043   4.4423  -0.3485
 8UF  H3   H  HCH3  0   0.262   2.7961  -2.7126   2.3575
 8UF  H4   H  HCH3  0   0.267   1.7894  -1.9115   3.5589
 8UF  H5   H  HCH3  0   0.268   1.2643  -1.9902   1.8788
 8UF  H6   H  HCH3  0   0.236   5.1297  -1.1190   0.3842
 8UF  H7   H  HCH3  0   0.236   5.6298  -1.5598  -1.2454
 8UF  H8   H  HCH3  0   0.226   5.4286   0.1347  -0.8253
 8UF  H9   H  HCR6  0   0.254  -0.0762   0.9415  -0.0041
 8UF  H10  H  HOH1  0   0.478  -9.2059   0.7356   1.5531
 8UF  H11  H  HCH2  0   0.291  -6.3721   2.3921   0.2178
 8UF  H12  H  HCH2  0   0.267  -5.9012   1.6192   1.7083
 8UF  H13  H  HCH1  0   0.232  -5.4428   0.4384  -1.0739
 8UF  H14  H  HCH2  0   0.239  -4.1048   2.4738  -0.7623
 8UF  H15  H  HCH2  0   0.221  -3.5438   1.9063   0.8050
 8UF  H16  H  HCH2  0   0.215  -2.9901   0.6247  -1.9103
 8UF  H17  H  HCH2  0   0.256  -1.8488   1.5053  -0.9070
 8UF  H18  H  HCH2  0   0.219  -4.4168  -0.4008   1.6708
 8UF  H19  H  HCH2  0   0.243  -5.5133  -1.3255   0.6536
 8UF  H20  H  HCH2  0   0.252  -3.2101  -2.1524   0.5422
 8UF  H21  H  HCH2  0   0.210  -3.8130  -1.6676  -1.0409
 8UF  H22  H  HCR6  0   0.282  -1.7636  -2.9529  -0.8056
 8UF  H23  H  HCH2  0   0.255   3.2921  -2.7536   0.0612
 8UF  H24  H  HCH2  0   0.256   3.1596  -3.0313  -1.6651
 8UF  H25  H  HCH3  0   0.234   3.9488   0.3129  -2.8818
 8UF  H26  H  HCH3  0   0.239   4.1064  -1.4144  -3.1658
 8UF  H27  H  HCH3  0   0.236   2.5062  -0.6948  -3.0334
 8UF  H28  H  HNR5  0   0.420   3.4936  -0.1543   4.1978
 8UF  C15  C  CH3   0  -0.663   5.0161  -0.8649  -0.6694

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
 8UF  O53  C52  double    1.206  0.020  1.206
 8UF  C52  O54  single    1.330  0.020  1.330
 8UF  C52  C51  single    1.504  0.020  1.504
 8UF  N11  C10  aromatic  1.347  0.020  1.347
 8UF  N11  N12  aromatic  1.335  0.020  1.335
 8UF  C51  C38  single    1.522  0.020  1.522
 8UF  C13  C10  single    1.487  0.020  1.487
 8UF  C39  C38  single    1.525  0.020  1.525
 8UF  C39  C40  single    1.522  0.020  1.522
 8UF  C10  C5   aromatic  1.386  0.020  1.386
 8UF  N12  C6   aromatic  1.305  0.020  1.305
 8UF  C38  C37  single    1.525  0.020  1.525
 8UF  C40  N35  single    1.450  0.020  1.450
 8UF  C6   C5   aromatic  1.394  0.020  1.394
 8UF  C6   O1   single    1.355  0.020  1.355
 8UF  C5   C4   single    1.502  0.020  1.502
 8UF  C37  C36  single    1.518  0.020  1.518
 8UF  N35  C19  single    1.391  0.020  1.391
 8UF  N35  C36  single    1.459  0.020  1.459
 8UF  C15  C14  single    1.520  0.020  1.520
 8UF  C20  C19  aromatic  1.406  0.020  1.406
 8UF  C20  C16  aromatic  1.376  0.020  1.376
 8UF  C19  C41  aromatic  1.402  0.020  1.402
 8UF  O1   C2   single    1.343  0.020  1.343
 8UF  C16  C4   single    1.513  0.020  1.513
 8UF  C16  C17  aromatic  1.390  0.020  1.390
 8UF  C4   C14  single    1.585  0.020  1.585
 8UF  C4   C3   single    1.520  0.020  1.520
 8UF  C41  C18  aromatic  1.385  0.020  1.385
 8UF  C14  C30  single    1.530  0.020  1.530
 8UF  C14  C44  single    1.543  0.020  1.543
 8UF  C17  C18  aromatic  1.373  0.020  1.373
 8UF  C17  C44  single    1.496  0.020  1.496
 8UF  C18  F29  single    1.346  0.020  1.346
 8UF  C2   C3   double    1.372  0.020  1.372
 8UF  C2   N7   single    1.339  0.020  1.339
 8UF  C3   C8   single    1.406  0.020  1.406
 8UF  C8   N9   triple    1.158  0.020  1.158
 8UF  N7   H1   single    0.890  0.020  1.040
 8UF  N7   H2   single    0.890  0.020  1.040
 8UF  C13  H3   single    0.970  0.020  1.090
 8UF  C13  H4   single    0.970  0.020  1.090
 8UF  C13  H5   single    0.970  0.020  1.090
 8UF  C15  H6   single    0.970  0.020  1.090
 8UF  C15  H7   single    0.970  0.020  1.090
 8UF  C15  H8   single    0.970  0.020  1.090
 8UF  C20  H9   single    0.930  0.020  1.080
 8UF  O54  H10  single    0.850  0.020  0.980
 8UF  C51  H11  single    0.970  0.020  1.090
 8UF  C51  H12  single    0.970  0.020  1.090
 8UF  C38  H13  single    0.970  0.020  1.090
 8UF  C37  H14  single    0.970  0.020  1.090
 8UF  C37  H15  single    0.970  0.020  1.090
 8UF  C36  H16  single    0.970  0.020  1.090
 8UF  C36  H17  single    0.970  0.020  1.090
 8UF  C39  H18  single    0.970  0.020  1.090
 8UF  C39  H19  single    0.970  0.020  1.090
 8UF  C40  H20  single    0.970  0.020  1.090
 8UF  C40  H21  single    0.970  0.020  1.090
 8UF  C41  H22  single    0.930  0.020  1.080
 8UF  C44  H23  single    0.970  0.020  1.090
 8UF  C44  H24  single    0.970  0.020  1.090
 8UF  C30  H25  single    0.970  0.020  1.090
 8UF  C30  H26  single    0.970  0.020  1.090
 8UF  C30  H27  single    0.970  0.020  1.090
 8UF  N11  H28  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
 8UF  O1   C2   N7   111.40  3.000
 8UF  N7   C2   C3   126.18  3.000
 8UF  O1   C2   C3   122.40  3.000
 8UF  C8   C3   C4   119.86  3.000
 8UF  C8   C3   C2   116.58  3.000
 8UF  C4   C3   C2   123.52  3.000
 8UF  C14  C4   C16  101.82  3.000
 8UF  C14  C4   C5   112.44  3.000
 8UF  C16  C4   C5   110.14  3.000
 8UF  C14  C4   C3   113.74  3.000
 8UF  C16  C4   C3   113.87  3.000
 8UF  C5   C4   C3   105.05  3.000
 8UF  C10  C5   C6   102.94  3.000
 8UF  C6   C5   C4   120.86  3.000
 8UF  C10  C5   C4   136.20  3.000
 8UF  O1   C6   N12  120.55  3.000
 8UF  O1   C6   C5   124.79  3.000
 8UF  N12  C6   C5   114.64  3.000
 8UF  H2   N7   H1   115.66  3.000
 8UF  H2   N7   C2   119.06  3.000
 8UF  H1   N7   C2   119.57  3.000
 8UF  N9   C8   C3   180.00  3.000
 8UF  N11  C10  C13  121.22  3.000
 8UF  C13  C10  C5   133.26  3.000
 8UF  N11  C10  C5   105.51  3.000
 8UF  H5   C13  H4   108.11  3.000
 8UF  H5   C13  H3   107.81  3.000
 8UF  H4   C13  H3   107.65  3.000
 8UF  H5   C13  C10  110.77  3.000
 8UF  H4   C13  C10  110.90  3.000
 8UF  H3   C13  C10  111.46  3.000
 8UF  C20  C16  C17  122.55  3.000
 8UF  C17  C16  C4   109.63  3.000
 8UF  C20  C16  C4   127.67  3.000
 8UF  C44  C17  C18  131.39  3.000
 8UF  C44  C17  C16  111.45  3.000
 8UF  C18  C17  C16  117.10  3.000
 8UF  F29  C18  C41  118.27  3.000
 8UF  F29  C18  C17  119.23  3.000
 8UF  C41  C18  C17  122.50  3.000
 8UF  H9   C20  C19  120.38  3.000
 8UF  H9   C20  C16  119.87  3.000
 8UF  C19  C20  C16  119.73  3.000
 8UF  H10  O54  C52  109.90  3.000
 8UF  C51  C52  O53  125.35  3.000
 8UF  C51  C52  O54  111.86  3.000
 8UF  O53  C52  O54  122.76  3.000
 8UF  H12  C51  H11  105.53  3.000
 8UF  H12  C51  C38  110.50  3.000
 8UF  H11  C51  C38  109.79  3.000
 8UF  H12  C51  C52  109.62  3.000
 8UF  H11  C51  C52  106.31  3.000
 8UF  C38  C51  C52  114.63  3.000
 8UF  H13  C38  C39  108.54  3.000
 8UF  H13  C38  C37  108.14  3.000
 8UF  C39  C38  C37  108.70  3.000
 8UF  H13  C38  C51  108.77  3.000
 8UF  C37  C38  C51  110.20  3.000
 8UF  C39  C38  C51  112.40  3.000
 8UF  H15  C37  H14  106.98  3.000
 8UF  H15  C37  C36  109.26  3.000
 8UF  H14  C37  C36  108.93  3.000
 8UF  H15  C37  C38  109.78  3.000
 8UF  H14  C37  C38  110.35  3.000
 8UF  C36  C37  C38  111.43  3.000
 8UF  H17  C36  H16  106.74  3.000
 8UF  H17  C36  N35  109.94  3.000
 8UF  H16  C36  N35  110.10  3.000
 8UF  H17  C36  C37  109.32  3.000
 8UF  H16  C36  C37  109.46  3.000
 8UF  N35  C36  C37  111.17  3.000
 8UF  H19  C39  H18  107.08  3.000
 8UF  H19  C39  C40  108.13  3.000
 8UF  H18  C39  C40  108.92  3.000
 8UF  H19  C39  C38  111.03  3.000
 8UF  H18  C39  C38  109.33  3.000
 8UF  C40  C39  C38  112.19  3.000
 8UF  H21  C40  H20  106.99  3.000
 8UF  H21  C40  N35  111.53  3.000
 8UF  H20  C40  N35  109.09  3.000
 8UF  H21  C40  C39  109.75  3.000
 8UF  H20  C40  C39  108.26  3.000
 8UF  N35  C40  C39  111.08  3.000
 8UF  C19  N35  C40  118.32  3.000
 8UF  C19  N35  C36  117.38  3.000
 8UF  C40  N35  C36  112.56  3.000
 8UF  C41  C19  N35  122.02  3.000
 8UF  C41  C19  C20  118.17  3.000
 8UF  N35  C19  C20  119.79  3.000
 8UF  H22  C41  C19  121.74  3.000
 8UF  H22  C41  C18  118.33  3.000
 8UF  C19  C41  C18  119.92  3.000
 8UF  H24  C44  H23  106.53  3.000
 8UF  H24  C44  C14  112.02  3.000
 8UF  H23  C44  C14  111.14  3.000
 8UF  H24  C44  C17  113.80  3.000
 8UF  H23  C44  C17  110.66  3.000
 8UF  C14  C44  C17  102.78  3.000
 8UF  C30  C14  C44  108.26  3.000
 8UF  C44  C14  C15  112.87  3.000
 8UF  C30  C14  C15  108.72  3.000
 8UF  C44  C14  C4   102.89  3.000
 8UF  C30  C14  C4   110.68  3.000
 8UF  C15  C14  C4   113.24  3.000
 8UF  H27  C30  H26  107.46  3.000
 8UF  H27  C30  H25  108.13  3.000
 8UF  H26  C30  H25  107.34  3.000
 8UF  H27  C30  C14  112.40  3.000
 8UF  H26  C30  C14  109.54  3.000
 8UF  H25  C30  C14  111.75  3.000
 8UF  H28  N11  N12  119.21  3.000
 8UF  H28  N11  C10  126.40  3.000
 8UF  N12  N11  C10  114.38  3.000
 8UF  N11  N12  C6   102.51  3.000
 8UF  C6   O1   C2   115.60  3.000
 8UF  H8   C15  H7   107.15  3.000
 8UF  H8   C15  H6   108.18  3.000
 8UF  H7   C15  H6   107.65  3.000
 8UF  H8   C15  C14  111.06  3.000
 8UF  H7   C15  C14  110.10  3.000
 8UF  H6   C15  C14  112.50  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
 8UF  CONST_01  N12  N11  C10  C5      0.00   0.0  0
 8UF  CONST_02  N11  N12  C6   C5      0.00   0.0  0
 8UF  CONST_03  C10  N11  N12  C6      0.00   0.0  0
 8UF  CONST_04  N11  C10  C5   C6      0.00   0.0  0
 8UF  CONST_05  N12  C6   C5   C10     0.00   0.0  0
 8UF  CONST_06  C41  C19  C20  C16     0.00   0.0  0
 8UF  CONST_07  C41  C18  C17  C16     0.00   0.0  0
 8UF  CONST_08  C19  C20  C16  C17     0.00   0.0  0
 8UF  CONST_09  C19  C41  C18  C17     0.00   0.0  0
 8UF  CONST_10  C20  C19  C41  C18     0.00   0.0  0
 8UF  CONST_11  C20  C16  C17  C18     0.00   0.0  0
 8UF  CONST_12  N11  C10  C5   C4    180.00   0.0  0
 8UF  CONST_13  N12  C6   C5   C4    180.00   0.0  0
 8UF  CONST_14  O1   C6   C5   C4      0.00   0.0  0
 8UF  CONST_15  N35  C19  C20  C16   180.00   0.0  0
 8UF  CONST_16  N35  C19  C41  C18   180.00   0.0  0
 8UF  CONST_17  C13  C10  C5   C4      0.00   0.0  0
 8UF  CONST_18  C13  C10  C5   C6    180.00   0.0  0
 8UF  CONST_19  N12  N11  C10  C13   180.00   0.0  0
 8UF  CONST_20  F29  C18  C17  C16   180.00   0.0  0
 8UF  CONST_21  F29  C18  C41  C19   180.00   0.0  0
 8UF  CONST_22  C44  C17  C18  F29     0.00   0.0  0
 8UF  CONST_23  H9   C20  C16  C4      0.00   0.0  0
 8UF  CONST_24  H28  N11  C10  C5    180.00   0.0  0
 8UF  CONST_25  H22  C41  C18  C17   180.00   0.0  0
 8UF  CONST_26  H10  O54  C52  O53     0.00   0.0  0
 8UF  Var_01    N12  C6   O1   C2   -160.54  30.0  1
 8UF  Var_02    C17  C44  C14  C4     31.57  30.0  1
 8UF  Var_03    O1   C2   C3   C4    -10.97  30.0  1
 8UF  Var_04    C14  C44  C17  C16   -20.07  30.0  1
 8UF  Var_05    C40  N35  C19  C20  -169.61  30.0  1
 8UF  Var_06    N35  C40  C39  C38    55.19  30.0  1
 8UF  Var_07    N35  C36  C37  C38   -56.41  30.0  1
 8UF  Var_08    C39  C40  N35  C36   -56.75  30.0  1
 8UF  Var_09    H1   N7   C2   C3      2.93  30.0  2
 8UF  Var_10    H6   C15  C14  C4     60.35  30.0  3
 8UF  Var_11    H25  C30  C14  C4     66.92  30.0  3
 8UF  Var_12    H3   C13  C10  C5     87.54  30.0  2
 8UF  Var_13    C38  C51  C52  O54   162.82  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
 8UF  chir_01  C4   C16  C14  C3   negativ
 8UF  chir_02  C38  C51  C39  C37  positiv

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
 8UF  plan-1  C4   0.020
 8UF  plan-1  C16  0.020
 8UF  plan-1  C17  0.020
 8UF  plan-1  C18  0.020
 8UF  plan-1  C20  0.020
 8UF  plan-1  N35  0.020
 8UF  plan-1  C19  0.020
 8UF  plan-1  C41  0.020
 8UF  plan-1  F29  0.020
 8UF  plan-1  C44  0.020
 8UF  plan-1  H9   0.020
 8UF  plan-1  H22  0.020
 8UF  plan-2  C4   0.020
 8UF  plan-2  C5   0.020
 8UF  plan-2  C6   0.020
 8UF  plan-2  C10  0.020
 8UF  plan-2  C13  0.020
 8UF  plan-2  N11  0.020
 8UF  plan-2  N12  0.020
 8UF  plan-2  O1   0.020
 8UF  plan-2  H28  0.020
 8UF  plan-3  O54  0.020
 8UF  plan-3  C52  0.020
 8UF  plan-3  O53  0.020
 8UF  plan-3  C51  0.020
 8UF  plan-3  H10  0.020

