# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 15:03:02 2021
#   Inital geometry file: a 126 line input string
#   Ligand name: N-(5-{[(5S)-7-(5-methylimidazo[1,2-a]pyrimidin-7-yl)-2,7-diazaspiro[4.4]nonan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)Nc1sc(CN2CC[C@]3(CCN(C3)c4cc(C)n5ccnc5n4)C2)cn1
#
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
 WG4  WG4  N-(5-{[(5S)-7-(5-methylimidazo[1,2-a]pyrimidin-7-yl)-2,7-diazaspiro[4.4]nonan-2-yl]methyl}-1,3-thiazol-2-yl)acetamide  ligand  54  29  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_WG4
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
 WG4  C1   C  CH3   0  -0.785  54.7235   -0.2489  273.0869
 WG4  C2   C  C     0   0.520  53.8037   -1.4094  272.8471
 WG4  C5   C  CR5   0   0.304  53.7950   -3.7516  272.2145
 WG4  C7   C  CR15  0  -0.041  53.5946   -5.8552  271.6611
 WG4  C8   C  CR5   0  -0.221  52.2743   -5.6066  271.8448
 WG4  N10  N  NT    0  -0.404  50.6310   -7.1484  272.9443
 WG4  C11  C  CH2   0  -0.288  49.9397   -6.2668  273.8641
 WG4  C12  C  CH2   0  -0.461  49.7227   -7.1444  275.1015
 WG4  C15  C  CH2   0  -0.289  52.1849   -9.9508  275.9348
 WG4  C17  C  CH2   0  -0.235  50.1071   -9.6527  274.7342
 WG4  C18  C  CR6   0   0.557  51.1212  -11.8864  274.8077
 WG4  C19  C  CR16  0  -0.506  52.2195  -12.7374  275.1716
 WG4  N22  N  N     0  -0.552  51.1056  -14.4936  274.1393
 WG4  C23  C  CR15  0  -0.139  50.7760  -15.7421  273.6501
 WG4  C24  C  CR15  0  -0.191  49.5676  -15.5647  273.0478
 WG4  O3   O  O     0  -0.453  52.5929   -1.3641  272.9581
 WG4  N4   N  NH1   0  -0.677  54.4314   -2.5651  272.4851
 WG4  N6   N  N     0  -0.423  54.4515   -4.8116  271.8685
 WG4  C9   C  CH2   0  -0.381  51.1291   -6.5715  271.7162
 WG4  C13  C  CT    0  -0.107  50.7523   -8.2865  274.9722
 WG4  C14  C  CH2   0  -0.474  51.6153   -8.5625  276.2003
 WG4  N16  N  NT    0  -0.502  51.1386  -10.5887  275.1467
 WG4  C20  C  CR6   0   0.436  52.1962  -14.0475  274.8263
 WG4  N25  N  N     0  -0.507  49.1322  -14.2744  273.1385
 WG4  C26  C  CR56  0   0.569  50.0709  -13.6342  273.8016
 WG4  N27  N  N     0  -0.528  50.0795  -12.3420  274.1373
 WG4  C28  C  CH2   0  -0.251  51.5850   -7.8714  273.7514
 WG4  S29  S  S2    0   0.217  52.0795   -3.9466  272.3115
 WG4  H1   H  HCH3  0   0.273  54.1512    0.6411  273.3317
 WG4  H3   H  HCH3  0   0.279  55.4075   -0.4667  273.9083
 WG4  H2   H  HCH3  0   0.276  55.3295   -0.0500  272.2021
 WG4  H5   H  HCR5  0   0.268  53.9951   -6.8137  271.3583
 WG4  H8   H  HCH2  0   0.200  50.5423   -5.3883  274.1412
 WG4  H9   H  HCH2  0   0.237  49.0094   -5.8991  273.4255
 WG4  H11  H  HCH2  0   0.245  49.8665   -6.5725  276.0189
 WG4  H10  H  HCH2  0   0.243  48.7070   -7.5424  275.1327
 WG4  H14  H  HCH2  0   0.254  52.3827  -10.4956  276.8602
 WG4  H15  H  HCH2  0   0.243  53.1241   -9.9003  275.3736
 WG4  H16  H  HCH2  0   0.236  49.2027   -9.7751  275.3410
 WG4  H17  H  HCH2  0   0.247  49.8267   -9.8026  273.6903
 WG4  H18  H  HCR6  0   0.289  53.0766  -12.3543  275.7041
 WG4  H19  H  HCH3  0   0.270  53.6859  -15.4500  274.2198
 WG4  H21  H  HCH3  0   0.275  54.0808  -14.5372  275.6802
 WG4  H20  H  HCH3  0   0.270  52.8962  -15.8466  275.7410
 WG4  H22  H  HCR5  0   0.293  51.4050  -16.6063  273.7731
 WG4  H23  H  HCR5  0   0.253  48.9822  -16.3209  272.5466
 WG4  H4   H  HNH1  0   0.428  55.4382   -2.5815  272.4001
 WG4  H6   H  HCH2  0   0.260  50.2918   -6.0988  271.1962
 WG4  H7   H  HCH2  0   0.261  51.4681   -7.3875  271.0719
 WG4  H12  H  HCH2  0   0.254  52.3961   -7.8158  276.3481
 WG4  H13  H  HCH2  0   0.250  50.9944   -8.5784  277.0997
 WG4  H24  H  HCH2  0   0.240  52.0011   -8.7202  273.2010
 WG4  H25  H  HCH2  0   0.206  52.4332   -7.2437  274.0734
 WG4  C21  C  CH3   0  -0.739  53.2748  -15.0213  275.1353

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
 WG4  C7   N6   aromatic  1.366  0.020  1.366
 WG4  C7   C8   aromatic  1.356  0.020  1.356
 WG4  N6   C5   aromatic  1.294  0.020  1.294
 WG4  C8   C9   single    1.503  0.020  1.503
 WG4  C8   S29  aromatic  1.735  0.020  1.735
 WG4  C9   N10  single    1.445  0.020  1.445
 WG4  C5   S29  aromatic  1.729  0.020  1.729
 WG4  C5   N4   single    1.373  0.020  1.373
 WG4  N4   C2   single    1.364  0.020  1.364
 WG4  C24  N25  aromatic  1.365  0.020  1.365
 WG4  C24  C23  aromatic  1.362  0.020  1.362
 WG4  N25  C26  aromatic  1.316  0.020  1.316
 WG4  N10  C11  single    1.450  0.020  1.450
 WG4  N10  C28  single    1.444  0.020  1.444
 WG4  C23  N22  aromatic  1.381  0.020  1.381
 WG4  C2   C1   single    1.500  0.020  1.500
 WG4  C2   O3   double    1.217  0.020  1.217
 WG4  C26  N22  aromatic  1.387  0.020  1.387
 WG4  C26  N27  aromatic  1.335  0.020  1.335
 WG4  N22  C20  aromatic  1.364  0.020  1.364
 WG4  C11  C12  single    1.532  0.020  1.532
 WG4  C28  C13  single    1.535  0.020  1.535
 WG4  N27  C18  aromatic  1.320  0.020  1.320
 WG4  C20  C21  single    1.486  0.020  1.486
 WG4  C20  C19  aromatic  1.355  0.020  1.355
 WG4  C18  C19  aromatic  1.436  0.020  1.436
 WG4  C18  N16  single    1.341  0.020  1.341
 WG4  C17  C13  single    1.530  0.020  1.530
 WG4  C17  N16  single    1.453  0.020  1.453
 WG4  C13  C12  single    1.543  0.020  1.543
 WG4  C13  C14  single    1.526  0.020  1.526
 WG4  N16  C15  single    1.457  0.020  1.457
 WG4  C14  C15  single    1.524  0.020  1.524
 WG4  C1   H1   single    0.970  0.020  1.090
 WG4  C1   H3   single    0.970  0.020  1.090
 WG4  C1   H2   single    0.970  0.020  1.090
 WG4  C7   H5   single    0.930  0.020  1.080
 WG4  C11  H8   single    0.970  0.020  1.090
 WG4  C11  H9   single    0.970  0.020  1.090
 WG4  C12  H11  single    0.970  0.020  1.090
 WG4  C12  H10  single    0.970  0.020  1.090
 WG4  C15  H14  single    0.970  0.020  1.090
 WG4  C15  H15  single    0.970  0.020  1.090
 WG4  C17  H16  single    0.970  0.020  1.090
 WG4  C17  H17  single    0.970  0.020  1.090
 WG4  C19  H18  single    0.930  0.020  1.080
 WG4  C21  H19  single    0.970  0.020  1.090
 WG4  C21  H21  single    0.970  0.020  1.090
 WG4  C21  H20  single    0.970  0.020  1.090
 WG4  C23  H22  single    0.930  0.020  1.080
 WG4  C24  H23  single    0.930  0.020  1.080
 WG4  N4   H4   single    0.860  0.020  1.020
 WG4  C9   H6   single    0.970  0.020  1.090
 WG4  C9   H7   single    0.970  0.020  1.090
 WG4  C14  H12  single    0.970  0.020  1.090
 WG4  C14  H13  single    0.970  0.020  1.090
 WG4  C28  H24  single    0.970  0.020  1.090
 WG4  C28  H25  single    0.970  0.020  1.090

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
 WG4  H2   C1   H3   107.39  3.000
 WG4  H2   C1   H1   109.04  3.000
 WG4  H3   C1   H1   108.92  3.000
 WG4  H2   C1   C2   110.61  3.000
 WG4  H3   C1   C2   110.51  3.000
 WG4  H1   C1   C2   110.30  3.000
 WG4  N4   C2   O3   120.91  3.000
 WG4  O3   C2   C1   124.52  3.000
 WG4  N4   C2   C1   114.57  3.000
 WG4  S29  C5   N6   115.21  3.000
 WG4  S29  C5   N4   123.10  3.000
 WG4  N6   C5   N4   121.69  3.000
 WG4  H5   C7   N6   119.14  3.000
 WG4  H5   C7   C8   124.10  3.000
 WG4  N6   C7   C8   116.75  3.000
 WG4  S29  C8   C9   123.47  3.000
 WG4  S29  C8   C7   108.73  3.000
 WG4  C9   C8   C7   127.78  3.000
 WG4  C28  N10  C9   116.56  3.000
 WG4  C28  N10  C11  105.37  3.000
 WG4  C9   N10  C11  117.43  3.000
 WG4  H9   C11  H8   107.38  3.000
 WG4  H9   C11  C12  113.35  3.000
 WG4  H8   C11  C12  109.35  3.000
 WG4  H9   C11  N10  110.86  3.000
 WG4  H8   C11  N10  112.58  3.000
 WG4  C12  C11  N10  103.39  3.000
 WG4  H10  C12  H11  106.85  3.000
 WG4  H10  C12  C13  110.70  3.000
 WG4  H11  C12  C13  111.75  3.000
 WG4  H10  C12  C11  111.33  3.000
 WG4  H11  C12  C11  111.11  3.000
 WG4  C13  C12  C11  105.17  3.000
 WG4  H15  C15  H14  107.58  3.000
 WG4  H15  C15  N16  111.03  3.000
 WG4  H14  C15  N16  111.72  3.000
 WG4  H15  C15  C14  111.58  3.000
 WG4  H14  C15  C14  112.00  3.000
 WG4  N16  C15  C14  102.98  3.000
 WG4  H17  C17  H16  107.59  3.000
 WG4  H17  C17  N16  111.44  3.000
 WG4  H16  C17  N16  110.91  3.000
 WG4  H17  C17  C13  112.33  3.000
 WG4  H16  C17  C13  111.20  3.000
 WG4  N16  C17  C13  103.40  3.000
 WG4  N27  C18  N16  118.20  3.000
 WG4  N16  C18  C19  119.95  3.000
 WG4  N27  C18  C19  121.85  3.000
 WG4  H18  C19  C20  118.85  3.000
 WG4  H18  C19  C18  121.47  3.000
 WG4  C20  C19  C18  119.68  3.000
 WG4  C26  N22  C20  121.10  3.000
 WG4  C20  N22  C23  131.69  3.000
 WG4  C26  N22  C23  107.21  3.000
 WG4  H22  C23  C24  132.38  3.000
 WG4  H22  C23  N22  123.10  3.000
 WG4  C24  C23  N22  104.52  3.000
 WG4  H23  C24  N25  121.33  3.000
 WG4  H23  C24  C23  126.52  3.000
 WG4  N25  C24  C23  112.14  3.000
 WG4  H4   N4   C5   115.54  3.000
 WG4  H4   N4   C2   119.64  3.000
 WG4  C5   N4   C2   124.83  3.000
 WG4  C7   N6   C5   110.37  3.000
 WG4  H7   C9   H6   106.25  3.000
 WG4  H7   C9   N10  108.03  3.000
 WG4  H6   C9   N10  108.23  3.000
 WG4  H7   C9   C8   107.05  3.000
 WG4  H6   C9   C8   110.29  3.000
 WG4  N10  C9   C8   116.49  3.000
 WG4  C28  C13  C14  112.47  3.000
 WG4  C14  C13  C17  101.67  3.000
 WG4  C28  C13  C17  110.28  3.000
 WG4  C14  C13  C12  116.34  3.000
 WG4  C17  C13  C12  113.12  3.000
 WG4  C28  C13  C12  103.21  3.000
 WG4  H13  C14  H12  107.77  3.000
 WG4  H13  C14  C13  110.10  3.000
 WG4  H12  C14  C13  112.96  3.000
 WG4  H13  C14  C15  110.02  3.000
 WG4  H12  C14  C15  112.32  3.000
 WG4  C13  C14  C15  103.65  3.000
 WG4  C18  N16  C17  122.84  3.000
 WG4  C17  N16  C15  112.42  3.000
 WG4  C18  N16  C15  124.72  3.000
 WG4  N22  C20  C21  118.09  3.000
 WG4  C21  C20  C19  124.62  3.000
 WG4  N22  C20  C19  117.28  3.000
 WG4  C26  N25  C24  105.42  3.000
 WG4  N27  C26  N25  127.04  3.000
 WG4  N27  C26  N22  122.26  3.000
 WG4  N25  C26  N22  110.71  3.000
 WG4  C26  N27  C18  117.83  3.000
 WG4  H25  C28  H24  107.21  3.000
 WG4  H25  C28  C13  109.80  3.000
 WG4  H24  C28  C13  113.38  3.000
 WG4  H25  C28  N10  112.72  3.000
 WG4  H24  C28  N10  111.02  3.000
 WG4  C13  C28  N10  102.80  3.000
 WG4  C8   S29  C5    88.94  3.000
 WG4  H20  C21  H21  108.41  3.000
 WG4  H20  C21  H19  107.41  3.000
 WG4  H21  C21  H19  108.44  3.000
 WG4  H20  C21  C20  111.05  3.000
 WG4  H21  C21  C20  110.54  3.000
 WG4  H19  C21  C20  110.88  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
 WG4  CONST_01  C8   C7   N6   C5      0.00   0.0  0
 WG4  CONST_02  C7   C8   S29  C5      0.00   0.0  0
 WG4  CONST_03  S29  C5   N6   C7      0.00   0.0  0
 WG4  CONST_04  N6   C5   S29  C8      0.00   0.0  0
 WG4  CONST_05  N25  C26  N27  C18   180.00   0.0  0
 WG4  CONST_06  N22  C26  N27  C18     0.00   0.0  0
 WG4  CONST_07  N22  C20  C19  C18     0.00   0.0  0
 WG4  CONST_08  C23  N22  C20  C19   180.00   0.0  0
 WG4  CONST_09  C26  N22  C20  C19     0.00   0.0  0
 WG4  CONST_10  C26  N27  C18  C19     0.00   0.0  0
 WG4  CONST_11  N25  C24  C23  N22     0.00   0.0  0
 WG4  CONST_12  C24  N25  C26  N22     0.00   0.0  0
 WG4  CONST_13  C26  N25  C24  C23     0.00   0.0  0
 WG4  CONST_14  N25  C26  N22  C23     0.00   0.0  0
 WG4  CONST_15  N27  C26  N22  C23   180.00   0.0  0
 WG4  CONST_16  N27  C26  N25  C24   180.00   0.0  0
 WG4  CONST_17  C26  N22  C23  C24     0.00   0.0  0
 WG4  CONST_18  C20  N22  C23  C24   180.00   0.0  0
 WG4  CONST_19  S29  C8   C7   N6      0.00   0.0  0
 WG4  CONST_20  N25  C26  N22  C20   180.00   0.0  0
 WG4  CONST_21  N27  C26  N22  C20     0.00   0.0  0
 WG4  CONST_22  N27  C18  C19  C20     0.00   0.0  0
 WG4  CONST_23  C26  N27  C18  N16   180.00   0.0  0
 WG4  CONST_24  C20  C19  C18  N16   180.00   0.0  0
 WG4  CONST_25  C9   C8   S29  C5    180.00   0.0  0
 WG4  CONST_26  N4   C5   N6   C7    180.00   0.0  0
 WG4  CONST_27  N4   C5   S29  C8    180.00   0.0  0
 WG4  CONST_28  C21  C20  C19  C18   180.00   0.0  0
 WG4  CONST_29  C23  N22  C20  C21     0.00   0.0  0
 WG4  CONST_30  C26  N22  C20  C21   180.00   0.0  0
 WG4  CONST_31  C9   C8   C7   N6    180.00   0.0  0
 WG4  CONST_32  H5   C7   N6   C5    180.00   0.0  0
 WG4  CONST_33  H23  C24  C23  N22   180.00   0.0  0
 WG4  CONST_34  H18  C19  C20  N22   180.00   0.0  0
 WG4  CONST_35  H22  C23  N22  C20     0.00   0.0  0
 WG4  CONST_36  N6   C5   N4   C2    180.00   0.0  0
 WG4  CONST_37  S29  C5   N4   C2      0.00   0.0  0
 WG4  CONST_38  H4   N4   C5   N6      0.00   0.0  0
 WG4  CONST_39  C5   N4   C2   C1    180.00   0.0  0
 WG4  CONST_40  O3   C2   N4   C5      0.00   0.0  0
 WG4  Var_01    C13  C12  C11  N10    20.03  30.0  1
 WG4  Var_02    C13  C28  N10  C11    45.62  30.0  1
 WG4  Var_03    C28  N10  C11  C12   -41.18  30.0  1
 WG4  Var_04    N27  C18  N16  C15   177.16  30.0  1
 WG4  Var_05    C13  C17  N16  C15    15.48  30.0  1
 WG4  Var_06    C14  C15  N16  C17     9.42  30.0  1
 WG4  Var_07    N16  C15  C14  C13   -30.58  30.0  1
 WG4  Var_08    N10  C9   C8   C7     98.47  30.0  2
 WG4  Var_09    C11  N10  C9   C8     68.83  30.0  3
 WG4  Var_10    H19  C21  C20  C19  -120.01  30.0  2
 WG4  Var_11    H1   C1   C2   O3     -2.34  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
 WG4  chir_01  C13  C17  C12  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
 WG4  plan-1  C5   0.020
 WG4  plan-1  C7   0.020
 WG4  plan-1  C8   0.020
 WG4  plan-1  N4   0.020
 WG4  plan-1  N6   0.020
 WG4  plan-1  C9   0.020
 WG4  plan-1  S29  0.020
 WG4  plan-1  H5   0.020
 WG4  plan-2  C1   0.020
 WG4  plan-2  C2   0.020
 WG4  plan-2  C5   0.020
 WG4  plan-2  O3   0.020
 WG4  plan-2  N4   0.020
 WG4  plan-2  H4   0.020
 WG4  plan-3  C18  0.020
 WG4  plan-3  C19  0.020
 WG4  plan-3  N22  0.020
 WG4  plan-3  C23  0.020
 WG4  plan-3  C24  0.020
 WG4  plan-3  N16  0.020
 WG4  plan-3  C20  0.020
 WG4  plan-3  N25  0.020
 WG4  plan-3  C26  0.020
 WG4  plan-3  N27  0.020
 WG4  plan-3  H18  0.020
 WG4  plan-3  H22  0.020
 WG4  plan-3  H23  0.020
 WG4  plan-3  C21  0.020

