# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 05:25:04 2020
#   Inital geometry file: a 133 line input string
#   Ligand name: 8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2ccc(cc2)c3cncc(Cl)c3N4CCC5(CCNC5=O)CC4
#
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
 4TV  4TV  8-{3-chloro-5-[4-(1-methyl-1H-pyrazol-4-yl)phenyl]pyridin-4-yl}-2,8-diazaspiro[4.5]decan-1-one  ligand  54  30  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4TV
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
 4TV  C1   C   CH3   0  -0.507   7.5294   1.5920   1.0045
 4TV  C3   C   CR15  0   0.014   5.3537   0.3896   0.7811
 4TV  C4   C   CR5   0  -0.134   4.1913   0.6126   0.0644
 4TV  C5   C   CR15  0  -0.101   4.4559   1.8179  -0.6173
 4TV  C7   C   CR6   0   0.098   2.9869  -0.2107   0.0290
 4TV  C8   C   CR16  0  -0.330   2.7570  -1.1943   0.9924
 4TV  C11  C   CR16  0  -0.259   0.8877  -0.8251  -1.0105
 4TV  C12  C   CR16  0  -0.319   2.0284  -0.0435  -0.9744
 4TV  C16  C   CR16  0  -0.052  -2.4868  -4.5409  -0.4699
 4TV  C17  C   CR6   0  -0.195  -2.8201  -3.1991  -0.3548
 4TV  C19  C   CR6   0   0.495  -1.8285  -2.2226  -0.1932
 4TV  C21  C   C     0  -0.311  -1.7480  -0.1866   1.1619
 4TV  C23  C   CR6   0  -0.265  -2.1938   2.0212   0.0294
 4TV  C24  C   CH2   0  -0.461  -3.4820   2.4478   0.7480
 4TV  C27  C   C     0   0.580  -1.5885   3.3608  -0.3836
 4TV  O28  O   O     0  -0.488  -0.4404   3.5405  -0.7568
 4TV  C30  C   C     0  -0.309  -3.0164  -0.1719  -0.9284
 4TV  N2   N   NR5   0  -0.266   6.1877   1.4032   0.5074
 4TV  N6   N   N     0  -0.278   5.6589   2.2808  -0.3393
 4TV  C9   C   CR16  0  -0.265   1.6206  -1.9851   0.9485
 4TV  C10  C   CR6   0   0.022   0.6663  -1.8125  -0.0515
 4TV  C13  C   CR6   0  -0.059  -0.5049  -2.7089  -0.1387
 4TV  C14  C   CR16  0  -0.099  -0.2876  -4.0772  -0.2296
 4TV  N15  N   N     0  -0.406  -1.2433  -4.9819  -0.4008
 4TV  N20  N   NR6   0  -0.515  -2.0732  -0.8694  -0.0792
 4TV  C22  C   C     0  -0.425  -1.2315   1.2180   0.8979
 4TV  C25  C   CH2   0  -0.261  -3.8403   3.7959   0.1211
 4TV  N26  N   NH1   0  -0.623  -2.5479   4.2946  -0.2944
 4TV  C29  C   C     0  -0.415  -2.4854   1.2191  -1.2510
 4TV  H1   H   HCH3  0   0.262   7.6160   2.5617   1.4899
 4TV  H2   H   HCH3  0   0.259   7.7496   0.8137   1.7291
 4TV  H3   H   HCH3  0   0.261   8.2494   1.5323   0.1907
 4TV  H4   H   HCR5  0   0.293   5.6391  -0.4133   1.4423
 4TV  H5   H   HCR5  0   0.257   3.8089   2.3647  -1.2869
 4TV  H6   H   HCR6  0   0.249   3.4697  -1.3434   1.7939
 4TV  H7   H   HCR6  0   0.255   0.1687  -0.6782  -1.8056
 4TV  H8   H   HCR6  0   0.246   2.1772   0.6982  -1.7490
 4TV  H9   H   HCR6  0   0.281  -3.2721  -5.2778  -0.5975
 4TV  H10  H   H     0   0.235  -2.6363  -0.1519   1.8094
 4TV  H11  H   H     0   0.263  -0.9943  -0.7565   1.7046
 4TV  H12  H   HCH2  0   0.255  -4.2948   1.7272   0.6622
 4TV  H13  H   HCH2  0   0.252  -3.2798   2.5829   1.8134
 4TV  H14  H   H     0   0.259  -3.1469  -0.7275  -1.8571
 4TV  H15  H   H     0   0.221  -4.0064  -0.0831  -0.4659
 4TV  H16  H   HCR6  0   0.255   1.4700  -2.7397   1.7109
 4TV  H17  H   HCR6  0   0.265   0.7304  -4.4511  -0.1958
 4TV  H18  H   H     0   0.240  -1.0687   1.7252   1.8526
 4TV  H19  H   H     0   0.257  -0.2658   1.1501   0.3935
 4TV  H20  H   HCH2  0   0.236  -4.5177   3.6890  -0.7308
 4TV  H21  H   HCH2  0   0.253  -4.3118   4.4718   0.8339
 4TV  H22  H   HNH1  0   0.395  -2.4101   5.2365  -0.6271
 4TV  H23  H   H     0   0.247  -3.2211   1.7359  -1.8742
 4TV  H24  H   H     0   0.244  -1.5683   1.1332  -1.8405
 4TV  CL1  CL  CL    0  -0.104  -4.5031  -2.8031  -0.3116

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
 4TV  C1   N2   single    1.443  0.020  1.443
 4TV  N2   N6   aromatic  1.329  0.020  1.329
 4TV  N2   C3   aromatic  1.341  0.020  1.341
 4TV  N6   C5   aromatic  1.319  0.020  1.319
 4TV  C3   C4   aromatic  1.384  0.020  1.384
 4TV  C5   C4   aromatic  1.410  0.020  1.410
 4TV  C4   C7   single    1.459  0.020  1.459
 4TV  C8   C7   aromatic  1.396  0.020  1.396
 4TV  C8   C9   aromatic  1.385  0.020  1.385
 4TV  C7   C12  aromatic  1.398  0.020  1.398
 4TV  C9   C10  aromatic  1.393  0.020  1.393
 4TV  C12  C11  aromatic  1.383  0.020  1.383
 4TV  C10  C11  aromatic  1.394  0.020  1.394
 4TV  C10  C13  single    1.477  0.020  1.477
 4TV  C14  C13  aromatic  1.388  0.020  1.388
 4TV  C14  N15  aromatic  1.327  0.020  1.327
 4TV  C13  C19  aromatic  1.411  0.020  1.411
 4TV  N15  C16  aromatic  1.321  0.020  1.321
 4TV  C30  N20  single    1.448  0.020  1.448
 4TV  C30  C29  single    1.523  0.020  1.523
 4TV  C19  N20  single    1.380  0.020  1.380
 4TV  C19  C17  aromatic  1.401  0.020  1.401
 4TV  N20  C21  single    1.453  0.020  1.453
 4TV  C24  C23  single    1.536  0.020  1.536
 4TV  C24  C25  single    1.529  0.020  1.529
 4TV  C16  C17  aromatic  1.387  0.020  1.387
 4TV  C29  C23  single    1.539  0.020  1.539
 4TV  C17  CL1  single    1.729  0.020  1.729
 4TV  C21  C22  single    1.520  0.020  1.520
 4TV  C23  C22  single    1.525  0.020  1.525
 4TV  C23  C27  single    1.527  0.020  1.527
 4TV  C25  N26  single    1.446  0.020  1.446
 4TV  C27  N26  single    1.342  0.020  1.342
 4TV  C27  O28  double    1.221  0.020  1.221
 4TV  C1   H1   single    0.970  0.020  1.090
 4TV  C1   H2   single    0.970  0.020  1.090
 4TV  C1   H3   single    0.970  0.020  1.090
 4TV  C3   H4   single    0.930  0.020  1.080
 4TV  C5   H5   single    0.930  0.020  1.080
 4TV  C8   H6   single    0.930  0.020  1.080
 4TV  C11  H7   single    0.930  0.020  1.080
 4TV  C12  H8   single    0.930  0.020  1.080
 4TV  C16  H9   single    0.930  0.020  1.080
 4TV  C21  H10  single    0.970  0.020  1.090
 4TV  C21  H11  single    0.970  0.020  1.090
 4TV  C24  H12  single    0.970  0.020  1.090
 4TV  C24  H13  single    0.970  0.020  1.090
 4TV  C30  H14  single    0.970  0.020  1.090
 4TV  C30  H15  single    0.970  0.020  1.090
 4TV  C9   H16  single    0.930  0.020  1.080
 4TV  C14  H17  single    0.930  0.020  1.080
 4TV  C22  H18  single    0.970  0.020  1.090
 4TV  C22  H19  single    0.970  0.020  1.090
 4TV  C25  H20  single    0.970  0.020  1.090
 4TV  C25  H21  single    0.970  0.020  1.090
 4TV  N26  H22  single    0.860  0.020  1.020
 4TV  C29  H23  single    0.970  0.020  1.090
 4TV  C29  H24  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
 4TV  H3   C1   H2   109.00  3.000
 4TV  H3   C1   H1   109.26  3.000
 4TV  H2   C1   H1   108.97  3.000
 4TV  H3   C1   N2   110.50  3.000
 4TV  H2   C1   N2   108.94  3.000
 4TV  H1   C1   N2   110.14  3.000
 4TV  H4   C3   N2   121.56  3.000
 4TV  H4   C3   C4   131.28  3.000
 4TV  N2   C3   C4   107.16  3.000
 4TV  C7   C4   C5   128.72  3.000
 4TV  C7   C4   C3   127.95  3.000
 4TV  C5   C4   C3   103.33  3.000
 4TV  H5   C5   N6   119.97  3.000
 4TV  H5   C5   C4   128.35  3.000
 4TV  N6   C5   C4   111.68  3.000
 4TV  C12  C7   C8   117.83  3.000
 4TV  C12  C7   C4   121.06  3.000
 4TV  C8   C7   C4   121.11  3.000
 4TV  H6   C8   C9   118.99  3.000
 4TV  H6   C8   C7   119.97  3.000
 4TV  C9   C8   C7   121.04  3.000
 4TV  H7   C11  C10  119.74  3.000
 4TV  H7   C11  C12  119.37  3.000
 4TV  C10  C11  C12  120.88  3.000
 4TV  H8   C12  C11  118.80  3.000
 4TV  H8   C12  C7   120.08  3.000
 4TV  C11  C12  C7   121.11  3.000
 4TV  H9   C16  N15  117.45  3.000
 4TV  H9   C16  C17  119.54  3.000
 4TV  N15  C16  C17  123.00  3.000
 4TV  CL1  C17  C19  121.75  3.000
 4TV  CL1  C17  C16  117.21  3.000
 4TV  C19  C17  C16  120.91  3.000
 4TV  N20  C19  C13  120.07  3.000
 4TV  N20  C19  C17  124.58  3.000
 4TV  C13  C19  C17  115.35  3.000
 4TV  H11  C21  H10  106.38  3.000
 4TV  H11  C21  C22  109.57  3.000
 4TV  H10  C21  C22  110.34  3.000
 4TV  H11  C21  N20  109.53  3.000
 4TV  H10  C21  N20  109.68  3.000
 4TV  C22  C21  N20  111.21  3.000
 4TV  C29  C23  C22  108.60  3.000
 4TV  C22  C23  C27  111.47  3.000
 4TV  C29  C23  C27  107.90  3.000
 4TV  C27  C23  C24  102.44  3.000
 4TV  C22  C23  C24  114.16  3.000
 4TV  C29  C23  C24  112.04  3.000
 4TV  H13  C24  H12  107.25  3.000
 4TV  H13  C24  C25  109.51  3.000
 4TV  H12  C24  C25  112.08  3.000
 4TV  H13  C24  C23  109.59  3.000
 4TV  H12  C24  C23  113.91  3.000
 4TV  C25  C24  C23  104.45  3.000
 4TV  N26  C27  O28  126.19  3.000
 4TV  O28  C27  C23  125.79  3.000
 4TV  N26  C27  C23  108.01  3.000
 4TV  H15  C30  H14  107.01  3.000
 4TV  H15  C30  C29  109.28  3.000
 4TV  H14  C30  C29  109.06  3.000
 4TV  H15  C30  N20  112.32  3.000
 4TV  H14  C30  N20  109.40  3.000
 4TV  C29  C30  N20  109.69  3.000
 4TV  N6   N2   C3   112.44  3.000
 4TV  C3   N2   C1   127.36  3.000
 4TV  N6   N2   C1   120.19  3.000
 4TV  N2   N6   C5   105.39  3.000
 4TV  H16  C9   C10  119.76  3.000
 4TV  H16  C9   C8   119.31  3.000
 4TV  C10  C9   C8   120.93  3.000
 4TV  C13  C10  C9   120.68  3.000
 4TV  C13  C10  C11  121.00  3.000
 4TV  C9   C10  C11  118.21  3.000
 4TV  C14  C13  C10  118.54  3.000
 4TV  C14  C13  C19  118.94  3.000
 4TV  C10  C13  C19  122.47  3.000
 4TV  H17  C14  N15  116.41  3.000
 4TV  H17  C14  C13  118.97  3.000
 4TV  N15  C14  C13  124.58  3.000
 4TV  C14  N15  C16  117.19  3.000
 4TV  C30  N20  C21  114.85  3.000
 4TV  C21  N20  C19  119.44  3.000
 4TV  C30  N20  C19  122.64  3.000
 4TV  H19  C22  H18  107.49  3.000
 4TV  H19  C22  C23  109.14  3.000
 4TV  H18  C22  C23  110.30  3.000
 4TV  H19  C22  C21  108.87  3.000
 4TV  H18  C22  C21  109.13  3.000
 4TV  C23  C22  C21  111.80  3.000
 4TV  H21  C25  H20  107.59  3.000
 4TV  H21  C25  N26  111.14  3.000
 4TV  H20  C25  N26  111.31  3.000
 4TV  H21  C25  C24  112.34  3.000
 4TV  H20  C25  C24  112.23  3.000
 4TV  N26  C25  C24  102.26  3.000
 4TV  H22  N26  C25  122.62  3.000
 4TV  H22  N26  C27  122.04  3.000
 4TV  C25  N26  C27  114.71  3.000
 4TV  H24  C29  H23  107.10  3.000
 4TV  H24  C29  C30  109.56  3.000
 4TV  H23  C29  C30  108.52  3.000
 4TV  H24  C29  C23  109.30  3.000
 4TV  H23  C29  C23  110.80  3.000
 4TV  C30  C29  C23  111.45  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
 4TV  CONST_01  C5   N6   N2   C3      0.00   0.0  0
 4TV  CONST_02  N6   C5   C4   C3      0.00   0.0  0
 4TV  CONST_05  N6   N2   C3   C4      0.00   0.0  0
 4TV  CONST_06  N2   N6   C5   C4      0.00   0.0  0
 4TV  CONST_07  C9   C8   C7   C4    180.00   0.0  0
 4TV  CONST_08  C11  C12  C7   C4    180.00   0.0  0
 4TV  CONST_09  N2   C3   C4   C5      0.00   0.0  0
 4TV  CONST_12  N2   C3   C4   C7    180.00   0.0  0
 4TV  CONST_13  N6   C5   C4   C7    180.00   0.0  0
 4TV  CONST_14  C10  C9   C8   C7      0.00   0.0  0
 4TV  CONST_15  C10  C11  C12  C7      0.00   0.0  0
 4TV  CONST_16  C11  C12  C7   C8      0.00   0.0  0
 4TV  CONST_17  C11  C10  C9   C8      0.00   0.0  0
 4TV  CONST_18  C13  C10  C9   C8    180.00   0.0  0
 4TV  CONST_21  C9   C8   C7   C12     0.00   0.0  0
 4TV  CONST_22  C9   C10  C11  C12     0.00   0.0  0
 4TV  CONST_23  C13  C10  C11  C12   180.00   0.0  0
 4TV  CONST_24  C13  C14  N15  C16     0.00   0.0  0
 4TV  CONST_25  C13  C19  C17  C16     0.00   0.0  0
 4TV  CONST_26  C10  C13  C19  C17   180.00   0.0  0
 4TV  CONST_27  C14  C13  C19  C17     0.00   0.0  0
 4TV  CONST_28  C14  N15  C16  C17     0.00   0.0  0
 4TV  CONST_30  N15  C14  C13  C19     0.00   0.0  0
 4TV  CONST_31  N15  C16  C17  C19     0.00   0.0  0
 4TV  CONST_33  N15  C14  C13  C10   180.00   0.0  0
 4TV  CONST_34  N20  C19  C17  C16   180.00   0.0  0
 4TV  CONST_35  N20  C19  C13  C10     0.00   0.0  0
 4TV  CONST_36  N20  C19  C13  C14   180.00   0.0  0
 4TV  CONST_37  C25  N26  C27  C23     0.00   0.0  0
 4TV  CONST_38  C5   N6   N2   C1    180.00   0.0  0
 4TV  CONST_39  C4   C3   N2   C1    180.00   0.0  0
 4TV  CONST_40  CL1  C17  C19  C13   180.00   0.0  0
 4TV  CONST_41  CL1  C17  C16  N15   180.00   0.0  0
 4TV  CONST_42  N20  C19  C17  CL1     0.00   0.0  0
 4TV  CONST_43  C25  N26  C27  O28   180.00   0.0  0
 4TV  CONST_44  H5   C5   C4   C3    180.00   0.0  0
 4TV  CONST_45  H6   C8   C7   C4      0.00   0.0  0
 4TV  CONST_46  H8   C12  C7   C4      0.00   0.0  0
 4TV  CONST_47  H4   C3   C4   C5    180.00   0.0  0
 4TV  CONST_48  H16  C9   C8   C7    180.00   0.0  0
 4TV  CONST_49  H7   C11  C12  C7    180.00   0.0  0
 4TV  CONST_50  H17  C14  N15  C16   180.00   0.0  0
 4TV  CONST_51  H9   C16  C17  C19   180.00   0.0  0
 4TV  CONST_52  H22  N26  C27  C23   180.00   0.0  0
 4TV  Var_01    C30  N20  C19  C17   -43.96  30.0  2
 4TV  Var_02    C29  C30  N20  C19  -143.15  30.0  1
 4TV  Var_03    C22  C21  N20  C19   143.66  30.0  1
 4TV  Var_04    C24  C23  C22  C21    72.01  30.0  1
 4TV  Var_05    N26  C25  C24  C23   -27.23  30.0  1
 4TV  Var_06    N20  C30  C29  C23   -56.51  30.0  1
 4TV  Var_07    N20  C21  C22  C23    53.53  30.0  1
 4TV  Var_08    C30  C29  C23  C24   -71.41  30.0  1
 4TV  Var_09    N26  C27  C23  C24   -16.40  30.0  3
 4TV  Var_10    C27  N26  C25  C24    18.35  30.0  1
 4TV  Var_11    C25  C24  C23  C27    26.65  30.0  3
 4TV  Var_12    H1   C1   N2   C3   -124.56  30.0  2

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
 4TV  plan-1  C1   0.020
 4TV  plan-1  C3   0.020
 4TV  plan-1  C4   0.020
 4TV  plan-1  C5   0.020
 4TV  plan-1  C7   0.020
 4TV  plan-1  N2   0.020
 4TV  plan-1  N6   0.020
 4TV  plan-1  H4   0.020
 4TV  plan-1  H5   0.020
 4TV  plan-2  C4   0.020
 4TV  plan-2  C7   0.020
 4TV  plan-2  C8   0.020
 4TV  plan-2  C11  0.020
 4TV  plan-2  C12  0.020
 4TV  plan-2  C9   0.020
 4TV  plan-2  C10  0.020
 4TV  plan-2  C13  0.020
 4TV  plan-2  H6   0.020
 4TV  plan-2  H7   0.020
 4TV  plan-2  H8   0.020
 4TV  plan-2  H16  0.020
 4TV  plan-3  C23  0.020
 4TV  plan-3  C27  0.020
 4TV  plan-3  O28  0.020
 4TV  plan-3  C25  0.020
 4TV  plan-3  N26  0.020
 4TV  plan-3  H22  0.020
 4TV  plan-4  C16  0.020
 4TV  plan-4  C17  0.020
 4TV  plan-4  C19  0.020
 4TV  plan-4  C10  0.020
 4TV  plan-4  C13  0.020
 4TV  plan-4  C14  0.020
 4TV  plan-4  N15  0.020
 4TV  plan-4  N20  0.020
 4TV  plan-4  H9   0.020
 4TV  plan-4  H17  0.020
 4TV  plan-4  CL1  0.020

