# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 21:40:23 2022
#   Inital geometry file: a 93 line input string
#   Ligand name: 8-(2-chloranylethanoyl)-4-(furan-2-ylmethyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ClCC(=O)N1CCC2(CC1)SCC(=O)N2Cc3occc3
#
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
 J2C  J2C  "8-(2-chloroacetyl)-4-(furan-2-ylmethyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one"
  ligand  38  21  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J2C
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
 J2C  C12  C   CH2   0  -0.461   -8.2003  41.4196  81.4491
 J2C  N01  N   NT    0  -0.431   -4.1778  43.7490  82.5409
 J2C  C02  C   CH2   0  -0.336   -4.4056  42.6630  83.4762
 J2C  C03  C   CH2   0  -0.411   -5.6967  41.9264  83.1334
 J2C  C04  C   CT    0  -0.064   -5.6710  41.4147  81.6964
 J2C  C05  C   CH2   0  -0.393   -5.3209  42.5521  80.7359
 J2C  C06  C   CH2   0  -0.321   -4.0629  43.2951  81.1657
 J2C  N07  N   NT    0  -0.445   -6.9099  40.7600  81.3019
 J2C  C08  C   C     0   0.567   -6.8309  39.6412  80.5468
 J2C  C09  C   CH2   0  -0.675   -5.4062  39.1618  80.3849
 J2C  S10  S   S2    0   0.030   -4.4207  40.0647  81.5924
 J2C  O11  O   O     0  -0.462   -7.7831  39.0904  80.0309
 J2C  C13  C   CR5   0   0.395   -9.0945  40.7514  82.4297
 J2C  C14  C   CR15  0  -0.367  -10.2755  40.1037  82.2875
 J2C  C15  C   CR15  0  -0.335  -10.6703  39.6935  83.5973
 J2C  C16  C   CR15  0  -0.004   -9.6932  40.1207  84.4294
 J2C  O17  O   O     0  -0.406   -8.7354  40.7663  83.7318
 J2C  C19  C   CH2   0  -0.606   -4.4068  45.4675  84.2817
 J2C  O20  O   O     0  -0.474   -4.1237  45.9395  81.9811
 J2C  H1   H   HCH2  0   0.291   -8.0306  42.4593  81.7323
 J2C  H2   H   HCH2  0   0.295   -8.7114  41.4457  80.4857
 J2C  H3   H   HCH2  0   0.265   -3.5456  41.9868  83.4384
 J2C  H4   H   HCH2  0   0.284   -4.4617  43.0210  84.4994
 J2C  H5   H   HCH2  0   0.255   -6.5229  42.6292  83.2647
 J2C  H6   H   HCH2  0   0.270   -5.8486  41.1006  83.8287
 J2C  H7   H   HCH2  0   0.256   -6.1552  43.2606  80.6969
 J2C  H8   H   HCH2  0   0.263   -5.1847  42.1592  79.7259
 J2C  H9   H   HCH2  0   0.254   -3.1942  42.6341  81.0906
 J2C  H10  H   HCH2  0   0.279   -3.8844  44.1432  80.5119
 J2C  H11  H   HCH2  0   0.312   -5.3441  38.0905  80.5711
 J2C  H12  H   HCH2  0   0.307   -5.0778  39.3492  79.3603
 J2C  H13  H   HCR5  0   0.260  -10.8013  39.9377  81.3611
 J2C  H14  H   HCR5  0   0.261  -11.5583  39.1503  83.8767
 J2C  H15  H   HCR5  0   0.276   -9.5468  40.0425  85.4946
 J2C  H16  H   HCH2  0   0.314   -3.7804  44.9125  84.9761
 J2C  H17  H   HCH2  0   0.327   -4.1848  46.5264  84.3773
 J2C  CL1  CL  CL    0  -0.130   -6.1188  45.2373  84.7714
 J2C  C18  C   C     0   0.558   -4.2265  45.0653  82.8268

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
 J2C  O11  C08  double    1.215  0.020  1.215
 J2C  C09  C08  single    1.512  0.020  1.512
 J2C  C09  S10  single    1.801  0.020  1.801
 J2C  C08  N07  single    1.352  0.020  1.352
 J2C  C05  C06  single    1.523  0.020  1.523
 J2C  C05  C04  single    1.529  0.020  1.529
 J2C  C06  N01  single    1.453  0.020  1.453
 J2C  N07  C12  single    1.457  0.020  1.457
 J2C  N07  C04  single    1.456  0.020  1.456
 J2C  C12  C13  single    1.486  0.020  1.486
 J2C  S10  C04  single    1.843  0.020  1.843
 J2C  C04  C03  single    1.526  0.020  1.526
 J2C  O20  C18  double    1.221  0.020  1.221
 J2C  C14  C13  aromatic  1.354  0.020  1.354
 J2C  C14  C15  aromatic  1.428  0.020  1.428
 J2C  C13  O17  aromatic  1.351  0.020  1.351
 J2C  N01  C18  single    1.348  0.020  1.348
 J2C  N01  C02  single    1.451  0.020  1.451
 J2C  C18  C19  single    1.520  0.020  1.520
 J2C  C03  C02  single    1.526  0.020  1.526
 J2C  C15  C16  aromatic  1.353  0.020  1.353
 J2C  O17  C16  aromatic  1.349  0.020  1.349
 J2C  C12  H1   single    0.970  0.020  1.090
 J2C  C12  H2   single    0.970  0.020  1.090
 J2C  C02  H3   single    0.970  0.020  1.090
 J2C  C02  H4   single    0.970  0.020  1.090
 J2C  C03  H5   single    0.970  0.020  1.090
 J2C  C03  H6   single    0.970  0.020  1.090
 J2C  C05  H7   single    0.970  0.020  1.090
 J2C  C05  H8   single    0.970  0.020  1.090
 J2C  C06  H9   single    0.970  0.020  1.090
 J2C  C06  H10  single    0.970  0.020  1.090
 J2C  C09  H11  single    0.970  0.020  1.090
 J2C  C09  H12  single    0.970  0.020  1.090
 J2C  C14  H13  single    0.930  0.020  1.080
 J2C  C15  H14  single    0.930  0.020  1.080
 J2C  C16  H15  single    0.930  0.020  1.080
 J2C  C19  H16  single    0.970  0.020  1.090
 J2C  C19  H17  single    0.970  0.020  1.090
 J2C  C19  CL1  single    1.796  0.020  1.796

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
 J2C  H2   C12  H1   106.22  3.000
 J2C  H2   C12  C13  108.16  3.000
 J2C  H1   C12  C13  110.55  3.000
 J2C  H2   C12  N07  109.67  3.000
 J2C  H1   C12  N07  108.66  3.000
 J2C  C13  C12  N07  113.34  3.000
 J2C  C18  N01  C06  120.58  3.000
 J2C  C18  N01  C02  126.05  3.000
 J2C  C06  N01  C02  112.87  3.000
 J2C  H4   C02  H3   106.07  3.000
 J2C  H4   C02  C03  109.11  3.000
 J2C  H3   C02  C03  111.03  3.000
 J2C  H4   C02  N01  111.65  3.000
 J2C  H3   C02  N01  108.46  3.000
 J2C  C03  C02  N01  110.45  3.000
 J2C  H6   C03  H5   107.78  3.000
 J2C  H6   C03  C04  110.43  3.000
 J2C  H5   C03  C04  109.98  3.000
 J2C  H6   C03  C02  109.90  3.000
 J2C  H5   C03  C02  107.60  3.000
 J2C  C04  C03  C02  111.06  3.000
 J2C  S10  C04  N07  103.45  3.000
 J2C  S10  C04  C05  110.73  3.000
 J2C  N07  C04  C05  111.05  3.000
 J2C  S10  C04  C03  108.08  3.000
 J2C  N07  C04  C03  113.06  3.000
 J2C  C05  C04  C03  110.25  3.000
 J2C  H8   C05  H7   107.14  3.000
 J2C  H8   C05  C06  109.48  3.000
 J2C  H7   C05  C06  108.88  3.000
 J2C  H8   C05  C04  109.99  3.000
 J2C  H7   C05  C04  109.21  3.000
 J2C  C06  C05  C04  112.00  3.000
 J2C  H10  C06  H9   107.46  3.000
 J2C  H10  C06  C05  110.30  3.000
 J2C  H9   C06  C05  109.98  3.000
 J2C  H10  C06  N01  109.82  3.000
 J2C  H9   C06  N01  108.46  3.000
 J2C  C05  C06  N01  110.75  3.000
 J2C  C08  N07  C04  118.28  3.000
 J2C  C04  N07  C12  121.52  3.000
 J2C  C08  N07  C12  118.88  3.000
 J2C  O11  C08  C09  123.32  3.000
 J2C  C09  C08  N07  112.16  3.000
 J2C  O11  C08  N07  124.50  3.000
 J2C  H12  C09  H11  108.18  3.000
 J2C  H12  C09  S10  112.23  3.000
 J2C  H11  C09  S10  110.32  3.000
 J2C  H12  C09  C08  109.23  3.000
 J2C  H11  C09  C08  110.32  3.000
 J2C  S10  C09  C08  106.55  3.000
 J2C  C09  S10  C04   91.94  3.000
 J2C  O17  C13  C14  109.77  3.000
 J2C  O17  C13  C12  118.12  3.000
 J2C  C14  C13  C12  132.11  3.000
 J2C  H13  C14  C15  127.52  3.000
 J2C  H13  C14  C13  126.09  3.000
 J2C  C15  C14  C13  106.38  3.000
 J2C  H14  C15  C16  126.51  3.000
 J2C  H14  C15  C14  127.60  3.000
 J2C  C16  C15  C14  105.89  3.000
 J2C  H15  C16  O17  116.69  3.000
 J2C  H15  C16  C15  133.08  3.000
 J2C  O17  C16  C15  110.23  3.000
 J2C  C16  O17  C13  107.72  3.000
 J2C  CL1  C19  H17  107.21  3.000
 J2C  CL1  C19  H16  108.03  3.000
 J2C  H17  C19  H16  108.88  3.000
 J2C  CL1  C19  C18  109.89  3.000
 J2C  H17  C19  C18  108.54  3.000
 J2C  H16  C19  C18  114.07  3.000
 J2C  O20  C18  C19  118.92  3.000
 J2C  C19  C18  N01  117.75  3.000
 J2C  O20  C18  N01  123.33  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
 J2C  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 J2C  CONST_02  C15  C16  O17  C13     0.00   0.0  0
 J2C  CONST_03  C16  O17  C13  C14     0.00   0.0  0
 J2C  CONST_04  O17  C16  C15  C14     0.00   0.0  0
 J2C  CONST_05  O17  C13  C14  C15     0.00   0.0  0
 J2C  CONST_06  C09  C08  N07  C04     0.00   0.0  0
 J2C  CONST_07  C15  C14  C13  C12   180.00   0.0  0
 J2C  CONST_08  C16  O17  C13  C12   180.00   0.0  0
 J2C  CONST_09  C09  C08  N07  C12   180.00   0.0  0
 J2C  CONST_10  O11  C08  N07  C04   180.00   0.0  0
 J2C  CONST_11  H14  C15  C14  C13   180.00   0.0  0
 J2C  CONST_12  H15  C16  O17  C13   180.00   0.0  0
 J2C  CONST_13  H15  C16  C15  C14   180.00   0.0  0
 J2C  CONST_14  H13  C14  C15  C16   180.00   0.0  0
 J2C  CONST_15  H13  C14  C13  O17   180.00   0.0  0
 J2C  CONST_16  H14  C15  C16  O17   180.00   0.0  0
 J2C  CONST_17  O20  C18  N01  C02   180.00   0.0  0
 J2C  CONST_18  C19  C18  N01  C02     0.00   0.0  0
 J2C  CONST_19  O20  C18  N01  C06     0.00   0.0  0
 J2C  CONST_20  C19  C18  N01  C06   180.00   0.0  0
 J2C  CONST_21  O11  C08  N07  C12     0.00   0.0  0
 J2C  Var_01    C04  C05  C06  N01   -53.72  30.0  1
 J2C  Var_02    C04  C03  C02  N01    56.37  30.0  1
 J2C  Var_03    C05  C06  N01  C02    58.47  30.0  1
 J2C  Var_04    C05  C04  C03  C02   -52.25  30.0  1
 J2C  Var_05    N07  C04  C03  C02  -177.21  30.0  1
 J2C  Var_06    S10  C04  C03  C02    68.91  30.0  1
 J2C  Var_07    C06  C05  C04  C03    51.19  30.0  1
 J2C  Var_08    C08  N07  C04  C03  -139.81  30.0  3
 J2C  Var_09    C09  S10  C04  C03   145.16  30.0  3
 J2C  Var_10    C06  N01  C02  C03   -59.94  30.0  1
 J2C  Var_11    C08  C09  S10  C04   -22.17  30.0  1
 J2C  Var_12    C08  N07  C04  C05    95.66  30.0  3
 J2C  Var_13    C09  S10  C04  C05   -93.99  30.0  3
 J2C  Var_14    N07  C04  C05  C06   177.29  30.0  1
 J2C  Var_15    S10  C04  C05  C06   -68.37  30.0  1
 J2C  Var_16    S10  C09  C08  N07    13.10  30.0  1
 J2C  Var_17    C09  S10  C04  N07    25.05  30.0  3
 J2C  Var_18    S10  C04  N07  C08   -23.16  30.0  3
 J2C  Var_19    C05  C04  N07  C12   -71.05  30.0  3
 J2C  Var_20    S10  C04  N07  C12   170.13  30.0  3
 J2C  Var_21    C03  C04  N07  C12    53.47  30.0  3
 J2C  Var_22    C18  N01  C02  C03   111.94  30.0  1
 J2C  Var_23    C13  C12  N07  C04  -114.82  30.0  3
 J2C  Var_24    C18  N01  C06  C05  -113.90  30.0  1
 J2C  Var_25    C14  C13  C12  N07  -114.24  30.0  2
 J2C  Var_26    O17  C13  C12  N07    66.74  30.0  2
 J2C  Var_27    C13  C12  N07  C08    78.54  30.0  3
 J2C  Var_28    O11  C08  C09  S10  -168.25  30.0  1
 J2C  Var_29    H7   C05  C06  N01    67.16  30.0  1
 J2C  Var_30    H8   C05  C06  N01  -176.00  30.0  1
 J2C  Var_31    H5   C03  C02  N01   -64.05  30.0  1
 J2C  Var_32    H6   C03  C02  N01   178.86  30.0  1
 J2C  Var_33    H9   C06  N01  C02   -62.31  30.0  1
 J2C  Var_34    H10  C06  N01  C02  -179.46  30.0  1
 J2C  Var_35    H7   C05  C04  C03   -69.50  30.0  1
 J2C  Var_36    H8   C05  C04  C03   173.18  30.0  1
 J2C  Var_37    H9   C06  C05  C04    66.15  30.0  1
 J2C  Var_38    H10  C06  C05  C04  -175.50  30.0  1
 J2C  Var_39    H11  C09  S10  C04  -141.93  30.0  1
 J2C  Var_40    H12  C09  S10  C04    97.35  30.0  1
 J2C  Var_41    H3   C02  C03  C04   -63.99  30.0  1
 J2C  Var_42    H4   C02  C03  C04   179.45  30.0  1
 J2C  Var_43    H5   C03  C04  C05    66.75  30.0  1
 J2C  Var_44    H6   C03  C04  C05  -174.43  30.0  1
 J2C  Var_45    H3   C02  N01  C06    61.95  30.0  1
 J2C  Var_46    H4   C02  N01  C06   178.47  30.0  1
 J2C  Var_47    H11  C09  C08  N07   132.86  30.0  1
 J2C  Var_48    H12  C09  C08  N07  -108.35  30.0  1
 J2C  Var_49    H7   C05  C04  N07    56.60  30.0  1
 J2C  Var_50    H8   C05  C04  N07   -60.71  30.0  1
 J2C  Var_51    H5   C03  C04  N07   -58.21  30.0  1
 J2C  Var_52    H6   C03  C04  N07    60.61  30.0  1
 J2C  Var_53    H7   C05  C04  S10   170.94  30.0  1
 J2C  Var_54    H8   C05  C04  S10    53.63  30.0  1
 J2C  Var_55    H5   C03  C04  S10  -172.10  30.0  1
 J2C  Var_56    H6   C03  C04  S10   -53.27  30.0  1
 J2C  Var_57    H1   C12  N07  C04     8.49  30.0  3
 J2C  Var_58    H2   C12  N07  C04   124.21  30.0  3
 J2C  Var_59    H1   C12  N07  C08  -158.15  30.0  3
 J2C  Var_60    H2   C12  N07  C08   -42.43  30.0  3
 J2C  Var_61    H11  C09  C08  O11   -48.49  30.0  1
 J2C  Var_62    H12  C09  C08  O11    70.30  30.0  1
 J2C  Var_63    H1   C12  C13  C14   123.50  30.0  1
 J2C  Var_64    H2   C12  C13  C14     7.59  30.0  1
 J2C  Var_65    H1   C12  C13  O17   -55.52  30.0  1
 J2C  Var_66    H2   C12  C13  O17  -171.43  30.0  1
 J2C  Var_67    H9   C06  N01  C18   125.32  30.0  1
 J2C  Var_68    H10  C06  N01  C18     8.16  30.0  1
 J2C  Var_69    H3   C02  N01  C18  -126.17  30.0  1
 J2C  Var_70    H4   C02  N01  C18    -9.65  30.0  1
 J2C  Var_71    CL1  C19  C18  N01   -76.71  30.0  3
 J2C  Var_72    H16  C19  C18  N01    44.76  30.0  3
 J2C  Var_73    H17  C19  C18  N01   166.34  30.0  3
 J2C  Var_74    CL1  C19  C18  O20   103.82  30.0  3
 J2C  Var_75    H16  C19  C18  O20  -134.71  30.0  3
 J2C  Var_76    H17  C19  C18  O20   -13.13  30.0  3

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
 J2C  plan-1  C12  0.020
 J2C  plan-1  C13  0.020
 J2C  plan-1  C14  0.020
 J2C  plan-1  C15  0.020
 J2C  plan-1  C16  0.020
 J2C  plan-1  O17  0.020
 J2C  plan-1  H13  0.020
 J2C  plan-1  H14  0.020
 J2C  plan-1  H15  0.020
 J2C  plan-2  N01  0.020
 J2C  plan-2  C02  0.020
 J2C  plan-2  C06  0.020
 J2C  plan-2  C19  0.020
 J2C  plan-2  O20  0.020
 J2C  plan-2  C18  0.020
 J2C  plan-3  C12  0.020
 J2C  plan-3  C04  0.020
 J2C  plan-3  N07  0.020
 J2C  plan-3  C08  0.020
 J2C  plan-3  C09  0.020
 J2C  plan-3  O11  0.020

