# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Aug  1 04:55:56 2021
#   Inital geometry file: a 151 line input string
#   Ligand name: 5-{[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non-7-yl]methyl}thiophene-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)N(C(=O)[C@]12CN(C[C@H]2c3ccc(cc3)C#N)Cc4scc(c4)C(O)=O)c5cc(Cl)cc(Cl)c5
#
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
 2IC  2IC  '5-{[(5S,9R)-9-(4-cyanophenyl)-3-(3,5-dichlorophenyl)-1-methyl-2,4-dioxo-1,3,7-triazaspiro[4.4]non-7-yl]methyl}thiophene-3-carboxylic acid'  ligand  57  37  .  2022-07-22  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_2IC
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
 2IC  C2    C   CR6    0  -0.056   -6.6002  -0.7035  29.0458
 2IC  C3    C   CR16   0  -0.164   -5.9543  -0.1193  30.1240
 2IC  C8    C   CR6    0   0.323   -8.0925   1.1473  28.8932
 2IC  C9    C   CR16   0  -0.189   -7.6722  -0.0879  28.4243
 2IC  C12   C   CR5    0   0.725  -10.4505   1.9158  28.8559
 2IC  C14   C   CR5    0   0.003  -10.6227   2.5837  26.6382
 2IC  C15   C   CH2    0  -0.259  -10.7409   3.9597  25.9556
 2IC  N18   N   NT     0  -0.436  -11.3858   3.6944  24.6808
 2IC  C19   C   CH2   -1  -0.254  -10.9797   2.3626  24.2786
 2IC  C22   C   CH1    0  -0.332  -11.1904   1.5892  25.5684
 2IC  C24   C   CR6    0   0.131  -10.6487   0.1951  25.6856
 2IC  C27   C   CR16   0  -0.221  -10.6884  -1.9212  26.8616
 2IC  C30   C   CR16   0  -0.221   -9.0850  -1.5483  25.0910
 2IC  C32   C   CR16   0  -0.291   -9.5959  -0.2759  24.9021
 2IC  C34   C   CSP    0   0.057   -9.0807  -3.6711  26.2972
 2IC  CL1   CL  CL     0  -0.097   -6.0707  -2.2428  28.4716
 2IC  C5    C   CR6    0  -0.049   -6.4051   1.1142  30.5681
 2IC  C6    C   CR16   0  -0.218   -7.4674   1.7666  29.9630
 2IC  N11   N   NR5    0  -0.684   -9.1871   1.7682  28.2558
 2IC  N13   N   NR5    0  -0.519  -11.2597   2.4594  27.9263
 2IC  C25   C   CR16   0  -0.292  -11.1934  -0.6510  26.6534
 2IC  C29   C   CR6    0  -0.029   -9.6235  -2.3693  26.0808
 2IC  N35   N   NS     0  -0.247   -8.6404  -4.7209  26.4745
 2IC  C36   C   CH2    0  -0.313  -11.1830   4.7152  23.6860
 2IC  C39   C   CR5    0  -0.196  -11.9339   5.9613  24.0441
 2IC  S40   S   S2     0   0.266  -11.3733   7.5122  23.5389
 2IC  C41   C   CR15   0  -0.497  -12.6974   8.3092  24.2531
 2IC  C43   C   CR5    0   0.028  -13.5374   7.4210  24.8658
 2IC  C44   C   CR15   0  -0.203  -13.0945   6.0721  24.7417
 2IC  C46   C   C      0   0.512  -14.7662   7.7812  25.5881
 2IC  O47   O   O      0  -0.440  -15.4858   6.9719  26.1239
 2IC  O48   O   OH1    0  -0.595  -15.0006   9.0870  25.5903
 2IC  C50   C   CR5    0   0.566   -9.1865   2.2172  26.9653
 2IC  O51   O   O      0  -0.398   -8.2356   2.2739  26.2293
 2IC  C52   C   CH3    0  -0.547  -12.6685   2.6813  28.1428
 2IC  CL57  CL  CL     0  -0.098   -5.6119   1.8613  31.9071
 2IC  H3    H   HCR6   0   0.310   -5.1222  -0.6126  30.6067
 2IC  H9    H   HCR6   0   0.284   -8.1832  -0.5625  27.5979
 2IC  H151  H   HCH2   0   0.249   -9.7420   4.3997  25.8252
 2IC  H152  H   HCH2   0   0.266  -11.3178   4.6586  26.5630
 2IC  H191  H   HCH2   0   0.270  -11.6063   1.9885  23.4675
 2IC  H192  H   HCH2   0   0.227   -9.9333   2.3240  23.9408
 2IC  H22   H   HCH1   0   0.306  -12.2702   1.5445  25.7391
 2IC  H27   H   HCR6   0   0.287  -11.1168  -2.5605  27.6211
 2IC  H30   H   HCR6   0   0.287   -8.2658  -1.9008  24.4793
 2IC  H32   H   HCR6   0   0.271   -9.1594   0.3473  24.1345
 2IC  H6    H   HCR6   0   0.302   -7.7918   2.7401  30.3039
 2IC  H25   H   HCR6   0   0.273  -12.0359  -0.3198  27.2483
 2IC  H361  H   HCH2   0   0.278  -11.5515   4.3382  22.7276
 2IC  H362  H   HCH2   0   0.230  -10.1156   4.9462  23.5363
 2IC  H41   H   HCR5   0   0.309  -12.7854   9.3826  24.1880
 2IC  H44   H   HCR5   0   0.268  -13.6151   5.2218  25.1586
 2IC  HO48  H   HOH1   0   0.487  -15.8153   9.2757  26.0789
 2IC  H521  H   HCH3   0   0.277  -12.8430   2.9523  29.1805
 2IC  H522  H   HCH3   0   0.261  -13.0090   3.5054  27.5189
 2IC  H523  H   HCH3   0   0.254  -13.2672   1.8003  27.9068
 2IC  O56   O   O      0  -0.459  -10.7070   1.6045  29.9938

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
 2IC  C2   CL1   single    1.726  0.020  1.726
 2IC  C2   C9    aromatic  1.384  0.020  1.384
 2IC  C2   C3    aromatic  1.386  0.020  1.386
 2IC  C3   C5    aromatic  1.386  0.020  1.386
 2IC  C3   H3    single    0.930  0.020  1.080
 2IC  C8   C9    aromatic  1.386  0.020  1.386
 2IC  C8   N11   single    1.411  0.020  1.411
 2IC  C8   C6    aromatic  1.385  0.020  1.385
 2IC  C9   H9    single    0.930  0.020  1.080
 2IC  C12  N11   single    1.406  0.020  1.406
 2IC  C12  N13   single    1.347  0.020  1.347
 2IC  C12  O56   double    1.207  0.020  1.207
 2IC  C14  C22   single    1.567  0.020  1.567
 2IC  C14  C15   single    1.541  0.020  1.541
 2IC  C14  C50   single    1.518  0.020  1.518
 2IC  C14  N13   single    1.442  0.020  1.442
 2IC  C15  N18   single    1.453  0.020  1.453
 2IC  C15  H151  single    0.970  0.020  1.090
 2IC  C15  H152  single    0.970  0.020  1.090
 2IC  N18  C36   single    1.440  0.020  1.440
 2IC  N18  C19   single    1.449  0.020  1.449
 2IC  C19  C22   single    1.519  0.020  1.519
 2IC  C19  H191  single    0.970  0.020  1.090
 2IC  C19  H192  single    0.970  0.020  1.090
 2IC  C22  C24   single    1.500  0.020  1.500
 2IC  C22  H22   single    0.970  0.020  1.090
 2IC  C24  C32   aromatic  1.394  0.020  1.394
 2IC  C24  C25   aromatic  1.396  0.020  1.396
 2IC  C27  C29   aromatic  1.394  0.020  1.394
 2IC  C27  C25   aromatic  1.383  0.020  1.383
 2IC  C27  H27   single    0.930  0.020  1.080
 2IC  C30  C32   aromatic  1.384  0.020  1.384
 2IC  C30  C29   aromatic  1.394  0.020  1.394
 2IC  C30  H30   single    0.930  0.020  1.080
 2IC  C32  H32   single    0.930  0.020  1.080
 2IC  C34  N35   triple    1.152  0.020  1.152
 2IC  C34  C29   single    1.427  0.020  1.427
 2IC  C5   C6    aromatic  1.386  0.020  1.386
 2IC  C5   CL57  single    1.726  0.020  1.726
 2IC  C6   H6    single    0.930  0.020  1.080
 2IC  N11  C50   single    1.366  0.020  1.366
 2IC  N13  C52   single    1.443  0.020  1.443
 2IC  C25  H25   single    0.930  0.020  1.080
 2IC  C36  C39   single    1.498  0.020  1.498
 2IC  C36  H361  single    0.970  0.020  1.090
 2IC  C36  H362  single    0.970  0.020  1.090
 2IC  C39  C44   aromatic  1.359  0.020  1.359
 2IC  C39  S40   aromatic  1.725  0.020  1.725
 2IC  S40  C41   aromatic  1.702  0.020  1.702
 2IC  C41  C43   aromatic  1.367  0.020  1.367
 2IC  C41  H41   single    0.930  0.020  1.080
 2IC  C43  C46   single    1.470  0.020  1.470
 2IC  C43  C44   aromatic  1.425  0.020  1.425
 2IC  C44  H44   single    0.930  0.020  1.080
 2IC  C46  O47   double    1.208  0.020  1.208
 2IC  C46  O48   single    1.327  0.020  1.327
 2IC  O48  HO48  single    0.850  0.020  0.980
 2IC  C50  O51   double    1.204  0.020  1.204
 2IC  C52  H521  single    0.970  0.020  1.090
 2IC  C52  H522  single    0.970  0.020  1.090
 2IC  C52  H523  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
 2IC  CL1   C2   C9    119.01  3.000
 2IC  C9    C2   C3    121.53  3.000
 2IC  CL1   C2   C3    119.45  3.000
 2IC  H3    C3   C5    120.88  3.000
 2IC  H3    C3   C2    120.91  3.000
 2IC  C5    C3   C2    118.21  3.000
 2IC  N11   C8   C6    120.15  3.000
 2IC  C6    C8   C9    121.51  3.000
 2IC  N11   C8   C9    118.33  3.000
 2IC  H9    C9   C8    120.41  3.000
 2IC  H9    C9   C2    120.94  3.000
 2IC  C8    C9   C2    118.64  3.000
 2IC  O56   C12  N13   128.82  3.000
 2IC  O56   C12  N11   124.47  3.000
 2IC  N13   C12  N11   106.71  3.000
 2IC  C50   C14  N13   101.81  3.000
 2IC  N13   C14  C22   113.27  3.000
 2IC  C50   C14  C22   109.67  3.000
 2IC  N13   C14  C15   116.03  3.000
 2IC  C50   C14  C15   112.56  3.000
 2IC  C22   C14  C15   103.68  3.000
 2IC  H152  C15  H151  106.87  3.000
 2IC  H152  C15  N18   111.76  3.000
 2IC  H151  C15  N18   111.86  3.000
 2IC  H152  C15  C14   111.47  3.000
 2IC  H151  C15  C14   109.90  3.000
 2IC  N18   C15  C14   105.05  3.000
 2IC  C36   N18  C19   114.86  3.000
 2IC  C19   N18  C15   106.67  3.000
 2IC  C36   N18  C15   114.47  3.000
 2IC  H192  C19  H191  107.81  3.000
 2IC  H192  C19  C22   112.01  3.000
 2IC  H191  C19  C22   112.16  3.000
 2IC  H192  C19  N18   112.58  3.000
 2IC  H191  C19  N18   111.13  3.000
 2IC  C22   C19  N18   101.16  3.000
 2IC  H22   C22  C24   107.83  3.000
 2IC  H22   C22  C19   106.87  3.000
 2IC  C24   C22  C19   119.31  3.000
 2IC  H22   C22  C14   106.07  3.000
 2IC  C24   C22  C14   113.93  3.000
 2IC  C19   C22  C14   101.91  3.000
 2IC  C25   C24  C32   118.65  3.000
 2IC  C25   C24  C22   118.45  3.000
 2IC  C32   C24  C22   122.86  3.000
 2IC  H27   C27  C29   120.39  3.000
 2IC  H27   C27  C25   120.28  3.000
 2IC  C29   C27  C25   119.33  3.000
 2IC  H30   C30  C29   120.14  3.000
 2IC  H30   C30  C32   120.14  3.000
 2IC  C29   C30  C32   119.72  3.000
 2IC  H32   C32  C30   118.55  3.000
 2IC  H32   C32  C24   120.61  3.000
 2IC  C30   C32  C24   120.84  3.000
 2IC  N35   C34  C29   180.00  3.000
 2IC  CL57  C5   C6    119.16  3.000
 2IC  CL57  C5   C3    118.95  3.000
 2IC  C6    C5   C3    121.89  3.000
 2IC  H6    C6   C5    121.08  3.000
 2IC  H6    C6   C8    120.70  3.000
 2IC  C5    C6   C8    118.21  3.000
 2IC  C50   N11  C12   111.65  3.000
 2IC  C50   N11  C8    124.82  3.000
 2IC  C12   N11  C8    123.40  3.000
 2IC  C52   N13  C14   123.51  3.000
 2IC  C52   N13  C12   123.04  3.000
 2IC  C14   N13  C12   112.69  3.000
 2IC  H25   C25  C27   118.83  3.000
 2IC  H25   C25  C24   119.92  3.000
 2IC  C27   C25  C24   121.24  3.000
 2IC  C34   C29  C30   119.86  3.000
 2IC  C34   C29  C27   119.92  3.000
 2IC  C30   C29  C27   120.21  3.000
 2IC  H362  C36  H361  106.23  3.000
 2IC  H362  C36  C39   110.08  3.000
 2IC  H361  C36  C39   109.10  3.000
 2IC  H362  C36  N18   112.27  3.000
 2IC  H361  C36  N18   108.27  3.000
 2IC  C39   C36  N18   110.73  3.000
 2IC  C44   C39  S40   110.78  3.000
 2IC  S40   C39  C36   121.00  3.000
 2IC  C44   C39  C36   128.21  3.000
 2IC  C41   S40  C39    92.60  3.000
 2IC  H41   C41  C43   128.54  3.000
 2IC  H41   C41  S40   120.25  3.000
 2IC  C43   C41  S40   111.20  3.000
 2IC  C46   C43  C44   122.31  3.000
 2IC  C44   C43  C41   112.63  3.000
 2IC  C46   C43  C41   125.06  3.000
 2IC  H44   C44  C43   124.15  3.000
 2IC  H44   C44  C39   123.06  3.000
 2IC  C43   C44  C39   112.79  3.000
 2IC  O48   C46  O47   123.59  3.000
 2IC  O48   C46  C43   112.93  3.000
 2IC  O47   C46  C43   123.47  3.000
 2IC  HO48  O48  C46   109.96  3.000
 2IC  O51   C50  N11   126.39  3.000
 2IC  O51   C50  C14   127.18  3.000
 2IC  N11   C50  C14   106.41  3.000
 2IC  H523  C52  H522  108.41  3.000
 2IC  H523  C52  H521  108.65  3.000
 2IC  H522  C52  H521  107.97  3.000
 2IC  H523  C52  N13   112.29  3.000
 2IC  H522  C52  N13   109.63  3.000
 2IC  H521  C52  N13   109.78  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
 2IC  CONST_01  C6    C8   C9   C2      0.00   0.0  0
 2IC  CONST_02  C6    C5   C3   C2      0.00   0.0  0
 2IC  CONST_03  C8    C9   C2   C3      0.00   0.0  0
 2IC  CONST_04  C8    C6   C5   C3      0.00   0.0  0
 2IC  CONST_05  C5    C3   C2   C9      0.00   0.0  0
 2IC  CONST_06  C5    C6   C8   C9      0.00   0.0  0
 2IC  CONST_07  C29   C30  C32  C24     0.00   0.0  0
 2IC  CONST_08  C29   C27  C25  C24     0.00   0.0  0
 2IC  CONST_09  C32   C30  C29  C27     0.00   0.0  0
 2IC  CONST_10  C32   C24  C25  C27     0.00   0.0  0
 2IC  CONST_11  C25   C24  C32  C30     0.00   0.0  0
 2IC  CONST_12  C25   C27  C29  C30     0.00   0.0  0
 2IC  CONST_13  C41   C43  C44  C39     0.00   0.0  0
 2IC  CONST_14  C43   C41  S40  C39     0.00   0.0  0
 2IC  CONST_15  C43   C44  C39  S40     0.00   0.0  0
 2IC  CONST_16  C44   C43  C41  S40     0.00   0.0  0
 2IC  CONST_17  C44   C39  S40  C41     0.00   0.0  0
 2IC  CONST_18  N11   C8   C9   C2    180.00   0.0  0
 2IC  CONST_19  C30   C32  C24  C22   180.00   0.0  0
 2IC  CONST_20  C27   C25  C24  C22   180.00   0.0  0
 2IC  CONST_21  N11   C8   C6   C5    180.00   0.0  0
 2IC  CONST_22  N13   C12  N11  C8    180.00   0.0  0
 2IC  CONST_23  C14   C50  N11  C8    180.00   0.0  0
 2IC  CONST_24  C14   C50  N11  C12     0.00   0.0  0
 2IC  CONST_25  N11   C12  N13  C14     0.00   0.0  0
 2IC  CONST_26  C50   N11  C12  N13     0.00   0.0  0
 2IC  CONST_27  CL57  C5   C3   C2    180.00   0.0  0
 2IC  CONST_28  CL1   C2   C9   C8    180.00   0.0  0
 2IC  CONST_29  CL57  C5   C6   C8    180.00   0.0  0
 2IC  CONST_30  C34   C29  C30  C32   180.00   0.0  0
 2IC  CONST_31  C25   C27  C29  C34   180.00   0.0  0
 2IC  CONST_32  C5    C3   C2   CL1   180.00   0.0  0
 2IC  CONST_33  C43   C44  C39  C36   180.00   0.0  0
 2IC  CONST_34  C41   S40  C39  C36   180.00   0.0  0
 2IC  CONST_35  C46   C43  C44  C39   180.00   0.0  0
 2IC  CONST_36  C46   C43  C41  S40   180.00   0.0  0
 2IC  CONST_37  O56   C12  N11  C8      0.00   0.0  0
 2IC  CONST_38  O56   C12  N13  C14   180.00   0.0  0
 2IC  CONST_39  C52   N13  C12  N11   180.00   0.0  0
 2IC  CONST_40  O56   C12  N11  C50   180.00   0.0  0
 2IC  CONST_41  H9    C9   C2   C3    180.00   0.0  0
 2IC  CONST_42  H6    C6   C5   C3    180.00   0.0  0
 2IC  CONST_43  H3    C3   C2   C9    180.00   0.0  0
 2IC  CONST_44  H32   C32  C24  C22     0.00   0.0  0
 2IC  CONST_45  H25   C25  C24  C22     0.00   0.0  0
 2IC  CONST_46  H30   C30  C32  C24   180.00   0.0  0
 2IC  CONST_47  H27   C27  C25  C24   180.00   0.0  0
 2IC  CONST_48  H41   C41  S40  C39   180.00   0.0  0
 2IC  CONST_49  H44   C44  C39  S40   180.00   0.0  0
 2IC  CONST_50  O56   C12  N13  C52     0.00   0.0  0
 2IC  CONST_51  HO48  O48  C46  C43   180.00   0.0  0
 2IC  Var_01    C12   N11  C8   C9    109.80  30.0  2
 2IC  Var_02    C44   C39  C36  N18   -30.01  30.0  2
 2IC  Var_03    O47   C46  C43  C41  -179.72  30.0  2
 2IC  Var_04    H521  C52  N13  C12    34.95  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
 2IC  chir_01  C14  C15  C50  N13  negativ
 2IC  chir_02  N18  C36  C19  C15  negativ
 2IC  chir_03  C22  C14  C19  C24  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
 2IC  plan-1  C36   0.020
 2IC  plan-1  C39   0.020
 2IC  plan-1  S40   0.020
 2IC  plan-1  C41   0.020
 2IC  plan-1  C43   0.020
 2IC  plan-1  C44   0.020
 2IC  plan-1  C46   0.020
 2IC  plan-1  H41   0.020
 2IC  plan-1  H44   0.020
 2IC  plan-2  C2    0.020
 2IC  plan-2  C3    0.020
 2IC  plan-2  C8    0.020
 2IC  plan-2  C9    0.020
 2IC  plan-2  CL1   0.020
 2IC  plan-2  C5    0.020
 2IC  plan-2  C6    0.020
 2IC  plan-2  N11   0.020
 2IC  plan-2  CL57  0.020
 2IC  plan-2  H3    0.020
 2IC  plan-2  H9    0.020
 2IC  plan-2  H6    0.020
 2IC  plan-3  C22   0.020
 2IC  plan-3  C24   0.020
 2IC  plan-3  C27   0.020
 2IC  plan-3  C30   0.020
 2IC  plan-3  C32   0.020
 2IC  plan-3  C34   0.020
 2IC  plan-3  C25   0.020
 2IC  plan-3  C29   0.020
 2IC  plan-3  N35   0.020
 2IC  plan-3  H27   0.020
 2IC  plan-3  H30   0.020
 2IC  plan-3  H32   0.020
 2IC  plan-3  H25   0.020
 2IC  plan-4  C8    0.020
 2IC  plan-4  C12   0.020
 2IC  plan-4  C14   0.020
 2IC  plan-4  N11   0.020
 2IC  plan-4  N13   0.020
 2IC  plan-4  C50   0.020
 2IC  plan-4  O51   0.020
 2IC  plan-4  C52   0.020
 2IC  plan-4  O56   0.020
 2IC  plan-5  C43   0.020
 2IC  plan-5  C46   0.020
 2IC  plan-5  O47   0.020
 2IC  plan-5  O48   0.020
 2IC  plan-5  HO48  0.020

