# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Aug  4 01:06:55 2022
#   Inital geometry file: a 109 line input string
#   Ligand name: (5S)-6,6-dimethyl-8-[(4S)-7-(trifluoromethyl)imidazo[1,5-a]pyridin-5-yl]-1,3,8-triazaspiro[4.5]decane-2,4-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1(C)CN(CC[C@]12NC(=O)NC2=O)c3cc(cc4cncn34)C(F)(F)F
#
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
 YRM  YRM  "(5S)-6,6-dimethyl-8-[(4S)-7-(trifluoromethyl)imidazo[1,5-a]pyridin-5-yl]-1,3,8-triazaspiro[4.5]decane-2,4-dione"
  ligand  45  27  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_YRM
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
 YRM  C01  C  CR6   0   0.630  -32.0186  -28.0406  -33.1969
 YRM  C03  C  CH2   0  -0.299  -32.7259  -27.0624  -35.2869
 YRM  C04  C  CT    0  -0.087  -32.2391  -26.9873  -36.7410
 YRM  C05  C  CR5   0  -0.017  -31.0583  -25.9668  -36.7830
 YRM  C06  C  CH2   0  -0.415  -29.9759  -26.3452  -35.7625
 YRM  C07  C  CH2   0  -0.340  -30.5621  -26.5153  -34.3736
 YRM  C08  C  CH3   0  -0.644  -31.8221  -28.3911  -37.1906
 YRM  C09  C  CH3   0  -0.656  -33.4039  -26.5246  -37.6145
 YRM  C11  C  CR56  0   0.376  -31.3446  -29.5700  -31.4295
 YRM  C12  C  CR16  0  -0.441  -32.5557  -29.3366  -30.7430
 YRM  C13  C  CR6   0  -0.087  -33.4606  -28.4917  -31.2996
 YRM  C14  C  CR16  0  -0.465  -33.1780  -27.8201  -32.5279
 YRM  C15  C  CR15  0   0.068  -29.9371  -29.4095  -33.1253
 YRM  C17  C  CR15  0  -0.238  -30.2459  -30.3829  -31.2424
 YRM  C19  C  CR5   0   0.662  -31.2930  -23.7853  -37.6147
 YRM  C21  C  CR5   0   0.585  -30.4277  -25.8348  -38.1710
 YRM  C24  C  CT    0   1.056  -34.7783  -28.2150  -30.6574
 YRM  F25  F  F     0  -0.315  -34.9206  -26.9137  -30.3616
 YRM  F26  F  F     0  -0.314  -35.7941  -28.5261  -31.4759
 YRM  F27  F  F     0  -0.299  -34.9606  -28.9004  -29.5278
 YRM  N02  N  NT    0  -0.506  -31.6533  -27.4887  -34.4076
 YRM  N10  N  N     0  -0.574  -31.1180  -28.9385  -32.6478
 YRM  N16  N  N     0  -0.424  -29.4030  -30.2708  -32.2923
 YRM  N18  N  NR15  0  -0.665  -31.5185  -24.6079  -36.5725
 YRM  N20  N  NR15  0  -0.701  -30.6491  -24.5569  -38.5793
 YRM  O23  O  O     0  -0.467  -31.5690  -22.6121  -37.7265
 YRM  H1   H  HCH2  0   0.240  -33.1487  -26.0957  -34.9709
 YRM  H2   H  HCH2  0   0.274  -33.5385  -27.7898  -35.2354
 YRM  H3   H  HCH2  0   0.263  -29.4842  -27.2683  -36.0711
 YRM  H4   H  HCH2  0   0.269  -29.2123  -25.5652  -35.7353
 YRM  H5   H  HCH2  0   0.277  -29.7780  -26.8423  -33.6913
 YRM  H6   H  HCH2  0   0.249  -30.9287  -25.5551  -33.9842
 YRM  H7   H  HCH3  0   0.240  -30.9524  -28.7726  -36.6596
 YRM  H8   H  HCH3  0   0.233  -32.6471  -29.0793  -36.9975
 YRM  H9   H  HCH3  0   0.240  -31.6116  -28.4296  -38.2574
 YRM  H10  H  HCH3  0   0.240  -33.8275  -25.5756  -37.2858
 YRM  H11  H  HCH3  0   0.241  -33.1046  -26.4182  -38.6588
 YRM  H12  H  HCH3  0   0.245  -34.2023  -27.2680  -37.5867
 YRM  H13  H  HCR6  0   0.283  -32.7280  -29.8575  -29.8118
 YRM  H14  H  HCR6  0   0.295  -33.8829  -27.1105  -32.9379
 YRM  H15  H  HCR5  0   0.302  -29.5249  -29.1131  -34.0761
 YRM  H16  H  HCR5  0   0.266  -30.0510  -31.0373  -30.4068
 YRM  H17  H  HNR5  0   0.413  -31.9835  -24.2796  -35.7418
 YRM  H18  H  HNR5  0   0.423  -30.3207  -24.1752  -39.4553
 YRM  O22  O  O     0  -0.417  -29.8221  -26.6846  -38.7776

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
 YRM  O22  C21  double    1.207  0.020  1.207
 YRM  N20  C21  single    1.360  0.020  1.360
 YRM  N20  C19  single    1.393  0.020  1.393
 YRM  C21  C05  single    1.530  0.020  1.530
 YRM  C09  C04  single    1.528  0.020  1.528
 YRM  C19  O23  double    1.210  0.020  1.210
 YRM  C19  N18  single    1.347  0.020  1.347
 YRM  C08  C04  single    1.532  0.020  1.532
 YRM  C05  C04  single    1.561  0.020  1.561
 YRM  C05  N18  single    1.450  0.020  1.450
 YRM  C05  C06  single    1.535  0.020  1.535
 YRM  C04  C03  single    1.535  0.020  1.535
 YRM  C06  C07  single    1.517  0.020  1.517
 YRM  C03  N02  single    1.451  0.020  1.451
 YRM  C07  N02  single    1.463  0.020  1.463
 YRM  N02  C01  single    1.380  0.020  1.380
 YRM  C01  N10  aromatic  1.385  0.020  1.385
 YRM  C01  C14  aromatic  1.357  0.020  1.357
 YRM  C15  N10  aromatic  1.358  0.020  1.358
 YRM  C15  N16  aromatic  1.312  0.020  1.312
 YRM  N10  C11  aromatic  1.391  0.020  1.391
 YRM  C14  C13  aromatic  1.428  0.020  1.428
 YRM  N16  C17  aromatic  1.351  0.020  1.351
 YRM  C11  C17  aromatic  1.380  0.020  1.380
 YRM  C11  C12  aromatic  1.412  0.020  1.412
 YRM  F26  C24  single    1.341  0.020  1.341
 YRM  C13  C12  aromatic  1.357  0.020  1.357
 YRM  C13  C24  single    1.492  0.020  1.492
 YRM  C24  F27  single    1.334  0.020  1.334
 YRM  C24  F25  single    1.342  0.020  1.342
 YRM  C03  H1   single    0.970  0.020  1.090
 YRM  C03  H2   single    0.970  0.020  1.090
 YRM  C06  H3   single    0.970  0.020  1.090
 YRM  C06  H4   single    0.970  0.020  1.090
 YRM  C07  H5   single    0.970  0.020  1.090
 YRM  C07  H6   single    0.970  0.020  1.090
 YRM  C08  H7   single    0.970  0.020  1.090
 YRM  C08  H8   single    0.970  0.020  1.090
 YRM  C08  H9   single    0.970  0.020  1.090
 YRM  C09  H10  single    0.970  0.020  1.090
 YRM  C09  H11  single    0.970  0.020  1.090
 YRM  C09  H12  single    0.970  0.020  1.090
 YRM  C12  H13  single    0.930  0.020  1.080
 YRM  C14  H14  single    0.930  0.020  1.080
 YRM  C15  H15  single    0.930  0.020  1.080
 YRM  C17  H16  single    0.930  0.020  1.080
 YRM  N18  H17  single    0.860  0.020  1.020
 YRM  N20  H18  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
 YRM  N10  C01  N02  115.78  3.000
 YRM  N10  C01  C14  117.74  3.000
 YRM  N02  C01  C14  126.45  3.000
 YRM  H2   C03  H1   106.59  3.000
 YRM  H2   C03  N02  109.01  3.000
 YRM  H1   C03  N02  111.58  3.000
 YRM  H2   C03  C04  108.26  3.000
 YRM  H1   C03  C04  110.52  3.000
 YRM  N02  C03  C04  110.73  3.000
 YRM  C09  C04  C08  108.50  3.000
 YRM  C08  C04  C05  112.66  3.000
 YRM  C09  C04  C05  111.31  3.000
 YRM  C05  C04  C03  107.29  3.000
 YRM  C08  C04  C03  108.63  3.000
 YRM  C09  C04  C03  108.33  3.000
 YRM  N18  C05  C21  100.47  3.000
 YRM  N18  C05  C06  111.00  3.000
 YRM  C21  C05  C06  109.49  3.000
 YRM  C06  C05  C04  110.75  3.000
 YRM  N18  C05  C04  111.63  3.000
 YRM  C21  C05  C04  113.11  3.000
 YRM  H4   C06  H3   107.24  3.000
 YRM  H4   C06  C07  109.11  3.000
 YRM  H3   C06  C07  109.78  3.000
 YRM  H4   C06  C05  109.49  3.000
 YRM  H3   C06  C05  109.79  3.000
 YRM  C07  C06  C05  111.34  3.000
 YRM  H6   C07  H5   106.28  3.000
 YRM  H6   C07  N02  109.93  3.000
 YRM  H5   C07  N02  110.59  3.000
 YRM  H6   C07  C06  110.81  3.000
 YRM  H5   C07  C06  109.20  3.000
 YRM  N02  C07  C06  109.97  3.000
 YRM  H9   C08  H8   107.30  3.000
 YRM  H9   C08  H7   108.15  3.000
 YRM  H8   C08  H7   107.27  3.000
 YRM  H9   C08  C04  111.89  3.000
 YRM  H8   C08  C04  108.67  3.000
 YRM  H7   C08  C04  113.31  3.000
 YRM  H12  C09  H11  106.94  3.000
 YRM  H12  C09  H10  107.52  3.000
 YRM  H11  C09  H10  108.07  3.000
 YRM  H12  C09  C04  109.69  3.000
 YRM  H11  C09  C04  111.56  3.000
 YRM  H10  C09  C04  112.81  3.000
 YRM  N10  C11  C17  104.87  3.000
 YRM  C17  C11  C12  135.62  3.000
 YRM  N10  C11  C12  119.39  3.000
 YRM  H13  C12  C13  123.16  3.000
 YRM  H13  C12  C11  118.44  3.000
 YRM  C13  C12  C11  118.38  3.000
 YRM  C24  C13  C14  117.25  3.000
 YRM  C24  C13  C12  121.85  3.000
 YRM  C14  C13  C12  120.90  3.000
 YRM  H14  C14  C13  120.39  3.000
 YRM  H14  C14  C01  118.48  3.000
 YRM  C13  C14  C01  121.12  3.000
 YRM  H15  C15  N16  125.80  3.000
 YRM  H15  C15  N10  123.18  3.000
 YRM  N16  C15  N10  111.01  3.000
 YRM  H16  C17  N16  122.64  3.000
 YRM  H16  C17  C11  127.32  3.000
 YRM  N16  C17  C11  110.03  3.000
 YRM  O23  C19  N20  125.33  3.000
 YRM  O23  C19  N18  128.71  3.000
 YRM  N20  C19  N18  105.96  3.000
 YRM  O22  C21  N20  126.33  3.000
 YRM  N20  C21  C05  106.64  3.000
 YRM  O22  C21  C05  127.01  3.000
 YRM  F27  C24  F26  107.11  3.000
 YRM  F27  C24  F25  107.29  3.000
 YRM  F26  C24  F25  106.21  3.000
 YRM  F25  C24  C13  111.62  3.000
 YRM  F27  C24  C13  112.96  3.000
 YRM  F26  C24  C13  111.30  3.000
 YRM  C07  N02  C03  111.72  3.000
 YRM  C07  N02  C01  116.31  3.000
 YRM  C03  N02  C01  116.97  3.000
 YRM  C15  N10  C11  106.99  3.000
 YRM  C11  N10  C01  122.38  3.000
 YRM  C15  N10  C01  130.60  3.000
 YRM  C17  N16  C15  107.09  3.000
 YRM  H17  N18  C19  121.10  3.000
 YRM  H17  N18  C05  124.87  3.000
 YRM  C19  N18  C05  114.01  3.000
 YRM  H18  N20  C21  124.23  3.000
 YRM  H18  N20  C19  122.77  3.000
 YRM  C21  N20  C19  112.83  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
 YRM  CONST_01  N16  C15  N10  C01   180.00   0.0  0
 YRM  CONST_02  C17  C11  N10  C01   180.00   0.0  0
 YRM  CONST_03  C12  C11  N10  C01     0.00   0.0  0
 YRM  CONST_04  C12  C13  C14  C01     0.00   0.0  0
 YRM  CONST_05  C14  C01  N10  C11     0.00   0.0  0
 YRM  CONST_06  N16  C15  N10  C11     0.00   0.0  0
 YRM  CONST_07  C15  N16  C17  C11     0.00   0.0  0
 YRM  CONST_08  C14  C13  C12  C11     0.00   0.0  0
 YRM  CONST_09  C15  N10  C11  C12   180.00   0.0  0
 YRM  CONST_10  N16  C17  C11  C12   180.00   0.0  0
 YRM  CONST_11  N10  C01  C14  C13     0.00   0.0  0
 YRM  CONST_12  N10  C11  C12  C13     0.00   0.0  0
 YRM  CONST_13  C17  C11  C12  C13   180.00   0.0  0
 YRM  CONST_14  C15  N10  C01  C14   180.00   0.0  0
 YRM  CONST_15  C17  C11  N10  C15     0.00   0.0  0
 YRM  CONST_16  N10  C15  N16  C17     0.00   0.0  0
 YRM  CONST_17  N16  C17  C11  N10     0.00   0.0  0
 YRM  CONST_18  N02  C01  N10  C11   180.00   0.0  0
 YRM  CONST_19  N02  C01  C14  C13   180.00   0.0  0
 YRM  CONST_20  N02  C01  N10  C15     0.00   0.0  0
 YRM  CONST_21  C19  N20  C21  C05     0.00   0.0  0
 YRM  CONST_22  N20  C19  N18  C05     0.00   0.0  0
 YRM  CONST_23  N18  C19  N20  C21     0.00   0.0  0
 YRM  CONST_24  C24  C13  C14  C01   180.00   0.0  0
 YRM  CONST_25  C24  C13  C12  C11   180.00   0.0  0
 YRM  CONST_26  O23  C19  N18  C05   180.00   0.0  0
 YRM  CONST_27  O22  C21  N20  C19   180.00   0.0  0
 YRM  CONST_28  O23  C19  N20  C21   180.00   0.0  0
 YRM  CONST_29  H15  C15  N10  C01     0.00   0.0  0
 YRM  CONST_30  H15  C15  N10  C11   180.00   0.0  0
 YRM  CONST_31  H16  C17  C11  C12     0.00   0.0  0
 YRM  CONST_32  H14  C14  C13  C12   180.00   0.0  0
 YRM  CONST_33  H13  C12  C13  C14   180.00   0.0  0
 YRM  CONST_34  H16  C17  N16  C15   180.00   0.0  0
 YRM  CONST_35  H15  C15  N16  C17   180.00   0.0  0
 YRM  CONST_36  H13  C12  C11  C17     0.00   0.0  0
 YRM  CONST_37  H14  C14  C01  N02     0.00   0.0  0
 YRM  CONST_38  H14  C14  C01  N10   180.00   0.0  0
 YRM  CONST_39  H16  C17  C11  N10   180.00   0.0  0
 YRM  CONST_40  H13  C12  C11  N10   180.00   0.0  0
 YRM  CONST_41  H18  N20  C21  C05   180.00   0.0  0
 YRM  CONST_42  H18  N20  C19  N18   180.00   0.0  0
 YRM  CONST_43  H17  N18  C19  N20   180.00   0.0  0
 YRM  CONST_44  H18  N20  C21  O22     0.00   0.0  0
 YRM  CONST_45  H18  N20  C19  O23     0.00   0.0  0
 YRM  CONST_46  H17  N18  C19  O23     0.00   0.0  0
 YRM  Var_01    C04  C03  N02  C01  -158.23  30.0  1
 YRM  Var_02    C06  C07  N02  C01   161.53  30.0  1
 YRM  Var_03    C06  C07  N02  C03   -60.61  30.0  1
 YRM  Var_04    N10  C01  N02  C03   152.84  30.0  2
 YRM  Var_05    C14  C01  N02  C03   -24.95  30.0  2
 YRM  Var_06    C07  N02  C03  C04    64.21  30.0  1
 YRM  Var_07    N02  C03  C04  C05   -59.30  30.0  1
 YRM  Var_08    N02  C07  C06  C05    55.03  30.0  1
 YRM  Var_09    N10  C01  N02  C07   -71.54  30.0  2
 YRM  Var_10    C14  C01  N02  C07   110.68  30.0  2
 YRM  Var_11    N02  C03  C04  C08    62.76  30.0  1
 YRM  Var_12    N02  C03  C04  C09  -179.57  30.0  1
 YRM  Var_13    H1   C03  N02  C01    78.22  30.0  1
 YRM  Var_14    H2   C03  N02  C01   -39.23  30.0  1
 YRM  Var_15    H5   C07  N02  C01    40.84  30.0  1
 YRM  Var_16    H6   C07  N02  C01   -76.21  30.0  1
 YRM  Var_17    H5   C07  N02  C03   178.70  30.0  1
 YRM  Var_18    H6   C07  N02  C03    61.65  30.0  1
 YRM  Var_19    H1   C03  C04  C05    64.86  30.0  1
 YRM  Var_20    H2   C03  C04  C05  -178.75  30.0  1
 YRM  Var_21    H5   C07  C06  C05   176.55  30.0  1
 YRM  Var_22    H6   C07  C06  C05   -66.70  30.0  1
 YRM  Var_23    H1   C03  N02  C07   -59.35  30.0  1
 YRM  Var_24    H2   C03  N02  C07  -176.80  30.0  1
 YRM  Var_25    H3   C06  C07  N02   -66.75  30.0  1
 YRM  Var_26    H4   C06  C07  N02   175.99  30.0  1
 YRM  Var_27    F26  C24  C13  C12  -121.98  30.0  2
 YRM  Var_28    F27  C24  C13  C12    -1.45  30.0  2
 YRM  Var_29    F25  C24  C13  C12   119.55  30.0  2
 YRM  Var_30    F26  C24  C13  C14    58.54  30.0  2
 YRM  Var_31    F27  C24  C13  C14   179.07  30.0  2
 YRM  Var_32    F25  C24  C13  C14   -59.93  30.0  2
 YRM  Var_33    H10  C09  C04  C03    56.09  30.0  3
 YRM  Var_34    H11  C09  C04  C03   177.96  30.0  3
 YRM  Var_35    H12  C09  C04  C03   -63.74  30.0  3
 YRM  Var_36    H7   C08  C04  C03   -66.12  30.0  3
 YRM  Var_37    H8   C08  C04  C03    53.00  30.0  3
 YRM  Var_38    H9   C08  C04  C03   171.29  30.0  3
 YRM  Var_39    H10  C09  C04  C05   -61.64  30.0  3
 YRM  Var_40    H11  C09  C04  C05    60.22  30.0  3
 YRM  Var_41    H12  C09  C04  C05   178.53  30.0  3
 YRM  Var_42    H7   C08  C04  C05    52.60  30.0  3
 YRM  Var_43    H8   C08  C04  C05   171.73  30.0  3
 YRM  Var_44    H9   C08  C04  C05   -69.98  30.0  3
 YRM  Var_45    H1   C03  C04  C08  -173.08  30.0  1
 YRM  Var_46    H2   C03  C04  C08   -56.69  30.0  1
 YRM  Var_47    H1   C03  C04  C09   -55.41  30.0  1
 YRM  Var_48    H2   C03  C04  C09    60.98  30.0  1
 YRM  Var_49    H14  C14  C13  C24     2.63  30.0  1
 YRM  Var_50    H13  C12  C13  C24     0.05  30.0  1
 YRM  Var_51    H10  C09  C04  C08   173.85  30.0  3
 YRM  Var_52    H11  C09  C04  C08   -64.29  30.0  3
 YRM  Var_53    H12  C09  C04  C08    54.02  30.0  3
 YRM  Var_54    H7   C08  C04  C09   176.31  30.0  3
 YRM  Var_55    H8   C08  C04  C09   -64.57  30.0  3
 YRM  Var_56    H9   C08  C04  C09    53.72  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
 YRM  chir_01  C05  C04  N18  C06  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
 YRM  plan-1  C05  0.020
 YRM  plan-1  C19  0.020
 YRM  plan-1  C21  0.020
 YRM  plan-1  N18  0.020
 YRM  plan-1  N20  0.020
 YRM  plan-1  O23  0.020
 YRM  plan-1  H17  0.020
 YRM  plan-1  H18  0.020
 YRM  plan-1  O22  0.020
 YRM  plan-2  C01  0.020
 YRM  plan-2  C11  0.020
 YRM  plan-2  C12  0.020
 YRM  plan-2  C15  0.020
 YRM  plan-2  C17  0.020
 YRM  plan-2  N10  0.020
 YRM  plan-2  N16  0.020
 YRM  plan-2  H15  0.020
 YRM  plan-2  H16  0.020

