# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 14:23:57 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 6'-[(6-aminopyrimidin-4-yl)amino]-8'-methyl-2'H-spiro[cyclohexane-1,3'-imidazo[1,5-a]pyridine]-1',5'-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C2N(C(=O)C(=C1)Nc3cc(N)ncn3)C4(CCCCC4)NC2=O
#
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
 N45  N45  6'-[(6-aminopyrimidin-4-yl)amino]-8'-methyl-2'H-spiro[cyclohexane-1,3'-imidazo[1,5-a]pyridine]-1',5'-dione  ligand  45  25  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_N45
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
 N45  O2   O  O     0  -0.454  -3.8710  -2.2774  -0.9933
 N45  C10  C  CR5   0   0.508  -3.1086  -1.4182  -0.5943
 N45  C9   C  CR56  0   0.232  -1.6892  -1.5894  -0.2143
 N45  N4   N  N     0  -0.637  -1.2111  -0.3671   0.1587
 N45  C11  C  CR5   0   0.335  -2.2580   0.6749   0.0997
 N45  C14  C  CH2   0  -0.420  -1.9008   1.7944  -0.8830
 N45  C15  C  CH2   0  -0.457  -3.0069   2.8453  -0.9436
 N45  C16  C  CH2   0  -0.435  -3.3334   3.3949   0.4408
 N45  C13  C  CH2   0  -0.458  -3.6975   2.2758   1.4104
 N45  C12  C  CH2   0  -0.417  -2.5875   1.2311   1.4888
 N45  N5   N  NR15  0  -0.679  -3.3649  -0.1147  -0.4047
 N45  C8   C  CR6   0  -0.017  -0.9339  -2.7189  -0.2015
 N45  C17  C  CH3   0  -0.725  -1.4469  -4.0703  -0.6017
 N45  C7   C  CR16  0  -0.197   0.4121  -2.5405   0.2035
 N45  C2   C  CR6   0   0.118   0.9077  -1.3284   0.5776
 N45  C1   C  CR6   0   0.555   0.0716  -0.1370   0.6028
 N45  O1   O  O     0  -0.486   0.4545   0.9620   0.9821
 N45  N1   N  NH1   0  -0.734   2.2173  -1.1956   1.0411
 N45  C3   C  CR6   0   0.505   3.1560  -0.3628   0.5190
 N45  C5   C  CR16  0  -0.464   2.9922   0.2996  -0.6899
 N45  C6   C  CR6   0   0.485   4.0452   1.1176  -1.1046
 N45  N6   N  NH2   0  -0.831   3.9758   1.8390  -2.2409
 N45  N3   N  N     0  -0.478   5.1684   1.2408  -0.3769
 N45  C4   C  CR16  0   0.055   5.2120   0.5398   0.7399
 N45  N2   N  N     0  -0.486   4.2841  -0.2517   1.2404
 N45  H1   H  HCH2  0   0.255  -0.9743   2.2669  -0.5575
 N45  H2   H  HCH2  0   0.251  -1.7202   1.3595  -1.8687
 N45  H3   H  HCH2  0   0.249  -2.6867   3.6519  -1.6060
 N45  H4   H  HCH2  0   0.223  -3.9096   2.4257  -1.3993
 N45  H5   H  HCH2  0   0.221  -2.4642   3.9364   0.8281
 N45  H6   H  HCH2  0   0.240  -4.1494   4.1173   0.3753
 N45  H7   H  HCH2  0   0.249  -3.8691   2.6800   2.4097
 N45  H8   H  HCH2  0   0.223  -4.6427   1.8128   1.1085
 N45  H9   H  HCH2  0   0.249  -2.8705   0.4043   2.1444
 N45  H10  H  HCH2  0   0.255  -1.6934   1.6936   1.9049
 N45  H11  H  HNR5  0   0.419  -4.2711   0.2885  -0.5889
 N45  H12  H  HCH3  0   0.254  -1.8019  -4.0807  -1.6310
 N45  H13  H  HCH3  0   0.249  -0.6529  -4.8095  -0.5135
 N45  H14  H  HCH3  0   0.254  -2.2735  -4.3936   0.0296
 N45  H15  H  HCR6  0   0.284   1.0733  -3.3991   0.2174
 N45  H16  H  HNH1  0   0.399   2.5089  -1.7549   1.8280
 N45  H17  H  HCR6  0   0.271   2.1074   0.1853  -1.3010
 N45  H18  H  HNH2  0   0.399   3.2623   1.6345  -2.9188
 N45  H19  H  HNH2  0   0.391   4.8219   2.2524  -2.5938
 N45  H20  H  HCR6  0   0.248   6.1261   0.6265   1.3207

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
 N45  N6   C6   single    1.348  0.020  1.348
 N45  C5   C6   aromatic  1.396  0.020  1.396
 N45  C5   C3   aromatic  1.388  0.020  1.388
 N45  C6   N3   aromatic  1.344  0.020  1.344
 N45  O1   C1   double    1.224  0.020  1.224
 N45  C13  C16  single    1.525  0.020  1.525
 N45  C13  C12  single    1.526  0.020  1.526
 N45  C16  C15  single    1.525  0.020  1.525
 N45  C12  C11  single    1.532  0.020  1.532
 N45  N1   C3   single    1.359  0.020  1.359
 N45  N1   C2   single    1.396  0.020  1.396
 N45  C3   N2   aromatic  1.344  0.020  1.344
 N45  N3   C4   aromatic  1.319  0.020  1.319
 N45  C1   C2   single    1.456  0.020  1.456
 N45  C1   N4   single    1.377  0.020  1.377
 N45  C2   C7   double    1.362  0.020  1.362
 N45  C4   N2   aromatic  1.318  0.020  1.318
 N45  C15  C14  single    1.527  0.020  1.527
 N45  C11  C14  single    1.532  0.020  1.532
 N45  C11  N4   single    1.478  0.020  1.478
 N45  C11  N5   single    1.450  0.020  1.450
 N45  N4   C9   single    1.365  0.020  1.365
 N45  C7   C8   single    1.417  0.020  1.417
 N45  N5   C10  single    1.342  0.020  1.342
 N45  C9   C8   double    1.359  0.020  1.359
 N45  C9   C10  single    1.479  0.020  1.479
 N45  C8   C17  single    1.500  0.020  1.500
 N45  C10  O2   double    1.216  0.020  1.216
 N45  C14  H1   single    0.970  0.020  1.090
 N45  C14  H2   single    0.970  0.020  1.090
 N45  C15  H3   single    0.970  0.020  1.090
 N45  C15  H4   single    0.970  0.020  1.090
 N45  C16  H5   single    0.970  0.020  1.090
 N45  C16  H6   single    0.970  0.020  1.090
 N45  C13  H7   single    0.970  0.020  1.090
 N45  C13  H8   single    0.970  0.020  1.090
 N45  C12  H9   single    0.970  0.020  1.090
 N45  C12  H10  single    0.970  0.020  1.090
 N45  N5   H11  single    0.860  0.020  1.020
 N45  C17  H12  single    0.970  0.020  1.090
 N45  C17  H13  single    0.970  0.020  1.090
 N45  C17  H14  single    0.970  0.020  1.090
 N45  C7   H15  single    0.930  0.020  1.080
 N45  N1   H16  single    0.860  0.020  1.020
 N45  C5   H17  single    0.930  0.020  1.080
 N45  N6   H18  single    0.890  0.020  1.040
 N45  N6   H19  single    0.890  0.020  1.040
 N45  C4   H20  single    0.930  0.020  1.080

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
 N45  N5   C10  C9   105.03  3.000
 N45  C9   C10  O2   127.16  3.000
 N45  N5   C10  O2   127.80  3.000
 N45  C8   C9   N4   123.18  3.000
 N45  C8   C9   C10  129.20  3.000
 N45  N4   C9   C10  107.62  3.000
 N45  C1   N4   C11  123.70  3.000
 N45  C11  N4   C9   111.86  3.000
 N45  C1   N4   C9   124.36  3.000
 N45  N5   C11  C12  110.42  3.000
 N45  N5   C11  C14  110.66  3.000
 N45  C12  C11  C14  111.50  3.000
 N45  N5   C11  N4    99.82  3.000
 N45  C14  C11  N4   112.06  3.000
 N45  C12  C11  N4   111.84  3.000
 N45  H2   C14  H1   107.56  3.000
 N45  H2   C14  C15  110.97  3.000
 N45  H1   C14  C15  109.22  3.000
 N45  H2   C14  C11  109.06  3.000
 N45  H1   C14  C11  108.87  3.000
 N45  C15  C14  C11  111.07  3.000
 N45  H4   C15  H3   105.81  3.000
 N45  H4   C15  C16  109.84  3.000
 N45  H3   C15  C16  110.33  3.000
 N45  H4   C15  C14  110.49  3.000
 N45  H3   C15  C14  108.67  3.000
 N45  C16  C15  C14  111.54  3.000
 N45  H6   C16  H5   106.70  3.000
 N45  H6   C16  C13  110.20  3.000
 N45  H5   C16  C13  109.13  3.000
 N45  H6   C16  C15  110.12  3.000
 N45  H5   C16  C15  109.23  3.000
 N45  C13  C16  C15  111.34  3.000
 N45  H8   C13  H7   105.87  3.000
 N45  H8   C13  C12  110.64  3.000
 N45  H7   C13  C12  108.71  3.000
 N45  H8   C13  C16  109.94  3.000
 N45  H7   C13  C16  110.36  3.000
 N45  C12  C13  C16  111.18  3.000
 N45  H10  C12  H9   107.74  3.000
 N45  H10  C12  C13  109.02  3.000
 N45  H9   C12  C13  111.13  3.000
 N45  H10  C12  C11  108.90  3.000
 N45  H9   C12  C11  108.97  3.000
 N45  C13  C12  C11  111.00  3.000
 N45  H11  N5   C11  122.11  3.000
 N45  H11  N5   C10  122.27  3.000
 N45  C11  N5   C10  115.61  3.000
 N45  C7   C8   C17  120.98  3.000
 N45  C17  C8   C9   123.80  3.000
 N45  C7   C8   C9   115.22  3.000
 N45  H14  C17  H13  107.76  3.000
 N45  H14  C17  H12  107.31  3.000
 N45  H13  C17  H12  107.94  3.000
 N45  H14  C17  C8   111.86  3.000
 N45  H13  C17  C8   109.92  3.000
 N45  H12  C17  C8   111.86  3.000
 N45  H15  C7   C2   118.66  3.000
 N45  H15  C7   C8   118.91  3.000
 N45  C2   C7   C8   122.43  3.000
 N45  N1   C2   C1   117.09  3.000
 N45  C1   C2   C7   121.61  3.000
 N45  N1   C2   C7   121.16  3.000
 N45  O1   C1   C2   124.09  3.000
 N45  C2   C1   N4   113.13  3.000
 N45  O1   C1   N4   122.78  3.000
 N45  H16  N1   C3   116.09  3.000
 N45  H16  N1   C2   118.54  3.000
 N45  C3   N1   C2   125.37  3.000
 N45  N2   C3   C5   121.81  3.000
 N45  N2   C3   N1   115.11  3.000
 N45  C5   C3   N1   123.05  3.000
 N45  H17  C5   C6   120.74  3.000
 N45  H17  C5   C3   122.56  3.000
 N45  C6   C5   C3   116.69  3.000
 N45  N3   C6   N6   116.77  3.000
 N45  N3   C6   C5   121.54  3.000
 N45  N6   C6   C5   121.68  3.000
 N45  H19  N6   H18  116.37  3.000
 N45  H19  N6   C6   118.20  3.000
 N45  H18  N6   C6   119.75  3.000
 N45  C4   N3   C6   115.92  3.000
 N45  H20  C4   N2   115.92  3.000
 N45  H20  C4   N3   115.97  3.000
 N45  N2   C4   N3   128.11  3.000
 N45  C4   N2   C3   115.90  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
 N45  CONST_01  N3   C6   C5   C3      0.00   0.0  0
 N45  CONST_02  N3   C4   N2   C3      0.00   0.0  0
 N45  CONST_03  C4   N3   C6   C5      0.00   0.0  0
 N45  CONST_04  C4   N2   C3   C5      0.00   0.0  0
 N45  CONST_05  N2   C3   C5   C6      0.00   0.0  0
 N45  CONST_06  N2   C4   N3   C6      0.00   0.0  0
 N45  CONST_07  C2   C1   N4   C9      0.00   0.0  0
 N45  CONST_08  C11  N5   C10  C9      0.00   0.0  0
 N45  CONST_09  C2   C1   N4   C11   180.00   0.0  0
 N45  CONST_10  C6   C5   C3   N1    180.00   0.0  0
 N45  CONST_11  C4   N2   C3   N1    180.00   0.0  0
 N45  CONST_12  N6   C6   C5   C3    180.00   0.0  0
 N45  CONST_13  C4   N3   C6   N6    180.00   0.0  0
 N45  CONST_15  C5   C3   N1   C2      0.00   0.0  0
 N45  CONST_16  N2   C3   N1   C2    180.00   0.0  0
 N45  CONST_18  C11  N5   C10  O2    180.00   0.0  0
 N45  CONST_19  O1   C1   N4   C9    180.00   0.0  0
 N45  CONST_20  O1   C1   N4   C11     0.00   0.0  0
 N45  CONST_21  H20  C4   N2   C3    180.00   0.0  0
 N45  CONST_22  H17  C5   C6   N3    180.00   0.0  0
 N45  CONST_23  H11  N5   C10  C9    180.00   0.0  0
 N45  CONST_24  H18  N6   C6   C5      0.00   0.0  0
 N45  CONST_25  H19  N6   C6   C5    180.00   0.0  0
 N45  CONST_26  H16  N1   C3   C5    180.00   0.0  0
 N45  Var_01    C12  C11  N5   C10  -116.04  30.0  1
 N45  Var_02    C13  C12  C11  N4   -178.38  30.0  3
 N45  Var_03    C15  C14  C11  N4    179.05  30.0  3
 N45  Var_04    C16  C13  C12  C11   -55.67  30.0  1
 N45  Var_05    C16  C15  C14  C11    54.75  30.0  1
 N45  Var_06    C13  C16  C15  C14   -55.48  30.0  1
 N45  Var_07    C12  C13  C16  C15    55.87  30.0  1
 N45  Var_08    H12  C17  C8   C9     59.68  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
 N45  plan-1  N1   0.020
 N45  plan-1  C3   0.020
 N45  plan-1  C5   0.020
 N45  plan-1  C6   0.020
 N45  plan-1  N6   0.020
 N45  plan-1  N3   0.020
 N45  plan-1  C4   0.020
 N45  plan-1  N2   0.020
 N45  plan-1  H17  0.020
 N45  plan-1  H20  0.020
 N45  plan-2  C2   0.020
 N45  plan-2  N1   0.020
 N45  plan-2  C3   0.020
 N45  plan-2  H16  0.020
 N45  plan-3  C6   0.020
 N45  plan-3  N6   0.020
 N45  plan-3  H18  0.020
 N45  plan-3  H19  0.020
 N45  plan-4  O2   0.020
 N45  plan-4  C10  0.020
 N45  plan-4  C9   0.020
 N45  plan-4  N4   0.020
 N45  plan-4  C11  0.020
 N45  plan-4  N5   0.020
 N45  plan-4  C8   0.020
 N45  plan-4  C17  0.020
 N45  plan-4  C7   0.020
 N45  plan-4  C2   0.020
 N45  plan-4  C1   0.020
 N45  plan-4  O1   0.020
 N45  plan-4  N1   0.020
 N45  plan-4  H11  0.020
 N45  plan-4  H15  0.020

