# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 06:54:22 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: (4R)-2-amino-1,3',3'-trimethyl-7'-(pyrimidin-5-yl)-3',4'-dihydro-2'H-spiro[imidazole-4,1'-naphthalen]-5(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@]2(CC(C)(C)Cc3ccc(cc23)c4cncnc4)C1=O)N
#
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
 1M7  1M7  (4R)-2-amino-1,3',3'-trimethyl-7'-(pyrimidin-5-yl)-3',4'-dihydro-2'H-spiro[imidazole-4,1'-naphthalen]-5(1H)-one  ligand  46  25  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_1M7
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
 1M7  C1   C  CR6   0   0.095  -1.8403   0.9946  -0.0346
 1M7  C2   C  CR16  0  -0.309  -1.6254   2.3646  -0.1958
 1M7  C3   C  CR16  0  -0.300  -0.3398   2.8533  -0.3186
 1M7  C4   C  CR6   0   0.051   0.7702   2.0074  -0.3020
 1M7  C5   C  CR6   0   0.241   0.5623   0.6385  -0.1458
 1M7  C6   C  CR16  0  -0.367  -0.7350   0.1537  -0.0010
 1M7  C7   C  CH2   0  -0.467   2.1489   2.5832  -0.4549
 1M7  C8   C  CT    0  -0.124   3.2346   1.7228   0.1911
 1M7  C9   C  CH2   0  -0.373   3.0757   0.3089  -0.3688
 1M7  C10  C  CR5   0  -0.241   1.7171  -0.3495  -0.0785
 1M7  C11  C  CR6   0  -0.046  -3.2001   0.4545   0.1015
 1M7  C12  C  CR5   0   0.552   1.4936  -1.4532  -1.1195
 1M7  N13  N  NR5   0  -0.518   1.4155  -2.6088  -0.4032
 1M7  C14  C  CR5   0   0.656   1.5544  -2.2890   0.9471
 1M7  N15  N  N     0  -0.446   1.7178  -1.0441   1.1985
 1M7  O16  O  O     0  -0.437   1.4081  -1.3461  -2.3219
 1M7  C17  C  CH3   0  -0.554   1.1919  -3.9237  -0.9533
 1M7  N18  N  NH2   0  -0.848   1.4476  -3.2755   1.8594
 1M7  C19  C  CR16  0  -0.046  -3.5919  -0.7425  -0.4920
 1M7  N20  N  N     0  -0.386  -4.8157  -1.2358  -0.3720
 1M7  C21  C  CR16  0   0.049  -5.6753  -0.5258   0.3424
 1M7  N22  N  N     0  -0.387  -5.4238   0.6246   0.9478
 1M7  C23  C  CR16  0  -0.048  -4.1942   1.1041   0.8287
 1M7  C24  C  CH3   0  -0.645   4.6069   2.2528  -0.2216
 1M7  C25  C  CH3   0  -0.633   3.1265   1.7621   1.7152
 1M7  H1   H  HCR6  0   0.257  -2.4634   3.0488  -0.2388
 1M7  H2   H  HCR6  0   0.252  -0.1875   3.9199  -0.4338
 1M7  H3   H  HCR6  0   0.250  -0.8906  -0.9066   0.1654
 1M7  H4   H  HCH2  0   0.252   2.3699   2.6880  -1.5244
 1M7  H5   H  HCH2  0   0.248   2.1684   3.5968  -0.0451
 1M7  H6   H  HCH2  0   0.239   3.2159   0.3659  -1.4534
 1M7  H7   H  HCH2  0   0.246   3.8597  -0.3476   0.0176
 1M7  H8   H  HCH3  0   0.263   2.0391  -4.5813  -0.7599
 1M7  H9   H  HCH3  0   0.265   0.2880  -4.3709  -0.5409
 1M7  H10  H  HCH3  0   0.275   1.0707  -3.8313  -2.0288
 1M7  H11  H  HNH2  0   0.410   1.6709  -4.2209   1.5956
 1M7  H12  H  HNH2  0   0.403   1.7083  -3.0351   2.8018
 1M7  H13  H  HCR6  0   0.271  -2.8954  -1.3123  -1.0990
 1M7  H14  H  HCR6  0   0.268  -6.6793  -0.9232   0.4404
 1M7  H15  H  HCR6  0   0.276  -3.9830   2.0365   1.3424
 1M7  H16  H  HCH3  0   0.228   4.7361   3.2909   0.0915
 1M7  H17  H  HCH3  0   0.229   5.4082   1.6680   0.2349
 1M7  H18  H  HCH3  0   0.224   4.7381   2.2134  -1.3049
 1M7  H19  H  HCH3  0   0.233   2.1469   1.4558   2.0798
 1M7  H20  H  HCH3  0   0.222   3.8653   1.1005   2.1708
 1M7  H21  H  HCH3  0   0.220   3.3165   2.7740   2.0811

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
 1M7  O16  C12  double    1.210  0.020  1.210
 1M7  C24  C8   single    1.528  0.020  1.528
 1M7  C12  N13  single    1.362  0.020  1.362
 1M7  C12  C10  single    1.534  0.020  1.534
 1M7  C17  N13  single    1.443  0.020  1.443
 1M7  C9   C8   single    1.529  0.020  1.529
 1M7  C9   C10  single    1.537  0.020  1.537
 1M7  C7   C8   single    1.529  0.020  1.529
 1M7  C7   C4   single    1.502  0.020  1.502
 1M7  C8   C25  single    1.528  0.020  1.528
 1M7  N13  C14  single    1.395  0.020  1.395
 1M7  C10  C5   single    1.521  0.020  1.521
 1M7  C10  N15  single    1.454  0.020  1.454
 1M7  C4   C3   aromatic  1.396  0.020  1.396
 1M7  C4   C5   aromatic  1.393  0.020  1.393
 1M7  C3   C2   aromatic  1.381  0.020  1.381
 1M7  C5   C6   aromatic  1.392  0.020  1.392
 1M7  C2   C1   aromatic  1.396  0.020  1.396
 1M7  C6   C1   aromatic  1.389  0.020  1.389
 1M7  C19  N20  aromatic  1.325  0.020  1.325
 1M7  C19  C11  aromatic  1.392  0.020  1.392
 1M7  C14  N15  double    1.280  0.020  1.280
 1M7  C14  N18  single    1.348  0.020  1.348
 1M7  C1   C11  single    1.469  0.020  1.469
 1M7  N20  C21  aromatic  1.324  0.020  1.324
 1M7  C11  C23  aromatic  1.392  0.020  1.392
 1M7  C21  N22  aromatic  1.324  0.020  1.324
 1M7  C23  N22  aromatic  1.325  0.020  1.325
 1M7  C2   H1   single    0.930  0.020  1.080
 1M7  C3   H2   single    0.930  0.020  1.080
 1M7  C6   H3   single    0.930  0.020  1.080
 1M7  C7   H4   single    0.970  0.020  1.090
 1M7  C7   H5   single    0.970  0.020  1.090
 1M7  C9   H6   single    0.970  0.020  1.090
 1M7  C9   H7   single    0.970  0.020  1.090
 1M7  C17  H8   single    0.970  0.020  1.090
 1M7  C17  H9   single    0.970  0.020  1.090
 1M7  C17  H10  single    0.970  0.020  1.090
 1M7  N18  H11  single    0.890  0.020  1.040
 1M7  N18  H12  single    0.890  0.020  1.040
 1M7  C19  H13  single    0.930  0.020  1.080
 1M7  C21  H14  single    0.930  0.020  1.080
 1M7  C23  H15  single    0.930  0.020  1.080
 1M7  C24  H16  single    0.970  0.020  1.090
 1M7  C24  H17  single    0.970  0.020  1.090
 1M7  C24  H18  single    0.970  0.020  1.090
 1M7  C25  H19  single    0.970  0.020  1.090
 1M7  C25  H20  single    0.970  0.020  1.090
 1M7  C25  H21  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
 1M7  C11  C1   C6   120.77  3.000
 1M7  C11  C1   C2   120.92  3.000
 1M7  C6   C1   C2   118.32  3.000
 1M7  H1   C2   C3   119.57  3.000
 1M7  H1   C2   C1   120.37  3.000
 1M7  C3   C2   C1   120.06  3.000
 1M7  H2   C3   C4   119.08  3.000
 1M7  H2   C3   C2   119.26  3.000
 1M7  C4   C3   C2   121.66  3.000
 1M7  C7   C4   C5   121.67  3.000
 1M7  C5   C4   C3   118.56  3.000
 1M7  C7   C4   C3   119.77  3.000
 1M7  C10  C5   C6   118.46  3.000
 1M7  C6   C5   C4   119.52  3.000
 1M7  C10  C5   C4   121.98  3.000
 1M7  H3   C6   C5   119.34  3.000
 1M7  H3   C6   C1   118.77  3.000
 1M7  C5   C6   C1   121.87  3.000
 1M7  H5   C7   H4   105.85  3.000
 1M7  H5   C7   C8   110.53  3.000
 1M7  H4   C7   C8   108.83  3.000
 1M7  H5   C7   C4   109.49  3.000
 1M7  H4   C7   C4   108.71  3.000
 1M7  C8   C7   C4   113.15  3.000
 1M7  C25  C8   C24  108.90  3.000
 1M7  C25  C8   C9   112.43  3.000
 1M7  C24  C8   C9   108.37  3.000
 1M7  C25  C8   C7   110.90  3.000
 1M7  C9   C8   C7   106.97  3.000
 1M7  C24  C8   C7   109.18  3.000
 1M7  H7   C9   H6   106.83  3.000
 1M7  H7   C9   C10  108.05  3.000
 1M7  H6   C9   C10  108.81  3.000
 1M7  H7   C9   C8   110.57  3.000
 1M7  H6   C9   C8   107.53  3.000
 1M7  C10  C9   C8   114.75  3.000
 1M7  N15  C10  C12  104.62  3.000
 1M7  N15  C10  C9   111.72  3.000
 1M7  C12  C10  C9   107.99  3.000
 1M7  N15  C10  C5   110.46  3.000
 1M7  C9   C10  C5   112.61  3.000
 1M7  C12  C10  C5   109.07  3.000
 1M7  C23  C11  C19  115.01  3.000
 1M7  C23  C11  C1   122.52  3.000
 1M7  C19  C11  C1   122.47  3.000
 1M7  O16  C12  N13  126.42  3.000
 1M7  N13  C12  C10  105.19  3.000
 1M7  O16  C12  C10  128.39  3.000
 1M7  C17  N13  C14  126.41  3.000
 1M7  C14  N13  C12  108.00  3.000
 1M7  C17  N13  C12  125.57  3.000
 1M7  N18  C14  N15  126.07  3.000
 1M7  N18  C14  N13  118.66  3.000
 1M7  N15  C14  N13  115.19  3.000
 1M7  C14  N15  C10  106.98  3.000
 1M7  H10  C17  H9   108.49  3.000
 1M7  H10  C17  H8   108.29  3.000
 1M7  H9   C17  H8   109.28  3.000
 1M7  H10  C17  N13  108.49  3.000
 1M7  H9   C17  N13  111.00  3.000
 1M7  H8   C17  N13  111.21  3.000
 1M7  H12  N18  H11  114.34  3.000
 1M7  H12  N18  C14  115.99  3.000
 1M7  H11  N18  C14  119.50  3.000
 1M7  H13  C19  N20  116.61  3.000
 1M7  H13  C19  C11  120.61  3.000
 1M7  N20  C19  C11  122.78  3.000
 1M7  C21  N20  C19  116.67  3.000
 1M7  H14  C21  N22  116.94  3.000
 1M7  H14  C21  N20  116.96  3.000
 1M7  N22  C21  N20  126.10  3.000
 1M7  C23  N22  C21  116.71  3.000
 1M7  H15  C23  N22  116.67  3.000
 1M7  H15  C23  C11  120.59  3.000
 1M7  N22  C23  C11  122.73  3.000
 1M7  H18  C24  H17  107.89  3.000
 1M7  H18  C24  H16  107.73  3.000
 1M7  H17  C24  H16  107.60  3.000
 1M7  H18  C24  C8   111.31  3.000
 1M7  H17  C24  C8   111.13  3.000
 1M7  H16  C24  C8   111.02  3.000
 1M7  H21  C25  H20  107.69  3.000
 1M7  H21  C25  H19  107.74  3.000
 1M7  H20  C25  H19  107.37  3.000
 1M7  H21  C25  C8   110.21  3.000
 1M7  H20  C25  C8   110.65  3.000
 1M7  H19  C25  C8   112.97  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
 1M7  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 1M7  CONST_02  C4   C5   C6   C1     0.00   0.0  0
 1M7  CONST_03  N20  C19  C11  C1   180.00   0.0  0
 1M7  CONST_04  N22  C23  C11  C1   180.00   0.0  0
 1M7  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 1M7  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 1M7  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 1M7  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 1M7  CONST_11  C11  C1   C2   C3   180.00   0.0  0
 1M7  CONST_12  C11  C1   C6   C5   180.00   0.0  0
 1M7  CONST_15  C21  N20  C19  C11    0.00   0.0  0
 1M7  CONST_16  C21  N22  C23  C11    0.00   0.0  0
 1M7  CONST_17  N22  C21  N20  C19    0.00   0.0  0
 1M7  CONST_18  N22  C23  C11  C19    0.00   0.0  0
 1M7  CONST_19  C23  C11  C19  N20    0.00   0.0  0
 1M7  CONST_20  C23  N22  C21  N20    0.00   0.0  0
 1M7  CONST_21  C14  N13  C12  C10    0.00   0.0  0
 1M7  CONST_22  N13  C14  N15  C10    0.00   0.0  0
 1M7  CONST_23  N15  C14  N13  C12    0.00   0.0  0
 1M7  CONST_24  C17  N13  C12  C10  180.00   0.0  0
 1M7  CONST_25  N18  C14  N15  C10  180.00   0.0  0
 1M7  CONST_26  N18  C14  N13  C12  180.00   0.0  0
 1M7  CONST_27  O16  C12  N13  C14  180.00   0.0  0
 1M7  CONST_28  C17  N13  C14  N15  180.00   0.0  0
 1M7  CONST_29  H2   C3   C2   C1   180.00   0.0  0
 1M7  CONST_30  H13  C19  C11  C1     0.00   0.0  0
 1M7  CONST_31  H15  C23  C11  C1     0.00   0.0  0
 1M7  CONST_32  H3   C6   C1   C2   180.00   0.0  0
 1M7  CONST_33  H1   C2   C3   C4   180.00   0.0  0
 1M7  CONST_34  H14  C21  N20  C19  180.00   0.0  0
 1M7  CONST_35  C17  N13  C12  O16    0.00   0.0  0
 1M7  CONST_36  N18  C14  N13  C17    0.00   0.0  0
 1M7  CONST_38  H12  N18  C14  N13  180.00   0.0  0
 1M7  Var_01    C8   C7   C4   C3   153.76  30.0  1
 1M7  Var_02    C9   C8   C7   C4    53.15  30.0  1
 1M7  Var_03    C10  C9   C8   C7   -60.40  30.0  1
 1M7  Var_04    H16  C24  C8   C7    59.48  30.0  3
 1M7  Var_05    H19  C25  C8   C7    56.22  30.0  3
 1M7  Var_06    H8   C17  N13  C12  117.52  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
 1M7  chir_01  C10  C9  C5  N15  positiv

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
 1M7  plan-1  C1   0.020
 1M7  plan-1  C11  0.020
 1M7  plan-1  C19  0.020
 1M7  plan-1  N20  0.020
 1M7  plan-1  C21  0.020
 1M7  plan-1  N22  0.020
 1M7  plan-1  C23  0.020
 1M7  plan-1  H13  0.020
 1M7  plan-1  H14  0.020
 1M7  plan-1  H15  0.020
 1M7  plan-2  C1   0.020
 1M7  plan-2  C2   0.020
 1M7  plan-2  C3   0.020
 1M7  plan-2  C4   0.020
 1M7  plan-2  C5   0.020
 1M7  plan-2  C6   0.020
 1M7  plan-2  C7   0.020
 1M7  plan-2  C10  0.020
 1M7  plan-2  C11  0.020
 1M7  plan-2  H1   0.020
 1M7  plan-2  H2   0.020
 1M7  plan-2  H3   0.020
 1M7  plan-3  C10  0.020
 1M7  plan-3  C12  0.020
 1M7  plan-3  N13  0.020
 1M7  plan-3  C14  0.020
 1M7  plan-3  N15  0.020
 1M7  plan-3  O16  0.020
 1M7  plan-3  C17  0.020
 1M7  plan-3  N18  0.020
 1M7  plan-3  H11  0.020
 1M7  plan-3  H12  0.020

