# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:43:09 2020
#   Inital geometry file: a 125 line input string
#   Ligand name: 3-[(4R)-2'-amino-1',2,2-trimethyl-5'-oxo-1',2,3,5'-tetrahydrospiro[chromene-4,4'-imidazol]-6-yl]benzonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@]2(CC(C)(C)Oc3ccc(cc23)c4cccc(c4)C#N)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
 1M6  1M6  3-[(4R)-2'-amino-1',2,2-trimethyl-5'-oxo-1',2,3,5'-tetrahydrospiro[chromene-4,4'-imidazol]-6-yl]benzonitrile  ligand  47  27  .  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_1M6
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
 1M6  C1   C  CR6   0   0.085  -1.4536   0.6472  -0.2284
 1M6  C2   C  CR16  0  -0.305  -1.3733   2.0287  -0.4253
 1M6  C3   C  CR16  0  -0.351  -0.1507   2.6641  -0.4835
 1M6  C4   C  CR6   0   0.347   1.0331   1.9341  -0.3576
 1M6  C5   C  CR6   0   0.140   0.9790   0.5527  -0.1814
 1M6  C6   C  CR16  0  -0.372  -0.2656  -0.0622  -0.1071
 1M6  O7   O  O2    0  -0.486   2.1832   2.6260  -0.4246
 1M6  C8   C  CT    0   0.162   3.3647   2.0188   0.1327
 1M6  C9   C  CH2   0  -0.416   3.4670   0.5900  -0.3869
 1M6  C10  C  CR5   0  -0.206   2.2431  -0.2678  -0.0434
 1M6  C11  C  CR5   0   0.554   2.1988  -1.4536  -1.0167
 1M6  N12  N  NR5   0  -0.522   2.2799  -2.5604  -0.2289
 1M6  C13  C  CR5   0   0.667   2.3553  -2.1414   1.0991
 1M6  N14  N  N     0  -0.451   2.3374  -0.8722   1.2728
 1M6  C15  C  CR6   0   0.107  -2.7568  -0.0387  -0.1509
 1M6  C16  C  CH3   0  -0.554   2.2669  -3.9273  -0.6914
 1M6  N17  N  NH2   0  -0.848   2.3820  -3.0731   2.0708
 1M6  C18  C  CR16  0  -0.312  -3.8354   0.5601   0.4943
 1M6  C19  C  CR6   0   0.029  -5.0636  -0.0936   0.5615
 1M6  C20  C  CR16  0  -0.255  -5.2388  -1.3543  -0.0069
 1M6  C21  C  CR16  0  -0.229  -4.1655  -1.9507  -0.6463
 1M6  C22  C  CR16  0  -0.292  -2.9424  -1.3008  -0.7198
 1M6  O23  O  O     0  -0.432   2.1156  -1.4315  -2.2231
 1M6  C24  C  CH3   0  -0.667   4.5261   2.8449  -0.3946
 1M6  C25  C  CH3   0  -0.655   3.2999   2.1051   1.6535
 1M6  C26  C  CSP   0   0.052  -6.1546   0.5360   1.2346
 1M6  N27  N  NS    0  -0.250  -7.0358   1.0435   1.7762
 1M6  H1   H  HCR6  0   0.260  -2.2751   2.6163  -0.5433
 1M6  H2   H  HCR6  0   0.266  -0.0985   3.7356  -0.6295
 1M6  H3   H  HCR6  0   0.255  -0.3114  -1.1310   0.0719
 1M6  H4   H  HCH2  0   0.258   3.5820   0.6324  -1.4741
 1M6  H5   H  HCH2  0   0.262   4.3649   0.1142   0.0116
 1M6  H6   H  HCH3  0   0.263   3.1834  -4.4441  -0.4082
 1M6  H7   H  HCH3  0   0.266   1.4100  -4.4664  -0.2890
 1M6  H8   H  HCH3  0   0.276   2.1973  -3.9267  -1.7755
 1M6  H9   H  HNH2  0   0.411   2.7311  -3.9954   1.8688
 1M6  H10  H  HNH2  0   0.405   2.5913  -2.7410   2.9980
 1M6  H11  H  HCR6  0   0.280  -3.7213   1.5281   0.9644
 1M6  H12  H  HCR6  0   0.283  -6.1968  -1.8526   0.0490
 1M6  H13  H  HCR6  0   0.276  -4.2858  -2.9242  -1.1013
 1M6  H14  H  HCR6  0   0.267  -2.1261  -1.7769  -1.2482
 1M6  H15  H  HCH3  0   0.242   4.4335   3.8891  -0.0930
 1M6  H16  H  HCH3  0   0.236   5.4648   2.4640   0.0070
 1M6  H17  H  HCH3  0   0.239   4.5833   2.8033  -1.4832
 1M6  H18  H  HCH3  0   0.246   2.4466   1.5696   2.0665
 1M6  H19  H  HCH3  0   0.234   4.1988   1.6676   2.0886
 1M6  H20  H  HCH3  0   0.235   3.2451   3.1475   1.9709

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
 1M6  O23  C11  double    1.210  0.020  1.210
 1M6  C24  C8   single    1.520  0.020  1.520
 1M6  C11  N12  single    1.361  0.020  1.361
 1M6  C11  C10  single    1.535  0.020  1.535
 1M6  C16  N12  single    1.443  0.020  1.443
 1M6  C9   C8   single    1.524  0.020  1.524
 1M6  C9   C10  single    1.534  0.020  1.534
 1M6  O7   C8   single    1.440  0.020  1.440
 1M6  O7   C4   single    1.344  0.020  1.344
 1M6  N12  C13  single    1.395  0.020  1.395
 1M6  C8   C25  single    1.525  0.020  1.525
 1M6  C10  C5   single    1.513  0.020  1.513
 1M6  C10  N14  single    1.451  0.020  1.451
 1M6  C4   C5   aromatic  1.394  0.020  1.394
 1M6  C4   C3   aromatic  1.397  0.020  1.397
 1M6  C5   C6   aromatic  1.390  0.020  1.390
 1M6  C3   C2   aromatic  1.379  0.020  1.379
 1M6  C6   C1   aromatic  1.389  0.020  1.389
 1M6  C22  C21  aromatic  1.387  0.020  1.387
 1M6  C22  C15  aromatic  1.397  0.020  1.397
 1M6  C2   C1   aromatic  1.398  0.020  1.398
 1M6  C1   C15  single    1.475  0.020  1.475
 1M6  C21  C20  aromatic  1.384  0.020  1.384
 1M6  C13  N14  double    1.281  0.020  1.281
 1M6  C13  N17  single    1.346  0.020  1.346
 1M6  C15  C18  aromatic  1.392  0.020  1.392
 1M6  C20  C19  aromatic  1.394  0.020  1.394
 1M6  C18  C19  aromatic  1.393  0.020  1.393
 1M6  C19  C26  single    1.428  0.020  1.428
 1M6  C26  N27  triple    1.152  0.020  1.152
 1M6  C2   H1   single    0.930  0.020  1.080
 1M6  C3   H2   single    0.930  0.020  1.080
 1M6  C6   H3   single    0.930  0.020  1.080
 1M6  C9   H4   single    0.970  0.020  1.090
 1M6  C9   H5   single    0.970  0.020  1.090
 1M6  C16  H6   single    0.970  0.020  1.090
 1M6  C16  H7   single    0.970  0.020  1.090
 1M6  C16  H8   single    0.970  0.020  1.090
 1M6  N17  H9   single    0.890  0.020  1.040
 1M6  N17  H10  single    0.890  0.020  1.040
 1M6  C18  H11  single    0.930  0.020  1.080
 1M6  C20  H12  single    0.930  0.020  1.080
 1M6  C21  H13  single    0.930  0.020  1.080
 1M6  C22  H14  single    0.930  0.020  1.080
 1M6  C24  H15  single    0.970  0.020  1.090
 1M6  C24  H16  single    0.970  0.020  1.090
 1M6  C24  H17  single    0.970  0.020  1.090
 1M6  C25  H18  single    0.970  0.020  1.090
 1M6  C25  H19  single    0.970  0.020  1.090
 1M6  C25  H20  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
 1M6  C15  C1   C6   120.91  3.000
 1M6  C15  C1   C2   121.19  3.000
 1M6  C6   C1   C2   117.90  3.000
 1M6  H1   C2   C3   118.93  3.000
 1M6  H1   C2   C1   120.25  3.000
 1M6  C3   C2   C1   120.81  3.000
 1M6  H2   C3   C4   119.25  3.000
 1M6  H2   C3   C2   120.29  3.000
 1M6  C4   C3   C2   120.46  3.000
 1M6  O7   C4   C5   123.36  3.000
 1M6  C5   C4   C3   119.78  3.000
 1M6  O7   C4   C3   116.86  3.000
 1M6  C10  C5   C6   120.21  3.000
 1M6  C6   C5   C4   118.68  3.000
 1M6  C10  C5   C4   121.10  3.000
 1M6  H3   C6   C5   118.85  3.000
 1M6  H3   C6   C1   118.79  3.000
 1M6  C5   C6   C1   122.35  3.000
 1M6  C8   O7   C4   117.75  3.000
 1M6  C25  C8   C24  110.36  3.000
 1M6  C25  C8   C9   113.33  3.000
 1M6  C24  C8   C9   109.88  3.000
 1M6  C25  C8   O7   109.10  3.000
 1M6  C9   C8   O7   108.57  3.000
 1M6  C24  C8   O7   105.28  3.000
 1M6  H5   C9   H4   107.05  3.000
 1M6  H5   C9   C10  109.32  3.000
 1M6  H4   C9   C10  109.15  3.000
 1M6  H5   C9   C8   109.85  3.000
 1M6  H4   C9   C8   108.04  3.000
 1M6  C10  C9   C8   113.24  3.000
 1M6  N14  C10  C11  104.79  3.000
 1M6  N14  C10  C9   112.60  3.000
 1M6  C11  C10  C9   108.25  3.000
 1M6  N14  C10  C5   111.26  3.000
 1M6  C9   C10  C5   110.06  3.000
 1M6  C11  C10  C5   109.69  3.000
 1M6  O23  C11  N12  126.60  3.000
 1M6  N12  C11  C10  105.05  3.000
 1M6  O23  C11  C10  128.35  3.000
 1M6  C16  N12  C13  126.18  3.000
 1M6  C13  N12  C11  108.06  3.000
 1M6  C16  N12  C11  125.76  3.000
 1M6  N17  C13  N14  126.01  3.000
 1M6  N17  C13  N12  118.71  3.000
 1M6  N14  C13  N12  115.22  3.000
 1M6  C13  N14  C10  106.89  3.000
 1M6  C22  C15  C18  118.32  3.000
 1M6  C18  C15  C1   120.59  3.000
 1M6  C22  C15  C1   121.09  3.000
 1M6  H8   C16  H7   108.57  3.000
 1M6  H8   C16  H6   108.27  3.000
 1M6  H7   C16  H6   109.32  3.000
 1M6  H8   C16  N12  108.65  3.000
 1M6  H7   C16  N12  110.94  3.000
 1M6  H6   C16  N12  111.00  3.000
 1M6  H10  N17  H9   114.51  3.000
 1M6  H10  N17  C13  116.13  3.000
 1M6  H9   N17  C13  119.74  3.000
 1M6  H11  C18  C19  119.46  3.000
 1M6  H11  C18  C15  120.29  3.000
 1M6  C19  C18  C15  120.24  3.000
 1M6  C26  C19  C20  119.66  3.000
 1M6  C26  C19  C18  119.31  3.000
 1M6  C20  C19  C18  121.03  3.000
 1M6  H12  C20  C21  120.82  3.000
 1M6  H12  C20  C19  120.47  3.000
 1M6  C21  C20  C19  118.72  3.000
 1M6  H13  C21  C22  119.85  3.000
 1M6  H13  C21  C20  119.73  3.000
 1M6  C22  C21  C20  120.42  3.000
 1M6  H14  C22  C21  119.00  3.000
 1M6  H14  C22  C15  119.73  3.000
 1M6  C21  C22  C15  121.27  3.000
 1M6  H17  C24  H16  108.01  3.000
 1M6  H17  C24  H15  108.47  3.000
 1M6  H16  C24  H15  107.81  3.000
 1M6  H17  C24  C8   111.45  3.000
 1M6  H16  C24  C8   109.90  3.000
 1M6  H15  C24  C8   111.08  3.000
 1M6  H20  C25  H19  107.98  3.000
 1M6  H20  C25  H18  108.68  3.000
 1M6  H19  C25  H18  107.30  3.000
 1M6  H20  C25  C8   110.27  3.000
 1M6  H19  C25  C8   109.90  3.000
 1M6  H18  C25  C8   112.58  3.000
 1M6  N27  C26  C19  180.00  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
 1M6  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 1M6  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 1M6  CONST_03  C21  C22  C15  C1   180.00   0.0  0
 1M6  CONST_04  C19  C18  C15  C1   180.00   0.0  0
 1M6  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 1M6  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 1M6  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 1M6  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 1M6  CONST_11  C15  C1   C2   C3   180.00   0.0  0
 1M6  CONST_12  C15  C1   C6   C5   180.00   0.0  0
 1M6  CONST_15  C20  C21  C22  C15    0.00   0.0  0
 1M6  CONST_16  C20  C19  C18  C15    0.00   0.0  0
 1M6  CONST_17  C21  C22  C15  C18    0.00   0.0  0
 1M6  CONST_18  C21  C20  C19  C18    0.00   0.0  0
 1M6  CONST_19  C22  C21  C20  C19    0.00   0.0  0
 1M6  CONST_20  C22  C15  C18  C19    0.00   0.0  0
 1M6  CONST_21  C13  N12  C11  C10    0.00   0.0  0
 1M6  CONST_22  N12  C13  N14  C10    0.00   0.0  0
 1M6  CONST_23  N14  C13  N12  C11    0.00   0.0  0
 1M6  CONST_24  C26  C19  C18  C15  180.00   0.0  0
 1M6  CONST_25  C26  C19  C20  C21  180.00   0.0  0
 1M6  CONST_26  C16  N12  C11  C10  180.00   0.0  0
 1M6  CONST_27  N17  C13  N14  C10  180.00   0.0  0
 1M6  CONST_28  N17  C13  N12  C11  180.00   0.0  0
 1M6  CONST_29  O23  C11  N12  C13  180.00   0.0  0
 1M6  CONST_30  C16  N12  C13  N14  180.00   0.0  0
 1M6  CONST_31  H2   C3   C2   C1   180.00   0.0  0
 1M6  CONST_32  H14  C22  C15  C1     0.00   0.0  0
 1M6  CONST_33  H11  C18  C15  C1     0.00   0.0  0
 1M6  CONST_34  H3   C6   C1   C2   180.00   0.0  0
 1M6  CONST_35  H1   C2   C3   C4   180.00   0.0  0
 1M6  CONST_36  H13  C21  C22  C15  180.00   0.0  0
 1M6  CONST_37  H12  C20  C19  C18  180.00   0.0  0
 1M6  CONST_38  O23  C11  N12  C16    0.00   0.0  0
 1M6  CONST_39  N17  C13  N12  C16    0.00   0.0  0
 1M6  CONST_41  H10  N17  C13  N12  180.00   0.0  0
 1M6  Var_01    C9   C8   O7   C4    48.44  30.0  1
 1M6  Var_02    C10  C9   C8   O7   -58.29  30.0  1
 1M6  Var_03    H15  C24  C8   O7    59.20  30.0  3
 1M6  Var_04    H18  C25  C8   O7    61.65  30.0  3
 1M6  Var_05    H6   C16  N12  C11  119.83  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
 1M6  chir_01  C10  C9  C5  N14  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
 1M6  plan-1  C1   0.020
 1M6  plan-1  C15  0.020
 1M6  plan-1  C18  0.020
 1M6  plan-1  C19  0.020
 1M6  plan-1  C20  0.020
 1M6  plan-1  C21  0.020
 1M6  plan-1  C22  0.020
 1M6  plan-1  C26  0.020
 1M6  plan-1  N27  0.020
 1M6  plan-1  H11  0.020
 1M6  plan-1  H12  0.020
 1M6  plan-1  H13  0.020
 1M6  plan-1  H14  0.020
 1M6  plan-2  C1   0.020
 1M6  plan-2  C2   0.020
 1M6  plan-2  C3   0.020
 1M6  plan-2  C4   0.020
 1M6  plan-2  C5   0.020
 1M6  plan-2  C6   0.020
 1M6  plan-2  O7   0.020
 1M6  plan-2  C10  0.020
 1M6  plan-2  C15  0.020
 1M6  plan-2  H1   0.020
 1M6  plan-2  H2   0.020
 1M6  plan-2  H3   0.020
 1M6  plan-3  C10  0.020
 1M6  plan-3  C11  0.020
 1M6  plan-3  N12  0.020
 1M6  plan-3  C13  0.020
 1M6  plan-3  N14  0.020
 1M6  plan-3  C16  0.020
 1M6  plan-3  N17  0.020
 1M6  plan-3  O23  0.020
 1M6  plan-3  H9   0.020
 1M6  plan-3  H10  0.020

