# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 16:36:41 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: (4R)-2'-amino-6-(3-chlorophenyl)-1',2,2-trimethyl-2,3-dihydrospiro[chromene-4,4'-imidazol]-5'(1'H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@]2(CC(C)(C)Oc3ccc(cc23)c4cccc(Cl)c4)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
 1M5  1M5  (4R)-2'-amino-6-(3-chlorophenyl)-1',2,2-trimethyl-2,3-dihydrospiro[chromene-4,4'-imidazol]-5'(1'H)-one  ligand  46  26  .  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_1M5
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
 1M5  C1   C   CR6   0   0.085  -1.3128   0.6021  -0.1439
 1M5  C2   C   CR16  0  -0.306  -1.2515   1.9862  -0.3314
 1M5  C3   C   CR16  0  -0.351  -0.0379   2.6367  -0.4110
 1M5  C4   C   CR6   0   0.345   1.1568   1.9201  -0.3178
 1M5  C5   C   CR6   0   0.140   1.1221   0.5369  -0.1522
 1M5  C6   C   CR16  0  -0.372  -0.1134  -0.0932  -0.0549
 1M5  O7   O   O2    0  -0.486   2.2977   2.6259  -0.4052
 1M5  C8   C   CT    0   0.162   3.4970   2.0280   0.1218
 1M5  C9   C   CH2   0  -0.416   3.6049   0.6047  -0.4121
 1M5  C10  C   CR5   0  -0.206   2.3984  -0.2704  -0.0510
 1M5  C11  C   CR6   0   0.088  -2.6062  -0.1009  -0.0454
 1M5  C12  C   CH3   0  -0.667   4.6378   2.8717  -0.4225
 1M5  C13  C   CH3   0  -0.655   3.4639   2.1001   1.6444
 1M5  C14  C   CR5   0   0.554   2.3454  -1.4466  -1.0352
 1M5  N15  N   NR5   0  -0.522   2.4557  -2.5605  -0.2609
 1M5  C16  C   CR5   0   0.666   2.5567  -2.1541   1.0693
 1M5  N17  N   N     0  -0.450   2.5290  -0.8872   1.2565
 1M5  N18  N   NH2   0  -0.847   2.6152  -3.0958   2.0306
 1M5  O19  O   O     0  -0.433   2.2354  -1.4135  -2.2393
 1M5  C20  C   CH3   0  -0.554   2.4412  -3.9227  -0.7371
 1M5  C21  C   CR16  0  -0.274  -3.6802   0.4907   0.6213
 1M5  C22  C   CR6   0  -0.021  -4.8911  -0.1754   0.7057
 1M5  C23  C   CR16  0  -0.230  -5.0718  -1.4306   0.1469
 1M5  C24  C   CR16  0  -0.245  -4.0018  -2.0180  -0.5130
 1M5  C25  C   CR16  0  -0.305  -2.7839  -1.3638  -0.6124
 1M5  CL1  CL  CL    0  -0.130  -6.2095   0.5795   1.5436
 1M5  H1   H   HCR6  0   0.259  -2.1620   2.5647  -0.4251
 1M5  H2   H   HCR6  0   0.265  -0.0019   3.7100  -0.5489
 1M5  H3   H   HCR6  0   0.253  -0.1424  -1.1638   0.1161
 1M5  H4   H   HCH2  0   0.257   3.6965   0.6578  -1.5011
 1M5  H5   H   HCH2  0   0.262   4.5165   0.1363  -0.0365
 1M5  H6   H   HCH3  0   0.242   4.5389   3.9125  -0.1113
 1M5  H7   H   HCH3  0   0.236   5.5890   2.4992  -0.0430
 1M5  H8   H   HCH3  0   0.239   4.6730   2.8388  -1.5123
 1M5  H9   H   HCH3  0   0.246   2.6254   1.5519   2.0708
 1M5  H10  H   HCH3  0   0.234   4.3767   1.6686   2.0560
 1M5  H11  H   HCH3  0   0.235   3.4048   3.1390   1.9721
 1M5  H12  H   HNH2  0   0.411   2.9817  -4.0074   1.8108
 1M5  H13  H   HNH2  0   0.404   2.8431  -2.7684   2.9553
 1M5  H14  H   HCH3  0   0.263   3.3679  -4.4359  -0.4818
 1M5  H15  H   HCH3  0   0.266   1.5987  -4.4724  -0.3190
 1M5  H16  H   HCH3  0   0.276   2.3447  -3.9115  -1.8191
 1M5  H17  H   HCR6  0   0.276  -3.5643   1.4595   1.0895
 1M5  H18  H   HCR6  0   0.280  -6.0236  -1.9386   0.2195
 1M5  H19  H   HCR6  0   0.270  -4.1280  -2.9933  -0.9639
 1M5  H20  H   HCR6  0   0.257  -1.9740  -1.8323  -1.1565

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
 1M5  O19  C14  double    1.210  0.020  1.210
 1M5  C12  C8   single    1.520  0.020  1.520
 1M5  C14  N15  single    1.361  0.020  1.361
 1M5  C14  C10  single    1.535  0.020  1.535
 1M5  C20  N15  single    1.443  0.020  1.443
 1M5  C9   C8   single    1.524  0.020  1.524
 1M5  C9   C10  single    1.534  0.020  1.534
 1M5  N15  C16  single    1.395  0.020  1.395
 1M5  O7   C8   single    1.440  0.020  1.440
 1M5  O7   C4   single    1.344  0.020  1.344
 1M5  C8   C13  single    1.525  0.020  1.525
 1M5  C10  C5   single    1.514  0.020  1.514
 1M5  C10  N17  single    1.452  0.020  1.452
 1M5  C4   C5   aromatic  1.394  0.020  1.394
 1M5  C4   C3   aromatic  1.396  0.020  1.396
 1M5  C5   C6   aromatic  1.390  0.020  1.390
 1M5  C3   C2   aromatic  1.379  0.020  1.379
 1M5  C6   C1   aromatic  1.389  0.020  1.389
 1M5  C2   C1   aromatic  1.398  0.020  1.398
 1M5  C16  N17  double    1.281  0.020  1.281
 1M5  C16  N18  single    1.347  0.020  1.347
 1M5  C25  C24  aromatic  1.386  0.020  1.386
 1M5  C25  C11  aromatic  1.396  0.020  1.396
 1M5  C1   C11  single    1.475  0.020  1.475
 1M5  C24  C23  aromatic  1.388  0.020  1.388
 1M5  C11  C21  aromatic  1.396  0.020  1.396
 1M5  C23  C22  aromatic  1.386  0.020  1.386
 1M5  C21  C22  aromatic  1.385  0.020  1.385
 1M5  C22  CL1  single    1.735  0.020  1.735
 1M5  C2   H1   single    0.930  0.020  1.080
 1M5  C3   H2   single    0.930  0.020  1.080
 1M5  C6   H3   single    0.930  0.020  1.080
 1M5  C9   H4   single    0.970  0.020  1.090
 1M5  C9   H5   single    0.970  0.020  1.090
 1M5  C12  H6   single    0.970  0.020  1.090
 1M5  C12  H7   single    0.970  0.020  1.090
 1M5  C12  H8   single    0.970  0.020  1.090
 1M5  C13  H9   single    0.970  0.020  1.090
 1M5  C13  H10  single    0.970  0.020  1.090
 1M5  C13  H11  single    0.970  0.020  1.090
 1M5  N18  H12  single    0.890  0.020  1.040
 1M5  N18  H13  single    0.890  0.020  1.040
 1M5  C20  H14  single    0.970  0.020  1.090
 1M5  C20  H15  single    0.970  0.020  1.090
 1M5  C20  H16  single    0.970  0.020  1.090
 1M5  C21  H17  single    0.930  0.020  1.080
 1M5  C23  H18  single    0.930  0.020  1.080
 1M5  C24  H19  single    0.930  0.020  1.080
 1M5  C25  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
 1M5  C11  C1   C6   120.94  3.000
 1M5  C11  C1   C2   121.27  3.000
 1M5  C6   C1   C2   117.79  3.000
 1M5  H1   C2   C3   118.87  3.000
 1M5  H1   C2   C1   120.24  3.000
 1M5  C3   C2   C1   120.88  3.000
 1M5  H2   C3   C4   119.26  3.000
 1M5  H2   C3   C2   120.28  3.000
 1M5  C4   C3   C2   120.46  3.000
 1M5  O7   C4   C5   123.37  3.000
 1M5  C5   C4   C3   119.74  3.000
 1M5  O7   C4   C3   116.89  3.000
 1M5  C10  C5   C6   120.20  3.000
 1M5  C6   C5   C4   118.70  3.000
 1M5  C10  C5   C4   121.09  3.000
 1M5  H3   C6   C5   118.82  3.000
 1M5  H3   C6   C1   118.76  3.000
 1M5  C5   C6   C1   122.41  3.000
 1M5  C8   O7   C4   117.71  3.000
 1M5  C13  C8   C12  110.34  3.000
 1M5  C13  C8   C9   113.30  3.000
 1M5  C12  C8   C9   109.87  3.000
 1M5  C13  C8   O7   109.13  3.000
 1M5  C9   C8   O7   108.58  3.000
 1M5  C12  C8   O7   105.29  3.000
 1M5  H5   C9   H4   107.06  3.000
 1M5  H5   C9   C10  109.34  3.000
 1M5  H4   C9   C10  109.14  3.000
 1M5  H5   C9   C8   109.84  3.000
 1M5  H4   C9   C8   108.01  3.000
 1M5  C10  C9   C8   113.25  3.000
 1M5  N17  C10  C14  104.78  3.000
 1M5  N17  C10  C9   112.57  3.000
 1M5  C14  C10  C9   108.27  3.000
 1M5  N17  C10  C5   111.27  3.000
 1M5  C9   C10  C5   110.08  3.000
 1M5  C14  C10  C5   109.68  3.000
 1M5  C25  C11  C21  118.66  3.000
 1M5  C21  C11  C1   120.30  3.000
 1M5  C25  C11  C1   121.04  3.000
 1M5  H8   C12  H7   108.02  3.000
 1M5  H8   C12  H6   108.47  3.000
 1M5  H7   C12  H6   107.81  3.000
 1M5  H8   C12  C8   111.43  3.000
 1M5  H7   C12  C8   109.93  3.000
 1M5  H6   C12  C8   111.07  3.000
 1M5  H11  C13  H10  107.99  3.000
 1M5  H11  C13  H9   108.67  3.000
 1M5  H10  C13  H9   107.31  3.000
 1M5  H11  C13  C8   110.25  3.000
 1M5  H10  C13  C8   109.89  3.000
 1M5  H9   C13  C8   112.58  3.000
 1M5  O19  C14  N15  126.59  3.000
 1M5  N15  C14  C10  105.05  3.000
 1M5  O19  C14  C10  128.36  3.000
 1M5  C20  N15  C16  126.20  3.000
 1M5  C16  N15  C14  108.06  3.000
 1M5  C20  N15  C14  125.73  3.000
 1M5  N18  C16  N17  126.02  3.000
 1M5  N18  C16  N15  118.69  3.000
 1M5  N17  C16  N15  115.22  3.000
 1M5  C16  N17  C10  106.90  3.000
 1M5  H13  N18  H12  114.37  3.000
 1M5  H13  N18  C16  115.97  3.000
 1M5  H12  N18  C16  119.53  3.000
 1M5  H16  C20  H15  108.59  3.000
 1M5  H16  C20  H14  108.29  3.000
 1M5  H15  C20  H14  109.28  3.000
 1M5  H16  C20  N15  108.65  3.000
 1M5  H15  C20  N15  110.94  3.000
 1M5  H14  C20  N15  111.02  3.000
 1M5  H17  C21  C22  119.86  3.000
 1M5  H17  C21  C11  120.25  3.000
 1M5  C22  C21  C11  119.88  3.000
 1M5  CL1  C22  C23  119.32  3.000
 1M5  CL1  C22  C21  118.99  3.000
 1M5  C23  C22  C21  121.68  3.000
 1M5  H18  C23  C24  120.78  3.000
 1M5  H18  C23  C22  120.89  3.000
 1M5  C24  C23  C22  118.33  3.000
 1M5  H19  C24  C25  119.87  3.000
 1M5  H19  C24  C23  119.33  3.000
 1M5  C25  C24  C23  120.79  3.000
 1M5  H20  C25  C24  119.29  3.000
 1M5  H20  C25  C11  120.04  3.000
 1M5  C24  C25  C11  120.65  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
 1M5  CONST_01  C4   C5   C6   C1     0.00   0.0  0
 1M5  CONST_02  C4   C3   C2   C1     0.00   0.0  0
 1M5  CONST_03  C24  C25  C11  C1   180.00   0.0  0
 1M5  CONST_04  C22  C21  C11  C1   180.00   0.0  0
 1M5  CONST_05  C5   C4   C3   C2     0.00   0.0  0
 1M5  CONST_06  C5   C6   C1   C2     0.00   0.0  0
 1M5  CONST_09  C6   C5   C4   C3     0.00   0.0  0
 1M5  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 1M5  CONST_11  C11  C1   C2   C3   180.00   0.0  0
 1M5  CONST_12  C11  C1   C6   C5   180.00   0.0  0
 1M5  CONST_15  C23  C24  C25  C11    0.00   0.0  0
 1M5  CONST_16  C23  C22  C21  C11    0.00   0.0  0
 1M5  CONST_17  C24  C25  C11  C21    0.00   0.0  0
 1M5  CONST_18  C24  C23  C22  C21    0.00   0.0  0
 1M5  CONST_19  C25  C24  C23  C22    0.00   0.0  0
 1M5  CONST_20  C25  C11  C21  C22    0.00   0.0  0
 1M5  CONST_21  C16  N15  C14  C10    0.00   0.0  0
 1M5  CONST_22  N15  C16  N17  C10    0.00   0.0  0
 1M5  CONST_23  N17  C16  N15  C14    0.00   0.0  0
 1M5  CONST_24  CL1  C22  C21  C11  180.00   0.0  0
 1M5  CONST_25  CL1  C22  C23  C24  180.00   0.0  0
 1M5  CONST_26  C20  N15  C14  C10  180.00   0.0  0
 1M5  CONST_27  N18  C16  N17  C10  180.00   0.0  0
 1M5  CONST_28  N18  C16  N15  C14  180.00   0.0  0
 1M5  CONST_29  O19  C14  N15  C16  180.00   0.0  0
 1M5  CONST_30  C20  N15  C16  N17  180.00   0.0  0
 1M5  CONST_31  H2   C3   C2   C1   180.00   0.0  0
 1M5  CONST_32  H20  C25  C11  C1     0.00   0.0  0
 1M5  CONST_33  H17  C21  C11  C1     0.00   0.0  0
 1M5  CONST_34  H3   C6   C1   C2   180.00   0.0  0
 1M5  CONST_35  H1   C2   C3   C4   180.00   0.0  0
 1M5  CONST_36  H19  C24  C25  C11  180.00   0.0  0
 1M5  CONST_37  H18  C23  C22  C21  180.00   0.0  0
 1M5  CONST_38  C20  N15  C16  N18    0.00   0.0  0
 1M5  CONST_39  C20  N15  C14  O19    0.00   0.0  0
 1M5  CONST_41  H13  N18  C16  N15  180.00   0.0  0
 1M5  Var_01    C9   C8   O7   C4    48.54  30.0  1
 1M5  Var_02    C10  C9   C8   O7   -58.28  30.0  1
 1M5  Var_03    H6   C12  C8   O7    59.12  30.0  3
 1M5  Var_04    H9   C13  C8   O7    61.60  30.0  3
 1M5  Var_05    H14  C20  N15  C14  119.94  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
 1M5  chir_01  C10  C9  C5  N17  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
 1M5  plan-1  C1   0.020
 1M5  plan-1  C11  0.020
 1M5  plan-1  C21  0.020
 1M5  plan-1  C22  0.020
 1M5  plan-1  C23  0.020
 1M5  plan-1  C24  0.020
 1M5  plan-1  C25  0.020
 1M5  plan-1  CL1  0.020
 1M5  plan-1  H17  0.020
 1M5  plan-1  H18  0.020
 1M5  plan-1  H19  0.020
 1M5  plan-1  H20  0.020
 1M5  plan-2  C1   0.020
 1M5  plan-2  C2   0.020
 1M5  plan-2  C3   0.020
 1M5  plan-2  C4   0.020
 1M5  plan-2  C5   0.020
 1M5  plan-2  C6   0.020
 1M5  plan-2  O7   0.020
 1M5  plan-2  C10  0.020
 1M5  plan-2  C11  0.020
 1M5  plan-2  H1   0.020
 1M5  plan-2  H2   0.020
 1M5  plan-2  H3   0.020
 1M5  plan-3  C10  0.020
 1M5  plan-3  C14  0.020
 1M5  plan-3  N15  0.020
 1M5  plan-3  C16  0.020
 1M5  plan-3  N17  0.020
 1M5  plan-3  N18  0.020
 1M5  plan-3  O19  0.020
 1M5  plan-3  C20  0.020
 1M5  plan-3  H12  0.020
 1M5  plan-3  H13  0.020

