# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 02:13:21 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: (4R,4a'S,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1-methyl-3',4',4a',10a'-tetrahydro-1'H-spiro[imidazole-4,10'-pyrano[4,3-b]chromen]-5(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=N[C@@]2([C@H]3COCC[C@@H]3Oc4ccc(cc24)c5cccnc5F)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
 2EX  2EX  (4R,4a'S,10a'S)-2-amino-8'-(2-fluoropyridin-3-yl)-1-methyl-3',4',4a',10a'-tetrahydro-1'H-spiro[imidazole-4,10'-pyrano[4,3-b]chromen]-5(1H)-one  ligand  47  28  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2EX
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
 2EX  C1   C  CR6   0  -0.195   3.5652   0.6650  -0.1341
 2EX  C2   C  CR16  0  -0.174   4.4889   1.4113  -0.8585
 2EX  C3   C  CR16  0  -0.326   5.8064   0.9879  -0.9681
 2EX  C4   C  CR16  0  -0.058   6.1699  -0.1886  -0.3412
 2EX  N5   N  N     0  -0.419   5.3066  -0.9156   0.3663
 2EX  C6   C  CR6   0   0.562   4.0811  -0.4908   0.4510
 2EX  C7   C  CR6   0   0.095   2.1629   1.0928   0.0131
 2EX  C8   C  CR16  0  -0.298   1.8663   2.4236   0.3162
 2EX  C9   C  CR16  0  -0.347   0.5590   2.8507   0.4255
 2EX  C10  C  CR6   0   0.354  -0.4935   1.9549   0.2351
 2EX  C11  C  CR6   0   0.101  -0.2206   0.6218  -0.0758
 2EX  C12  C  CR16  0  -0.362   1.1036   0.2156  -0.1856
 2EX  O13  O  O2    0  -0.484  -1.7358   2.4592   0.3416
 2EX  C14  C  CH1   0   0.067  -2.8288   1.5494   0.3823
 2EX  C15  C  CH1   0  -0.326  -2.6356   0.3979  -0.5882
 2EX  C16  C  CR5   0  -0.162  -1.3412  -0.3742  -0.2963
 2EX  C17  C  CH2   0  -0.494  -4.0971   2.3053   0.0360
 2EX  C18  C  CH2   0  -0.198  -5.2638   1.3291  -0.0105
 2EX  O19  O  O2    0  -0.479  -5.0300   0.2771  -0.9233
 2EX  C20  C  CH2   0  -0.164  -3.8895  -0.4746  -0.5861
 2EX  N21  N  N     0  -0.456  -1.0483  -1.2952  -1.3727
 2EX  C22  C  CR5   0   0.665  -1.0363  -2.4739  -0.8660
 2EX  N23  N  NR5   0  -0.517  -1.2699  -2.5289   0.5065
 2EX  C24  C  CR5   0   0.563  -1.4598  -1.2566   0.9551
 2EX  O25  O  O     0  -0.429  -1.6658  -0.9242   2.1000
 2EX  N26  N  NH2   0  -0.849  -0.8753  -3.6219  -1.5437
 2EX  C27  C  CH3   0  -0.557  -1.3036  -3.7207   1.3203
 2EX  F28  F  F     0  -0.294   3.2678  -1.2501   1.1930
 2EX  H1   H  HCR6  0   0.281   4.1696   2.3222  -1.3488
 2EX  H2   H  HCR6  0   0.278   6.5298   1.5552  -1.5358
 2EX  H3   H  HCR6  0   0.278   7.1840  -0.5636  -0.4005
 2EX  H4   H  HCR6  0   0.261   2.6665   3.1340   0.4824
 2EX  H5   H  HCR6  0   0.267   0.3393   3.8840   0.6628
 2EX  H6   H  HCR6  0   0.255   1.3026  -0.8097  -0.4703
 2EX  H7   H  HCH1  0   0.242  -2.9128   1.1614   1.4049
 2EX  H8   H  HCH1  0   0.274  -2.5192   0.8131  -1.5972
 2EX  H9   H  HCH2  0   0.256  -4.3013   3.0775   0.7811
 2EX  H10  H  HCH2  0   0.241  -3.9839   2.7969  -0.9344
 2EX  H11  H  HCH2  0   0.209  -5.4503   0.9257   0.9950
 2EX  H12  H  HCH2  0   0.249  -6.1727   1.8370  -0.3333
 2EX  H13  H  HCH2  0   0.252  -3.7960  -1.2686  -1.3276
 2EX  H14  H  HCH2  0   0.207  -4.0275  -0.9474   0.3980
 2EX  H15  H  HNH2  0   0.407  -0.5625  -3.5422  -2.4973
 2EX  H16  H  HNH2  0   0.416  -0.5707  -4.4529  -1.0649
 2EX  H17  H  HCH3  0   0.267  -2.0274  -4.4336   0.9282
 2EX  H18  H  HCH3  0   0.265  -0.3226  -4.1928   1.3711
 2EX  H19  H  HCH3  0   0.277  -1.6035  -3.4441   2.3270

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
 2EX  O25  C24  double    1.210  0.020  1.210
 2EX  C18  C17  single    1.522  0.020  1.522
 2EX  C18  O19  single    1.412  0.020  1.412
 2EX  C17  C14  single    1.517  0.020  1.517
 2EX  C27  N23  single    1.444  0.020  1.444
 2EX  C14  O13  single    1.423  0.020  1.423
 2EX  C14  C15  single    1.518  0.020  1.518
 2EX  C24  N23  single    1.362  0.020  1.362
 2EX  C24  C16  single    1.536  0.020  1.536
 2EX  O19  C20  single    1.407  0.020  1.407
 2EX  O13  C10  single    1.345  0.020  1.345
 2EX  C20  C15  single    1.528  0.020  1.528
 2EX  N23  C22  single    1.393  0.020  1.393
 2EX  C10  C9   aromatic  1.395  0.020  1.395
 2EX  C10  C11  aromatic  1.396  0.020  1.396
 2EX  C15  C16  single    1.535  0.020  1.535
 2EX  C9   C8   aromatic  1.380  0.020  1.380
 2EX  C16  C11  single    1.515  0.020  1.515
 2EX  C16  N21  single    1.447  0.020  1.447
 2EX  C11  C12  aromatic  1.389  0.020  1.389
 2EX  C8   C7   aromatic  1.397  0.020  1.397
 2EX  C2   C3   aromatic  1.388  0.020  1.388
 2EX  C2   C1   aromatic  1.391  0.020  1.391
 2EX  C12  C7   aromatic  1.390  0.020  1.390
 2EX  C7   C1   single    1.473  0.020  1.473
 2EX  C22  N21  double    1.283  0.020  1.283
 2EX  C22  N26  single    1.343  0.020  1.343
 2EX  C3   C4   aromatic  1.382  0.020  1.382
 2EX  C1   C6   aromatic  1.394  0.020  1.394
 2EX  C4   N5   aromatic  1.332  0.020  1.332
 2EX  C6   N5   aromatic  1.300  0.020  1.300
 2EX  C6   F28  single    1.337  0.020  1.337
 2EX  C2   H1   single    0.930  0.020  1.080
 2EX  C3   H2   single    0.930  0.020  1.080
 2EX  C4   H3   single    0.930  0.020  1.080
 2EX  C8   H4   single    0.930  0.020  1.080
 2EX  C9   H5   single    0.930  0.020  1.080
 2EX  C12  H6   single    0.930  0.020  1.080
 2EX  C14  H7   single    0.970  0.020  1.090
 2EX  C15  H8   single    0.970  0.020  1.090
 2EX  C17  H9   single    0.970  0.020  1.090
 2EX  C17  H10  single    0.970  0.020  1.090
 2EX  C18  H11  single    0.970  0.020  1.090
 2EX  C18  H12  single    0.970  0.020  1.090
 2EX  C20  H13  single    0.970  0.020  1.090
 2EX  C20  H14  single    0.970  0.020  1.090
 2EX  N26  H15  single    0.890  0.020  1.040
 2EX  N26  H16  single    0.890  0.020  1.040
 2EX  C27  H17  single    0.970  0.020  1.090
 2EX  C27  H18  single    0.970  0.020  1.090
 2EX  C27  H19  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
 2EX  C7   C1   C6   123.43  3.000
 2EX  C6   C1   C2   114.68  3.000
 2EX  C7   C1   C2   121.88  3.000
 2EX  H1   C2   C3   120.05  3.000
 2EX  H1   C2   C1   119.43  3.000
 2EX  C3   C2   C1   120.51  3.000
 2EX  H2   C3   C4   120.62  3.000
 2EX  H2   C3   C2   121.11  3.000
 2EX  C4   C3   C2   118.26  3.000
 2EX  H3   C4   N5   116.55  3.000
 2EX  H3   C4   C3   121.09  3.000
 2EX  N5   C4   C3   122.36  3.000
 2EX  C6   N5   C4   117.86  3.000
 2EX  F28  C6   N5   115.08  3.000
 2EX  F28  C6   C1   118.58  3.000
 2EX  N5   C6   C1   126.33  3.000
 2EX  C12  C7   C8   118.07  3.000
 2EX  C12  C7   C1   121.86  3.000
 2EX  C8   C7   C1   120.03  3.000
 2EX  H4   C8   C9   119.01  3.000
 2EX  H4   C8   C7   120.09  3.000
 2EX  C9   C8   C7   120.89  3.000
 2EX  H5   C9   C10  119.31  3.000
 2EX  H5   C9   C8   120.34  3.000
 2EX  C10  C9   C8   120.34  3.000
 2EX  O13  C10  C11  123.81  3.000
 2EX  C11  C10  C9   119.75  3.000
 2EX  O13  C10  C9   116.44  3.000
 2EX  C16  C11  C12  120.07  3.000
 2EX  C12  C11  C10  118.90  3.000
 2EX  C16  C11  C10  121.03  3.000
 2EX  H6   C12  C11  118.22  3.000
 2EX  H6   C12  C7   119.69  3.000
 2EX  C11  C12  C7   122.04  3.000
 2EX  C14  O13  C10  118.17  3.000
 2EX  H7   C14  C17  108.97  3.000
 2EX  H7   C14  C15  109.72  3.000
 2EX  C17  C14  C15  109.78  3.000
 2EX  H7   C14  O13  108.16  3.000
 2EX  C15  C14  O13  111.65  3.000
 2EX  C17  C14  O13  108.50  3.000
 2EX  H8   C15  C20  107.73  3.000
 2EX  H8   C15  C16  106.00  3.000
 2EX  C20  C15  C16  113.87  3.000
 2EX  H8   C15  C14  108.32  3.000
 2EX  C16  C15  C14  111.54  3.000
 2EX  C20  C15  C14  109.14  3.000
 2EX  C24  C16  N21  104.84  3.000
 2EX  N21  C16  C15  110.45  3.000
 2EX  C24  C16  C15  112.26  3.000
 2EX  N21  C16  C11  112.15  3.000
 2EX  C15  C16  C11  108.70  3.000
 2EX  C24  C16  C11  108.43  3.000
 2EX  H10  C17  H9   107.86  3.000
 2EX  H10  C17  C18  109.91  3.000
 2EX  H9   C17  C18  109.33  3.000
 2EX  H10  C17  C14  109.88  3.000
 2EX  H9   C17  C14  110.67  3.000
 2EX  C18  C17  C14  109.17  3.000
 2EX  H12  C18  H11  107.48  3.000
 2EX  H12  C18  O19  107.08  3.000
 2EX  H11  C18  O19  110.24  3.000
 2EX  H12  C18  C17  110.45  3.000
 2EX  H11  C18  C17  109.72  3.000
 2EX  O19  C18  C17  111.76  3.000
 2EX  C20  O19  C18  112.16  3.000
 2EX  H14  C20  H13  107.82  3.000
 2EX  H14  C20  O19  110.01  3.000
 2EX  H13  C20  O19  107.19  3.000
 2EX  H14  C20  C15  110.46  3.000
 2EX  H13  C20  C15  110.15  3.000
 2EX  O19  C20  C15  111.09  3.000
 2EX  C22  N21  C16  107.03  3.000
 2EX  N26  C22  N23  118.92  3.000
 2EX  N26  C22  N21  125.96  3.000
 2EX  N23  C22  N21  115.07  3.000
 2EX  C27  N23  C24  125.60  3.000
 2EX  C24  N23  C22  108.12  3.000
 2EX  C27  N23  C22  126.29  3.000
 2EX  O25  C24  N23  126.29  3.000
 2EX  N23  C24  C16  104.92  3.000
 2EX  O25  C24  C16  128.79  3.000
 2EX  H16  N26  H15  114.97  3.000
 2EX  H16  N26  C22  120.14  3.000
 2EX  H15  N26  C22  116.59  3.000
 2EX  H19  C27  H18  108.39  3.000
 2EX  H19  C27  H17  108.47  3.000
 2EX  H18  C27  H17  109.36  3.000
 2EX  H19  C27  N23  108.59  3.000
 2EX  H18  C27  N23  111.28  3.000
 2EX  H17  C27  N23  110.67  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
 2EX  CONST_01  C4   C3   C2   C1     0.00   0.0  0
 2EX  CONST_02  C9   C8   C7   C1   180.00   0.0  0
 2EX  CONST_03  C11  C12  C7   C1   180.00   0.0  0
 2EX  CONST_04  C4   N5   C6   C1     0.00   0.0  0
 2EX  CONST_05  N5   C4   C3   C2     0.00   0.0  0
 2EX  CONST_08  N5   C6   C1   C2     0.00   0.0  0
 2EX  CONST_09  C7   C1   C2   C3   180.00   0.0  0
 2EX  CONST_10  C6   C1   C2   C3     0.00   0.0  0
 2EX  CONST_11  C6   N5   C4   C3     0.00   0.0  0
 2EX  CONST_12  C7   C1   C6   N5   180.00   0.0  0
 2EX  CONST_15  C10  C9   C8   C7     0.00   0.0  0
 2EX  CONST_16  C10  C11  C12  C7     0.00   0.0  0
 2EX  CONST_17  C11  C10  C9   C8     0.00   0.0  0
 2EX  CONST_18  C11  C12  C7   C8     0.00   0.0  0
 2EX  CONST_19  C12  C11  C10  C9     0.00   0.0  0
 2EX  CONST_20  C12  C7   C8   C9     0.00   0.0  0
 2EX  CONST_21  C22  N23  C24  C16    0.00   0.0  0
 2EX  CONST_22  N23  C22  N21  C16    0.00   0.0  0
 2EX  CONST_23  C24  N23  C22  N21    0.00   0.0  0
 2EX  CONST_24  F28  C6   C1   C2   180.00   0.0  0
 2EX  CONST_25  F28  C6   N5   C4   180.00   0.0  0
 2EX  CONST_26  F28  C6   C1   C7     0.00   0.0  0
 2EX  CONST_27  C27  N23  C24  C16  180.00   0.0  0
 2EX  CONST_28  N26  C22  N21  C16  180.00   0.0  0
 2EX  CONST_29  C27  N23  C22  N21  180.00   0.0  0
 2EX  CONST_30  O25  C24  N23  C22  180.00   0.0  0
 2EX  CONST_31  N26  C22  N23  C24  180.00   0.0  0
 2EX  CONST_32  H2   C3   C2   C1   180.00   0.0  0
 2EX  CONST_33  H4   C8   C7   C1     0.00   0.0  0
 2EX  CONST_34  H6   C12  C7   C1     0.00   0.0  0
 2EX  CONST_35  H3   C4   C3   C2   180.00   0.0  0
 2EX  CONST_36  H1   C2   C3   C4   180.00   0.0  0
 2EX  CONST_37  H5   C9   C8   C7   180.00   0.0  0
 2EX  CONST_38  C27  N23  C24  O25    0.00   0.0  0
 2EX  CONST_39  C27  N23  C22  N26    0.00   0.0  0
 2EX  CONST_40  H15  N26  C22  N21    0.00   0.0  0
 2EX  Var_01    O19  C18  C17  C14  -56.53  30.0  1
 2EX  Var_02    H13  C20  O19  C18  179.03  30.0  1
 2EX  Var_03    H17  C27  N23  C22  -55.58  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
 2EX  chir_01  C14  C17  O13  C15  positiv
 2EX  chir_02  C15  C14  C20  C16  positiv
 2EX  chir_03  C16  C11  C15  C24  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
 2EX  plan-1  C1   0.020
 2EX  plan-1  C2   0.020
 2EX  plan-1  C3   0.020
 2EX  plan-1  C4   0.020
 2EX  plan-1  N5   0.020
 2EX  plan-1  C6   0.020
 2EX  plan-1  C7   0.020
 2EX  plan-1  F28  0.020
 2EX  plan-1  H1   0.020
 2EX  plan-1  H2   0.020
 2EX  plan-1  H3   0.020
 2EX  plan-2  C1   0.020
 2EX  plan-2  C7   0.020
 2EX  plan-2  C8   0.020
 2EX  plan-2  C9   0.020
 2EX  plan-2  C10  0.020
 2EX  plan-2  C11  0.020
 2EX  plan-2  C12  0.020
 2EX  plan-2  O13  0.020
 2EX  plan-2  C16  0.020
 2EX  plan-2  H4   0.020
 2EX  plan-2  H5   0.020
 2EX  plan-2  H6   0.020
 2EX  plan-3  C16  0.020
 2EX  plan-3  N21  0.020
 2EX  plan-3  C22  0.020
 2EX  plan-3  N23  0.020
 2EX  plan-3  C24  0.020
 2EX  plan-3  O25  0.020
 2EX  plan-3  N26  0.020
 2EX  plan-3  C27  0.020
 2EX  plan-3  H15  0.020
 2EX  plan-3  H16  0.020

