# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 22:36:21 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 4-[(1S,5R,6R)-6-amino-1-methyl-3-azabicyclo[3.2.0]hept-3-yl]-6-fluoro-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNc1cc(F)cc2c1[nH]c3nc(Oc4cnc(C)nc4)nc(N5C[C@@H]6[C@H](N)C[C@]6(C)C5)c23
#
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
 920  920  4-[(1S,5R,6R)-6-amino-1-methyl-3-azabicyclo[3.2.0]hept-3-yl]-6-fluoro-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine  ligand  58  33  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_920
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
 920  F31  F  F     0  -0.328  -4.7200  -2.9242   0.0594
 920  C6   C  CR6   0   0.560  -3.3898  -2.7852  -0.1096
 920  C1   C  CR16  0  -0.561  -2.6882  -3.9046  -0.5428
 920  C5   C  CR16  0  -0.614  -2.8193  -1.5691   0.1724
 920  C4   C  CR56  0   0.061  -1.4331  -1.4703  -0.0172
 920  C9   C  CR56  0  -0.093  -0.4597  -0.4251   0.1800
 920  C10  C  CR6   0   0.468  -0.4206   0.9475   0.5160
 920  N22  N  NR5   0  -0.498  -1.5013   1.7553   0.5511
 920  C26  C  CH2   0  -0.310  -2.5573   1.7018  -0.4579
 920  C25  C  CR15  0  -0.259  -3.6140   2.6464   0.0948
 920  C28  C  CH1   0  -0.062  -4.1335   3.7241  -0.8705
 920  N29  N  NH2   0  -0.804  -4.3969   3.3576  -2.2394
 920  C27  C  CH2   0  -0.460  -2.9431   4.6200  -0.4522
 920  C24  C  CR5   0  -0.071  -2.7678   3.7313   0.8059
 920  C30  C  CH3   0  -0.669  -3.3818   4.3298   2.0559
 920  C23  C  CH2   0  -0.255  -1.3811   3.1264   1.0432
 920  N11  N  N     0  -0.505   0.7587   1.5044   0.8189
 920  C12  C  CR6   0   0.563   1.8514   0.7883   0.6555
 920  N13  N  N     0  -0.503   1.9802  -0.4327   0.1984
 920  C8   C  CR56  0   0.493   0.8009  -1.0153  -0.0141
 920  N7   N  NR15  0  -0.757   0.6442  -2.2942  -0.4089
 920  C3   C  CR56  0   0.287  -0.7041  -2.6057  -0.4070
 920  C2   C  CR6   0   0.361  -1.3025  -3.8438  -0.6921
 920  N32  N  NH1   0  -0.682  -0.5557  -4.9074  -1.1254
 920  C33  C  CH3   0  -0.538  -1.1403  -6.2202  -1.2507
 920  O14  O  O2    0  -0.491   2.9727   1.4634   0.9966
 920  C15  C  CR6   0   0.233   4.1822   0.8511   0.8265
 920  C20  C  CR16  0  -0.065   4.7916   0.7601  -0.4139
 920  N19  N  N     0  -0.400   5.9907   0.2245  -0.5532
 920  C18  C  CR6   0   0.351   6.6003  -0.2279   0.5427
 920  C21  C  CH3   0  -0.728   7.9536  -0.8374   0.3663
 920  N17  N  N     0  -0.402   6.0888  -0.1749   1.7662
 920  C16  C  CR16  0  -0.076   4.8822   0.3592   1.9083
 920  H1   H  HCR6  0   0.286  -3.2302  -4.8198  -0.7382
 920  H2   H  HCR6  0   0.266  -3.4185  -0.7650   0.5730
 920  H3   H  HCH2  0   0.242  -2.1491   2.0420  -1.4181
 920  H4   H  HCH2  0   0.271  -2.9307   0.6975  -0.6258
 920  H5   H  HCR5  0   0.246  -4.3531   2.1088   0.6944
 920  H6   H  HCH1  0   0.240  -5.0575   4.1367  -0.4589
 920  H7   H  HNH2  0   0.348  -4.8157   4.1393  -2.7272
 920  H8   H  HNH2  0   0.339  -3.5324   3.1645  -2.7297
 920  H10  H  HCH2  0   0.230  -2.1018   4.5320  -1.1444
 920  H11  H  HCH2  0   0.238  -3.1426   5.6804  -0.2864
 920  H12  H  HCH3  0   0.230  -3.4326   3.5936   2.8603
 920  H13  H  HCH3  0   0.232  -2.7914   5.1771   2.4103
 920  H14  H  HCH3  0   0.231  -4.3947   4.6924   1.8712
 920  H15  H  HCH2  0   0.248  -1.1017   3.1143   2.0985
 920  H16  H  HCH2  0   0.236  -0.6057   3.6819   0.5076
 920  H17  H  HNR5  0   0.414   1.4120  -2.9134  -0.6105
 920  H18  H  HNH1  0   0.383   0.4084  -4.9166  -0.8373
 920  H19  H  HCH3  0   0.225  -1.5808  -6.5900  -0.3186
 920  H20  H  HCH3  0   0.239  -1.9166  -6.2278  -2.0166
 920  H21  H  HCH3  0   0.261  -0.3637  -6.9144  -1.5609
 920  H22  H  HCR6  0   0.290   4.3013   1.1343  -1.3068
 920  H23  H  HCH3  0   0.257   8.6229  -0.1448  -0.1445
 920  H24  H  HCH3  0   0.251   8.3906  -1.1062   1.3245
 920  H25  H  HCH3  0   0.259   7.8894  -1.7352  -0.2505
 920  H26  H  HCR6  0   0.290   4.4667   0.4045   2.9098

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
 920  C33  N32  single    1.443  0.020  1.443
 920  F31  C6   single    1.348  0.020  1.348
 920  C1   C6   aromatic  1.390  0.020  1.390
 920  C1   C2   aromatic  1.395  0.020  1.395
 920  C6   C5   aromatic  1.373  0.020  1.373
 920  N32  C2   single    1.370  0.020  1.370
 920  C2   C3   aromatic  1.404  0.020  1.404
 920  C5   C4   aromatic  1.403  0.020  1.403
 920  C3   C4   aromatic  1.404  0.020  1.404
 920  C3   N7   aromatic  1.384  0.020  1.384
 920  C4   C9   aromatic  1.442  0.020  1.442
 920  N7   C8   aromatic  1.348  0.020  1.348
 920  C9   C8   aromatic  1.405  0.020  1.405
 920  C9   C10  aromatic  1.414  0.020  1.414
 920  C8   N13  aromatic  1.332  0.020  1.332
 920  C26  N22  single    1.462  0.020  1.462
 920  C26  C25  single    1.521  0.020  1.521
 920  C10  N22  single    1.350  0.020  1.350
 920  C10  N11  aromatic  1.339  0.020  1.339
 920  N22  C23  single    1.462  0.020  1.462
 920  N13  C12  aromatic  1.310  0.020  1.310
 920  C23  C24  single    1.531  0.020  1.531
 920  C25  C24  single    1.549  0.020  1.549
 920  C25  C28  single    1.537  0.020  1.537
 920  N11  C12  aromatic  1.317  0.020  1.317
 920  C12  O14  single    1.353  0.020  1.353
 920  C24  C30  single    1.516  0.020  1.516
 920  C24  C27  single    1.550  0.020  1.550
 920  O14  C15  single    1.366  0.020  1.366
 920  C28  N29  single    1.441  0.020  1.441
 920  C28  C27  single    1.548  0.020  1.548
 920  C20  C15  aromatic  1.385  0.020  1.385
 920  C20  N19  aromatic  1.321  0.020  1.321
 920  C15  C16  aromatic  1.379  0.020  1.379
 920  N19  C18  aromatic  1.333  0.020  1.333
 920  C16  N17  aromatic  1.327  0.020  1.327
 920  C18  N17  aromatic  1.327  0.020  1.327
 920  C18  C21  single    1.495  0.020  1.495
 920  C1   H1   single    0.930  0.020  1.080
 920  C5   H2   single    0.930  0.020  1.080
 920  C26  H3   single    0.970  0.020  1.090
 920  C26  H4   single    0.970  0.020  1.090
 920  C25  H5   single    0.970  0.020  1.090
 920  C28  H6   single    0.970  0.020  1.090
 920  N29  H7   single    0.890  0.020  1.040
 920  N29  H8   single    0.890  0.020  1.040
 920  C27  H10  single    0.970  0.020  1.090
 920  C27  H11  single    0.970  0.020  1.090
 920  C30  H12  single    0.970  0.020  1.090
 920  C30  H13  single    0.970  0.020  1.090
 920  C30  H14  single    0.970  0.020  1.090
 920  C23  H15  single    0.970  0.020  1.090
 920  C23  H16  single    0.970  0.020  1.090
 920  N7   H17  single    0.860  0.020  1.020
 920  N32  H18  single    0.890  0.020  1.040
 920  C33  H19  single    0.970  0.020  1.090
 920  C33  H20  single    0.970  0.020  1.090
 920  C33  H21  single    0.970  0.020  1.090
 920  C20  H22  single    0.930  0.020  1.080
 920  C21  H23  single    0.970  0.020  1.090
 920  C21  H24  single    0.970  0.020  1.090
 920  C21  H25  single    0.970  0.020  1.090
 920  C16  H26  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
 920  C5   C6   C1   124.58  3.000
 920  C5   C6   F31  118.41  3.000
 920  C1   C6   F31  117.00  3.000
 920  H1   C1   C2   121.02  3.000
 920  H1   C1   C6   118.99  3.000
 920  C2   C1   C6   119.97  3.000
 920  H2   C5   C4   123.10  3.000
 920  H2   C5   C6   120.35  3.000
 920  C4   C5   C6   116.45  3.000
 920  C3   C4   C9   105.88  3.000
 920  C9   C4   C5   134.41  3.000
 920  C3   C4   C5   119.58  3.000
 920  C8   C9   C10  114.57  3.000
 920  C10  C9   C4   139.03  3.000
 920  C8   C9   C4   106.39  3.000
 920  N11  C10  N22  116.77  3.000
 920  N11  C10  C9   118.82  3.000
 920  N22  C10  C9   124.42  3.000
 920  C23  N22  C26  109.03  3.000
 920  C23  N22  C10  120.29  3.000
 920  C26  N22  C10  122.59  3.000
 920  H4   C26  H3   106.24  3.000
 920  H4   C26  C25  113.08  3.000
 920  H3   C26  C25  112.57  3.000
 920  H4   C26  N22  112.92  3.000
 920  H3   C26  N22  108.90  3.000
 920  C25  C26  N22  103.20  3.000
 920  H5   C25  C24  117.52  3.000
 920  H5   C25  C28  117.44  3.000
 920  C24  C25  C28   88.96  3.000
 920  H5   C25  C26  111.32  3.000
 920  C28  C25  C26  116.22  3.000
 920  C24  C25  C26  102.84  3.000
 920  H6   C28  C27  109.28  3.000
 920  H6   C28  N29  107.41  3.000
 920  C27  C28  N29  123.00  3.000
 920  H6   C28  C25  108.30  3.000
 920  C27  C28  C25   88.63  3.000
 920  N29  C28  C25  118.68  3.000
 920  H8   N29  H7   105.50  3.000
 920  H8   N29  C28  110.63  3.000
 920  H7   N29  C28  109.69  3.000
 920  H11  C27  H10  108.37  3.000
 920  H11  C27  C24  117.02  3.000
 920  H10  C27  C24  112.38  3.000
 920  H11  C27  C28  117.57  3.000
 920  H10  C27  C28  111.98  3.000
 920  C24  C27  C28   88.54  3.000
 920  C23  C24  C30  113.26  3.000
 920  C30  C24  C27  113.40  3.000
 920  C23  C24  C27  117.04  3.000
 920  C27  C24  C25   88.12  3.000
 920  C30  C24  C25  115.71  3.000
 920  C23  C24  C25  106.81  3.000
 920  H14  C30  H13  107.39  3.000
 920  H14  C30  H12  107.79  3.000
 920  H13  C30  H12  108.01  3.000
 920  H14  C30  C24  111.56  3.000
 920  H13  C30  C24  110.80  3.000
 920  H12  C30  C24  111.12  3.000
 920  H16  C23  H15  107.30  3.000
 920  H16  C23  C24  111.43  3.000
 920  H15  C23  C24  112.70  3.000
 920  H16  C23  N22  111.70  3.000
 920  H15  C23  N22  109.63  3.000
 920  C24  C23  N22  104.12  3.000
 920  C12  N11  C10  118.47  3.000
 920  O14  C12  N13  118.15  3.000
 920  O14  C12  N11  112.65  3.000
 920  N13  C12  N11  129.18  3.000
 920  C8   N13  C12  112.09  3.000
 920  N7   C8   N13  124.37  3.000
 920  N13  C8   C9   126.03  3.000
 920  N7   C8   C9   109.56  3.000
 920  H17  N7   C3   127.21  3.000
 920  H17  N7   C8   123.62  3.000
 920  C3   N7   C8   109.06  3.000
 920  C2   C3   N7   127.84  3.000
 920  N7   C3   C4   108.91  3.000
 920  C2   C3   C4   123.22  3.000
 920  N32  C2   C3   121.09  3.000
 920  C3   C2   C1   116.10  3.000
 920  N32  C2   C1   122.79  3.000
 920  H18  N32  C33  113.88  3.000
 920  H18  N32  C2   116.03  3.000
 920  C33  N32  C2   120.87  3.000
 920  H21  C33  H20  107.68  3.000
 920  H21  C33  H19  108.34  3.000
 920  H20  C33  H19  108.00  3.000
 920  H21  C33  N32  108.45  3.000
 920  H20  C33  N32  110.84  3.000
 920  H19  C33  N32  113.35  3.000
 920  C15  O14  C12  118.60  3.000
 920  C16  C15  C20  117.11  3.000
 920  C16  C15  O14  120.76  3.000
 920  C20  C15  O14  122.03  3.000
 920  H22  C20  N19  117.59  3.000
 920  H22  C20  C15  121.03  3.000
 920  N19  C20  C15  121.38  3.000
 920  C18  N19  C20  117.78  3.000
 920  N17  C18  C21  118.30  3.000
 920  C21  C18  N19  117.09  3.000
 920  N17  C18  N19  124.61  3.000
 920  H25  C21  H24  108.57  3.000
 920  H25  C21  H23  107.09  3.000
 920  H24  C21  H23  108.87  3.000
 920  H25  C21  C18  110.42  3.000
 920  H24  C21  C18  111.16  3.000
 920  H23  C21  C18  110.61  3.000
 920  C16  N17  C18  117.72  3.000
 920  H26  C16  N17  117.62  3.000
 920  H26  C16  C15  120.97  3.000
 920  N17  C16  C15  121.40  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
 920  CONST_01  C3   C2   C1   C6     0.00   0.0  0
 920  CONST_02  C3   C4   C5   C6     0.00   0.0  0
 920  CONST_03  C9   C4   C5   C6   180.00   0.0  0
 920  CONST_04  C4   C5   C6   C1     0.00   0.0  0
 920  CONST_05  C4   C3   C2   C1     0.00   0.0  0
 920  CONST_06  N7   C3   C2   C1   180.00   0.0  0
 920  CONST_07  C2   C1   C6   C5     0.00   0.0  0
 920  CONST_08  C2   C3   C4   C5     0.00   0.0  0
 920  CONST_09  N7   C3   C4   C5   180.00   0.0  0
 920  CONST_10  C8   C9   C4   C5   180.00   0.0  0
 920  CONST_11  C10  C9   C4   C5     0.00   0.0  0
 920  CONST_12  C8   N7   C3   C4     0.00   0.0  0
 920  CONST_13  N7   C8   C9   C4     0.00   0.0  0
 920  CONST_14  N13  C8   C9   C4   180.00   0.0  0
 920  CONST_15  N11  C10  C9   C4   180.00   0.0  0
 920  CONST_16  C2   C3   C4   C9   180.00   0.0  0
 920  CONST_17  N7   C3   C4   C9     0.00   0.0  0
 920  CONST_18  C3   N7   C8   C9     0.00   0.0  0
 920  CONST_19  C12  N13  C8   C9     0.00   0.0  0
 920  CONST_20  C12  N11  C10  C9     0.00   0.0  0
 920  CONST_21  C3   C4   C9   C10  180.00   0.0  0
 920  CONST_22  N7   C8   C9   C10  180.00   0.0  0
 920  CONST_23  N13  C8   C9   C10    0.00   0.0  0
 920  CONST_24  N13  C12  N11  C10    0.00   0.0  0
 920  CONST_25  C8   C9   C10  N11    0.00   0.0  0
 920  CONST_26  C8   N13  C12  N11    0.00   0.0  0
 920  CONST_27  N7   C8   N13  C12  180.00   0.0  0
 920  CONST_28  C3   N7   C8   N13  180.00   0.0  0
 920  CONST_29  C2   C3   N7   C8   180.00   0.0  0
 920  CONST_30  C3   C4   C9   C8     0.00   0.0  0
 920  CONST_31  C18  N19  C20  C15    0.00   0.0  0
 920  CONST_32  C18  N17  C16  C15    0.00   0.0  0
 920  CONST_33  N17  C16  C15  C20    0.00   0.0  0
 920  CONST_34  N17  C18  N19  C20    0.00   0.0  0
 920  CONST_35  C16  C15  C20  N19    0.00   0.0  0
 920  CONST_36  C16  N17  C18  N19    0.00   0.0  0
 920  CONST_37  N22  C10  C9   C4     0.00   0.0  0
 920  CONST_38  C8   C9   C10  N22  180.00   0.0  0
 920  CONST_39  C12  N11  C10  N22  180.00   0.0  0
 920  CONST_40  C2   C1   C6   F31  180.00   0.0  0
 920  CONST_41  C4   C5   C6   F31  180.00   0.0  0
 920  CONST_42  N32  C2   C1   C6   180.00   0.0  0
 920  CONST_43  N32  C2   C3   C4   180.00   0.0  0
 920  CONST_44  O14  C12  N11  C10  180.00   0.0  0
 920  CONST_45  O14  C12  N13  C8   180.00   0.0  0
 920  CONST_46  N32  C2   C3   N7     0.00   0.0  0
 920  CONST_47  N19  C20  C15  O14  180.00   0.0  0
 920  CONST_48  N17  C16  C15  O14  180.00   0.0  0
 920  CONST_49  C21  C18  N19  C20  180.00   0.0  0
 920  CONST_50  C16  N17  C18  C21  180.00   0.0  0
 920  CONST_51  H2   C5   C6   C1   180.00   0.0  0
 920  CONST_52  H1   C1   C6   C5   180.00   0.0  0
 920  CONST_53  H17  N7   C3   C4   180.00   0.0  0
 920  CONST_54  H26  C16  C15  C20  180.00   0.0  0
 920  CONST_55  H22  C20  N19  C18  180.00   0.0  0
 920  CONST_56  C33  N32  C2   C1     0.00   0.0  0
 920  CONST_57  C33  N32  C2   C3   180.00   0.0  0
 920  Var_01    C26  N22  C10  C9   -41.07  30.0  2
 920  Var_02    C25  C26  N22  C10  173.05  30.0  1
 920  Var_03    C24  C23  N22  C10  175.14  30.0  1
 920  Var_04    C20  C15  O14  C12   78.54  30.0  2
 920  Var_05    H23  C21  C18  N19   54.80  30.0  2
 920  Var_06    H19  C33  N32  C2   -56.96  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
 920  chir_01  C25  C26  C24  C28  negativ
 920  chir_02  C28  N29  C25  C27  negativ
 920  chir_03  C24  C27  C25  C23  negativ

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
 920  plan-1  O14  0.020
 920  plan-1  C15  0.020
 920  plan-1  C20  0.020
 920  plan-1  N19  0.020
 920  plan-1  C18  0.020
 920  plan-1  C21  0.020
 920  plan-1  N17  0.020
 920  plan-1  C16  0.020
 920  plan-1  H22  0.020
 920  plan-1  H26  0.020
 920  plan-2  F31  0.020
 920  plan-2  C6   0.020
 920  plan-2  C1   0.020
 920  plan-2  C5   0.020
 920  plan-2  C4   0.020
 920  plan-2  C9   0.020
 920  plan-2  C10  0.020
 920  plan-2  N22  0.020
 920  plan-2  N11  0.020
 920  plan-2  C12  0.020
 920  plan-2  N13  0.020
 920  plan-2  C8   0.020
 920  plan-2  N7   0.020
 920  plan-2  C3   0.020
 920  plan-2  C2   0.020
 920  plan-2  N32  0.020
 920  plan-2  O14  0.020
 920  plan-2  H1   0.020
 920  plan-2  H2   0.020
 920  plan-2  H17  0.020
 920  plan-3  C2   0.020
 920  plan-3  N32  0.020
 920  plan-3  C33  0.020
 920  plan-3  H18  0.020

