# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 15:39:32 2020
#   Inital geometry file: a 128 line input string
#   Ligand name: 6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-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]6CCN[C@H]6C5)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
 DOO  DOO  6-fluoro-4-[(3aR,6aR)-hexahydropyrrolo[3,4-b]pyrrol-5(1H)-yl]-N-methyl-2-[(2-methylpyrimidin-5-yl)oxy]-9H-pyrimido[4,5-b]indol-8-amine  ligand  55  32  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DOO
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
 DOO  F30  F  F     0  -0.328  -4.9610  -2.3404  -0.2200
 DOO  C6   C  CR6   0   0.565  -3.6273  -2.3304  -0.0265
 DOO  C1   C  CR16  0  -0.561  -3.0270  -3.5425   0.2962
 DOO  C5   C  CR16  0  -0.610  -2.9543  -1.1436  -0.1752
 DOO  C4   C  CR56  0   0.058  -1.5682  -1.1849   0.0330
 DOO  C7   C  CR56  0  -0.094  -0.5101  -0.2115  -0.0565
 DOO  C13  C  CR6   0   0.471  -0.3620   1.1687  -0.3059
 DOO  N22  N  NT    0  -0.509  -1.3963   2.0367  -0.3479
 DOO  C26  C  CH2   0  -0.309  -2.4699   2.0555   0.6375
 DOO  C25  C  CH1   0  -0.276  -3.5047   2.9563  -0.0200
 DOO  C27  C  CH2   0  -0.458  -4.3754   3.7922   0.9260
 DOO  C28  C  CH2   0  -0.329  -4.0782   5.2419   0.5019
 DOO  N29  N  NH1   0  -0.584  -2.7202   5.2440  -0.0292
 DOO  C24  C  CH1   0  -0.130  -2.6243   3.9940  -0.7719
 DOO  C23  C  CH2   0  -0.293  -1.2117   3.4012  -0.8220
 DOO  N12  N  N     0  -0.501   0.8597   1.6622  -0.5332
 DOO  C11  C  CR6   0   0.561   1.8930   0.8533  -0.4023
 DOO  N10  N  N     0  -0.496   1.9182  -0.4070  -0.0458
 DOO  C8   C  CR56  0   0.496   0.6947  -0.9141   0.1033
 DOO  N9   N  NR15  0  -0.759   0.4286  -2.2070   0.3758
 DOO  C3   C  CR56  0   0.286  -0.9407  -2.4070   0.3231
 DOO  C2   C  CR6   0   0.365  -1.6448  -3.6130   0.4736
 DOO  N31  N  NH1   0  -0.682  -0.9992  -4.7729   0.8094
 DOO  C32  C  CH3   0  -0.554  -1.6867  -6.0406   0.7792
 DOO  O14  O  O2    0  -0.491   3.0692   1.4668  -0.6632
 DOO  C15  C  CR6   0   0.238   4.2226   0.7439  -0.5445
 DOO  C20  C  CR16  0  -0.063   4.8725   0.2624  -1.6636
 DOO  N19  N  N     0  -0.398   6.0223  -0.3894  -1.5679
 DOO  C18  C  CR6   0   0.352   6.5301  -0.5711  -0.3534
 DOO  C21  C  CH3   0  -0.711   7.8377  -1.2869  -0.2446
 DOO  N17  N  N     0  -0.399   5.9690  -0.1381   0.7738
 DOO  C16  C  CR16  0  -0.052   4.8231   0.5153   0.6804
 DOO  H1   H  HCR6  0   0.287  -3.6466  -4.4243   0.3839
 DOO  H2   H  HCR6  0   0.265  -3.4774  -0.2515  -0.4876
 DOO  H3   H  HCH2  0   0.270  -2.8341   1.0635   0.8880
 DOO  H4   H  HCH2  0   0.247  -2.1023   2.5077   1.5694
 DOO  H5   H  HCH1  0   0.261  -4.1065   2.3723  -0.7200
 DOO  H6   H  HCH2  0   0.241  -5.4347   3.5464   0.8521
 DOO  H7   H  HCH2  0   0.232  -4.0797   3.6355   1.9663
 DOO  H8   H  HCH2  0   0.226  -4.7693   5.5485  -0.2886
 DOO  H9   H  HCH2  0   0.242  -4.1741   5.9612   1.3152
 DOO  H10  H  HNH1  0   0.339  -2.0735   5.2172   0.7529
 DOO  H12  H  HCH1  0   0.259  -3.0091   4.1591  -1.7814
 DOO  H13  H  HCH2  0   0.236  -0.5285   3.9615  -0.1721
 DOO  H14  H  HCH2  0   0.262  -0.7830   3.4006  -1.8227
 DOO  H15  H  HNR5  0   0.410   1.1397  -2.9039   0.5237
 DOO  H16  H  HNH1  0   0.377  -0.0282  -4.8297   0.5521
 DOO  H17  H  HCH3  0   0.231  -2.1149  -6.2791  -0.2003
 DOO  H18  H  HCH3  0   0.268  -0.9783  -6.8223   1.0409
 DOO  H19  H  HCH3  0   0.249  -2.4922  -6.0637   1.5142
 DOO  H20  H  HCR6  0   0.274   4.4585   0.4114  -2.6557
 DOO  H21  H  HCH3  0   0.255   8.6617  -0.5715  -0.2925
 DOO  H22  H  HCH3  0   0.247   7.9161  -1.8139   0.7039
 DOO  H23  H  HCH3  0   0.247   7.9674  -1.9924  -1.0625
 DOO  H24  H  HCR6  0   0.272   4.3709   0.8705   1.6008

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
 DOO  C32  N31  single    1.442  0.020  1.442
 DOO  F30  C6   single    1.348  0.020  1.348
 DOO  C1   C6   aromatic  1.391  0.020  1.391
 DOO  C1   C2   aromatic  1.395  0.020  1.395
 DOO  N31  C2   single    1.369  0.020  1.369
 DOO  C6   C5   aromatic  1.372  0.020  1.372
 DOO  C2   C3   aromatic  1.405  0.020  1.405
 DOO  C5   C4   aromatic  1.402  0.020  1.402
 DOO  C3   C4   aromatic  1.404  0.020  1.404
 DOO  C3   N9   aromatic  1.385  0.020  1.385
 DOO  C4   C7   aromatic  1.441  0.020  1.441
 DOO  N9   C8   aromatic  1.348  0.020  1.348
 DOO  C7   C8   aromatic  1.404  0.020  1.404
 DOO  C7   C13  aromatic  1.410  0.020  1.410
 DOO  C8   N10  aromatic  1.333  0.020  1.333
 DOO  C23  N22  single    1.456  0.020  1.456
 DOO  C23  C24  single    1.533  0.020  1.533
 DOO  C13  N22  single    1.351  0.020  1.351
 DOO  C13  N12  aromatic  1.337  0.020  1.337
 DOO  N22  C26  single    1.457  0.020  1.457
 DOO  N10  C11  aromatic  1.310  0.020  1.310
 DOO  C26  C25  single    1.521  0.020  1.521
 DOO  N12  C11  aromatic  1.319  0.020  1.319
 DOO  C11  O14  single    1.352  0.020  1.352
 DOO  C24  C25  single    1.555  0.020  1.555
 DOO  C24  N29  single    1.457  0.020  1.457
 DOO  C25  C27  single    1.534  0.020  1.534
 DOO  O14  C15  single    1.366  0.020  1.366
 DOO  N29  C28  single    1.458  0.020  1.458
 DOO  C20  C15  aromatic  1.381  0.020  1.381
 DOO  C20  N19  aromatic  1.325  0.020  1.325
 DOO  C15  C16  aromatic  1.383  0.020  1.383
 DOO  C27  C28  single    1.540  0.020  1.540
 DOO  N19  C18  aromatic  1.329  0.020  1.329
 DOO  C16  N17  aromatic  1.322  0.020  1.322
 DOO  C18  N17  aromatic  1.331  0.020  1.331
 DOO  C18  C21  single    1.495  0.020  1.495
 DOO  C1   H1   single    0.930  0.020  1.080
 DOO  C5   H2   single    0.930  0.020  1.080
 DOO  C26  H3   single    0.970  0.020  1.090
 DOO  C26  H4   single    0.970  0.020  1.090
 DOO  C25  H5   single    0.970  0.020  1.090
 DOO  C27  H6   single    0.970  0.020  1.090
 DOO  C27  H7   single    0.970  0.020  1.090
 DOO  C28  H8   single    0.970  0.020  1.090
 DOO  C28  H9   single    0.970  0.020  1.090
 DOO  N29  H10  single    0.890  0.020  1.040
 DOO  C24  H12  single    0.970  0.020  1.090
 DOO  C23  H13  single    0.970  0.020  1.090
 DOO  C23  H14  single    0.970  0.020  1.090
 DOO  N9   H15  single    0.860  0.020  1.020
 DOO  N31  H16  single    0.890  0.020  1.040
 DOO  C32  H17  single    0.970  0.020  1.090
 DOO  C32  H18  single    0.970  0.020  1.090
 DOO  C32  H19  single    0.970  0.020  1.090
 DOO  C20  H20  single    0.930  0.020  1.080
 DOO  C21  H21  single    0.970  0.020  1.090
 DOO  C21  H22  single    0.970  0.020  1.090
 DOO  C21  H23  single    0.970  0.020  1.090
 DOO  C16  H24  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
 DOO  C5   C6   C1   124.55  3.000
 DOO  C5   C6   F30  118.44  3.000
 DOO  C1   C6   F30  117.00  3.000
 DOO  H1   C1   C2   121.07  3.000
 DOO  H1   C1   C6   118.84  3.000
 DOO  C2   C1   C6   120.08  3.000
 DOO  H2   C5   C4   123.09  3.000
 DOO  H2   C5   C6   120.53  3.000
 DOO  C4   C5   C6   116.31  3.000
 DOO  C3   C4   C7   105.83  3.000
 DOO  C7   C4   C5   134.18  3.000
 DOO  C3   C4   C5   119.87  3.000
 DOO  C8   C7   C13  114.82  3.000
 DOO  C13  C7   C4   138.54  3.000
 DOO  C8   C7   C4   106.57  3.000
 DOO  N12  C13  N22  117.20  3.000
 DOO  N12  C13  C7   119.16  3.000
 DOO  N22  C13  C7   123.63  3.000
 DOO  C23  N22  C26  107.55  3.000
 DOO  C26  N22  C13  123.45  3.000
 DOO  C23  N22  C13  121.00  3.000
 DOO  H4   C26  H3   107.00  3.000
 DOO  H4   C26  C25  110.51  3.000
 DOO  H3   C26  C25  114.35  3.000
 DOO  H4   C26  N22  109.40  3.000
 DOO  H3   C26  N22  113.03  3.000
 DOO  C25  C26  N22  102.50  3.000
 DOO  H5   C25  C24  111.03  3.000
 DOO  H5   C25  C27  111.96  3.000
 DOO  C24  C25  C27  104.83  3.000
 DOO  H5   C25  C26  109.58  3.000
 DOO  C27  C25  C26  116.25  3.000
 DOO  C24  C25  C26  102.65  3.000
 DOO  H7   C27  H6   107.17  3.000
 DOO  H7   C27  C28  110.18  3.000
 DOO  H6   C27  C28  112.41  3.000
 DOO  H7   C27  C25  110.82  3.000
 DOO  H6   C27  C25  112.77  3.000
 DOO  C28  C27  C25  103.52  3.000
 DOO  H9   C28  H8   107.38  3.000
 DOO  H9   C28  N29  110.66  3.000
 DOO  H8   C28  N29  108.95  3.000
 DOO  H9   C28  C27  113.51  3.000
 DOO  H8   C28  C27  109.94  3.000
 DOO  N29  C28  C27  106.35  3.000
 DOO  H10  N29  C24  109.15  3.000
 DOO  H10  N29  C28  108.22  3.000
 DOO  C24  N29  C28  104.22  3.000
 DOO  H12  C24  C23  110.65  3.000
 DOO  H12  C24  N29  108.54  3.000
 DOO  C23  C24  N29  114.15  3.000
 DOO  H12  C24  C25  110.37  3.000
 DOO  N29  C24  C25  106.79  3.000
 DOO  C23  C24  C25  106.23  3.000
 DOO  H14  C23  H13  107.44  3.000
 DOO  H14  C23  C24  113.15  3.000
 DOO  H13  C23  C24  110.92  3.000
 DOO  H14  C23  N22  110.41  3.000
 DOO  H13  C23  N22  111.39  3.000
 DOO  C24  C23  N22  103.59  3.000
 DOO  C11  N12  C13  118.21  3.000
 DOO  O14  C11  N10  118.18  3.000
 DOO  O14  C11  N12  112.59  3.000
 DOO  N10  C11  N12  129.22  3.000
 DOO  C8   N10  C11  112.26  3.000
 DOO  N9   C8   N10  124.67  3.000
 DOO  N10  C8   C7   125.79  3.000
 DOO  N9   C8   C7   109.49  3.000
 DOO  H15  N9   C3   127.17  3.000
 DOO  H15  N9   C8   123.67  3.000
 DOO  C3   N9   C8   109.03  3.000
 DOO  C2   C3   N9   127.99  3.000
 DOO  N9   C3   C4   108.91  3.000
 DOO  C2   C3   C4   123.06  3.000
 DOO  N31  C2   C3   121.15  3.000
 DOO  C3   C2   C1   116.07  3.000
 DOO  N31  C2   C1   122.75  3.000
 DOO  H16  N31  C32  113.89  3.000
 DOO  H16  N31  C2   116.11  3.000
 DOO  C32  N31  C2   120.97  3.000
 DOO  H19  C32  H18  107.69  3.000
 DOO  H19  C32  H17  108.01  3.000
 DOO  H18  C32  H17  108.28  3.000
 DOO  H19  C32  N31  110.89  3.000
 DOO  H18  C32  N31  108.45  3.000
 DOO  H17  C32  N31  113.35  3.000
 DOO  C15  O14  C11  118.52  3.000
 DOO  C16  C15  C20  117.12  3.000
 DOO  C16  C15  O14  122.06  3.000
 DOO  C20  C15  O14  120.76  3.000
 DOO  H20  C20  N19  117.68  3.000
 DOO  H20  C20  C15  120.90  3.000
 DOO  N19  C20  C15  121.42  3.000
 DOO  C18  N19  C20  117.70  3.000
 DOO  N17  C18  C21  117.57  3.000
 DOO  C21  C18  N19  117.79  3.000
 DOO  N17  C18  N19  124.63  3.000
 DOO  H23  C21  H22  109.44  3.000
 DOO  H23  C21  H21  107.57  3.000
 DOO  H22  C21  H21  107.53  3.000
 DOO  H23  C21  C18  111.11  3.000
 DOO  H22  C21  C18  111.00  3.000
 DOO  H21  C21  C18  110.07  3.000
 DOO  C16  N17  C18  117.78  3.000
 DOO  H24  C16  N17  117.58  3.000
 DOO  H24  C16  C15  121.07  3.000
 DOO  N17  C16  C15  121.36  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
 DOO  CONST_01  C3   C2   C1   C6      0.00   0.0  0
 DOO  CONST_02  C3   C4   C5   C6      0.00   0.0  0
 DOO  CONST_03  C7   C4   C5   C6    180.00   0.0  0
 DOO  CONST_04  C4   C5   C6   C1      0.00   0.0  0
 DOO  CONST_05  C4   C3   C2   C1      0.00   0.0  0
 DOO  CONST_06  N9   C3   C2   C1    180.00   0.0  0
 DOO  CONST_07  C2   C1   C6   C5      0.00   0.0  0
 DOO  CONST_08  C2   C3   C4   C5      0.00   0.0  0
 DOO  CONST_09  N9   C3   C4   C5    180.00   0.0  0
 DOO  CONST_10  C8   C7   C4   C5    180.00   0.0  0
 DOO  CONST_11  C13  C7   C4   C5      0.00   0.0  0
 DOO  CONST_12  C8   N9   C3   C4      0.00   0.0  0
 DOO  CONST_13  N9   C8   C7   C4      0.00   0.0  0
 DOO  CONST_14  N10  C8   C7   C4    180.00   0.0  0
 DOO  CONST_15  N12  C13  C7   C4    180.00   0.0  0
 DOO  CONST_16  C2   C3   C4   C7    180.00   0.0  0
 DOO  CONST_17  N9   C3   C4   C7      0.00   0.0  0
 DOO  CONST_18  C3   N9   C8   C7      0.00   0.0  0
 DOO  CONST_19  C11  N10  C8   C7      0.00   0.0  0
 DOO  CONST_20  C11  N12  C13  C7      0.00   0.0  0
 DOO  CONST_21  C3   C4   C7   C13   180.00   0.0  0
 DOO  CONST_22  N9   C8   C7   C13   180.00   0.0  0
 DOO  CONST_23  N10  C8   C7   C13     0.00   0.0  0
 DOO  CONST_24  N10  C11  N12  C13     0.00   0.0  0
 DOO  CONST_25  C8   C7   C13  N12     0.00   0.0  0
 DOO  CONST_26  C8   N10  C11  N12     0.00   0.0  0
 DOO  CONST_27  N9   C8   N10  C11   180.00   0.0  0
 DOO  CONST_28  C3   N9   C8   N10   180.00   0.0  0
 DOO  CONST_29  C2   C3   N9   C8    180.00   0.0  0
 DOO  CONST_30  C3   C4   C7   C8      0.00   0.0  0
 DOO  CONST_31  C18  N19  C20  C15     0.00   0.0  0
 DOO  CONST_32  C18  N17  C16  C15     0.00   0.0  0
 DOO  CONST_33  N17  C16  C15  C20     0.00   0.0  0
 DOO  CONST_34  N17  C18  N19  C20     0.00   0.0  0
 DOO  CONST_35  C16  C15  C20  N19     0.00   0.0  0
 DOO  CONST_36  C16  N17  C18  N19     0.00   0.0  0
 DOO  CONST_37  N22  C13  C7   C4      0.00   0.0  0
 DOO  CONST_38  C8   C7   C13  N22   180.00   0.0  0
 DOO  CONST_39  C11  N12  C13  N22   180.00   0.0  0
 DOO  CONST_40  C2   C1   C6   F30   180.00   0.0  0
 DOO  CONST_41  C4   C5   C6   F30   180.00   0.0  0
 DOO  CONST_42  N31  C2   C1   C6    180.00   0.0  0
 DOO  CONST_43  N31  C2   C3   C4    180.00   0.0  0
 DOO  CONST_44  O14  C11  N12  C13   180.00   0.0  0
 DOO  CONST_45  O14  C11  N10  C8    180.00   0.0  0
 DOO  CONST_46  N31  C2   C3   N9      0.00   0.0  0
 DOO  CONST_47  N19  C20  C15  O14   180.00   0.0  0
 DOO  CONST_48  N17  C16  C15  O14   180.00   0.0  0
 DOO  CONST_49  C21  C18  N19  C20   180.00   0.0  0
 DOO  CONST_50  C16  N17  C18  C21   180.00   0.0  0
 DOO  CONST_51  H2   C5   C6   C1    180.00   0.0  0
 DOO  CONST_52  H1   C1   C6   C5    180.00   0.0  0
 DOO  CONST_53  H15  N9   C3   C4    180.00   0.0  0
 DOO  CONST_54  H24  C16  C15  C20   180.00   0.0  0
 DOO  CONST_55  H20  C20  N19  C18   180.00   0.0  0
 DOO  CONST_56  C32  N31  C2   C1      0.00   0.0  0
 DOO  CONST_57  C32  N31  C2   C3    180.00   0.0  0
 DOO  Var_01    C23  N22  C13  C7   -169.87  30.0  2
 DOO  Var_02    C24  C23  N22  C13   177.12  30.0  1
 DOO  Var_03    C25  C26  N22  C13  -167.52  30.0  1
 DOO  Var_04    N29  C28  C27  C25   -28.69  30.0  1
 DOO  Var_05    C24  N29  C28  C27    38.90  30.0  1
 DOO  Var_06    C20  C15  O14  C11   102.50  30.0  2
 DOO  Var_07    H21  C21  C18  N19    89.90  30.0  2
 DOO  Var_08    H17  C32  N31  C2     57.48  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
 DOO  chir_01  C25  C26  C24  C27  positiv
 DOO  chir_02  C24  N29  C23  C25  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
 DOO  plan-1  O14  0.020
 DOO  plan-1  C15  0.020
 DOO  plan-1  C20  0.020
 DOO  plan-1  N19  0.020
 DOO  plan-1  C18  0.020
 DOO  plan-1  C21  0.020
 DOO  plan-1  N17  0.020
 DOO  plan-1  C16  0.020
 DOO  plan-1  H20  0.020
 DOO  plan-1  H24  0.020
 DOO  plan-2  F30  0.020
 DOO  plan-2  C6   0.020
 DOO  plan-2  C1   0.020
 DOO  plan-2  C5   0.020
 DOO  plan-2  C4   0.020
 DOO  plan-2  C7   0.020
 DOO  plan-2  C13  0.020
 DOO  plan-2  N22  0.020
 DOO  plan-2  N12  0.020
 DOO  plan-2  C11  0.020
 DOO  plan-2  N10  0.020
 DOO  plan-2  C8   0.020
 DOO  plan-2  N9   0.020
 DOO  plan-2  C3   0.020
 DOO  plan-2  C2   0.020
 DOO  plan-2  N31  0.020
 DOO  plan-2  O14  0.020
 DOO  plan-2  H1   0.020
 DOO  plan-2  H2   0.020
 DOO  plan-2  H15  0.020
 DOO  plan-3  C2   0.020
 DOO  plan-3  N31  0.020
 DOO  plan-3  C32  0.020
 DOO  plan-3  H16  0.020

