# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 03:31:03 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: N-[4-(dimethylphosphoryl)phenyl]-9-[(E)-2-(5-methyl-1H-indazol-4-yl)ethenyl]-9H-purin-6-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2[nH]ncc2c1\C=C\n3cnc4c(Nc5ccc(cc5)[P](C)(C)=O)ncnc34
#
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
 B90  B90  N-[4-(dimethylphosphoryl)phenyl]-9-[(E)-2-(5-methyl-1H-indazol-4-yl)ethenyl]-9H-purin-6-amine  ligand  54  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_B90
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
 B90  N1    N  N     0  -0.237   7.8070  -2.6056   0.8820
 B90  C2    C  CR15  0  -0.121   6.6556  -2.1272   0.4793
 B90  C3    C  CR56  0  -0.149   6.7449  -0.7416   0.1727
 B90  C4    C  CR56  0   0.465   8.0901  -0.4234   0.4459
 B90  N5    N  NR15  0  -0.582   8.6694  -1.5829   0.8674
 B90  C6    C  CR6   0   0.000   5.8270   0.2428  -0.2852
 B90  C7    C  CR6   0   0.073   6.3196   1.5300  -0.4792
 B90  C8    C  CR16  0  -0.255   7.6820   1.8067  -0.1919
 B90  C9    C  CR16  0  -0.301   8.5854   0.8738   0.2719
 B90  C10   C  CH3   0  -0.794   5.4767   2.6430  -1.0200
 B90  C14   C  C1    0  -0.372   4.4789  -0.1844  -0.5352
 B90  C15   C  C1    0   0.043   3.3731   0.5116  -0.3434
 B90  N16   N  NR5   0  -0.598   2.1419   0.0443  -0.5819
 B90  C17   C  CR15  0   0.152   1.7309  -1.0774  -1.2468
 B90  N18   N  N     0  -0.486   0.4419  -1.2413  -1.2596
 B90  C19   C  CR56  0  -0.059  -0.0188  -0.1354  -0.5667
 B90  C20   C  CR56  0   0.564   1.0141   0.6733  -0.1532
 B90  C21   C  CR6   0   0.523  -1.2841   0.2933  -0.2158
 B90  N22   N  N     0  -0.544  -1.4191   1.4376   0.4609
 B90  C23   C  CR16  0   0.127  -0.3391   2.1324   0.7922
 B90  N24   N  N     0  -0.513   0.9157   1.8134   0.5397
 B90  N25   N  NH1   0  -0.704  -2.3634  -0.5042  -0.5774
 B90  C26   C  CR6   0   0.299  -3.7289  -0.3645  -0.3402
 B90  C27   C  CR16  0  -0.338  -4.6066  -1.4198  -0.7690
 B90  C28   C  CR16  0  -0.253  -5.9663  -1.3618  -0.5610
 B90  C29   C  CR6   0  -0.171  -6.5215  -0.2726   0.0835
 B90  C30   C  CR16  0  -0.246  -5.6809   0.7508   0.5024
 B90  C31   C  CR16  0  -0.238  -4.3105   0.7236   0.3069
 B90  P36   P  P     0   0.988  -8.3147  -0.3010   0.3245
 B90  C37   C  CH3   0  -0.877  -8.5635  -0.1074   2.1310
 B90  C41   C  CH3   0  -0.851  -8.9207   1.2800  -0.3686
 B90  O45   O  O     0  -0.810  -8.9416  -1.4837  -0.2482
 B90  H2    H  HCR5  0   0.265   5.8001  -2.7814   0.4231
 B90  HN5   H  HNR5  0   0.416   9.6197  -1.7343   1.1495
 B90  H8    H  HCR6  0   0.248   8.0457   2.8182  -0.3613
 B90  H9    H  HCR6  0   0.254   9.6245   1.1359   0.4748
 B90  H10   H  HCH3  0   0.248   4.9192   3.1380  -0.1962
 B90  H10A  H  HCH3  0   0.251   6.0779   3.4110  -1.5181
 B90  H10B  H  HCH3  0   0.256   4.7512   2.3248  -1.7514
 B90  H14   H  H     0   0.286   4.3925  -1.1994  -0.8667
 B90  H15   H  H     0   0.290   3.3427   1.5003   0.0640
 B90  H17   H  HCR5  0   0.320   2.4201  -1.7483  -1.7033
 B90  H23   H  HCR6  0   0.280  -0.5216   3.0415   1.3431
 B90  HN25  H  HNH1  0   0.419  -2.0887  -1.3382  -1.0696
 B90  H27   H  HCR6  0   0.268  -4.1908  -2.2876  -1.2689
 B90  H28   H  HCR6  0   0.282  -6.6138  -2.1632  -0.8937
 B90  H30   H  HCR6  0   0.265  -6.0944   1.6179   1.0044
 B90  H31   H  HCR6  0   0.287  -3.6888   1.5279   0.6493
 B90  H37   H  HCH3  0   0.234  -8.0518   0.7623   2.5445
 B90  H37A  H  HCH3  0   0.268  -9.6264  -0.0079   2.3570
 B90  H37B  H  HCH3  0   0.308  -8.1808  -0.9981   2.6275
 B90  H41   H  HCH3  0   0.307  -8.7536   1.2927  -1.4430
 B90  H41A  H  HCH3  0   0.297  -9.9905   1.3554  -0.1794
 B90  H41B  H  HCH3  0   0.217  -8.4323   2.1517   0.0631

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
 B90  N1   C2    aromatic  1.310  0.020  1.310
 B90  N1   N5    aromatic  1.338  0.020  1.338
 B90  C2   C3    aromatic  1.422  0.020  1.422
 B90  C3   C4    aromatic  1.409  0.020  1.409
 B90  C3   C6    aromatic  1.422  0.020  1.422
 B90  C4   N5    aromatic  1.363  0.020  1.363
 B90  C4   C9    aromatic  1.399  0.020  1.399
 B90  C6   C7    aromatic  1.392  0.020  1.392
 B90  C6   C14   single    1.436  0.020  1.436
 B90  C7   C8    aromatic  1.420  0.020  1.420
 B90  C7   C10   single    1.497  0.020  1.497
 B90  C8   C9    aromatic  1.379  0.020  1.379
 B90  C14  C15   double    1.321  0.020  1.321
 B90  C15  N16   single    1.338  0.020  1.338
 B90  N16  C17   aromatic  1.367  0.020  1.367
 B90  N16  C20   aromatic  1.361  0.020  1.361
 B90  C17  N18   aromatic  1.299  0.020  1.299
 B90  N18  C19   aromatic  1.384  0.020  1.384
 B90  C19  C20   aromatic  1.375  0.020  1.375
 B90  C19  C21   aromatic  1.381  0.020  1.381
 B90  C20  N24   aromatic  1.338  0.020  1.338
 B90  C21  N22   aromatic  1.336  0.020  1.336
 B90  C21  N25   single    1.390  0.020  1.390
 B90  N22  C23   aromatic  1.326  0.020  1.326
 B90  C23  N24   aromatic  1.319  0.020  1.319
 B90  N25  C26   single    1.393  0.020  1.393
 B90  C26  C27   aromatic  1.438  0.020  1.438
 B90  C26  C31   aromatic  1.393  0.020  1.393
 B90  C27  C28   aromatic  1.377  0.020  1.377
 B90  C28  C29   aromatic  1.382  0.020  1.382
 B90  C29  C30   aromatic  1.389  0.020  1.389
 B90  C29  P36   single    1.810  0.020  1.810
 B90  C30  C31   aromatic  1.385  0.020  1.385
 B90  P36  C37   single    1.834  0.020  1.834
 B90  P36  C41   single    1.830  0.020  1.830
 B90  P36  O45   double    1.456  0.020  1.456
 B90  C2   H2    single    0.930  0.020  1.080
 B90  N5   HN5   single    0.860  0.020  1.020
 B90  C8   H8    single    0.930  0.020  1.080
 B90  C9   H9    single    0.930  0.020  1.080
 B90  C10  H10   single    0.970  0.020  1.090
 B90  C10  H10A  single    0.970  0.020  1.090
 B90  C10  H10B  single    0.970  0.020  1.090
 B90  C14  H14   single    0.930  0.020  1.080
 B90  C15  H15   single    0.930  0.020  1.080
 B90  C17  H17   single    0.930  0.020  1.080
 B90  C23  H23   single    0.930  0.020  1.080
 B90  N25  HN25  single    0.860  0.020  1.020
 B90  C27  H27   single    0.930  0.020  1.080
 B90  C28  H28   single    0.930  0.020  1.080
 B90  C30  H30   single    0.930  0.020  1.080
 B90  C31  H31   single    0.930  0.020  1.080
 B90  C37  H37   single    0.970  0.020  1.090
 B90  C37  H37A  single    0.970  0.020  1.090
 B90  C37  H37B  single    0.970  0.020  1.090
 B90  C41  H41   single    0.970  0.020  1.090
 B90  C41  H41A  single    0.970  0.020  1.090
 B90  C41  H41B  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
 B90  N5    N1   C2    106.49  3.000
 B90  H2    C2   C3    129.02  3.000
 B90  H2    C2   N1    119.45  3.000
 B90  C3    C2   N1    111.53  3.000
 B90  C6    C3   C4    121.50  3.000
 B90  C6    C3   C2    134.72  3.000
 B90  C4    C3   C2    103.78  3.000
 B90  C9    C4   N5    132.57  3.000
 B90  C9    C4   C3    121.54  3.000
 B90  N5    C4   C3    105.88  3.000
 B90  HN5   N5   C4    128.19  3.000
 B90  HN5   N5   N1    119.49  3.000
 B90  C4    N5   N1    112.31  3.000
 B90  C14   C6   C7    125.67  3.000
 B90  C14   C6   C3    117.14  3.000
 B90  C7    C6   C3    117.18  3.000
 B90  C10   C7   C8    117.94  3.000
 B90  C10   C7   C6    122.59  3.000
 B90  C8    C7   C6    119.45  3.000
 B90  H8    C8   C9    117.53  3.000
 B90  H8    C8   C7    118.06  3.000
 B90  C9    C8   C7    124.40  3.000
 B90  H9    C9   C8    121.61  3.000
 B90  H9    C9   C4    122.47  3.000
 B90  C8    C9   C4    115.92  3.000
 B90  H10B  C10  H10A  105.54  3.000
 B90  H10B  C10  H10   107.26  3.000
 B90  H10A  C10  H10   107.47  3.000
 B90  H10B  C10  C7    113.86  3.000
 B90  H10A  C10  C7    112.12  3.000
 B90  H10   C10  C7    110.23  3.000
 B90  H14   C14  C15   118.47  3.000
 B90  H14   C14  C6    114.30  3.000
 B90  C15   C14  C6    127.15  3.000
 B90  H15   C15  N16   111.37  3.000
 B90  H15   C15  C14   124.48  3.000
 B90  N16   C15  C14   124.09  3.000
 B90  C20   N16  C17   106.46  3.000
 B90  C20   N16  C15   123.03  3.000
 B90  C17   N16  C15   130.51  3.000
 B90  H17   C17  N18   123.95  3.000
 B90  H17   C17  N16   122.07  3.000
 B90  N18   C17  N16   113.98  3.000
 B90  C19   N18  C17   102.97  3.000
 B90  C21   C19  C20   115.40  3.000
 B90  C21   C19  N18   132.85  3.000
 B90  C20   C19  N18   111.74  3.000
 B90  N24   C20  C19   126.98  3.000
 B90  N24   C20  N16   128.18  3.000
 B90  C19   C20  N16   104.83  3.000
 B90  N25   C21  N22   123.00  3.000
 B90  N25   C21  C19   117.85  3.000
 B90  N22   C21  C19   119.15  3.000
 B90  C23   N22  C21   119.52  3.000
 B90  H23   C23  N24   117.56  3.000
 B90  H23   C23  N22   115.55  3.000
 B90  N24   C23  N22   126.88  3.000
 B90  C23   N24  C20   112.04  3.000
 B90  HN25  N25  C26   115.71  3.000
 B90  HN25  N25  C21   113.00  3.000
 B90  C26   N25  C21   131.25  3.000
 B90  C31   C26  C27   117.18  3.000
 B90  C31   C26  N25   124.52  3.000
 B90  C27   C26  N25   118.29  3.000
 B90  H27   C27  C28   118.82  3.000
 B90  H27   C27  C26   119.39  3.000
 B90  C28   C27  C26   121.79  3.000
 B90  H28   C28  C29   119.11  3.000
 B90  H28   C28  C27   120.86  3.000
 B90  C29   C28  C27   120.03  3.000
 B90  P36   C29  C30   124.82  3.000
 B90  P36   C29  C28   116.61  3.000
 B90  C30   C29  C28   118.57  3.000
 B90  H30   C30  C31   117.30  3.000
 B90  H30   C30  C29   119.89  3.000
 B90  C31   C30  C29   122.81  3.000
 B90  H31   C31  C30   120.92  3.000
 B90  H31   C31  C26   119.47  3.000
 B90  C30   C31  C26   119.61  3.000
 B90  O45   P36  C41   114.23  3.000
 B90  O45   P36  C37   114.51  3.000
 B90  C41   P36  C37   103.71  3.000
 B90  O45   P36  C29   112.77  3.000
 B90  C41   P36  C29   105.32  3.000
 B90  C37   P36  C29   105.31  3.000
 B90  H37B  C37  H37A  108.81  3.000
 B90  H37B  C37  H37   108.33  3.000
 B90  H37A  C37  H37   107.81  3.000
 B90  H37B  C37  P36   108.36  3.000
 B90  H37A  C37  P36   110.23  3.000
 B90  H37   C37  P36   113.21  3.000
 B90  H41B  C41  H41A  108.44  3.000
 B90  H41B  C41  H41   108.28  3.000
 B90  H41A  C41  H41   108.77  3.000
 B90  H41B  C41  P36   113.16  3.000
 B90  H41A  C41  P36   108.62  3.000
 B90  H41   C41  P36   109.48  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
 B90  CONST_01  C4   C3   C2   N1      0.00   0.0  0
 B90  CONST_02  C6   C3   C2   N1    180.00   0.0  0
 B90  CONST_03  C3   C4   N5   N1      0.00   0.0  0
 B90  CONST_04  C9   C4   N5   N1    180.00   0.0  0
 B90  CONST_05  C4   N5   N1   C2      0.00   0.0  0
 B90  CONST_06  N5   C4   C3   C2      0.00   0.0  0
 B90  CONST_07  C9   C4   C3   C2    180.00   0.0  0
 B90  CONST_08  C7   C6   C3   C2    180.00   0.0  0
 B90  CONST_09  N5   N1   C2   C3      0.00   0.0  0
 B90  CONST_10  C8   C9   C4   C3      0.00   0.0  0
 B90  CONST_11  C8   C7   C6   C3      0.00   0.0  0
 B90  CONST_12  C7   C6   C3   C4      0.00   0.0  0
 B90  CONST_13  C7   C8   C9   C4      0.00   0.0  0
 B90  CONST_14  C6   C3   C4   N5    180.00   0.0  0
 B90  CONST_15  C8   C9   C4   N5    180.00   0.0  0
 B90  CONST_16  C9   C4   C3   C6      0.00   0.0  0
 B90  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 B90  CONST_18  C19  N18  C17  N16     0.00   0.0  0
 B90  CONST_19  N18  C19  C20  N16     0.00   0.0  0
 B90  CONST_20  C21  C19  C20  N16   180.00   0.0  0
 B90  CONST_21  C23  N24  C20  N16   180.00   0.0  0
 B90  CONST_22  C19  C20  N16  C17     0.00   0.0  0
 B90  CONST_23  N24  C20  N16  C17   180.00   0.0  0
 B90  CONST_24  C20  C19  N18  C17     0.00   0.0  0
 B90  CONST_25  C21  C19  N18  C17   180.00   0.0  0
 B90  CONST_26  C20  N16  C17  N18     0.00   0.0  0
 B90  CONST_27  N24  C20  C19  N18   180.00   0.0  0
 B90  CONST_28  N22  C21  C19  N18   180.00   0.0  0
 B90  CONST_29  C23  N24  C20  C19     0.00   0.0  0
 B90  CONST_30  C23  N22  C21  C19     0.00   0.0  0
 B90  CONST_31  N22  C21  C19  C20     0.00   0.0  0
 B90  CONST_32  N22  C23  N24  C20     0.00   0.0  0
 B90  CONST_33  N24  C20  C19  C21     0.00   0.0  0
 B90  CONST_34  N24  C23  N22  C21     0.00   0.0  0
 B90  CONST_35  C29  C28  C27  C26     0.00   0.0  0
 B90  CONST_36  C29  C30  C31  C26     0.00   0.0  0
 B90  CONST_37  C30  C31  C26  C27     0.00   0.0  0
 B90  CONST_38  C30  C29  C28  C27     0.00   0.0  0
 B90  CONST_39  C31  C26  C27  C28     0.00   0.0  0
 B90  CONST_40  C31  C30  C29  C28     0.00   0.0  0
 B90  CONST_41  C14  C6   C3   C2      0.00   0.0  0
 B90  CONST_42  C10  C7   C6   C3    180.00   0.0  0
 B90  CONST_43  C14  C6   C3   C4    180.00   0.0  0
 B90  CONST_44  C14  C6   C7   C8    180.00   0.0  0
 B90  CONST_45  C10  C7   C8   C9    180.00   0.0  0
 B90  CONST_46  N18  C17  N16  C15   180.00   0.0  0
 B90  CONST_47  C19  C20  N16  C15   180.00   0.0  0
 B90  CONST_48  N24  C20  N16  C15     0.00   0.0  0
 B90  CONST_49  N25  C21  C19  N18     0.00   0.0  0
 B90  CONST_50  N25  C21  C19  C20   180.00   0.0  0
 B90  CONST_51  N25  C21  N22  C23   180.00   0.0  0
 B90  CONST_52  C28  C27  C26  N25   180.00   0.0  0
 B90  CONST_53  C30  C31  C26  N25   180.00   0.0  0
 B90  CONST_54  P36  C29  C28  C27   180.00   0.0  0
 B90  CONST_55  P36  C29  C30  C31   180.00   0.0  0
 B90  CONST_56  HN5  N5   N1   C2    180.00   0.0  0
 B90  CONST_57  H9   C9   C4   C3    180.00   0.0  0
 B90  CONST_58  H2   C2   C3   C4    180.00   0.0  0
 B90  CONST_59  H8   C8   C9   C4    180.00   0.0  0
 B90  CONST_60  H17  C17  N18  C19   180.00   0.0  0
 B90  CONST_61  H23  C23  N24  C20   180.00   0.0  0
 B90  CONST_62  H28  C28  C27  C26   180.00   0.0  0
 B90  CONST_63  H30  C30  C31  C26   180.00   0.0  0
 B90  CONST_64  H31  C31  C26  C27   180.00   0.0  0
 B90  CONST_65  H27  C27  C28  C29   180.00   0.0  0
 B90  Var_01    C26  N25  C21  C19   178.01  30.0  2
 B90  Var_02    C27  C26  N25  C21  -175.70  30.0  2
 B90  Var_03    N16  C15  C14  C6   -179.08   0.0  2
 B90  Var_04    C15  C14  C6   C3    145.32  30.0  2
 B90  Var_05    C17  N16  C15  C14   -12.18  30.0  2
 B90  Var_06    C37  P36  C29  C28   123.73  30.0  2
 B90  Var_07    H10  C10  C7   C6     86.00  30.0  2
 B90  Var_08    H37  C37  P36  C29    53.20  30.0  3
 B90  Var_09    H41  C41  P36  C29    65.84  30.0  3

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
 B90  plan-1  N25  0.020
 B90  plan-1  C26  0.020
 B90  plan-1  C27  0.020
 B90  plan-1  C28  0.020
 B90  plan-1  C29  0.020
 B90  plan-1  C30  0.020
 B90  plan-1  C31  0.020
 B90  plan-1  P36  0.020
 B90  plan-1  H27  0.020
 B90  plan-1  H28  0.020
 B90  plan-1  H30  0.020
 B90  plan-1  H31  0.020
 B90  plan-2  N1   0.020
 B90  plan-2  C2   0.020
 B90  plan-2  C3   0.020
 B90  plan-2  C4   0.020
 B90  plan-2  N5   0.020
 B90  plan-2  C6   0.020
 B90  plan-2  C7   0.020
 B90  plan-2  C8   0.020
 B90  plan-2  C9   0.020
 B90  plan-2  C10  0.020
 B90  plan-2  C14  0.020
 B90  plan-2  H2   0.020
 B90  plan-2  HN5  0.020
 B90  plan-2  H8   0.020
 B90  plan-2  H9   0.020
 B90  plan-3  C15  0.020
 B90  plan-3  N16  0.020
 B90  plan-3  C17  0.020
 B90  plan-3  N18  0.020
 B90  plan-3  C19  0.020
 B90  plan-3  C20  0.020
 B90  plan-3  C21  0.020
 B90  plan-3  N22  0.020
 B90  plan-3  C23  0.020
 B90  plan-3  N24  0.020
 B90  plan-3  N25  0.020
 B90  plan-3  H17  0.020
 B90  plan-3  H23  0.020
 B90  plan-4  C6   0.020
 B90  plan-4  C14  0.020
 B90  plan-4  C15  0.020
 B90  plan-4  N16  0.020
 B90  plan-4  H14  0.020
 B90  plan-4  H15  0.020

