# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 19:51:37 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 9-cyclopentyl-N~8~-(2-fluorophenyl)-N~2~-(4-methoxyphenyl)-9H-purine-2,8-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(Nc2ncc3nc(Nc4ccccc4F)n(C5CCCC5)c3n2)cc1
#
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
 JBI  JBI  9-cyclopentyl-N~8~-(2-fluorophenyl)-N~2~-(4-methoxyphenyl)-9H-purine-2,8-diamine  ligand  54  31  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_JBI
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
 JBI  C1    C  CR56  0   0.504  -0.1457  -0.2229   0.1419
 JBI  F1    F  F     0  -0.321  -6.1173  -0.3327  -0.3694
 JBI  N1    N  N     0  -0.469   2.1212   1.1519   0.1685
 JBI  O1    O  O2    0  -0.474   8.5392   0.7399   0.0027
 JBI  C2    C  CR56  0   0.087  -0.2306   1.1749   0.1101
 JBI  N2    N  N     0  -0.497   0.9581  -0.9284   0.1824
 JBI  C3    C  CR16  0  -0.075   0.9776   1.8349   0.1286
 JBI  N3    N  NR5   0  -0.597  -1.4319  -0.6788   0.1197
 JBI  C4    C  CR6   0   0.575   2.0695  -0.1776   0.1917
 JBI  N4    N  N     0  -0.531  -1.5468   1.5716   0.0619
 JBI  C5    C  CR5   0   0.733  -2.2220   0.4581   0.0647
 JBI  N5    N  NH1   0  -0.765   3.2315  -0.8927   0.2231
 JBI  C6    C  CH1   0  -0.123  -1.8115  -2.0821   0.1600
 JBI  N6    N  NH1   0  -0.821  -3.5727   0.3374   0.0202
 JBI  C7    C  CR6   0   0.333   4.5509  -0.4385   0.1522
 JBI  C8    C  CR6   0   0.212  -4.5236   1.3516   0.0030
 JBI  C9    C  CH2   0  -0.489  -2.7777  -2.4699   1.3109
 JBI  C10   C  CH2   0  -0.465  -3.9031  -3.2751   0.6466
 JBI  C11   C  CH2   0  -0.445  -3.2876  -3.7884  -0.6556
 JBI  C12   C  CH2   0  -0.463  -2.4486  -2.6096  -1.1351
 JBI  C13   C  CR6   0   0.455  -5.8552   0.9793  -0.1933
 JBI  C14   C  CR16  0  -0.400  -6.8929   1.8798  -0.2128
 JBI  C15   C  CR16  0  -0.262  -6.6134   3.2296  -0.0346
 JBI  C16   C  CR16  0  -0.257  -5.3019   3.6314   0.1599
 JBI  C17   C  CR16  0  -0.306  -4.2621   2.7100   0.1812
 JBI  C18   C  CR16  0  -0.277   4.9935   0.7582   0.7230
 JBI  C19   C  CR16  0  -0.340   6.3261   1.1193   0.6483
 JBI  C20   C  CR6   0   0.363   7.2628   0.2989   0.0196
 JBI  C21   C  CR16  0  -0.373   6.8329  -0.9014  -0.5364
 JBI  C22   C  CR16  0  -0.327   5.4911  -1.2534  -0.4719
 JBI  C23   C  CH3   0  -0.435   9.5097  -0.0503  -0.6508
 JBI  H3    H  HCR6  0   0.268   1.0486   2.9172   0.1089
 JBI  HN5   H  HNH1  0   0.401   3.1010  -1.8847   0.1008
 JBI  H6    H  HCH1  0   0.294  -0.8693  -2.6068   0.3124
 JBI  HN6   H  HNH1  0   0.421  -3.9395  -0.5959  -0.0590
 JBI  H9    H  HCH2  0   0.268  -2.2396  -3.0848   2.0315
 JBI  H9A   H  HCH2  0   0.256  -3.1451  -1.6051   1.8648
 JBI  H10   H  HCH2  0   0.255  -4.2754  -4.0753   1.2859
 JBI  H10A  H  HCH2  0   0.220  -4.7635  -2.6378   0.4215
 JBI  H11   H  HCH2  0   0.233  -2.6444  -4.6488  -0.4528
 JBI  H11A  H  HCH2  0   0.247  -4.0337  -4.1007  -1.3862
 JBI  H12   H  HCH2  0   0.230  -3.0905  -1.8589  -1.6058
 JBI  H12A  H  HCH2  0   0.263  -1.6922  -2.8753  -1.8732
 JBI  H14   H  HCR6  0   0.284  -7.9039   1.5276  -0.3698
 JBI  H15   H  HCR6  0   0.267  -7.4170   3.9525  -0.0491
 JBI  H16   H  HCR6  0   0.263  -5.0719   4.6792   0.2992
 JBI  H17   H  HCR6  0   0.298  -3.2477   3.0417   0.3326
 JBI  H18   H  HCR6  0   0.267   4.2999   1.4136   1.2261
 JBI  H19   H  HCR6  0   0.261   6.6508   2.0516   1.0938
 JBI  H21   H  HCR6  0   0.278   7.5178  -1.5737  -1.0354
 JBI  H22   H  HCR6  0   0.267   5.1770  -2.1882  -0.9211
 JBI  H23   H  HCH3  0   0.258  10.4546   0.4806  -0.5621
 JBI  H23A  H  HCH3  0   0.225   9.6168  -1.0358  -0.1891
 JBI  H23B  H  HCH3  0   0.226   9.2814  -0.1840  -1.7119

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
 JBI  N2   C1    aromatic  1.311  0.020  1.311
 JBI  C1   N3    aromatic  1.365  0.020  1.365
 JBI  C1   C2    aromatic  1.401  0.020  1.401
 JBI  C13  F1    single    1.349  0.020  1.349
 JBI  C4   N1    aromatic  1.331  0.020  1.331
 JBI  N1   C3    aromatic  1.333  0.020  1.333
 JBI  O1   C20   single    1.350  0.020  1.350
 JBI  O1   C23   single    1.412  0.020  1.412
 JBI  C2   C3    aromatic  1.377  0.020  1.377
 JBI  C2   N4    aromatic  1.376  0.020  1.376
 JBI  N2   C4    aromatic  1.341  0.020  1.341
 JBI  C3   H3    single    0.930  0.020  1.080
 JBI  C6   N3    single    1.454  0.020  1.454
 JBI  N3   C5    aromatic  1.386  0.020  1.386
 JBI  N5   C4    single    1.365  0.020  1.365
 JBI  C5   N4    aromatic  1.302  0.020  1.302
 JBI  C5   N6    single    1.357  0.020  1.357
 JBI  C7   N5    single    1.397  0.020  1.397
 JBI  N5   HN5   single    0.860  0.020  1.020
 JBI  C12  C6    single    1.537  0.020  1.537
 JBI  C6   C9    single    1.552  0.020  1.552
 JBI  C6   H6    single    0.970  0.020  1.090
 JBI  N6   C8    single    1.390  0.020  1.390
 JBI  N6   HN6   single    0.860  0.020  1.020
 JBI  C18  C7    aromatic  1.398  0.020  1.398
 JBI  C7   C22   aromatic  1.392  0.020  1.392
 JBI  C17  C8    aromatic  1.395  0.020  1.395
 JBI  C8   C13   aromatic  1.397  0.020  1.397
 JBI  C10  C9    single    1.535  0.020  1.535
 JBI  C9   H9    single    0.970  0.020  1.090
 JBI  C9   H9A   single    0.970  0.020  1.090
 JBI  C11  C10   single    1.529  0.020  1.529
 JBI  C10  H10   single    0.970  0.020  1.090
 JBI  C10  H10A  single    0.970  0.020  1.090
 JBI  C11  C12   single    1.524  0.020  1.524
 JBI  C11  H11   single    0.970  0.020  1.090
 JBI  C11  H11A  single    0.970  0.020  1.090
 JBI  C12  H12   single    0.970  0.020  1.090
 JBI  C12  H12A  single    0.970  0.020  1.090
 JBI  C13  C14   aromatic  1.374  0.020  1.374
 JBI  C15  C14   aromatic  1.390  0.020  1.390
 JBI  C14  H14   single    0.930  0.020  1.080
 JBI  C16  C15   aromatic  1.385  0.020  1.385
 JBI  C15  H15   single    0.930  0.020  1.080
 JBI  C17  C16   aromatic  1.389  0.020  1.389
 JBI  C16  H16   single    0.930  0.020  1.080
 JBI  C17  H17   single    0.930  0.020  1.080
 JBI  C19  C18   aromatic  1.383  0.020  1.383
 JBI  C18  H18   single    0.930  0.020  1.080
 JBI  C19  C20   aromatic  1.395  0.020  1.395
 JBI  C19  H19   single    0.930  0.020  1.080
 JBI  C20  C21   aromatic  1.391  0.020  1.391
 JBI  C21  C22   aromatic  1.389  0.020  1.389
 JBI  C21  H21   single    0.930  0.020  1.080
 JBI  C22  H22   single    0.930  0.020  1.080
 JBI  C23  H23   single    0.970  0.020  1.090
 JBI  C23  H23A  single    0.970  0.020  1.090
 JBI  C23  H23B  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
 JBI  N3    C1   N2    127.91  3.000
 JBI  N3    C1   C2    106.01  3.000
 JBI  N2    C1   C2    126.08  3.000
 JBI  C4    N1   C3    118.63  3.000
 JBI  C23   O1   C20   118.21  3.000
 JBI  N4    C2   C3    134.58  3.000
 JBI  N4    C2   C1    110.28  3.000
 JBI  C3    C2   C1    115.14  3.000
 JBI  C4    N2   C1    113.37  3.000
 JBI  H3    C3   C2    122.37  3.000
 JBI  H3    C3   N1    117.11  3.000
 JBI  C2    C3   N1    120.52  3.000
 JBI  C6    N3   C5    130.09  3.000
 JBI  C5    N3   C1    105.30  3.000
 JBI  C6    N3   C1    124.60  3.000
 JBI  N5    C4   N2    114.35  3.000
 JBI  N5    C4   N1    119.39  3.000
 JBI  N2    C4   N1    126.26  3.000
 JBI  C5    N4   C2    104.45  3.000
 JBI  N6    C5   N4    126.31  3.000
 JBI  N6    C5   N3    119.73  3.000
 JBI  N4    C5   N3    113.96  3.000
 JBI  HN5   N5   C7    115.85  3.000
 JBI  HN5   N5   C4    113.74  3.000
 JBI  C7    N5   C4    129.24  3.000
 JBI  H6    C6   C12   108.13  3.000
 JBI  H6    C6   C9    108.32  3.000
 JBI  C12   C6   C9    106.33  3.000
 JBI  H6    C6   N3    104.06  3.000
 JBI  C9    C6   N3    115.10  3.000
 JBI  C12   C6   N3    114.59  3.000
 JBI  HN6   N6   C8    115.24  3.000
 JBI  HN6   N6   C5    116.62  3.000
 JBI  C8    N6   C5    128.05  3.000
 JBI  C22   C7   C18   118.07  3.000
 JBI  C22   C7   N5    118.05  3.000
 JBI  C18   C7   N5    123.82  3.000
 JBI  C17   C8   C13   117.16  3.000
 JBI  C13   C8   N6    117.35  3.000
 JBI  C17   C8   N6    125.49  3.000
 JBI  H9A   C9   H9    106.14  3.000
 JBI  H9A   C9   C10   112.87  3.000
 JBI  H9    C9   C10   110.63  3.000
 JBI  H9A   C9   C6    112.84  3.000
 JBI  H9    C9   C6    108.91  3.000
 JBI  C10   C9   C6    105.46  3.000
 JBI  H10A  C10  H10   106.24  3.000
 JBI  H10A  C10  C11   109.69  3.000
 JBI  H10   C10  C11   112.99  3.000
 JBI  H10A  C10  C9    111.10  3.000
 JBI  H10   C10  C9    112.44  3.000
 JBI  C11   C10  C9    104.45  3.000
 JBI  H11A  C11  H11   107.55  3.000
 JBI  H11A  C11  C12   112.80  3.000
 JBI  H11   C11  C12   110.07  3.000
 JBI  H11A  C11  C10   113.05  3.000
 JBI  H11   C11  C10   110.06  3.000
 JBI  C12   C11  C10   103.29  3.000
 JBI  H12A  C12  H12   106.44  3.000
 JBI  H12A  C12  C11   113.99  3.000
 JBI  H12   C12  C11   110.06  3.000
 JBI  H12A  C12  C6    111.52  3.000
 JBI  H12   C12  C6    111.73  3.000
 JBI  C11   C12  C6    103.21  3.000
 JBI  C14   C13  C8    123.18  3.000
 JBI  C14   C13  F1    119.25  3.000
 JBI  C8    C13  F1    117.56  3.000
 JBI  H14   C14  C15   121.50  3.000
 JBI  H14   C14  C13   119.63  3.000
 JBI  C15   C14  C13   118.87  3.000
 JBI  H15   C15  C16   120.78  3.000
 JBI  H15   C15  C14   119.88  3.000
 JBI  C16   C15  C14   119.34  3.000
 JBI  H16   C16  C17   118.76  3.000
 JBI  H16   C16  C15   120.02  3.000
 JBI  C17   C16  C15   121.22  3.000
 JBI  H17   C17  C16   120.16  3.000
 JBI  H17   C17  C8    119.61  3.000
 JBI  C16   C17  C8    120.23  3.000
 JBI  H18   C18  C19   119.09  3.000
 JBI  H18   C18  C7    120.47  3.000
 JBI  C19   C18  C7    120.44  3.000
 JBI  H19   C19  C20   119.36  3.000
 JBI  H19   C19  C18   119.44  3.000
 JBI  C20   C19  C18   121.20  3.000
 JBI  C21   C20  C19   118.69  3.000
 JBI  C21   C20  O1    124.68  3.000
 JBI  C19   C20  O1    116.63  3.000
 JBI  H21   C21  C22   118.40  3.000
 JBI  H21   C21  C20   121.67  3.000
 JBI  C22   C21  C20   119.93  3.000
 JBI  H22   C22  C21   118.65  3.000
 JBI  H22   C22  C7    119.68  3.000
 JBI  C21   C22  C7    121.67  3.000
 JBI  H23B  C23  H23A  108.66  3.000
 JBI  H23B  C23  H23   108.68  3.000
 JBI  H23A  C23  H23   108.69  3.000
 JBI  H23B  C23  O1    111.97  3.000
 JBI  H23A  C23  O1    112.10  3.000
 JBI  H23   C23  O1    106.63  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
 JBI  CONST_01  N1   C4   N2   C1     0.00   0.0  0
 JBI  CONST_02  N4   C5   N3   C1     0.00   0.0  0
 JBI  CONST_03  N1   C3   C2   C1     0.00   0.0  0
 JBI  CONST_04  C5   N4   C2   C1     0.00   0.0  0
 JBI  CONST_05  N4   C2   C3   N1   180.00   0.0  0
 JBI  CONST_06  C4   N2   C1   C2     0.00   0.0  0
 JBI  CONST_07  C5   N3   C1   C2     0.00   0.0  0
 JBI  CONST_08  C4   N1   C3   C2     0.00   0.0  0
 JBI  CONST_09  N3   C5   N4   C2     0.00   0.0  0
 JBI  CONST_10  C5   N3   C1   N2   180.00   0.0  0
 JBI  CONST_11  C3   C2   C1   N2     0.00   0.0  0
 JBI  CONST_12  N4   C2   C1   N2   180.00   0.0  0
 JBI  CONST_13  C3   N1   C4   N2     0.00   0.0  0
 JBI  CONST_14  N3   C1   C2   C3   180.00   0.0  0
 JBI  CONST_15  C5   N4   C2   C3   180.00   0.0  0
 JBI  CONST_16  C4   N2   C1   N3   180.00   0.0  0
 JBI  CONST_17  N4   C2   C1   N3     0.00   0.0  0
 JBI  CONST_18  C20  C19  C18  C7     0.00   0.0  0
 JBI  CONST_19  C20  C21  C22  C7     0.00   0.0  0
 JBI  CONST_20  C15  C16  C17  C8     0.00   0.0  0
 JBI  CONST_21  C15  C14  C13  C8     0.00   0.0  0
 JBI  CONST_22  C16  C17  C8   C13    0.00   0.0  0
 JBI  CONST_23  C16  C15  C14  C13    0.00   0.0  0
 JBI  CONST_24  C17  C8   C13  C14    0.00   0.0  0
 JBI  CONST_25  C17  C16  C15  C14    0.00   0.0  0
 JBI  CONST_26  C21  C22  C7   C18    0.00   0.0  0
 JBI  CONST_27  C21  C20  C19  C18    0.00   0.0  0
 JBI  CONST_28  C22  C7   C18  C19    0.00   0.0  0
 JBI  CONST_29  C22  C21  C20  C19    0.00   0.0  0
 JBI  CONST_30  C6   N3   C1   C2   180.00   0.0  0
 JBI  CONST_31  C6   N3   C1   N2     0.00   0.0  0
 JBI  CONST_32  C6   N3   C5   N4   180.00   0.0  0
 JBI  CONST_33  N5   C4   N2   C1   180.00   0.0  0
 JBI  CONST_34  N6   C5   N3   C1   180.00   0.0  0
 JBI  CONST_35  C17  C8   C13  F1   180.00   0.0  0
 JBI  CONST_36  C15  C14  C13  F1   180.00   0.0  0
 JBI  CONST_37  C18  C19  C20  O1   180.00   0.0  0
 JBI  CONST_38  C22  C21  C20  O1   180.00   0.0  0
 JBI  CONST_39  N6   C5   N4   C2   180.00   0.0  0
 JBI  CONST_40  N5   C4   N1   C3   180.00   0.0  0
 JBI  CONST_41  C19  C18  C7   N5   180.00   0.0  0
 JBI  CONST_42  C21  C22  C7   N5   180.00   0.0  0
 JBI  CONST_43  N6   C5   N3   C6     0.00   0.0  0
 JBI  CONST_44  C16  C17  C8   N6   180.00   0.0  0
 JBI  CONST_45  C14  C13  C8   N6   180.00   0.0  0
 JBI  CONST_46  H3   C3   C2   C1   180.00   0.0  0
 JBI  CONST_47  H19  C19  C18  C7   180.00   0.0  0
 JBI  CONST_48  H21  C21  C22  C7   180.00   0.0  0
 JBI  CONST_49  H16  C16  C17  C8   180.00   0.0  0
 JBI  CONST_50  H14  C14  C13  C8   180.00   0.0  0
 JBI  CONST_51  H17  C17  C8   C13  180.00   0.0  0
 JBI  CONST_52  H15  C15  C14  C13  180.00   0.0  0
 JBI  CONST_53  H22  C22  C7   C18  180.00   0.0  0
 JBI  CONST_54  H18  C18  C19  C20  180.00   0.0  0
 JBI  Var_01    C10  C11  C12  C6    40.67  30.0  1
 JBI  Var_02    C11  C10  C9   C6    22.09  30.0  1
 JBI  Var_03    C12  C11  C10  C9   -39.19  30.0  1
 JBI  Var_04    C7   N5   C4   N1    -4.44  30.0  2
 JBI  Var_05    C8   N6   C5   N3   177.88  30.0  2
 JBI  Var_06    C18  C7   N5   C4    35.84  30.0  1
 JBI  Var_07    C17  C8   N6   C5    -7.70  30.0  2
 JBI  Var_08    H23  C23  O1   C20  179.29  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
 JBI  chir_01  C6  N3  C12  C9  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
 JBI  plan-1  F1   0.020
 JBI  plan-1  N6   0.020
 JBI  plan-1  C8   0.020
 JBI  plan-1  C13  0.020
 JBI  plan-1  C14  0.020
 JBI  plan-1  C15  0.020
 JBI  plan-1  C16  0.020
 JBI  plan-1  C17  0.020
 JBI  plan-1  H14  0.020
 JBI  plan-1  H15  0.020
 JBI  plan-1  H16  0.020
 JBI  plan-1  H17  0.020
 JBI  plan-2  O1   0.020
 JBI  plan-2  N5   0.020
 JBI  plan-2  C7   0.020
 JBI  plan-2  C18  0.020
 JBI  plan-2  C19  0.020
 JBI  plan-2  C20  0.020
 JBI  plan-2  C21  0.020
 JBI  plan-2  C22  0.020
 JBI  plan-2  H18  0.020
 JBI  plan-2  H19  0.020
 JBI  plan-2  H21  0.020
 JBI  plan-2  H22  0.020
 JBI  plan-3  C1   0.020
 JBI  plan-3  N1   0.020
 JBI  plan-3  C2   0.020
 JBI  plan-3  N2   0.020
 JBI  plan-3  C3   0.020
 JBI  plan-3  N3   0.020
 JBI  plan-3  C4   0.020
 JBI  plan-3  N4   0.020
 JBI  plan-3  C5   0.020
 JBI  plan-3  N5   0.020
 JBI  plan-3  C6   0.020
 JBI  plan-3  N6   0.020
 JBI  plan-3  H3   0.020

