# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 03:47:30 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: N-[2-(3-fluorophenyl)ethyl]-N'-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethane-1,2-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(CCNCCNc2ccnc(n2)n3ccnc3)c1
#
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
 6J0  6J0  N-[2-(3-fluorophenyl)ethyl]-N'-[2-(1H-imidazol-1-yl)pyrimidin-4-yl]ethane-1,2-diamine  ligand  43  24  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6J0
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
 6J0  N01   N  N     0  -0.446   7.0932  -2.6022  -0.1971
 6J0  C02   C  CR15  0   0.114   5.9485  -1.9878  -0.1422
 6J0  N03   N  NR5   0  -0.522   6.1086  -0.6375  -0.0459
 6J0  C04   C  CR15  0  -0.094   7.4627  -0.3936  -0.0410
 6J0  C05   C  CR15  0  -0.212   8.0471  -1.6164  -0.1343
 6J0  C1'   C  CR6   0   0.138  -5.7111   0.4084  -0.2869
 6J0  N11   N  N     0  -0.474   5.4781   1.5746   0.1220
 6J0  C12   C  CR6   0   0.638   5.0870   0.3200   0.0342
 6J0  N13   N  N     0  -0.506   3.8621  -0.1530   0.0120
 6J0  C14   C  CR6   0   0.562   2.8646   0.7385   0.0836
 6J0  C15   C  CR16  0  -0.438   3.1536   2.1165   0.1821
 6J0  C16   C  CR16  0  -0.017   4.4801   2.4615   0.1961
 6J0  N17   N  NH1   0  -0.655   1.6199   0.2573   0.0545
 6J0  C18   C  CH2   0  -0.277   0.4259   1.0665   0.1394
 6J0  C19   C  CH2   0  -0.294  -0.8088   0.1892   0.0078
 6J0  C2'   C  CR16  0  -0.463  -6.3626  -0.2251   0.7687
 6J0  N20   N  NH1   0  -0.603  -2.0007   1.0021   0.1110
 6J0  C21   C  CH2   0  -0.249  -3.2219   0.2469  -0.0892
 6J0  C22   C  CH2   0  -0.530  -4.4386   1.1692  -0.0467
 6J0  C3'   C  CR6   0   0.539  -7.5076  -0.9550   0.5161
 6J0  C4'   C  CR16  0  -0.426  -8.0411  -1.0874  -0.7510
 6J0  C5'   C  CR16  0  -0.225  -7.3868  -0.4547  -1.7996
 6J0  C6'   C  CR16  0  -0.320  -6.2346   0.2848  -1.5721
 6J0  F7'   F  F     0  -0.319  -8.1273  -1.5563   1.5469
 6J0  H02   H  HCR5  0   0.291   4.9747  -2.4487  -0.1683
 6J0  H04   H  HCR5  0   0.297   7.8671   0.6002   0.0277
 6J0  H05   H  HCR5  0   0.259   9.1018  -1.8415  -0.1601
 6J0  H15   H  HCR6  0   0.289   2.3833   2.8698   0.2458
 6J0  H16   H  HCR6  0   0.277   4.7688   3.5033   0.2718
 6J0  HN17  H  HNH1  0   0.398   1.5267  -0.7464   0.0228
 6J0  H18   H  HCH2  0   0.239   0.3960   1.6039   1.0940
 6J0  H18A  H  HCH2  0   0.245   0.4163   1.8164  -0.6561
 6J0  H19   H  HCH2  0   0.238  -0.8009  -0.2940  -0.9736
 6J0  H19A  H  HCH2  0   0.209  -0.7677  -0.6181   0.7565
 6J0  H2'   H  HCR6  0   0.270  -5.9842  -0.1437   1.7809
 6J0  HN20  H  HNH1  0   0.345  -2.0293   1.4287   1.0307
 6J0  H21   H  HCH2  0   0.228  -3.1739  -0.2354  -1.0700
 6J0  H21A  H  HCH2  0   0.203  -3.3495  -0.5612   0.6482
 6J0  H22   H  HCH2  0   0.249  -4.3194   1.9464  -0.8040
 6J0  H22A  H  HCH2  0   0.247  -4.4794   1.6688   0.9253
 6J0  H4'   H  HCR6  0   0.277  -8.9418  -1.6643  -0.9145
 6J0  H5'   H  HCR6  0   0.266  -7.7850  -0.5399  -2.8022
 6J0  H6'   H  HCR6  0   0.253  -5.7395   0.7771  -2.4002

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
 6J0  N01  C02   aromatic  1.300  0.020  1.300
 6J0  N01  C05   aromatic  1.373  0.020  1.373
 6J0  C02  N03   aromatic  1.363  0.020  1.363
 6J0  N03  C04   aromatic  1.376  0.020  1.376
 6J0  N03  C12   single    1.402  0.020  1.402
 6J0  C04  C05   aromatic  1.358  0.020  1.358
 6J0  C1'  C2'   aromatic  1.393  0.020  1.393
 6J0  C1'  C22   single    1.502  0.020  1.502
 6J0  C1'  C6'   aromatic  1.393  0.020  1.393
 6J0  N11  C12   aromatic  1.317  0.020  1.317
 6J0  N11  C16   aromatic  1.337  0.020  1.337
 6J0  C12  N13   aromatic  1.313  0.020  1.313
 6J0  N13  C14   aromatic  1.340  0.020  1.340
 6J0  C14  C15   aromatic  1.411  0.020  1.411
 6J0  C14  N17   single    1.335  0.020  1.335
 6J0  C15  C16   aromatic  1.371  0.020  1.371
 6J0  N17  C18   single    1.445  0.020  1.445
 6J0  C18  C19   single    1.520  0.020  1.520
 6J0  C19  N20   single    1.446  0.020  1.446
 6J0  C2'  C3'   aromatic  1.381  0.020  1.381
 6J0  N20  C21   single    1.450  0.020  1.450
 6J0  C21  C22   single    1.527  0.020  1.527
 6J0  C3'  C4'   aromatic  1.381  0.020  1.381
 6J0  C3'  F7'   single    1.345  0.020  1.345
 6J0  C4'  C5'   aromatic  1.389  0.020  1.389
 6J0  C5'  C6'   aromatic  1.388  0.020  1.388
 6J0  C02  H02   single    0.930  0.020  1.080
 6J0  C04  H04   single    0.930  0.020  1.080
 6J0  C05  H05   single    0.930  0.020  1.080
 6J0  C15  H15   single    0.930  0.020  1.080
 6J0  C16  H16   single    0.930  0.020  1.080
 6J0  N17  HN17  single    0.860  0.020  1.020
 6J0  C18  H18   single    0.970  0.020  1.090
 6J0  C18  H18A  single    0.970  0.020  1.090
 6J0  C19  H19   single    0.970  0.020  1.090
 6J0  C19  H19A  single    0.970  0.020  1.090
 6J0  C2'  H2'   single    0.930  0.020  1.080
 6J0  N20  HN20  single    0.890  0.020  1.040
 6J0  C21  H21   single    0.970  0.020  1.090
 6J0  C21  H21A  single    0.970  0.020  1.090
 6J0  C22  H22   single    0.970  0.020  1.090
 6J0  C22  H22A  single    0.970  0.020  1.090
 6J0  C4'  H4'   single    0.930  0.020  1.080
 6J0  C5'  H5'   single    0.930  0.020  1.080
 6J0  C6'  H6'   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
 6J0  C05   N01  C02  105.69  3.000
 6J0  H02   C02  N03  122.10  3.000
 6J0  H02   C02  N01  126.33  3.000
 6J0  N03   C02  N01  111.57  3.000
 6J0  C12   N03  C04  126.56  3.000
 6J0  C12   N03  C02  126.50  3.000
 6J0  C04   N03  C02  106.95  3.000
 6J0  H04   C04  C05  132.43  3.000
 6J0  H04   C04  N03  122.29  3.000
 6J0  C05   C04  N03  105.28  3.000
 6J0  H05   C05  C04  127.59  3.000
 6J0  H05   C05  N01  121.89  3.000
 6J0  C04   C05  N01  110.52  3.000
 6J0  C6'   C1'  C22  120.72  3.000
 6J0  C6'   C1'  C2'  118.88  3.000
 6J0  C22   C1'  C2'  120.37  3.000
 6J0  C16   N11  C12  114.45  3.000
 6J0  N13   C12  N11  128.40  3.000
 6J0  N13   C12  N03  115.63  3.000
 6J0  N11   C12  N03  115.97  3.000
 6J0  C14   N13  C12  116.99  3.000
 6J0  N17   C14  C15  122.98  3.000
 6J0  N17   C14  N13  116.95  3.000
 6J0  C15   C14  N13  120.06  3.000
 6J0  H15   C15  C16  120.96  3.000
 6J0  H15   C15  C14  122.64  3.000
 6J0  C16   C15  C14  116.39  3.000
 6J0  H16   C16  C15  120.03  3.000
 6J0  H16   C16  N11  116.27  3.000
 6J0  C15   C16  N11  123.70  3.000
 6J0  HN17  N17  C18  118.87  3.000
 6J0  HN17  N17  C14  116.46  3.000
 6J0  C18   N17  C14  124.57  3.000
 6J0  H18A  C18  H18  107.29  3.000
 6J0  H18A  C18  C19  109.01  3.000
 6J0  H18   C18  C19  109.64  3.000
 6J0  H18A  C18  N17  110.41  3.000
 6J0  H18   C18  N17  110.39  3.000
 6J0  C19   C18  N17  110.05  3.000
 6J0  H19A  C19  H19  106.60  3.000
 6J0  H19A  C19  N20  113.21  3.000
 6J0  H19   C19  N20  108.55  3.000
 6J0  H19A  C19  C18  109.49  3.000
 6J0  H19   C19  C18  109.07  3.000
 6J0  N20   C19  C18  109.80  3.000
 6J0  H2'   C2'  C3'  120.00  3.000
 6J0  H2'   C2'  C1'  120.69  3.000
 6J0  C3'   C2'  C1'  119.31  3.000
 6J0  HN20  N20  C21  108.70  3.000
 6J0  HN20  N20  C19  108.92  3.000
 6J0  C21   N20  C19  113.05  3.000
 6J0  H21A  C21  H21  106.37  3.000
 6J0  H21A  C21  C22  109.40  3.000
 6J0  H21   C21  C22  109.03  3.000
 6J0  H21A  C21  N20  112.79  3.000
 6J0  H21   C21  N20  108.45  3.000
 6J0  C22   C21  N20  110.65  3.000
 6J0  H22A  C22  H22  107.18  3.000
 6J0  H22A  C22  C21  109.28  3.000
 6J0  H22   C22  C21  108.88  3.000
 6J0  H22A  C22  C1'  109.99  3.000
 6J0  H22   C22  C1'  110.01  3.000
 6J0  C21   C22  C1'  111.38  3.000
 6J0  F7'   C3'  C4'  118.84  3.000
 6J0  F7'   C3'  C2'  118.57  3.000
 6J0  C4'   C3'  C2'  122.59  3.000
 6J0  H4'   C4'  C5'  121.40  3.000
 6J0  H4'   C4'  C3'  120.75  3.000
 6J0  C5'   C4'  C3'  117.85  3.000
 6J0  H5'   C5'  C6'  119.95  3.000
 6J0  H5'   C5'  C4'  119.37  3.000
 6J0  C6'   C5'  C4'  120.68  3.000
 6J0  H6'   C6'  C5'  119.76  3.000
 6J0  H6'   C6'  C1'  119.55  3.000
 6J0  C5'   C6'  C1'  120.69  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
 6J0  CONST_01  C04   N03  C02  N01     0.00   0.0  0
 6J0  CONST_02  C12   N03  C02  N01   180.00   0.0  0
 6J0  CONST_03  N03   C04  C05  N01     0.00   0.0  0
 6J0  CONST_04  C04   C05  N01  C02     0.00   0.0  0
 6J0  CONST_05  C05   C04  N03  C02     0.00   0.0  0
 6J0  CONST_06  N11   C12  N03  C02   180.00   0.0  0
 6J0  CONST_07  N13   C12  N03  C02     0.00   0.0  0
 6J0  CONST_08  C05   N01  C02  N03     0.00   0.0  0
 6J0  CONST_09  C16   N11  C12  N03   180.00   0.0  0
 6J0  CONST_10  C14   N13  C12  N03   180.00   0.0  0
 6J0  CONST_11  N11   C12  N03  C04     0.00   0.0  0
 6J0  CONST_12  N13   C12  N03  C04   180.00   0.0  0
 6J0  CONST_13  C12   N03  C04  C05   180.00   0.0  0
 6J0  CONST_14  C4'   C3'  C2'  C1'     0.00   0.0  0
 6J0  CONST_15  C4'   C5'  C6'  C1'     0.00   0.0  0
 6J0  CONST_16  C14   N13  C12  N11     0.00   0.0  0
 6J0  CONST_17  C14   C15  C16  N11     0.00   0.0  0
 6J0  CONST_18  C15   C16  N11  C12     0.00   0.0  0
 6J0  CONST_19  C15   C14  N13  C12     0.00   0.0  0
 6J0  CONST_20  C16   N11  C12  N13     0.00   0.0  0
 6J0  CONST_21  C16   C15  C14  N13     0.00   0.0  0
 6J0  CONST_22  C5'   C6'  C1'  C2'     0.00   0.0  0
 6J0  CONST_23  C5'   C4'  C3'  C2'     0.00   0.0  0
 6J0  CONST_24  C6'   C1'  C2'  C3'     0.00   0.0  0
 6J0  CONST_25  C6'   C5'  C4'  C3'     0.00   0.0  0
 6J0  CONST_26  F7'   C3'  C2'  C1'   180.00   0.0  0
 6J0  CONST_27  N17   C14  N13  C12   180.00   0.0  0
 6J0  CONST_28  N17   C14  C15  C16   180.00   0.0  0
 6J0  CONST_29  C3'   C2'  C1'  C22   180.00   0.0  0
 6J0  CONST_30  C5'   C6'  C1'  C22   180.00   0.0  0
 6J0  CONST_31  F7'   C3'  C4'  C5'   180.00   0.0  0
 6J0  CONST_32  H04   C04  C05  N01   180.00   0.0  0
 6J0  CONST_33  H05   C05  N01  C02   180.00   0.0  0
 6J0  CONST_34  H02   C02  N03  C04   180.00   0.0  0
 6J0  CONST_35  H5'   C5'  C6'  C1'   180.00   0.0  0
 6J0  CONST_36  H15   C15  C16  N11   180.00   0.0  0
 6J0  CONST_37  H16   C16  N11  C12   180.00   0.0  0
 6J0  CONST_38  H6'   C6'  C1'  C2'   180.00   0.0  0
 6J0  CONST_39  H4'   C4'  C3'  C2'   180.00   0.0  0
 6J0  CONST_40  H2'   C2'  C3'  C4'   180.00   0.0  0
 6J0  CONST_41  C18   N17  C14  N13   180.00   0.0  0
 6J0  CONST_42  C18   N17  C14  C15     0.00   0.0  0
 6J0  CONST_43  HN17  N17  C14  N13     0.00   0.0  0
 6J0  Var_01    C21   C22  C1'  C2'    85.34  30.0  2
 6J0  Var_02    N20   C21  C22  C1'   178.57  30.0  1
 6J0  Var_03    C19   C18  N17  C14   177.31  30.0  3
 6J0  Var_04    N20   C19  C18  N17   179.26  30.0  3
 6J0  Var_05    C21   N20  C19  C18   176.35  30.0  3
 6J0  Var_06    C22   C21  N20  C19  -176.82  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
 6J0  plan-1  N01   0.020
 6J0  plan-1  C02   0.020
 6J0  plan-1  N03   0.020
 6J0  plan-1  C04   0.020
 6J0  plan-1  C05   0.020
 6J0  plan-1  C12   0.020
 6J0  plan-1  H02   0.020
 6J0  plan-1  H04   0.020
 6J0  plan-1  H05   0.020
 6J0  plan-2  C1'   0.020
 6J0  plan-2  C2'   0.020
 6J0  plan-2  C22   0.020
 6J0  plan-2  C3'   0.020
 6J0  plan-2  C4'   0.020
 6J0  plan-2  C5'   0.020
 6J0  plan-2  C6'   0.020
 6J0  plan-2  F7'   0.020
 6J0  plan-2  H2'   0.020
 6J0  plan-2  H4'   0.020
 6J0  plan-2  H5'   0.020
 6J0  plan-2  H6'   0.020
 6J0  plan-3  N03   0.020
 6J0  plan-3  N11   0.020
 6J0  plan-3  C12   0.020
 6J0  plan-3  N13   0.020
 6J0  plan-3  C14   0.020
 6J0  plan-3  C15   0.020
 6J0  plan-3  C16   0.020
 6J0  plan-3  N17   0.020
 6J0  plan-3  H15   0.020
 6J0  plan-3  H16   0.020
 6J0  plan-4  C14   0.020
 6J0  plan-4  N17   0.020
 6J0  plan-4  C18   0.020
 6J0  plan-4  HN17  0.020

