# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 21:20:32 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-(3-fluorophenyl)-N-{2-[2-(5-methyl-1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cncn1c2nccc(CCNCCCc3cccc(F)c3)n2
#
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
 7F5  7F5  3-(3-fluorophenyl)-N-{2-[2-(5-methyl-1H-imidazol-1-yl)pyrimidin-4-yl]ethyl}propan-1-amine  ligand  47  25  .  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_7F5
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
 7F5  N01   N  N     0  -0.438   5.6900  -2.9118  -0.2891
 7F5  C02   C  CR15  0   0.105   4.8064  -1.9754  -0.1410
 7F5  N03   N  NR5   0  -0.573   5.3734  -0.7301  -0.1887
 7F5  C04   C  CR5   0   0.283   6.7360  -0.9111  -0.3793
 7F5  C05   C  CR15  0  -0.260   6.8907  -2.2631  -0.4315
 7F5  C06   C  CH3   0  -0.710   7.7738   0.1490  -0.4513
 7F5  C1'   C  CR6   0   0.151  -5.6647  -0.7743  -0.2492
 7F5  N11   N  N     0  -0.427   5.2367   1.5694  -0.4783
 7F5  C12   C  CR6   0   0.616   4.6473   0.4620  -0.0751
 7F5  N13   N  N     0  -0.454   3.4304   0.3440   0.4219
 7F5  C14   C  CR6   0   0.322   2.7019   1.4524   0.5207
 7F5  C15   C  CR16  0  -0.387   3.2277   2.6798   0.1315
 7F5  C16   C  CR16  0   0.006   4.5185   2.6796  -0.3602
 7F5  C17   C  CH2   0  -0.524   1.3108   1.3139   1.0499
 7F5  C18   C  CH2   0  -0.250   0.4188   0.5214   0.0948
 7F5  N19   N  NH1   0  -0.604  -0.9393   0.4786   0.5944
 7F5  C2'   C  CR16  0  -0.468  -6.3911   0.2711  -0.8150
 7F5  C20   C  CH2   0  -0.257  -1.8328  -0.2839  -0.2572
 7F5  C21   C  CH2   0  -0.434  -3.2749  -0.1561   0.2064
 7F5  C22   C  CH2   0  -0.511  -4.2319  -0.9915  -0.6453
 7F5  C3'   C  CR6   0   0.539  -7.6928   0.4893  -0.4097
 7F5  C4'   C  CR16  0  -0.428  -8.3152  -0.2922   0.5441
 7F5  C5'   C  CR16  0  -0.224  -7.5867  -1.3325   1.1058
 7F5  C6'   C  CR16  0  -0.324  -6.2762  -1.5721   0.7155
 7F5  F7'   F  F     0  -0.319  -8.3792   1.5015  -0.9686
 7F5  H02   H  HCR5  0   0.289   3.7455  -2.1106  -0.0079
 7F5  H05   H  HCR5  0   0.258   7.8180  -2.8009  -0.5611
 7F5  H06   H  HCH3  0   0.249   7.7584   0.7993   0.4229
 7F5  H06A  H  HCH3  0   0.249   8.7503  -0.3313  -0.4952
 7F5  H06B  H  HCH3  0   0.252   7.6651   0.7831  -1.3290
 7F5  H16   H  HCR6  0   0.285   4.9937   3.6004  -0.6771
 7F5  H15   H  HCR6  0   0.283   2.6572   3.5933   0.2139
 7F5  H17   H  HCH2  0   0.262   1.3528   0.8027   2.0160
 7F5  H17A  H  HCH2  0   0.255   0.8769   2.3004   1.2192
 7F5  H18   H  HCH2  0   0.228   0.4072   1.0155  -0.8817
 7F5  H18A  H  HCH2  0   0.204   0.8565  -0.4754  -0.0660
 7F5  HN19  H  HNH1  0   0.340  -0.9375   0.0628   1.5190
 7F5  H20   H  HCH2  0   0.219  -1.7503   0.1100  -1.2751
 7F5  H20A  H  HCH2  0   0.193  -1.5530  -1.3480  -0.3193
 7F5  H21   H  HCH2  0   0.227  -3.3604  -0.4670   1.2526
 7F5  H21A  H  HCH2  0   0.229  -3.5703   0.8960   0.1685
 7F5  H22   H  HCH2  0   0.245  -3.9763  -2.0501  -0.5506
 7F5  H22A  H  HCH2  0   0.243  -4.1003  -0.7304  -1.6988
 7F5  H6'   H  HCR6  0   0.251  -5.7230  -2.3895   1.1616
 7F5  H5'   H  HCR6  0   0.265  -8.0517  -1.9618   1.8533
 7F5  H4'   H  HCR6  0   0.277  -9.3381  -0.0970   0.8378
 7F5  H2'   H  HCR6  0   0.268  -5.9450   0.9085  -1.5695

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
 7F5  N01  C02   aromatic  1.296  0.020  1.296
 7F5  N01  C05   aromatic  1.372  0.020  1.372
 7F5  C02  N03   aromatic  1.369  0.020  1.369
 7F5  C02  H02   single    0.930  0.020  1.080
 7F5  N03  C04   aromatic  1.388  0.020  1.388
 7F5  N03  C12   single    1.400  0.020  1.400
 7F5  C04  C05   aromatic  1.362  0.020  1.362
 7F5  C04  C06   single    1.485  0.020  1.485
 7F5  C05  H05   single    0.930  0.020  1.080
 7F5  C06  H06   single    0.970  0.020  1.090
 7F5  C06  H06A  single    0.970  0.020  1.090
 7F5  C06  H06B  single    0.970  0.020  1.090
 7F5  C1'  C2'   aromatic  1.393  0.020  1.393
 7F5  C1'  C22   single    1.502  0.020  1.502
 7F5  C1'  C6'   aromatic  1.393  0.020  1.393
 7F5  N11  C12   aromatic  1.318  0.020  1.318
 7F5  N11  C16   aromatic  1.328  0.020  1.328
 7F5  C12  N13   aromatic  1.320  0.020  1.320
 7F5  N13  C14   aromatic  1.330  0.020  1.330
 7F5  C14  C15   aromatic  1.391  0.020  1.391
 7F5  C14  C17   single    1.495  0.020  1.495
 7F5  C15  C16   aromatic  1.381  0.020  1.381
 7F5  C15  H15   single    0.930  0.020  1.080
 7F5  C16  H16   single    0.930  0.020  1.080
 7F5  C17  C18   single    1.528  0.020  1.528
 7F5  C17  H17   single    0.970  0.020  1.090
 7F5  C17  H17A  single    0.970  0.020  1.090
 7F5  C18  N19   single    1.448  0.020  1.448
 7F5  C18  H18   single    0.970  0.020  1.090
 7F5  C18  H18A  single    0.970  0.020  1.090
 7F5  N19  C20   single    1.451  0.020  1.451
 7F5  N19  HN19  single    0.890  0.020  1.040
 7F5  C2'  C3'   aromatic  1.381  0.020  1.381
 7F5  C2'  H2'   single    0.930  0.020  1.080
 7F5  C20  C21   single    1.520  0.020  1.520
 7F5  C20  H20   single    0.970  0.020  1.090
 7F5  C20  H20A  single    0.970  0.020  1.090
 7F5  C21  C22   single    1.529  0.020  1.529
 7F5  C21  H21   single    0.970  0.020  1.090
 7F5  C21  H21A  single    0.970  0.020  1.090
 7F5  C22  H22   single    0.970  0.020  1.090
 7F5  C22  H22A  single    0.970  0.020  1.090
 7F5  C3'  C4'   aromatic  1.381  0.020  1.381
 7F5  C3'  F7'   single    1.345  0.020  1.345
 7F5  C4'  C5'   aromatic  1.389  0.020  1.389
 7F5  C4'  H4'   single    0.930  0.020  1.080
 7F5  C5'  C6'   aromatic  1.388  0.020  1.388
 7F5  C5'  H5'   single    0.930  0.020  1.080
 7F5  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
 7F5  C05   N01  C02   105.48  3.000
 7F5  H02   C02  N03   121.74  3.000
 7F5  H02   C02  N01   126.49  3.000
 7F5  N03   C02  N01   111.77  3.000
 7F5  C12   N03  C04   129.15  3.000
 7F5  C12   N03  C02   123.83  3.000
 7F5  C04   N03  C02   107.02  3.000
 7F5  C06   C04  C05   128.86  3.000
 7F5  C06   C04  N03   126.84  3.000
 7F5  C05   C04  N03   104.26  3.000
 7F5  H05   C05  C04   126.63  3.000
 7F5  H05   C05  N01   121.90  3.000
 7F5  C04   C05  N01   111.47  3.000
 7F5  H06B  C06  H06A  108.30  3.000
 7F5  H06B  C06  H06   107.33  3.000
 7F5  H06A  C06  H06   107.95  3.000
 7F5  H06B  C06  C04   112.65  3.000
 7F5  H06A  C06  C04   108.28  3.000
 7F5  H06   C06  C04   112.16  3.000
 7F5  C6'   C1'  C22   121.23  3.000
 7F5  C6'   C1'  C2'   118.82  3.000
 7F5  C22   C1'  C2'   119.91  3.000
 7F5  C16   N11  C12   115.69  3.000
 7F5  N13   C12  N11   127.07  3.000
 7F5  N13   C12  N03   115.63  3.000
 7F5  N11   C12  N03   117.30  3.000
 7F5  C14   N13  C12   117.29  3.000
 7F5  C17   C14  C15   122.19  3.000
 7F5  C17   C14  N13   117.31  3.000
 7F5  C15   C14  N13   120.50  3.000
 7F5  H15   C15  C16   121.39  3.000
 7F5  H15   C15  C14   121.69  3.000
 7F5  C16   C15  C14   116.92  3.000
 7F5  H16   C16  C15   120.92  3.000
 7F5  H16   C16  N11   116.57  3.000
 7F5  C15   C16  N11   122.50  3.000
 7F5  H17A  C17  H17   107.50  3.000
 7F5  H17A  C17  C18   109.49  3.000
 7F5  H17   C17  C18   109.39  3.000
 7F5  H17A  C17  C14   109.96  3.000
 7F5  H17   C17  C14   108.68  3.000
 7F5  C18   C17  C14   111.71  3.000
 7F5  H18A  C18  H18   106.43  3.000
 7F5  H18A  C18  N19   113.37  3.000
 7F5  H18   C18  N19   108.13  3.000
 7F5  H18A  C18  C17   109.20  3.000
 7F5  H18   C18  C17   109.25  3.000
 7F5  N19   C18  C17   110.32  3.000
 7F5  HN19  N19  C20   108.72  3.000
 7F5  HN19  N19  C18   108.98  3.000
 7F5  C20   N19  C18   113.00  3.000
 7F5  H2'   C2'  C3'   119.97  3.000
 7F5  H2'   C2'  C1'   120.63  3.000
 7F5  C3'   C2'  C1'   119.40  3.000
 7F5  H20A  C20  H20   106.02  3.000
 7F5  H20A  C20  C21   109.83  3.000
 7F5  H20   C20  C21   108.96  3.000
 7F5  H20A  C20  N19   112.59  3.000
 7F5  H20   C20  N19   108.08  3.000
 7F5  C21   C20  N19   111.16  3.000
 7F5  H21A  C21  H21   106.58  3.000
 7F5  H21A  C21  C22   109.71  3.000
 7F5  H21   C21  C22   109.16  3.000
 7F5  H21A  C21  C20   109.06  3.000
 7F5  H21   C21  C20   109.98  3.000
 7F5  C22   C21  C20   112.20  3.000
 7F5  H22A  C22  H22   106.65  3.000
 7F5  H22A  C22  C21   109.32  3.000
 7F5  H22   C22  C21   109.54  3.000
 7F5  H22A  C22  C1'   109.53  3.000
 7F5  H22   C22  C1'   109.89  3.000
 7F5  C21   C22  C1'   111.78  3.000
 7F5  F7'   C3'  C4'   118.87  3.000
 7F5  F7'   C3'  C2'   118.57  3.000
 7F5  C4'   C3'  C2'   122.56  3.000
 7F5  H4'   C4'  C5'   121.42  3.000
 7F5  H4'   C4'  C3'   120.75  3.000
 7F5  C5'   C4'  C3'   117.83  3.000
 7F5  H5'   C5'  C6'   119.96  3.000
 7F5  H5'   C5'  C4'   119.32  3.000
 7F5  C6'   C5'  C4'   120.72  3.000
 7F5  H6'   C6'  C5'   119.78  3.000
 7F5  H6'   C6'  C1'   119.55  3.000
 7F5  C5'   C6'  C1'   120.68  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
 7F5  CONST_01  C04  N03  C02  N01     0.00   0.0  0
 7F5  CONST_02  C12  N03  C02  N01   180.00   0.0  0
 7F5  CONST_03  N03  C04  C05  N01     0.00   0.0  0
 7F5  CONST_04  C04  C05  N01  C02     0.00   0.0  0
 7F5  CONST_05  C05  C04  N03  C02     0.00   0.0  0
 7F5  CONST_08  C05  N01  C02  N03     0.00   0.0  0
 7F5  CONST_09  C16  N11  C12  N03   180.00   0.0  0
 7F5  CONST_10  C14  N13  C12  N03   180.00   0.0  0
 7F5  CONST_13  C12  N03  C04  C05   180.00   0.0  0
 7F5  CONST_14  C4'  C3'  C2'  C1'     0.00   0.0  0
 7F5  CONST_15  C4'  C5'  C6'  C1'     0.00   0.0  0
 7F5  CONST_16  C14  N13  C12  N11     0.00   0.0  0
 7F5  CONST_17  C14  C15  C16  N11     0.00   0.0  0
 7F5  CONST_18  C15  C16  N11  C12     0.00   0.0  0
 7F5  CONST_19  C15  C14  N13  C12     0.00   0.0  0
 7F5  CONST_20  C16  N11  C12  N13     0.00   0.0  0
 7F5  CONST_21  C16  C15  C14  N13     0.00   0.0  0
 7F5  CONST_22  C5'  C6'  C1'  C2'     0.00   0.0  0
 7F5  CONST_23  C5'  C4'  C3'  C2'     0.00   0.0  0
 7F5  CONST_24  C6'  C1'  C2'  C3'     0.00   0.0  0
 7F5  CONST_25  C6'  C5'  C4'  C3'     0.00   0.0  0
 7F5  CONST_26  C06  C04  C05  N01   180.00   0.0  0
 7F5  CONST_27  C06  C04  N03  C02   180.00   0.0  0
 7F5  CONST_28  C12  N03  C04  C06     0.00   0.0  0
 7F5  CONST_29  F7'  C3'  C2'  C1'   180.00   0.0  0
 7F5  CONST_30  C17  C14  N13  C12   180.00   0.0  0
 7F5  CONST_31  C17  C14  C15  C16   180.00   0.0  0
 7F5  CONST_32  C3'  C2'  C1'  C22   180.00   0.0  0
 7F5  CONST_33  C5'  C6'  C1'  C22   180.00   0.0  0
 7F5  CONST_34  F7'  C3'  C4'  C5'   180.00   0.0  0
 7F5  CONST_35  H05  C05  N01  C02   180.00   0.0  0
 7F5  CONST_36  H02  C02  N03  C04   180.00   0.0  0
 7F5  CONST_37  H5'  C5'  C6'  C1'   180.00   0.0  0
 7F5  CONST_38  H15  C15  C16  N11   180.00   0.0  0
 7F5  CONST_39  H16  C16  N11  C12   180.00   0.0  0
 7F5  CONST_40  H6'  C6'  C1'  C2'   180.00   0.0  0
 7F5  CONST_41  H4'  C4'  C3'  C2'   180.00   0.0  0
 7F5  CONST_42  H2'  C2'  C3'  C4'   180.00   0.0  0
 7F5  Var_01    C18  C17  C14  N13   -66.54  30.0  2
 7F5  Var_02    C21  C22  C1'  C2'    86.98  30.0  2
 7F5  Var_03    H06  C06  C04  N03    54.71  30.0  2
 7F5  Var_04    C20  C21  C22  C1'  -175.48  30.0  1
 7F5  Var_05    N19  C18  C17  C14  -176.36  30.0  3
 7F5  Var_06    C20  N19  C18  C17  -178.87  30.0  3
 7F5  Var_07    C21  C20  N19  C18  -172.78  30.0  3
 7F5  Var_08    C22  C21  C20  N19  -177.95  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
 7F5  plan-1  N01  0.020
 7F5  plan-1  C02  0.020
 7F5  plan-1  N03  0.020
 7F5  plan-1  C04  0.020
 7F5  plan-1  C05  0.020
 7F5  plan-1  C06  0.020
 7F5  plan-1  C12  0.020
 7F5  plan-1  H02  0.020
 7F5  plan-1  H05  0.020
 7F5  plan-2  C1'  0.020
 7F5  plan-2  C2'  0.020
 7F5  plan-2  C22  0.020
 7F5  plan-2  C3'  0.020
 7F5  plan-2  C4'  0.020
 7F5  plan-2  C5'  0.020
 7F5  plan-2  C6'  0.020
 7F5  plan-2  F7'  0.020
 7F5  plan-2  H6'  0.020
 7F5  plan-2  H5'  0.020
 7F5  plan-2  H4'  0.020
 7F5  plan-2  H2'  0.020
 7F5  plan-3  N03  0.020
 7F5  plan-3  N11  0.020
 7F5  plan-3  C12  0.020
 7F5  plan-3  N13  0.020
 7F5  plan-3  C14  0.020
 7F5  plan-3  C15  0.020
 7F5  plan-3  C16  0.020
 7F5  plan-3  C17  0.020
 7F5  plan-3  H16  0.020
 7F5  plan-3  H15  0.020

