# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:54:02 2022
#   Inital geometry file: a 103 line input string
#   Ligand name: 3-(3-fluorophenyl)-N-{[2-(1H-imidazol-1-yl)pyrimidin-4-yl]methyl}propan-1-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1cccc(CCCNCc2ccnc(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
 S8F  S8F  3-(3-fluorophenyl)-N-{[2-(1H-imidazol-1-yl)pyrimidin-4-yl]methyl}propan-1-amine  ligand  41  23  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S8F
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
 S8F  N01   N  N     0  -0.444   4.4006  -3.1879  -0.0104
 S8F  C02   C  CR15  0   0.114   3.7818  -2.0644   0.1983
 S8F  N03   N  NR5   0  -0.529   4.4936  -1.0043  -0.2828
 S8F  C04   C  CR15  0  -0.094   5.6477  -1.5128  -0.8345
 S8F  C05   C  CR15  0  -0.210   5.5672  -2.8565  -0.6549
 S8F  C1'   C  CR6   0   0.151  -4.6073   0.2299   0.3852
 S8F  N11   N  N     0  -0.438   4.9551   1.2080  -0.7584
 S8F  C12   C  CR6   0   0.634   4.1148   0.3407  -0.2246
 S8F  N13   N  N     0  -0.442   2.9620   0.5945   0.3575
 S8F  C14   C  CR6   0   0.295   2.5886   1.8694   0.4208
 S8F  C15   C  CR16  0  -0.383   3.3914   2.8716  -0.1068
 S8F  C16   C  CR16  0   0.006   4.5822   2.4788  -0.6922
 S8F  C17   C  CH2   0  -0.322   1.2738   2.1706   1.0808
 S8F  N18   N  NH1   0  -0.595   0.1953   1.4617   0.4266
 S8F  C19   C  CH2   0  -0.256  -1.0703   1.5987   1.1236
 S8F  C2'   C  CR16  0  -0.470  -4.8865  -1.1074   0.6552
 S8F  C20   C  CH2   0  -0.439  -2.1731   0.8445   0.3988
 S8F  C21   C  CH2   0  -0.509  -3.5141   0.9451   1.1270
 S8F  C3'   C  CR6   0   0.539  -5.8665  -1.7542  -0.0727
 S8F  C4'   C  CR16  0  -0.428  -6.5895  -1.1279  -1.0688
 S8F  C5'   C  CR16  0  -0.224  -6.3059   0.2053  -1.3351
 S8F  C6'   C  CR16  0  -0.322  -5.3268   0.8776  -0.6176
 S8F  F7'   F  F     0  -0.319  -6.1260  -3.0448   0.2027
 S8F  H02   H  HCR5  0   0.294   2.8279  -1.9395   0.6843
 S8F  H04   H  HCR5  0   0.300   6.3946  -0.8871  -1.2894
 S8F  H05   H  HCR5  0   0.261   6.2849  -3.6043  -0.9537
 S8F  H15   H  HCR6  0   0.286   3.1005   3.9111  -0.0669
 S8F  H16   H  HCR6  0   0.288   5.2580   3.2071  -1.1246
 S8F  H17   H  HCH2  0   0.256   1.3326   1.8299   2.1191
 S8F  H17A  H  HCH2  0   0.226   1.1297   3.2594   1.1184
 S8F  HN18  H  HNH1  0   0.345   0.0914   1.8192  -0.5163
 S8F  H19   H  HCH2  0   0.222  -0.9482   1.1872   2.1309
 S8F  H19A  H  HCH2  0   0.194  -1.3732   2.6500   1.2555
 S8F  H2'   H  HCR6  0   0.268  -4.3471  -1.6409   1.4289
 S8F  H20   H  HCH2  0   0.229  -2.2843   1.2417  -0.6153
 S8F  H20A  H  HCH2  0   0.231  -1.8866  -0.2055   0.2947
 S8F  H21   H  HCH2  0   0.245  -3.7832   1.9976   1.2490
 S8F  H21A  H  HCH2  0   0.245  -3.4116   0.5293   2.1326
 S8F  H4'   H  HCR6  0   0.276  -7.3526  -1.6635  -1.6176
 S8F  H5'   H  HCR6  0   0.265  -6.8581   0.7224  -2.1089
 S8F  H6'   H  HCR6  0   0.251  -5.1197   1.9180  -0.8370

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
 S8F  N01  C02   aromatic  1.299  0.020  1.299
 S8F  N01  C05   aromatic  1.373  0.020  1.373
 S8F  C02  N03   aromatic  1.365  0.020  1.365
 S8F  N03  C04   aromatic  1.377  0.020  1.377
 S8F  N03  C12   single    1.399  0.020  1.399
 S8F  C04  C05   aromatic  1.358  0.020  1.358
 S8F  C1'  C2'   aromatic  1.393  0.020  1.393
 S8F  C1'  C21   single    1.502  0.020  1.502
 S8F  C1'  C6'   aromatic  1.394  0.020  1.394
 S8F  N11  C12   aromatic  1.320  0.020  1.320
 S8F  N11  C16   aromatic  1.326  0.020  1.326
 S8F  C12  N13   aromatic  1.316  0.020  1.316
 S8F  N13  C14   aromatic  1.330  0.020  1.330
 S8F  C14  C15   aromatic  1.388  0.020  1.388
 S8F  C14  C17   single    1.502  0.020  1.502
 S8F  C15  C16   aromatic  1.384  0.020  1.384
 S8F  C17  N18   single    1.447  0.020  1.447
 S8F  N18  C19   single    1.451  0.020  1.451
 S8F  C19  C20   single    1.520  0.020  1.520
 S8F  C2'  C3'   aromatic  1.382  0.020  1.382
 S8F  C20  C21   single    1.529  0.020  1.529
 S8F  C3'  C4'   aromatic  1.381  0.020  1.381
 S8F  C3'  F7'   single    1.345  0.020  1.345
 S8F  C4'  C5'   aromatic  1.389  0.020  1.389
 S8F  C5'  C6'   aromatic  1.388  0.020  1.388
 S8F  C02  H02   single    0.930  0.020  1.080
 S8F  C04  H04   single    0.930  0.020  1.080
 S8F  C05  H05   single    0.930  0.020  1.080
 S8F  C15  H15   single    0.930  0.020  1.080
 S8F  C16  H16   single    0.930  0.020  1.080
 S8F  C17  H17   single    0.970  0.020  1.090
 S8F  C17  H17A  single    0.970  0.020  1.090
 S8F  N18  HN18  single    0.890  0.020  1.040
 S8F  C19  H19   single    0.970  0.020  1.090
 S8F  C19  H19A  single    0.970  0.020  1.090
 S8F  C2'  H2'   single    0.930  0.020  1.080
 S8F  C20  H20   single    0.970  0.020  1.090
 S8F  C20  H20A  single    0.970  0.020  1.090
 S8F  C21  H21   single    0.970  0.020  1.090
 S8F  C21  H21A  single    0.970  0.020  1.090
 S8F  C4'  H4'   single    0.930  0.020  1.080
 S8F  C5'  H5'   single    0.930  0.020  1.080
 S8F  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
 S8F  C05   N01  C02  105.74  3.000
 S8F  H02   C02  N03  122.05  3.000
 S8F  H02   C02  N01  126.45  3.000
 S8F  N03   C02  N01  111.51  3.000
 S8F  C12   N03  C04  126.80  3.000
 S8F  C12   N03  C02  126.24  3.000
 S8F  C04   N03  C02  106.96  3.000
 S8F  H04   C04  C05  132.29  3.000
 S8F  H04   C04  N03  122.48  3.000
 S8F  C05   C04  N03  105.23  3.000
 S8F  H05   C05  C04  127.58  3.000
 S8F  H05   C05  N01  121.86  3.000
 S8F  C04   C05  N01  110.56  3.000
 S8F  C6'   C1'  C21  120.64  3.000
 S8F  C6'   C1'  C2'  118.83  3.000
 S8F  C21   C1'  C2'  120.48  3.000
 S8F  C16   N11  C12  115.49  3.000
 S8F  N13   C12  N11  127.57  3.000
 S8F  N13   C12  N03  116.17  3.000
 S8F  N11   C12  N03  116.26  3.000
 S8F  C14   N13  C12  116.86  3.000
 S8F  C17   C14  C15  121.91  3.000
 S8F  C17   C14  N13  117.33  3.000
 S8F  C15   C14  N13  120.76  3.000
 S8F  H15   C15  C16  121.37  3.000
 S8F  H15   C15  C14  121.66  3.000
 S8F  C16   C15  C14  116.97  3.000
 S8F  H16   C16  C15  120.98  3.000
 S8F  H16   C16  N11  116.67  3.000
 S8F  C15   C16  N11  122.35  3.000
 S8F  H17A  C17  H17  106.44  3.000
 S8F  H17A  C17  N18  113.77  3.000
 S8F  H17   C17  N18  108.45  3.000
 S8F  H17A  C17  C14  109.18  3.000
 S8F  H17   C17  C14  107.91  3.000
 S8F  N18   C17  C14  110.83  3.000
 S8F  HN18  N18  C19  108.91  3.000
 S8F  HN18  N18  C17  108.91  3.000
 S8F  C19   N18  C17  112.74  3.000
 S8F  H19A  C19  H19  106.21  3.000
 S8F  H19A  C19  C20  109.33  3.000
 S8F  H19   C19  C20  109.46  3.000
 S8F  H19A  C19  N18  112.78  3.000
 S8F  H19   C19  N18  108.01  3.000
 S8F  C20   C19  N18  110.90  3.000
 S8F  H2'   C2'  C3'  119.92  3.000
 S8F  H2'   C2'  C1'  120.76  3.000
 S8F  C3'   C2'  C1'  119.32  3.000
 S8F  H20A  C20  H20  106.67  3.000
 S8F  H20A  C20  C21  109.77  3.000
 S8F  H20   C20  C21  109.16  3.000
 S8F  H20A  C20  C19  109.38  3.000
 S8F  H20   C20  C19  109.60  3.000
 S8F  C21   C20  C19  112.12  3.000
 S8F  H21A  C21  H21  106.65  3.000
 S8F  H21A  C21  C20  109.32  3.000
 S8F  H21   C21  C20  109.41  3.000
 S8F  H21A  C21  C1'  109.96  3.000
 S8F  H21   C21  C1'  109.53  3.000
 S8F  C20   C21  C1'  111.82  3.000
 S8F  F7'   C3'  C4'  118.81  3.000
 S8F  F7'   C3'  C2'  118.57  3.000
 S8F  C4'   C3'  C2'  122.62  3.000
 S8F  H4'   C4'  C5'  121.47  3.000
 S8F  H4'   C4'  C3'  120.71  3.000
 S8F  C5'   C4'  C3'  117.82  3.000
 S8F  H5'   C5'  C6'  119.88  3.000
 S8F  H5'   C5'  C4'  119.45  3.000
 S8F  C6'   C5'  C4'  120.67  3.000
 S8F  H6'   C6'  C5'  119.71  3.000
 S8F  H6'   C6'  C1'  119.56  3.000
 S8F  C5'   C6'  C1'  120.73  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
 S8F  CONST_01  C04  N03  C02  N01    0.00   0.0  0
 S8F  CONST_02  C12  N03  C02  N01  180.00   0.0  0
 S8F  CONST_03  N03  C04  C05  N01    0.00   0.0  0
 S8F  CONST_04  C04  C05  N01  C02    0.00   0.0  0
 S8F  CONST_05  C05  C04  N03  C02    0.00   0.0  0
 S8F  CONST_06  N11  C12  N03  C02  180.00   0.0  0
 S8F  CONST_07  N13  C12  N03  C02    0.00   0.0  0
 S8F  CONST_08  C05  N01  C02  N03    0.00   0.0  0
 S8F  CONST_09  C16  N11  C12  N03  180.00   0.0  0
 S8F  CONST_10  C14  N13  C12  N03  180.00   0.0  0
 S8F  CONST_11  N11  C12  N03  C04    0.00   0.0  0
 S8F  CONST_12  N13  C12  N03  C04  180.00   0.0  0
 S8F  CONST_13  C12  N03  C04  C05  180.00   0.0  0
 S8F  CONST_14  C4'  C3'  C2'  C1'    0.00   0.0  0
 S8F  CONST_15  C4'  C5'  C6'  C1'    0.00   0.0  0
 S8F  CONST_16  C14  N13  C12  N11    0.00   0.0  0
 S8F  CONST_17  C14  C15  C16  N11    0.00   0.0  0
 S8F  CONST_18  C15  C16  N11  C12    0.00   0.0  0
 S8F  CONST_19  C15  C14  N13  C12    0.00   0.0  0
 S8F  CONST_20  C16  N11  C12  N13    0.00   0.0  0
 S8F  CONST_21  C16  C15  C14  N13    0.00   0.0  0
 S8F  CONST_22  C5'  C6'  C1'  C2'    0.00   0.0  0
 S8F  CONST_23  C5'  C4'  C3'  C2'    0.00   0.0  0
 S8F  CONST_24  C6'  C1'  C2'  C3'    0.00   0.0  0
 S8F  CONST_25  C6'  C5'  C4'  C3'    0.00   0.0  0
 S8F  CONST_26  F7'  C3'  C2'  C1'  180.00   0.0  0
 S8F  CONST_27  C17  C14  N13  C12  180.00   0.0  0
 S8F  CONST_28  C17  C14  C15  C16  180.00   0.0  0
 S8F  CONST_29  C3'  C2'  C1'  C21  180.00   0.0  0
 S8F  CONST_30  C5'  C6'  C1'  C21  180.00   0.0  0
 S8F  CONST_31  F7'  C3'  C4'  C5'  180.00   0.0  0
 S8F  CONST_32  H04  C04  C05  N01  180.00   0.0  0
 S8F  CONST_33  H05  C05  N01  C02  180.00   0.0  0
 S8F  CONST_34  H02  C02  N03  C04  180.00   0.0  0
 S8F  CONST_35  H5'  C5'  C6'  C1'  180.00   0.0  0
 S8F  CONST_36  H15  C15  C16  N11  180.00   0.0  0
 S8F  CONST_37  H16  C16  N11  C12  180.00   0.0  0
 S8F  CONST_38  H6'  C6'  C1'  C2'  180.00   0.0  0
 S8F  CONST_39  H4'  C4'  C3'  C2'  180.00   0.0  0
 S8F  CONST_40  H2'  C2'  C3'  C4'  180.00   0.0  0
 S8F  Var_01    N18  C17  C14  N13  -57.58  30.0  2
 S8F  Var_02    C20  C21  C1'  C2'   91.17  30.0  2
 S8F  Var_03    C19  C20  C21  C1'  178.40  30.0  2
 S8F  Var_04    C19  N18  C17  C14  173.28  30.0  3
 S8F  Var_05    C20  C19  N18  C17  179.75  30.0  3
 S8F  Var_06    C21  C20  C19  N18  178.75  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
 S8F  plan-1  N01  0.020
 S8F  plan-1  C02  0.020
 S8F  plan-1  N03  0.020
 S8F  plan-1  C04  0.020
 S8F  plan-1  C05  0.020
 S8F  plan-1  C12  0.020
 S8F  plan-1  H02  0.020
 S8F  plan-1  H04  0.020
 S8F  plan-1  H05  0.020
 S8F  plan-2  C1'  0.020
 S8F  plan-2  C2'  0.020
 S8F  plan-2  C21  0.020
 S8F  plan-2  C3'  0.020
 S8F  plan-2  C4'  0.020
 S8F  plan-2  C5'  0.020
 S8F  plan-2  C6'  0.020
 S8F  plan-2  F7'  0.020
 S8F  plan-2  H2'  0.020
 S8F  plan-2  H4'  0.020
 S8F  plan-2  H5'  0.020
 S8F  plan-2  H6'  0.020
 S8F  plan-3  N03  0.020
 S8F  plan-3  N11  0.020
 S8F  plan-3  C12  0.020
 S8F  plan-3  N13  0.020
 S8F  plan-3  C14  0.020
 S8F  plan-3  C15  0.020
 S8F  plan-3  C16  0.020
 S8F  plan-3  C17  0.020
 S8F  plan-3  H15  0.020
 S8F  plan-3  H16  0.020

