# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:43:58 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 4-[1-(cyclopropylmethyl)-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2n(CC3CC3)cnc2c4ccc(F)cc4
#
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
 SB5  SB5  4-[1-(cyclopropylmethyl)-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyrimidin-2-amine  ligand  39  23  .  2022-09-22  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SB5
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
 SB5  FA1   F  F     0  -0.316  -0.8193   0.3169   5.6496
 SB5  CA1   C  CR16  0  -0.400   0.0214  -0.5548   3.6385
 SB5  CA2   C  CR6   0   0.512  -0.9533   0.1440   4.3241
 SB5  CA3   C  CR16  0  -0.401  -2.0645   0.6618   3.6878
 SB5  CA4   C  CR16  0  -0.281  -2.1919   0.4772   2.3196
 SB5  CA5   C  CR6   0   0.035  -1.2228  -0.2113   1.5878
 SB5  CA6   C  CR16  0  -0.297  -0.1234  -0.7319   2.2716
 SB5  CB1   C  CR16  0  -0.015   3.1755  -1.3062  -1.1825
 SB5  NB2   N  N     0  -0.451   3.7153  -0.2491  -0.6039
 SB5  CB3   C  CR6   0   0.539   2.8588   0.6653  -0.1282
 SB5  NB4   N  N     0  -0.450   1.5270   0.5992  -0.2097
 SB5  CB5   C  CR6   0   0.184   1.0085  -0.4735  -0.7930
 SB5  CB6   C  CR16  0  -0.382   1.8075  -1.4893  -1.3077
 SB5  NC1   N  NR5   0  -0.443  -1.1647  -0.7514  -2.0015
 SB5  CC2   C  CR5   0   0.289  -0.4553  -0.5414  -0.8451
 SB5  CC3   C  CR5   0   0.085  -1.4026  -0.3981   0.1467
 SB5  NC4   N  N     0  -0.454  -2.6510  -0.4989  -0.3941
 SB5  CC5   C  CR15  0   0.092  -2.4696  -0.6965  -1.6726
 SB5  CE1   C  CH1   0  -0.246  -0.1718   0.5590  -3.8284
 SB5  CE2   C  CH2   0  -0.488  -0.3248   0.9229  -5.2724
 SB5  CE3   C  CH2   0  -0.481  -1.1682   1.5989  -4.2338
 SB5  HCA1  H  HCR6  0   0.280   0.8740  -0.9670   4.1617
 SB5  HCA3  H  HCR6  0   0.279  -2.8177   1.2015   4.2466
 SB5  HCA4  H  HCR6  0   0.259  -3.0577   0.8807   1.8121
 SB5  HCA6  H  HCR6  0   0.255   0.6266  -1.3056   1.7447
 SB5  HCB1  H  HCR6  0   0.273   3.8634  -2.0559  -1.5588
 SB5  HCB6  H  HCR6  0   0.274   1.3976  -2.3860  -1.7470
 SB5  HN71  H  HNH2  0   0.398   4.3655   1.7708   0.6749
 SB5  HN72  H  HNH2  0   0.397   2.7847   2.3813   0.9626
 SB5  HCC5  H  HCR5  0   0.287  -3.2482  -0.8096  -2.4126
 SB5  HCD1  H  HCH2  0   0.278   0.1274  -1.5346  -3.4439
 SB5  HCD2  H  HCH2  0   0.277  -1.4823  -1.1295  -3.9955
 SB5  HCE1  H  HCH1  0   0.269   0.7274   0.9151  -3.3372
 SB5  HC21  H  HCH2  0   0.258   0.4701   1.4892  -5.7393
 SB5  HC22  H  HCH2  0   0.251  -0.8039   0.2060  -5.9285
 SB5  HC31  H  HCH2  0   0.247  -2.2196   1.3395  -4.1866
 SB5  HC32  H  HCH2  0   0.257  -0.9546   2.6307  -3.9879
 SB5  CD1   C  CH2   0  -0.346  -0.6599  -0.7863  -3.3661
 SB5  NB7   N  NH2   0  -0.824   3.3856   1.7576   0.4530

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
 SB5  FA1  CA2   single    1.343  0.020  1.343
 SB5  CA1  CA2   aromatic  1.381  0.020  1.381
 SB5  CA1  CA6   aromatic  1.386  0.020  1.386
 SB5  CA1  HCA1  single    0.930  0.020  1.080
 SB5  CA2  CA3   aromatic  1.381  0.020  1.381
 SB5  CA3  CA4   aromatic  1.386  0.020  1.386
 SB5  CA3  HCA3  single    0.930  0.020  1.080
 SB5  CA4  CA5   aromatic  1.396  0.020  1.396
 SB5  CA4  HCA4  single    0.930  0.020  1.080
 SB5  CA5  CA6   aromatic  1.395  0.020  1.395
 SB5  CA5  CC3   single    1.464  0.020  1.464
 SB5  CA6  HCA6  single    0.930  0.020  1.080
 SB5  CB1  NB2   aromatic  1.320  0.020  1.320
 SB5  CB1  CB6   aromatic  1.386  0.020  1.386
 SB5  CB1  HCB1  single    0.930  0.020  1.080
 SB5  NB2  CB3   aromatic  1.340  0.020  1.340
 SB5  CB3  NB4   aromatic  1.336  0.020  1.336
 SB5  CB3  NB7   single    1.345  0.020  1.345
 SB5  NB4  CB5   aromatic  1.327  0.020  1.327
 SB5  CB5  CB6   aromatic  1.391  0.020  1.391
 SB5  CB5  CC2   single    1.466  0.020  1.466
 SB5  CB6  HCB6  single    0.930  0.020  1.080
 SB5  NB7  HN71  single    0.890  0.020  1.040
 SB5  NB7  HN72  single    0.890  0.020  1.040
 SB5  NC1  CC2   aromatic  1.373  0.020  1.373
 SB5  NC1  CC5   aromatic  1.347  0.020  1.347
 SB5  NC1  CD1   single    1.455  0.020  1.455
 SB5  CC2  CC3   aromatic  1.379  0.020  1.379
 SB5  CC3  NC4   aromatic  1.364  0.020  1.364
 SB5  NC4  CC5   aromatic  1.306  0.020  1.306
 SB5  CC5  HCC5  single    0.930  0.020  1.080
 SB5  CD1  CE1   single    1.504  0.020  1.504
 SB5  CD1  HCD1  single    0.970  0.020  1.090
 SB5  CD1  HCD2  single    0.970  0.020  1.090
 SB5  CE1  CE2   single    1.497  0.020  1.497
 SB5  CE1  CE3   single    1.496  0.020  1.496
 SB5  CE1  HCE1  single    0.970  0.020  1.090
 SB5  CE2  CE3   single    1.499  0.020  1.499
 SB5  CE2  HC21  single    0.970  0.020  1.090
 SB5  CE2  HC22  single    0.970  0.020  1.090
 SB5  CE3  HC31  single    0.970  0.020  1.090
 SB5  CE3  HC32  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
 SB5  HCA1  CA1  CA6   120.71  3.000
 SB5  HCA1  CA1  CA2   120.58  3.000
 SB5  CA6   CA1  CA2   118.71  3.000
 SB5  CA3   CA2  CA1   121.91  3.000
 SB5  CA3   CA2  FA1   119.11  3.000
 SB5  CA1   CA2  FA1   118.98  3.000
 SB5  HCA3  CA3  CA4   120.80  3.000
 SB5  HCA3  CA3  CA2   120.60  3.000
 SB5  CA4   CA3  CA2   118.60  3.000
 SB5  HCA4  CA4  CA5   119.58  3.000
 SB5  HCA4  CA4  CA3   119.14  3.000
 SB5  CA5   CA4  CA3   121.28  3.000
 SB5  CC3   CA5  CA6   122.10  3.000
 SB5  CC3   CA5  CA4   119.58  3.000
 SB5  CA6   CA5  CA4   118.30  3.000
 SB5  HCA6  CA6  CA5   120.38  3.000
 SB5  HCA6  CA6  CA1   118.42  3.000
 SB5  CA5   CA6  CA1   121.19  3.000
 SB5  HCB1  CB1  CB6   120.22  3.000
 SB5  HCB1  CB1  NB2   116.48  3.000
 SB5  CB6   CB1  NB2   123.29  3.000
 SB5  CB3   NB2  CB1   116.13  3.000
 SB5  NB7   CB3  NB4   117.20  3.000
 SB5  NB7   CB3  NB2   117.21  3.000
 SB5  NB4   CB3  NB2   125.57  3.000
 SB5  CB5   NB4  CB3   117.17  3.000
 SB5  CC2   CB5  CB6   121.77  3.000
 SB5  CC2   CB5  NB4   116.31  3.000
 SB5  CB6   CB5  NB4   121.91  3.000
 SB5  HCB6  CB6  CB5   122.62  3.000
 SB5  HCB6  CB6  CB1   121.43  3.000
 SB5  CB5   CB6  CB1   115.92  3.000
 SB5  CD1   NC1  CC5   124.47  3.000
 SB5  CD1   NC1  CC2   127.90  3.000
 SB5  CC5   NC1  CC2   106.78  3.000
 SB5  CC3   CC2  NC1   105.47  3.000
 SB5  CC3   CC2  CB5   130.95  3.000
 SB5  NC1   CC2  CB5   123.56  3.000
 SB5  NC4   CC3  CC2   109.62  3.000
 SB5  NC4   CC3  CA5   120.79  3.000
 SB5  CC2   CC3  CA5   129.55  3.000
 SB5  CC5   NC4  CC3   105.79  3.000
 SB5  HCC5  CC5  NC4   125.90  3.000
 SB5  HCC5  CC5  NC1   121.79  3.000
 SB5  NC4   CC5  NC1   112.31  3.000
 SB5  HCE1  CE1  CE3   116.53  3.000
 SB5  HCE1  CE1  CE2   116.22  3.000
 SB5  CE3   CE1  CE2    60.11  3.000
 SB5  HCE1  CE1  CD1   115.05  3.000
 SB5  CE3   CE1  CD1   119.27  3.000
 SB5  CE2   CE1  CD1   118.74  3.000
 SB5  HC22  CE2  HC21  114.20  3.000
 SB5  HC22  CE2  CE3   117.98  3.000
 SB5  HC21  CE2  CE3   118.45  3.000
 SB5  HC22  CE2  CE1   117.93  3.000
 SB5  HC21  CE2  CE1   117.93  3.000
 SB5  CE3   CE2  CE1    59.92  3.000
 SB5  HC32  CE3  HC31  114.19  3.000
 SB5  HC32  CE3  CE2   118.45  3.000
 SB5  HC31  CE3  CE2   117.90  3.000
 SB5  HC32  CE3  CE1   118.02  3.000
 SB5  HC31  CE3  CE1   117.90  3.000
 SB5  CE2   CE3  CE1    59.98  3.000
 SB5  HCD2  CD1  HCD1  106.72  3.000
 SB5  HCD2  CD1  CE1   110.41  3.000
 SB5  HCD1  CD1  CE1   110.98  3.000
 SB5  HCD2  CD1  NC1   106.68  3.000
 SB5  HCD1  CD1  NC1   109.53  3.000
 SB5  CE1   CD1  NC1   112.29  3.000
 SB5  HN72  NB7  HN71  117.58  3.000
 SB5  HN72  NB7  CB3   119.28  3.000
 SB5  HN71  NB7  CB3   119.22  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
 SB5  CONST_01  CA4   CA3  CA2  CA1     0.00   0.0  0
 SB5  CONST_02  CA4   CA5  CA6  CA1     0.00   0.0  0
 SB5  CONST_03  CC3   CA5  CA6  CA1   180.00   0.0  0
 SB5  CONST_04  CA5   CA6  CA1  CA2     0.00   0.0  0
 SB5  CONST_05  CA5   CA4  CA3  CA2     0.00   0.0  0
 SB5  CONST_06  CA6   CA1  CA2  CA3     0.00   0.0  0
 SB5  CONST_07  CA6   CA5  CA4  CA3     0.00   0.0  0
 SB5  CONST_08  CC3   CA5  CA4  CA3   180.00   0.0  0
 SB5  CONST_11  CB5   CC2  CC3  CA5     0.00   0.0  0
 SB5  CONST_12  NC1   CC2  CC3  CA5   180.00   0.0  0
 SB5  CONST_13  CC5   NC4  CC3  CA5   180.00   0.0  0
 SB5  CONST_16  NB4   CB3  NB2  CB1     0.00   0.0  0
 SB5  CONST_17  NB4   CB5  CB6  CB1     0.00   0.0  0
 SB5  CONST_18  CC2   CB5  CB6  CB1   180.00   0.0  0
 SB5  CONST_19  CB5   CB6  CB1  NB2     0.00   0.0  0
 SB5  CONST_20  CB5   NB4  CB3  NB2     0.00   0.0  0
 SB5  CONST_21  CB6   CB1  NB2  CB3     0.00   0.0  0
 SB5  CONST_22  CB6   CB5  NB4  CB3     0.00   0.0  0
 SB5  CONST_23  CC2   CB5  NB4  CB3   180.00   0.0  0
 SB5  CONST_26  CC5   NC1  CC2  CB5   180.00   0.0  0
 SB5  CONST_27  NC4   CC3  CC2  CB5   180.00   0.0  0
 SB5  CONST_30  NC4   CC3  CC2  NC1     0.00   0.0  0
 SB5  CONST_31  CC3   NC4  CC5  NC1     0.00   0.0  0
 SB5  CONST_32  NC4   CC5  NC1  CC2     0.00   0.0  0
 SB5  CONST_33  CC5   NC4  CC3  CC2     0.00   0.0  0
 SB5  CONST_34  CC5   NC1  CC2  CC3     0.00   0.0  0
 SB5  CONST_35  CA6   CA1  CA2  FA1   180.00   0.0  0
 SB5  CONST_36  CA4   CA3  CA2  FA1   180.00   0.0  0
 SB5  CONST_37  NB7   CB3  NB2  CB1   180.00   0.0  0
 SB5  CONST_38  NB7   CB3  NB4  CB5   180.00   0.0  0
 SB5  CONST_39  CD1   NC1  CC2  CB5     0.00   0.0  0
 SB5  CONST_40  CD1   NC1  CC2  CC3   180.00   0.0  0
 SB5  CONST_41  CD1   NC1  CC5  NC4   180.00   0.0  0
 SB5  CONST_42  HCA3  CA3  CA2  CA1   180.00   0.0  0
 SB5  CONST_43  HCA6  CA6  CA1  CA2   180.00   0.0  0
 SB5  CONST_44  HCA4  CA4  CA3  CA2   180.00   0.0  0
 SB5  CONST_45  HCA1  CA1  CA2  CA3   180.00   0.0  0
 SB5  CONST_46  HCB6  CB6  CB1  NB2   180.00   0.0  0
 SB5  CONST_47  HCB1  CB1  NB2  CB3   180.00   0.0  0
 SB5  CONST_48  HCC5  CC5  NC1  CC2   180.00   0.0  0
 SB5  CONST_49  HN71  NB7  CB3  NB2     0.00   0.0  0
 SB5  CONST_50  HN72  NB7  CB3  NB2   180.00   0.0  0
 SB5  Var_01    CE2   CE1  CD1  NC1  -147.05  30.0  3
 SB5  Var_02    CE1   CD1  NC1  CC2   -67.57  30.0  2
 SB5  Var_03    CE3   CE2  CE1  CD1   109.14  30.0  1
 SB5  Var_04    HC31  CE3  CE2  CE1  -107.78  30.0  1

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
 SB5  chir_01  CE1  CD1  CE2  CE3  both

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
 SB5  plan-1  CA5   0.020
 SB5  plan-1  CB5   0.020
 SB5  plan-1  NC1   0.020
 SB5  plan-1  CC2   0.020
 SB5  plan-1  CC3   0.020
 SB5  plan-1  NC4   0.020
 SB5  plan-1  CC5   0.020
 SB5  plan-1  HCC5  0.020
 SB5  plan-1  CD1   0.020
 SB5  plan-2  FA1   0.020
 SB5  plan-2  CA1   0.020
 SB5  plan-2  CA2   0.020
 SB5  plan-2  CA3   0.020
 SB5  plan-2  CA4   0.020
 SB5  plan-2  CA5   0.020
 SB5  plan-2  CA6   0.020
 SB5  plan-2  CC3   0.020
 SB5  plan-2  HCA1  0.020
 SB5  plan-2  HCA3  0.020
 SB5  plan-2  HCA4  0.020
 SB5  plan-2  HCA6  0.020
 SB5  plan-3  CB1   0.020
 SB5  plan-3  NB2   0.020
 SB5  plan-3  CB3   0.020
 SB5  plan-3  NB4   0.020
 SB5  plan-3  CB5   0.020
 SB5  plan-3  CB6   0.020
 SB5  plan-3  CC2   0.020
 SB5  plan-3  HCB1  0.020
 SB5  plan-3  HCB6  0.020
 SB5  plan-3  NB7   0.020
 SB5  plan-4  CB3   0.020
 SB5  plan-4  HN71  0.020
 SB5  plan-4  HN72  0.020
 SB5  plan-4  NB7   0.020

