# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 22 11:56:03 2022
#   Inital geometry file: a 105 line input string
#   Ligand name: 4-[4-(4-fluorophenyl)-1-piperidin-4-yl-1H-imidazol-5-yl]pyrimidin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1nccc(n1)c2n(cnc2c3ccc(F)cc3)C4CCNCC4
#
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
 SB4  SB4  4-[4-(4-fluorophenyl)-1-piperidin-4-yl-1H-imidazol-5-yl]pyrimidin-2-amine  ligand  44  25  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SB4
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
 SB4  CA1   C  CH2   0  -0.428  -0.6954  -1.1690  -3.7040
 SB4  CA2   C  CH2   0  -0.295  -0.0720  -1.0743  -5.0900
 SB4  NA3   N  NH1   0  -0.597  -0.5611   0.1106  -5.7682
 SB4  CA4   C  CH2   0  -0.298  -0.1890   1.3252  -5.0684
 SB4  CA5   C  CH2   0  -0.422  -0.8240   1.3404  -3.6838
 SB4  CA6   C  CH1   0  -0.120  -0.3878   0.0980  -2.9127
 SB4  CB1   C  CR16  0  -0.282  -2.1821   0.5711   2.8383
 SB4  CB2   C  CR16  0  -0.401  -2.1376   0.4891   4.2217
 SB4  CB3   C  CR6   0   0.512  -1.1410  -0.2666   4.8071
 SB4  CB4   C  CR16  0  -0.400  -0.2013  -0.9448   4.0550
 SB4  CB5   C  CR16  0  -0.295  -0.2626  -0.8541   2.6735
 SB4  CB6   C  CR6   0   0.035  -1.2432  -0.0872   2.0424
 SB4  CC1   C  CR16  0  -0.383   1.8526  -1.1325  -0.8707
 SB4  CC2   C  CR6   0   0.180   1.1149  -0.1527  -0.2120
 SB4  NC3   N  N     0  -0.452   1.6826   0.7109   0.6186
 SB4  CC4   C  CR6   0   0.543   3.0008   0.5989   0.8091
 SB4  NC5   N  N     0  -0.451   3.8011  -0.2976   0.2152
 SB4  CC6   C  CR16  0  -0.015   3.2137  -1.1433  -0.6116
 SB4  NC7   N  NH2   0  -0.825   3.5746   1.4762   1.6485
 SB4  ND1   N  NR5   0  -0.464  -0.9806   0.0516  -1.5789
 SB4  CD2   C  CR15  0   0.091  -2.2965   0.1665  -1.3124
 SB4  ND3   N  N     0  -0.454  -2.5467   0.1421  -0.0298
 SB4  CD4   C  CR5   0   0.082  -1.3363   0.0120   0.5841
 SB4  CD5   C  CR5   0   0.286  -0.3389  -0.0423  -0.3669
 SB4  H11   H  HCH2  0   0.249  -0.3094  -2.0468  -3.1805
 SB4  H12   H  HCH2  0   0.235  -1.7776  -1.2951  -3.7994
 SB4  H21   H  HCH2  0   0.194   1.0260  -1.0838  -4.9870
 SB4  H22   H  HCH2  0   0.242  -0.3418  -1.9566  -5.6726
 SB4  HN3   H  HNH1  0   0.357  -0.2028   0.1370  -6.7133
 SB4  H41   H  HCH2  0   0.195   0.9027   1.4372  -4.9599
 SB4  H42   H  HCH2  0   0.242  -0.5400   2.1872  -5.6380
 SB4  H51   H  HCH2  0   0.231  -1.9114   1.3645  -3.7912
 SB4  H52   H  HCH2  0   0.252  -0.5219   2.2403  -3.1446
 SB4  H6    H  HCH1  0   0.267   0.6925   0.1637  -2.7682
 SB4  HB1   H  HCR6  0   0.258  -2.9587   1.1613   2.3704
 SB4  HB2   H  HCR6  0   0.278  -2.8668   1.0067   4.8309
 SB4  HB4   H  HCR6  0   0.279   0.5596  -1.5448   4.5371
 SB4  HB5   H  HCR6  0   0.256   0.4570  -1.4098   2.0883
 SB4  HC6   H  HCR6  0   0.274   3.8537  -1.8780  -1.0879
 SB4  HN71  H  HNH2  0   0.399   4.5335   1.3522   1.9205
 SB4  HN72  H  HNH2  0   0.398   2.9969   2.0775   2.2088
 SB4  H2    H  HCR5  0   0.289  -3.0383   0.2708  -2.0893
 SB4  FB7   F  F     0  -0.316  -1.0871  -0.3522   6.1469
 SB4  HC1   H  HCR6  0   0.277   1.3970  -1.8646  -1.5211

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
 SB4  CA1  CA2   single    1.523  0.020  1.523
 SB4  CA1  CA6   single    1.525  0.020  1.525
 SB4  CA1  H11   single    0.970  0.020  1.090
 SB4  CA1  H12   single    0.970  0.020  1.090
 SB4  CA2  NA3   single    1.450  0.020  1.450
 SB4  CA2  H21   single    0.970  0.020  1.090
 SB4  CA2  H22   single    0.970  0.020  1.090
 SB4  NA3  CA4   single    1.450  0.020  1.450
 SB4  NA3  HN3   single    0.890  0.020  1.040
 SB4  CA4  CA5   single    1.523  0.020  1.523
 SB4  CA4  H41   single    0.970  0.020  1.090
 SB4  CA4  H42   single    0.970  0.020  1.090
 SB4  CA5  CA6   single    1.526  0.020  1.526
 SB4  CA5  H51   single    0.970  0.020  1.090
 SB4  CA5  H52   single    0.970  0.020  1.090
 SB4  CA6  ND1   single    1.460  0.020  1.460
 SB4  CA6  H6    single    0.970  0.020  1.090
 SB4  CB1  CB2   aromatic  1.386  0.020  1.386
 SB4  CB1  CB6   aromatic  1.396  0.020  1.396
 SB4  CB1  HB1   single    0.930  0.020  1.080
 SB4  CB2  CB3   aromatic  1.381  0.020  1.381
 SB4  CB2  HB2   single    0.930  0.020  1.080
 SB4  CB3  CB4   aromatic  1.382  0.020  1.382
 SB4  CB3  FB7   single    1.344  0.020  1.344
 SB4  CB4  CB5   aromatic  1.386  0.020  1.386
 SB4  CB4  HB4   single    0.930  0.020  1.080
 SB4  CB5  CB6   aromatic  1.396  0.020  1.396
 SB4  CB5  HB5   single    0.930  0.020  1.080
 SB4  CB6  CD4   single    1.465  0.020  1.465
 SB4  CC1  CC2   aromatic  1.392  0.020  1.392
 SB4  CC1  CC6   aromatic  1.386  0.020  1.386
 SB4  CC1  HC1   single    0.930  0.020  1.080
 SB4  CC2  NC3   aromatic  1.326  0.020  1.326
 SB4  CC2  CD5   single    1.466  0.020  1.466
 SB4  NC3  CC4   aromatic  1.337  0.020  1.337
 SB4  CC4  NC5   aromatic  1.341  0.020  1.341
 SB4  CC4  NC7   single    1.343  0.020  1.343
 SB4  NC5  CC6   aromatic  1.321  0.020  1.321
 SB4  CC6  HC6   single    0.930  0.020  1.080
 SB4  NC7  HN71  single    0.860  0.020  1.020
 SB4  NC7  HN72  single    0.860  0.020  1.020
 SB4  ND1  CD2   aromatic  1.348  0.020  1.348
 SB4  ND1  CD5   aromatic  1.375  0.020  1.375
 SB4  CD2  ND3   aromatic  1.307  0.020  1.307
 SB4  CD2  H2    single    0.930  0.020  1.080
 SB4  ND3  CD4   aromatic  1.363  0.020  1.363
 SB4  CD4  CD5   aromatic  1.379  0.020  1.379

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
 SB4  H12   CA1  H11   107.38  3.000
 SB4  H12   CA1  CA6   109.91  3.000
 SB4  H11   CA1  CA6   110.34  3.000
 SB4  H12   CA1  CA2   109.45  3.000
 SB4  H11   CA1  CA2   109.97  3.000
 SB4  CA6   CA1  CA2   109.76  3.000
 SB4  H22   CA2  H21   106.80  3.000
 SB4  H22   CA2  NA3   109.12  3.000
 SB4  H21   CA2  NA3   112.74  3.000
 SB4  H22   CA2  CA1   109.54  3.000
 SB4  H21   CA2  CA1   108.79  3.000
 SB4  NA3   CA2  CA1   109.78  3.000
 SB4  HN3   NA3  CA4   109.77  3.000
 SB4  HN3   NA3  CA2   109.81  3.000
 SB4  CA4   NA3  CA2   111.84  3.000
 SB4  H42   CA4  H41   106.83  3.000
 SB4  H42   CA4  CA5   109.43  3.000
 SB4  H41   CA4  CA5   108.80  3.000
 SB4  H42   CA4  NA3   109.09  3.000
 SB4  H41   CA4  NA3   112.74  3.000
 SB4  CA5   CA4  NA3   109.88  3.000
 SB4  H52   CA5  H51   107.80  3.000
 SB4  H52   CA5  CA6   110.03  3.000
 SB4  H51   CA5  CA6   110.61  3.000
 SB4  H52   CA5  CA4   109.98  3.000
 SB4  H51   CA5  CA4   109.00  3.000
 SB4  CA6   CA5  CA4   109.39  3.000
 SB4  H6    CA6  ND1   106.42  3.000
 SB4  H6    CA6  CA5   107.50  3.000
 SB4  ND1   CA6  CA5   111.80  3.000
 SB4  H6    CA6  CA1   108.55  3.000
 SB4  ND1   CA6  CA1   111.44  3.000
 SB4  CA5   CA6  CA1   110.89  3.000
 SB4  HB1   CB1  CB6   119.57  3.000
 SB4  HB1   CB1  CB2   119.13  3.000
 SB4  CB6   CB1  CB2   121.29  3.000
 SB4  HB2   CB2  CB3   120.62  3.000
 SB4  HB2   CB2  CB1   120.79  3.000
 SB4  CB3   CB2  CB1   118.59  3.000
 SB4  FB7   CB3  CB4   118.96  3.000
 SB4  FB7   CB3  CB2   119.12  3.000
 SB4  CB4   CB3  CB2   121.92  3.000
 SB4  HB4   CB4  CB5   120.76  3.000
 SB4  HB4   CB4  CB3   120.52  3.000
 SB4  CB5   CB4  CB3   118.71  3.000
 SB4  HB5   CB5  CB6   120.35  3.000
 SB4  HB5   CB5  CB4   118.45  3.000
 SB4  CB6   CB5  CB4   121.19  3.000
 SB4  CD4   CB6  CB5   122.15  3.000
 SB4  CD4   CB6  CB1   119.54  3.000
 SB4  CB5   CB6  CB1   118.29  3.000
 SB4  HC1   CC1  CC6   121.44  3.000
 SB4  HC1   CC1  CC2   122.58  3.000
 SB4  CC6   CC1  CC2   115.95  3.000
 SB4  CD5   CC2  NC3   116.21  3.000
 SB4  CD5   CC2  CC1   121.90  3.000
 SB4  NC3   CC2  CC1   121.87  3.000
 SB4  CC4   NC3  CC2   117.19  3.000
 SB4  NC7   CC4  NC5   117.30  3.000
 SB4  NC7   CC4  NC3   117.11  3.000
 SB4  NC5   CC4  NC3   125.57  3.000
 SB4  CC6   NC5  CC4   116.11  3.000
 SB4  HC6   CC6  NC5   116.51  3.000
 SB4  HC6   CC6  CC1   120.19  3.000
 SB4  NC5   CC6  CC1   123.30  3.000
 SB4  HN72  NC7  HN71  118.15  3.000
 SB4  HN72  NC7  CC4   119.60  3.000
 SB4  HN71  NC7  CC4   119.77  3.000
 SB4  CD5   ND1  CD2   106.70  3.000
 SB4  CD5   ND1  CA6   128.17  3.000
 SB4  CD2   ND1  CA6   125.05  3.000
 SB4  H2    CD2  ND3   125.22  3.000
 SB4  H2    CD2  ND1   122.49  3.000
 SB4  ND3   CD2  ND1   112.29  3.000
 SB4  CD4   ND3  CD2   105.88  3.000
 SB4  CD5   CD4  ND3   109.59  3.000
 SB4  CD5   CD4  CB6   129.64  3.000
 SB4  ND3   CD4  CB6   120.74  3.000
 SB4  CD4   CD5  ND1   105.53  3.000
 SB4  CD4   CD5  CC2   130.33  3.000
 SB4  ND1   CD5  CC2   124.14  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
 SB4  CONST_01  CB4   CB3  CB2  CB1    0.00   0.0  0
 SB4  CONST_02  CB4   CB5  CB6  CB1    0.00   0.0  0
 SB4  CONST_05  CB5   CB6  CB1  CB2    0.00   0.0  0
 SB4  CONST_06  CD4   CB6  CB1  CB2  180.00   0.0  0
 SB4  CONST_07  CB5   CB4  CB3  CB2    0.00   0.0  0
 SB4  CONST_08  CB6   CB1  CB2  CB3    0.00   0.0  0
 SB4  CONST_09  CB6   CB5  CB4  CB3    0.00   0.0  0
 SB4  CONST_10  CD4   CB6  CB5  CB4  180.00   0.0  0
 SB4  CONST_13  CD2   ND3  CD4  CB6  180.00   0.0  0
 SB4  CONST_14  CC2   CD5  CD4  CB6    0.00   0.0  0
 SB4  CONST_15  ND1   CD5  CD4  CB6  180.00   0.0  0
 SB4  CONST_16  CC4   NC3  CC2  CC1    0.00   0.0  0
 SB4  CONST_19  CC4   NC5  CC6  CC1    0.00   0.0  0
 SB4  CONST_20  NC5   CC6  CC1  CC2    0.00   0.0  0
 SB4  CONST_21  NC5   CC4  NC3  CC2    0.00   0.0  0
 SB4  CONST_22  CD2   ND1  CD5  CC2  180.00   0.0  0
 SB4  CONST_23  ND3   CD4  CD5  CC2  180.00   0.0  0
 SB4  CONST_24  CC6   CC1  CC2  NC3    0.00   0.0  0
 SB4  CONST_27  CC6   NC5  CC4  NC3    0.00   0.0  0
 SB4  CONST_28  CD5   CC2  NC3  CC4  180.00   0.0  0
 SB4  CONST_29  CD5   CC2  CC1  CC6  180.00   0.0  0
 SB4  CONST_30  CD4   ND3  CD2  ND1    0.00   0.0  0
 SB4  CONST_31  ND3   CD4  CD5  ND1    0.00   0.0  0
 SB4  CONST_32  CD4   CD5  ND1  CD2    0.00   0.0  0
 SB4  CONST_33  CD5   CD4  ND3  CD2    0.00   0.0  0
 SB4  CONST_34  CD5   ND1  CD2  ND3    0.00   0.0  0
 SB4  CONST_35  ND3   CD2  ND1  CA6  180.00   0.0  0
 SB4  CONST_36  CC2   CD5  ND1  CA6    0.00   0.0  0
 SB4  CONST_37  CD4   CD5  ND1  CA6  180.00   0.0  0
 SB4  CONST_38  FB7   CB3  CB2  CB1  180.00   0.0  0
 SB4  CONST_39  FB7   CB3  CB4  CB5  180.00   0.0  0
 SB4  CONST_40  NC7   CC4  NC3  CC2  180.00   0.0  0
 SB4  CONST_41  NC7   CC4  NC5  CC6  180.00   0.0  0
 SB4  CONST_42  H2    CD2  ND1  CA6    0.00   0.0  0
 SB4  CONST_43  HB5   CB5  CB6  CB1  180.00   0.0  0
 SB4  CONST_44  HB4   CB4  CB3  CB2  180.00   0.0  0
 SB4  CONST_45  HB1   CB1  CB2  CB3  180.00   0.0  0
 SB4  CONST_46  HB2   CB2  CB3  CB4  180.00   0.0  0
 SB4  CONST_47  HC6   CC6  CC1  CC2  180.00   0.0  0
 SB4  CONST_48  HC1   CC1  CC2  NC3  180.00   0.0  0
 SB4  CONST_49  HN71  NC7  CC4  NC3  180.00   0.0  0
 SB4  CONST_50  HN72  NC7  CC4  NC3    0.00   0.0  0
 SB4  Var_01    CA4   NA3  CA2  CA1   62.15  30.0  1
 SB4  Var_02    CA5   CA4  NA3  CA2  -62.51  30.0  1
 SB4  Var_03    CA6   CA1  CA2  NA3  -56.99  30.0  1
 SB4  Var_04    CA6   CA5  CA4  NA3   57.42  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
 SB4  chir_01  CA6  CA1  CA5  ND1  negativ

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
 SB4  plan-1  CA6   0.020
 SB4  plan-1  CB6   0.020
 SB4  plan-1  CC2   0.020
 SB4  plan-1  ND1   0.020
 SB4  plan-1  CD2   0.020
 SB4  plan-1  ND3   0.020
 SB4  plan-1  CD4   0.020
 SB4  plan-1  CD5   0.020
 SB4  plan-1  H2    0.020
 SB4  plan-2  CB1   0.020
 SB4  plan-2  CB2   0.020
 SB4  plan-2  CB3   0.020
 SB4  plan-2  CB4   0.020
 SB4  plan-2  CB5   0.020
 SB4  plan-2  CB6   0.020
 SB4  plan-2  CD4   0.020
 SB4  plan-2  HB1   0.020
 SB4  plan-2  HB2   0.020
 SB4  plan-2  HB4   0.020
 SB4  plan-2  HB5   0.020
 SB4  plan-2  FB7   0.020
 SB4  plan-3  CC1   0.020
 SB4  plan-3  CC2   0.020
 SB4  plan-3  NC3   0.020
 SB4  plan-3  CC4   0.020
 SB4  plan-3  NC5   0.020
 SB4  plan-3  CC6   0.020
 SB4  plan-3  NC7   0.020
 SB4  plan-3  CD5   0.020
 SB4  plan-3  HC6   0.020
 SB4  plan-3  HC1   0.020
 SB4  plan-4  CC4   0.020
 SB4  plan-4  NC7   0.020
 SB4  plan-4  HN71  0.020
 SB4  plan-4  HN72  0.020

