# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 08:02:51 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 4-[1-(cyclopropylmethyl)-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc(cc1)c2ncn(CC3CC3)c2c4ccncc4
#
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
 SB6  SB6  4-[1-(cyclopropylmethyl)-4-(4-fluorophenyl)-1H-imidazol-5-yl]pyridine  ligand  38  22  .  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_SB6
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
 SB6  FA1   F  F     0  -0.316   0.4894   0.6218  -5.6827
 SB6  CA1   C  CR16  0  -0.399   1.8270   0.7681  -3.7573
 SB6  CA2   C  CR6   0   0.513   0.6516   0.3804  -4.3713
 SB6  CA3   C  CR16  0  -0.396  -0.3591  -0.2557  -3.6776
 SB6  CA4   C  CR16  0  -0.303  -0.1818  -0.5089  -2.3261
 SB6  CA5   C  CR6   0   0.019   0.9851  -0.1229  -1.6653
 SB6  CA6   C  CR16  0  -0.281   1.9858   0.5109  -2.4046
 SB6  CB1   C  CR16  0  -0.056  -3.4272  -0.8845   1.2554
 SB6  NB2   N  N     0  -0.406  -3.9221   0.2614   0.8040
 SB6  CB3   C  CR16  0  -0.054  -3.0582   1.1594   0.3428
 SB6  CB4   C  CR16  0  -0.354  -1.6875   0.9635   0.3203
 SB6  CB5   C  CR6   0   0.087  -1.1677  -0.2393   0.7939
 SB6  CB6   C  CR16  0  -0.363  -2.0736  -1.1851   1.2681
 SB6  NC1   N  NR5   0  -0.441   1.0003  -0.8105   1.8974
 SB6  CC2   C  CR5   0   0.307   0.2760  -0.4798   0.7790
 SB6  CC3   C  CR5   0   0.083   1.1982  -0.3965  -0.2424
 SB6  NC4   N  N     0  -0.453   2.4483  -0.6499   0.2439
 SB6  CC5   C  CR15  0   0.091   2.2918  -0.8820   1.5195
 SB6  CE1   C  CH1   0  -0.243   0.2215   0.5088   3.8181
 SB6  CE2   C  CH2   0  -0.488   0.4633   0.7834   5.2701
 SB6  CE3   C  CH2   0  -0.481   1.3408   1.4120   4.2301
 SB6  HCA1  H  HCR6  0   0.279   2.6063   1.2637  -4.3217
 SB6  HCA3  H  HCR6  0   0.280  -1.2650  -0.5644  -4.1826
 SB6  HCA4  H  HCR6  0   0.261  -0.9628  -1.0337  -1.7931
 SB6  HCA6  H  HCR6  0   0.259   2.9015   0.8139  -1.9146
 SB6  HCB1  H  HCR6  0   0.268  -4.1430  -1.6125   1.6211
 SB6  HCB3  H  HCR6  0   0.268  -3.4742   2.0908  -0.0245
 SB6  HCB4  H  HCR6  0   0.271  -1.0362   1.7404  -0.0572
 SB6  HCB6  H  HCR6  0   0.275  -1.7441  -2.1527   1.6214
 SB6  HCC5  H  HCR5  0   0.286   3.0788  -1.1143   2.2217
 SB6  HCD1  H  HCH2  0   0.277  -0.3279  -1.5141   3.3463
 SB6  HCD2  H  HCH2  0   0.277   1.3325  -1.3242   3.8599
 SB6  HCE1  H  HCH1  0   0.268  -0.6481   0.9881   3.3806
 SB6  HE21  H  HCH2  0   0.258  -0.2480   1.4073   5.7949
 SB6  HE22  H  HCH2  0   0.250   0.8846  -0.0125   5.8729
 SB6  HE31  H  HCH2  0   0.247   2.3548   1.0423   4.1315
 SB6  HE32  H  HCH2  0   0.256   1.2362   2.4714   4.0366
 SB6  CD1   C  CH2   0  -0.346   0.5380  -0.8573   3.2763

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
 SB6  FA1  CA2   single    1.343  0.020  1.343
 SB6  CA1  CA2   aromatic  1.382  0.020  1.382
 SB6  CA1  CA6   aromatic  1.386  0.020  1.386
 SB6  CA1  HCA1  single    0.930  0.020  1.080
 SB6  CA2  CA3   aromatic  1.381  0.020  1.381
 SB6  CA3  CA4   aromatic  1.386  0.020  1.386
 SB6  CA3  HCA3  single    0.930  0.020  1.080
 SB6  CA4  CA5   aromatic  1.396  0.020  1.396
 SB6  CA4  HCA4  single    0.930  0.020  1.080
 SB6  CA5  CA6   aromatic  1.396  0.020  1.396
 SB6  CA5  CC3   single    1.465  0.020  1.465
 SB6  CA6  HCA6  single    0.930  0.020  1.080
 SB6  CB1  NB2   aromatic  1.327  0.020  1.327
 SB6  CB1  CB6   aromatic  1.387  0.020  1.387
 SB6  CB1  HCB1  single    0.930  0.020  1.080
 SB6  NB2  CB3   aromatic  1.329  0.020  1.329
 SB6  CB3  CB4   aromatic  1.385  0.020  1.385
 SB6  CB3  HCB3  single    0.930  0.020  1.080
 SB6  CB4  CB5   aromatic  1.393  0.020  1.393
 SB6  CB4  HCB4  single    0.930  0.020  1.080
 SB6  CB5  CB6   aromatic  1.393  0.020  1.393
 SB6  CB5  CC2   single    1.464  0.020  1.464
 SB6  CB6  HCB6  single    0.930  0.020  1.080
 SB6  NC1  CC2   aromatic  1.373  0.020  1.373
 SB6  NC1  CC5   aromatic  1.348  0.020  1.348
 SB6  NC1  CD1   single    1.455  0.020  1.455
 SB6  CC2  CC3   aromatic  1.379  0.020  1.379
 SB6  CC3  NC4   aromatic  1.365  0.020  1.365
 SB6  NC4  CC5   aromatic  1.306  0.020  1.306
 SB6  CC5  HCC5  single    0.930  0.020  1.080
 SB6  CD1  CE1   single    1.503  0.020  1.503
 SB6  CD1  HCD1  single    0.970  0.020  1.090
 SB6  CD1  HCD2  single    0.970  0.020  1.090
 SB6  CE1  CE2   single    1.497  0.020  1.497
 SB6  CE1  CE3   single    1.496  0.020  1.496
 SB6  CE1  HCE1  single    0.970  0.020  1.090
 SB6  CE2  CE3   single    1.499  0.020  1.499
 SB6  CE2  HE21  single    0.970  0.020  1.090
 SB6  CE2  HE22  single    0.970  0.020  1.090
 SB6  CE3  HE31  single    0.970  0.020  1.090
 SB6  CE3  HE32  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
 SB6  HCA1  CA1  CA6   120.76  3.000
 SB6  HCA1  CA1  CA2   120.61  3.000
 SB6  CA6   CA1  CA2   118.63  3.000
 SB6  CA3   CA2  CA1   121.91  3.000
 SB6  CA3   CA2  FA1   119.00  3.000
 SB6  CA1   CA2  FA1   119.09  3.000
 SB6  HCA3  CA3  CA4   120.66  3.000
 SB6  HCA3  CA3  CA2   120.64  3.000
 SB6  CA4   CA3  CA2   118.69  3.000
 SB6  HCA4  CA4  CA5   120.31  3.000
 SB6  HCA4  CA4  CA3   118.47  3.000
 SB6  CA5   CA4  CA3   121.20  3.000
 SB6  CC3   CA5  CA6   119.67  3.000
 SB6  CC3   CA5  CA4   122.01  3.000
 SB6  CA6   CA5  CA4   118.30  3.000
 SB6  HCA6  CA6  CA5   119.59  3.000
 SB6  HCA6  CA6  CA1   119.15  3.000
 SB6  CA5   CA6  CA1   121.26  3.000
 SB6  HCB1  CB1  CB6   119.71  3.000
 SB6  HCB1  CB1  NB2   116.63  3.000
 SB6  CB6   CB1  NB2   123.66  3.000
 SB6  CB3   NB2  CB1   117.33  3.000
 SB6  HCB3  CB3  CB4   119.72  3.000
 SB6  HCB3  CB3  NB2   116.66  3.000
 SB6  CB4   CB3  NB2   123.62  3.000
 SB6  HCB4  CB4  CB5   120.94  3.000
 SB6  HCB4  CB4  CB3   120.00  3.000
 SB6  CB5   CB4  CB3   119.06  3.000
 SB6  CC2   CB5  CB6   122.24  3.000
 SB6  CC2   CB5  CB4   120.42  3.000
 SB6  CB6   CB5  CB4   117.34  3.000
 SB6  HCB6  CB6  CB5   121.38  3.000
 SB6  HCB6  CB6  CB1   119.62  3.000
 SB6  CB5   CB6  CB1   118.99  3.000
 SB6  CD1   NC1  CC5   124.65  3.000
 SB6  CD1   NC1  CC2   127.74  3.000
 SB6  CC5   NC1  CC2   106.86  3.000
 SB6  CC3   CC2  NC1   105.37  3.000
 SB6  CC3   CC2  CB5   131.10  3.000
 SB6  NC1   CC2  CB5   123.48  3.000
 SB6  NC4   CC3  CC2   109.72  3.000
 SB6  NC4   CC3  CA5   120.93  3.000
 SB6  CC2   CC3  CA5   129.33  3.000
 SB6  CC5   NC4  CC3   105.74  3.000
 SB6  HCC5  CC5  NC4   125.87  3.000
 SB6  HCC5  CC5  NC1   121.84  3.000
 SB6  NC4   CC5  NC1   112.29  3.000
 SB6  HCE1  CE1  CE3   116.35  3.000
 SB6  HCE1  CE1  CE2   116.06  3.000
 SB6  CE3   CE1  CE2    60.10  3.000
 SB6  HCE1  CE1  CD1   115.14  3.000
 SB6  CE3   CE1  CD1   119.36  3.000
 SB6  CE2   CE1  CD1   118.83  3.000
 SB6  HE22  CE2  HE21  114.16  3.000
 SB6  HE22  CE2  CE3   117.80  3.000
 SB6  HE21  CE2  CE3   118.66  3.000
 SB6  HE22  CE2  CE1   117.87  3.000
 SB6  HE21  CE2  CE1   118.03  3.000
 SB6  CE3   CE2  CE1    59.91  3.000
 SB6  HE32  CE3  HE31  114.09  3.000
 SB6  HE32  CE3  CE2   118.56  3.000
 SB6  HE31  CE3  CE2   117.89  3.000
 SB6  HE32  CE3  CE1   118.01  3.000
 SB6  HE31  CE3  CE1   117.97  3.000
 SB6  CE2   CE3  CE1    59.99  3.000
 SB6  HCD2  CD1  HCD1  106.65  3.000
 SB6  HCD2  CD1  CE1   110.46  3.000
 SB6  HCD1  CD1  CE1   110.95  3.000
 SB6  HCD2  CD1  NC1   106.82  3.000
 SB6  HCD1  CD1  NC1   109.45  3.000
 SB6  CE1   CD1  NC1   112.29  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
 SB6  CONST_01  CA4   CA3  CA2  CA1     0.00   0.0  0
 SB6  CONST_02  CA4   CA5  CA6  CA1     0.00   0.0  0
 SB6  CONST_03  CC3   CA5  CA6  CA1   180.00   0.0  0
 SB6  CONST_04  CA5   CA6  CA1  CA2     0.00   0.0  0
 SB6  CONST_05  CA5   CA4  CA3  CA2     0.00   0.0  0
 SB6  CONST_06  CA6   CA1  CA2  CA3     0.00   0.0  0
 SB6  CONST_07  CA6   CA5  CA4  CA3     0.00   0.0  0
 SB6  CONST_08  CC3   CA5  CA4  CA3   180.00   0.0  0
 SB6  CONST_11  CB5   CC2  CC3  CA5     0.00   0.0  0
 SB6  CONST_12  NC1   CC2  CC3  CA5   180.00   0.0  0
 SB6  CONST_13  CC5   NC4  CC3  CA5   180.00   0.0  0
 SB6  CONST_16  CB4   CB3  NB2  CB1     0.00   0.0  0
 SB6  CONST_17  CB4   CB5  CB6  CB1     0.00   0.0  0
 SB6  CONST_18  CC2   CB5  CB6  CB1   180.00   0.0  0
 SB6  CONST_19  CB5   CB6  CB1  NB2     0.00   0.0  0
 SB6  CONST_20  CB5   CB4  CB3  NB2     0.00   0.0  0
 SB6  CONST_21  CB6   CB1  NB2  CB3     0.00   0.0  0
 SB6  CONST_22  CB6   CB5  CB4  CB3     0.00   0.0  0
 SB6  CONST_23  CC2   CB5  CB4  CB3   180.00   0.0  0
 SB6  CONST_26  CC5   NC1  CC2  CB5   180.00   0.0  0
 SB6  CONST_27  NC4   CC3  CC2  CB5   180.00   0.0  0
 SB6  CONST_30  NC4   CC3  CC2  NC1     0.00   0.0  0
 SB6  CONST_31  CC3   NC4  CC5  NC1     0.00   0.0  0
 SB6  CONST_32  NC4   CC5  NC1  CC2     0.00   0.0  0
 SB6  CONST_33  CC5   NC4  CC3  CC2     0.00   0.0  0
 SB6  CONST_34  CC5   NC1  CC2  CC3     0.00   0.0  0
 SB6  CONST_35  CA6   CA1  CA2  FA1   180.00   0.0  0
 SB6  CONST_36  CA4   CA3  CA2  FA1   180.00   0.0  0
 SB6  CONST_37  CD1   NC1  CC2  CB5     0.00   0.0  0
 SB6  CONST_38  CD1   NC1  CC2  CC3   180.00   0.0  0
 SB6  CONST_39  CD1   NC1  CC5  NC4   180.00   0.0  0
 SB6  CONST_40  HCA3  CA3  CA2  CA1   180.00   0.0  0
 SB6  CONST_41  HCA6  CA6  CA1  CA2   180.00   0.0  0
 SB6  CONST_42  HCA4  CA4  CA3  CA2   180.00   0.0  0
 SB6  CONST_43  HCA1  CA1  CA2  CA3   180.00   0.0  0
 SB6  CONST_44  HCB3  CB3  NB2  CB1   180.00   0.0  0
 SB6  CONST_45  HCB6  CB6  CB1  NB2   180.00   0.0  0
 SB6  CONST_46  HCB4  CB4  CB3  NB2   180.00   0.0  0
 SB6  CONST_47  HCB1  CB1  NB2  CB3   180.00   0.0  0
 SB6  CONST_48  HCC5  CC5  NC1  CC2   180.00   0.0  0
 SB6  Var_01    CE2   CE1  CD1  NC1  -146.87  30.0  3
 SB6  Var_02    CE1   CD1  NC1  CC2   -68.48  30.0  2
 SB6  Var_03    CE3   CE2  CE1  CD1   109.22  30.0  1
 SB6  Var_04    HE31  CE3  CE2  CE1  -107.89  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
 SB6  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
 SB6  plan-1  CA5   0.020
 SB6  plan-1  CB5   0.020
 SB6  plan-1  NC1   0.020
 SB6  plan-1  CC2   0.020
 SB6  plan-1  CC3   0.020
 SB6  plan-1  NC4   0.020
 SB6  plan-1  CC5   0.020
 SB6  plan-1  HCC5  0.020
 SB6  plan-1  CD1   0.020
 SB6  plan-2  FA1   0.020
 SB6  plan-2  CA1   0.020
 SB6  plan-2  CA2   0.020
 SB6  plan-2  CA3   0.020
 SB6  plan-2  CA4   0.020
 SB6  plan-2  CA5   0.020
 SB6  plan-2  CA6   0.020
 SB6  plan-2  CC3   0.020
 SB6  plan-2  HCA1  0.020
 SB6  plan-2  HCA3  0.020
 SB6  plan-2  HCA4  0.020
 SB6  plan-2  HCA6  0.020
 SB6  plan-3  CB1   0.020
 SB6  plan-3  NB2   0.020
 SB6  plan-3  CB3   0.020
 SB6  plan-3  CB4   0.020
 SB6  plan-3  CB5   0.020
 SB6  plan-3  CB6   0.020
 SB6  plan-3  CC2   0.020
 SB6  plan-3  HCB1  0.020
 SB6  plan-3  HCB3  0.020
 SB6  plan-3  HCB4  0.020
 SB6  plan-3  HCB6  0.020

