# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 14:14:26 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Fc1ccc2[nH]c(NCCCNCc3cc(Cl)cc(Cl)c3)nc2n1
#
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
 4RQ  4RQ  N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine  ligand  40  24  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4RQ
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
 4RQ  N1   N   NH1   0  -0.683  -2.7964   0.4935  -0.4902
 4RQ  N2   N   NH1   0  -0.602   1.9651  -0.1584   0.3252
 4RQ  C3   C   CR56  0   0.265  -6.0247  -0.1590   0.6384
 4RQ  C4   C   CR5   0   0.700  -4.1175   0.3997  -0.2982
 4RQ  C5   C   CH2   0  -0.275  -1.8093   0.1576   0.5144
 4RQ  C6   C   CH2   0  -0.484  -0.4181   0.1668  -0.0955
 4RQ  C7   C   CH2   0  -0.250   0.6490  -0.1705   0.9331
 4RQ  C10  C   CR16  0  -0.249   4.6033   0.6714  -0.3787
 4RQ  C12  C   CR16  0  -0.193   6.9524   0.0763  -0.4537
 4RQ  C15  C   CR56  0   0.287  -6.2164   0.5338  -0.5745
 4RQ  C13  C   CR6   0  -0.027   6.7177  -0.8333   0.5644
 4RQ  C11  C   CR6   0  -0.023   5.8737   0.8180  -0.9092
 4RQ  CL   CL  CL    0  -0.118   6.1310   1.9623  -2.1840
 4RQ  C14  C   CR16  0  -0.259   5.4579  -1.0080   1.1127
 4RQ  C9   C   CR6   0   0.062   4.3916  -0.2485   0.6436
 4RQ  C8   C   CH2   0  -0.297   3.0300  -0.4025   1.2711
 4RQ  N    N   NR15  0  -0.739  -4.6584  -0.2236   0.7845
 4RQ  N3   N   N     0  -0.527  -5.0265   0.8697  -1.1349
 4RQ  N4   N   N     0  -0.466  -7.4194   0.8037  -1.0687
 4RQ  C    C   CR6   0   0.529  -8.4254   0.3821  -0.3500
 4RQ  F    F   F     0  -0.312  -9.6388   0.6618  -0.8532
 4RQ  C2   C   CR16  0  -0.202  -7.1019  -0.5940   1.3739
 4RQ  C1   C   CR16  0  -0.484  -8.3628  -0.3068   0.8515
 4RQ  H1   H   HNH1  0   0.403  -2.5145   1.1002  -1.2440
 4RQ  H2   H   HNH1  0   0.347   2.0012  -0.8629  -0.4028
 4RQ  H4   H   HCH2  0   0.240  -1.8525   0.8553   1.3590
 4RQ  H5   H   HCH2  0   0.242  -2.0232  -0.8398   0.9073
 4RQ  H6   H   HCH2  0   0.240  -0.3847  -0.5534  -0.9184
 4RQ  H7   H   HCH2  0   0.240  -0.2053   1.1522  -0.5195
 4RQ  H8   H   HCH2  0   0.198   0.4094  -1.1339   1.4096
 4RQ  H9   H   HCH2  0   0.226   0.6359   0.5784   1.7309
 4RQ  H10  H   HCR6  0   0.276   3.7770   1.2592  -0.7541
 4RQ  H11  H   HCR6  0   0.299   7.9382   0.1996  -0.8795
 4RQ  H12  H   HCR6  0   0.278   5.3044  -1.7336   1.9011
 4RQ  H13  H   HCH2  0   0.254   2.9418   0.3333   2.0775
 4RQ  H14  H   HCH2  0   0.223   2.9700  -1.3879   1.7570
 4RQ  H15  H   HNR5  0   0.430  -4.1605  -0.6523   1.5484
 4RQ  H17  H   HCR6  0   0.285  -6.9946  -1.1306   2.3069
 4RQ  H18  H   HCR6  0   0.281  -9.2644  -0.6086   1.3645
 4RQ  CL1  CL  CL    0  -0.117   8.0380  -1.7842   1.1564

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
 4RQ  F    C    single    1.343  0.020  1.343
 4RQ  C1   C    aromatic  1.386  0.020  1.386
 4RQ  C1   C2   aromatic  1.395  0.020  1.395
 4RQ  C    N4   aromatic  1.306  0.020  1.306
 4RQ  C2   C3   aromatic  1.375  0.020  1.375
 4RQ  N4   C15  aromatic  1.328  0.020  1.328
 4RQ  C3   C15  aromatic  1.410  0.020  1.410
 4RQ  C3   N    aromatic  1.376  0.020  1.376
 4RQ  C15  N3   aromatic  1.358  0.020  1.358
 4RQ  N    C4   aromatic  1.361  0.020  1.361
 4RQ  N3   C4   aromatic  1.322  0.020  1.322
 4RQ  C4   N1   single    1.338  0.020  1.338
 4RQ  N1   C5   single    1.448  0.020  1.448
 4RQ  C5   C6   single    1.519  0.020  1.519
 4RQ  C6   C7   single    1.520  0.020  1.520
 4RQ  C7   N2   single    1.450  0.020  1.450
 4RQ  N2   C8   single    1.445  0.020  1.445
 4RQ  CL1  C13  single    1.731  0.020  1.731
 4RQ  CL   C11  single    1.732  0.020  1.732
 4RQ  C13  C12  aromatic  1.385  0.020  1.385
 4RQ  C13  C14  aromatic  1.385  0.020  1.385
 4RQ  C12  C11  aromatic  1.386  0.020  1.386
 4RQ  C11  C10  aromatic  1.384  0.020  1.384
 4RQ  C14  C9   aromatic  1.391  0.020  1.391
 4RQ  C10  C9   aromatic  1.391  0.020  1.391
 4RQ  C9   C8   single    1.507  0.020  1.507
 4RQ  N1   H1   single    0.890  0.020  1.040
 4RQ  N2   H2   single    0.890  0.020  1.040
 4RQ  C5   H4   single    0.970  0.020  1.090
 4RQ  C5   H5   single    0.970  0.020  1.090
 4RQ  C6   H6   single    0.970  0.020  1.090
 4RQ  C6   H7   single    0.970  0.020  1.090
 4RQ  C7   H8   single    0.970  0.020  1.090
 4RQ  C7   H9   single    0.970  0.020  1.090
 4RQ  C10  H10  single    0.930  0.020  1.080
 4RQ  C12  H11  single    0.930  0.020  1.080
 4RQ  C14  H12  single    0.930  0.020  1.080
 4RQ  C8   H13  single    0.970  0.020  1.090
 4RQ  C8   H14  single    0.970  0.020  1.090
 4RQ  N    H15  single    0.860  0.020  1.020
 4RQ  C2   H17  single    0.930  0.020  1.080
 4RQ  C1   H18  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
 4RQ  H1   N1   C5   117.90  3.000
 4RQ  H1   N1   C4   115.19  3.000
 4RQ  C5   N1   C4   123.86  3.000
 4RQ  H2   N2   C8   109.05  3.000
 4RQ  H2   N2   C7   109.13  3.000
 4RQ  C8   N2   C7   113.15  3.000
 4RQ  C2   C3   N    134.95  3.000
 4RQ  N    C3   C15  104.45  3.000
 4RQ  C2   C3   C15  120.60  3.000
 4RQ  N3   C4   N    113.14  3.000
 4RQ  N3   C4   N1   124.27  3.000
 4RQ  N    C4   N1   122.58  3.000
 4RQ  H5   C5   H4   107.22  3.000
 4RQ  H5   C5   C6   109.21  3.000
 4RQ  H4   C5   C6   109.97  3.000
 4RQ  H5   C5   N1   109.13  3.000
 4RQ  H4   C5   N1   111.11  3.000
 4RQ  C6   C5   N1   110.14  3.000
 4RQ  H7   C6   H6   107.19  3.000
 4RQ  H7   C6   C7   109.00  3.000
 4RQ  H6   C6   C7   109.97  3.000
 4RQ  H7   C6   C5   109.84  3.000
 4RQ  H6   C6   C5   109.03  3.000
 4RQ  C7   C6   C5   111.71  3.000
 4RQ  H9   C7   H8   106.29  3.000
 4RQ  H9   C7   C6   109.46  3.000
 4RQ  H8   C7   C6   109.52  3.000
 4RQ  H9   C7   N2   108.11  3.000
 4RQ  H8   C7   N2   112.72  3.000
 4RQ  C6   C7   N2   110.59  3.000
 4RQ  H10  C10  C9   119.88  3.000
 4RQ  H10  C10  C11  120.71  3.000
 4RQ  C9   C10  C11  119.41  3.000
 4RQ  H11  C12  C11  121.28  3.000
 4RQ  H11  C12  C13  121.26  3.000
 4RQ  C11  C12  C13  117.46  3.000
 4RQ  N4   C15  N3   126.15  3.000
 4RQ  N3   C15  C3   110.95  3.000
 4RQ  N4   C15  C3   122.90  3.000
 4RQ  C14  C13  CL1  119.27  3.000
 4RQ  C14  C13  C12  121.86  3.000
 4RQ  CL1  C13  C12  118.86  3.000
 4RQ  CL   C11  C12  118.67  3.000
 4RQ  C12  C11  C10  122.11  3.000
 4RQ  CL   C11  C10  119.22  3.000
 4RQ  H12  C14  C9   120.20  3.000
 4RQ  H12  C14  C13  120.13  3.000
 4RQ  C9   C14  C13  119.67  3.000
 4RQ  C8   C9   C14  119.76  3.000
 4RQ  C8   C9   C10  120.73  3.000
 4RQ  C14  C9   C10  119.49  3.000
 4RQ  H14  C8   H13  105.79  3.000
 4RQ  H14  C8   C9   108.95  3.000
 4RQ  H13  C8   C9   108.10  3.000
 4RQ  H14  C8   N2   113.59  3.000
 4RQ  H13  C8   N2   108.01  3.000
 4RQ  C9   C8   N2   112.08  3.000
 4RQ  H15  N    C4   126.97  3.000
 4RQ  H15  N    C3   126.25  3.000
 4RQ  C4   N    C3   106.78  3.000
 4RQ  C15  N3   C4   104.68  3.000
 4RQ  C    N4   C15  115.29  3.000
 4RQ  C1   C    F    117.97  3.000
 4RQ  C1   C    N4   127.04  3.000
 4RQ  F    C    N4   114.99  3.000
 4RQ  H17  C2   C1   120.99  3.000
 4RQ  H17  C2   C3   122.73  3.000
 4RQ  C1   C2   C3   116.28  3.000
 4RQ  H18  C1   C2   121.27  3.000
 4RQ  H18  C1   C    120.84  3.000
 4RQ  C2   C1   C    117.89  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
 4RQ  CONST_01  C    C1   C2   C3      0.00   0.0  0
 4RQ  CONST_02  C    N4   C15  C3      0.00   0.0  0
 4RQ  CONST_03  C4   N3   C15  C3      0.00   0.0  0
 4RQ  CONST_04  N3   C4   N    C3      0.00   0.0  0
 4RQ  CONST_05  C2   C3   N    C4    180.00   0.0  0
 4RQ  CONST_06  C15  C3   N    C4      0.00   0.0  0
 4RQ  CONST_07  N4   C15  N3   C4    180.00   0.0  0
 4RQ  CONST_08  C13  C12  C11  C10     0.00   0.0  0
 4RQ  CONST_09  C13  C14  C9   C10     0.00   0.0  0
 4RQ  CONST_10  C9   C14  C13  C12     0.00   0.0  0
 4RQ  CONST_11  C9   C10  C11  C12     0.00   0.0  0
 4RQ  CONST_12  C1   C    N4   C15     0.00   0.0  0
 4RQ  CONST_13  C1   C2   C3   C15     0.00   0.0  0
 4RQ  CONST_14  N    C4   N3   C15     0.00   0.0  0
 4RQ  CONST_15  C14  C13  C12  C11     0.00   0.0  0
 4RQ  CONST_16  C14  C9   C10  C11     0.00   0.0  0
 4RQ  CONST_17  C1   C2   C3   N     180.00   0.0  0
 4RQ  CONST_18  N4   C15  C3   N     180.00   0.0  0
 4RQ  CONST_19  N3   C15  C3   N       0.00   0.0  0
 4RQ  CONST_20  C    N4   C15  N3    180.00   0.0  0
 4RQ  CONST_21  C2   C3   C15  N3    180.00   0.0  0
 4RQ  CONST_22  C2   C1   C    N4      0.00   0.0  0
 4RQ  CONST_23  C2   C3   C15  N4      0.00   0.0  0
 4RQ  CONST_24  C3   N    C4   N1    180.00   0.0  0
 4RQ  CONST_25  C15  N3   C4   N1    180.00   0.0  0
 4RQ  CONST_26  F    C    N4   C15   180.00   0.0  0
 4RQ  CONST_27  C11  C12  C13  CL1   180.00   0.0  0
 4RQ  CONST_28  C9   C14  C13  CL1   180.00   0.0  0
 4RQ  CONST_29  CL   C11  C12  C13   180.00   0.0  0
 4RQ  CONST_30  C8   C9   C14  C13   180.00   0.0  0
 4RQ  CONST_31  C8   C9   C10  C11   180.00   0.0  0
 4RQ  CONST_32  C9   C10  C11  CL    180.00   0.0  0
 4RQ  CONST_33  C2   C1   C    F     180.00   0.0  0
 4RQ  CONST_34  H18  C1   C2   C3    180.00   0.0  0
 4RQ  CONST_35  H11  C12  C11  C10   180.00   0.0  0
 4RQ  CONST_36  H12  C14  C9   C10   180.00   0.0  0
 4RQ  CONST_37  H10  C10  C11  C12   180.00   0.0  0
 4RQ  CONST_38  H17  C2   C3   C15   180.00   0.0  0
 4RQ  CONST_39  H15  N    C3   C15   180.00   0.0  0
 4RQ  CONST_40  N    C4   N1   C5      0.00   0.0  0
 4RQ  CONST_41  N3   C4   N1   C5    180.00   0.0  0
 4RQ  CONST_42  H1   N1   C4   N     180.00   0.0  0
 4RQ  Var_01    C14  C9   C8   N2   -149.27  30.0  2
 4RQ  Var_02    C6   C5   N1   C4    171.11  30.0  3
 4RQ  Var_03    C9   C8   N2   C7   -174.27  30.0  3
 4RQ  Var_04    C7   C6   C5   N1    179.52  30.0  3
 4RQ  Var_05    C5   C6   C7   N2    179.85  30.0  1
 4RQ  Var_06    C8   N2   C7   C6    176.90  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
 4RQ  plan-1  C10  0.020
 4RQ  plan-1  C12  0.020
 4RQ  plan-1  C13  0.020
 4RQ  plan-1  C11  0.020
 4RQ  plan-1  CL   0.020
 4RQ  plan-1  C14  0.020
 4RQ  plan-1  C9   0.020
 4RQ  plan-1  C8   0.020
 4RQ  plan-1  H10  0.020
 4RQ  plan-1  H11  0.020
 4RQ  plan-1  H12  0.020
 4RQ  plan-1  CL1  0.020
 4RQ  plan-2  N1   0.020
 4RQ  plan-2  C3   0.020
 4RQ  plan-2  C4   0.020
 4RQ  plan-2  C15  0.020
 4RQ  plan-2  N    0.020
 4RQ  plan-2  N3   0.020
 4RQ  plan-2  N4   0.020
 4RQ  plan-2  C    0.020
 4RQ  plan-2  F    0.020
 4RQ  plan-2  C2   0.020
 4RQ  plan-2  C1   0.020
 4RQ  plan-2  H15  0.020
 4RQ  plan-2  H17  0.020
 4RQ  plan-2  H18  0.020
 4RQ  plan-3  N1   0.020
 4RQ  plan-3  C4   0.020
 4RQ  plan-3  C5   0.020
 4RQ  plan-3  H1   0.020

